Veris VIS-NIR Operating Instructions
Operating Instructions
VIS/NIR Spectrophotometer
Table of Contents
Section 1
1-2 Warranty
1-3 Safety
Section 2
2-1 System Overview
2-6 Software Installation Guide
2-11 Configuring Ocean Optics Spectrometer
2-15 Setting port order
2-16 Setting Integration Time
Section 3
3-1 Field Operations--Electronics
3-13 Bench top usage
3-15 Test/Example data
3-16 Field Operations—NIRS and EC Mobile Sensor Platform
Section 4
4-1 Maintenance and Lubrication
4-8 NIRS Wear-plate replacement
4-11 Shank Removal
4-14 Case Removal
Section 5
5-1 Troubleshooting
5-6 Procedure #1 Checking Ocean Optic Spec
5-8 Procedure #2 Checking Hamamatsu Spec
5-10 Procedure #3 Shutter Movement
5-12 Procedure #4 Troubleshooting with HyperTerminal
5-16 Procedure #5 Fuse Replacement
5-20 Procedure #6 Checking voltage on Hamamatsu
5-21 Procedure #7 Replacing halogen lamp
5-23 Glossary
5-24 Field Auxiliary output definitions
5-27 Program modifications
Pub.# OM17-NIR Shank
Pub# OM17-NIR Shank
Section 1
MSP with Near Infrared Spectrophotometer
Warranty
Veris Technologies warrants this product to be free of defects in materials and
workmanship for a period of one (1) year from the date of delivery to the purchaser.
Veris Technologies will repair or replace any product returned to Salina, Kansas, which
appears upon inspection to be defective in materials or workmanship. Veris
Technologies will have shall have no obligation under this warranty for the cost of labor,
down-time, transportation charges, or for the repair or replacement of any product that
has been misused, carelessly handled, modified, or altered.
ALL OTHER WARRANTIES OF ANY KIND, WHETHER EXPRESSED OR IMPLIED,
INCLUDING BUT NOT LIMITED TO ANY IMPLIED WARRANTY OF
MERCHANTABILITY OR OF FITNESS FOR A PARTICULAR PURPOSE AND ALL
CLAIMS FOR CONSEQUENTIAL DAMAGES, ARE SPECIFICALLY DISCLAIMED AND
EXCLUDED.
Safety
Important! Read the following SAFETY PROCEDURES before operating the Veris
MSP:
• Read and understand all instructions on safety decals
1-2
Pub# OM17-NIR Shank
• Escaping fluid under pressure can penetrate the skin causing serious injury. Avoid
the hazard by relieving pressure before disconnecting hydraulic lines. Use a piece of
paper or cardboard, NOT BODY PARTS, to check for suspected leaks.
• Wear protective gloves and safety glasses or goggles when working with hydraulic and
high-pressure wash systems.
• If an accident occurs, see a doctor immediately. Any fluid injected into the skin must
be surgically removed within a few hours or gangrene may result.
• Pinch point hazard: to prevent injury, stand clear when raising or lowering any part of
the Veris MSP.
• Install all transport locks before transporting or working underneath.
• Detach and store implements in an area where children normally do not play. Secure
implement by using blocks and supports.
• Read Operations Manual before operating machine
• Review safety instructions with operators before operating machine and at least
annually
• Never stand on or use tire as a step
• Do not tow the implement on public roads without the optional light package, or without
the proper safety equipment and licensing as required by your State Department of
Transportation. Always use safety chain.
• Riders obstruct the operator’s view. They could be struck by foreign objects or
thrown from the machine.
• Never allow children to operate equipment.
• To prevent possible electrical shock, or damage to the instrument, do not connect to
any power source greater than twelve (12) volts DC.
• Do not grease or oil implement while it is in operation.
• Disk edges are sharp. Be careful when working in this area.
• Disconnect battery ground cable (-) before servicing or adjusting electrical systems or
before welding on implement.
• Remove buildup of mud, oil or debris.
• Be prepared if a fire starts.
• Keep a first aid kit and fire extinguisher handy.
