User Manual - Pembroke Instruments
Contents
1. SERIES IMAGING SPECTROMETERS AND SPECTRONON SOFTWARE User Manual Document Change History Version Number Date Contributor Description V1 0 3 12 07 Cws Document Creation V1 1 9 12 08 Cws Updated V1 2 5 28 09 RCS Updates Updated 5 28 2009 Copyright and License Spectronon Resonon s hyperspectral image acquisition and analysis software c 2005 2007 Resonon Below are thanks and credit to underlying libraries as well as links to their licenses The Spectronon EULA follows Spectronon is built proudly and primarily with Python Python license www python org download releases 2 4 2 license learn more www python org Spectronon was written by Resonon and employs the fine libraries listed below each with links to the accompanying license numpy BSD license http en wikipedia org wiki BSD license learn more http www numpy org wxPython wxWidgets license http wxwidgets org about newlicen htm learn more http www wxpython org matplotlib matplotlib license http matplotlib sourceforge net license html learn more http matplotlib sourceforge net pywin32 Python license http www python org download releases 2 4 2 license learn more http sourceforge net projects pywin32 PIL c Secret Labs AB and Fredrik Lundh http www pythonware com products pil license htm learn more http www pythonware com products pil The Full copyright is included at the bottom of th2. 8 Then press the Set Black Body Temperature button 14 When prompted enter the Color Temperature of the reference light source In order to produce absolute units of radiance keep the exposure settings of the system at the same level they were at when the datacube of interest was collected Position the imager to ensure that the reference light is filling the field of view Collect a data cube in Radiance mode and find the peak intensity value Scale this number by the intensity reading of your reference light in W m sr Using the Unit Conversion tool within the Process to new Cube menu produce a new datacube using this number as the conversion factor Collecting and Saving Data Collecting Data To collect data click the Start and Stop Recording button 14 The stage will begin moving and lines of image data will be displayed the data window default the image data is represented by a True Color rendering of the scene More information on Renders and Filters is available in Chapter 4 To stop press the button again The stage should move back to its starting location To adjust the starting location of the stage press the Move Stage buttons shown below Lb Once the Start Recording button is pressed data recording will continue until the button is pressed again If you would like to record a specific number of frames enter in the desired number of frames in the Frame Number window show below lo
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4. If zero is entered the software will record indefinitely A non zero number allows the software to allocate the necessary resources for the data which improves performance A scan can be stopped at anytime using the stop button Saving Data Once data has been collected it is temporarily stored and represented in the left side of Spectronon called the Resource Tree as shown below 15 eimialalcie eel Se Current Scan Current Scan True Color To save the data right click on the Current Scan item colored blue above Select Save Cube or Save Cube As to save to disk You may also select the menu item Cube gt Save Cube instead of the right clicking method If you would like to only save a portion of the cube click the Select Areas tool on the toolbar Select the portion of the image you would like to save by dragging a square over the area Right click inside of the square and select Crop Into New Cube Alternatively you may select the menu item Selection Crop Into New Cube Once this is done right click on the newly generated cube in the Resource Tree and save as described above Saturation Alarm The Saturation Alarm Ol warns the user of potentially erroneous data due to detector saturation or bit overflow This icon will turn yellow when saturation or bit overflow occurs Detector saturation happens because too much light is incident on the detector for the given gain and exposure settings Satura
5. To Flip or Rotate the image use these tools Selecting Regions of Interest A Region of Interest is a selectable group of pixels within the datacube The associated spectra from these pixels can then be saved averaged or copied to the clipboard To select a Region of Interest select either the Or tools from the menu bar Click and drag a rectangle of interest with the first tool or click and drag any shape with the second Once selected right click within the selected areas for options Spectral Plot and XY Plotter Windows Plotting Data to the Spectral Plot and XY Plotter Windows The Spectral Plot window shows the spectrum of a selected pixel or the spectrum open in the Resource Tree far left side of the Spectronon window To show the spectrum of a pixel within the Render select the Inspector tool e Click a point inside of the Render to see the spectrum of that pixel One can also click and hold while dragging to update the Spectral Plot window continuously The X and Y Plotter Windows show cross sections of the current Render X and Y cross sections respectively at the point of the Inspector tool pointer The black line in the X or Y Plotter window represents the location of the Inspector tool pointer in the alternate dimension Y or X respectively 19 Zooming and Panning Zooming and Panning function in the plotting windows just as in the render window To zoom in select the Zoom In tool from the toolbar
6. 6 U S GOVERNMENT END USERS The Software is a commercial item as that term is defined in 48 CFR 2 101 Oct 2006 consisting of commercial computer software and commercial computer software documentation as such terms are used in 48 CFR 12 212 Oct 2006 and 48 CFR 227 7202 Oct 2006 Consistent with 48 CFR 12 212 48 CFR 27 405 b 2 and 48 CFR 227 7202 all U S government end users acquire the Software with only those rights as set forth in this Agreement 7 DISCLAIMER OF WARRANTY THE SOFTWARE IS PROVIDED AS IS WITH ALL FAULTS TO THE EXTENT PERMITTED BY LAW RESONON AND RESONON S DISTRI BUTORS and LI CENSORS HEREBY DISCLAIM ALL WARRANTIES WHETHER EXPRESS OR IMPLIED INCLUDING WITHOUT LIMITATION WARRANTIES THAT THE SOFTWARE IS FREE OF DEFECTS MERCHANTABLE FIT FOR A PARTICULAR PURPOSE AND NON INFRINGING YOU BEAR THE ENTIRE RISK AS TO SELECTING THE SOFTWARE FOR YOUR PURPOSES AND AS TO THE QUALITY AND PERFORMANCE OF THE SOFTWARE THIS LIMITATION WILL APPLY NOTWITHSTANDING THE FAILURE OF ESSENTIAL PURPOSE OF ANY REMEDY SOME JURISDICTIONS DO NOT ALLOW THE EXCLUSION OR LIMITATION OF IMPLIED WARRANTIES SO THIS DISCLAIMER MAY NOT APPLY TO YOU 8 LIMITATION OF LIABILITY EXCEPT AS REQUIRED BY LAW RESONON AND ITS DISTRIBUTORS DIRECTORS LICENSORS CONTRIBUTORS AND AGENTS COLLECTIVELY THE RESONON GROUP WILL NOT BE LIABLE FOR ANY INDIRECT SPECIAL INCIDENTAL CONSEQUENTIAL OR EXEMPLARY DAMAGES ARISING OUT OF OR IN ANY WAY RELATI
