Poly Pen Device
Specifications
- Device: PolyPen
- Model: SpectraPen
- Communication: USB
- Software: SpectraPen software
- GPS module included
Product Information
General Description
The PolyPen device is a versatile tool for measurement and
analysis. It comes with a GPS module for location tracking and
utilizes USB communication for data transfer.
Technical Specification
The device specifications include:
- Model: SpectraPen
- Communication: USB
- Software: SpectraPen software
Device Description
The PolyPen device is designed for accurate measurement and
analysis. It comes with a GPS module for precise location
tracking.
List of Equipment and Customer Information
The package includes the PolyPen device, USB cable, GPS module,
and user manual with detailed customer information.
Care and Maintenance
Regular care and maintenance of the PolyPen device are essential
to ensure accurate measurements. Clean the device with a soft, dry
cloth and store it in a safe place when not in use.
Product Usage Instructions
Getting Started
To start using the PolyPen device:
- Calibrate the device following the instructions provided in
section 4.1. - Perform measurements as outlined in section 4.2.
Menu Description
The menu options on the PolyPen device allow you to navigate
different settings and functions. Refer to section 5 for detailed
menu descriptions.
PC Communication
Connect the PolyPen device to your PC using the USB cable to
transfer data and communicate with the SpectraPen software.
SpectraPen Software
The SpectraPen software enables data visualization, transfer,
and online control. Install the software as per the instructions in
section 7.1 for full functionality.
GPS Module
The GPS module included with the PolyPen device allows for
precise location tracking during operation. Follow the instructions
in section 8.1 for GPS/PolyPen operation.
Frequently Asked Questions (FAQ)
Q: How often should I calibrate the PolyPen device?
A: It is recommended to calibrate the device before each
measurement session to ensure accuracy.
Q: Can I use the PolyPen without the GPS module?
A: While the GPS module enhances location tracking, the device
can still function without it for basic measurements.
Manual Version: 2023/04 © PSI (Photon Systems Instruments), spol. s r.o. www.psi.cz This document and its parts can be copied or provided to a third party only with the express permission of PSI. The contents of this manual have been verified to correspond to the specifications of the device. However, deviations cannot be ruled out. Therefore, a complete correspondence between the manual and the real device cannot be guaranteed. The information in this manual is regularly checked, and corrections may be made in subsequent versions. The visualizations shown in this manual are only illustrative. This manual is an integral part of the purchase and delivery of equipment and its accessories and both Parties must abide by it.
Page | 2
TABLE OF CONTENT
1
Information before using PolyPen device …………………………………………………………………………………. 4
2
General Description………………………………………………………………………………………………………………. 5
2.1
Technical Specification …………………………………………………………………………………………………………………7
3
Device Description………………………………………………………………………………………………………………… 8
3.1
List of equipment and customer information…………………………………………………………………………………..9
3.2
Care and maintenance………………………………………………………………………………………………………………….9
4
Getting started …………………………………………………………………………………………………………………… 10
4.1
Calibration………………………………………………………………………………………………………………………………… 10
4.2
Measurement ……………………………………………………………………………………………………………………………11
5
Menu description ……………………………………………………………………………………………………………….. 12
6
PC communication………………………………………………………………………………………………………………. 14
6.1
USB connection………………………………………………………………………………………………………………………….14
6.2
Driver installation ………………………………………………………………………………………………………………………15
7
SpectraPen software …………………………………………………………………………………………………………… 17
7.1
Software installation…………………………………………………………………………………………………………………..17
7.2
Software menu ………………………………………………………………………………………………………………………….20
7.3
Data transfer and visualization …………………………………………………………………………………………………….21
7.4
Online control ……………………………………………………………………………………………………………………………25
7.5
Firmware update ……………………………………………………………………………………………………………………….27
8
GPS module ……………………………………………………………………………………………………………………….. 27
8.1
GPS/PolyPen operation……………………………………………………………………………………………………………….27
9
Warranty terms and conditions …………………………………………………………………………………………….. 29
10
Troubleshooting and Customer Support …………………………………………………………………………………. 29
11
Appendix …………………………………………………………………………………………………………………………… 30
11.1 Programming custom index in PolyPen …………………………………………………………………………………………30
11.1.1 Function description …………………………………………………………………………………………………………………..31
12
List of figures ……………………………………………………………………………………………………………………… 33
Page | 3
1 INFORMATION BEFORE USING POLYPEN DEVICE
Read this manual carefully before operating the device. If you are not sure about something in the manual, contact the manufacturer for clarification.
By accepting the device, the customer agrees to follow the instructions in this guide.
Always follow corresponding manuals while working with the PolyPen device or doing the maintenance. It is forbidden to interfere with the hardware or software of the PolyPen device in any way without previous agreement with the manufacturer.
The following table presents basic highlight symbols used in this manual:
Symbol
Description
Important information, read carefully.
Complementary and additional information. Tab. 1 Used symbols.