1-3
Pub# OM17-NIR Shank
Spectrometer case
EC
Lamp
Temperature
Motor
GPS
Spare
Auxiliary case
USB ports
Section 2
System Overview
Description:
The Veris Spectrophotometer acquires absorbance measurements of soil while being
pulled through the field. Alternatively, the unit can be set up in stationary mode in a
laboratory to acquire absorbance measurements of samples.
System diagram
Figure 1
Figures 2 and 3
2-1
Figure 4
Shank module
#30267
Cable that includes fiber, motor
control and lamp power
Garmin GPS
# 21221
GPS adaptor cable #30727
Note: This adaptor cable is
required in order for
compatibility with the provided
Garmin GPS.
Shank bench top
stand
#33204
GPS serial adaptor cable
#35482
This will connect the serial port of a GPS to the GPS
port on the auxiliary case, for using an alternate GPS
to the Garmin. External power is required for the GPS
to function.
Figure 5
Pub# OM17-NIR Shank
Figure 6
Figure 7
2-2
Figure 8
External reference blocks
and reference block holder
which are used to calibrate
instrument during the system
check.
External reference block
holder
Soil temperature sensor
#30276
5-meter USB cables
#30281
Pub# OM17-NIR Shank
Figure 9
Figure 10
Figure 11
2-3
Figure 12
USB repeaters
#32891
These are to be used only when the
regular 5-meter long USB cables
are not long enough.
15-amp power supply
#34669
This will power the instrument
in a bench top setting.
Power cable
#33158
This is used to power the
instrument from a vehicle (for
field use).
Note: Only use 15-amp fuse
Power cable for 15-amp power supply
Figure 13
Pub# OM17-NIR Shank
Figure 14
Figure 15
2-4
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Wearplate assembly
#31934
For serial #s 1001 thru 1005
Wearplate assembly
#35488
For serial #s 1006 and beyond
Figures 16 & 17
Note: For computers outside the United States of America, please make the
following change to the computer’s regional settings before installing the Veris
Spectrophotometer Software.
Step 1: Open control panel and double click on Regional and Language Options
Step 2: Click on Customize, the following screen will appear. The Decimal symbol
needs to be a “.” while the Digit grouping symbol needs to be a “,”. The will ensure
proper operation of the software. Once the changes have been made click OK and
proceed with installation.
2-5
Veris Spectrophotometer Software Installation
The Veris
Spectrophotometer
Software installer will
guide the user through
installation of the Veris
operating software and
the necessary drivers
needed to run the
spectrometers. Note:
Do not plug in USB
cables for cases at
this time.
Keep the default
directory and click next
Veris Spectrophotometer
Software V1.77 and up will
run on either Windows XP,
Vista or 7—32 bit operating
systems only
Figure 18
Pub# OM17-NIR Shank
Figure 19
Figure 20
2-6
Now the ocean optics
drivers will be installed.
Select language and
continue.
Leave the default
directory and click next
Select next to
complete install
Figure 21
Figure 22
Pub# OM17-NIR Shank
Figure 23
2-7
Figure 24
At this point it is
OK to restart the
computer
Select Install the
software automatically,
then click Next to
complete the hardware
installation.
Next the Hamamatsu
Minispectrometer
installation guide will
appear. Click next two
process through the
installer
Pub# OM17-NIR Shank
Figure 25
Once the restart is complete, plug in the USB cables for the auxiliary and spectrometer
cases
MS Windows may then bring up the following screens about the Ocean Optics
spectrometer and the Hamamatsu spectrometer.
Figure 26
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Pub# OM17-NIR Shank
Windows will
automatically find the
correct drivers for the
Ocean Optics USB4000.
For the Hamamatsu
installation select Install
the software
automatically then Next
to complete installation.
If this screen appears
asking for the driver
version to be installed
always use the
specu1a.inf, then
select Next.
Figure 27
After completing the Ocean Optics MS Windows installer, the Hamamatsu installer may
appear. Note: These installers may appear in any order.
Figure 28
Figure 29
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Pub# OM17-NIR Shank
The master_veris_standards
file is specific to your external
references and is provided by
Veris.
