AVASOFT for AvaSpec-USB2 version 7.5 USER`S MANUAL

AVASOFT for AvaSpec-USB2 version 7.5 USER`S MANUAL
AVASOFT for AvaSpec-USB2
version 7.5
USER’S MANUAL
December 2009
Sunrise
Dec-09
Avantes
www.avantes.com
[email protected]
0
AVASOFT INSTALLATION
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0.1 Installation program
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0.2 Bluetooth installation
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0.3 Launching the software
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1
QUICK START: MEASURING AND SAVING A SPECTRUM
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MAIN WINDOW
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2.1
Menu bar
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2.2
Button bar
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2.3
Edit bar
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2.4
Graphical region
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2.5
Status bar
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2.6
Find peaks or valleys by CTRL or SHIFT + left mouse button click
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3
MENU OPTIONS
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3.1 File Menu
3.1.1
File Menu: Start New Experiment
3.1.2
File Menu: Load Dark
3.1.3
File Menu: Load Reference
3.1.4
File Menu: Load Experiment
3.1.5
File Menu: Save Dark
3.1.6
File Menu: Save Reference
3.1.7
File Menu: Save Experiment
3.1.8
File Menu: Print
3.1.9
File Menu: Black and White printer
3.1.10 File Menu: Display Saved Graph
3.1.11 File Menu: Display 3D Graph
3.1.12 File Menu: Convert Graph – Include ASCII Header
3.1.13 File Menu: Convert Graph - to ASCII
3.1.14 File Menu: Convert Graph - to ASCII Equi distance
3.1.15 File Menu: Convert Graph - to J-CAMP
3.1.16 File Menu: Convert Graph - to Excel
3.1.17 File Menu: Save Graph to .RTF
3.1.18 File Menu: Exit
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3.2 Setup Menu
3.2.1
Setup Menu: Hardware
3.2.2
Setup Menu: Wavelength Calibration Coefficients
3.2.3
Setup Menu: Smoothing and Spline
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3.2.4
Setup Menu: Use 16bit ADC in 14bit mode (HW rev 1D and later)
3.2.5
Setup Menu: Correct for Dynamic Dark
3.2.6
Setup Menu: Subtract Saved Dark
3.2.7
Setup Menu: Strobe Enable
3.2.8
Setup Menu: PWM (AvaLight-LED) control
3.2.9
Setup Menu: Options
3.2.9.1
Setup Menu: Options – Check on Saturation
3.2.9.2
Setup Menu: Options – Full Width Half Max
3.2.9.3
Setup Menu: Options - Integrals
3.2.9.4
Setup Menu: Options – Autosave Spectra Periodically
3.2.9.5
Setup Menu: Options - Correct for Drift
3.2.9.6
Setup Menu: Options - Automatic Save Dark by TTL shutter
3.2.9.7
Setup Menu: Options - External Trigger Setting
3.2.9.8
Setup Menu: Options - Auto configure Integration time
3.2.9.9
Setup Menu: Options – Use Custom Reflection Reference
3.2.9.10 Setup Menu: Options – Suppress Save Comments
3.2.9.11 Setup Menu: Options – View Reflectance instead of Transmittance
3.2.9.12 Setup Menu: Options – Battery Voltage Monitoring
3.2.9.13 Setup Menu: Options – Merge Channel Settings
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3.3 View Menu
3.3.1
View Menu: Scope Mode
3.3.2
View Menu: Absorbance Mode
3.3.3
View Menu: Transmittance/Reflectance Mode
3.3.4
View Menu: Irradiance Mode
3.3.5
View Menu: Change Graph Scale
3.3.6
View Menu: Graphic Reset
3.3.7
View Menu: Autoscale Y-axis
3.3.8
View Menu: Goto Preset Scale
3.3.9
View Menu: Grid Enable
3.3.10 View Menu: Progress Bar Enable
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APPLICATIONS
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4.1 Applications: History Channel Functions
4.1.1
History Application: Function Entry
4.1.2
History Application: Start Measuring
4.1.3
History Application: Display Saved History Graph
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4.2 Applications: Wavelength Calibration
4.2.1
Calibrate Wavelength Application: Perform New Calibration
4.2.2
Calibrate Wavelength Application: Restore Original Calibration
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4.3 Applications: Color Measurement
4.3.1
Color of an Object - Background
4.3.2
Menu option: Color Measurement
4.3.2.1
LABChart
4.3.2.2
Time Series
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4.4 Applications: Absolute Irradiance Application
4.4.1
Background
4.4.2
Quick Start
4.4.3
Load Intensity Calibration
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4.4.4
4.4.4.1
4.4.4.2
4.4.5
4.4.5.1
4.4.5.2
4.4.6
4.4.7
4.4.7.1
4.4.7.2
Perform Intensity Calibration
Start Intensity Calibration
Save Intensity Calibration
Irradiance Chart
Irradiance Chart Settings
Irradiance Chart Display
Time Series Measurement
Auto Adjust Integrationtime
Auto Adjust Integrationtime Settings
Measuring with Auto Adjust Integrationtime
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4.5 Applications: Process Control Application
4.5.1
Digital Output signals
4.5.2
Analog Output signals
4.5.3
Using the Process Control Application in AvaSoft
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4.6 Applications: Excel Output
4.6.1
Select Source Data
4.6.2
Enable Excel Output
4.6.3
Settings
4.6.4
Start Output
4.6.5
Stop Output
4.6.6
Limitations and Optimization Notes
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4.7 Applications: Chemometry
4.7.1 Quick Start: How to make concentration measurements with AvaSoft-Chem
4.7.2
Calibration Settings
4.7.2.1
Start New Calibration
4.7.2.2
Modifying a calibration
4.7.3
Enabling the application
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4.8 Applications: Laser Induced Breakdown Spectroscopy (AvaSpec-2048/2048L/3648*)
4.8.1
Libs Settings
4.8.2
Enabling and running the application
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4.9 Applications: Store To Ram
4.9.1
Introduction
4.9.2
Quick Start
4.9.3
Main Window
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5
HELP
APPENDIX A
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TROUBLESHOOTING
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How to rectify an incorrect (USB) installation
APPENDIX B
ERROR MESSAGES
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0
AvaSoft Installation
Before you connect the AvaSpec spectrometer to the USB port of your computer, you need to install the
AvaSoft software first.
AVASOFT version 7 is a 32-bit application and can be installed under the following operating systems:
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Windows 95/98/Me
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Windows NT/2000
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XP/Vista/Windows7 x32 (32-bit O/S)
•
XP/Vista/Windows7 x64 (64-bit O/S)
If the operating system is Windows 95 or Windows NT4.0, use a standard RS-232 cable (with male and
female DB-9 connectors) to connect the AvaSpec to the serial port of the computer.
0.1 Installation program
With each new spectrometer system, an AVANTES PRODUCT CD-ROM is included. One of the options in the
main menu which is shown after the CD-ROM is inserted in the CD-ROM drive, is to install AvaSoft
software. After selecting this option, a submenu is displayed in which the spectrometer configuration can
be selected.
The AvaSpec-USB2 group of spectrometers should be selected to install AvaSoft7 for one of the following
spectrometer types:
AvaSpec-102/128/256/1024/2048/2048L/2048x14/3648/NIR256-USB2.
Instructions below are for the AvaSpec-USB2 spectrometers, -Bluetooth® instructions are found in section
0.2.
Installation Dialogs
The setup program will check the system
configuration of the computer. If no problems
are detected, the first dialog is the “Welcome”
dialog with some general information.
In the next dialog, the destination directory for
the AvaSoft software can be changed. The
default destination directory is
C:\AVASOFT7USB2. If you want to install the
software to a different directory, click the
Browse button, select a new directory and click
OK. If the specified directory does not exist, it
will be created.
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In the next dialog, the name for the program manager group can be changed. The default name for this is
“AVANTES Software”.
After this, the “Start Installation” dialog is shown. After clicking the “next” button, the installation
program starts installing files.
During this installation, the installation program will check if the most recent USB driver has been
installed already at the PC. If no driver is found, or if the driver needs to be upgraded, the Device Driver
Installation Wizard is launched automatically, click Next. If the Operating System is Windows Vista, it will
display a message that it can’t verify the publisher of the driver software, select “Install this driver
software anyway”.
After the drivers have been installed successfully, the dialog at the right is displayed, click Finish.
After all files have been installed, the “Installation Complete” dialog shows up. Click Finish.
Connecting the hardware
Connect the USB connector to a USB port on your computer with the supplied USB cable. Windows will
display the “Found New Hardware” dialog. Select the (default) option to install the software
automatically, and click next. After the Hardware Wizard has completed, the following dialog is
displayed:
Click Finish to complete the installation.
Please note that if the spectrometer is
Connected to another USB port to which it has not
been connected before, the “Found New Hardware
Wizard” will need to install the software for this port
as well. For this reason, this Wizard will run
“NrOfChannel” times for a multichannel AvaSpecUSB2 spectrometer system. This, because inside the
housing, the USB ports for each spectrometer channel
is connected to a USB-Hub.
Windows Vista will install the driver automatically,
without displaying the “Found New Hardware Wizard”
dialogs
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0.2 Bluetooth installation
The AvaSpec spectrometers with Bluetooth® wireless data transfer support are shipped with a Bluesoleil
BS001 USB dongle. The Bluetooth® drivers can be installed from the Avantes product CD-ROM. This section
describes how to setup Bluetooth® data communication with the AvaSpec-BT spectrometer.
Install AvaSoft for USB2 spectrometers from the Avantes Product CD-ROM
Insert the Avantes Product CD-ROM in the CD drive of your PC, select “Software Installation” and install
AvaSoft.
Install Bluetooth® drivers
The option to install the Bluesoleil Bluetooth Drivers can also be found in the “Software Installation”
section of the Avantes Product CD-ROM. Click this option to install the Bluetooth drivers for the BS001 USB
dongle. After the installation has been completed you will be asked to restart the computer. After the
restart, insert the BS001 USB dongle.
The “Bluetooth Places” Window in the figure below can be opened by double clicking the
bluetooth icon at the desktop. In this window, go to the Bluetooth menu and select “Display
Classic View”
A shortcut to setup the Classic View is to right click the Bluetooth icon in the taskbar which shows the
same option
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Connect the 12 VDC external power supply or batterypack to the AvaSpec-BT
First make sure that the Batterypack is completely charged, if not connect the batterypack to the charger
and let it charge until the LED on the charger starts to flicker (trickle-charge mode). Now connect the
batterypack to the AvaSpec-BT and switch on the batterypack (switch on the frontside) and switch on the
AvaSpec-BT to external power. In the Classic View, the AvaSpec will initially be displayed as a Bluetooth
Device. The icon is a question mark.
By double clicking the question mark icon, the serial port icon will be high lighted:
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By double clicking the Serial Port icon, the connection will be established and a virtual serial port number
will be assigned:
This serial port number (COM21 in this example) will be needed later on in AvaSoft. The color of the
Bluetooth Device icon changes to green, and a dotted line with moving red dot between the PC (yellow
bowl in the center) and the Bluetooth Device (AvaSpec) illustrates that the connection has been
established successfully
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Starting AvaSoft
AvaSoft can be started after data communication has been established. The first time that AvaSoft is
started for the Bluetooth spectrometer, it will show the dialog below.
Click the option: “Retry to establish communication through RS-232 or Bluetooth”. A list with available
comports will be displayed. In our example, COM21 has been selected for the Bluetooth® data
communication. Select the right COM port from the list and click OK. AvaSoft will now read the
configuration data from the spectrometer (this can take about 15 seconds), after which measurements can
be started.
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0.3 Launching the software
AvaSoft can be started from Windows Start Menu. Under Start-programs, the group “AVANTES Software”
has been added. This group contains two icons. With the red “V” icon, AvaSoft is started. The AvaSoft
Help icon can be used to activate the AvaSoft helpfiles (these helpfiles can also be activated from the
Help menu after starting AvaSoft).
After starting the AvaSoft 7 software, all connected spectrometers will be recognized automatically. The
number of detected spectrometers and their status will be displayed in the welcome dialog. After a few
seconds, the main window will be displayed and the spectrometer names (default serialnr) will appear in
the legend at the right hand of the screen. More detailed information about the spectrometer(s) is shown
after clicking the menu option Setup-Hardware. In this dialog, a user defined name can be defined for
each spectrometer.
After clicking the start button, the spectra for all connected spectrometers will be displayed in the main
window.
After clicking the OK button, the main window is displayed. Refer to section 2 for a description about the
main window components. A “Quick Start” can be found in section 1, if you want to start measuring
immediately. Detailed information about the menu options is found in section 3. Depending on the AvaSoft
version (Basic or Full) and the extra add-on modules that were ordered for your spectrometer, up to nine
applications are available in AvaSoft, which are described in sections 4.1 to 4.9:
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History (standard in AvaSoft FULL)
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Wavelength Calibration (standard in AvaSoft FULL)
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Color Measurement (add-on module)
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Irradiance Measurement (add-on module)
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Process Control (add-on module)
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Excel Output (add-on module)
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Chemometry (add-on module)
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Laser Induced Breakdown Spectroscopy (LIBS, standard in AvaSoft FULL)
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Store to RAM (standard in AvaSoft FULL)
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1
Quick Start: Measuring and saving a spectrum
1. After starting AvaSoft, the green Start button needs to be clicked to start measuring.
2. Connect a fiber or probe to the light source and to the spectrometer input port(s) and set up the
experiment for taking a reference spectrum.
3. Optimal smoothing is preset and stored on board in the EEPROM.
4. Now turn on the light source. Usually some sort of spectrum may be seen on the screen, but it is
possible that too much or too little light reaches the spectrometer at the present data collection
settings. Too much light means that, over a certain wavelength range, the signal is saturated shown as
a straight line at the maximum counts and the appearance of the label “saturated” in the statusbar of
the spectrometer channel. This can usually be solved by a shorter integration time. The integration
time can be changed in the main window, in the white box below the start/stop button or the Autoconfigure Integration time button can be used (see 2.1). The new integration time can be entered in
the box, and will take effect once you press the ‘Enter’ key or leave the box. Try to adjust the
integration time, such that the maximum count over the wavelength range is around 90% of the full
ADC scale (14750 counts for the 14bit ADC, 59000 counts for the 16bit ADC). When at minimum
integration the signal is still too high, an attenuator, a neutral density filter or fibers with a smaller
diameter may be used. When not enough light reaches the spectrometer, likewise a longer integration
time should be entered.
5. When a good spectrum is displayed, turn off the light source.
6. Now save the Dark data. This is be done by File-Save-Dark from the menu or by clicking the black
square on the left top of the screen with the mouse. Always use Save Dark after the integration time
has been changed.
7. Turn on the light source again. Save the present spectrum as a reference by choosing File SaveReference from the menu or by clicking at the white square (next to the black one). Always use Save
Reference after the integration time has been changed. Now the Transmittance/reflectance (T/R
button) or Absorbance (A button) spectra can be obtained online. To have a better look at the
amplitude versus wavelength, the cursor button can be clicked. A vertical line is displayed in the
graph. If the mouse cursor is placed nearby this line, the shape of the mouse cursor changes from an
arrow to a ‘drag’ shape. If this shape is displayed, the left mouse button can be used to drag (keep
left mouse button down) the line with the mouse towards a new position. Moving this line shows the
corresponding values of wavelength and amplitude in the main screen. By clicking the red stop button,
the data acquisition is stopped and the last acquired spectrum is shown in static mode. The data
acquisition can be started again by clicking the same button, which now shows a green ‘Start’.
8. To save the spectrum (in the mode chosen before), choose File-Save-Experiment from the menu, or
click the Save Experiment button from the button bar.
9. To improve the Signal/Noise ratio, a number of spectra may be averaged. To do this, the value in the
white average box in the main window (next to integration time) can be increased. The new value will
take effect when you press the ‘Enter’ key or leave the box.
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2 Main Window
2.1 Menu bar
The menus and submenus are described in section 3.
2.2 Button bar
Start/Stop button
The Start/Stop button can be used to display data real-time or to take a snapshot
Cursor button
After clicking the cursor button, a vertical line is displayed in the graph. If the mouse cursor is placed
nearby this line, the shape of the mouse cursor changes from an arrow to a ‘drag’ shape. If this shape is
displayed, the left mouse button can be used to drag (keep left mouse button down) the line with the
mouse towards a new position. Moving this line shows the
corresponding values of wavelength and amplitude in the main screen.
As an alternative for dragging the line, the small step and big step
arrow buttons may be used, or the left and right arrow keys on the
keyboard. The step size for the arrow buttons can be changed by
holding down the CTRL-key while clicking at a (single or double) arrow
button.
Save reference and dark buttons
The reference button is the white button at the left top of the screen. It needs to be clicked to save the
reference data. The same result can be achieved with the option File-Save Reference. The dark button is
the black button at the left top of the screen. It needs to be clicked to save the dark data. The same
result can be achieved with the option File-Save Dark.
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Save experiment button
By clicking the Save Experiment button an experiment is saved. The same result can be achieved with the
option File-Save Experiment.
Print button
By clicking the Print button a graph that is displayed on the monitor will be printed. The same result can
be achieved with the option File-Print.
Scope button
By clicking the S button, the data will be presented in Scope Mode. The same result can be achieved with
the option View-Scope Mode.
Absorbance button
By clicking the A button, the data will be presented in Absorbance Mode. The same result can be achieved
with the option View-Absorbance Mode.
Transmission button
By clicking the T button, the data will be presented in Transmittance Mode. The same result can be
achieved with the option View-Transmittance Mode.
Irradiance button
By clicking the I button, the data will be presented in Irradiance Mode. The same result can be achieved
with the option View-Irradiance Mode.
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Autoscale Y-axis button
By clicking this button, the graph will be rescaled on-line. A maximum signal will be shown at about 75%
of the vertical scale. The same result can be achieved with the option View-Autoscale Y-axis
Change Graph Scale button
By clicking this button, a dialog will be shown in which the range can be changed for both X- and Y-axis.
This range can be saved as well and restored any time by clicking the Goto Preset Scale button (see
below). The menu option with the same functionality is View-Change Graph Scale.
Goto Preset Scale button
By clicking this button, the scale for X- and Y-axis will be set to a range that has been set before. The
same result can be achieved with the menu option View-Goto Preset Scale
Graphic Reset button
By clicking this button, the X- and Y-axis will be reset to their default values. The same result can be
achieved with the option View-Graphic Reset
Auto Configure Integration time button
After this button is clicked, AvaSoft starts searching for an optimal integration time. Depending on the
maximum counts in the last scan, the integration time will be increased/decreased automatically until a
scope signal of about 90% of the full scale is measured. During the search routine, the changes in
integration time can be followed in the integration time edit box in the edit bar. A dialog will display the
new integration time if the search is ready. The routine can be aborted by clicking the button again
before the search has ended.
H.C.F. button
The History Channel Function button allows you to switch directly to the history channel function screen
to start measuring immediately. Of course first the functions need to be defined.
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The two buttons below are available only if AvaSoft has been ordered together with the color
application add-on:
Color Chart button
The Color Chart button allows you to switch directly to the Color Chart screen and starts measuring
immediately.
Color of Object versus Time button
The Color of Object versus time button allows you to switch directly to the time measurement of color
parameters and starts measuring immediately.
2.3 Edit bar
-single channel
-multi channel
The edit bar shows the following parameters:
Integration time[ms]
This option changes the CCD readout frequency and therefore the exposure- or integration time of the
CCD detector. The longer the integration time, the more light is exposed to the detector during a single
scan, so the higher the signal. If the integration time is set too long, too much light reaches the detector.
The result is that, over some wavelength range, the signal extends the maximum counts (65535 for the
16bit ADC, 16383 for the 14bit ADC) or in extreme case shows as a straight line at any arbitrary height,
even near zero. Entering a shorter integration time can usually solve this. Try to adjust the integration
time, such that the maximum count over the wavelength range is around 90% of the full ADC scale (14750
counts for the 14bit ADC, 59000 counts for the 16bit ADC). When at minimum integration the signal is still
too high, an attenuator, a neutral density filter or fibers with a smaller diameter may be used. When not
enough light reaches the spectrometer, likewise a longer integration time should be entered. It’s also
possible to let AvaSoft search for a good integration time by clicking the ‘∫AC’ button, or by using the
menu option Setup-Options-Auto Configure Integration time.
If measurements are done in a mode in which reference and dark data are required (all modes except
Scope mode), then new reference and dark spectra need to be saved after the integration time has been
changed.
Average
With this option, the number of scans to average can be set. A spectrum will be displayed after every #
scans. This spectrum is the average of the # scans.
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Wavelength [nm]
The wavelength shows the position of the cursor, which becomes visible if the cursor button is down. The
amplitude of the signal, which is given in the statusbar at the bottom of the main window, is the
amplitude at the wavelength shown in this field.
Multichannel only
For multichannel spectrometers the integration time
and averaging can be set for all channels at the same
value by clicking to All.
If the dashed box is clicked, different integration
time and averaging can be set per channel .
2.4 Graphical region
The graphical region displays
the data in an XY-diagram,
with at the X-axis the
wavelength in nanometers,
and at the Y-axis the detector
counts. After loading or
saving a reference and dark
spectrum, other units can be
selected at the Y-axis:
Absorbance Units, Percentage
Transmittance, or Relative
Irradiance.
Display saved Graph and
Line style editor
By clicking on the legend with the right mouse button, multiple spectra,
that were saved earlier can be displayed.
New in AvaSoft 7 is that displayed graphs can be deleted or
properties of the displayed graphs, such as line style or color
or comments can be changed. This is done by clicking with
the right mouse button on the line in the graphical display. A
small line edit box will appear.
Now the line can be deactivated or the line properties can be
changed as depicted in the border editor or the comments
can be edited.
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Zoom features
Zoom in: select a region to be expanded to the full graph. To select this region, click the left mouse
button in the white graphical region and drag it downwards and to the right. After releasing the left
mouse button within the graphic display, both the X- and Y-axis will be rescaled to the new values of the
selected region.
Zoom out: drag with the left mouse button within the white rectangle, but in stead of dragging the mouse
downwards and to the right, drag it in another direction. After releasing the mouse button, both the Xand Y-axis will be reset to their default values.
Move X-Y: dragging with the right mouse button results in moving the complete spectrum up or down and
to the left or right.
Move-Y: if a mouse-wheel is available on the mouse being used, then the spectrum can be moved up or
down by moving the mouse wheel.
2.5 Status bar
For each selected spectrometer channel, a statusbar at the bottom of the main window shows the name
label of the connected spectrometer channel, the file to which the data will be saved, amplitude at
current wavelength, the current settings for the smoothing and spline parameters, the line color and style
in the graphical display, the real integration time and averages per channel and final the number of scans
taken since the start button was clicked. The field at the right is used to indicate that the spectrometer is
receiving too much light at a certain wavelength range (=16383 counts with the spectrometer boards rev
1B and rev 1C and 65535 counts for the spectrometer boards rev 1D and later. These ADC counts are
before correcting for dynamic dark, smoothing or averaging), in which case the label “saturated” will
become visible.
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2.6 Find peaks or valleys by CTRL or SHIFT + left mouse button click
This option can be used in all modes (Scope, Absorbance, Transmittance or Irradiance) and for all
displayed graphics. When the left mouse button is clicked in the graphical region, while the CTRL key is
down, AvaSoft will follow the following procedure to run to the closest peak:
1. The wavelength is determined from the position the mouse click occurred.
2. The data from closest pixel is retrieved
3. The direction to search for the peak is determined from the neighbor pixels. If both neighbor pixels
have a lower value at the Y-axis than the current pixel, the current pixel is already a peak. If only one
of the neighbor pixel values is higher than the current pixel value, the peak will be searched in the
direction of this higher pixel. If both neighbor pixels have a higher value at the Y-axis than the current
pixel, the current pixel is in a valley. The peak will in this case be searched in the direction of this
neighbor pixel with the highest value.
4. The cursor starts moving in the direction, as determined under 3), until it reaches a pixel of which the
value is not higher than the last one evaluated. At this pixel the cursor stops.
By holding down the SHIFT key instead of the CTRL key, the same procedure will be used to move to the
closest valley.
If more than one spectrum is being displayed, a dialog, as
shown at the right, pops up in which the spectrum for which
the peakfinder needs to be activated can be selected out of
all displayed spectra.
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3
Menu Options
In sections 3.1 to 3.3 the main menu options (File, Setup and View Menu) and their submenu's are
described in detail.
3.1 File Menu
3.1.1
File Menu: Start New Experiment
After selecting this option, a dialog box appears in which a new experiment name can be entered. The
experiment name will be saved as a filename with the extension *.kon. This extension does not need to be
entered.
After clicking the save button,
the current filename will be built
up from the experiment name
that has been entered, and a
sequence number, starting at
0001.
Example: if the experiment name
is “test”, the first graphic file
that will be saved in scope mode,
will be called test0001.ROH, the
sequence number will be
automatically incremented, so
the next file that will be saved in
scope mode will be called
test0002.ROH etc. For detailed
information on graphic filenames,
see File-Save Experiment. Note that the dialog allows you to select different folders or drives to save the
experiments to, as well as creating a new folder name for the new experiment. For USB2 platform the
default directory is “data”.
After closing the dialog box by clicking the save button, the new experiment name, followed by its
sequence number, is displayed in the lower left of the status bar. By clicking the cancel button, the old
experiment name will be restored.
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3.1.2
File Menu: Load Dark
With this option, dark data can be loaded, that have been saved before. If AvaSoft is in static mode, the
dark data that will be loaded are shown on the screen first.
3.1.3
File Menu: Load Reference
With this option, reference data can be loaded, that have been saved before. If AvaSoft is in static mode,
the reference data that will be loaded are shown on the screen first.
3.1.4
File Menu: Load Experiment
With this option, an
experiment can be loaded,
that has been used before.
This way more spectra can be
saved to an existing
experiment. An experiment
name has the file extension "*.kon". After choosing this
option, a dialog box shows all
experiments that were saved
earlier in the current
experiment directory. If the
experiment name that needs
to be loaded is in this
directory, select it and click
the save button. If the
experiment name that needs
to be loaded is in another drive and/or directory, move to this directory by clicking the
behind the
current foldername. For detailed information on graphic filenames, see File-Save Experiment.
3.1.5
File Menu: Save Dark
With this option, dark data are saved. The name of the dark data file is "serialnr.drk".
The dark data files will be saved in the experiment directory that has been picked by the option File-LoadExperiment or File-Start New-Experiment.
3.1.6
File Menu: Save Reference
With this option, reference data are saved. The name of the reference data file is "serialnr.ref".
The reference data files will be saved in the experiment directory that has been picked by the option FileLoad-Experiment or File-Start New-Experiment
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3.1.7
File Menu: Save Experiment
With this option, spectral data is saved. All graphic files will be saved in the experiment directory that has
been picked by the option File-Load-Experiment or File-Start New-Experiment.