Page | 4
2 GENERAL DESCRIPTION
PolyPen RP400 & RP410 (in further text – PolyPen) is a portable, handheld spectroradiometer. The PolyPen features a complete system primarily designed for a measurement of spectral reflectance of leaves or other planar samples. The system is convenient for both, indoor as well as field applications. The PolyPen is a self-contained instrument powered by a Lithium-ion battery which is rechargeable via a PC and a USB cable. However, it does not require a PC for operation. Reflectance spectra and calculated reflectance indices are instantly displayed on the PolyPen touch screen and all stored in the device internal memory. Integrated USB communication allows data transfer to a PC at a later time. Measured spectra and calculated indices are stored as full spectrum and individual values (respectively). The PolyPen device integrates an internal light source (Xenon incandescent lamp) with radiation range 380 1050 nm. Two versions of detectors are available for UV/VIS and NIR spectral regions. The built-in GPS module and splash-proof case are ideal for field use of the PolyPen and make this device well suited for wide scope of environmental, agricultural and ecological applications such as monitoring of artificial lighting used in horticulture industry or light source testing.
PolyPen versions: PolyPen RP 410 UVIS PolyPen RP 410 NIR
Spectral response range: 380 to 790 nm. Spectral response range: 640 to 1050 nm.
PolyPen measures:
Transmittance calculated using the following formula T= I/I0 Where: I0 is reference light intensity I is measured light intensity Absorbance calculated using the following formula A=log (I0/I) Where: I0 is reference light intensity I is measured light intensity
The PolyPen device incorporates formulas of commonly used reflectance indices (e.g., NDVI, NDGI, PRI etc.) directly in its software and displays values of the selected indices instantly. The PolyPen allow calculation of the following pre-defined vegetation indices:
Normalized Difference Vegetation Index (NDVI)
Reference: Rouse et al. (1974) Equation: NDVI = (RNIR – RRED) / (RNIR + RRED)
Simple Ratio Index (SR)
Reference: Jordan (1969); Rouse et al. (1974) Equation: SR = RNIR / RRED Modified Chlorophyll Absorption in Reflectance Index (MCARI1) Reference: Haboudane et al. (2004) Equation: MCARI1 = 1.2 * [2.5 * (R790 – R670) – 1.3 * (R790 – R550)]
Optimized Soil-Adjusted Vegetation Index (OSAVI)
Reference: Rondeaux et al. (1996) Equation: OSAVI = (1 + 0.16) * (R790 – R670) / (R790 – R670 + 0.16) Greenness Index (G) Equation: G = R554 / R677 Modified Chlorophyll Absorption in Reflectance Index (MCARI) Reference: Daughtry et al. (2000) Equation: MCARI = [(R700 – R670) – 0.2 * (R700 – R550)] * (R700 / R670)
Page | 5
Transformed CAR Index (TCARI) Reference: Haboudane et al. (2002) Equation: TSARI = 3 * [(R700 – R670) – 0.2 * (R700 – R550) * (R700 / R670)] Triangular Vegetation Index (TVI) Reference:Broge and Leblanc (2000) Equation: TVI = 0.5 * [120 * (R750 – R550) – 200 * (R670 – R550)]
Zarco-Tejada & Miller Index (ZMI)
Reference: Zarco-Tejada et al. (2001) Equation: ZMI = R750 / R710 Simple Ratio Pigment Index (SRPI) Reference: Peñuelas et al. (1995) Equation: SRPI = R430 / R680 Normalized Phaeophytinization Index (NPQI) Reference: Barnes et al. (1992) Equation: NPQI = (R415 – R435) / (R415 + R435) Photochemical Reflectance Index (PRI) Reference: Gamon et al. (1992) Equation: PRI = (R531 – R570) / (R531 + R570) Normalized Pigment Chlorophyll Index (NPCI) Reference: Peñuelas et al. (1994) Equation: NPCI = (R680 – R430) / (R680 + R430) Carter Indices Reference: Carter (1994), Carter et al. (1996)
Equation: Ctr1 = R695 / R420; Ctr2 = R695 / R760
Pigment specific normalized difference a (PSNDa) Reference: Blackburn (1998)
Equation: PSNDa = (R790 – R680) / (R790 + R680)
Structure Insensitive Pigment Index (SIPI) Reference: Peñuelas et al. (1995) Equation: SIPI = (R790 – R450) / (R790 – R650) Gitelson and Merzlyak Indices Reference: Gitelson & Merzlyak (1997)
Equation: GM1 = R750 / R550; GM2 = R750 / R700
Anthocyanin Reflectance Indices (ARI1; ARI2) Reference: Gitelson et al. (2001) Equation: ARI1 = 1/R550-1/R700; ARI2 = R790*(1/R550-1/R700) Carotenoid Reflectance Indices (CRI1; CRI2) Reference: Gitelson et al. (2002) Equation: CRI1 = 1 /R510 -1 /R550; CRI2 = 1 /R510 -1 /R700 Renormalized Difference Vegetation Index (RDVI) Reference: Roujean & Breon (1995) Equation: RDVI = (R780 – R670) / ((R780 + R670)^0.5)
indices measured also by RP 410 NIR
Page | 6
2.1 TECHNICAL SPECIFICATION
Spectral range
Spectral response half width Spectral straylight Scanning speed
Dynamic range
Size of aperture Light source Light source spectral range Internal memory capacity Internal data logging Data transfer PC software Battery type Battery capacity Max. charging current Charging
Battery life
Sample holder Display
Built in GPS module
Size Weight
Operating conditions
Storage conditions
Warranty
380 nm 790 nm (RP 410 UVIS) 640 nm 1050 nm (RP 410 NIR)
8 nm
