AVASOFT for AvaSpec-USB1 version 7.5 USER`S MANUAL

AVASOFT for AvaSpec-USB1 version 7.5 USER`S MANUAL
AVASOFT for AvaSpec-USB1
version 7.5
USER’S MANUAL
November 2010
Nov-10
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0
AVASOFT INSTALLATION
4
0.1
Installation program
4
0.2
Launching the software
6
1
QUICK START: MEASURING AND SAVING A SPECTRUM
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2
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: Convert Graph – Include ASCII Header
3.1.12
File Menu: Convert Graph - to ASCII
3.1.13
File Menu: Convert Graph - to ASCII Equidistance
3.1.14
File Menu: Convert Graph - to J-CAMP
3.1.15
File Menu: Convert Graph - to Excel
3.1.16
File Menu: Save Graph to .RTF
3.1.17
File Menu: Exit
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3.1 Setup Menu
3.2.1
Setup Menu: Hardware
3.2.2
Setup Menu: Wavelength Calibration Coefficients
3.2.3
Setup Menu: Smoothing and Spline
3.2.4
Setup Menu: Correct for Dynamic Dark (AvaSpec-2048 only)
3.2.5
Setup Menu: Subtract Saved Dark
3.2.6
Setup Menu: Strobe Enable (DO1)
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3.2.7
Setup Menu: 1 kHz Enable (DO2)
3.2.8
Setup Menu: Options
3.2.8.1
Setup Menu: Options – Check on Saturation
3.2.8.2
Setup Menu: Options – Full Width Half Max
3.2.8.3
Setup Menu: Options - Integrals
3.2.8.4
Setup Menu: Options – Autosave Spectra Periodically
3.2.8.5
Setup Menu: Options - Correct for Drift
3.2.8.6
Setup Menu: Options - Automatic Save Dark by TTL shutter
3.2.8.7
Setup Menu: Options - External Trigger Setting
3.2.8.8
Setup Menu: Options - Auto configure Integration time
3.2.8.9
Setup Menu: Options – Use Custom Reflection Reference
3.2.8.10 Setup Menu: Options – Suppress Save Comments
3.2.8.11 Setup Menu: Options – View Reflectance instead of Transmittance
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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: Channel
3.3.6
View Menu: Change Graph Scale
3.3.7
View Menu: Graphic Reset
3.3.8
View Menu: Autoscale Y-axis
3.3.9
View Menu: Goto Preset Scale
3.3.10
View Menu: Grid Enable
3.3.11
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
4.4.4
Perform Intensity Calibration
4.4.4.1
Start Intensity Calibration
4.4.4.2
Save Intensity Calibration
4.4.5
Irradiance Chart
4.4.5.1
Irradiance Chart Settings
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4.4.5.2
Irradiance Chart Display
4.4.6
Time Series Measurement
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4.5 Applications: Process Control Application
4.5.1
Digital Output signals
4.5.2
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 Oxygen application
4.7.1
Quick Start: How to take oxygen measurements with AvaSoft-Oxy
4.7.2
Enabling the application
4.7.3
Settings
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4.8 Chemometry
4.8.1
Quick Start: How to make concentration measurements with AvaSoft-Chem
4.8.2
Calibration Settings
4.8.2.1
Start New Calibration
4.8.2.2
Modifying a calibration
4.8.3
Enabling the application
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5
HELP
APPENDIX A
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TROUBLESHOOTING
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How to rectify an incorrect (USB) installation
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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:
•
Windows 95/98/Me
•
Windows NT/2000
•
XP/Vista/Windows 7 x86 (32 bit O/S)
•
XP/Vista/Windows 7 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-USB1 group of spectrometers should be selected to install AvaSoft for one
of the following spectrometer types:
•
AvaSpec-102 or AvaSpec-102-y
•
AvaSpec-128 or AvaSpec-128-y
•
AvaSpec-256 or AvaSpec-256-y
•
AvaSpec-1024 or AvaSpec-1024-y
•
AvaSpec-2048 or AvaSpec-2048-y
•
AvaSpec-2048FT or AvaSpec-2048FT-y
In which y represents the number of spectrometer channels.
Instructions below are for the AvaSpec-USB1. Please refer to the AvaSpec USB2 manual if you have an
AvaSpec-USB2 spectrometer.