Saving graphic files if one spectrometer channel is enabled
First, a window appears in which a line of comments can be entered to the saved graph. Next, two files
will be saved: the first file contains the saved spectrum data. The name of this first file starts with the
experiment name, directly followed by the sequence number of the saved spectrum. The extension of this
first file depends on the current measuring mode, as shown below:
Extension
Mode
ROH
Scope Mode
ABS
Absorbance
TRM
Transmittance/Reflectance
IRR
Irradiance
The second file contains the line of comments, which may have been added to this graph. The name of
this second file is, except for the extension, the same as the name of the first file (experiment name and
sequence number). The extension of this second file also depends on the measuring mode, as shown
below:
Extension
Mode
RCM
Scope Mode
ACM
Absorbance
TCM
Transmittance/Reflectance
ICM
Irradiance
Example: suppose the name of our experiment is "avantes". Then, saving one spectrum in scope mode, one
in absorbance mode and two in transmittance mode results in the following files:
avantes0001.roh:
spectrum data in scope mode
avantes0001.rcm:
comments for the spectrum saved in avantes0001.roh
avantes0001.abs:
spectrum data in absorbance mode
avantes0001.acm:
comments for the spectrum saved in avantes0001.abs
avantes0001.trm:
spectrum transmittance mode
avantes0001.tcm:
comments for the spectrum saved in avantes0001.trm
avantes0002.trm:
spectrum data in transmittance mode
avantes0002.tcm:
comments for the spectrum saved in avantes0002.trm
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After leaving the application and opening AvaSoft the next time, saving graphics in scope, absorbance and
transmittance mode, will then result in respectively the data-files avantes0002.roh, avantes0002.abs and
avantes0003.trm, as well as the comment files avantes0002.rcm, avantes0002.acm and avantes0003.tcm.
Before saving, the name of the graphic file is displayed in the statusbar at the bottom of the screen. After
saving, the sequence number is automatically incremented by one.
Saving graphic files if multiple spectrometer channels have been enabled
If graphic files are saved while more than one channel is viewed at the same time (see option ViewChannel), then the graphic filename for each channel that is displayed gets a different sequence number.
For example, the result of saving one experiment in triple view mode is three graphic data files and three
comment files, for instance:
avantes0002.roh: spectrum data in scope mode (e.g. spectrometer 1 or Master Channel)
avantes0003.roh: spectrum data in scope mode (e.g. spectrometer 2 or Slave1 Channel)
avantes0004.roh: spectrum data in scope mode (e.g. spectrometer 3 or Slave2 Channel)
avantes0002.rcm: comments for the spectrum saved in avantes0002.roh
avantes0003.rcm: comments for the spectrum saved in avantes0003.roh
avantes0004.rcm: comments for the spectrum saved in avantes0004.roh
For each channel a different comment line can be entered.
To make it easier to select the graphic files later on with the option File-Display Saved Graph, all
comment lines start with a short name for the channel at which the graph has been saved: M for Master,
S1 for Slave1 and so on.
After saving, the sequence numbers in this example (triple view mode) will automatically have been
increased to 0005, 0006 and 0007, for resp. Master, Slave1 and Slave2.
Starting with version 7.4, the spectra from multiple spectrometer channels with consecutive wavelength
ranges can (under certain conditions) be merged and saved to one file. Consult section 3.2.9.13 for
details.
3.1.8
File Menu: Print
After selecting the print menu option,
the background colors in the
graphical region will become white. If
the menu option “Black and White
printer” (see next section) has been
marked, the line style for the spectra
will also change from colored to
black. A dialog will be shown in which
the title for the printout can be
entered. In the next window, the
printer settings can be changed (e.g.
portrait or landscape printing,
printing quality etc.). After clicking
OK in the printer settings dialog, the
graph will be printed, and the original
graph colors will be restored on the
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monitor.
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3.1.9
File Menu: Black and White printer
The default setting in AvaSoft is to print the spectra in the same color as they appear on the monitor.
However, if a color printer is not available, the menu option “Black and White printer” can be enabled. If
this option is enabled, different line styles will be printed if more than one spectrum is displayed, e.g.
dash-dash, dot-dot, dash-dot. To enable this option, click the menu option and a checkmark appears in
front of it.
3.1.10 File Menu: Display Saved Graph
This option requires that graphic
files were saved earlier by using
the option File-Save Experiment.
After choosing this option, a
window shows all files in the
current measure mode. In the
example at the right, the measure
mode is “scope”, so the extension
of the earlier saved spectra is
*.roh.
To select graphic files that were
saved in another measure mode,
e.g. absorbance, click
behind
the Graph - …Mode, and pick the
desired measure mode.
To select graphic files from another folder or drive, click
behind the current foldername.
If a graphic file is marked by a (single) mouse click on the filename, the comment line for this file appears
at the top of the graphical region in the main window. Selecting multiple filenames can be realized by
using the CTRL or SHIFT key in combination with the mouse. If the CTRL key is pressed, all the files that
are clicked by the mouse will be selected for displaying. If the SHIFT key is pressed, all the files in
between two clicked files will be selected for displaying.
Select the name of the file(s) to be displayed and click the Open button. To leave this dialog without
displaying graphic files, click the CANCEL button.
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In the figure at the right, two
graphic files were selected in
scope mode. The comments
that were saved with these
graphs are displayed at the top
of the graphical region,
together with information about
amplitude at current
wavelength (amp), integration
time (it) and smoothing (s)
settings at the moment that the
file was saved and the name of
the graphic file. If the active
spectrometer channels (e.g.
Master) have not been
unselected with the View
Channel option, the actual data
for the activated channel(s) will
be displayed in the same graph
as the selected graphic files. By
clicking the green start button, the online measurements can be compared directly to the graphics that
were saved before.
New in AvaSoft 7 is that displayed graphs can be deleted or properties
of the displayed graphs, such as line style or color or comments can
be changed. This is done by clicking with the right mouse button on
the line in the graphical display. A small line edit box will appear.
Now the line can be deactivated or the line properties can be
changed as depicted in the border editor or the comments
can be edited.
The menu option File-Display Saved Graph is preceded by a
checkmark as long as the earlier saved graphics are displayed.
To clear these earlier saved graphics, select again the menu
option File-Display Saved Graph, after which the checkmark
disappears, and only the spectra for the active spectrometer
channel(s) will be displayed.
Starting with version 7.4, so-called merged files can be displayed. These contain spectra from multiple
channels, combined in a single graph. Consult section 3.2.9.13 for details.
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3.1.11 File Menu: Display 3D Graph
The 3D Graph option allows you to load a large number of existing AvaSoft graphs into a 3D view. You can
view the 3D graph from different sides and zoom in on a section of the graph.
The manipulation of the 3D graph is done indirectly, with two separate 2D graphs.
The graphs can be saved as 3 JPEG files, embedded in a single .RTF file. This file can be loaded into
Microsoft Word, for text editing, extraction of the JPEG files, resizing etc.
Introduction
This option allows you to visualize data that was saved earlier, with a single 3D and two 2D graphs. You
can select the files in the menu, with ‘File’, ‘Load into 3D Graph’. A standard windows dialog will appear.
You can select the file type in the bottom combo box, all four types of AvaSoft files can be selected
(Scope, Absorbance, Transmittance/Reflectance and Irradiance). Select multiple files with the mouse in
the standard Windows way, by holding down the Shift or Ctrl key.
There is a limit to the amount of input files that the windows dialog can handle. The exact number of files
that can be handled depends on the combined length of the filenames. If you want to handle thousands of
files at a time, use short names like ‘a00001.roh’, ‘a00002.roh’ etc. With this naming scheme, which is
the shortest that can be used in the Store To Ram application, we have been able to read 2520 files at a
time. Selecting more files will generate the following error:
The order in which these files are added to the 3D view can be either alphabetically, or on the basis of
the date/time stamp that each file has in the directory. A complication with the last criterion is the fact
that windows only has a 2 second resolution in this date/time stamp. If you have saved the files with e.g.
the Store To Ram application, you could have many files with an identical date/time stamp. In that case,
it is better to use an alphabetical order.
The files that are read are checked for their wavelength range, and also for the embedded serial number
of the spectrometer they originated from. If they are found to be from multiple spectrometers, you will
have to select between these spectrometers.
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You cannot display spectra from multiple spectrometers in the same 3D graph.
The handling of the graphs is patterned after the one in the Store To Ram application:
The view of the 3D graph can be adjusted by inverting the Depth axis and the X axis. These axes can also
be transposed, which enables a side view of the graph.
The Y axis is auto scaled by default, this can be undone by unchecking the option in the ‘Adjust View’
box.
The 2D graphs both have a scrollbar, which allows you to change the third dimension. It is also possible to
display the position of each 2D graph in the 3D graph by displaying a separate highlighted line that
sections the 3D graph. This feature is turned on and off with the ‘3D’ checkbox at the top-right position of
each 2D graph.
The amount of data in the 3D graph and the second 2D graph (Counts vs. Measurement #) has been limited
to prevent computer overload. If more data is present, only one out a calculated number of scans or
pixels is shown. Zooming the graphs will reveal more detail. The fraction of the data that is shown is
indicated in the title of the relevant axis.
E.g. ‘Measurement # (1/10)’ means that only one out of every 10 scans is shown.
Note that the first 2D graph (Counts vs. Wavelength) always shows all of the data present. It is therefore
possible to show this graph as a highlighted line in the 3D graph that shows more detail than the 3D graph
itself shows. Zooming in will show more detail in the 3D graph, which will eventually correct the
discrepancy.
The 3D graph does not allow direct manipulation with the mouse. You can zoom both 2D graphs and the
3D graph will zoom to the selected range. The selected range will then also be shown in the manual
selection boxes described below.
Unzooming the 2D graphs will also unzoom the 3D graph.
Note that zooming and unzooming the 2D graphs is performed the same way as in the main screen of
AvaSoft:
You zoom the graph by clicking the top-left corner of your area to select, hold down the left mouse
button, then draw a rectangle and release the mouse button at the lower-right corner of the area to
select.
You unzoom the graph by clicking anywhere on the graph, hold down the left mouse button, then drag a
rectangle towards the top and left and release the mouse button at any position.
You can pan the 2D graphs by holding down the right mouse button.
It is also possible to manually select the ranges by entering values in the ‘Select Measurement # Range’,
‘Select Wavelength Range’ and ‘Select Counts Range’ boxes, and pressing the ‘Zoom’ button. Note that
changing the ‘Select Counts Range’ will only have an effect if the ‘Autoscale Y-axis’ option is unchecked.
The ‘Unzoom’ button will undo all your changes.
You can save the graphs to disk by pressing the ‘Save Graphs’ button. You can first enter a comment line,
which will be included on the page. Next, you can enter the filename that will be used to save the graphs.
The three graphs will be saved in JPEG format, embedded in a single, one page .RTF file. You can open
this file with Microsoft Word, edit it, extract the graphs, change the size of the graphs, etc.
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Quick Start
1.
2.
3.
4.
5.
Select the input file sort order in the upper right corner.
Select ‘File’, ‘Load into 3D Graph’ in the menu.
Select the files to show in the standard Windows dialog.
Inspect the data by zooming the 2D graphs with your mouse. Scroll the 2D graphs with their
scrollbars, see where the line is located in the 3D graph by selecting the 3D checkbox in either
2D graph. The data that is changed when scrolling the 2D graphs with their respective
scrollbars is also shown in the boxes to the right of each 2D graph.
Save the graphs by pressing the ‘Save Graphs’ button in the upper right corner.
Main Window
The upper right of the window is used to select the
Input File Sort Order, to adjust the view of the 3D
graph, and to manually make a selection from the
scans.
The Input File Sort Order selects the way the input
files selected from the input dialog are sorted. You
can select between alphabetical sort order and file
date/time sort order. Windows only offers a
resolution of 2 seconds in the file date/time stamp.
Especially when you save files with the Store To
Ram application, many files will have an identical
date/time stamp. Be sure to select alphabetical
order in that case.
The Adjust View checkboxes allow viewing the 3D
graph from all sides. The Autoscale Y axis button is
checked by default. Unselecting it will only yield a
satisfactory image if the Y range is positioned at an
edge of the graph, otherwise there will be other
readings filling the entire screen behind the
selected lines.
Manually change the scan selections by changing the values in the ‘Select Range’ fields and pressing the
‘Zoom’ button. ‘Unzoom’ will undo any change made.
Note that manually changing the ‘Select Count Range’ will only have an effect if the ‘Autoscale Y Axis’
box is unchecked.
The 2D graphs each have a scrollbar that changes the respective third dimension. The position of the
scrollbar is reflected in the boxes to the right of each 2D graph. Change the scrollbar in the standard
Windows ways: Clicking the arrows will cause a change of a single unit, clicking between the arrows and
the thumb will change 10 units, dragging the thumb will select a new position in the readings relative to
the position of the thumb. You can also use the keyboard to change the scrollbar, the Up and Down keys
will give a single unit change, the PageUp and PageDown keys will give a change of 10 units, the Home and
End keys will move to the first and last reading. Checking the 3D boxes in the upper right corner of each
graph will show the graph as a highlighted line in the 3D graph.
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The Measurement # axis of the right 2D graph has a maximum number of points. If this is exceeded, only
one out of a calculated number of points will be shown. This ratio is added to the title of the axis, e.g.
‘Measurement # (1/10)’ means that only one out of 10 points is shown. In this case, zooming the right 2D
graph will reveal more detail.
Zooming the 2D graphs with the mouse can also be used to select a wavelength and measurement # range.
The selection will also be shown in the 3D graph. Zooming and Unzooming is done in the regular AvaSoft
way. You can also pan the graph by dragging the mouse while holding the right mouse key down. This has
no effect on the 3D graph.
The 3D graph cannot be manipulated directly. It is redrawn after the 2D graphs are zoomed, or after the
ranges are manually changed, and the ‘Zoom’ button is pressed. The view of the graph can be changed in
a basic number of ways, to allow a view of all sides. A highlighted line can be shown in the 3D graph for
both 2D lines.
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3.1.12 File Menu: Convert Graph – Include ASCII Header
Converting the spectra to ASCII and ASCII-Equidistance can be done with or without header information. If
the ASCII files are further processed by other software, the header is often not compatible. The option
“Include ASCII Header” is preceded by a checkmark by default. If the header information should be left
out, click the “Include ASCII Header” to toggle the checkmark.
3.1.13 File Menu: Convert Graph - to ASCII
This option requires that
graphic files were saved
earlier by using the option
File-Save Experiment. After
choosing this option, a
window shows all files in the
current measure mode. In the
example at the right, the
measure mode is “scope”, so
the extension of the earlier
saved spectra is *.roh.
To select graphic files that
were saved in another
measure mode, e.g.
absorbance, click
behind
the Graph - …Mode, and pick
the desired measure mode.
behind the current foldername. If a graphic
To select graphic files from another folder or drive, click
file is marked by a (single) mouse click on the filename, the comment line for this file appears at the top
of the graphical region in the main window. Selecting multiple filenames can be realized by using the
CTRL or SHIFT key in combination with the mouse.
If the CTRL key is pressed, all the files that are clicked by the mouse will be selected for conversion. If
the SHIFT key is pressed, all the files in between two clicked files will be selected for conversion.
Select the name of the file(s) to be converted to ASCII and click the Open button. To leave this dialog
without converting files, click the CANCEL button. The extension of the text files depends on the
extension of the binary graphic file as shown below:
Extension binary file
Extension text-file
ROH
TRT
ABS
TAT
TRM
TTT
IRR
TIT
All text files start with a header with information for the graphic file that has been converted. The header
shows:
-
the comment line
-
the integration time
-
the number of scans that has been averaged
-
the number of pixels used for smoothing
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-
the serial number of the spectrometer that was used to save the data
The data in a *.TRT file is given in two columns. The first column gives the wavelength in nanometers, the
second one the scope data.
The data in the *.TAT, *.TTT files is presented in five columns. The first column gives the wavelength in
nanometers. The second to fourth column give respectively the dark, reference and scope data. The fifth
column shows the calculated value for absorbance (in a *.TAT file) or transmittance (in a *.TTT file).
The format for the irradiance text files (*.TIT) depends on the availability of AvaSoft-IRRAD. The absolute
irradiance text file that will be generated if AvaSoft-IRRAD is available shows six columns. The first two
columns are the wavelength and dark data. The third column is the transfer function from counts to
microwatts. The fourth column contains the measured counts. In column five and six, the calculated
irradiance values are given in microwatts per square centimeter (column 5) and in photon counts (column
6). The relative irradiance text file that will be generated if AvaSoft-IRRAD is not available shows five
columns. The first column gives the wavelength in nanometers. The second to fourth column give
respectively the dark, reference and scope data. The fifth column shows the calculated value for relative
irradiance.
Starting with version 7.4, so-called merged files can be converted. These contain spectra from multiple
channels, combined in a single graph. Consult section 3.2.9.13 for details.
3.1.14 File Menu: Convert Graph - to ASCII Equi distance
This option requires that graphic files were
saved earlier by using the option File-Save
Experiment. After selecting the option “File/
Convert Graph/To ASCII – Equi distance”, the
wavelength range for which the
data should be converted, and the distance
between two successive data points can be
entered in the dialog as shown at the right.
After clicking the OK button, you can select the
files which need to be converted. Selecting
these files is the same as for converting to ASCII
without the equi distance feature (section
3.1.13).
Also the information in the header file is the same as for converting to ASCII without the equi distance
feature. The data in the *.TRT, *.TAT, *.TTT and *.TIT files is presented in two columns. The first column
gives the equally spaced wavelength in nanometers. The second column shows the interpolated value for
scopedata (in a *.TRT file), absorbance (in a *.TAT file), transmittance (in a *.TTT file) or irradiance (in a
*.TIT file).
Starting with version 7.4, so-called merged files can be converted. These contain spectra from multiple
channels, combined in a single graph. Consult section 3.2.9.13 for details.
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3.1.15 File Menu: Convert Graph - to J-CAMP
JCAMP-DX is a standard file format for
exchange of spectra between different
spectrometer systems and computers. A
JCAMP-DX spectrum is a text file, which
can be viewed, corrected and annotated
with a text editor. A lot of other
elaborate spectrometer software
programs, like Grams32 and OPUS, are
capable of importing files in JCAMP-DX
format.
The J-Camp format requires an equal
distance between the data points at the
X-axis (wavelength). Converting the CCDpixels to wavelength points is not a
linear function, so before writing to the
J-Camp format, the data points are linearized first.
This option requires that graphic files were saved earlier by using the option File-Save Experiment. After
choosing this option, a window shows all files in the current measure mode. In the example at the right,
the measure mode is “scope”, so the extension of the earlier saved spectra is *.roh.
To select graphic files that were saved in another measure mode, e.g. absorbance, click
Graph - …Mode, and pick the desired measure mode.
behind the
If a graphic file is marked by a (single) mouse click on the filename, the comment line for this file appears
at the top of the graphical region in the main window. Selecting multiple filenames can be realized by
using the CTRL or SHIFT key in combination with the mouse. If the CTRL key is pressed, all the files that
are clicked by the mouse will be selected for conversion. If the SHIFT key is pressed, all the files in
between two clicked files will be selected for conversion.
Select the name of the file(s) to be converted to J-Camp and click the Open button. To leave this dialog
without converting files, click the CANCEL button. The text files in J-Camp format require an extension
DX. If, for example a file AVANTES0001.trm and another file AVANTES0001.abs are both converted to JCamp, the result will be AVANTES0001.dx in both cases.
Starting with version 7.4, so-called merged files can be converted. These contain spectra from multiple
channels, combined in a single graph. Consult section 3.2.9.13 for details.
3.1.16 File Menu: Convert Graph - to Excel
This option requires that graphic files were saved earlier by using the option File-Save Experiment. After
choosing this option, a window shows all files in the current measure mode. In the example below, the
measure mode is “scope”, so the extension of the earlier saved spectra is *.roh.
To select graphic files that were saved in another measure mode, e.g. absorbance, click
Graph - …Mode, and pick the desired measure mode.
behind the
If a graphic file is marked by a (single) mouse click on the filename, the comment line for this file appears
at the top of the graphical region in the main window. Selecting multiple filenames can be realized by
using the CTRL or SHIFT key in combination with the mouse. If the CTRL key is pressed, all the files that
are clicked by the mouse will be selected for conversion. If the SHIFT key is pressed, all the files in
between two clicked files will be selected for conversion.
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Select the name of the file(s) to be converted to Excel and click the Open button
If not already open, Excel will be opened by AvaSoft and the conversion will be done in 2 steps:
• In step1 all files that have been selected will be sorted into groups with the same serial number AND
wavelength calibration coefficients. For example, in a 4 channel system, there will generally be 4
groups.
• In step2, a sheet will be created in Excel for each group with the name of the serial number and the
data of all selected files that belong to this sheet is written to Excel.
The first six rows in each Excel sheet are reserved for: Filename, Mode/Unit, Integration Time,
NrOfAverages, Smoothing, and comments (the comments that were saved with the file) The first column
represents the wavelength, the other columns the data.
If for a certain channel the wavelength calibration is changed, then the data does not fit into the same
sheet with the old wavelength calibration (because there is only one column with wavelength). In that
case a new sheet is generated with serialnumber with suffix _1 (e.g. 0706005U1_1), after a next change
_2, etc... Since the AvaSpec spectrometers have a very stable wavelength calibration, which normally
does not need to be changed, the _1 etc.. will not often show up.
Irradiance files: files that have been saved in the irradiance chart (absolute irradiance application) can
have a number of different units. During the conversion to Excel, the unit is read and the calculated data
for that unit (emitted/received power or energy, photons etc..) is written to Excel. The unit is displayed
in the second row. An absolute irradiance file that is saved in the main window is always in uwatts/cm2.
Without the AvaSoft-IRRAD, the unit in irradiance mode will be relative irradiance.
Limitations: An Excel sheet includes 256 columns. Therefore, a maximum of 255 files (1 column for
wavelength) can be transferred into one sheet.
Starting with version 7.4, so-called merged files can be converted. These contain spectra from multiple
channels, combined in a single graph. Consult section 3.2.9.13 for details.
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3.1.17 File Menu: Save Graph to .RTF
This menu option allows you to save the main screen to disk. The graph will be saved in JPEG format,
embedded in a one page .RTF file. You can open this file with Microsoft Word, edit it, extract the graph,
change the size of the graph, etc.
3.1.18 File Menu: Exit
Closes AvaSoft.
The measurement settings are saved to EEProm before
the software is closed. During the process of saving it
is very important that the spectrometer is not
powered off. A dialog as shown at the right will
become visible as long as data are saved (< 1 sec for
USB2), about 8 sec for RS232/bluetooth connection.
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3.2 Setup Menu
3.2.1
Setup Menu: Hardware
This option shows all connected spectrometers and allows you to change the name of the channel and to
deactivate and activate spectrometers. For synchronization of scans a master sync spectrometer needs to
be dedicated, in Multichannel platforms usually the spectrometer from the left as seen from the front is
assigned as master sync by Avantes.
For the NIR2.2/2.5 and the TE Cooled USB2 spectrometers, the Setpoint temperature can be entered at
which the detector will be held constant.
AvaSpec-3648 mode
The Toshiba detector, as implemented in the AvaSpec-3648, can be used in 2 different control modes:
1. The Prescan mode (default mode).
In this mode the Toshiba detector will generate automatically an additional prescan for every
request from the PC, the first scan contains non-linear data and will be rejected, the 2nd scan
contains linear data and will be showed on the screen and/or saved. This prescan mode is default
and should be used in most applications, like with averaging (only one prescan is generated for a
nr of averages), with the use of an AvaLight-XE (one or more flashes per scan) and with
multichannel spectrometers. The advantage of this mode is a very stable and linear spectrum. The
disadvantage of this mode is that a minor (<5%) image of the previous scan (ghostspectrum) is
included in the signal.
This mode cannot be used for fast external trigger and accurate timing, since the start of the scan
is always delayed with the integration time (min. 3.7 ms).
2. The Clear-Buffer mode.
In this mode the Toshiba detector buffer will be cleared, before a scan is taken. This clear-buffer
mode should be used when timing is important, like with fast external triggering. The advantage
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of this mode is that a scan will start at the time of an external trigger, the disadvantage of this
mode is that after clearing the buffer, the detector will have a minor threshold, in which small
signals (<500 counts) will not appear and with different integration times the detector is not
linear.
3.2.2
Setup Menu: Wavelength Calibration Coefficients
After clicking this option, a dialog is shown in which the wavelength calibration coefficients can be
changed manually.
Background
The wavelength λ that corresponds to a pixel number (pixnr) in the detector in the spectrometer can be
calculated by the following equation:
λ = Intercept + X1*pixnr + X2*pixnr2 + X3*pixnr3 + X4*pixnr4
in which Intercept and X1 to X4 correspond to
Intercept and First to Fourth Coefficient in the
figure at the right. For example, if we want to
calculate the wavelength at pixel number 1000,
using the numbers in the figure at the right, the
wavelength becomes:
λ=
384,054 + 0,136492*1000 +
-6,71259E-6*1E6 +
-5,66234E-10*1E9
=
513,267 nm.
The ‘Restore Factory Settings’ button restores
for all spectrometer channels the original
wavelength calibration coefficients that were saved to the EEPROM during factory calibration.
The “Process data only when in following wavelength range” option can be used to transfer only a limited
number of pixels from the spectrometer to the PC. This can significantly speed up the transfer time (e.g.
for the AvaSpec-2048 from 30 ms at full wavelength range down to 14 ms for a small selection of 10
pixels). A second advantage is data reduction, because only the spectral data will be saved at the pixels
for which the wavelength is in the specified wavelength range.
3.2.3
Setup Menu: Smoothing and Spline
The Cubic Spline Interpolation Algorithm can be
applied to get a better estimation for the spectral
data between the pixels on the detector array.
Smoothing is a procedure, which averages the
spectral data over a number of pixels on the
detector array. For example, if the smoothing
parameter is set to 2, the spectral data for all
pixels xn on the detector array will be averaged
with their neighbor pixels xn-2, xn-1, xn+1 and xn+2.
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Cubic Spline Interpolation
In the figure at the right, the effect of spline interpolation is illustrated. The Master data shows the AD
counts for 4 pixels, connected by a straight line (linear interpolation). The Slave1 data is for these 4 pixels
exactly the same as for the Master data, but this time the cubic spline interpolation algorithm has been
applied, resulting in data which is
smooth in the first derivative and
continuous in the second
derivative.
The spline interpolation can be
useful for applications in which
the output of line sources, like
laser diodes is displayed, or for
other applications, which require
a high resolution. Note that for
the AvaSpec-2048 with 2048
pixels, the effect of spline
interpolation is not visible if the
data is shown at full scale. The
monitor resolution is much less
than 2048 pixels. The effect of
spline interpolation can only be
visualized if the number of
detector pixels that are displayed
is smaller than the number of monitor pixels at the x-axis.
Smoothing
To get a smoother spectrum without losing information it is important to set in the software the right
smoothing parameter. The optimal smoothing parameter depends on the distance between the pixels at
the detector array and the light beam that enters the spectrometer. For the AvaSpec-2048, the distance
between the pixels on the CCD-array is 14 micron.
With a 200 micron fiber (no slit installed) connected, the optical pixel resolution is about 14.3 CCD-pixels.
With a smoothing parameter set to 7, each pixel will be averaged with 7 left and 7 right neighbor pixels.
Averaging over 15 pixels with a pitch distance between the CCD pixels of 14 micron will cover 15*14 = 210
micron at the CCD array. Using a fiber diameter of 200 micron means that we will lose resolution when
setting the smoothing parameter to 7. Theoretically the optimal smoothing parameter is therefore 6. The
formula is ((slit size/pixel size) – 1)/2
In the table below, the recommended smoothing values for the AvaSpecs spectrometer are listed as
function of the light beam that enters the spectrometer. This light beam is the fiber core diameter, or if a
smaller slit has been installed in the spectrometer, the slit width. Note that this table shows the optimal
smoothing without losing resolution. If resolution is not an important issue, a higher smoothing parameter
can be set to decrease noise against the price of less resolution.
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Slit or
Fiber
AvaSpec-102
AvaSpec-128
10µm
25µm
Pixel 77 µm
n.a.
n.a.
50µm
AvaSpec-3648
AvaSpecNIR256
Pixel 63.5 µm Pixel 25 µm
n.a.
n.a.
n.a.
0
AvaSpec-2048
AvaSpec-2048L
AvaSpec-2048x14
Pixel 14 µm
0
0-1
Pixel 8 µm
0
1
Pixel 50 µm
n.a.
n.a.