Installation of Calibration Files
This must be complete for the software to be operational
Copy the master_veris_standards.txt file from the calibration CD into the C:\Veris
directory
Figure 30
Figure 31
Figure 32
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Configuring Ocean Optics Spectrometer
Step 1: Open OOIBase32 Software (only necessary for Veris Spectrophotometer
Software V1.76 and below)
Start Ocean Optics software (Start programs Ocean Optics OOIBase32)
a. If software asks for a default spectrometer file click cancel
Figure 33
If it asks for a spectrometer configuration click, OK
Figure 34
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Pub# OM17-NIR Shank
If software asks for a default spectrometer file click Cancel
Figure 35
Step 2: Open Configuration
Click on Spectrometer in the toolbar at the top and then select Configure
Figure 36
On the configuration screen select the A/D Interface tab
Figure 37
Note: Under Spectrometer Type if USB4000/HR4000 is not available select S4000
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Under serial # only one spectrometer number should be present. If no serial number is
present close out of the software, unplug the USB cable and reinsert the USB cable,
wait to see if windows recognizes a new device, then proceed to the open the Ocean
Optics software and try again.
Click OK and a spectrum will be present on the screen.
Figure 38
Example of spectrum that should be shown on screen (when light is on at shank).
Step 3: Save Configuration
Figure 39
2-13
Pub# OM17-NIR Shank
Click on Spectrometer then Save Configuration As.
Figure 40
The Save Spectrometer Configuration should automatically fill in the file name with the
serial number. Click Save.
Figure 41
Choose yes to make the spectrometer configuration the default settings.
The spectrometer has now been configured.
Figure 42
Exit the software.
2-14
Setting port order
Auxiliary case ports
Spectrometer case ports
The software could increment the
number of the ports by one
depending on the computer. For
example, the device manager
shows ports 20,21,22,23,9 but the
software shows 21,22,23,24,10.
Just use the incremented numbers
if this situation occurs.
- Check Device Manager for port order (Start settings control panel
system hardware tab device manager double click ports)
- Ports will be listed in order, as they should be set in software.
Pub# OM17-NIR Shank
Figure 43
In this example the order to set the ports would be as follows: (see Figure 5.) Different
computers will have the ports in different orders; however if the software is used on one
computer only, the ports will never change. The ports will always be in the order of
spare, GPS, temp, control, and spectrometer. For future reference, make note of the
com port order your computer is using.
Spare: COM20
GPS: COM11
Temp: COM12
Control: COM13
Spectrometer: COM8
The last port (COM9) will not be used.
2-15
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Example of ref spectra shown
in system check and acquisition
with correct integration time set.
Ocean Optics Integration time
Hamamatsu Integration time
Setting Integration Time:
The integration time is the amount of time the spectrometers collect the spectral data for
averaging. It is important to have this set correctly because too much light will saturate
the spectrometer, while too little light won’t allow the full range of the detector to be
used. The integration time needs to be set before acquiring spectral data. This is
especially important for users switching between probe and shank modules as
the optics are different and the amount of light seen by each device varies.
Step 1: Open the Veris Spectrophotometer Software and start the system check. After
the first Dark and Reference measurements are stored check the ref spectra display
(example shown below). The two peaks shown should be around 40000.00 counts.
The first peak is controlled by the Ocean Optics (oo) int time, while the second peak is
controlled by the Hamamatsu (ham) int time. If peaks are too high, then lower the
integration time. If peaks are too low then raise the integration time.
Step 2: Once it has been determined which way to move the integration time, exit the
software and open the acq_settings.txt file located in the C:\Veris directory.
0.010 12.000 5.000 8.000 0.150 0.150 0.300 0.150 2.000
Example of data stored in acq_settings.txt
The second value represents the ham integration time, while the third value represents
the oo integration time. Raise or lower these values then save the file, open the Veris
Spectrophotometer Software, run a dark and reference measurement, and then check
these values again to see how the peaks changed.
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Pub# OM17-NIR Shank
Folder icon to select working
directory.
A field folder must be selected
before any steps can be
completed. Note: Each field or
site must have its own folder.
Once the desired
directory is found,
click on current folder.