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:\AVASOFT7USB1. 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.
Windows Vista will install the driver automatically,
without displaying the “Found New Hardware
Wizard” dialogs
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0.2
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 AvaSoft, the dialog at the right will
be shown to indicate that the USB connection has
been detected (a similar dialog will be shown if
the serial RS-232 interface is used):
If more than one AvaSpec spectrometer is connected to your PC, the
dialog at the right will be shown which allows you to select the
spectrometer serial number for which you want to use AvaSoft. With USB1
platform spectrometers you can run multiple spectrometers
simultaneously, just by restarting AvaSoft multiple times. 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 eight applications are available in AvaSoft, which are
described in sections 4.1 to 4.8:
•
History (standard in AvaSoft FULL)
•
Wavelength Calibration (standard in AvaSoft FULL)
•
Color Measurement (add-on module)
•
Irradiance Measurement (add-on module)
•
Process Control (add-on module)
•
Excel Output (add-on module)
•
Oxygen (add-on module)
•
Chemometry (add-on module)
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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. Adjust the Smoothing Parameters in the Setup menu (section 3.2.3) to optimize smoothing for the
Fiber/Slit diameter that is used.
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. This is
shown as a straight line at the maximum counts and by 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 Auto-configure Integration time button can be used (see 2.1). 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 14500 counts. 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 value
can only be changed in static mode. When AvaSoft is acquiring data, the average box becomes gray.
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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.
Channel button
After clicking the Channel button, a dialog is shown in which the spectrometer channels can be selected,
for which data will be acquired and displayed. The same result can be achieved with the option ViewChannel.
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 14500 counts 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
When AvaSoft is acquiring data, the edit fields are gray and non-editable. By clicking the red STOP
button, data acquisition is stopped and the edit fields become white and editable. 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 exceeds the maximum counts
(16383) 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 14500 counts. 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.
2.4 Graphical region
The graphical region
displays the data in an XYdiagram, with at the X-axis
the wavelength in
nanometers, and at the Yaxis 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 legenda 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 occur.
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 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.
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
information about the file to which the data will be saved, amplitude at current wavelength, and the
current settings for the smoothing and spline parameters. The field at the right of the Spline setting is
used to indicate that the spectrometer is receiving too much light at a certain wavelength range (=16383
counts before correcting for dynamic dark, smoothing or averaging), in which case the label “saturated”
will become visible. See also section 3.2.8.1: check on saturation.
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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 then 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 submenus 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. The default folder in which data is saved is called “data <serialnumber>”, in which
<serialnumber> refers to the serial number of the AvaSpec spectrometer that is being used (0208006A1
in the figure above).
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 "dark*.dat", where * represents
the number of the slave channel for which the dark data has been saved (*=0 represents the master
channel).
The dark data files will be saved in the experiment directory that has been picked by the option FileLoad-Experiment 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 "ref*.dat", where *
represents the number of the slave channel for which the reference data has been saved (*=0 represents
the master channel).
The reference data files will be saved in the experiment directory that has been picked by the option
File-Load-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.
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
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.
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3.1.11 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.
3.1.12 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
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-
the number of pixels used for smoothing
-
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.
3.1.13 File Menu: Convert Graph - to ASCII Equidistance
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 – Equidistance”, 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
equidistance feature (section 3.1.12).
Also the information in the header file is the
same as for converting to ASCII without the equidistance 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).
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3.1.14 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.
3.1.15 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.
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3.1.16 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.
3.1.17 File Menu: Exit
Closes AvaSoft.
3.1 Setup Menu
3.2.1
Setup Menu: Hardware
This menu option displays a list of AvaSpec serial numbers that are
connected to the PC’s USB port(s) and COM port(s) and which are not
used by another (instance of the) application. This option can be
used to allocate a spectrometer to an application (for example if one
spectrometer is running with AvaSoft-Full and another spectrometer
needs to run with AvaSoft-Raman software). But it can also be used
to run multiple spectrometers simultaneously, just by restarting
AvaSoft multiple times.
After clicking the OK button, AvaSoft will communicate with the
spectrometer serial number that has been activated in the dialog.
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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 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.
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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.
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 CCDpixels. 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
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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.