0
0
0-1
1-2
2-3
0
100µm
0-1
0-1
1-2
3
5-6
0-1
200µm
1
1
3-4
6-7
12
1-2
400µm
2
2-3
7-8
13-14
24-25
3-4
500µm
3
3-4
9-10
17
31
4-5
600µm
3-4
4
11-12
21
37
5-6
3.2.4
AvaSpec-256
AvaSpec-1024
Setup Menu: Use 16bit ADC in 14bit mode (HW rev 1D and later)
The 14bit AD Converter used with the as5216 boards revision 1B and 1C inside the AvaSpec-USB2 has been
replaced by a 16bit ADC since the release of the as5216 board revision 1D. Therefore, the default range in
Scope Mode for an AvaSpec-USB2 has changed from a 14bit range (0..16383) to 16bit (0..65535).
If the menu option “Use 16bit ADC in 14bit mode” is enabled (preceded by a checkmark), the 16bit range
AD Counts will be converted to a 14bit range by the as5216.dll (divide by 4.0). This option has been added
for customers who have been already working with earlier versions of the AvaSpec-USB2 with 14bit ADC,
and want to be able to compare the data in scope mode between both spectrometers. Note that by
setting the 16bit ADC into 14bit mode, you will not lose resolution because the numbers are not truncated
or rounded to integer numbers, e.g. 5 counts in 16bit mode will become 1.25 counts in 14-bit mode.
If multiple AvaSpec-USB2 spectrometers are connected simultaneously and one or more devices do not
support the 16bit ADC (rev 1B or rev 1C as5216 board), all spectrometers will be set automatically to 14bit
mode (range 0..16383 AD counts).
3.2.5
Setup Menu: Correct for Dynamic Dark
The pixels of the detector are thermally sensitive, which causes a small dark current, even without
exposure to light. To get an approximation of this dark current, the signal of some optical black pixels of
the detector can be taken and subtracted from the raw scope data. This will happen if the correct for
dynamic dark option is enabled. As these optical black pixels have the same thermal behaviour as the
active pixels, the correction is dynamic.
Some detector types (AvaSpec-2048/2048L/3648/2048x14) include dedicated optical black pixels. New in
AvaSoft 7.5 is the dynamic dark correction support for the NIR256-2.0/2.2/2.5. For these detectors, a few
datapixels can be blackened during fabrication of the optical bench. These blackened pixels can then be
used for dynamic dark correction.
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For spectrometers with dedicated optical black or blackened pixels, the correct for dynamic dark option
can be switched on or off by clicking this menu option. The option is on if the menu option is preceded by
a checkmark which is the default state. If the connected spectrometers don’t have optical black or
blackened pixels, the correct for dynamic dark menu option will not be available.
Note that this option is different from the dark current that needs to be saved before any transmittance
or absorbance measurements can be taken (File-Save Dark). If the correct for dynamic dark option has
been changed, it will be necessary to save a new dark and reference spectrum because the raw data has
been changed.
3.2.6
Setup Menu: Subtract Saved Dark
This option is used to subtract the dark spectrum that has been saved (File-Save Dark) from the raw scope
data. After starting AvaSoft, this menu option is always unselected, because a dark spectrum needs to be
saved or loaded before it can be subtracted.
If this menu option is preceded by a checkmark, the scope data is corrected with the saved dark.
3.2.7
Setup Menu: Strobe Enable
This option can be used to enable or disable an external strobe (e.g. the AvaLight-XE) attached to an
AvaSpec spectrometer. The measured light intensity of the AvaLight-XE is independent of the integration
time in AvaSoft. To increase light intensity, the number of pulses per integration interval should be
increased. The maximum frequency at which the AvaLight-XE operates is 100 Hz. This means that the
minimum integration time for 1 pulse per scan is 10 ms. When setting the number of pulses e.g. to 3, the
minimum integration time becomes 30 ms. It is recommended to keep the integration time as low as
possible to avoid unnecessary increase of noise.
Strobe (AvaLight-XE) Control
The AvaLight-XE needs to be attached to AvaSpec-USB2 by
connecting an IC-DB26-2 interface cable between the high density
26 pole Sub-D connectors at the AvaSpec-USB2 and the 15-pole DB
connector of the AvaLight -XE. If used with a multichannel system,
make sure that the AvaLight-XE is connected to the master sync
spectrometer, only the number of flashes per scan set for the
master synch spectrometer will determine flash rate. To disable
the strobe, simply enter 0 under the NrOfFlashes.
3.2.8
Setup Menu: PWM (AvaLight-LED) control
The AvaLight-LED needs to be attached to a AvaSpecUSB2 by connecting an IC-DB26-2 interface cable
between the high density 26 pole Sub-D connectors at
the AvaSpec-USB2 and the 15-pole DB connector of
the AvaLight –LED (DO1 – pin11).
The frequency can be set between 500 Hz and 300
kHz, the duty cycle between 0 and 100%.
If used with a multichannel system, all channels can
have their own independent PWM setting for both frequency and duty cycle.
To disable the PWM output, simply enter 0 under the Duty Cycle.
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3.2.9
Setup Menu: Options
All options described in this section are standard included in
AvaSoft FULL version. In AvaSoft BASIC, these features are
not available.
3.2.9.1 Setup Menu: Options – Check on Saturation
The 14-bit A/D converter in AvaSpec-USB2 HW rev 1B and 1C results in raw Scope pixel values between 0
and 16383 counts. If the value of 16383 counts is measured at one or more pixels, then these pixels are
called to be saturated or overexposed. The range for the 16-bit A/D converter in the AvaSpec-USB2 HW
rev 1D and later results in Scope pixel values between 0 and 65535. In this case the pixels are saturated at
65535 counts (see also section 3.2.4 about the 16bit ADC mode). Since saturated pixels can disturb the
measurement results, a lot of attention has been given in AvaSoft (and the driver packages AS161.DLL/AS-5216.DLL) to detect saturation and to notify the user if a measurement contains saturated
pixels. This notification is done in such a way that the user can always decide to ignore the saturation, for
example if the saturation happens at pixels that are not in the wavelength range where the user is
interested in. Saturation can usually be solved by selecting a shorter integration time. When at minimum
integration the signal is still too high, an attenuator, a neutral density filter or fibers with a smaller
diameter may be used.
In AvaSoft, different levels of saturation detection can be set, as shown in the figure at the right.
Saturation detection levels
The default level of saturation detection is “Detect
Saturated Pixels at saturation level”. Only for
AvaSpec-2048 spectrometers, the third (autocorrect
inverted pixels) level is available. The reason for
this is that if the detector type in the AvaSpec-2048
(Sony-ILX554) is heavily saturated (at a light
intensity of approximately 5 times the intensity at
which saturation starts), it will return values <
saturation level. The other detector types in the
AvaSpec-102, 256, 1024 and 3648 do not show this
effect, so no correction is needed. Normally, you
don’t need to use this third level for the AvaSpec2048, but when measuring a peaky spectrum with
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some heavily saturated peaks, the autocorrect can be used. To illustrate this, a strong peak from the
AvaLight-CAL calibration line source was heavily saturated at 435.84 nm. This caused the most heavily
saturated pixels to return inverted (<16383 counts) pixel values (figure below at the left). In the right
figure, the saturation detection has been set to the third level, which will not only detect the saturated
pixels at 16383 counts, but also detect and correct the inverted saturated pixels. Disadvantage of the
autocorrect detection level is that processing the saturated scans by the application takes more time.
Saturation Notification
If the saturation detection has not been switched off, the spectrometer channel statusbar will show the
text label “saturated” as long as one or more pixels of that spectrometer channel are saturated:
This is useful for measurements in transmittance, absorbance and irradiance mode, because in these
modes saturation can not be observed by looking at the number of counts, like in scope mode. But even in
scope mode, a spectrum can contain saturated pixels also when this is not directly obvious from the
graph. Examples are:
•
Smoothing. The maximum pixel value of a peak can be saturated, but is averaged with neighbor
pixels which may not be saturated.
•
The correct for dynamic dark algorithm subtracts the dark values that are measured at the optical
black pixels from the spectral data. Therefore, the saturation level of 16383 (65535 in 16 bit mode)
counts will never be reached with correct for dynamic dark ON. The saturation detection in AvaSoft
is done before the data is corrected for dynamic dark, so it will also detect saturation with dynamic
dark ON.
•
Monitor resolution. The CCD contains 2048/3648 pixels which is a lot more than the monitor pixels
in the graph. Since not each CCD pixels can be drawn at the monitor, a sharp peak at one CCD pixel
can be saturated although this is not visible at the monitor. Use the zoom function if you want to
verify if this is the cause of saturation.
•
Zoomed in. Saturation can also happen at a wavelength range that is not visible because the graph
is not at full scale.
Under all these circumstances, the “saturation” label will be shown in the statusbar of the spectrometer
channel for which one or more pixels are saturated. During time series measurements (History Channel
Functions, color versus time, irradiance versus time) the saturation detection will be done only for the
relevant wavelength range. The relevant wavelength range in color measurements is from 380 to 780 nm.
For History Channel Functions, the relevant wavelength range is set by the user. For example, when
monitoring an integral between 500 and 505 nm, saturation detection and notification will be done only
for this range. If saturated, the saturation label will become visible in the History Channel output. If the
time series measurements are saved online to Excel, the font color in Excel will be red for a history
channel as long as the output for that channel is saturated.
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3.2.9.2 Setup Menu: Options – Full Width Half Max
The Full Width Half Maximum of a peak is the bandwidth (in nanometers) for which the intensity is higher
than half of the maximum intensity of that peak. The FWHM can be calculated in Scope or Irradiance
Mode. This utility is used mostly measuring the output of laser diodes. During FWHM calculations, the
intensity needs to be corrected for the dark data. Therefore it is recommended to enable the option
Subtract Saved Dark.
The FWHM can be displayed in two different ways:
Show all FWHM and Peaks in Table
This option allows you to open the table in which Wavelength, Intensity and FWHM are displayed and
updated after each scan (see figure below).
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The results can be saved any time by clicking the Save As button. The file is a textfile with the file
extension .fwm. It can be opened with any texteditor, e.g. notepad.
The channel selector at the top of the FWHM dialog can be useful if there are multiple spectrometers
connected, and you want to switch between channels.
The cursor (vertical green line which is enabled/disabled by the cursor button) will be positioned
automatically on a peak if one of the peaks in the FWHM dialog is clicked with the left mouse button. The
cursor needs to be enabled by clicking the cursor button
Display FWHM in Graph after selection
The dialog at the right appears when clicking this option.
After clicking the OK button, the Full Width Half Max
values are calculated for a number of peaks. To mark a
peak for which the FWHM values need to be calculated,
press the ALT key, and click with the left mouse button on
this peak. If only one spectrometer channel is enabled,
and there are no earlier saved graphs being displayed, then the FWHM value of the marked peak will be
shown directly on top of the peak. Furthermore, this peak will be yellow marked over the width of the
FWHM value (it may be necessary to zoom in on the peak to be able to view that the peak is marked).
If more than one spectrum is being displayed, a dialog, as shown at
the right, pops up in which the spectrum for which the FWHM needs
to be activated can be selected out of all displayed spectra.
In the figure below, 2 peaks have been selected for FWHM
calculation. The FWHM values are given in the same color the
spectrum is drawn in.
To disable the FWHM calculation, the menu option (which is marked
as long as the FWHM is enabled), needs to be reselected.
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3.2.9.3 Setup Menu: Options - Integrals
This utility can be used for measuring the
total amount of energy coming into the
spectrometer. Up to 10 integrals can be
displayed simultaneously. The integral
calculations are enabled after they have
been defined in the dialog that is shown
at the right. This dialog is displayed after
activating the menu option SetupOptions-Integrals. In the example at the
right, two integrals have been defined
(the first 2 are marked by the “Enable”
checkbox in the first column). In the
second column, a spectrum can be
chosen out of all spectra that are at that
moment displayed in the
main window in AvaSoft. A full list of the
spectra to choose from (this includes
earlier saved spectra like integral 2 in
the example) is displayed after clicking
on the arrow button at the right side of the second column. In the third and fourth column, the
wavelength range can be entered over which the integral should be calculated. Finally, a multiplication
factor can be entered for scaling purpose. After clicking the OK button, the integral values are given as
shown in the figure below.
To disable the integral calculation, the menu option (which is marked as long as the Integrals are
enabled), needs to be reselected.
To measure the integral versus time, up to 8 different functions can be entered in the History application.
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3.2.9.4 Setup Menu: Options – Autosave Spectra Periodically
With this option complete spectra will be saved
automatically in time. The following parameters
can be set:
•
Time delay before first scan needs to be
entered in seconds. After clicking the OK
button, AvaSoft waits for this number of
seconds, before the first scan is saved.
•
Time delay between scans needs to be
entered in seconds. This defines the time
between saving two subsequent spectra. If
this number is set to zero, AvaSoft will save
the spectra as fast as possible.
•
Number of scans to save: the number of spectra that needs to be saved can be entered.
On top of the parameters that appear at the right, a checkbox shows: Save As Fast As Possible (no screen
updates).
If the white checkbox in front of this text line is marked, the Automatic Save option will always save the
number of scans that have been entered as fast as possible. To do so, the time delay between scans is
automatically changed to 0 milliseconds at the moment the checkbox is clicked. With this option selected,
the spectra will be saved 5 to 10 times faster, compared to if this option is not selected. This speed
increase has been achieved by mainly two reasons:
1) During the saving of the number of scans that has been entered, the screen update, which is very
time-consuming, is not activated. Instead, the main window is temporarily minimized, and the number
of scans to save is counted down in a new dialog.
2) No comment files will be generated.
Other factors that have a positive effect on the speed of the data acquisition, and which can be set in
AvaSoft are:
• Smoothing parameters.
• Integration time.
• Averaging.
• Number of pixels to transfer (section 3.2.2)
Furthermore, it is recommended to keep the number of files in your experiment directory small (a few
hundred maximum), because a large number of files in the same experiment directory have a negative
effect on the system speed
If the automatic saving needs to be aborted before all spectra have been saved, the “Autosave Spectra
Periodically” menu option can be selected again and the value 0 can be entered for the number of spectra
to be saved.
Note that with the Store to RAM application (section 4.9), the fastest data acquisition can be achieved.
AvaSoft Store To Ram allows you to measure a fixed amount of scans in scope mode as fast as possible,
without the overhead of USB communications. The scans are stored in the internal memory of the AS5216,
and the results are only sent to the computer after the last measurement has been made.
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Save on Digital In
The DB26 connector pins 7, 16 and 24 may be
used to connect external switches, such as
photoswitches, to save a spectrum,
reference or dark. This is especially useful
for automated sampling in a process control
environment with periodical updates of dark
and reference signals. It is recommended to
enable the Automatic save dark by TTL
shutter in combination with the save dark on
digital in setting.
3.2.9.5 Setup Menu: Options - Correct for Drift
Introduction
When measuring the reflectance of a white reference tile or the transmittance of a reference solution
against time, the output should theoretically remain 100% +/- noise. In practice the output value will not
remain exactly fluctuating round 100%, but the signal can slowly drift away. The cause for this drift in the
measurement system can be a change in temperature in the optical bench which causes micro bending of
the components that focus the light at the detector, but also a drift in the light source that is used to
illuminate the reference sample.
To correct for the drift in the system, it needs to be measured first. If a 2-or multiple-channel
spectrometer is available, the measured deviation from 100% at a reference channel can be used to
compensate the measured data at the sample channel. The sample and reference data can be measured
simultaneously and the measured data at the reference sample can be used directly to correct the sample
data. Disadvantage of the “correct for drift by spectrometer channel” is that the data for reference and
sample are measured by using two optical benches which may react differently on temperature changes.
If the drift is mainly caused by the light source (such as a difference in flash intensity of the AvaLight-XE),
this method of correction is recommended.
A disadvantage of this method is that it will not correct for drift caused by temperature changes of the
optical bench.
Correct for Drift by Spectrometer Channel
This option is only available if the spectrometer system has one or more slave
channels. One spectrometer channel will be used as a reference channel,
which will continuously measure the reference spectrum (e.g. the white tile in
reflectance measurements or the cuvette holding the reference solution in
transmittance measurements). Changes in this reference signal, e.g. because
of drift in the lightsource, will be used to correct the data of the other
(selected) spectrometer channels. The wavelength range over which the data
can be corrected will be the overlapping wavelength range between reference
spectrometer channel and the spectrometer channel to be corrected.
If this option is activated, a dialog is shown in which the reference channel
and one or more (depending on the number of spectrometer channels that are
available) channels to be corrected can be selected. After selecting the right
setup, and clicking the OK button, AvaSoft shows the following information:
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Turn on your light source, choose the right integration time and save reference. Then turn off the light
source and save dark. After clicking OK, AvaSoft enables the spectrometer channels that are relevant in
the correct for drift application. After saving the reference and dark files, a message dialog shows that
the data will be corrected for drift. The menu option will be preceded by a checkmark. To disable the
correct for drift option, the menu option (if preceded by a checkmark) needs to be clicked.
3.2.9.6 Setup Menu: Options - Automatic Save Dark by TTL shutter
To use the automatic save dark option, an interface cable needs to be connected from the spectrometer
to the light source with shutter (AvaLight-HAL-S, AvaLight-DHc, AvaLight-D(H)-S-(DUV) ). The interface
cable between TTL-shutter and spectrometer is a 26 pin to 15 pin cable (IC-DB26-2).
The TTL switch at the lightsource needs to be in TTL-position. In AvaSoft, the menu option ‘save
automatic dark by TTL shutter’ needs to be enabled in the menu setup-options. If this option is enabled,
the TTL will close the shutter of the light source at the moment the dark data is saved. After the dark has
been saved, the shutter will be opened automatically.
3.2.9.7 Setup Menu: Options - External Trigger Setting
If the external trigger setting is enabled the spectrometer will wait until a TTL signal at pin 6 of the DB26
connector gets high and will then start the integration time. The delay between the rising edge of the TTL
pulse and the start of the integration time cycle depends on the spectrometer type, as shown in the table
below.
Spectrometer Type
Minimum Delay [µs]
Maximum Delay [µs]
AvaSpec-128-USB2
9
60
AvaSpec-256-USB2
0.80
0.84
AvaSpec-1024-USB2
0.80
0.84
AvaSpec-2048-USB2
1.28
1.30
AvaSpec-2048L-USB2
3.28
3.30
AvaSpec-3648-USB2 (clearbuffer mode)
0.28
0.30
AvaSpec-NIR-256
0
600
AvaSpec-2048x14-USB2
0
2170
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NrOfScans
If a number of scans is set to a value higher than 1, the spectrometer will accumulate multiple scans on
every rising edge of the external TTL trigger. This setting is overruled when level triggered is enabled.
Save Spectrum
If this box is checked, the scans that the spectrometer will accumulate will be saved to the hard disk. If
NrOfScans>1 the datasaving will be done as fast as possible without screen updates.
Edge Triggered
When this mode is selected the one or multiple scans will be started at the rising edge of a TTL pulse at
pin 6 of the DB26 connector. The delay between the rising edge and the actual start of the integration
time can be found in the table above.
Level Triggered
When this mode is selected the spectrometer will start to accumulate data (take scans at the selected
integration time) at the rising edge of the TTL pulse and will continue to do so as long as the TTL signal
remains high. When the signal becomes low, the average of the accumulated data (except for the last
scan) will be displayed or saved. This mode is especially useful for conveying belt applications, when a
product needs to be scanned, independent of the transport speed.
3.2.9.8 Setup Menu: Options - Auto configure Integration time
After this menu option is clicked, AvaSoft starts searching for an optimal integration time. Depending on
the maximum counts in the last scan, the integration time will be increased/decreased automatically until
an optimal signal is measured.
The changing values of the actual integration time during the search can be followed in the integration
time field at the edit bar. If the auto configure integration time routine needs to be aborted before an
optimal integration time has been found, click the ‘∫AC’ button (which is in the down position during the
search), or reselect the menu option Setup-Options-Auto Configure Integration time.
When the maximum peak is around 90% of the full ADC scale (14750 counts for the 14bit ADC, 59000
counts for the 16bit ADC), the new integration time is displayed. Since the integration time has changed,
new reference and dark spectra need to be saved, before switching to transmittance or absorbance mode
is possible. For this reason this option is only available in scope mode.
3.2.9.9 Setup Menu: Options – Use Custom Reflection Reference
In Transmittance/Reflectance Mode, the transmittance/reflectance at pixel n is calculated using the
current sample, reference and dark data sets in the following equation:
 samplen − dark n 

Tn = C n * 
 ref n − dark n 
Cn is the Custom Reflectance Reference factor at pixel n. In earlier versions of AvaSoft, this factor was set
to 100 for each pixel and could not be modified. In AvaSoft version 6 and later, the custom reflectance
reference factor is default set to 100, but can be set to different values if needed. If the reflectance
spectrum of a “white” calibration tile is known, the data can be read from a file, or entered in a table in
AvaSoft. The resulting custom reference data can be saved and loaded under a user defined filename.
Click the “Enable Custom Standard” radio button, and then OK in the Custom Reflectance Settings dialog
to use the customized reference data in AvaSoft.
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The status of this option is shown in the
button bar by the addition of a green
border to the white button. If the
border is absent, 100% reflectance will
be assumed for the reference tile. If
the border is present, like in the figure
above, customized reflectance values
will be used for all calculations.
3.2.9.10
Setup Menu: Options – Suppress Save Comments
This option, if preceded by a checkmark, disables the appearance of the comments dialog box if an
experiment is saved as described in section 3.1.7.
By default this option is OFF. After clicking the menu option it will be enabled (preceded by a
checkmark).
3.2.9.11
Setup Menu: Options – View Reflectance instead of Transmittance
Although mathematically equivalent, the experimental setup for a measurement in reflectance or
transmittance mode is different, and therefore the possibility to select the name “Reflectance” instead of
“Transmittance” is implemented. By default the option is not preceded by a checkmark, meaning the
program will use Transmittance mode. By clicking the menu option, a checkmark will appear and the
program will use the name Reflectance instead of Transmittance. The effect of the change is twofold:
•
•
In Reflectance/Transmittance mode, the Reflectance name will shown at the Y-Axis
The Caption at the Reflectance/Transmittance button will change from T to R, and the corresponding
menu option under View will change from “Transmittance mode” to “Reflectance mode”.
3.2.9.12
Setup Menu: Options – Battery Voltage Monitoring
This option enables you to monitor the voltage level of a battery pack that is used with the AvaSpec. Two
voltage threshold levels for up to eight spectrometers are saved on disk. The program will issue a warning
level when the first threshold level is passed. When the second threshold level is passed, the program will
stop scanning, besides issuing a warning.
Introduction
The 12/24V battery packs for use with AvaSpecs and AvaLights need to be recharged if the battery voltage
becomes too low. The battery voltage monitoring option will help in reminding you when it is time to
recharge the battery pack.
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The option uses one of the analog inputs of the AvaSpec to monitor the battery voltage. Two alarm levels
are maintained per spectrometer, an Alarm trigger level and a Shutdown trigger level. You can select
between the spectrometer that are attached in the drop-down box at the upper left of the form.
The default trigger levels are 94.17 and 90.00 % of full charge. You can edit these levels if necessary, and
the levels can be saved to disk in a .ini file. Press the ‘Save Settings’ button to save the levels and status,
before closing the form or selecting another spectrometer in the drop-down box.
The monitoring can be switched on and off per spectrometer with the ‘Alarm Status’ radiobutton. It can
be started and stopped altogether with the ‘Start/Stop Voltage Monitoring’ button.
When the measured voltage is lower than the alarm trigger level, both a visual and audio warning will be
issued. At this moment, you can disable the monitoring if you want to, by selecting ‘Off’ in the ‘Alarm
Status’, and pressing the ‘Save Settings’ button, or by pressing the ‘Stop Voltage Monitoring’ button.
When you continue measuring with the voltage monitoring switched on, eventually the measured voltage
will be lower than the shutdown trigger level. An error message will be issued, and the program will stop
scanning.
Quick Start
1.
2.
3.
4.
5.
6.
Connect the monitoring cable of the battery pack to the HD26 plug of your AvaSpec.
Select ‘Setup’, ‘Options’, ‘Battery Voltage Monitoring’
Check if the Alarm Status for your spectrometer is set to ‘On’
Press the ‘Save Settings’ button
Press the ‘Start Voltage Monitoring’ button
Press the ‘Close Form’ button
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Main Window
Select the spectrometer with which you want to monitor the battery voltage in the drop-down box at the
upper left of the form.
The monitoring can be switched on and off per channel with the ‘Alarm Status’ radio button at the upper
right of the form.
The current battery voltage is displayed in the first box in the middle of the form.
The trigger levels can be edited in the other boxes in the middle.
Save the settings per spectrometer by pressing the ‘Save Settings’ button. Save your settings before you
switch to another spectrometer.
Start or Stop the voltage monitoring altogether by pressing the ‘Start/Stop Voltage Monitoring’ button
Close the form by pressing the ‘Close Form’ button.
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3.2.9.13
Setup Menu: Options – Merge Channel Settings
3.2.9.13.1. Introduction
Merging spectra in a multichannel spectrometer system
Multichannel spectrometer systems are often setup to achieve a high resolution over a wide range, e.g.
Master: UE 230 to 310 nm
Slave1: UE 303 to 410 nm
Slave2: VE 401 to 490 nm
Slave3: VE 485 to 555 nm
Another example is the UV/VIS/NIR range (e.g. 200-2500nm) which requires at least two different
detectors and therefore different channels.
In both examples, there is an overlapping wavelength range between consecutive channels for which the
results should be the same, especially when measurements are taken in absorbance, transmittance,
reflectance or irradiance mode.
In the application software, it would be convenient if the spectral data in the overlapping range could be
handled as a single spectrum. It is possible to define a group of spectrometer channels that are combined
into a single spectrum (in abs, trm, irr – mode). The combined spectrum will replace the individual
spectra.
It is now also possible to save this combined spectrum, and display it in AvaSoft. Export to ASCII, Excel and
J-Camp is also supported.
3.2.9.13.2. Merge settings and requirements
In the 4-channel example above, it is easy to identify the overlapping ranges (303-310nm, 401-410nm, and
485-490nm). But if e.g. a 5th channel would be added with the range 200-700nm, the data for this
channel should clearly not be merged with the high resolution channels. Also, if a 4-channel-spectrometer
system holds 2xUV/VIS (200-1100nm) and 2xNIR (1000-2200nm) channel, we need to define which
spectrometer channels should be merged into one spectrum. In this example, two merged UV/VIS/NIR
spectra are required.
In AvaSoft, we have created the option to define for each channel whether it should be treated as an
individual channel, or be placed in one of the (max 2) merge groups. For the examples mentioned above,
the spectrometer channels can be allocated as shown in the following tables:
Example1:
Channel
1
2
3
4
5
Wavelength Range
200-700
230-310
303-410
401-490
485-555
Individual
X
O
O
O
O
Group1<name1> Group2 <name2>
O
O
X
O
X
O
X
O
X
O
Example2:
Channel
1
2
3
4
Wavelength Range
200-1100
200-1100
1000-2200
1000-2200
Individual
O
O
O
O
Group1 <name1>
X
O
X
O
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O
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In AvaSoft, the Merge Spectrometer Channels Settings dialog will be displayed after clicking the menu
option: “Setup – Options – Merge Channel Setting”:
It is required to run the spectrometer channels in SYNC mode, if channels need to be merged. If a red
warning shows up like in the figure above, enter the “Setup-Hardware” menu options and make sure the
checkmark “Synchronize scans between all spectrometers” is enabled:
Sync mode requires that the spectrometer channels are connected to each other with sync cables which
would always be the case in a dedicated AvaSpec multichannel system. However, when setting up your
own multiple channel system by combining a number of single channel systems, make sure that all
channels are connected with sync cables.