-30 dB About 100 ms High gain: 1:4300 Low gain: 1:13000 7 mm Xenon incandescent lamp 380-1050 nm Up to 16 Mbit Up to 4,000 measurements USB cable SpectraPen 1.1 (Windows 7 and higher) Li-Ion rechargeable battery 2600 mAh 0.5 A Via USB port – PC, power bank, USB charger, etc. 48 hours typical with full operation Low battery indicator Mechanical leaf clip Touchscreen 240 x 320 pixel; 65535 colors Ultra-high sensitivity down to -165dBm High accuracy of <1.5 m in 50% of trials 150 x 75 x 40 mm 300 g Temperature: 0 to +55 °C Relative humidity: 0 to 95 % (non-condensing) Temperature: -10 to +60 °C Relative humidity: 0 to 95 % (non-condensing) 1year parts and labor
Page | 7
3 DEVICE DESCRIPTION
Fig. 1 Device description. Leaf clip PolyPen is equipped with a non-destructive leaf-clip sample holder. Color touch screen display PolyPen is operated via a touch screen by using a supplied stylus. The software operation instructions are available on page 17.
No sharp objects should be used when operating the PolyPen via touch screen. It is recommended to use provided stylus when making selections on the touch screen. USB Connector USB connector is used for operation of the PolyPen device directly from PC via the SpectraPen software and for re-charging the device batteries. Please note that PolyPen device is automatically re-charged when connected to the PC via the USB connector. Power button Power button is the main Switch ON/OFF button.
Page | 8
Optical sensor and light source The optical sensor of the PolyPen and the light source, are placed inside of the device. See schematic drawing of the principle of reflectance measurement in PolyPen in Fig. 2. The light source is oriented in 35° to the normal line intersecting the detector.
The sensor should be always dust and dirt free.
Fig. 2 Schema of reflectance measurement.
3.1 LIST OF EQUIPMENT AND CUSTOMER INFORMATION
Standard version of the PolyPen device package consists: · PolyPen · Reflectance standard (Spectralon®) · Stylus · Carrying Case · Textile Strap for Comfortable Wearing · PolyPen Operating Manual (on a USB flash disc) · SpectraPen software and driver (on a USB flash disc) · USB cable · Other Accessories or Optional Features (according to your specific order)
For data download via USB connection, the USB driver needs to be installed on the PC. It can be found on the installation disk (USB driver folder). If any item is missing, please, contact the manufacturer. Also check the carton for any visible external damage. If any damage is found, notify the carrier and the manufacturer immediately. The carton and all packing materials should be retained for inspection by the carrier or insurer. For customer support, please write to: support@psi.cz
3.2 CARE AND MAINTENANCE
PolyPen device · Never submerge the device in water! · The device should not come in contact with any organic solvents, strong acids or bases. · Keep the optical sensor clean and dry. If cleaning is needed, use soft, non-abrasive tissue. · Do not use sharp objects for touch screen operation.
Page | 9
Li-ion battery · Avoid fully discharging of the battery. · Do not keep the battery at full charge for long periods of time. Allow for it to discharge. · High temperatures shorten battery life. · If the battery can no longer be charged, please contact PSI for replacement battery.
4 GETTING STARTED
To switch ON the PolyPen, press the Power button until the device logo shows up. Follow next steps to perform the measurements. In case the device battery is not charged, connect the PolyPen with USB cable via USB port to the PC and charge the battery.
The measurements with the PolyPen cannot be made until the calibration is performed.
4.1 CALIBRATION
The calibration of the white reflectance standard is an indispensable part of a correct calculation of reflectance spectrum. The calibration scan must be performed always after the device switched ON or it should be periodically repeated upon certain time period of the device operation. The calibration is not needed for a simple measurement of spectra of external light sources. For calibration of device use special reflectance standard Spectralon®* (Fig. 3).
Fig. 3 Reflectance standard Spectralon. * Spectralon® is a registered trademark of Labsphere.
Spectralon® standard is spectrally flat over UV-VIS-NIR spectrum and optically flat to +/- 1 % over the photopic region of the spectrum.
Please follow the instructions below for device calibration: · In the main window go to > Calibrate >press OK (Fig. 4). · Use the Spectralon® standard (Fig. 3) for white calibration. For dark calibration close the leaf clip only (“standard” is on bottom part
of the leafclip). · Close leaf clip. · Press OK and wait until the calibration step is completed. · Calibration is automatically stored into the device memory. · After the calibration step is performed, Main window icon Calibrate will change into Get reflectance (Fig. 4). Get Reflectance
shows up after successful calibration, measures and stores reflectance spectrum. · The device is now ready to measure other samples.