BEFORE STARTING:
1. Before taking any
data let system run
for 20 minutes to
allow the
spectrometers to
stabilize.
2. Connect
spectrometers to
PC.
3. Open Veris software
4. The port order must
be set (see Setting
Port Order). This
needs to be done
the first time the
software is run on a
machine, after that
the port order will be
stored for future use.
Port terminology
may be labeled
COM or ASRL.
Both are acceptable
if port number is
correct.
Press EXIT or F12 when ready to quit the software; this will
ensure the port order will be saved.
Section 3
Field Operations: Electronics
Operating software – Software that will guide the user through the field usage steps.
This will need to be completed every time the software is started. Open Veris operating
software:
Figure 1
Figure 2
3-1
Pub# OM17-NIR Shank
Indicator light will be
yellow or green
Number of times each
ER has been sampled
1) System Check – This step calibrates the spectra data to known standards to ensure
data integrity. This is accomplished by A) manually placing four external reference
standards against the window and collecting spectra measurements for each standard,
then B) transforming the data to a master set of data provided by Veris.
A) After the Dark and Reference cycle has completed and the ref check light has turned
green, the system is ready for the external references. Before running the external
references make sure the window on the shank and the window on the references are
clean. References can be checked in any order and as many times as necessary.
When program state reads REST, the ref check light is green, and controller is in
neutral (N), place the correct external reference under shank and then press the
corresponding external reference button. If the External Reference (ER) failure light is
yellow, check to make sure the correct external reference was placed under the shank
and that the correct external reference button was pressed, then run the external
reference again. When ER light turns green or yellow, proceed to next reference. Once
each external reference has been run at least once, press end or F12. This will exit this
program and initiate the create transform program, which will take the data just acquired
and compare it to the master data to create a current transform. If the transform is
created successfully, then that transform will be applied to all spectra data acquired
during the acquisition.
Placing the reference holder beneath shank ER held securely beneath shank
Figures 3 & 4
Place the ER securely onto the shank wearplate. The dowel pins on the ER fit into four
allen-head screws on the wearplate. This aligns the ER in the correct position, and
magnets hold the ER firmly in place. The reference material goes towards the front of
the shank and lines up directly underneath the sapphire window on the wearplate. The
allen-head screws can get packed with soil after the system has had soil contact. A flathead screwdriver can be used to remove the soil so the ER can be put in place.
Figure 5
3-2
Pub# OM17-NIR Shank
External
Reference buttons
Failure light
Number of times
each reference
has been ran,
since system
check was
opened.
Manually stores
dark/reference
data. This should
be done if there is
a failed reference
check. This could
be caused by the
shank steps not
being within
specification, or
one of the
spectrometers is
not running. Try to
clear out the
reference by
pressing F2. If
problem persists
shut down system
and restart.
Auxiliary data can be scrolled through by the up and
down arrows on the left of the indicator. Data
corresponds to chart listed on the right of indicator.
Note: a reading of –1.50 indicates failure of that
component or communication problem. See
Glossary for Auxiliary data information table.
Ref check graph:
This should be close to
a straight line except
for the edges and the
center. The reference
check light will indicate
if this is an acceptable
reference check.
Root mean squared
error of current
external reference.
By default the RMSE
should be within .10
for references 1,2,& 4
and within .15 for
reference 3.
Reference check light is
green for good references
and red for a failed
reference. If a reference
fails, press F2 to store a
new dark and reference.
Ref check light
Graph that compares current
external reference to master
reference. These should
correlate to one another if
system check has been
completed before.
A yellow ER light
indicates possible
problem. Regard as a
good reference unless
transform step fails.
Shank steps should
be 5.2 cm within +.03 cm. If steps are
not within this range
then press F2 to
store another
dark/ref.
Figure 6
3-3
B) Transform step.
Raw master and
slave data
(external
reference). The
master is black
and the slave is
grey.
Master and slave
data with
transform applied
master is black
and slave is grey.
Root mean
squared error for
current transform.
Maximum allowed
RMSE for a good
transform.
Compares the
offset of the
previous transform
the current
transform
Indicates when transform is
complete. READY TO
MOVE TO NEXT STEP—
DATA ACQUISITION.