If all spectrometer channels need to be merged into a single spectrum, select all checkmarks in the same
merge group in the merge spectrometer channels settings dialog (merge1 or merge2). Other selections,
like in the example1 and example2 tables at the previous page are possible as well, but there are a few
requirements that should be met:
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1. There should not be a “gap” in the wavelength range of the merged spectrum. For example, the
full ranges for the two channels in the settings dialog are 165.4-730.3nm for channel 1 and 184.1
to 1100.0nm for channel 2. To illustrate merging, the start wavelength for the 2nd channel will be
set to 700nm (under Setup-Wavelength Calibration Coefficients), resulting in a 30nm overlap
range. If channel 2 starts e.g. at 740nm, there would be a 10nm gap between the channels which
is not allowed.
2. A merge group can be empty (e.g. merge2 in the example above), or it should hold 2 or more
spectrometer channels. A single spectrometer channel in a merge group is not allowed. If a
spectrometer should be processed individually, place it into the “Individual” column.
3. If more than two spectrometer channels are placed into the same merge group, each overlapping
wavelength range should hold the data for two spectrometer channels. For example, if the 4channel system with 2 UV/VIS (200-1100nm) and 2 NIR channels (1000-2200nm) are all placed in
merge1, the data for all 4 channels is available in the overlapping range from 1000-1100nm, which
is not allowed (and also not desirable!). If all channels should be merged into a single spectrum in
a 3-channel system with e.g. the ranges 200-500nm, 300-600nm and 400-700nm, part of the
overlap range (400-500nm) would hold data for all 3 channels. If this hypothetical situation
occurs, it can be solved by using only channel 1 and 3 for merging (and place channel 2 in the
individual column), or by changing the start/stop wavelength for one or more channels, such that
only 2 channels are available in each overlap range.
AvaSoft will check if the requirements mentioned above are met, and it will display an error message and
the cause of the error if wrong settings are entered.
The merge spectrometer channels dialog allows you to enter a virtual “combined channel” name for each
merge group. This name can be used as an identifier when displaying saved graphs, or converting the
graphs to ASCII, Excel or JCAMP.
The “Apply merging also in Scopemode” checkmark can be enabled if you also want to merge the raw data
in scopemode. Due to different sensitivity of gratings, detectors, mirrors, fiber optics and possibly other
settings (e.g. integration time), the raw data in scopemode will probably not match in the overlapping
wavelength range, and therefore merging data in scopemode does not make much sense. However for
some applications, like LIBS, it is more important to identify the location of the spectral peaks than the
peak intensity. In such applications, multichannel systems are often used because of the higher peak
resolution, and it is convenient to merge these channels into a single spectrum, also in scopemode. It is
recommended in this case to save a dark spectrum for all channels and use the option “Subtract Saved
Dark” to let the spectrum start at a baseline near zero.
Of course “Apply merging also in Scopemode” can also be selected to do a quick test to see how merging
affects the raw spectra in the overlapping range(s) in scopemode.
Finally, make sure the “Enable” checkbox is marked in the “Merge Spectrometer Channel Settings” dialog
and click the OK button to save the settings and start measuring in merge mode.
3.2.9.13.3. Processing scans in merge mode
The AvaSpec-USB2 spectrometer channels can all be setup for different integration time and averages. In
Sync mode, the start of a measurement cycle is the same for each channel. The arrival of the scans is
sequential. (The as5216 DLL will signal the application that new data is available with special Windows
messages.) If the system is not in merge mode, each channel will process new data immediately after
AvaSoft receives a dataready message from the DLL.
In merge mode, recalculating the intensity in the overlapping range can only be done if the data for all
channels since the last synchronized measurement started is available in the application. Therefore, data
processing in merge mode is only done after the data for all channels has been received by the
application.
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In merge mode, all individual channels are still visible and the processed scans will be displayed over the
range specified by the start- and stop wavelength for each channel (under setup – wavelength calibration
coefficients). The line properties (color, style) for each spectrometer channel can still be set per channel,
and saving reference and dark has not change either. There are only two main changes when comparing
the processed scans in merge mode and the traditional non-merged measurements:
1) Recalculating the intensity in the overlapping wavelength range(s)
2) Saving the spectra of all spectrometer channels in the same merge group into a single file
3.2.9.13.3.1 Recalculating the intensity in the overlapping wavelength range(s)
Under perfect conditions, recalculation of the intensity in the overlapping range should not be needed in
absorbance, transmittance or irradiance mode, because the intensities measured by both channels in the
overlapping range should be the same. However, due to small imperfections like second order effects,
stray light, nonlinearity effects and/or temperature drift, minor discontinuities between the intensity of
the two channels in the overlapping range may occur. AvaSoft will recalculate the intensity in such a way
that a smooth transition between the overlapping channels will take place.
An example of such a discontinuity in irradiance mode is shown in the figure below.
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In merge mode, the discontinuity in the overlap range is removed as shown in the figure below:
Note that the overlap range is determined by the start- and stop wavelength for each spectrometer
channel. To minimize recalculation of the intensity, select the start- and stop wavelength such that only a
small overlap range remains. The quality of the signal in terms of signal/noise should be used to decide
for which spectrometer channel the wavelength range should be reduced. An example is a dual channel
UV/VIS/NIR spectrometer system with a 200-1100nm range at channel 1 and 1000-2200nm range at
channel 2. The full range for the 200-1100nm channel (UA grating) is probably 200 to 1300nm, but the
factory setting for the stop wavelength is only1100nm, because the CCD is insensitive at wavelengths over
1100nm.
It is not a good idea to use the signal between 1100 and 1300nm when merging this channel with the NIR
channel, as this signal is of poor quality. The remaining overlap range between 1000nm (start of NIR
channel) and 1100nm can be reduced further. If the quality of channel 1 between 1050 and 1100nm is
lower than the quality of the NIR channel, set the stop wavelength for channel 1 to 1050nm. Likewise, if
the contribution of the NIR channel around 1000nm should be reduced, increase the start wavelength for
channel 2.
When leaving the overlap range between 1000 and 1100nm, the data for both channels in this range will
be merged such that the intensity gradually changes from channel 1 to channel 2, using the data from
both channels in the overlap range as input.
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The figure below illustrates how merging handles a huge discontinuity between two overlapping channels.
Since this screenshot was taken in scopemode, such a discontinuity is normal (see section 3.2.9.13.2). The
only purpose for merging these spectra in scopemode is to illustrate how the two channels (blue and red)
are merged into a single spectrum (purple).
3.2.9.13.3.2 Saving the spectra of all spectrometer channels in the same merge group into one file
In merge mode, the spectra of all spectrometer channels in the same merge group are saved in the same
file. Files that are saved in merge mode can be recognized by the addition of an ‘X’ to the file extension:
.ROHX, .ABSX, .TRMX, IRRX. If merge mode is not enabled, the traditional file format and extensions
(without ‘X’) are used. Also spectrometer channels that are placed in the individual column in the merge
settings dialog are saved as merged files.
The status bar for each spectrometer channel shows the name of the file the next scan will be saved in.
Before AvaSoft 7.4 (and also when not in merge mode) the filename for each spectrometer channel
needed to be unique which was realised by auto incrementing the sequence number in the filename.
In merge mode, the spectra of spectrometer channels in the same merge group will have the same
filename, as shown in the figure below:
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In a 4-channel system, in which two merge groups have been defined, saving the spectra should result in
two files, each holding the data for two spectrometer channels:
In the example above, the spectrometer channels 0610063U1 and 0802555U1 are in merge group merge1,
and channels 0807017U1 and 0707083U1 are in merge group merge2.
When saving merged files, the data for all pixels of all channels are saved. An 8-channel AvaSpec-3648 for
which all channels are in the same merge group and set to their full range will yield files with 29184 data
points!
The main reason for developing the merge utility was the ability to analyze the spectra of a multichannel
system as a single spectrum. Therefore, when analyzing the saved spectra (displaying, comparing with
other spectra, converting to ASCII, Excel, Jcamp etc..) the file is handled as a single spectrum. Detailed
information about the data origin (which channels and settings were used when saving the file) can still be
obtained and displayed, but the spectral data will always be represented as a single spectrum (wavelength
+ intensity).
A detailed description about displaying and converting the graphs saved in merge mode can be found
below in section 3.2.9.13.4 and 3.2.9.13.5.
3.2.9.13.4. Displaying merged spectra
The (merged) spectra to be displayed can be selected after clicking the menu option “File-Display Saved
Graph”. New in AvaSoft 7.4 is that the merged files (with an additional ‘X’ in their file extension) will also
be listed in the Open Dialog that shows up. Multiple non-merged and merged files can be selected and will
be displayed after clicking the “Open” button.
A small difference between the displayed non-merged and merged graphic files is that in the non-merged
files the graph title already displays the main measurement parameters settings such as integration time
(it), averaging (av) and smoothing (s). Since merged spectra can hold different settings for up to 8
channels, there is too much information to be displayed in the graph title.
Therefore, detailed information about these settings can be viewed in a separate information dialog which
will be displayed after selecting “Show Info” from the popup menu that shows up when right-clicking the
spectral line of interest.
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3.2.9.13.5. Converting merged spectra to ASCII, ASCII-equidistance, Excel and Jcamp-DX
Converting the merged spectra to ASCII and ASCII-Equidistance can be done with or without header
information. If the ASCII files are further processed by other software, the header is often not compatible.
The option “Include ASCII Header” is preceded by a checkmark by default. If the header information
should be left out, click the “Include ASCII Header” to toggle the checkmark.
The “To ASCII” and “To ASCII – Equidistance” menu options can then be clicked to export the data to an
ASCII file. To distinguish the merged ASCII files from the non-merged, an ‘X’ is added to the file extension
for the merged ASCII files. An overview of the file extensions in the different measure modes is given in
the table below:
Measure mode
Scopemode
Absorbance
Transmittance
Irradiance
Binary file
Not Merged
ROH
ABS
TRM
IRR
Binary file
Merged
ROHX
ABSX
TRMX
IRRX
Text file
Not Merged
TRT
TAT
TTT
TIT
Text file
Merged
TRTX
TATX
TTTX
TITX
The header in a merged ASCII file includes the following information
The data for all measure modes is given in two columns, separated by a semi-colon(;). The first column
holds the wavelength in nm, the second column holds the intensity.
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Converting merged spectra to Excel
Converting a merged file to Excel is similar to a non-merged conversion to Excel. The header is more
comprehensive, because it includes the main parameter settings for all spectrometer channels, but the
data format is the same.
All the selected files that share the same merge group name (e.g. merge2) and wavelength data (first
column) will be exported to the same tab sheet in Excel.
However, if the same merge group name is found in different files, but the wavelength data between
those files is different, then a new tab sheet is created with the merge group name appended with a
sequence number like merge1_1 in the figure above. The reason for different wavelength data in the same
merge group can be a change in spectrometer channels in the merge group, a change in start/stop
wavelength in one or more channels, or e.g. a new wavelength calibration.
Individually processed channels yield files in the merged file format which include only 1 spectrometer
channel. (They were placed in the individual column in the merge settings). These files are exported to
the tab sheet <serialnr> followed by an x, like 0610063U1x in the figure above.
Converting merged spectra to JCAMP
The JCAMP-DX format requires a .dx file extension which can become troublesome if files with the same
filename but with different file extensions are converted to Jcamp. For example AVANTES0001.ABS and
AVANTES0001.ABSX or AVANTES0001.TRM will all be converted to AVANTES0001.dx and this file will then
only contain the last conversion. DX files have a fixed format and the wavelength column is linearized in
the conversion.
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3.3 View Menu
3.3.1
View Menu: Scope Mode
The display is set to Scope Mode, showing a real time raw data signal, with on the Y-axes the read out of
the AD-converter and on the X-axes the calculated wavelength.
3.3.2 View Menu: Absorbance Mode
In Absorbance Mode, the absorbance at pixel n is calculated using the current sample, reference and dark
data sets in the following equation:
 samplen − dark n
An = − log
 ref n − dark n
3.3.3



View Menu: Transmittance/Reflectance Mode
In Transmittance Mode, the transmittance at pixel n is calculated using the current sample, reference and
dark data sets in the following equation:
 samplen − dark n
Tn = 100 * 
 ref n − dark n



As described in section 3.2.9.9, the reference (white) percentage of 100 can be customized. The
percentage of transmittance is mathematically equivalent to the percentage of reflectance and can also
be used for reflectance experiments (see also section 3.2.9.11).
3.3.4 View Menu: Irradiance Mode
If the Absolute Irradiance Measurements Module has been ordered with AvaSoft, this option will show the
absolute energy output in µWatt/cm2/nm. An elaborate description about the experimental setup in case
of absolute irradiance can be found in section 4.4.
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If the absolute irradiance application is not available, a light source of known color temperature is
needed as a reference, for example the AvaLight-HAL with color temperatures of 2850K at default jumper
setting. The relative radiance energy at wavelength λ is then calculated using the current sample, the
reference and the dark data sets:
S λ = Bλ * (sampleλ − dark λ )
Where Bλ is the computed component of the spectral distribution of the blackbody radiant emmittance (at
user selected temperature in degrees Kelvin), divided by the current reference data at wavelength λ
How to take relative irradiance measurements with AvaSoft
1.
Start the AvaSoft software, and click the Start button in the main window.
2.
Connect a fiber to the Spectrometer input port.
3.
Adjust the Smoothing Parameters in the Setup menu to optimize smoothing for the Fiber/Slit
diameter that is used.
4.
Set up the experiment such that the other end of the fiber points at the sample of light to be
determined (use a fixture for the best results). Usually some sort of spectrum may be seen on the
screen, but it is possible that too much or too little light reaches the spectrometer at the present
data collection settings. Too much light means that, over a certain wavelength range, the signal is
overloaded shown as a straight line at any arbitrary height, even near zero. This can usually be
solved by a shorter integration time. The integration time can be changed in the main window, in
the white box below the start/stop button. If AvaSoft is collecting data, the start/stop button shows
a red ‘stop’ and the integration time box is gray, indicating that it cannot be changed. After
clicking the ‘stop’ button the data acquisition stops and the integration time can be changed. The
result of the changed integration time can be viewed after clicking the green ‘start’ button. Try to
adjust the integration time, such that the maximum count over the wavelength range is around 90%
of the full ADC scale (14750 counts for the 14bit ADC, 59000 counts for the 16bit ADC). When at
minimum integration the signal is still too high, fibers with a smaller diameter can be used. When
not enough light reaches the spectrometer, likewise a longer integration time should be entered.
5.
When a good spectrum is displayed, turn off the light source.
6.
Now save the Dark data. This is done by File-Save Dark from the menu or by clicking the black
square on the left top of the screen with the mouse.
7.
Turn on the reference light source of known color temperature (2850K for AvaLight-HAL with
default jumper setting) and set up the fiber end that is not connected to the spectrometer, so that
a good spectrum is displayed on the screen. Note that the integration time or fiber type may not be
changed while measuring the reference data. If there is too much light, adjust the focusing of the
light source, so less light is coupled into the fiber. As long as only light from the reference light
source and no ambient light is coupled into the fiber, this will not influence the spectral
distribution, only its height. Try to set up the fiber such that the maximum count over the
wavelength range is around 90% of the full ADC scale, which is 14750 counts for the 14bit ADC,
59000 counts for the 16bit ADC).
8.
Save the Reference data. This is done by File-Save Reference from the menu or by clicking the
white square on the left top of the screen with the mouse.
9.
Note that the whole operation of saving a reference file does not need to be carried out each time
a new experiment is started. The reference data are saved in a file called ref*.dat and can be
loaded next time by choosing the option File-Load Reference. After saving or loading reference and
dark the irradiance mode can be chosen by clicking the ‘I’ button or by the menu option ViewIrradiance mode. First a message box appears in which the value of the color temperature in Kelvin
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of the light source that has been used as a reference can be entered. If light from the reference
light source is viewed, the Planck-curve for the color temperature of the reference light source is
displayed. The maximum of the reference Planck-curve has been set to 100.
3.3.5
View Menu: Change Graph Scale
After selecting this option, a dialog is shown in which the
range for both X- and Y-axis can be changed. To switch to the
full scale, the View-Graphic Reset option, or the mouse
zoom-out feature can be used. By clicking the Save button in
this dialog, the settings for X-axis and Y-Axis will be saved to
a file and can be restored in the future by selecting the menu
option “View-Goto Preset Scale” or by clicking the
corresponding button in the button bar.
3.3.6
View Menu: Graphic Reset
When selecting this option, the graph will be reset to the default X- and Y-axes.
3.3.7
View Menu: Autoscale Y-axis
By using this option, the graph will be rescaled on-line. A maximum signal will be shown at about 75% of
the vertical scale.
3.3.8
View Menu: Goto Preset Scale
By clicking this menu option, the scale for X- and Y-axis will be set to a range that has been set before.
The same result can be achieved by clicking the Goto Preset Scale Button in the button bar.
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3.3.9
View Menu: Grid Enable
With the Grid Enable option activated, a grid will be displayed in the graph as shown in the figure below.
3.3.10 View Menu: Progress Bar Enable
If using long integration times or a high number of averages, it can take a few or more seconds before a
new scan is received by the application. To get an indication about how much time it will take until the
next scan arrives, a progress bar can be displayed. After enabling the progress bar by clicking the menu
option, it will be displayed after the next scan has arrived. The progress bar will be shown only if the time
between scans is more than one second. The time between scans is roughly the integration time,
multiplied with the number of averages. However, if the number of averages is high, the time between
scans can get longer because of the overhead time that is spent on transmitting the high number of
average spectra to the PC.
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4
Applications
4.1 Applications: History Channel Functions
4.1.1
History Application: Function Entry
With the History Application, the
output of self defined functions
or integrals can be followed in a
graph against time. Up to 8
functions can be followed
simultaneously.
The functions are defined in the
dialog at the right, which is
shown after the History-Function
Entry option has been chosen.
The functions F1 to F8 can be
selected by clicking the
corresponding TAB sheet at the
top of this dialog.
Furthermore, a number of
general (function independent)
parameters can be entered,
below of the function TAB sheets.
Function Type
The first time that the Function
Entry dialog is activated, all 8
functions are not activated (Function Type = None). To define a function, the Function Type radio button
needs to be changed from None to: Integral, User Defined , View Spectrum or Peak. After defining the
function type, the Measure Mode, Function Definition and Function Display Settings can be set.
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Measure Mode
The four possible modes (Scope, Absorbance, Transmittance or Irradiance) are described in section 3.3.1
to 3.3.4. Note that if the selected measure mode is Absorbance, Transmittance or Irradiance a reference
and dark spectrum needs to be saved or loaded before the History Channel Measurements can be started.
Function Definition
The parameters that need to be entered in the Function Definition Box depend on the Function Type that
has been chosen: Integral, User Defined, View Spectrum or Peak.
Function Definition-Integral
In case a function is defined to display the integral versus time, the following parameters can be set:
Spectrometer Channel. The default is Master, but in case more channels are available, this can be
changed to Slave1, Slave2…..up to Slave7.
The “from” and “to” edit boxes may be changed to specify the wavelength range in nanometer over which
the integral needs to be calculated.
Finally, a multiplication factor can be entered. The value entered here is multiplied with the calculated
integral.
Function Definition-User Defined
If you want to display the output of a self defined function against time, a function needs to be defined
first. You can either enter a user defined input function in the dialog box, or assign a script to the history
channel.
Input Functions:
A comprehensive example of an input function is given in the dialog, but it illustrates only a few of the
functions AvaSoft can handle. A list of allowed operators and functions is given below:
Operators:
*, /, +,Functions:
log(x) = natural log
log10(x) = log base 10
exp(x) = e to the power of x
sqrt(x) = square root
Additionally, the wavelength signal for master and slave channel(s) can be entered by:
m(wavelength in nm) = master
s1(wavelength in nm) = slave1, s2(wavelength in nm) = slave2, etc.
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For example: the function that needs to be entered to follow the intensity of the HG peak against time at
the second slave channel is: s2(253.65)
Scripts:
A scripting feature has been added to allow you to use more complicated calculations with many more
mathematical and logical functions. Scripts will also allow you to combine the results of several history
channels.
AvaSoft uses the Microsoft VBScript language that comes with your copy of Windows. We have included a
help file for VBScript for your reference. You can reach it from the main menu by selecting ‘Help’,
‘VBScript’. It lists among other things all available operators and functions.
When you edit a script, either the previous script for the channel will be shown, or a new starter script
will be generated if there is no previous script. AvaSoft includes a simple script editor. The scripts are
plain ASCII files, named Fx_script.txt, where x is the history channel number, from 1 to 8.
A starter script has the following contents:
Function F2(value)
F2=0
End Function
You can elaborate on this function, as long as there is a value assigned to F2 in the end. In this case, F2
will be assigned the value 0.
You can refer to the other history channels with the predefined variables F1 to F8. If you want to use data
from the spectrometer, you will need to assign other history channels to e.g. wavelength values or
integrals. The following script defines the function value for F3 as the quotient of F1 and F2.
Function F3(value)
F3=F1/F2
End Function
Please do not refer to the function value for the script itself. You can also not refer to other functions, if
these are themselves assigned to a script. This will result in a scripting run-time error. If you want to use
code from another script, please copy the necessary lines from that script into the one your working with.
Please understand that a script is executed by an interpreter, on a line by line basis. If you make a syntax
error in your script, it will usually only show at the moment the line with the error is executed, as a runtime error.
Nothing will stop you, for instance, from entering the following script for function 3:
Function F3(value)
F3=F1/0
End Function
Running this script will result in
the run-time error at the right:
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If you refer to channels that are undefined (Function Type ‘None’), they will be handled as uninitialized
variables by VBScript, with value 0. This is the case for all uninitialized variables you might use in your
scripts.
Finally, a small example to monitor the integral of a peak between 522 nm and 550 nm, in which an offset
is subtracted. The offset area is the area below of the straight line between the output at 522 nm and the
output at 550 nm.
F1 is defined as a user defined input function: m(522)
F2 is defined as a user defined input function: m(550)
F3 is defined as the zero-based integral between 522 nm and 550 nm.
The script for function F4 can then be written as:
Function F4(value)
If F1 > F2 Then
offset = 28*(F2 + (0.5*(F1-F2)))
Else
offset = 28*(F1 + (0.5*(F2-F1)))
End If
F4 = F3 - offset
End Function
Function Definition-View Spectrum
The View Spectrum function does not display function output against time. Instead, the wavelength range
that has been entered in the Function Definition Box will be displayed at the X-axis. The spectrum for the
selected spectrometer channel will be displayed in the selected measure mode. In combination with
AvaSoft-XLS, the View Spectrum mode can also be used to export the spectra online to Excel (section 4.6)
If the History Channel Functions are used to track the intensity or wavelength of a peak (see below for the
Function Definition – Peak), a graphical feature can be used to visualize the peak changes in a spectrum.
The number of peaks to display in the spectrum can be entered. This number (between 0 and 100) is the
number of vertical lines that will be drawn in the spectrum, each vertical line representing one of the
detected peaks in the past.
• The height of the vertical line is equal to the peak intensity.
• The wavelength at which the vertical line is drawn in the spectrum corresponds to the wavelength of
the detected peak.
• The color of a vertical line represents the oldness of the peak: Most recent peak is red, going back in
time followed by orange, green and blue. All older peaks are gray colored, from light gray (oldest
peak) to dark gray (one peak older than blue).
The time interval at which the vertical lines are updated is the same as the time interval at which the
function output is saved (to be entered under Save every x Seconds under Save Function Output).
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For example, suppose the function output will be saved every 3 seconds, and the Nr of peaks to display
has been set to 10 in function F1. After starting the History Channel Measurements, the peak in the
spectrum drawn for F1, will be marked by a red vertical line immediately. In the next 3 seconds, the
spectral peak may vary in height or position but the red vertical line remains at the same place and
height. After 3 seconds, the red vertical line becomes orange, and a new red line will be drawn at the
position and with the height of the peak detected at that moment (t=3). After 6 seconds another line is
drawn and the colors are shifted again, so that red is most recent, then orange, then green. At t=27
seconds, the 10th vertical line is drawn, again red for the most recent, the oldest is now represented by a
light gray color. At t=30 seconds, the oldest peak is removed from the list (since in this example the Nr of
peaks to display is 10), a new one is added and the colors are shifted according to the definition etc….
Function Definition-Peak
In case a function is defined to display a peak versus time, the following parameters can be set:
The Spectrometer Channel. The default is Master, but in case more channels are available, this can be
changed to Slave1, Slave2….. up to Slave7.
The “from” and “to” edit boxes may be changed to specify the wavelength range in nanometer, which will
be evaluated in the peak search. Finally, a selection can be made to define the Peak Output: Wavelength
or Intensity.
If both wavelength and intensity need to be followed against time, one of the functions (F1..F8) can be
used to follow the peak wavelength, and another function to follow the peak intensity. To visualize the
peak changes, a third function can be set to “View Spectrum” with e.g. the wavelength range set to 455457 as well and the nr of peaks to display set to 10. In the figure above, the resulting output will be the
wavelength of the highest peak between 455 and 457 nanometer. If the intensity button had been
selected, the function output would have been the intensity of the highest peak between 455 and 457
nanometer.
Function Display Setting
For Integral, User Defined and Peak functions, the output can be displayed graphically against time. The
amount of time that will be displayed at the X-axis can be set manually by clicking the Fixed radiobutton.
If set to Auto, the time axis will be set to 1 minute. This option is not available if the View Spectrum
Function Type has been selected, because the X-axis range is in that case in nanometers, and determined
by the wavelength range as described above.
The Y-Axis can also be set to Fixed or to Auto. The Auto option will set the Y-axis range to the minimum
and maximum function values that are in the list of measured datapoints.
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Function Independent Parameters
Function Independent Parameters - Display no graphics to speed up data processing
Below the TAB sheets for function definition an option can be enabled or disabled to speed up data
processing by not displaying the graphics during the measurements. If an application requires fast data
processing (e.g. more than 10 scans per second), this option should be enabled. If saved to an output file,
the data can be displayed graphically after the time series experiment has been ended, as described in
section 4.1.3: History-Display Saved History Graph.
Function Independent Parameters - Save Function Output
The results of a time series experiment will be saved to an ASCII-file if the radio button “Save Function
Output” has been selected. A number of seconds between saving can be entered for data reduction, in
case measurements are carried out over long periods. Entering a value of zero results in saving every scan.
The name of the file to which the data will be saved, can be changed after clicking the “Change Output
File…” button. Last option in the “Save Function Output” box is to enable or disable the possibility to
create a backup file during the measurements. If this option is enabled, AvaSoft will create a backup file
with the same filename, but with the extension *.bak (also in ASCII). This backup file is updated every
scan and can be used in case the filename that has been selected has failed to save the data, for instance
because of a power failure during the measurements.
Save HCF…/Load HCF buttons
AvaSoft automatically saves all parameters (function definition, save options) to the file hcf.ini, and
restores these parameters, the next time AvaSoft is started. With the Save HCF… and Load HCF… buttons,
it’s also possible to save these parameter settings to (and load from) a file with the extension *.hcf. With
this feature it is possible to save for each experiment a different HCF file, so it can be loaded a next time
the same settings are required. The left figure below shows the dialog in which the name of the hcf file
can be entered after clicking the save HCF… button. The right figure below, which is displayed after
clicking the Load HCF… button, illustrates how to select an earlier saved HCF file.
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After the definition of one or more functions, the OK button is clicked to confirm, the CANCEL button to
leave the dialog without changes. If the OK button is clicked, AvaSoft performs a number of checks on the
data that has been entered. If no warnings show up, the parameters that have been entered are accepted,
and the measurement can be started by the History – Start Measuring menu option.