Page | 10
4.2 MEASUREMENT
Fig. 4 PolyPen calibration. PolyPen is a complex system for a measurement of reflectance spectra of planar samples such as leaves. Besides the whole spectrum information, the PolyPen incorporates pre-defined formulas for calculation of commonly used plant reflectance indices (e.g., NDVI, NDGI, PRI, Greenness Index, etc.) directly in its software. The measured data are instantly displayed in graphs or data sheets on the device screen display. They are also stored in the device memory for later re-collection or transfer to a PC. Please follow these instructions to perform a measurement: · Insert a leaf sample into the leaf clip. The leaf clip is important for the sample stabilization. · In the main window select > Get Reflectance > press OK. · Press OK and wait until the measurement is completed. · Measurements are automatically stored into the device memory and displayed on the screen. · Currently displayed graph represents transmittance data. Displayed graph would be switched to absorbance data in Options menu
(more information in chapter 5). Transmittance mode corresponds with reflectance in case of PolyPen device. The measured spectral data are normalized to the white calibration standard by the linear calculation: T = I/I0, where I means the signal measured from the sample and I0 is the ideal reflectance signal from the standard. Absorbance data are normalized to the white calibration standard as the logarithmic ratio: A = log(I0/I). This visualization mode does not have a special meaning in case of PolyPen device, as this function is important for the trans-illumination geometry measurement in PolyPen-Aqua. Indices table displays a group of selected indices calculated for actual measured data (Fig. 5). To define the indices of interest, go to Options > Settings > Indexes. You can select two indices that are currently displayed. However, all indices are calculated and stored in the device memory. Entire list of the indices can be displayed after a data download to PC. The software also allows a calculation of custom indices defined by user (please refer to page 30).
Fig. 5 Indices table.
Page | 11
5 MENU DESCRIPTION
Device · Calibrate calibration can be run any time by pressing Device > Calibrate after inserting appropriate standard in the leaf clip.
(Fig. 6).
Fig. 6 Calibration of the device. Data · Browse displays data browse dialog box. The user can browse the list of stored data, select the set of data files and view the light
spectra in Transmittance or Absorbance mode (Options > Settings > > Graph). Color classification of each data file helps user to discriminate between individual modes. Up to 3 sets of collected data can be displayed at once by checking off the last column in the data table. · Erase erase function is used to delete the internal data memory. · Memory info displays info on amount of used internal memory of the PolyPen.
Fig. 7 Menu – Data. Options · Settings function is used to set various variables for the light measurements and for the device settings.
o Indices – Select indexes to be calculated and displayed on the main screen (Fig. 8).
Page | 12
Fig. 8 Settings – Indices selection.
o Graph displays options for setting the wavelength range and graph features (Fig. 9). Zoom enable enables the zoom feature. Select an area (in the right-down direction) of the displayed graph, which you want to zoom in. Reverse these steps if you want to return to the original graph size. Marker enable enables to display exact numeric value for the point selected in the Scope graph window. Exact wavelength and light irradiance are displayed for the point, which is selected by touching on the display. In top right corner of the LCD display the exact value of wavelength in nm is shown for the user selected position in spectra. In addition, light irradiance for the given nm is shown. Smoothing enables noise reduction of the graphical display (only on display) by smoothing the noise in the spectrum at the expense of spectral resolution. Data are not affected (calculated as moving average). Absorbance switches to absorbance mode of spectrum visualization, the raw spectral data are calculated according to the formula (A = log(I0/I)). Wavelength range defines the range of wavelengths considered for light scope and light meter measurements. Desired wavelength range can be adjusted by selecting the wavelength and by using the arrows up and down.
o Time – Set the actual time and date (all data files are stored by time and date signature). To change time, touch on one of the values and adjust it using the arrows (Fig. 9).
Fig. 9 Settings Graph ant Time o LCD is used to adjust LCD display control settings (Fig. 10). Backlight intensity move slider to adjust backlight intensity. Backlight time-out move slider to adjust backlight time-out (time of inactivity required before backlight will dim out to save battery life). o Device Average Average function is used for adjusting the number of scans for each reading. Averaging of more scans results in a higher signal-to-noise ratio but increases the time required for each reading that appears on the screen. Move slider to set the number of measurements to be acquired for averaged values (Fig. 10). Data are affected.
Page | 13
GPS enables the GPS module (Fig. 10). The GPS coordinates cannot be displayed at the device display, but they are exported together with data and visualized in SpectraPen software.
Fig. 10 Settings LCD and Device Help · About…- information about the device, hardware and software version (Fig. 11).
Fig. 11 About
6 PC COMMUNICATION
6.1 USB CONNECTION
PolyPen comes with the USB cable that is required for charging of the Li-ion battery and can also be used for data transfer to the PC after completion of measurements. To connect the USB cable with the PolyPen device follow the picture instructions below. Please note that a lock in system is used to secure the USB cable to the PolyPen and extreme caution has to be used when setting up this connection to avoid damage to the cable pins.