Slit or
Fiber
AvaSpec-102
AvaSpec-128
Pixel 77 µm
AvaSpec-256
AvaSpec-1024
Pixel 25 µm
AvaSpec-2048
n.a.
0
0
0-1
10µm
25µm
n.a.
n.a.
Pixel 63.5
µm
n.a.
n.a.
Pixel 14 µm
50µm
0
0
0-1
1-2
100µm
0-1
0-1
1-2
3
200µm
1
1
3-4
6-7
400µm
2
2-3
7-8
13-14
500µm
3
3-4
9-10
17
600µm
3-4
4
11-12
21
The best way to determine the optimal smoothing parameter is to look at the resolution with a linesource like the AvaLight-CAL calibration lamp. Displaying the resolution in nanometers at Full Width Half
Max can be activated by the menu option Setup/Options/Full Width Half Max. First look at the FWHM
value of one or more peaks without smoothing (smoothing = 0). Then increase the smoothing parameter
and look at the effect of the increase on the FWHM value(s). In order to get an optimal smoothing
without losing resolution, the smoothing parameter should be increased, as long as the resolution does
not become worse.
3.2.4
Setup Menu: Correct for Dynamic Dark (AvaSpec-2048 only)
The pixels of the CCD detector (AvaSpec-2048) are thermally sensitive, which causes a small dark
current, even without light exposure. To get an approximation of this dark current, the signal of the first
14 optical black pixels of the CCD-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 14 pixels have the same thermal
behaviour as the active pixels, the correction is dynamic.
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.
If this menu option is preceded by a checkmark, the scope data is corrected with the dynamic dark
algorithm. It is recommended to leave this setting checked, which is the default state.
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3.2.5
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 up 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.
3.2.6
Setup Menu: Strobe Enable (DO1)
This option can be used to enable or disable an external strobe (e.g. the AvaLight-XE) attached to an
AvaSpec spectrometer.
The AvaLight-XE needs to be attached to the AvaSpec by connecting an IC-DB15-2 interface cable to the
high density 15 pole Sub-D connectors at the AvaLight-XE. The measured light intensity of the AVALIGHTXE is independent of the integration time in AvaSoft. To increase light intensity, the number of pulses
per integration interval should be increased. When clicking the “Strobe Enable” menu option, a dialog is
shown in which this number of pulses can be set.
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.
If this menu option is preceded by a checkmark, the strobe control function has been enabled. To
disable the strobe, simply click the menu option when preceded by a checkmark.
3.2.7
Setup Menu: 1 kHz Enable (DO2)
Pin 2 of the high density 15 pole Sub-D connector at the AvaSpec can be used to generate an 1 kHz
signal. This signal can be used to control an AvaLight-LED light source in pulsed mode.
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3.2.8
Setup Menu: Options
All options described in this section are standard included in AvaSoft FULL version. In AvaSoft BASIC,
these features are not available.
3.2.8.1 Setup Menu: Options – Check on Saturation
The 14-bit A/D converter in the AvaSpec-USB1 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. Since saturated pixels can disturb the measurement results, a lot of attention
has been given in AvaSoft (and the driver packages AS-161.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 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, and there are also different options for
notification, 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 <16383 counts. The other
detector types in the AvaSpec-102, 256 and
1024 do not show this effect, and don’t need to
be corrected for this. Normally, you don’t need
to use this third level for the AvaSpec-2048, but
when measuring a peaky spectrum with 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.
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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:
•
Averaging. If the measured spectrum is the average of a number of scans, some scans may contain
saturated pixels, while the end result does not show a graph that reaches the maximum counts.
•
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 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 pixels which is a lot more than the monitor pixels in the
graph. Since not each CCD pixel 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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Additional information about the saturated wavelength ranges can be visualized and/or saved by
enabling the following options:
Visualize saturated pixels areas in graph
By enabling this option, the spectrum in the main window will be displayed with a thicker line for these
wavelength ranges where the saturation occurs. In time series measurements, the function output values
that were calculated using saturated data are marked with a black dot.
Log saturated pixel areas to screen
By enabling the second option, a small window appears in which the spectrometer
channel number (0 = Master, 1 = Slave1 etc…) and wavelength range for the saturated
pixels are given.