4.1.2 History Application: Start Measuring
This option displays the output against time for the history functions that have been defined in the History
Channel Function Entry dialog box. If the option “Display no graphics to speed up data processing” has
been marked in the function entry dialog, the function output will be shown by numbers only, which are
updated each time a new scan is saved to the output file.
There are six buttons at the top of this window: an Exit button, a Pause/Start button, a Save Reference
button, a Save Dark button, an Info button and a Print button.
If the red Exit button is clicked, the time measurements are ended and the main window and menu is
activated again. The yellow Pause button can be used to stop the time measurements temporarily. After
clicking the Pause button, data acquisition stops and the text on the button changes to a green Start. If
the Start button is clicked, data acquisition is activated again and the text changes back to the yellow
Pause again.
The Save Reference and Save
Dark buttons have the same
functionality as in the main
window. The Info button
shows the Function Entry
dialog, in which all
parameters can be viewed
(not edited) while the
measurement is running.
By clicking the Print button,
the graphics that are
displayed can be printed
during the run. First the
printer specific dialog shows
up in which the print options
can be set. For example, if
only one graph of the four in
the figure above need to be
printed, this graph can be
selected by the page(s)
radiobutton. All graphics are
printed full size on a different page.
Zoom features
In each graph the same zoom features apply as in the main window (except for scaling the Y-axis with the
mouse wheel). However, zooming in over the X-axis while the measurement is running and the X-axis is
already scrolling will not be possible, because in that case the X-axis is updated with each new scan.
Clicking the pause button to take a snapshot will solve this problem.
Zoom in: select a region to be expanded to the full graph. To select this region, click the left mouse
button in the white graphics region and drag it downwards and to the right. After releasing the left mouse
button, both the X- and Y-axis will be rescaled to the new values of the selected region.
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Zoom out: drag with the left mouse button within the white graphics region, but in stead of dragging the
mouse downwards and to the right, drag it into another direction. After releasing the mouse button, both
the X- and Y-axis will be reset to their default values.
Move X-Y: dragging with the right mouse button results in moving the complete spectrum up or down and
to the left or right.
4.1.3
History Application: Display Saved History Graph
If time measurement data have been saved, the
resulting ASCII file can be displayed graphically by
selecting this file in the dialog that is shown after
clicking the “Display Saved History Graph” menu
option.
After clicking the “Open” button, the function output
of the functions with function type “Integral” or
“User Defined” is displayed against time. Both X- and
Y-axis are set to their full scale, which is determined
by the minimum and maximum values in the list.
The zoom features, as described in section 4.1.2, can be applied, to zoom in on an interesting time
interval. A description for the print button can also be found in section 4.1.2.
Since the History Channels Output file is in ASCII, this file can be easily imported in a spreadsheet program
like Microsoft Excel. The data in the file can also be viewed with a text editor, like Microsoft Word, or
with Notepad. An example of the file format is given on the next page:
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History Channel Functions Measurement Report
Measurements started at 29/06/01 Time: 15:06:29
Integration time: 3 ms
Average
: 1 scans
Description of the Functions:
FUNCTION 1: User Defined Function: m(400). Scope Mode.
FUNCTION 2: User Defined Function: m(500). Absorbance Mode.
FUNCTION 3: User Defined Function: m(600). Transmittance Mode.
FUNCTION 4: User Defined Function: m(700). Irradiance Mode.
FUNCTION 5: Integral Master Channel, between 380,0 and 780,0 nm. Multiplied with: 1,000. Transmittance
Mode.
FUNCTION 6: View Spectrum in Transmittance Mode. No Data Saved
FUNCTION 7:Not Activated
FUNCTION 8:Not Activated
Time
SecondsF1
F2
15:06:29
0,62
79,79
15:06:30
0,77
15:06:30
F3
F4
F5
-2,294E-3
100,8
74,11
40192
81,84
-2,059E-3
100,9
74,17
40236
0,92
81,79
-3,756E-3
100,2
73,77
40201
15:06:30
1,07
84,69
-3,209E-3
101,0
73,43
40202
15:06:30
1,22
82,19
-7,877E-4
100,3
74,11
40188
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4.2 Applications: Wavelength Calibration
Please refer to section 3.2.2 for a description about the polynomial that converts the pixelnumber on the
detector into the corresponding wavelength at the X-axis in AvaSoft.
If a Wavelength Calibration light source is available, together with suitable optical fibers, an automatic
wavelength calibration can be performed. The peaks for the Mercury-Argon calibration source (AvaLightCAL) are by default loaded in AvaSoft. It’s also possible to import the peaks that will be used in the
calibration from file by selecting the “File” radio button at the right of the “Find Peaks” button. This
option also allows you to import peaks from different calibration sources such as the Avalight-CAL-NEON
or AvaLight-CAL-AR. The files that can be imported are in ASCII format and can be edited with any text
editor, e.g. Notepad. The extension for these files is “.lit” and the data is presented in three columns:
<wavelength in nm> <intensity in arbitrary units> <peak order>
An important precondition for a successful auto calibration is the absence of saturation. The easiest way
to assure this is to select the ‘check on saturation’ option (section 3.2.9.1). If the spectrometer is
saturated at minimum integration time, a fiber with smaller core diameter (e.g. FC-IR008-2) needs to be
used. As an alternative, the incoming light can be attenuated e.g. by using an attenuator (FOA-Inline) or
neutral density filter.
4.2.1
Calibrate Wavelength Application: Perform New Calibration
The procedure to perform an auto calibration is as follows:
- Connect the fiber to the AvaLight-CAL light
source and to the spectrometer channel to be
calibrated.
- Choose a suitable integration time so as not
to saturate the detector. The peaks can be
seen in scope mode.
- Select the menu option ‘Wavelength
Calibration-Perform New Calibration’.
- The auto calibration routine will now search
for a number of peaks; initially it will look for
5 peaks in the data from the Master channel.
- The spectrometer channel and the number of
peaks to look for can be altered. A new
search can be performed by pressing the ‘Find
Peaks’ button. The peaks are shown in 3
columns. The first column shows the position
of the peaks found. The second column shows
the position of a suggested standard peak, if
available. The last column lists the difference
between the first two columns. You can edit
the values of the second column by selecting them with the mouse.
- Select the polynomial order. In most cases a third order polynomial will show an excellent fit (see
figure above)
- The “include 2nd order peaks” option can be enabled if second or third order peaks should be added
to the list of available literature peaks (e.g. 507.30 nm as second order peak for 253.65). In most
spectrometers, the second order effects are eliminated by filters or coatings, but if these options
have not been added to the spectrometer, and second order peaks are available, then these can be
included in the calibration. The central column cells will be marked green if a second order peak is
found and yellow if a third order peak is found.
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-
Press the ‘Calculate’ button. If your calibration is successful,
you will be asked to confirm new coefficients.
Select ‘OK’ and the new calibration will be applied
immediately.
At least 3 peaks are needed to successfully complete a new
calibration. Try to calibrate with more peaks. Selecting too many
peaks can however lead to peaks that cannot be matched with
standard wavelengths.
4.2.2
Calibrate Wavelength Application: Restore Original Calibration
This option enables the user to restore the calibration coefficients to their original values, i.e. the values
that AvaSoft was shipped with. If a new calibration was performed with a limited number of peaks, or
over a limited wavelength range, the results could be less favorable.
This option allows the user to undo unwanted changes to the calibration.
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4.3 Applications: Color Measurement
The AvaSoft Color Application has been developed to perform on-line color measurements with a
spectrometer system. It can be used for reflective color measurements, in earlier versions of AvaSoft
called “color of object measurements”. The CIE 1976 L*a*b* color parameters are calculated, as well as
other frequently used parameters, like Hue, Chroma and X, Y, Z.
These parameters can be displayed in a CIELAB chart or in a graph versus time. It’s also possible to save
the measured L*a*b* values online to a database and use one of the products from the database as a
reference color. By comparing the measured L*a*b* values to the stored database values, color differences
(∆ELab, ∆L*, ∆a*, or ∆b*) can be measured as well.
Emissive color measurements can be done to measure the color of a light source (e.g. LED’s). These
measurements require an irradiance spectrum to calculate the color parameters x, y and z. With AvaSoft’s
Irradiance application, it is possible to perform irradiance measurements with a lot higher accuracy than
when using the relative irradiance mode (which assumes a perfect blackbody light source with known
color temperature). For this reason the emissive color or “color of light” calculation is one of the features
in the Irradiance Application.
4.3.1
Color of an Object - Background
The color of an object can be expressed by the CIE 1976 (L*a*b*) color space. L* describes the lightness of
the color. A positive value of a* describes the redness of the color, a negative a* the greenness. Similarly,
yellowness or blueness is expressed by coordinate b*, which is positive for yellow and negative for blue.
The L*a*b* values are derived from the CIE tristimulus values X, Y and Z of the sample (object) and the
standard illuminant tristimulus values Xn, Yn and Zn.
The standard illuminant tristimulus values for Xn, Yn, and Zn are constant and depend only on the type of
standard illuminant that has been chosen.
The CIE tristimulus values X, Y and Z of the color of an object are obtained by multiplying the relative
power P of a standard illuminant, the reflectance R (or the transmittance) of the object, and the CIE
standard observer functions xλ, yλ and zλ (2 degrees or 10 degrees angle). The integral of these products
over all the wavelengths in the visible spectrum (380 to 780 nm with a 5 nm interval) gives the tristimulus
values.
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The chromaticity coordinates x, y and z are obtained by taking the ratios of the tristimulus values (X, Y
and Z) to their sum:
x=
X
(X + Y + Z )
y=
Y
(X + Y + Z )
z=
Z
(X + Y + Z )
Another well known way to present the color parameters a* and b* is by their hue angle (h*) and Chroma
(C*).
Hue angle is measured in degrees starting with h*=0 in the red direction (+a*) and increasing
counterclockwise:
h * = arctan
b*
a*
Chroma is defined as the length of the line from the point a*=b*=0 to the sample point:
2
C * = a* + b*
2
To describe color differences, a well known parameter is ∆ELab, which is defined as:
∆E Lab = (∆L*) 2 + (∆a*) 2 + (∆b*) 2
In which,
∆L*, ∆a* and ∆b* represent the difference in L*a*b* values between the reference color and the actual
measured L*a*b* values.
4.3.2
Menu option: Color Measurement
After selecting the menu option “Applications-Color Measurement” a dialog is displayed in which the input
parameters can be set. The dialog shows two tabbed pages: one is called “LABChart” and shows the input
parameters for displaying the color measurements in a color chart; the other one is called “Time Series”
and shows all input parameters for displaying up to eight color parameters in a graph versus time. The
input parameters will be described in detail in sections 4.3.2.1 (LABChart) and 4.3.2.2 (Time Series).
The color measurements are started by clicking the OK button. AvaSoft returns to the main window if the
Cancel button is clicked.
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4.3.2.1 LABChart
The color measurements in the LABChart are started by clicking the OK button in the figure above. The
following parameters can be set before the measurements are started:
•
Spectrometer Channel. If the spectrometer system contains one or more slave spectrometer
channels, the spectrometer channel on which the color will be measured can be selected from the
drop down box at the upper left corner (showing by default “Master”). Make sure white reference and
dark spectra have been saved before for the selected spectrometer channel.
•
Illuminant. The CIE Standard sources A, B or C or one of the illuminants D50, D55, D65 or D75 can be
selected by clicking one of the radio buttons. The default is D65, which is the most widely used
illuminant. It represents the power distribution of average daylight, with a correlated color
temperature of 6500K. The D50, D55 and D75 have correlated color temperatures of 5000K, 5500K and
7500K. The CIE Standard sources A, B or C represent respectively: Incandescent light (2854K
blackbody), Simulated noon sunlight and Simulated overcast sky daylight. Note that there is no
relation between the illuminant chosen here and the light source that is used for measuring the color
of an object. The selected illuminant is used in calculation of the color parameters. These color
parameters will be different if for example A will be selected instead of D65, just as the color of an
object will look different in average daylight or in incandescent light (2854K blackbody).
•
CIE Standard Observer. The original CIE standard observer functions xλ, yλ and zλ were defined in
1931, and are known as the 2 degrees standard observer values. The 2 degrees corresponds with the
angle of vision that was used in the experiments to determine these standard observer values. In
1964, the CIE recommended the use of different observer values for a higher correlation with visual
perception for large samples. These are known as the 1964 supplementary standard observer, or 10
degrees observer values. Both standards are still in use, and in AvaSoft, the CIE standard observer can
be selected by clicking one of the radiobuttons. The default is 2 degrees.
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•
Display settings. The measurement results can be displayed graphically in 3 charts:
1) the LABChart in which a* and b* are shown by a moving dot in a CIELAB graph
2) the Measured Color Panel, which displays the color which is being measured. Note that the
displayed color on the monitor may not match exactly the color of the object (depends on
monitor), but it will give a good impression.
3) The Reference Color Panel, which displays the reference color that has been selected under the
“reference color” setting.
The graphical display can be enabled or disabled by a mouse click for each graph separately.
•
Display following Color Parameters. The values of the color parameters that are enabled will be
displayed below of the charts during the measurements
•
Save Settings. The color parameters can be
saved to an ASCII file during the
measurements. The current name and location
of this ASCII file is shown under save setting.
This filename (and path) can be changed by
clicking the “Change Output File” button. The
next dialog will be displayed:
To start a new file for saving the color
parameters, enter a filename that does not
already exists (AvaSoft will add the .txt
extension), and click Open.
If an existing file is selected, the color parameters that will be saved are appended to this file. This
way experiments that were saved before can be proceeded, using the same output file.
•
Reference Color
The reference color can be set to compare the L*, a* and b* color parameters during the online
measurements with the LREF, aREF and bREF of the reference color. The color differences can be
shown during the measurements by dL (=L*-LREF), da (=a*-aREF), db (=b*-bREF) and/or dE
(=√ (dL2+da2+db2)).
The reference color can be entered manually under “Current Reference Color” in the figure above, or
it can be selected from a database file. The database file is a list of reference colors that were saved
before to this file, all with a unique ProductID. By default the name of the database file is
“empty.pct”. By clicking the DB button, a different database file can be selected, or a new file can be
created.
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To start a new database file for saving reference
colors, enter a filename that does not already exists
(AvaSoft will add the .pct extension), and click Open.
To open an existing file simply double click on the
filename, or select it and click the Open button. The
file example.pct can be found in AvaSoft’s main
directory and contains a few measured reference
colors.
To select a reference color from the database file,
click the select button, below of the DB button.
The contents of the database file will be
displayed as shown in the figure below:
To select one of the products from the list, click
on one of the numbers (1..11) in the first (gray)
column.
To delete a product from the list, select it and
click the delete key on the keyboard.
To search for a certain productID or number, click
the Find button.
To sort the records by ProductID, L-REF, a-REF or
b-REF, click on the corresponding column header.
A yellow marked ‘1’ will be shown in the column
header. By clicking again at the header which is
already marked, the sorting direction will be
converted.
By clicking the Cancel button, the selected
product will not be moved to the current
reference color in the LABChart settings dialog,
and changes (e.g. deleting a product from the
list) will be ignored.
By clicking the OK button, the current reference color in the LABChart settings dialog is changed to the
color which has been selected.
To add the current reference color (specified in the LABChart settings dialog) to the database file, the
Add button (below of the select button) can be clicked. If the ProductID already exists, a dialog will be
shown in which the choice can be made to overwrite the old color parameters with the new ones, or to
keep the old values for this productID. As an alternative, a reference color can be added to the database
during the online measurements. This can be done only if in the LABChart settings dialog, the option “Add
new reference colors to DB when measuring” is enabled.
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After all settings are filled in correctly the
measurements can be started by clicking the OK
button, or using the Enter key on the keyboard. A
shortcut to start measuring with LABChart directly
(omitting the settings dialog) is clicking the
LABChart button in AvaSoft’s main window.
The figure at the right shows all color parameters
and all 3 charts were enabled. The measurements
in the figure are performed with the Master
spectrometer channel and illuminant D65 has been
selected. The color parameters are calculated
with the 2 degrees CIE standard observer values.
The filename to which data will be saved can be
found in the lower left corner.
The button bar in the LABChart shows the following buttons:
• The Exit button is clicked to stop the color measurements and return to AvaSoft’s main window.
• The white and dark reference buttons have the same functionality as in AvaSoft’s main window.
• The “Save as reference color” button is used to update the current reference color. After clicking this
button, a dialog is displayed in which a name for
the ProductID needs to be entered. If the
productID already exists in the database file and
if the option “Add new reference colors to DB
when measuring” is enabled in the LABChart
settings dialog, then a dialog will be shown in
which the choice can be made to overwrite the
old color parameters with the new ones, or to
keep the old values for this productID (see figure
at the right).
• The select button can be used to select a new
reference color from the database, as described
in detail on the previous page.
• Each time the Save button is clicked, a new record is added to the Filename in the lower left corner.
One record contains the following fields: Date, Time, Comments, L, a, b, h, c, X, Y, Z, RefProductID,
Lref, aRef, bRef, dL, da, db, dE, Channel, Illuminant and Observer. The Comments field contains the
text that is entered in the dialog that is shown after clicking the Save button.
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4.3.2.2 Time Series
With time series color
measurements, up to 8 color
parameters or color differences
can be followed simultaneously in
a graph against time. The time
series settings are defined in the
dialog above, which is shown after
clicking the Time Series TAB page.
The functions F1 to F8 can be
selected by clicking the
corresponding TAB sheet at the
top of this dialog. Furthermore, a
number of general (function
independent) parameters can be
entered, below of the function
TAB sheets. The following features
can be set separately for all
functions F1 to F8:
•
Spectrometer Channel. If the spectrometer system contains one or more slave spectrometer
channels, the spectrometer channel on which the color will be measured can be selected from the
drop down box at the upper left corner (showing by default “Master”). Make sure white reference and
dark spectra have been saved before for the selected spectrometer channel.
•
Illuminant. The CIE Standard sources A, B or C or one of the illuminants D50, D55, D65 or D75 can be
selected by clicking one of the radio buttons. The default is D65, which is the most widely used
illuminant. It represents the power distribution of average daylight, with a correlated color
temperature of 6500K. The D50, D55 and D75 have correlated color temperatures of 5000K, 5500K and
7500K. The CIE Standard sources A, B or C represent respectively: Incandescent light (2854K
blackbody), Simulated noon sunlight and Simulated overcast sky daylight. Note that there is no
relation between the illuminant chosen here and the light source that is used for measuring the color
of an object. The selected illuminant is used in calculation of the color parameters. These color
parameters will be different if for example A will be selected instead of D65, just as the color of an
object will look different in average daylight or in incandescent light (2854K blackbody).
•
CIE Standard Observer. The original CIE standard observer functions xλ, yλ and zλ were defined in
1931, and are known as the 2 degrees standard observer values. The 2 degrees corresponds with the
angle of vision that was used in the experiments to determine these standard observer values. In
1964, the CIE recommended the use of different observer values for a higher correlation with visual
perception for large samples. These are known as the 1964 supplementary standard observer, or 10
degrees observer values. Both standards are still in use, and in AvaSoft, the CIE standard observer can
be selected by clicking one of the radiobuttons. The default is 2 degrees.
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•
Function display settings. For each function, one of the color parameters can be selected. Functions
for which the color parameter has been set to “None” will be disabled. If one of the color difference
parameters (dL, da, db or dE) is selected, the reference color to which the measured color needs to
be compared needs to be defined as well. Therefore the reference color definition box (figure below)
will be displayed if dL, da, db or dE is clicked.
For each function, a different reference color can be selected. A detailed description about the DB,
Select and Add button can be found in the previous section.
The color parameters that have been set in the functions can be displayed graphically against time.
The amount of time that will be displayed at the X-axis can be set manually by clicking the Fixed
radiobutton (see figure below). If set to Auto, the time axis will be set to 1 minute. The Y-Axis can
also be set to Fixed or to Auto. The Auto option will set the Y-axis range to the minimum and
maximum function values that are in the list of measured datapoints.
Function Independent Parameters
Function Independent Parameters - Display no graphics to speed up data processing
Below the TAB sheets for function definition an option can be enabled or disabled to speed up data
processing by not displaying the graphics during the measurements. If an application requires fast data
processing, this option should be enabled. If saved to an output file, the data can be displayed graphically
after the time series experiment has been ended, as described in section 4.1.3: History-Display Saved
History Graph.
Function Independent Parameters - Save Function Output
The results of a time series color experiment will be saved to an ASCII-file if the radio button “Save
Function Output” has been selected. A number of seconds between saving can be entered for data
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reduction, in case measurements are carried out over long periods. Entering a value of zero results in
saving every scan. The name of the file to which the data will be saved, can be changed after clicking the
“Change Output File…” button. Last option in the “Save Function Output” box is to enable or disable the
possibility to create a backup file during the measurements. If this option is enabled, AvaSoft will create a
backup file with the same filename, but with the extension *.bak (also in ASCII). This backup file is
updated every scan and can be used in case the filename that has been selected has failed to save the
data, for instance because of a power failure during the measurements.
Save Setting/Load Settings buttons
AvaSoft automatically saves all parameters (color parameters, save options) to the file cootime.ini, and
restores these parameters, the next time AvaSoft is started. With the Save Settings and Load Settings
buttons, it’s also possible to save these parameter settings to (and load from) a file with the extension
*.coo. With this feature it is possible to save for each experiment a different *.coo file, so it can be
loaded a next time the same settings are required. The left figure below shows the dialog in which the
name of the file can be entered after clicking the Save Settings button. The right figure below, which is
displayed after clicking the Load Settings button, illustrates how to select an earlier saved *.coo file.
After the definition of one or more functions, the OK button is clicked to start measuring, the CANCEL
button to leave the dialog and return to AvaSoft’s main window.
After starting the color measurements by clicking OK, the output of the selected color parameters will be
displayed against time. If the option “Display no graphics to speed up data processing” has been marked in
the function entry dialog, the function output will be shown by numbers only, which are updated each
time a new scan is saved to the output file.
There are six buttons at the top of this window (see figure below): an Exit button, a Pause/Start button, a
Save Reference button, a Save Dark button, an Info button and a Print button.
If the red Exit button is clicked, the time measurements are ended and the main window and menu is
activated. The yellow Pause button can be used to stop the time measurements temporarily. After
clicking the Pause button, data acquisition stops and the text on the button changes to a green Start. If
the Start button is clicked, data acquisition is activated again and the text changes back to the yellow
Pause again.
The Save Reference and Save Dark buttons have the same functionality as in the main window.
The Info button shows the dialog, in which all parameters can be viewed (not edited) while the
measurement is running.
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By clicking the Print button, the
graphics that are displayed can be
printed during the run. First the printer
specific dialog shows up in which the
print options can be set. For example, if
only one graph of the four in the figure
above need to be printed, this graph can
be selected by the page(s) radiobutton.
All graphics are printed full size on a
different page.
At the right top of each graph, a color
indicator panel shows the color of the
sample being measured. If the function
output is a color difference value, like
dE in the figure above, then a second
color indicator panel is shown for the
reference color.
If time measurement data have been saved, the resulting ASCII file can be displayed graphically by
selecting this file in the dialog that is shown after clicking the menu option: Application-History-Display
Saved History Graph.
After clicking the “Open” button in this dialog, the function output is displayed against time. Both X- and
Y-axis are set to their full scale, which is determined by the minimum and maximum values in the list.
Zoom features
In each graph the same zoom features apply as in the main window (except for scaling the Y-axis with the
mouse wheel). However, zooming in over the X-axis while the measurement is running and the X-axis is
already scrolling will not be possible, because in that case the X-axis is updated with each new scan.
Clicking the pause button to take a snapshot will solve this problem.
Zoom in: select a region to be expanded to the full graph. To select this region, click the left mouse
button in the white graphics region and drag it downwards and to the right. After releasing the left mouse
button, both the X- and Y-axis will be rescaled to the new values of the selected region.
Zoom out: drag with the left mouse button within the white graphics region, but in stead of dragging the
mouse downwards and to the right, drag it into another direction. After releasing the mouse button, both
the X- and Y-axis will be reset to their default values.
Move X-Y: dragging with the right mouse button results in moving the complete spectrum up or down and
to the left or right.
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4.4 Applications: Absolute Irradiance Application
AvaSoft-IRRAD has been developed to perform on-line absolute irradiance measurements with an Avantes
spectrometer system. A calibrated light source AvaLight-HAL-CAL or AvaLight-DH-CAL with known energy
output (in µWatt/cm2/nm) is used as a reference. Also the calibration of an Avantes spectrometer system
can be done in our calibration lab, after which this calibration can be loaded.
Color of light parameters can be expressed by the chromaticity coordinated x, y and z. These chromaticity
coordinates are obtained by taking the ratios of the tristimulus values (X, Y and Z) to their sum. The
tristimulus values X, Y and Z and the spectral irradiance are computed in a wavelength range from 380 nm
to 780 nm, using a 1 nm interval. These parameters, as well as the coordinates u, v and the color
temperature of an external light source can be calculated and displayed in real-time. For LED
measurements, the Dominant Wavelength and Purity are interesting parameters, which can be calculated
as well. The Color Rendering Index (CRI) is a measure of the color rendering properties of a light source.
The same experimental set up (spectrometer with fiber optics and cosine corrector or integrating sphere)
is used to calculate the photometric and/or radiometric parameters of the light to be measured. The
calculated output can be displayed and saved in three ways:
•
In the main Window the data can be displayed as spectral irradiance in µWatt/cm2/nm versus
wavelength.
•
The measurement results can also be displayed in an irradiance chart (figure above), which shows the
chromaticity diagram, the irradiance spectrum, the spectrum in scope mode and many parameters for
colorimetry, photometry, radiometry and peak measurements. Up to 10 different radiometric
parameters and/or wavelength ranges can be selected for which the output will be displayed.
•
In Time Measurement mode, up to 8 functions can be displayed simultaneously against time. For each
function, a different radiometric, photometric, color coordinate or peak output parameter and/or
wavelength range may be selected, as well as a different spectrometer channel.
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4.4.1
Background
Before irradiance measurements can be done, an intensity calibration is required. The intensity
calibration contains the data transfer function for each pixel. The data transfer function is used to
convert the scope data (A/D Counts) into irradiance data (in µWatt/cm2) . To be able to calculate the
transfer function, a calibrated light source, with known output (in µWatt/cm2/nm) needs to be available.
When saving the A/D Counts with the reference light source on and off, we know the relation between the
A/D Counts and µWatt/cm2:


Caldata n


 refcal n − darkcal n 
Caldatan
refcaln
darkcaln
= Intensity of the calibrated light source at pixel n (in µWatt/cm2) from lampfile
= A/D Counts at pixel n that were saved with the reference light source on
= A/D Counts at pixel n that were saved with the reference light source off
When measuring the A/D counts received from a light source different from the calibrated light source
(but of course with the same fiber optic cable and diffuser), this relation can be used to measure the
intensity at every pixel n (in µWatt/cm2). If samplen is the measured A/D counts at pixel n when looking
at the sample light source, and darkn is the measured A/D Counts with the sample light source off, then
the equation for intensity In (in µWatt/cm2) becomes:
 samplen − dark n 

I n = Caldata n * 
 refcal n − darkcal n 
If during the intensity calibration a different integration time was used (e.g. 100ms) from the integration
time during the sample measurements (e.g. 2 ms), a factor needs to be added to the equation to
compensate for this. In the example the factor is 100/2 = 50.