When connecting the USB cable take extra caution to prevent damage to the cable connector pins. Ensure correct orientation of the cable as shown in the pictures below so the circled portion of the plug and the cable in photo A and B are perfectly lined up prior to pushing them together. Once this connection is achieved the cable may be secured in position by turning the metal cover of the cable and locking the cable in position.
Page | 14
To connect PolyPen with your computer please follow steps below in Fig. 12:
Fig. 12 How to connect PolyPen with PC. A) connector on the PolyPen device. B) Portion of the USB cable with pins. C E) Position the cable horizontally and line up the green circled parts of the cable and the connector, plug in the inlet and screw the securing screw. F) Correct connection of the USB cable and Pen device.
6.2 DRIVER INSTALLATION
For successful USB connection of the PolyPen to the PC computer the USB driver and the SpectraPen software, included on the USB disk, need to be first installed on the PC. Without the driver installed the PolyPen device will not be recognized by the computer and the connection to the software will be not possible. · Press Start and Select Control Panels (Fig. 13)
Fig. 13 Control panel. Page | 15
· Navigate through System and security, System to Device manager (Fig. 14). Fig. 14 System window. · Connect the PolyPen to the PC. You should see that PSI USB Device appears in the list. Right click on it and select Update Driver
Software (Fig. 15)
Fig. 15 PSI USB device. · Click Browse my computer for driver software and select Driver folder on the PolyPen installation disk. Allow the installation even if
the warning message appears (Fig. 16).
Fig. 16 Choose the driver from the USB disc. · Installation of the driver is now complete (Fig. 17)
Page | 16
Fig. 17 Complete installation. In case this driver installation is not successful the driver may be downloaded directly from PSI websites www.psi.cz.
Once the device is properly connected to the computer, the indicating icon appears in upper right corner on the PolyPen display (Fig. 18).
Fig. 18 Device connect.
7 SPECTRAPEN SOFTWARE
7.1 SOFTWARE INSTALLATION
1. Copy the SpectraPen software provided on the USB flash disk to your computer and launch the SpectraPen program. 2. To connect and recognize the PolyPen device in the SpectraPen software, proceeds first with the registration of the SpectraPen
software (Fig. 19). · Select: Help > Register · Enter: your serial registration number (found in a text file on the USB flash disk drive included with the device). · Select: OK
Page | 17
Fig. 19 SW registration. Please note that the serial (registration) number for the PolyPen may be found in the file SN.txt, which is included on the enclosed USB flash disk. Please Note: it is not possible to download data from the PolyPen device without software registration.
3. Connect the USB cable to the computer. Then switch on the PolyPen by pressing the Power button for a couple of seconds. 4. Ensure the PC and the PolyPen are properly paired (see chapter 6). 5. Connect PolyPen device in SpectraPen software, Device > Connect (Fig. 20).
Fig. 20 SW connection. 6. When the device is properly connected the left bottom corner of the SW window will display “PolyPen” (Fig. 21). Otherwise,
notification “Device: Not Connected” is displayed (Fig. 22).
Page | 18
Fig. 21 PolyPen connected. Fig. 22 Connection failed. Page | 19
7.2 SOFTWARE MENU
MENU: File
Load
Loads previously saved data files.
Save
Saves data to hard disc.
Export
Exports data in .txt format.
Export to JSON Exports data in JavaScript Object Notation.
Close
Closes the current experiment.
Close All
Closes all open experiments.
Exit
Exits the program.
MENU: Device
Connect
Detects and connects the device.
Update Firmware Used for firmware updates. *
Attach GPS File Memory Erase
Used to download data from the GPS module of the old version of the SpectraPen – LM 500. Erases data from the SpectraPen memory.
Online Control Online control of SP device.
* For more information on firmware updating, see Chapter 7.5 of this Operation Manual.
MENU: Setup Update Software
Settings
Used for software updates.
On/Off Auto memory erase after download. Selection of separator for the csv file after its export and following opening in Excel (TAB, SEMICOLON, COMMA, SPACE).
MENU: Help Registration
About
Used for the SpectraPen software registration. Offers basic information about the program.
Fig. 23 Menu File. Fig. 24 Menu Device.
Fig. 25 Menu Setup. Fig. 26 Menu Help.
Page | 20
7.3 DATA TRANSFER AND VISUALIZATION
1. After completion of measurement PolyPen may be connected to PC for data download and further analysis. 2. Launch the SpectraPen software on the computer and Connect the device. Go to Device> Connect. 3. To transfer your data from the PolyPen device to your PC use the Download function. Select icon on left side of screen or go to File
and select Load if you want to process data stored on PC. 4. All data stored currently in the PolyPen device will be downloaded and shown in the main window view. The data are store and
displayed/listed with the time stamp of measurement. Please note that if there are no data stored in the memory, the download function is not active.
5. Visualization modes: Scope (Fig. 27) mode window is always displayed as the default. To visualize the measured data in transmittance or absorbance mode, go to Transmittance or Absorbance bookmark.