Log saturated pixel areas to file on “Save Measurement”
The third option can be used to create a file to which the saturated wavelength ranges will be written
when a measurement is saved in AvaSoft. When saving spectra in the main window (Save button, or
menu option File-Save-Experiment), the name of the logfile becomes equal to the experimentname, but
with the extension *.sat. For example if a graph in absorbance mode is saved to test0001.abs and if this
spectrum contains saturated data, then additional lines will be written to the textfile test.sat.
If time series measurements, color measurements, irradiance measurements are saved to file, the data
will also be checked on saturation and if saturation occurs, additional lines will be written to a logfile
with the same filename as the measurement results, but with the extension *.sat (e.g. History.sat).
The files with extension *.sat can be openend with any textfile editor, for example Notepad.
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3.2.8.2 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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3.2.8.3 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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3.2.8.4 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 has 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.
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3.2.8.5 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. This can be done with a 2-channel
Fiber Optic Switch (FOS-2-INLINE-UV/VIS) in which case one channel is connected to the reference
sample and the other channel to the sample that needs to be measured. By regularly switching channels
(manually or automatically), the measured deviation from 100% at the reference channel can be used to
compensate the measured data at the sample channel. The same principle can be used if a 2-or
multiple-channel spectrometer is available. In that case 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. The advantage of the “correct
for drift by FOS-2-INLINE-UV/VIS” is that it will also correct for drift caused by temperature changes of
the optical bench. Disadvantage is that the correction is sequentially, so not every scan is immediately
corrected. Moreover, there needs to be time available to switch channels.
Correct for Drift by FOS-2-INLINE-UV/VIS
The FOS-2-INLINE-UV/VIS is a 2 channel fiber optic switch. Switching between the optical channels can
be done manually, or by a TTL signal (see operating manual or FOS-2-INLINE-UV/VIS hardware manual).
By connecting an IC-DB15-2 interface cable between the AvaSpec and FOS-2 (or an IC-DB15-FOS2-2 if a
shutter needs to be controlled as well from the AvaSpec), the spectrometer can control the position of
the switch. In AvaSoft, the bottom channel has been defined as reference channel, while the top
channel should be connected to the optical path that is used to measure the samples.
The Correct for Drift with the FOS-2 can be done in two different ways.
1. By regularly switching to the FOS reference channel, the measured spectrum can be compared to the
saved FOS reference spectrum. The differences can be used to correct the data that is measured at
the FOS sample channel. To be able to correct the sample data, the following data needs to be
available:
o
Dark spectrum FOS sample channel
o
Dark spectrum FOS reference channel (if integration time at reference channel is
different from integration time at sample channel)
o
Reference spectrum at FOS reference channel
2. In Transmittance/Reflectance or Absorbance mode, the measured spectrum at the FOS reference
channel can be used as a new reference for the FOS sample channel. To be able to correct for the
difference in sensitivity between both FOS channels, the reference material (white tile or blank)
needs to be saved at the FOS reference channel as well as at the FOS sample channel. This option
requires an equal integration time for FOS reference and sample channel. The following data needs
to be available:
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Dark spectrum at FOS sample or reference channel
o
Reference spectrum FOS sample channel
o
Reference spectrum at FOS reference channel
The difference between these two methods of correction is that in the first method there is no relation
between the data measured at both channels. Avasoft uses only the differences measured in time at the
FOS reference channel to correct the data measured at the sample channel. In the second correction
method, the correction factor between the both FOS channels is determined first, and then the (white)
reference measured at the FOS reference channel is recalculated and saved as a new reference for the
FOS sample channel.
Since for both methods a dark spectrum needs to be available, save dark before enabling the Correct for
Drift by FOS-2-INLINE-UV/VIS menu option. After clicking the menu option, the following dialog will be
shown:
If the interface cable between AvaSpec and FOS-2 and the Power Supply are properly connected, the
FOS-2 will close top (=sample) channel and open the bottom (=reference) channel. As long as the FOS
settings dialog is not closed, the FOS-2 remains in this position.
If you want to use the second method to correct for drift (by saving a new reference, see previous page),
click the checkbox “FOS Reference = Sample Reference” at the bottom of the dialog. When using the
first correction method, the integration time for the FOS reference channel can be set to a different
value as for the FOS sample channel. Remember to save a new dark and reference for the FOS reference
channel after changing the integration time. Determine a good integration time and save a FOS
reference by clicking the white button. Then switch off the light source and save a FOS dark spectrum by
clicking the black button.