Calculating the intensity (in µWatt/cm2) from the measured sample spectrum (in A/D Counts) can
therefore be done by the following equation:
 samplen − dark n 
 * factor
I n = Caldata n * 
refcal
darkcal
−
n
n 

From the irradiance spectrum (in µWatt/cm2), a lot of light output parameters can be calculated:
colorimetric, photometric and radiometric.
Below, short background information is given about the colorimetric, radiometric and photometric
parameters. We also describe the definition of the peak parameters that can be measured as well.
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Colorimetry
The color of light can be expressed by the chromaticity coordinates x, y and z. These chromaticity
coordinates are obtained by taking the ratios of the tristimulus values (X, Y and Z) to their sum:
x=
X
(X + Y + Z )
y=
Y
(X + Y + Z )
z=
Z
(X + Y + Z )
The tristimulus values X, Y and Z are computed by:
X = k * ∑ I λ * xλ
Y = k * ∑ I λ * yλ
Z = k * ∑ I λ * zλ
where:
k
=
constant (= 1/(Σyλ ) = 0.00934
Iλ
=
Spectral irradiance at wavelength λ
xλ, yλ, zλ =
CIE 1931 or 1964 Standard Observer value (2 or 10 degrees angle) at wavelength λ
The tristimulus values X, Y and Z and the spectral irradiance are computed in a wavelength range from
380 nm to 780 nm, using a 1 nm interval.
The CIE1960 UCS color coordinates u and v are calculated by:
u=
4x
(− 2 x + 12 y + 3)
v=
6y
(− 2 x + 12 y + 3)
The equation that is used for calculating the color temperature is empirical and assumes a black body
radiator:
p = ((x-0.332)/(y-0.1858))
Color Temp =5520.33-(6823.3*p)+(3525*p2)-(449*p3)
The Color Rendering Index (CRI) is a measure of the color rendering properties of a light source. The CIE
has defined 14 standard color samples and the CRI is defined as the mean value of the color rendering
values of the first 8 of these standard CIE samples.
A CRI of 100 indicates that the sample sources have identical color coordinates under the light source to
be tested and the reference light source. A CRI value of 50 is assigned to the CIE standard warm white
fluorescent lamp.
The CRI calculation method used is based on the CIE 13.3-1995 standard.
A reference light source is calculated on the basis of the color temperature of the light source to be
tested. The color temperature calculation is done with the McCamy algorithm described above.
For color temperatures under 5000K, a standard Planckian radiator is calculated with a color temperature
that equals the color temperature of the sample light source. For color temperatures between 5000K and
25000K, a standard daylight distribution is calculated, again with an identical color temperature.
The 14 standard CIE samples are then ‘illuminated’ with both light sources, and from the difference in
chromaticity values the 14 Special Rendering Indices are calculated, the first 8 of which yield the CRI.
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In LED measurements, the Dominant Wavelength and Purity (also known as HelmHoltz coordinates) are
often used to describe a color. The Dominant Wavelength can be calculated for a measured sample point S
with chromaticity coordinates (Sx,Sy) by drawing a straight line from the midpoint in the chromaticity
diagram (E with x=y=0.333) through S towards the edge of the Chromaticity Diagram (spectrum locus). The
points at the spectrum locus correspond with a wavelength and the interception of the straight line
through E and S with the locus is called the Dominant Wavelength.
Purity, is the distance from the midpoint (E) to the sample point (S), divided by that from the midpoint (E)
to the spectrum locus (DW):
Purity = (E-S) / (E-DW)
The method described above is used for all colors with a Dominant Wavelength from 380 to 699
nanometer. If the x,y coordinates are in the triangle area encompassed by the 3 points E, A and B, then
the Dominant Wavelength can not be calculated because the interception point through E and S with the
spectrum locus (between A and B) does not correspond with a wavelength. In that case the
Complementary Dominant Wavelength (CDW) is used. The line from E through S is extended backward in
order to determine the Complementary Dominant Wavelength (CDW).
DW
S
E
B
A
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Peak Measurements
A typical spectral power distribution of a (green) LED is
shown in the figure at the right. A number of peak
parameters can be calculated from this spectrum:
FWHM and Center Wavelength
The Full Width Half Maximum of a peak is the bandwidth (in
nanometers) for which the intensity is higher than half of the
maximum intensity of that peak. The Center Wavelength is
the wavelength halfway between the left and right
wavelength where the intensity is half of the maximum
intensity.
Peak Wavelength
Wavelength at the maximum spectral power
Centroid Wavelength
The total spectral power left and right from the centroid
wavelength (integral) is the same.
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Radiometry
The radiometric parameters can be grouped into three categories:
•
Radiant Flux [µWatt]: The radiant flux is the total optical power emitted from a source in all
directions. The best way to measure the power emitted by a source is to measure the source inside
an integrating sphere. This is often done when measuring LED’s. It is also possible to calculate the
flux of a source by measuring the irradiance at the surface of the diffuser (cosine corrector or
integrating sphere sample port) at a certain distance from a light source. An important assumption
in this calculation is that the source should be isotropic and the distance between diffuser and
source should be greater than five times the largest dimension of the source (approximation of
point source).
•
Radiant Intensity [µWatt/sr]: The radiant intensity is the optical power per unit solid angle. It is
used to quantify the optical power that is emitted by a source into a certain direction. Radiant
intensity is calculated from the measured irradiance by multiplication with the square of the
distance between source and diffuser surface. It is assumed that the source is a pointsource.
•
Irradiance [µWatt/cm2]: Irradiance is used to measure the power that is received by a surface.
Radiometric measurement can be done in different setups, like with fiber optic cosine corrector or
integrating sphere. Both setups can be used to measure the irradiance spectrum received at the surface of
the diffuser (cosine corrector or integrating sphere sample port) at a certain distance from a light source.
When measuring at a certain distance from the source, the radiant intensity and flux can be calculated as
described above. When measuring a light source inside an integrating sphere, the radiant flux can be
measured, but radiant intensity and irradiance parameters cannot be measured.
Radiometric parameters calculated from the power distribution
The power distribution can be easily converted in an energy distribution by multiplying the power with
the integration time. The result is the amount of energy that has been emitted or received during one
integration time cycle.
Another radiometric parameter that can be calculated from the irradiance spectrum, is the number of
photons that is received by a surface. Since the number of photons per nanometer is a huge number (even
with very low light intensity), the number of Avogadro is used to express the number of photons in mols,
or as in our application in µmols. The number of photons per nanometer can be calculated from the
wavelength dependent photon energy, and the absolute light energy that is measured. A detailed
description how this is done can be found at the next page.
The photon count distribution [µMol/(s.m2.nm)] shows the photon flux received per square meter. Other
photon count units that can be calculated from this are:
•
[µMol/(s.nm)]
photon flux received at diffuser surface
•
[µMol/( m2.nm)] photons received per square meter during one integration cycle
•
[µMol/nm]
photons received at diffuser surface during one integration cycle
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How to convert a power distribution [µWatt/(cm2.nm)] into a photon count distribution
[µMol/(s.m2.nm)]
Photon energy E(λ) = h.c/λ e
Where:
h = Planck´s constant 6,626 068 76 x10-34
c = velocity of light 2,998 x108 m/s
λ = wavelength in meters
For example, the photon energy at 250 nm and at 1000 nm is:
E(250) = (6,626 x 10-34. 2,998 x 108)/ 250.10-9 = 7,946 x10-19 (Joule/photon)
E(1000)= (6,626 x 10-34. 2,998 x 108)/ 1000.10-9 = 1,986 x10-19 (Joule/photon)
(1)
(2)
1eV = 1,60207 x 10-19 Joule, so the photon energy expressed in eV/photon becomes:
E(250) = 7,946 x10-19 /1,60207 x 10-19 = 4,9592 (eV/photon)
E(1000)= 1,986 x10-19 /1,60207 x 10-19 = 1,2398 (eV/photon)
(3)
(4)
Suppose we measure 20 µWatt/cm2 at a certain wavelength
20 µWatt/cm2 = 20 µJoule/s/cm2 = 0.2 Joule/s/m2
= 0.2/(1,60207 x 10-19 ) eV/s/m2
= 1,248 . 1018 eV/s/m2
(5)
Knowing the photon energy at 250 nm and at 1000 nm from (3) and (4), the number of photons
that correspond with 20 µWatt/cm2 at 250 nm and at 1000 nm can be calculated from (5) by:
for 250 nm
for 1000 nm
: #photons = 1,248 . 1018 / 4,9592 = 2,517 . 1017 photons/s/m2
: #photons = 1,248 . 1018 / 1,2398 = 1,007 . 1018 photons/s/m2
With 1 mol = 6,02308 x1023 (Number of Avogadro)
1 µmol = 6,02308 x1017
So, the number of photons, expressed in µmol/s/m2, when measuring 20 µWatt/cm2 at wavelength
250 nm and also 20 µWatt/cm2 at 1000 nm becomes:
for 250 nm
: 2,517 . 1017 / 6,02308 .1017 = 0,418 µmol/s/m2
for 1000 nm
: 1,007 . 1018 / 6,02308 .1017 = 1,672 µmol/s/m2
.
In the table below, the radiometric parameters that can be measured in AvaSoft are listed. Note that a
wavelength range needs to be specified over which the parameter spectral output will be integrated. In
the first column (Hardware setup), “inside sphere” refers to measurements that are done with the light
source inside an integrating sphere, while “outside sphere or cc” refers to measurements that are done
with a light source at a certain distance from the sphere or with a cosine corrector
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Hardware Setup
Parameter
Unit
Description
inside sphere
Radiant Flux
(Power emitted)
µWatt
Total optical power emitted from a source
inside sphere
Energy emitted
µJoule
Total optical energy emitted from a source,
calculated by multiplication of the power with
the integration time
outside sphere or
cc
Radiant Flux
(Power emitted)
µWatt
Total optical power emitted from a source,
calculated by multiplication of radiant intensity
with the solid angle of the light source
outside sphere or
cc
Energy emitted
µJoule
Total optical energy emitted from a source,
calculated by multiplication of the power with
the integration time
outside sphere or
cc
Radiant Intensity µWatt/sr
Optical power per unit solid angle, calculated by
multiplication of irradiance with the square
distance between point source and diffuser
surface
outside sphere or
cc
Radiant Energy
µJoule/sr
Total optical energy emitted from a source,
calculated by multiplication of the radiant
intensity with the integration time
outside sphere or
cc
Power received
µWatt
Power received at diffuser surface
outside sphere or
cc
Energy received
µJoule
Energy received at diffuser surface, calculated
by multiplication of the power with the
integration time
outside sphere or
cc
Irradiance
µWatt/cm2
Power received per square centimeter
outside sphere or
cc
Energy/cm2
µJoule/cm2
Energy received per square centimeter,
calculated by multiplication of irradiance with
the integration time
outside sphere or
cc
Photon Flux/m2
µMol/(s.m2)
Photons received per second and per square
meter, see for calculation previous page
outside sphere or
cc
Photon Flux
µMol/s
Photons received per second at diffuser surface
outside sphere or
cc
Photons/m2
µMol/m2
Photons received per square meter during one
integration time cycle
outside sphere or
cc
Photons
µMol
Photons received at diffuser surface during one
integration time cycle
Photometry
Photometry is the measurement of visible light. Unlike radiometry, it is not a purely physical
measurement and is calculated considering a 'standard' human visual perception. This is attained by
multiplying the radiometric data by the luminous efficacy curve (see figure below) and integrating the
product over the visible range (380 – 780 nm).
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Luminous efficacy curve
700
Luminous efficacy [lumens/watt]
600
500
400
300
200
100
0
380
430
480
530
580
630
680
730
780
Wavelength [nm]
The three categories that were defined for the radiometric parameters can also be used for the
photometric parameters.
•
The photometric equivalent for the Radiant Flux [µWatt] is the Luminous Flux, expressed in Lumens.
•
The photometric equivalent for the Radiant Intensity [µWatt/sr] is the Luminous Intensity,
expressed in Lumens/sr. This unit is equal to Candela.
•
The photometric equivalent for Irradiance [µWatt/cm2] is called Illuminance, expressed in
Lumens/m2. This unit is equal to Lux.
Since the geometry of the three categories is the same for radiometry and photometry, the same can be
written about the hardware setup: luminous flux can be measured inside an integrating sphere. When
measuring a source at a certain distance from the integrating sphere or cosine corrector, the luminous
flux can be calculated, assuming that the source is an isotropic point source. The Luminous Intensity
[Candela] and Illuminance [Lux] of a sphere can be measured outside the integrating sphere or with a
cosine corrector.
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4.4.2
Quick Start
Quick Start (1): Perform absolute irradiance measurements using a calibrated lamp
1. Start the AvaSoft software, and click the Start button in the main window.
2. Connect a fiber to the Spectrometer input port.
3. Start the Absolute Irradiance Application software by clicking the menu option: Application/Absolute
Irradiance. Click the “Perform Intensity Calibration” button.
4. Select the spectrometer channel that will be calibrated, the calibration lamp file and enter the
diameter of the fiber/cosine corrector or integrating sphere sample port that is used, as described in
section 4.4.4.
5. Turn on the reference light source (e.g. AvaLight-HAL-CAL or AvaLight-HAL-CAL-ISP). If a cosine
corrector is used at the end of the fiber, mount it directly on the reference light source. If an
integrating sphere is used at the end of the fiber, put the integrating sphere sample port over the
light output port.
6. Verify that the calibration lamp is ON for at least 15 minutes, and click the “Start Intensity
Calibration” button. Try to adjust the integration time while looking at the reference light, such that
the maximum count over the wavelength range is around 90% of the full ADC scale, which is 14750
counts for the 14bit ADC, 59000 counts for the 16bit ADC. It’s also possible to let AvaSoft search for
an optimal integration time by clicking the ‘∫AC’ button.
7. Adjust the Smoothing Parameter to optimize smoothing for the Fiber/Slit diameter that is used.
8. If a good reference signal is displayed, click the white “Save Reference” button. A white line will
mark the reference spectrum. Then switch off the calibration lamp, wait until the spectrum becomes
flat, near the bottom of the scale, and click the black button to save a dark spectrum. A black line
will mark the dark spectrum.
9. Click the “Save Intensity Calibration” button. A dialog shows up in which the current settings in this
intensity calibration are shown. If the calibration has been performed with diffuser, the intensity
calibration data will be saved to an ASCII file with extension *.dfr, with bare fiber this extension will
be *.fbr. The name of the intensity calibration file can be entered after clicking the “Save As”
button. With USB2 spectrometers, the intensity calibration can also be saved to EEProm by clicking
the “Save to EEProm” button. Click the Close button to Close the dialog.
10. Switch to the Irradiance Chart TAB to enter the hardware setup and select the colorimetric,
radiometric, photometric and/or peak parameters of interest (see section 4.4.5.1) . Then click OK.
11. Measure the output parameters in the experiment. If needed, change the integration time, such that
the maximum in Scope Mode is around 90% of the full ADC scale, which is 14750 counts for the 14bit
ADC, 59000 counts for the 16bit ADC). Block the light path to the spectrometer, and save a dark
spectrum. If the (ir)radiance of the light to be measured needs to be displayed against time, click the
time measurement TAB in the settings dialog as described in section 4.4.6.
12. The intensity calibration as performed under point 9 can be loaded in future experiments by selecting
the option “Load Intensity Calibration”, as described below under Quick Start (2). For the USB2
spectrometers, the intensity calibration that has been stored in the EEProm is loaded automatically
during the initialization of AvaSoft. After loading an intensity calibration, a dark spectrum needs to be
saved before switching to Irradiance mode.
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Quick Start (2): Perform absolute irradiance measurements by loading an intensity calibration
1. Start the AvaSoft software, and click the Start button in the main window.
2. Connect the same fiber (and diffuser or integrating sphere) that was used during the intensity
calibration that will be loaded to the Spectrometer input port.
3. Start the Absolute Irradiance Application software by clicking the menu option: Application/Absolute
Irradiance. If an intensity calibration has been stored in EEProm before, this will be autoloaded at
AvaSoft program initialization. Click the “Load Intensity Calibration” button. A dialog shows up in
which the intensity calibration file can be selected. Select the file and click the open button.
4. Switch to the Irradiance Chart TAB to enter the hardware setup and select the colorimetric,
radiometric, photometric and/or peak parameters of interest (see section 4.4.5.1) . Then click OK.
5. Measure the output parameters in the experiment. If needed, change the integration time, such that
the maximum in Scope Mode is around around 90% of the full ADC scale (14750 counts for the 14bit
ADC, 59000 counts for the 16bit ADC). Block the light path to the spectrometer, and save a dark
spectrum. If the (ir)radiance of the light to be measured needs to be displayed against time, click the
time measurement TAB in the settings dialog as described in section 4.4.6.
4.4.3
Load Intensity Calibration
By selecting the menu option ApplicationAbsolute Irradiance Measurement, a window
is shown in which the intensity calibration
that was saved before can be loaded by
clicking the “Load” button. An intensity
calibration file contains the data which is
necessary to convert the Scope data to
Irradiance data. If the spectrometer system
has one or more slave channels, it is
important to know that the calibration data
for each spectrometer channel are saved in a
separate file. To measure irradiance data at
more spectrometer channels simultaneously,
the calibration files for each spectrometer
channels needs to be loaded first. After loading an intensity calibration file, a graph is displayed which
shows the data transfer function for the loaded channel. The irradiance spectrum is calculated by
multiplying the measured scope data (from which a saved dark spectrum is subtracted) with this data
transfer function.
The intensity calibration is by default loaded from
Eeprom. However, if multiple calibrations are available
for a spectrometer, the eeprom calibration can be
overruled by loading a calibration from file. The
filename that holds the intensity calibration needs to
include the serialnumber of the spectrometer channel.
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If the intensity calibration has been loaded, the “Irradiance Chart” and “Irradiance Time Series” tabs will
be enabled. The “Auto Adjust Integrationtime TAB will become available as well. Clicking the irradiance
chart or time series tabs allows you to change the settings, before the measurements are started by
clicking the OK button. The irradiance chart and time series settings will be described in sections 4.4.5
and 4.4.6.
The Auto Adjust Integrationtime Settings tab can be clicked to enable the Auto Adjust Integrationtime
feature and to set the parameters that control the change of integration time. A detailed description
about this feature can be found in section 4.4.7.
4.4.4
Perform Intensity Calibration
If a calibrated light source such as the AvaLight-HAL-CAL
or AvaLight-DH-CAL is available, an intensity calibration
can be performed. By selecting the menu option
Application-Absolute Irradiance Measurement, a window
is shown in which the settings for the intensity calibration
become visible after clicking the “Perform Intensity
Calibration” button. The following settings need to be
entered before starting the intensity calibration:
•
Spectrometer channel
•
Calibration Lampfile
•
CC-UV/VIS, Fiber or AvaSphere sample port diameter
For a single channel spectrometer, the spectrometer
channel will always be set to “Master”. For multichannel spectrometer systems, the spectrometer channel
for which the intensity calibration will be performed can be selected from the list (Master, Slave1…).
Calibration Lamp
The energy output (in µWatt/cm2/nm)
for the calibration lamp that will be
used can be found in a file with the
extension *.lmp. This file needs to be
selected by clicking the “Select”
button.
After the calibration file has been
selected, the data can be viewed,
edited and/or saved under a different
filename by clicking the “View/Edit
Lamp Data” button.
A dialog with the intensity versus
wavelength values for the selected
calibration light source is shown, as well
as a graph in which the intensity is displayed versus wavelength:
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If needed, the data can be edited and saved under another filename by clicking the Save As… button.
Before the changed data takes effect, the new filename needs to be loaded with the Select lamp option
described above.
CC-UV/VIS, Fiber or AvaSphere sample port diameter
The hardware setup for which the calibration lamp has been calibrated (CC-UV/VIS cosine corrector, bare
fiber or integrating sphere), should match the hardware setup that is used during the intensity calibration.
The diameter of the cosine corrector (3900 micron), bare fiber, or AvaSphere (6000, 10000 or 15000
micron for respectively AvaSphere-30, AvaSphere-50 and AvaSphere-80) needs to be entered in micron.
It is important that the hardware setup that is used during the calibration, is the same as the hardware
setup in the (ir)radiance measurements.
4.4.4.1 Start Intensity Calibration
Verify that the calibration is ON for at least 15
minutes, and that the hardware has been setup
correctly. Then click the button “Start
Calibration”. As a result, the Scope data (A/D
Counts) for the selected spectrometer channel
will be displayed graphically.
Set the smoothing parameter to optimize
smoothing for the fiber/slit diameter used (see
also section 3.2.3).
Set the integration time such that a good
reference signal is measured (maximum
around 90% of the full ADC scale, which is
14750 counts for the 14bit ADC, 59000 counts
for the 16bit ADC). It’s also possible to let
AvaSoft search for an optimal integration time
by clicking the AutoConfigure Integration time
(‘∫AC’) button.
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Set the number of scans to Average to a high number to reduce the noise during the intensity calibration.
If a good reference signal is displayed, click the white “Save Reference” button in the dialog above. A
white line will mark the reference spectrum. Then switch off the calibration lamp, wait until the
spectrum becomes flat, near the bottom of the scale, and click the black button to save a dark spectrum.
A black line will mark the dark spectrum.
4.4.4.2 Save Intensity Calibration
If reference and dark data have been
saved in the figure above, the intensity
calibration can be saved by clicking the
“Save Calibration” button.
A dialog shows up in which the current
settings in this intensity calibration are
shown. If the calibration has been
performed with diffuser, the intensity
calibration data will be saved to an ASCII
file with extension *.dfr, with bare fiber
this extension will be *.fbr. The name of
the intensity calibration file can be
entered after clicking the “Save As”
button. The intensity calibration can be
saved to Eeprom by clicking the Save To
EEPROM button. When saving an intensity
calibration to file, make sure to include the serialnr into the filename.
The following data will be saved to the intensity calibration file:
•
Name of light source calibration file (*.lmp)
•
Spectrometer channel (0=Master, 1=Slave1 etc..)
•
Integration time in milliseconds
•
Diameter of diffuser surface in microns
•
TOTAL_PIXELS (=2048 for AvaSpec-2048) values,
which represent the dynamic range (reference
minus dark data) at each pixel during the
intensity calibration, divided by the intensity of
the calibrated light source that was used.
•
Setting for the Smoothing parameter during the
intensity calibration.
After an intensity calibration has been performed, a
graph is displayed which shows the data transfer
function for the spectrometer channel. The irradiance
spectrum is calculated by multiplying the measured
scope data (from which a saved dark spectrum is
subtracted) with this data transfer function.
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If the intensity calibration has been performed, the “Irradiance Chart” and “Irradiance Time Series” tabs will
be enabled. Clicking one of these tabs allows you to change the settings for the irradiance chart or time series
measurements, after which the measurements can be started by clicking the OK button. The irradiance chart
and time series settings will be described in sections 4.4.5 and 4.4.6.
4.4.5
Irradiance Chart
4.4.5.1 Irradiance Chart Settings
After an intensity calibration has been performed or loaded, the “Irradiance
Chart TAB” becomes available in the Irradiance Settings dialog. By clicking
the TAB, the Irradiance Chart settings are displayed. The figure at the right
shows the settings for Spectrometer Channel, Hardware Setup, Parameter
group, Graphics and Save Settings.
The Spectrometer Channel setting can be changed, if for a multichannel
spectrometer system calibrations have been performed or loaded for more
than one channel.
The Hardware setup setting is an important parameter, because as
described in section 4.4.1 (background) it determines the radiometric and
photometric parameters that can be measured, as well as the way these are
calculated. If an AvaSphere is used, it is important to know if the light
source is measured inside the sphere (like often is done with LED’s), or
outside the sphere. This setting can be entered after clicking the AvaSphere
button and then inside or outside sphere.
The Parameter group setting determines which parameters will be shown in
the irradiance chart. By clicking one of the group parameters, the detailed
settings for this group become visible. A description about these
parameters and how they are calculated can be found in section 4.4.1.
By default, only the Colorimetric parameters are enabled.
The parameters that are enabled in the figure above will be displayed in the Irradiance Chart.
The detailed setting for the radiometric parameters is done while measuring, in the irradiance chart
dialog. If the hardware setup is not “source inside sphere”, you can already select if you want to measure
only radiometric parameters received at the diffuser surface, or also calculate the power and/or energy
emitted by the source. An important assumption when calculating the emitted power or energy is that the
source should be an isotropic point source.
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If the hardware setup is “source inside sphere”, the detailed setting for the radiometric parameters
(emitted power in µWatt or emitted energy in µJoule) is done while measuring, in the irradiance chart
dialog.
The same difference in hardware setup determines which photometric parameters can be measured. If
the hardware setup is not “source inside sphere”, the Illuminance in Lux can be measured. The Luminous
flux (the photometric equivalent of radiometric Power) can be measured at the diffuser surface, but it
can also be calculated how much lumens are emitted by the source. An important assumption is that the
source should be an isotropic point source. In this setup the Luminous Intensity in Candela can be
measured as well. If the hardware setup is “source inside sphere”, only the Lumens emitted by the source
can be measured.
The peak parameter group allows you to enable/disable the following peak information.
Detailed settings, like the wavelength range and the radiometric output parameter for which the peak(s)
are calculated can be done in the Irradiance chart dialog.
The Graphics setting determines which graph will be displayed in the irradiance chart dialog.
The Save Settings are used to enter the name of the textfile to which the results of the irradiance chart
measurements will be saved. By default this name is irrchart.txt, but by clicking the “Change Output File”
button, this filename can be changed.
By enabling the “Save Irradiance Spectrum” option, a complete
irradiance spectrum will be saved together with the parameter
results. The name of the irradiance spectrum file will start with the
filename that has been entered (irrchart in the figure at the right),
followed by a sequence number and the extension *.irr. The
irradiance spectrum files can be saved and loaded from the irradiance
chart dialog.
Likewise, the complete irradiance chart window can be saved as a
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picture together with the parameter results. The name of the picture will start with the filename that has
been entered (irrchart in the figure at the right), followed by a sequence number and the extension *.jpg.
If all settings have been entered, the measurements can be started by clicking the OK button. To be able
to measure the right A/D counts (corrected for the dark spectrum), a warning will be displayed if a dark
spectrum has not been saved:
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4.4.5.2 Irradiance Chart Display
The irradiance chart displays the
graphics and output parameters
that were selected in the settings
dialog. Moreover, up to ten
radiometric parameters can be
selected, each with a user defined
wavelength range. The
measurement results can be saved,
and earlier saved spectra can be
graphically displayed and compared
to the measured spectrum. The
integration time and number of
scans to average can be changed to
optimize the AD Counts for each
sample.
The figure at the right shows the
result for a typical LED
measurement inside an Avasphere.
If the light
source is
measured
outside the
sphere or
with a cosine corrector, and the radiant flux [µWatt], radiant intensity [µWatt/sr], luminous flux [Lumens]
or luminous intensity [Candela] need to be calculated, then the distance (in meter) and geometry of the
lamp (in steradians) can be entered in the irradiance chart window as well. The geometry of the point
source is default 4π steradians and is needed only for the radiant and luminous flux calculations.
In this section, the following items from the irradiance chart window will be described:
•
Add/Edit radiometric parameters
•
Graphics
•
Button bar
The other output parameters are displayed according to the settings in the irradiance chart settings
dialog. Background information about all output parameters can be found in section 4.4.1.
Add/Edit radiometric parameters
There are two ways to monitor the radiometric parameters. The first one is by defining up to ten different
parameters or wavelength ranges in the radiometry box at the right side of the irradiance chart window.
The second one is by selecting a radiometric parameter in the graph after which the spectrum for the
selected parameter will be displayed (see below under graphics).
To define an output parameter at one of the ten lines in the radiometry box, simply double click the line
or click the Edit button on top and enter the line number. A dialog will be shown in which the radiometric
parameter and wavelength range can be specified.