This compares the slope
of the previous transform
to the current transform
Previous transform will
be a straight line the first
time system is ran.
External
reference data
that was just
taken.
Master data file, which
will be used to transform
slave (master file
provided by Veris)
Indicates if transform is acceptable.
Figure 7
Master data file is provided by Veris.
Pub# OM17-NIR Shank
Once the transform is complete press close window or F12. If the transform was
successful, the software will inform the user and continue on to acquisition. If the
transform failed, the program will enter the system check again so the references can
be ran once more. If the transform fails again, either there is a system problem
(spectrometer malfunction, window is dirty, or references not taken properly) or the
tolerance for the maximum allowed RMSE could be set too low; see program
modifications to change this.
3-4
Pub# OM17-NIR Shank
Before mapping complete the following:
Start system at least 20 minutes before starting to map to ensure the spectrometers
have stabilized
Make sure auxiliary sensor data is coming in (see Glossary for auxiliary sensor data
definition).
Make sure all auxiliary lights are green.
Complete all steps above. Make sure Reference Check (Ref Check) light is green, and
GPS data are being received.
Set depth so that EC coulters penetrate approximately 1.5"
Make sure the implement frame is level with the ground surface
Pull forward with shank in ground. The absorbance should not rise more than 0.1.
2) Data Acquisition--electronics – The collection of spectral and auxiliary data in the
field. Data is streamed to a file in a compact format.
Pressing LOG button or ESC key stores spectrum data as absorbance and auxiliary
data, which includes EC data, until LOG button or ESC key has been pressed again. No
data can be logged if there is no GPS signal or there is a bad ref check. No data,
including EC data, will be stored unless it program is in LOG mode. Whenever shank is
raised out of the soil, press LOG button or ESC key to stop logging, re-press LOG
button or ESC key to re-start logging when shank is in soil.
System will automatically collect a dark and reference every 10 minutes—the next time
the LOG button or ESC key is pressed after a 10-minute period. Before re-starting at
the end of each round, check to make sure system isn’t collecting a dark and reference.
If an extra dark and reference is desired, pressing F2 or Dark & Ref stores a new
reference and dark spectrum. Pressing F4 or sample will store a reference, dark, then
transformed spectrum data as absorbance into the acquisition_samples file located in
the field directory.
When all data have been acquired press F12 or End to return to the main interface.
Soil EC is recorded simultaneously with NIR data, provided the unit is equipped with soil
EC coulter module, and cables are connected properly. When EC is being collected, EC
values will appear in the shallow and deep EC windows, as shown in Figure 10. Note:
unit must be in Log mode for EC to be recorded. Also, see Maintenance section for
information on testing EC system output.
3-5
Ref check light This
green light indicates a
good reference
These indicate the temperatures and the
humidity of the system. If they are not
within range (see specifications) the
indicator light will be red, if this occurs
the system should be shut down.
Dark spectrum
that was stored
when program
state was in dark
mode
Reference
spectrum that
was stored when
program state
was in reference
mode.
Ref check
compares the
previous
reference data
to current
reference.
As in system check, this should be close to a straight line
except for the edges and the center. A bad reference is
indicated by the ref check light at the top of the screen. If this
situation occurs, press F2 to store a new dark and reference.
Pressing LOG
or ESC stores
spectrum data
as absorbance
and auxiliary
data, which
includes EC
data, until
LOG or ESC
has been hit
again. No data
can be logged
if there is no
GPS signal or
there is a bad
ref check. Use
LOG to store
data while
mapping a
field. No data,
including EC
data, will be
stored unless
it program is in
LOG mode.
Auxiliary data indicator
Auxiliary data can
be scrolled
through by
pressing the up or
down arrow to the
left of the indicator.
The auxiliary data
corresponds to the
chart listed on the
right of the
indicator.
Figure 8
EC indicators
Log and GPS
lights—must be
green for data to
be recorded
Pub# OM17-NIR Shank
As long as the acquisition software is closed properly using F12, all data is saved and
the acquisition can be opened at a later time with new data being appended to the data
taken previously.
3-6
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