Fig. 27 Scope spectra. 6. All data that are downloaded are displayed in the Scope window after download from the PolyPen. The user can select the set of
measurements to be displayed by marking and unmarking the data from the selection list. See selection in the list of measured data in Fig. 27. 7. Right click on list of measured data enables edit data name, delete selected measurement or show and hide all measured data in the graph Select all measure and Clear all measure (Fig. 28).
Page | 21
Fig. 28 Option for list of data.
Fig. 29 Marker function. 8. In the graph marker feature is available, which enables display of the numeric values for wavelength and transmittance or absorbance
for the selected wavelength of the scan (Fig. 29). Use the mouse to select the given point. In top right corner of the graph (green rectangle) is displayed exact value for the selected point on the x-axis and y-axis. 9. To zoom in on the data displayed in the graph select an area of the displayed graph. To reverse these steps and return to original display use minus icon in the corners of the zoom area marked with green rectangles in Fig. 30.
Page | 22
Fig. 30 Zoom function. 10. To view the spectral data in parameter values (Fig. 32) click to button with two arrows (Fig. 31). If you want to calculate your own
index, you can do it from the raw data in Excel or you can add this formula to the Config/Formulas.txt in the PolyPen program folder. Syntax is very simple, for example: Transmittance:CRI2:Caroteniod Reflectance Index 2:1/Transmittance[510nm]-1/Transmittance[700nm] Each parameter is separated with colon: the first one is data set, which will be used as source data (leave their Transmittance); the second is name of the created parameter; the third is description of created parameter and the last one is formula of the new parameter. After you edit the Formulas file, restart the SpectraPen software. Your index should appear in the list and also in the exported data.
Fig. 31 Switch to vegetation indices. Page | 23
Fig. 32 Vegetation indices. 11. To Save the experiment select File>Save. All data stored in the device memory will be saved irrespective of the data selection in the
SpectraPen software. The file will be stored as .spec. Spec files stores all Transmittance and numeric data. 12. Select File>Export to export the data in .txt format. Export function allows the user to specify the type of data. The options are: Spectrum (Fig. 33) all raw scope data for entire range of measured wavelengths are exported including data for the dark scan. Spectrum Scope scope data normalized to dark spectrum scan are exported for all acquired scans or set of selected measurements. Spectrum Transmittance transmittance data for all measurements are exported. The transmittance data are normalized to white calibration standard and thus express the reflectance from the sample. Spectrum Absorbance absorbance data for all measurement are exported. Data in absorbance mode are normalized to white calibration standard by logarithmic calculation. Computed Data (Fig. 34) export of the reflectance indices for Scope, Transmittance or Absorbance of all of the measurements. Export interpolation interpoled data are read every 1 nm, they are the same such as raw data.
Fig. 33 Export table.
Page | 24
Fig. 34 Export Computed data selection and choosing of exported values.
7.4 ONLINE CONTROL
Menu Online Control This function can be used for remote – online control of the PolyPen device after connection with the PC. Online control enables to make changes in device setting and also perform remote measurement using PC. Select: Menu > Device > Online Control (Fig. 35)
Fig. 35 Online Control. Remote measurement (Fig. 36) Using this function Reflectance and Absorbance can be measured.
Please note that the Calibration should be done manually prior the remote measurement. · For manual remote measurement click on Get button (Fig. 36 – 1). · Setting for automated remote measurement is possible using the button with three dots (Fig. 36 – 3). Here the time interval (Fig.
36 – 5) of the measurement is set. To apply this setting use the option Use settings (Fig. 36- 4) and confirm by clicking OK (Fig. 36 6). The measurement stars immediately and continues until it is manually stopped (Stop button). · Use the export option for exporting the data to .csv file. · Clear function serves for erasing of data measured by Online Control.
Page | 25
Fig. 36 Setting of reflectance or absorbance measurements in online control. Settings (Fig. 37) Here the following functions may be set up for remote operation of the PolyPen: · Time synchronization of the device and PC (Fig. 37 – 1) · GPS built-in module activation (Fig. 37 2; more information about the GPS module in chapter 8) · Averaging of measurement, set from 1 to 10 measurements (Fig. 37 – 3)
Fig. 37 Settings of online control. Page | 26
7.5 FIRMWARE UPDATE
All data in the PolyPen memory are erased during the firmware update! Before starting any firmware update, download all your data from the PolyPen memory to the computer and save! Before firmware update ask the manufacturer for appropriate version of the firmware for your particular device. Incompatible firmware version can cause device malfunction.
1. Starting Update · Select: Setup > Update Firmware From File 2. Selecting .bxn file · Find firmware update file: Binary file (with the extension .bxn) · Select: Open. 3. Finishing Upload · Select: OK to start uploading of the update · The bottom bar indicates the upload progress (Fig. 38)
Fig. 38 Firmware update running.
8 GPS MODULE
PolyPen device has integrated GPS module which may be turned on during the measurement for mapping of the collected data to specific field position. When GPS module is turned on, the map coordinates will be automatically saved with all collected data and will be downloaded during data download.