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The wavelength range is the spectral range over which
the radiometric output will be integrated. For
example, by specifying the UV-C, UV-B and UV-A
wavelength ranges at three different lines, the
irradiance for these spectral ranges can me measured
simultaneously (assuming the spectrometer wavelength
range includes the specified ranges and has also been
calibrated for these ranges).
Note that the available parameters depend on the
settings in the irradiance chart settings dialog. For
example, to be able to measure the radiant intensity,
the “Calculate Power and/or Energy emitted by a
source” option should be enabled.
Graphics
Chromaticity diagram
Radiometric Graph
Scope Data Graph
The chromaticity diagram is used to visualize the colorimetric measurements. According to what has been
selected in the irradiance chart settings dialog, it will display the locus for the 2 or 10 degrees standard
observer. The measured (x,y) coordinates will be displayed in the diagram and a line will be drawn from
the midpoint (x=y=1/3) through the measured (x,y) to the edge of the locus, which represents the
dominant wavelength.
The scope data graph displays the raw A/D counts that are received from the spectrometer. This graph
can be used to determine if a good integration time has been set. If the integration time is too low, the
radiometric spectrum will be noisy, if the integration time is set too high, the spectrometer detector can
be saturated, in which case a saturated label will appear in the Scope Data Graph.
The radiometric graph displays the spectrum for the
selected radiometric parameter. Just like with selecting the
radiometric parameter in the radiometry box, the available
parameters depend on the settings in the irradiance chart
settings dialog. In the figure at the right, an LED is
measured inside an integrating sphere, in which case only
the Radiant Flux (emitted power in µWatt) and the emitted
energy during one integration cycle (in µJoule) can be
selected. See also the radiometric table in section 4.4.1.
The selected parameter in the radiometric graph is also
used to determine the peaks in the peak measurement box.
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The radiometric spectra can be saved and loaded by the “Save” and “Open Saved Graph” buttons (see
below under button bar).
Button bar
The Exit button will close the irradiance chart and return to the AvaSoft main Window.
The Pause button will stop data processing to be able to take a snapshot at the spectrum and/or output
parameters.
The Info button shows information about the current settings, as shown in the dialog below:
The last line in this dialog: “Save irradiance spectrum?: Yes”
refers to the save setting in section 4.4.5.1. If this option is
enabled then all (displayed) parameters will be saved in this
example to irrchart2.txt and the spectrum for the selected
parameter in the radiometric graph will be saved to
irrchart2xxxx.irr, in which xxxx represents the sequence
number.
If the “Save irradiance spectrum” option is not enabled, only
the displayed output parameters will be saved.
By clicking the save dark (black) button, a new dark spectrum will be saved. It is recommended to save a
new dark spectrum each time after changing the integration time.
Clicking the save data button will add the measured data to the textfile. A user comment can be added to
the saved data. If a radiometric spectrum and/or irradiance chart picture (.jpg) have been saved with the
output parameters, the name of these/this file is also saved in the textfile.
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The “Display Saved Graph” button can be clicked to load a radiometric spectrum that was saved before.
In the open file dialog, the radiometric spectra that were saved before will be listed. By single clicking a
file name, the comment for this file will be displayed in the graph. By double clicking the file name, or by
clicking the Open button, the radiometric spectrum will be displayed. This can be repeated for a second
filename, which allows you to compare the output of the two spectra graphically. The online measured
spectrum will be displayed in the same graph and can be compared to earlier saved spectra as well.
The filename and comments for the displayed spectra appear on top of the
graph, the text colors are the same as the colors used to draw the spectra. By
clicking the (blue or green) filename with the right mouse button, a popup
menu for this radiometric spectrum is presented, with the menu options shown
in the figure at the right:
The “Show Info” menu option displays the hardware
settings, measurement parameters and save settings for
the spectrum, as shown in the dialog at the left.
The Measurement parameters displays the unit of the
intensity of the displayed saved spectrum. This can be a
different unit than the selected unit for the online
measured spectra. Also, if comparing two saved spectra
graphically, be aware that these were saved in the same
radiometric unit.
The other menu options in the popup menu, “Convert to ASCII” and “Convert to Excel” can be used to
export the data from the (binary) file with extension *.IRR to a textfile (*.txt) or to a file that can be
opened with Excel (*.xls). The “Remove from Chart” menu option clears the saved spectrum.
At the right side of the button bar, the integration time and number of scans to average can be changed.
The Auto Configure Integration time button can be used to let AvaSoft search for integration time such
that the maximum output in scope mode (A/D Counts) is around 90% of the full ADC scale (14750 counts
for the 14bit ADC, 59000 counts for the 16bit ADC).
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4.4.6
Time Series Measurement
After an intensity calibration has been performed or loaded, the “Irradiance Time Series TAB” becomes
available in the Irradiance Settings dialog. By clicking the TAB, the Irradiance Time Series settings are
displayed.
With time series irradiance measurements, up to 8 radiometric parameters can be followed
simultaneously in a graph against time. The functions F1 to F8 can be selected by clicking the
corresponding TAB sheet at the top of the Time Series settings dialog.
Furthermore, a number of general (function independent) parameters can be entered, below of the
function TAB sheets. The following features can be set separately for all functions F1 to F8:
•
•
•
Enable/Disable function. The radiometric parameters can be set after clicking the Enable button.
Hardware Setup. The Hardware setup setting is an important parameter, because as described in
section 4.4.1 (background) it determines the radiometric and photometric parameters that can be
measured, as well as the way these are calculated. If an AvaSphere is used, it is important to know
if the light source is measured inside the sphere (like often is done with LED’s), or outside the
sphere. This setting can be entered after clicking the AvaSphere button and then inside or outside
sphere.
Spectrometer Channel. If the spectrometer system contains one or more slave spectrometer
channels, for which also an intensity calibration has been loaded or performed, the spectrometer
channel on which the output parameter will be measured can be selected from the drop down box
at the left (showing by default “Master”).
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•
Parameter. The number of available parameters and the way these are calculated depend on the
hardware setup. The figure above shows the settings that are available when measuring with a
cosine corrector, or with an integrating sphere at a certain distance from the light source. For each
function F1..F8, one of the 35 available parameters can be selected. See section 4.4.1 for
background information about these parameters. The colorimetric parameters can be calculated by
using the 2 degrees standard observer values or the 10 degrees. If one of the radiometric
parameters is selected, the wavelength range needs to be specified. The wavelength range is the
spectral range over which the radiometric output will be integrated. If the source is not inside an
integrating sphere, the radiant intensity (in µWatts/sr) and radiant energy (in µJoule/sr) can be
calculated if the distance from source to diffuser surface has been specified. The radiant flux
(µWatts emitted) and emitted energy (µJoule e.) can be calculated if the geometry of the lamp (in
steradians) is specified. Distance and Geometry can be entered if the parameter is selected for
which these data entries are relevant. If one of the peak parameters is selected, the wavelength
range needs to be entered over which the (highest) peak will be calculated. Moreover, the
radiometric parameter should be specified to determine a peak parameter. Photometric parameters
do not need a wavelength range because for these parameters the range is always from 380 to 780
nm. However, since emitted Lumens and Candela are the photometric equivalent of radiant flux
and radiant intensity, the geometry (for emitted Lumens) and distance (for emitted Lumens and
Candela) needs to be specified if the source is not measured inside an integrating sphere. If a
source is measured inside an integrating sphere, the radiometric parameters that can be measured
are limited to radiant flux (µWatts emitted) and emitted energy (µJoule e.), and the photometric
parameter that can be measured in this hardware setup is emitted Lumen.
•
Function display settings. The parameters that have been set in the functions can be displayed
graphically against time. The amount of time that will be displayed at the X-axis can be set
manually under the X-axis setting. The Y-Axis can be set to a fixed range or to Autoscale. The
Autoscale option will set the Y-axis range to the minimum and maximum function values that are in
the list of measured datapoints.
Function Independent Parameters
Function Independent Parameters - Display no graphics to speed up data processing
Below the TAB sheets for function definition an option can be enabled or disabled to speed up data
processing by not displaying the graphics during the measurements. If an application requires fast data
processing, this option should be enabled. If saved to an output file, the data can be displayed graphically
after the time series experiment has been ended, as described in section 4.1.3: History-Display Saved
History Graph.
Function Independent Parameters - Save Function Output
The results of a time series color experiment will be saved to an ASCII-file if the radio button “Save
Function Output” has been selected. A number of seconds between saving can be entered for data
reduction, in case measurements are carried out over long periods. Entering a value of zero results in
saving every scan. The name of the file to which the data will be saved, can be changed after clicking the
“Change Output File…” button.
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Last option in the “Save Function Output” box is to enable or disable the possibility to create a backup
file during the measurements. If this option is enabled, AvaSoft will create a backup file with the same
filename, but with the extension *.bak (also in ASCII). This backup file is updated every scan and can be
used in case the filename that has been selected has failed to save the data, for instance because of a
power failure during the measurements.
Save ICF/Load ICF buttons
AvaSoft automatically saves all parameters (irradiance parameters, save options) to the file irrtime62.ini,
and restores these parameters, the next time AvaSoft is started. With the Save ICF and Load ICF buttons,
it’s also possible to save these parameter settings to (and load from) a file with the extension*.icf. With
this feature it is possible to save for each experiment a different *.icf file, so it can be loaded a next time
the same settings are required.
After the definition of one or more functions, the OK button is clicked to start measuring, the CANCEL
button to leave the dialog and return to AvaSoft’s main window.
After starting the irradiance measurements by clicking OK, the output of the selected parameters will be
displayed against time. If the option “Display no graphics to speed up data processing” has been marked in
the function entry dialog, the function output will be shown by numbers only, which are updated each
time a new scan is saved to the output file.
There are six buttons at the top of this window (see figure below): an Exit button, a Pause/Start button, a
Save Reference button, a Save Dark button, an Info button and a Print button.
If the red Exit button is clicked, the time measurements are ended and the main window and menu is
activated. The yellow Pause button can be used to stop the time measurements temporarily. After
clicking the Pause button, data acquisition stops and the text on the button changes to a green Start. If
the Start button is clicked, data acquisition is activated again and the text changes back to the yellow
Pause again.
The Save Reference and Save Dark buttons have the same functionality as in the main window.
The Info button shows the dialog, in which all parameters can be viewed (not edited) while the
measurement is running.
By clicking the Print button, the
graphics that are displayed can be
printed during the run. First the
printer specific dialog shows up in
which the print options can be set.
For example, if only one graph of
the four in the figure above need to
be printed, this graph can be
selected by the page(s) radiobutton.
All graphics are printed full size on
a different page.
If time measurement data have
been saved, the resulting ASCII file
can be displayed graphically by
selecting this file in the dialog that
is shown after clicking the menu
option: Application-History-Display
Saved History Graph. After clicking
the “Open” button in this dialog,
the function output is displayed against time. Both X- and Y-axis are set to their full scale, which is
determined by the minimum and maximum values in the list.
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Zoom features
In each graph the same zoom features apply as in the main window (except for scaling the Y-axis with the
mouse wheel). However, zooming in over the X-axis while the measurement is running and the X-axis is
already scrolling will not be possible, because in that case the X-axis is updated with each new scan.
Clicking the pause button to take a snapshot will solve this problem.
Zoom in: select a region to be expanded to the full graph. To select this region, click the left mouse
button in the white graphics region and drag it downwards and to the right. After releasing the left mouse
button, both the X- and Y-axis will be rescaled to the new values of the selected region.
Zoom out: drag with the left mouse button within the white graphics region, but in stead of dragging the
mouse downwards and to the right, drag it into another direction. After releasing the mouse button, both
the X- and Y-axis will be reset to their default values.
Move X-Y: dragging with the right mouse button results in moving the complete spectrum up or down and
to the left or right.
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4.4.7
Auto Adjust Integrationtime
Introduction
In Irradiance mode, the integration time should be selected such that the maximum intensity of the ADC
Counts is around 90% of the full scale.
In experiments where the light intensity varies slowly during a long period of time (e.g. solar
measurements over 24 hours), it is possible to setup the software in such a way that the integration time
is autoadjusted if the maximum of the measured intensity in the previous scan is outside certain limits.
Normally, when changing the integration time manually, it is always recommended to save a new dark
spectrum. If the integration time is automatically changed, the dark spectrum at the new integration time
can also be different. To avoid recording a new dark spectrum after each change of integration time, a
dark calibration can be done at minimum integration time and long integration time. This dark calibration
can be saved to EEProm for all pixels. During the measurements, the dark data is then calculated by
interpolating the saved dark spectra at different integration times.
4.4.7.1 Auto Adjust Integrationtime Settings
The Settings window as displayed in the figure below is activated by clicking the “Auto Adjust
Integrationtime Settings” TAB in the Irradiance settings dialog.
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The Auto Adjust Integrationtime feature can be switched on or off by clicking the “Apply” checkbox at
the top of the Settings windows.
In the limits box, you can change the percentages at which the integration time will be changes. For
example, if the full scale is 65535 ADC Counts, and the switching limits are 80% and 90% like in the figure
above, the integration time will be increased for the next scan if the maximum Counts measured is lower
than 0.80*65535 = 52428. Likewise, if the maximum is more than 0.90*65535 = 58982 Counts, the
integration time will be decreased in the next scan.
The maximum integrationtime setting will be applied if the calculated integration time for the next scan
is longer than this user specified value. This is a useful setting e.g. in a 24 hours/day solar measurements
in which case the calculated integration time would otherwise become many minutes during the night.
The user specified maximum integration time will also serve as “long” integration time setting during the
dark calibration (see below).
If the “Recalculate Averages” checkbox is enabled, the number of averages will be recalculated after
each change of integration time. The number of averages will be set such that at the new integration
time, the total scan duration is close to the user specified duration time (e.g. 10 averages if the
calculated integration time is 100ms and the scan duration is 1000ms).
The Dark Calibration is needed to calculate a dark spectrum after each change of integration time. The
currently available dark calibration spectra and integration times can be displayed in the graph. In the
figure above, the dark spectra at 1.10ms and 1000ms (dynamic dark correction ON) for channel 0807040U2
are displayed. A new dark calibration can be done for all channels (in a multichannel system)
simultaneously by clicking the Start Dark Calibration button. A reminder will be displayed to block light
input for all connected spectrometer channels. Then, a few scans are taken at minimum integration time,
followed by a few scans at the integration time that has been entered in the maximum integration time
edit box. During the calibration, a counter will be updated after each scan in the dark calibration status
box, and the measured dark scans are displayed in the graph for each channel.
The dark calibration can always be aborted during the calibration by clicking the Abort Dark Calibration
button (e.g. if the light input for one or more channels was not blocked).
If the dark calibration is ready, the dialog at the right
will be displayed. By clicking Yes, the new dark spectra
and corresponding integration times are saved to
eeprom and will be used to calculate a new dark
spectrum after each change of integration time if the
Auto Adjust Integration time feature is enabled
4.4.7.2 Measuring with Auto Adjust Integrationtime
If the Auto Adjust Integrationtime option is enabled, and a valid dark calibration has been saved to
EEProm, the maximum ADC Counts will be evaluated after each scan and compared against the limits that
have been entered in the settings dialog. In Absolute Irradiance mode (main window) and when measuring
in the Absolute Irradiance Application (irradiance chart and time series measurement) the integration
time will be adjusted if the maximum ADC Counts level is not inside the user specified range. See also the
example given in the description of the limits settings above.
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4.5 Applications: Process Control Application
Avasoft Process Control allows you to operate digital outputs corresponding with preset levels of your
history channels. You can use all eight history channels, as well as the output functions of the Time Series
from both the Color and the Irradiance applications. The output of two History Channel Functions can be
converted to analog output signals (0..5V).
4.5.1
Digital Output signals
AvaSoft supports 8 built-in digital outputs on the AvaSpec, one per history channel. The output pins on the
High Density 26-pole Sub-D connector which are used for the process control application are listed in the
table below.
HD DB26 pins used by AvaSoft
Process Control
HCF# connector
pin
1
2
2
20
3
3
4
21
5
13
6
4
7
22
8
25
GND
4.5.2
8
Analog Output signals
Pin 17 and 26 of the HD DB26 connector can be used to convert maximal two History Channel Function
output signals into a 0-5V signal. The analog output resolution is 8-bit (0.02V steps)
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4.5.3
Using the Process Control Application in AvaSoft
The Process Control application needs to be activated by selecting ‘Application’, ‘Process Control’,
‘Enable’. A checkmark will appear before the menu entry to show that the option is enabled.
To set minimum and maximum threshold values for each of the History functions, select ‘Application’,
‘Process Control’, ‘Digital Output Settings’.
The box shows 16 values, corresponding with a minimum and maximum
threshold value for the 8 history channels. All 16 values can be edited by
clicking them with the mouse. In addition, in the third column, you can
select whether or not to invert the signal that is output. For each
channel, the minimum threshold value may not exceed the maximum
threshold value. You cannot leave fields blank, in that case, enter 0.
After selecting OK, the settings are written to a binary file called
‘digital.ini’.
The minimum and maximum threshold values are indicated in the history
graphs with horizontal lines.
If ‘Invert’ is not selected, the corresponding output pin will be set high if
the history channel output value lies between the minimum and
maximum value. It will be set low if the history channel output value exceeds the maximum value OR is
smaller than the minimum value.
If ‘Invert’ is selected, the corresponding output pin will be set high if the history channel output value
exceeds the maximum value OR is smaller than the minimum value. It will be set low if the history
channel output value lies between the minimum and maximum value.
If you want to monitor both threshold
values, you can assign two (identically
configured) history channels.
To monitor a single level, set one
threshold value to the desired level,
and the other one to a value that is
out of range, e.g. Min to –99999999
and Max to 1000, or Min to 2000 and
Max to 99999999.
That way, you will only need a single
channel per threshold value.
An example of running the History
Channel functions together with the
digital output signals in the Process
Control application is shown in the
figure at the right.
In this example, two History Channel functions were defined. The threshold values for function F1 were
set at 99.5 and 100.5 percent transmittance, for function F5 at 0 and 58. These values are represented by
the horizontal lines in the graphs.
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To specify the History Channel Function range(s) that
should be converted into a 0-5V analog output signal,
select ‘Application’, ‘Process Control’, ‘Analog Output
Settings’.
Two analog output signals can be assigned to any history
channel. The Chan-0 output is sent to pin 17, and the
Chan-1 output to pin 26 of the HD DB26 connector
The calculated voltage will be printed between parentheses after the function value in the History
Channel and Time Series (color and irradiance application) screens:
In this example, with the Min and Max Function Range settings according to the Analog Settings dialog
above, the voltage at pin 17 and pin 26 are calculated by:
F1: Output = 62.943, corresponds to 5.0*(62.943 - 50.0)/(100.0 - 50.0) = 1.29V
F2: Output = 69.192, corresponds to 5.0*(69.192- -100.0)/(100.0- -100.0) = 4.23V
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4.6 Applications: Excel Output
AvaSoft XLS is an add-on application that enables Avasoft Full to output history channel data and/or
complete spectra to Microsoft Excel.
It uses OLE-Automation, which is a technology that enables AvaSoft to remotely control Excel, opening
sheets and copying data into cells.
On modern hardware, we have been able to copy complete 2048 pixel spectra to Excel with as little as 50
msec. overhead per scan.
4.6.1
Select Source Data
Besides enabling Excel output, you
will have to select your source data.
This is done in the same way it
would be done without the Excel
output option, with the input
screens you use to define History
Channel Functions, and Time Series
in the Color and Irradiance
applications.
The only difference is the ‘Save
Function Output’ box, which is not
used by the Excel Output option.
This part is replaced by a separate
dialog, which will be described
under ‘Settings’.
4.6.2
Enable Excel Output
Enable the option by selecting ‘Application’, ‘Excel Output’, ‘Enable’.
A checkmark will appear before the menu entry ‘Enable’ to show the status of the option.
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4.6.3
Settings
AvaSoft will write the data to three differently formatted sheets, depending on user input in History
Channel Function Entry and the Settings dialog.
You can enter the Settings dialog by selecting ‘Application’, ‘Excel Output’, ‘Settings’.
First, select the mode you want.
Export mode
You can select Export Mode by selecting the top radio button. In this mode, a predefined number of scans
will be logged to new worksheets that Excel will open.
Depending on your choice of history channel, one of two formats of sheet (or both) will be opened by
Excel.
If you select regular history channels, without selecting ‘View Spectrum’, the sheet will be formatted
horizontally, with the program adding a new row for each measurement written.
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The sheet will be called ‘AvaSoft Data’, the columns contain the following data:
Column A contains a data/time value, formatted as ‘dd:mm:yyyy hh:mm:ss’.
This is a floating point value, in which the integer part is the day number, starting at January 1, 1900 with
day 1. The fractional part represents a decimal time value, where 0.5 is 12:00 h. noon and 0.75 is 18:00 h.
This way, differences in date/time can be readily calculated by subtracting values, which would be much
more difficult if this was a text representation.
Column B contains a time value, representing the elapsed milliseconds since midnight. This value does not
have a one millisecond resolution. Remember that Windows is not a real-time operating system. It can,
however, be used as a reasonably accurate indicator of the time that passes between scans.
Columns C through J contain the 8 different History Channel values. For unselected History Channels, a
value of 0 will be entered in the sheet.
If you select ‘View Spectrum’ in your choice of History Channels, the sheet will be formatted vertically. As
Excel only offers 256 columns per sheet, we need to write a spectrum (which can hold more than 2000
pixels) in a column instead of a row, and add more columns as time passes.
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Since there is a maximum of 256 columns per sheet, new sheets will be added after column 256 (‘IV’) is
filled.
The first sheet will be called ‘F1’ for history channel 1, ‘F2’ for history channel 2, etc. If extra sheets are
added, a suffix will be added to this name, e.g. F1_01, F1_02 etc.
If the function type “View Spectrum” has been selected for more than one History Channel Function (e.g.
Master channel for F1, Slave1 channel for F2), then the different history channel sheets (named F1 and F2)
are located in separate workbooks, and must be saved under separate filenames. This is also the case for
the sheet with 8 History Channel values, described before.
Rows 1 and 2 contain the date/time stamp and the elapsed millisecond value, as described in the previous
section.
Column A of the first sheet holds the wavelength scale. The wavelength range matches the wavelength
range as specified in the History Channel Functions.
The lower left half of the Settings dialog can be used to enter the number of scans you want to export to
Excel, and the time interval (in seconds) between two scans you want to log.
Default values are 1000 scans and no interval, meaning as fast as possible.
Continuous Mode
You can select Continuous Mode by selecting the bottom radio button. In this mode, data will be written
to a single sheet, each scan overwriting the previous one.
In the lower right part of the Settings dialog, you can select the workbook the sheet will be added to,
thereby enabling you to use your own calculations and graphs in Excel on live data from AvaSoft.
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Press the ‘Select File’ button to select the workbook. Please save an empty workbook using Excel if you
don’t have a previous workbook to open.
AvaSoft will check if a sheet named ‘AvaSoft Data’ is present, and will add this sheet if it is not present.
This way, links to the sheet can be preserved between sessions.
The sheet contains the following data, at fixed positions:
A3
: Date / Time stamp
This is a floating point value, in which the integer part is the day number, starting at January 1, 1900 with
day 1. The fractional part represents a decimal time value, where 0.5 is 12:00 h. noon and 0.75 is 18:00 h.
This way, differences in date/time can be readily calculated by subtracting values, which would be much
more difficult if this was a text representation.
B3
: Time in milliseconds after midnight
This value does not have a one millisecond resolution. Remember that Windows is not a real-time
operating system. It can, however, be used as a reasonably accurate indicator of the time that passes
between scans.
C5-C*** : Wavelength scale (in nm) for first History Channel spectrum
D3
: Value for first History Channel (0 if spectrum is selected)
D5-D*** : Spectrum for first History Channel.
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E5-E*** : Wavelength scale (in nm) for second History Channel spectrum
(empty if spectrum is not selected)
F3
: Value for second History Channel
F5-F*** : Spectrum for second History Channel
(empty if spectrum is not selected)
etc.
*** : depends on the wavelength range selected.
4.6.4
Start Output
You start the output the usual way, with ‘Application’, ‘History’,
‘Start measuring’.
You can also use the corresponding button on the Button Bar.
Please do not perform large alterations of the worksheet, while data
is being transmitted. An error ‘Call was rejected by callee’ will be
issued if Excel is too busy.
Moving around the worksheet should not pose any problems.
Save any alterations to your worksheet before starting the transfer to Excel. You do not have to close the
worksheet or close Excel.
4.6.5
Stop Output
If you want to stop the transfer to Excel give focus to AvaSoft and press ‘Exit’. It may take a few seconds
before the buttons appear.
Excel will not be closed by AvaSoft. Save your work and close Excel the same way you would when working
with Excel manually.
We have included a sample worksheet, called ‘Continuous.xls’, which demonstrates linking to the ‘AvaSoft
Data’ sheet. In this case, two graphs are drawn from the columns for Channel 1 and 2. The graph and data
are continuously updated while data is being transferred to Excel.
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4.6.6
Limitations and Optimization Notes
As all scans are stored in memory, it is possible to overflow internal memory with scans in Export mode.
Therefore, a limit to the number of scans to store in Excel has been built in. Before a new sheet is added,
the amount of memory Excel uses is determined. If this number is larger than half the physical memory
installed in the machine, output to Excel will stop.
On a 128 MB machine, this corresponds with 7-8 complete sheets (of 256 columns and 2000 rows), roughly
2000 full scans. Limiting the wavelength range will extend your range of scans accordingly.
Of course, adding more Ram to your machine will also help raise this limit. On a 3.5 GB machine with
Excel 2003, it is possible to save more than 100 complete sheets (of 256 columns and 2000 rows).
We have, however, seen limitations in the amount of memory that Excel can use. It looks like there is an
internal limit that is hit before internal memory runs out. After this Excel issues an ‘Out of Memory’
message and is no longer functional. E.g. saving your data to disk is not possible anymore.
For this reason, an absolute limit to the number of cells used has also been built in.
For greatest speed, it is important to give the focus to Excel. If you set the focus to AvaSoft, Windows will
dramatically lower Excel’s priority. You can verify this by looking at the ‘Filling Cells’ progress bar in the
lower left corner of your worksheet.
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4.7 Applications: Chemometry
AvaSoft-Chem was developed to enable on-line concentration measurements with a spectrometer system.
According to Lambert-Beer’s law, there is a linear relationship between absorbance and concentration.
A = ε*c*l
Where A is the absorbance (or extinction), ε is the extinction coefficient of the compound to be
measured, c is the concentration and l is the optical path length.
In practice, this relationship is only linear at reasonably low absorbance levels (say less than 2). The
wavelength at which the absorbance is measured must of course be kept constant.
To take concentration measurements, you will need a spectrometer with either a cuvette-holder or a dipprobe and a suitable light source.
If you use cuvettes, remember that glass cuvettes will absorb UV light. If your wavelength is in the UV
range, use quartz or polystyrene ones instead.
AvaSoft-Chem can display and save the calculated concentration in two ways:
-
The concentration can be displayed and saved on-line in a separate display window, for up to eight
spectrometer channels (if available).
You can select up to eight history channels that can display and save concentration values against
time. This application can be combined with the Excel and Process-Control applications.
4.7.1 Quick Start: How to make concentration measurements with AvaSoft-Chem
1. Start the AvaSoft software and click the Start button in the main window.
2. Set up the absorbance experiment with a cuvette holder or a dip-probe measuring the sample with
the lowest concentration, usually your reference. Switch on the light source.
3. Adjust the integration time to get a good reference signal with a maximum around 14500 counts.
The easiest way to do this is by using the “AutoConfigure Integration time” option.