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The FOS correction mode, as shown in the FOS settings dialog can be set to “Software” or to “Auto”.
This setting determines when AvaSoft should switch channels during the measurements.
If set to “Software”, the user determines when to switch channels. The dialog below will be shown after
the OK button has been clicked in the FOS Settings dialog.
As long as the Reference channel is
the Active FOS Channel, the data
processing does not occur in the main
window, but a small graph as shown in
the figure at the right shows the A/D
Counts measured at the FOS-reference
channel. When clicking the Sample
channel radio button, the FOS-2
switches channels, and the
(corrected) data will be processed as
usual. A small window will remain
visible in which the FOS channel can be switched back to the FOS reference channel and measure a new
reference spectrum.
If set to “Auto”, switching of channels will be done after a preset number of seconds. Furthermore, you
can select if you want to update the FOS reference
spectra once every x seconds or only take one sample
measurement once every x seconds. In figure at the
right, the sample channel will be measured during most
of the 60 seconds. Once every 60 seconds, the FOS
switches to the FOS reference channel to take a new
FOS reference spectrum that will be used for the
correction.
After clicking OK in the FOS Settings dialog, the FOS will display one of the two dialogs below. As long as
the sample channel is active (right dialog), the measurement results will be processed as usual. As long
as the reference channel is active (left dialog), the measurement results will be used to update the
reference spectrum and the A/D Counts of this spectrum will be displayed in the dialog.
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Correct for Drift by Spectrometer Channel
This option is 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:
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.
3.2.8.6 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 for the USB1 platform a 15 to 15 pin cable (IC-DB15-2).
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.
3.2.8.7 Setup Menu: Options - External Trigger Setting
The DB15 connector on the
AvaSpec spectrometer uses two
pins for digital IN
communication: pin 4 and 8.
Pin 4 is used for the Hardware
Trigger mode and pin 8 is a
regular digital for which the
status can be polled. In AvaSoft,
two functions have been defined
for using the digital in at pin 8.
A lot more (customer specific)
features can be easily implemented. For generating a +5V signal at pin 8 manually, the handheld
pushbutton cable IC-Extrig-2 may be ordered, or if the “Automatic Save Dark by TTL shutter” option
needs to be supported as well, an “IC-DB15-Extrig-2” Y-cable can be ordered. The different options,
which are shown in the dialog above, are described below.
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Perform scans continuously, save first available spectrum if TTL signal is high (pin 8)
In this mode, AvaSoft will poll the status of pin 8 after each arriving scan. If the status of pin 8 is HIGH
(+5V), the spectrum (or spectra in case more spectrometer channels are active) will be saved
automatically, as described in section 3.1.7. A comment dialog will not be shown, instead the
spectrometer channel number and a time stamp will be written to the comment file. Note that the
spectrum will be saved only if the signal is high at the moment of polling, which is the moment that
AvaSoft receives a new spectrum from the data acquisition driver. If a short TTL pulse is generated at
pin 8, there is a big chance that the spectrum is not saved. To save one spectrum, the duration of the
TTL signal should therefore be as long as the product of integration time and number of scans to
average. In time critical situations, it is recommended to use the External Hardware Trigger Mode.
Perform scans continuously, save first available spectrum as Reference if TTL signal is high (pin 8)
For absorbance or reflectance/transmittance measurements, it is recommended to update the reference
data regularly, to exclude effects like drift in the light source or e.g. temperature effects of the
detector or in the optical bench. In most cases, reference is saved manually by clicking the white
reference button. This reference data will be saved automatically if this external trigger option is
selected and the status of pin 8 is HIGH (+5V) at the moment that a new spectrum is available. For the
required TTL signal duration and timing, see the above description for saving spectra at high TTL signal.
External Hardware Trigger, perform a single scan at rising edge of TTL pulse (pin 4)
By selecting the external hardware trigger option, the data acquisition mode of the spectrometer is
changed. There will be no data acquisition until a TTL pulse is received at pin 4 of the DB15 connector.