For proper GPS reading, the time in your PolyPen and in your computer must be synchronized. Preset time and time zone must correspond to GPS time (time zone) in your location.
8.1 GPS/POLYPEN OPERATION
1. Check the time setting on the PolyPen device: Settings > Date & Time 2. Switch the GPS module “ON” on the PolyPen device by following these steps in the PolyPen menu: · Select: Options > Settings > Device · Click on the check box for GPS (Fig. 39-A) · Wait until the GPS position is found. The GPS module is ready when the icon of the position flag, in upper menu, stops flashing (Fig.
39-B).
Page | 27
Fig. 39 GPS activation and Active GPS For proper function of the GPS module the PolyPen device may need a clear view of the sky to acquire satellite signal.
1. Perform the selected measurements. 2. Connect the PolyPen to the computer and open the SpectraPen software to proceed with download of the measured data. Data
measured with activated GPS module are downloaded with GPS coordinates (Fig. 40).
Fig. 40 Data with GPS coordinates.
Page | 28
9 WARRANTY TERMS AND CONDITIONS
· This Limited Warranty applies only to the PolyPen device. It is valid for one year from the date of shipment. · If at any time within this warranty period the instrument does not function as warranted, return it and the manufacturer will repair
or replace it at no charge. The customer is responsible for shipping and insurance charges (for the full product value) to PSI. The manufacturer is responsible for shipping and insurance on return of the instrument to the customer. · No warranty will apply to any instrument that has been (i) modified, altered, or repaired by persons unauthorized by the manufacturer; (ii) subjected to misuse, negligence, or accident; (iii) connected, installed, adjusted, or used otherwise than in accordance with the instructions supplied by the manufacturer. · The warranty is return-to-base only and does not include on-site repair charges such as labor, travel, or other expenses associated with the repair or installation of replacement parts at the customer’s site. · The manufacturer repairs or replaces faulty instruments as quickly as possible; the maximum time is one month. · The manufacturer will keep spare parts or their adequate substitutes for a period of at least five years. · Returned instruments must be packaged sufficiently so as not to assume any transit damage. If damage is caused due to insufficient packaging, the instrument will be treated as an out-of-warranty repair and charged as such. · PSI also offers out-of-warranty repairs. These are usually returned to the customer on a cash-on-delivery basis. · Wear & Tear Items (such as sealing, tubing, padding, etc.) are excluded from this warranty. The term Wear & Tear denotes the damage that naturally and inevitably occurs as a result of normal use or aging even when an item is used competently and with care and proper maintenance.
10 TROUBLESHOOTING AND CUSTOMER SUPPORT
In case of problems with the PolyPen visit FAQ on our websites (http://psi.cz/support/faq) or contact customer support by email to support@psi.cz , or contact your local distributor.
Page | 29
11 APPENDIX
11.1 PROGRAMMING CUSTOM INDEX IN POLYPEN
The SpectraPen software enables programming custom indexes, which can be used for wide range of calculation based on the measured spectrum. 1. Go to the main SpectraPen folder in your PC (Usually in Program Files). 2. Open the file Config > Formulas.txt. 3. Write your index into this .txt file and save it (Fig. 41). Index example: Transmitance:SAVI:Soil-Adjusted Vegetation Index: (1+0.5)*(Transmitance[780nm]-Transmitance[670nm])/(Transmitance[780nm]+Transmitance[670nm]+0.5) Transmitance source data SAVI name of the index in the SpectraPen software and in exported data Soil-Adjusted Vegetation Index full name of the index (not showed) (1+0.5)*(Transmitance[780nm]-Transmitance[670nm])/(Transmitance[780nm]+Transmitance[670nm]+0.5) equation for calculation; calculated from 670 and 780 nm of Transmittance spectra)
Fig. 41 Formulas configuration file adding new index. 1. Restart the SpectraPen Software. 2. The new index appears in the selected bookmark in the data (Fig. 42). 3. For export of this index choose the option “Computed values” and selected spectrum in the export table.
Page | 30
Fig. 42 Downloaded data with newly defined index.
11.1.1 FUNCTION DESCRIPTION
Different mathematical functions can be used in SpectraPen software syntax to create new custom formulas.
min, max min(value1, value2) value1 – number, variable, function value2 number, variable, function – only one value can be function! min(array) array array of numbers
example1: max(Transmitance example2: min(Irradiance) example3: min(Transmitance[760nm], max(Transmitance[450], Transmitance[680])) example4: max(Transmitance[550nm], (5+4)*4) __________________________________________________________________________ ln the natural (base e) logarithm of specified number
ln(value) value number, variable, function
example1: ln(5) example2: ln(Transmitance[760nm]) example3: ln(max(Transmitance[550nm], Transmitace[480nm])) example4: ln((5+4)*4) __________________________________________________________________________ log the logarithm of specified number in a specified base.