4. Adjust the number of averages. The higher the better, however the time for a single absorbance
reading must remain practical. If you want to change it, first press the Stop button, and press the
Start button again after changing the Average value in the Edit-bar.
5. Switch off the light source and save a dark spectrum, switch it back on and save a reference.
6. Change to Absorbance mode by clicking the ‘A’ button in the button bar. Measure the absorbance
of a sample with a high concentration to find the wavelength and bandwidth of an absorbance
peak to use (most of the time, the wavelength with the highest absorbance is used.
7. Calibrate your absorbance readings in the ‘Chemometry Settings’ form (section 4.7.2). You can
also just use a previous calibration line, as it can be saved to disk under a user defined filename
and reloaded at the start of the application.
8. Enable the Concentration measurements by selecting ‘Application’, ‘Chemometry’, ‘Enable’ from
the main menu. After the application is enabled, it is also possible to select ‘Chem’ as a History
Channel function.
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4.7.2
Calibration Settings
The dialog at the right is shown
after selecting ‘Application’,
‘Chemometry’, ‘Settings’ for the
first time. An example calibration
file (example0.cal) has been
created in the folder “chem”,
which holds the data that is
presented in the dialog. Note that
the example is only illustrative. You
need to measure a number of
samples with known concentration
to create your own calibration
file(s), as described in section
4.7.2.1. After a calibration has
been saved, it will be loaded
automatically the next time the
application is started. Once a calibration has been saved, it can be loaded later on and modified if
needed. Section 4.7.2.2 describes how to modify a previous saved calibration file.
4.7.2.1 Start New Calibration
A new calibration is started by
clicking the “Start New Calibration
(Clear Data)” button. All data fields
for the selected spectrometer
channel will be cleared. Enter the
wavelength for the measurements in
the ‘Peak at’ field and the width of
the peak that will be used in the
‘Width’ field. The program will
integrate the absorbance values from
“Peak minus Width” to “Peak plus
Width” and uses this integral as the
absorbance value in the
concentration calculations.
The unit of concentration can be entered in the ‘Conc. Unit’ field. This is just a text, no adjustments will
be made if you change this value.
Enter the known concentration values for the available standards in the central column of the calibration
points table. You can include the reference sample with zero concentration in these measurements.
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After this, the dialog contains for
example the data shown in the
figure at the right.
If the zero concentration
(reference) sample is included, like
in the example at the right, set up
the experiment to measure this
reference. Use the keyboard or
mouse to point out the row in the
table for which sample the
absorbance value will be measured.
When moving through the rows in
the table, the text in the button
“Read Absorbance for point x”, will
be updated for the sample that will
be measured. In the example, we
start with measuring the absorbance of point 1, which is the reference sample. Click the “Read
Absorbance for point 1” button to import the measured absorbance into the left column in the table. If
the reference is measured, the value should be very close to 0.000. The measured absorbance and
corresponding concentration will be visualized as a new point in the graph. Now move the cursor in the
table to the second row, setup the experiment for measuring the sample of known concentration for point
2 (30 mmol/l in the example above), and click the “Read Absorbance for point 1” button to import the
measured absorbance into the left column in the table for point 2. Repeat these steps for the other
samples of known concentration. For a linear calibration line, at least two samples are needed, but the
more points added, the more reliable the calibration line will be.
After the samples have been
measured, click the “Calculate New
Calibration Line” button. As a
result, a red line will be fit through
the measured data, and you will be
asked to save the calibration or
not.
The figure at the right shows that
the calibration line fits very well
through the measured points, so we
click yes to confirm that we want
to save the calibration.
If during the measurements an
incorrect calibration point was
measured, for example because of
mixing up the samples or measuring
the concentration at the wrong
row, this will become clear from the graph. You can then select either directly the “No” button, or select
the “Yes” button and modify the calibration line later on.
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After clicking “Yes”, a dialog is
shown in which the name of the
calibration file can be entered.
Type in the name you will use for
this calibration line (MyFirst in the
figure at the right), then click the
“Save” button. As a result, the file
MyFirst.cal will be created, and the
calibration line will become the
actual calibration line that will be
used to calculate the concentration
levels for the specified
spectrometer channel (Master in
this example).
After a calibration line is saved, it
will become the actual calibration
line, which is blue colored. This
actual line will be used for
concentration calculations.
Furthermore, the Calibration Line
coefficients are shown in the lower
right corner of the dialog and the
predicted concentration values that
have been calculated by using the
calibration coefficients, have been
added for the standards into the
right column of the table.
By comparing the predicted values
with the actual concentration
values, you can get an impression
about the quality of your calibration
line.
The actual calibration line will be automatically loaded the next time AvaSoft is started. By clicking the
Load button, other calibrations that were saved before can be loaded after which the loaded calibration
line becomes the actual line.
4.7.2.2 Modifying a calibration
The actual calibration line can be modified by changing the fit order of the calibration line or by adding or
deleting calibration points.
Fit order
The default fit order is linear. Using a second order (parabolic curve) makes it possible to compensate for
non-linearity in e.g. your dip-probe. To illustrate this, the calibration from the previous section was
loaded (MyFirst.cal), and the fit order was changed from first order to second order. After clicking the
“Calculate New Calibration Line” button, the new standard deviation showed a much better fit then the
previous (linear) fit. After saving this calibration line to “MySecond.cal” the predicted concentrations
showed also a much better fit for the quadratic model. However, certainly with this few calibration
points, the second order option should be used with care, as it will happily draw a well fitting calibration
curve also through outliers.
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Adding/deleting calibration points
Adding and deleting calibration points from/to the actual calibration line is very simple and very well
visualized in the graphical display. To add new calibration points to a calibration, just load the calibration
file, move the cursor to the next row in the table (row 5 in our example), fill in the sample concentration
in the center column and read the absorbance into the first column by clicking the “Read Absorbance for
point 5” button. A new red point will mark the calibration point in the graph. New points can be added up
to 30 standard samples. The “Calculate New Calibration Line” will display a new red line next to the
actual blue calibration line before raising the dialog
with the question if the new calibration data should be
saved or not. This may be helpful to see if the new
points are correctly measured, or that one or more new
points induce a strong increase of the standard
deviation. For example, in the figure at the right the
error was caused by typing in the value of 60 in the
center column instead of the correct value of 40. To
delete one or more calibration points from the actual calibration, just delete the value for that point in
the left or second column.
4.7.3
Enabling the application
Enable the application by selecting ‘Application’, ‘Chemometry’, ‘Enable’ from the main menu. A
checkmark will appear before the menu entry to show that the option is enabled.
A separate Concentration display will appear, for each spectrometer channel enabled.
By clicking the “Save Concentration” button in the upper left corner, a
new line (record) will be added to the chem output file (text file, ascii
format) that is displayed in the box below of the save button (newout.txt in
the figure above). This box also displays the current number of records that
have been saved to this file before.
A new Filename for saving the output can be selected by clicking the “New
Filename” button. If a filename is entered that does not yet exist, then
you will start with an empty file (header only) with 0 records. If a filename
is selected that already exists, the nr of records in this file will be
displayed and new measurements will be added to the existing ones.
The following information will be saved with each click on the Save
Concentration Button:
Date
Time
Comments
Concentration Unit
CalibrationFilename
SpectrometerName
- Current Date
- Current Time
- Comment line, entered by user (right from Save button)
- Unit entered in the CHEM Settings, during the CHEM calibration
- Name of the calibration filename that is used in the calculation
- Name of the Spectrometer used when saving the concentration
The columns in the textfile are separated by blanks (not TABS), so if you want to open the textfile in
Excel, you can select “blanks” when Excel asks how the columns are separated. The file can always be
opened with any text editor, for example “Notepad”.
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After enabling the chemometry
application, you can select
‘Chem’ as a function type in
the Function Entry dialog of the
History application.
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4.8 Applications: Laser Induced Breakdown Spectroscopy (AvaSpec-2048/2048L/3648*)
The start of the integration time can be delayed in relation to an event like a laser pulse or flash light.
This feature can be used for Laser Induced Breakdown Spectroscopy.
Programmable delay: -21 nanosec to +89 seconds in 21 nanosec steps, jitter = 0
This portion of the plasma emission is not included in the integration time
In LIBS measurements, the laser light should not be included in the integration time cycle. Instead, the
integration time starts a user programmable delay after the laser pulse. There are two ways in which the
LIBS measurements can be setup:
1) The AvaSpec spectrometer controls the timing for the laser. In this mode, the spectrometer sends a
TTL Output signal to fire the laser and the integration time delay is synchronized with this output
signal.
2) The timing is controlled by the laser or external pulse generator and synchronized with the AvaSpec
spectrometer by running the spectrometer in external trigger mode. In this mode, the spectrometer
receives a TTL-input signal from the laser, or simultaneously with the laser. The integration time
delay is synchronized with this input signal.
Advantage of using the TTL-output signal from the spectrometer to fire the laser are:
•
No jitter between TTL-Output and start of integration time. The output signal and start of the
Integration time cycle are both synchronized with the 48 MHz FPGA clock in the spectrometer.
However, if there is a large jitter in the laser between receiving the TTL signal from the
spectrometer and firing the laser pulse, there is no advantage in the zero jitter at the
spectrometer. If the timing is controlled by the laser, the jitter between the asynchronized external
trigger input and the start of the integration time will be 21 ns.
•
The integration time delay can be set very short or even negative (in which case the integration
time cycle starts before the laser is fired). If the timing is controlled by the laser or pulse
generator, there will be a minimum integration delay which depends on the spectrometer type: the
minimum delay for the AvaSpec-3648-USB2*, AvaSpec-2048-USB2 and AvaSpec-2048L-USB2 is
respectively 0.28, 1.28 and 3.28 µs.
The hardware setup and other settings will be described in section 4.8.1. After enabling the LIBS
application (section 4.8.2), the specified number of measurements can be started.
* AvaSpec-3648-USB2 in clear-buffer mode only, for advantages/disadvantages, see section 3.2.1
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4.8.1
Libs Settings
The LIBS settings dialog is displayed after clicking the menu option “Application – LIBS – Settings”. The
following settings can be entered:
The Hardware Setup refers to the two options to setup a LIBS measurement, as described at the previous
page.
The General Settings include:
•
Number of Measurements. One measurement includes NrOfAverage scans. The average parameter is
set in the main windows edit bar. For example, if 10 measurements are required and the average
parameter is set to 16, a total of 160 scans will be done.
•
Fixed/Variable integration time delay. If the “Use Variable Integrationtime Delay” box is checked,
the integration time during the first and last measurement need to be entered. The integration
time delay for all measurements in between will be linearly interpolated. Leave the “Use Variable
Integrationtime Delay” box unchecked if the measurements should be performed at fixed
integration time delay, and enter the required fixed Integration time delay.
•
AutoSave Spectra. If this box is checked, the spectra will be saved after each measurement and can
be displayed afterwards with the menu option File-Display Saved Graph.
•
Disable Graphical Output for high speed measurements. The graphical output is the most time
consuming event at short integration times, so if high speed measurements are required, check this
box to process the data without updating the graphics during the measurements.
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The LIBS settings in the lower box of the window, as shown in the figure above and described below, are
only relevant if the TTL-Out at pin 23 is used to trigger the laser.
The Pulse Width parameter is the pulse width in microseconds for the TTL-Out at pin 23.
When using the TTL-Out at pin 23, there are three possibilities how to start and control a sequence of
measurements:
Software controlled
A measurement sequence can be fully controlled by software if the spectrometer is not setup in hardware
trigger mode (“Setup – Options – External Trigger Setting” is not Enabled), and the checkbox in the LIBS
Settings above: “In Hardware Trigger Mode, perform one SingleScan…” is left blank. The frequency of the
TTL-Out at pin 23 is determined by the “Time Between Scans [ms]” parameter.
A measurement sequence is started by clicking the Start button in the LIBS progress dialog as described in
section 4.8.2
Start First Scan on Hardware Trigger, every next scan by software
A measurement sequence can be setup such that the first scan is started after the spectrometer receives
an external hardware trigger at pin 6. Then every next scan in the measurement sequence is started by
the software, using the “Time between Scans [ms]” parameter to determine the frequency of the TTL-Out
at pin 23. To use this mode, enable the hardware trigger mode (“Setup – Options – External Trigger
Setting” is Enabled), and the checkbox in the LIBS Settings above: “In Hardware Trigger Mode, perform
one SingleScan…” is left blank.
A measurement sequence is started by clicking the Start button in the LIBS progress dialog as described in
section 4.8.2, followed by an external trigger at pin 6 to start the sequence.
Start Every Scan on Hardware Trigger, optionally use the Laser Delay parameter
By selecting the checkbox in the LIBS Settings above: “In Hardware Trigger Mode, perform one
SingleScan…”, the spectrometer will be setup in external trigger mode and requires one external trigger
input at pin 6 for each scan, so totally NrOfMeasurement*NrOfAverage trigger signals to complete the
sequence. The “Time Between scans [ms]” parameter becomes irrelevant when using this setting, because
the frequency will be determined by the frequency of the trigger pulses received at pin 6.
An additional parameter called “LaserDelay [µs]” can be specified when using this mode. The LaserDelay
parameter is the time in microseconds between receiving the external trigger at pin 6 and sending out the
Laser pulse at pin 23 to fire the laser.
A measurement sequence is started by clicking the Start button in the LIBS progress dialog as described in
section 4.8.2, followed by external trigger pulses at pin 6 for each scan in the measurement sequence.
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4.8.2
Enabling and running the application
The LIBS application is started by clicking the menu option
“Application – LIBS – Settings”. The LIBS Progress window at
the right will be displayed.
The buttons in the dialog have the same functionality as in
the main window. Access to the main window is not possible
during the LIBS measurements.
After clicking the Start button in this dialog, the LIBS
measurements are started.
If the spectrometer controls the timing by the TTL-Out at pin
23, the spectrometer starts sending these signals to the laser
and starts its integration time cycle the user specified
Integration Delay period after each TTL-Out.
If the timing is controlled by the laser or external pulse generator, the spectrometer will wait for the
external trigger pulse and it will start the integration time cycle the user specified Integration Delay
period after receiving the external trigger input. Then it will wait again for the next external trigger pulse
to arrive.
After each scan, the “Performed Nr of Average” number is updated, and after Nr of Average scans, the
“Performed Nr of Measurements” number as well as the graphical output is updated.
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4.9 Applications: Store To Ram
4.9.1
Introduction
This application requires an AvaSpec-USB2 spectrometer, with firmware version 0.20 or later. A firmware
upgrade utility can be downloaded from our website.
As the application is rather demanding on your computer, it is advisable to use a recent model PC with
good graphics performance, preferably with a dedicated graphics card.
AvaSoft Store To Ram allows you to measure a fixed amount of scans as fast as possible, without the
overhead of USB communications. The scans are stored in the internal memory of the AS5216, and the
results are only sent to the computer after the last measurement has been made.
You can, for example, store as much as 19784 full pixel scans with the AvaSpec 102, which has 102 pixels
and a fastest integration cycle of 0.1 msec. By limiting the wavelength range in the measurement
(‘Setup’, ‘Wavelength Calibration Coefficients’, change the ‘Start at’ and ‘Stop at’ fields) you can extend
the number of scans to a maximum of 65504 scans.
When you use a spectrometer with more pixels, the number of full pixel scans is proportionally less:
For example, with the AvaSpec-2048-USB2, the number of full pixel scans is 1013, and the fastest
integration cycle is 1.1 msec.
If you enter more scans, the application will return the maximum amount that could be made with the
selected wavelength range, and change the number in the edit field.
All spectrometers allow you to extend the amount of Store To Ram scans by limiting the wavelength
range.
Note that the time needed to transport the data to the computer, after the measurement has been made,
can be as long as 50 seconds, if you select a very large number of scans.
After the scans have been sent to the computer, the AvaSoft Store To Ram application allows you to make
a range selection in the scans, and save the selected scans to .ROH files on disk.
These files can then be processed further in AvaSoft, or easily read into Excel and processed there.
The data are visualized with a single 3D and two 2D graphs.
The view of the 3D graph can be adjusted by inverting the Depth axis and the X axis. These axes can also
be transposed, which enables a side view of the graph.
The Y axis is auto scaled by default, this can be undone by unchecking the option in the ‘Adjust View’
box.
The 2D graphs both have a scrollbar, which allows you to change the third dimension. It is also possible to
display the position of each 2D graph in the 3D graph by displaying a separate highlighted line that
sections the 3D graph. This feature is turned on and off with the ‘3D’ checkbox at the top-right position of
each 2D graph.
The amount of data in the 3D graph and the second 2D graph (Counts vs. Time) has been limited to
prevent computer overload. If more data is present, only one out a calculated number of scans or pixels is
shown. Zooming the graphs will reveal more detail. The fraction of the data that is shown is indicated in
the title of the relevant axis.
E.g. ‘Time [ms] (1/10)’ means that only one out of every 10 scans is shown.
Note that the first 2D graph (Counts vs. Wavelength) always shows all of the data present. It is therefore
possible to show this graph as a highlighted line in the 3D graph that shows more detail than the 3D graph
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itself shows. Zooming in will show more detail in the 3D graph, which will eventually correct the
discrepancy.
The 3D graph does not allow direct manipulation with the mouse. You can zoom both 2D graphs and the
3D graph will zoom to the selected range. The selected range will then also be shown in the manual
selection boxes described below.
Unzooming the 2D graphs will also unzoom the 3D graph.
Note that zooming and unzooming the 2D graphs is performed the same way as in the main screen of
AvaSoft:
You zoom the graph by clicking the top-left corner of your area to select, hold down the left mouse
button, then draw a rectangle and release the mouse button at the lower-right corner of the area to
select.
You unzoom the graph by clicking anywhere on the graph, hold down the left mouse button, then drag a
rectangle towards the top and left and release the mouse button at any position.
You can pan the 2D graphs by holding down the right mouse button.
It is also possible to manually select the ranges by entering values in the ‘Select Time Range’, ‘Select
Wavelength Range’ and ‘Select Counts Range’ boxes, and pressing the ‘Zoom’ button. Note that changing
the ‘Select Counts Range’ will only have an effect if the ‘Autoscale Y-axis’ option is unchecked. The
‘Unzoom’ button will undo all your changes.
After your selection is made, you can save the scans to disk by pressing the ‘Save’ button. Each scan will
result in two files written to disk. The .ROH file contains the spectrometer setup and the data from the
scan itself. The .RCM file contains the timestamp from the scan, as a microsecond offset value from the
first scan.
If you save the .ROH files to Excel, using AvaSoft ‘File’-‘Convert Graph’-‘to Excel’, the timestamp values
from the .RCM files will be written into Excel in row 6 of each data column, allowing you to use these
timestamp values in calculations.
The files are numbered consecutively, a five digit number is affixed to the filename you enter in the
dialog. The starting number of the sequence is the lower limit of the range of selected scans. Only the
presence of a previous version of this file will trigger an overwrite warning in the dialog. All consecutive
scans will silently overwrite previous versions with the same filename.
Note that the scans that are saved in the .ROH files are all full scans, only the values entered in ‘Select
Time Range’ have an effect here. If you want to limit the wavelength range in the .ROH files, you will
have to do this in the AvaSoft setup screen, as described above.
Although it is possible to use the Store To Ram application to measure huge amounts of scans with a
limited wavelength range, we strongly advise you to save only a limited amount of scans.
If you select 50000 scans to save, the huge number of small files to save will bring your computer to a
near standstill.
For this reason, a warning has been built in when you want to save more than 2500 scans.
You can save the graphs to disk by pressing the ‘Save Graphs’ button. You can first enter a comment line,
which will be included on the page. Next, you can enter the filename that will be used to save the graphs.
The three graphs will be saved in JPEG format, embedded in a single, one page .RTF file. You can open
this file with Microsoft Word, edit it, extract the graphs, change the size of the graphs, etc.
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4.9.2
Quick Start
1. Select wavelength range and integration time in AvaSoft. (Averaging is not possible with Store To
Ram measurements, this setting has no effect.) Adjust your light source and take some readings to
check whether the signal level is satisfactory. Stop the regular AvaSoft readings. (The Start/Stop
button should read ‘Start’)
2. Start the Store To Ram application by selecting it in the menu with ‘Application’, ‘Store To Ram’.
3. Select the channel (if you have more than one) and enter the number of scans to read. This value
is set to 100 by default. The integration time setting in the Store To Ram form is automatically
copied from the main AvaSoft form. You can change this value here, but it will only be used in the
Store To Ram application.
4. Press the ‘Start’ button. After the measurement has been made, the readings are transmitted to
the PC and the graphs will be drawn. Depending on the duration of an integration cycle and the
number of readings, this can take anywhere between a second and many minutes. The ‘Stop’
button can be pressed whenever you want to stop a pending measurement with a long integration
time.
5. Make a selection from the readings by zooming the 2D graphs with your mouse. Only the time
range selection will be reflected in the saved output. Scroll the 2D graphs with their scrollbars,
see where the line is located in the 3D graph by selecting the 3D checkbox in either 2D graph.
6. Save your selection to disk by pressing the ‘Save Scans’ button.
7. When needed, save the graphs to disk by pressing the ‘Save Graphs’ button.
8. Load a single scan into AvaSoft with ‘File’, ‘Display Saved Graph’.
9. Look at a 3D display of the saved graphs with ‘File’, ‘Display 3D Graph’.
10. Load multiple scans into Excel with ‘File’, ‘Convert Graph’, ‘To Excel’.
4.9.3
Main Window
The upper left of the window is used to control the measurement
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The upper right of the window is used to adjust the view of the 3D
graph, and to manually make a selection from the scans.
The Adjust View checkboxes allow viewing the 3D graph from all
sides. The Autoscale Y axis button is checked by default.
Unselecting it will only yield a satisfactory image if the Y range is
positioned at an edge of the graph, otherwise there will be other
readings filling the entire screen behind the selected lines.
Manually change the scan selections by changing the values in the
‘Select Range’ fields and pressing the ‘Zoom’ button. ‘Unzoom’
will undo any change made.
Note that manually changing the ‘Select Count Range’ will only
have an effect if the ‘Autoscale Y Axis’ box is unchecked.
The 2D graphs each have a scrollbar that changes the respective third dimension.
The position of the scrollbar is reflected in the boxes underneath each 2D graph. Change the scrollbar in
the standard Windows ways: Clicking the arrows will cause a change of a single unit, clicking between the
arrows and the thumb will change 10 units, dragging the thumb will select a new position in the readings
relative to the position of the thumb. You can also use the keyboard to change the scrollbar, the Up and
Down keys will give a single unit change, the PageUp and PageDown keys will give a change of 10 units,
the Home and End keys will move to the first and last reading. Checking the 3D boxes in the upper right
corner of each graph will show the graph as a highlighted line in the 3D graph.
The Time axis of the right 2D graph has a maximum number of points. If this is exceeded, only one out of
a calculated number of points will be shown. This ratio is added to the title of the axis, e.g. ‘Time [ms]
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(1/10)’ means that only one out of 10 points is shown. In this case, zooming the right 2D graph will reveal
more detail.
Zooming the 2D graphs with the mouse can also be used to select a wavelength and time range. The
selection will also be shown in the 3D graph. Zooming and Unzooming is done in the regular AvaSoft way.
You can also pan the graph by dragging the mouse while holding the right mouse key down. This has no
effect on the 3D graph.
The 3D graph cannot be manipulated directly. It is redrawn after the 2D graphs are zoomed, or after the
ranges are manually changed, and the ‘Zoom’ button is pressed. The view of the graph can be changed in
a basic number of ways, to allow a view of all sides. A highlighted line can be shown in the 3D graph for
both 2D lines.
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5
Help
After clicking the Help-Contents menu option, the AvaSoft FULL manual will be displayed in HTML format.
At the left side the Help Contents displays all sections to which the user can browse to a specific topic.
Instead of browsing through the contents to a specific topic, the search TAB can be selected, as illustrated
in the figure below. After typing in a keyword (e.g. concentration), and clicking the List Topics button, a
list of all topics containing this keyword is shown. By selecting a topic at the left (double click), the
information is displayed at the right, in which the keyword is marked in the text.
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As described in section 4.1.1, the History Channel Functions have been extended with the possibility to
define a function with the support of a VB Script. We have included a help file for VBScript for your
reference. You can reach it from the main menu by selecting ‘Help’, ‘VBScript’. It lists among other things
all available operators and functions:
Finally, the third Help submenu is the About Box which shows some information about the AvaSoft version
that is being used, the serial numbers of the spectrometers that are connected, detector types, firmware
and FPGA versions, the Windows version of the computer and the available memory:
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Appendix A
Troubleshooting
How to rectify an incorrect (USB) installation
Any USB device requires that the USB drivers need to be
installed before the device is connected to the computer. If
you accidentally connected the AvaSpec spectrometer to
the USB port of your PC before installing AvaSoft, the USB
drivers cannot be found, and the spectrometer cannot be
found by the (later installed) software. To rectify an
incorrect installation follow these steps:
1. Navigate to the Device Manager. For Windows2000/XP
systems, right click on My Computer, select Properties
(or open the system icon from the Control Panel). Then
select Hardware tab and click on Device Manager
button.
2. Scroll down until you see Other devices
3. Under Other devices you will see USB device with a
large question mark, right click the USB device and
select the uninstall option.
4. A warning box will appear to ask if it is OK to remove
the device, click OK.
5. Unplug the AvaSpec spectrometer from your PC and
reinstall the AvaSoft software.
6. Now you can plug the AvaSpec spectrometer to the USB
port again. Windows will display the “Found New
Hardware” (USB device) dialog. Proceed with the
installation as described in section 0.1 under
“Connecting the Hardware”
7. The AvaSoft software can now be started and will
detect the spectrometer at the USB port. If not, please have a look at the Device Manager, which
should contain the Avantes Spectrometers Class, as illustrated in the figure below. The figures shows
that 4 USB ports are connected to an AvaSpec spectrometer: one AvaSpec-USB1, and three AvaSpecUSB2 spectrometers
Don’t hesitate to contact us if the problem remains
unsolved.
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Appendix B
Error Messages
AvaSoft can display error messages containing a number. The following table lists these numbers and a
description of the error:
Error code
-1
-2
-3
-4
-5
-6
-7
-8
-9
-10
-11
-12
-13
-14
-15
-16
-17
-18
-19
-20
-21
-100
-101
-102
-110
-111
-112
-113
-114
-115
Description
Function called with invalid parameter
Function called to use 16bit ADC mode, with 14bit ADC hardware
Opening communication failed or time-out during communication occurred
AvsHandle is unknown in the DLL
Function is called while result of previous function is not received yet
No answer received from device
Reserved
No measurement data is received at the point AVS_GetScopeData is called
Allocated buffer size too small
Measurement preparation failed because pixel range is invalid
Measurement preparation failed because integration time is invalid for selected sensor
Measurement preparation failed because of invalid combination of parameters
(e.g. integration time > 600 seconds or averages > 5000)
Reserved
Measurement preparation failed because no measurement buffers are available
Unknown error reason received from spectrometer
Error in communication occurred
No more spectra available in RAM, all read or measurement not started yet
DLL version information can not be retrieved
Memory allocation error in the DLL
Function called before AVS_Init is called
Function failed because AS5216 is in wrong state (e.g. AVS_StartMeasurement while
measurement is pending)
NrOfPixel in Device data incorrect
Gain Setting Out of Range
Offset Setting Out of Range
Use of Saturation Detection Level 2 is not compatible with the Averaging function
Use of Averaging is not compatible with the StoreToRam function
Use of the Synchronize setting is not compatible with the StoreToRam function
Use of Level Triggering is not compatible with the StoreToRam function
Use of Saturation Detection Level 2 Parameter is not compatible with the StoreToRam
function
The StoreToRam function is only supported with firmware version 0.20.0.0 or later
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