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
AvaSpec-102
AvaSpec-256
AvaSpec-1024
AvaSpec-2048 (S/N <= 0405054S1)
AvaSpec-2048 (S/N > 0405054S1)
AvaSpec-2048FT
Minimum Delay [µs]
1000
1000
4000
2000
1.26
1.26
Maximum Delay [µs]
1500
1500
4500
2500
1.30
1.30
For example, the integration time (as set in AvaSoft) starts for a standard AvaSpec-102 after 1.0 to 1.5
ms after receiving the TTL pulse at pin 4 of the DB15 connector. After the integration time expires, the
data is processed by AvaSoft and the spectrometer waits for a next pulse. The external hardware trigger
is useful to observe short pulse events (i.e. laser pulses, etc.). To measure a laser pulse, the AvaSpec2048FT includes an option to send out a TTL-pulse at pin DO2 to fire the laser just before the integration
time cycle starts (delay = -42 ns). By setting the delay between the TTL-out at DO2 and the start of the
integration time to a positive value, the AvaSpec-2048FT can be used in LIBS application (Laser-induced
breakdown spectroscopy), where the laser pulse itself should not be measured, but the plasma emission
e.g. 1 µs after firing the laser. For details about the delay settings for the AvaSpec-2048FT in external
hardware trigger mode, see below. For LIBS measurements with the USB2 platform spectrometers, refer
to the USB2 manual.
If the white “automatic save on trigger” box is marked, each spectrum that will be recorded in external
hardware trigger mode will be saved automatically.
Make sure that, before the External Hardware Trigger is selected and confirmed by the clicking the OK
button, a +5V TTL pulse can be set on pin 4. To leave the external trigger mode, the “External Trigger
Setting” menu option needs to be selected, and the “None” radiobutton needs to be clicked, followed by
the OK button. However, the spectrometer firmware will not return to normal acquisition mode before it
receives the TTL pulse at pin 4.
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AvaSpec-2048FT and external hardware trigger
The AvaSec-2048FT has been developed for the LIBS (Laser-induced breakdown spectroscopy)
applications, but can of course also be used in applications that need a fast response to an external
trigger signal, such as when measuring products at a conveying belt.
If the AvaSpec-2048FT scanning is controlled by an external hardware trigger signal at pin 4 of the DB15
connector, it will carry out the following events after receiving this trigger signal:
1. First it will respond by putting a TTL output signal at pin 2 of the DB15 connector. This TTL
output can be used to fire the laser in the LIBS application.
2. The integration time cycle starts a user defined delay after the TTL output to the laser has been
given. The minimum period for this delay is –42 nanoseconds, in which case the laser pulse
itself will be measured because the integration time will start 42 ns before the TTL-out at DO2.
The setting of the delay period can be increased with 42 nanoseconds steps. The maximum delay
is 2730583 ns. A frequently used delay setting in LIBS applications is 1000 ns. There is no jitter
on the delay period, which makes to AvaSpec-2048FT not only suitable for simple classification,
but also for precise quantitative analytical applications.
The software programmable delay between the output at DO2 (to fire the laser) and the start of the
integration time is used to avoid the measurement of the first period directly after the laser pulse, in
which the plasma emission shows a high intensity, but without the useful information. The figure below
shows an example of the plasma emission intensity after the laser pulse. The integration time for the
AvaSpec-2048FT can be set from 2 ms to 60000 ms. In LIBS applications, the minimum integration time
of 2ms is used.
Programmable delay: -42 ns to +2730583 ns in 42 ns steps, jitter = 0 ns
This portion of the plasma emission is not included in the integration time
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To set the delay in AvaSoft, select the
external hardware trigger option in the
External Trigger Setting dialog, as
shown in the figure. Enter the delay (in
nanoseconds) between the output that
will be given at pin 2 to fire the laser
and the start of the integration time
cycle. If you want the spectra to be
saved automatically, enable the
“Automatically save on Hardware
Trigger” option. Then click OK.
When measuring in external hardware mode, the data acquisition is controlled by the external trigger
pulse input. Therefore, the Start/Stop button will be disabled. The edit bar will show the current
setting for the delay (1000 ns in the figure below).