logB(value) B base – number value number, variable, function
example1: log2(5) example2: log5(Transmitance[760nm]) example3: log10(max(Transmitance[550nm], Transmitance[480nm])) example4: log10((5+4)*4) __________________________________________________________________________
Page | 31
sqrt the square root of a specified number sqrt(value) value number, variable, function
example1: sqrt(5) example2: sqrt(Transmitance[760nm]) example3: sqrt(max(Transmitance[550nm], Transmitance[480nm])) example4: sqrt(((5+4)*4) + 6) ____________________________________________________________________________ ^ – specified number raised to the specified power
value^power value number, variable, function power number, variable, function
example1: Transmitance[760nm]^ Transmitance[550nm] example2: min(Transmitance[760nm], Transmitance[550nm])^max(Transmitance[435nm], Transmitance[430nm]) example3: Transmitance[760nm]^0.5 ___________________________________________________________________________ integral – express the area under the curve of a graph of the function in the interval
integral(function_values, from, to) function_values input values for integral compute from,to limit values
example1: integral(IrradianceL, 360nm, 700nm) example2: integral(IrradianceE, 360nm, 700nm) * IrradianceE[450]
Page | 32
12 LIST OF FIGURES
Fig. 1 Device description…………………………………………………………………………………………………………………………………………………………..8 Fig. 2 Schema of reflectance measurement. ……………………………………………………………………………………………………………………………….9 Fig. 3 Reflectance standard Spectralon. ……………………………………………………………………………………………………………………………………10 Fig. 4 PolyPen calibration. ………………………………………………………………………………………………………………………………………………………11 Fig. 5 Indices table. ………………………………………………………………………………………………………………………………………………………………..11 Fig. 6 Calibration of the device. ……………………………………………………………………………………………………………………………………………….12 Fig. 7 Menu – Data. ………………………………………………………………………………………………………………………………………………………………..12 Fig. 8 Settings – Indices selection. …………………………………………………………………………………………………………………………………………….13 Fig. 9 Settings Graph ant Time………………………………………………………………………………………………………………………………………………13 Fig. 10 Settings LCD and Device …………………………………………………………………………………………………………………………………………….14 Fig. 11 About ………………………………………………………………………………………………………………………………………………………………………..14 Fig. 12 How to connect PolyPen with PC. ………………………………………………………………………………………………………………………………….15 Fig. 13 Control panel………………………………………………………………………………………………………………………………………………………………15 Fig. 14 System window. ………………………………………………………………………………………………………………………………………………………….16 Fig. 15 PSI USB device. ……………………………………………………………………………………………………………………………………………………………16 Fig. 16 Choose the driver from the USB disc. …………………………………………………………………………………………………………………………….16 Fig. 17 Complete installation. ………………………………………………………………………………………………………………………………………………….17 Fig. 18 Device connect……………………………………………………………………………………………………………………………………………………………17 Fig. 19 SW registration. ………………………………………………………………………………………………………………………………………………………….18 Fig. 20 SW connection. …………………………………………………………………………………………………………………………………………………………..18 Fig. 21 PolyPen connected………………………………………………………………………………………………………………………………………………………19 Fig. 22 Connection failed. ……………………………………………………………………………………………………………………………………………………….19 Fig. 23 Menu File. ………………………………………………………………………………………………………………………………………………………………….20 Fig. 24 Menu Device. ……………………………………………………………………………………………………………………………………………………………..20 Fig. 25 Menu Setup………………………………………………………………………………………………………………………………………………………………..20 Fig. 26 Menu Help………………………………………………………………………………………………………………………………………………………………….20 Fig. 27 Scope spectra. …………………………………………………………………………………………………………………………………………………………….21 Fig. 28 Option for list of data. ………………………………………………………………………………………………………………………………………………….22 Fig. 29 Marker function. …………………………………………………………………………………………………………………………………………………………22 Fig. 30 Zoom function. ……………………………………………………………………………………………………………………………………………………………23 Fig. 31 Switch to vegetation indices. ………………………………………………………………………………………………………………………………………..23 Fig. 32 Vegetation indices……………………………………………………………………………………………………………………………………………………….24 Fig. 33 Export table………………………………………………………………………………………………………………………………………………………………..24 Fig. 34 Export Computed data selection and choosing of exported values. …………………………………………………………………………………25 Fig. 35 Online Control. ……………………………………………………………………………………………………………………………………………………………25 Fig. 36 Setting of reflectance or absorbance measurements in online control. ………………………………………………………………………………26 Fig. 37 Settings of online control. …………………………………………………………………………………………………………………………………………….26 Fig. 38 Firmware update running. ……………………………………………………………………………………………………………………………………………27 Fig. 39 GPS activation and Active GPS ………………………………………………………………………………………………………………………………………28 Fig. 40 Data with GPS coordinates……………………………………………………………………………………………………………………………………………28 Fig. 41 Formulas configuration file adding new index. ……………………………………………………………………………………………………………..30 Fig. 42 Downloaded data with newly defined index……………………………………………………………………………………………………………………31
Page | 33
Documents / Resources
 | Poly Pen Device |
References
- mailto:support@psi.czpsi.cz
- psi.cz/support/faqpsi.cz
- Photon Systems Instrumentswww.psi.cz
- Photon Systems Instrumentswww.psi.cz
- User Manualmanual.tools