Trigger checkbox
As long as the spectrometer is in this mode, you cannot send commands from AvaSoft to the
spectrometer. So if you need to change the delay, you will first need to disable the external trigger
mode. This can be done in the external trigger mode dialog, by selecting the “None” button, but a
shortcut with the same effect is to click the Trigger checkbox in the edit bar of the main window. Note
that one more trigger pulse is needed before the external trigger mode is disabled. The reason for this is
that the spectrometer can only react on an external trigger at pin 4 before it can respond to the
“disable external trigger mode” command.
After disabling External Trigger mode and providing one more trigger, an edit box will show up with the
current delay setting (see figure below). The delay setting can be changed in this edit box (-42 to
2730583 nanoseconds)
After changing the delay, you can enable the external hardware trigger by clicking the Trigger checkbox.
Note that the resolution of the delay in nanoseconds is steps of 41.67 ns, with an offset of –41.67 ns. So
if you enter e.g. a delay of 800 ns, the software will calculate the closest step (= -41.67+20*41.67 = 792
ns).
For the spectra that are saved in external hardware trigger mode, a comment file will be created
automatically, in which the date, time and delay are shown. This may help to compare the spectra that
were recorded with different delay settings to determine an optimal delay (File-Display Saved Graph).
The optimal delay period depends on the material and the laser in the LIBS application.
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3.2.8.8 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 14000 counts, a dialog is shown in which the new integration time is
given. 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.
3.2.8.9 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, 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.
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.
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3.2.8.10
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).
3.2.8.11
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”.
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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 3.2.8.9, 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 3.2.8.11).
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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.
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
14000. 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 14000 counts.
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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 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: Channel
After selecting this option, a dialog is shown in which the channels to be displayed can
be selected. Depending on the number of available channels in the spectrometer system
that is used, up to 8 spectrometer channels can be selected. If displaying graphs that
were saved before (File-Display Saved Graph), the active channels also remain visible, to
be able to measure online against a saved graph background. To view only the saved
graphs, all active channels need to be unselected.
3.3.6
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.
3.3.7
View Menu: Graphic Reset
When selecting this option, the graph will be reset to the default X- and Y-axes.
3.3.8
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.
3.3.9
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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3.3.10 View Menu: Grid Enable
With the Grid Enable option activated, a grid will be displayed in the graph as shown in the figure below.
3.3.11 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 HistoryFunction 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 run-time 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 overexposure. The easiest
way to assure this is to select the ‘check on saturation’ option (section 3.2.8.1). If the spectrometer is
overexposed 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.
Please consider the following points to avoid some pitfalls:
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 (default
C:\AvaSpec60) 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: HistoryDisplay 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 Xand 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 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 14000 counts. 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.
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 14000 counts. 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). 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. 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 14000 A/D counts. 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.
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If the intensity calibration has been loaded, the “Irradiance Chart” and “Irradiance Time Series” tabs
will be enabled. Clicking the irradiance chart or time series tabs allows you to change the settings, 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.
4.4.4
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 (maximum around 14000 –
15000 counts) is measured. 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 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) will be around 14500 counts. Do not forget to
save a new dark spectrum (black button) after changing the integration time.
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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: HistoryDisplay 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 an .ini file, 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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4.5 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.
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 15-pole Sub-D connector which are used for the process control application are listed in
the table below. So, pin 5 is used to monitor the thresholds that are set for History Channel Function F1
etc..
HD DB15 pins used by AvaSoft
Process Control
HCF# connector
pin
1
5
2
6
3
7
4
9
5
11
6
12
7
14
8
15
GND
10
An IC-DB15-2 interface cable is available to connect all pins to your process equipment
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4.5.2
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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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 Oxygen application
Avasoft-Oxygen has been developed to perform on-line absolute oxygen measurements with a
spectrometer system. Oxygen probes are based on the quenching effect of oxygen on the fluorescence of
a ruthenium complex. The AvaLight-LED-475 light source used, emits light with a wavelength of
approximately 475 nm. Measurements of the fluorescence are performed at approximately 600 nm. A
high signal corresponds with a low oxygen level and vice versa.
The calculated oxygen level can be displayed and saved in two ways:
• The oxygen level can be displayed on-line in a separate display window, with up to eight channels.
• You can select up to eight history channels that can display and save oxygen levels against time. This
application can be combined with the Excel and Process-Control applications.
4.7.1
Quick Start: How to take oxygen measurements with AvaSoft-Oxy
1. Start the AvaSoft software, and click the Start button in the main window.
2. Connect one leg of the bifurcated fiber optic cable to the input of your spectrometer, and the
other leg to your blue LED lightsource. Use an SMA interconnect (ME-FI-SM-MM) to connect the
oxygen probe to the common part of the bifurcated cable.
3. Set the Smoothing Parameters in the setup menu (‘Setup’, ‘Smoothing and Spline’) to 10.
4. Before oxygen measurements can be performed, the oxygen probe must be calibrated at two
known levels of oxygen, such as 0.0 percent oxygen and 100.0 percent oxygen. Although zero
oxygen level is recommended for the low concentration, any value can be used for the
standards, as long as they are sufficiently different. The levels for the low and high oxygen
standard, as well as the unit need to be entered in the Oxygen Settings dialog. The settings
dialog is opened by selecting ‘Application’, ‘Oxygen’, ‘Settings’ from the main menu.
The probe must be shielded from ambient light to obtain reliable data. To determine if ambient
light is entering the probe, the blue LED can be turned off. The spectrum should appear to be
flat, near the bottom of the scale.
First save a dark level, switch off the LED light source and click ‘File’, ‘Save’, ‘Dark’ or click the
‘Save Dark’ button in the button bar.
Then start with the standard in the lower end of your oxygen range. Select a suitable setting for
integration time, try to get a large dynamic range. Higher oxygen levels will give lower signal
levels. Averaging can be increased to e.g. 10 to improve the stability of the signal.
5. Your displayed spectrum should now like the figure below. The peak to the left is the 475 nm
LED peak. It can be higher or lower than your fluorescence peak, depending on the oxygen
probes.
The peak in the middle is your fluorescence peak, at about 600 nm.
6. If you have a stable signal, click the ‘Low Oxygen’ button and acknowledge reading the standard
with the ‘OK’ button.
7. Repeat the above for the high oxygen standard. The peak at 600nm should be considerably lower
at the high oxygen level. Click the ‘High Oxygen’ button and acknowledge with ‘OK’.
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8. Calculate K and I0 values by clicking the ‘Calculate’ button.
9. Save the values for the calibration by clicking the ‘Save Channel’ button. Close the settings
dialog by clicking the ‘Close Form’ button.
10. Enable the Oxygen measurements by selecting “Application’, ‘Oxygen’, ‘Enable’ from the main
menu. After the application is enabled, it is also possible to select ‘Oxygen’ as a History Channel
function.
4.7.2
Enabling the application
Enable the application by selecting ‘Application’, ‘Oxygen’, ‘Enable’ from the main menu. A checkmark
will appear before the menu entry to show that the option is enabled. After enabling, you can select
‘Oxygen’ as a function type in the Function Entry dialog of the History Application.
4.7.3
Settings
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This dialog is shown after selecting ‘Application’, ‘Oxygen’, ‘Settings’ from the main menu. The settings
are read from the oxygen.ini file on disk. You can use different standards and units for each of the 8
spectrometer channels.
The LED Control option allows you to switch the LED to ON by the software, only when a measurement is
done. This option requires a special version of the LED light source (AvaLight-LED-475-p14), in which it
can be controlled by pin 14 of the DB15 connector in TTL position.
Note that it is perfectly possible to enter your own values for K and I0 in the edit boxes and work with
these values. You can save these values or calculate new ones by performing a new calibration. Always
save changes with the ‘Save Channel’ button.
Remember that the K and I0 values are dependent on many parameters, such as probe quality, fiber
diameter and positioning, integration time, dark settings, light source intensity, ambient light,
temperature, oxygen standard values used etc.
Therefore, it is highly recommended to calibrate as often as possible.
Choose the standards in the range of your measurements, and try to make the difference in signal over
this range as large as possible.
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4.8 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
dip-probe 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.
4.8.1
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 4.8.2). 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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4.8.2
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
4.8.2.1. 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 4.8.2.2 describes how to modify a previous saved calibration file.
4.8.2.1 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 fitted
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.
4.8.2.2 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.
4.8.3
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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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 number of the spectrometer that is connected, detector type,
firmware version, AS161.DLL version, 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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