7. Click in the appropriate plot window or click and drag a rectangle in the plot window to zoom to that area Select the Zoom Out tool and click to zoom out To Pan select the Pan tool then click and drag in the plot window Clearing the Spectral Plot Window To clear the Spectral Plot or XY Plotter Windows select the Plot menu item then Clear opectral Plot This is useful to force a rescale of the Spectral Plot Renders and Filters A Render is a 2D representation of a datacube This representation can be monochrome or full color be one or more bands of a datacube or contain the results of analysis A Filter is a set of rules that apply to a Render to alter its appearance In this section two examples of using Renders and Filters will be presented The Color Infrared CIR Render The Color Infrared Render maps an infrared band 860 nm of the datacube to the red color channel of the display a red band 650 nm to the green color channel and a green band 550 nm to the blue color channel This Render may be useful in viewing scenes containing vegetation as chlorophyll is very reflective at 860 nm making plant life appear red in this Render To try the CIR Render open the datacube eaf small bip located in the C Program Files Spectronon examples folder The datacube will show up in the left side Resource Tree and a True Color render of the datacube will appear Right click on the leaf_small object in the Resource Tree and se
8. Once a spectrum has been added to the Spectra List in the Resource Tree by encircling the Region of Interest with the Lasso or Rectangular Area tool and right clicking in its center it can be save to disk as either a Spectrum file for opening later in Spectronon or as text for importing into Excel or other graphing program Similarly the entire Spectral Plot window can be saved as an image or as text This is done by choosing the Plotters menu item then choose the plot you wish to save then selecting either Save as Image or Save as Text 21 Advanced Data Manipulation and Analysis This chapter provides an overview of advanced data analysis features of Spectronon Topics in this chapter are e Binning e Spectral Correction Spectral Angle Map Render e Adding Functionality Through Plugins Cube Tools Cube tools are datacube processing methods that return a new datacube as a result This resultant datacube may be a resampling of the original cube like the Binning example below or it may be an entirely different cube such as a colorspace conversion tool Binning The Binning tool is used to average spectral or spatial channels together to reduce the size of the cube or to increase the signal to noise ratio To use the Binning tool right click on the cube of interest in the Resource Tree Select Process to New Cube gt Utilities gt Bin Cube Alternatively you may select the menu item Proc
9. is complete press the Response Correction Cube button This will instruct you to place the white reference e g Teflon in front of the imager Make sure the reference target fills the field of view of the imager Press OK to continue Once complete the Response Correction button will show a red checkmark The data will now be automatically corrected for the illumination spectrum and instrument response The resultant data is in units of 0 4095 representing Reflectance from 0 100 In Float Mode covered in Chapter 6 the units are 0 1 0 Anytime the aperture gain exposure time or light source changes the Dark Current and Response Correction collection processes as described above must be repeated Radiance In Radiance Mode data is recorded in relative units of Radiance To produce absolute units of radiance additional steps are required This will be discussed later In order to use Radiance Mode a black body light source with a calibrated color temperature or a radiance calibration standard is necessary First set up the imager so the field of view is filled by the reference light source The intensity of the reference light should be adjusted to approximate the intensity of the scene illumination Set your exposure using the Autoexposure feature as described above Cover the lens and collect a Dark Current correction cube Then collect the Radiance Correction cube by pressing the Response Correction Cube button
10. the exposure and gain 12 Adjusting the Aperture The aperture of most objective lenses can be adjusted across a wide range For the Pika ll f s below f 3 are not recommended and for the f Zs below 1 2 are not recommended because this will increase the amount of scattered light inside of the instrument Choosing an f is a trade the higher the f the less light the instrument will collect but the depth of focus of the instrument will increase A smaller f means more light will be collected but the depth of focus will be shorter For cases in which the user wishes to post correct the data from a reference object in the scene for example when the user is using the Rotation Stage and the Teflon reference does not fill the entire field of view it is required that the f be set no lower than 1 4 for good results Again after adjusting the aperture you will need to run AutoExposure to set optimum exposure and gain levels Modes Pika imaging spectrometers can collect data in 3 modes Raw Data Reflectance and Irradiance To select the mode of operation navigate to the Mode menu item and select the desired mode Each mode is described below Raw Data In Raw Data mode data is recorded without any processing The result is thus a product of the reflectance of the object the spatial and spectral distribution of the lightning and the response of the instrument Reflectance For many applications the absolu
11. NG TO THIS AGREEMENT OR THE USE OF OR INABILITY TO USE THE SOFTWARE INCLUDING WITHOUT LIMITATION DAMAGES FOR LOSS OF GOODWILL WORK STOPPAGE LOST PROFITS LOSS OF DATA AND COMPUTER FAILURE OR MALFUNCTION EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGES AND REGARDLESS OF THE THEORY CONTRACT TORT OR OTHERWISE UPON WHICH SUCH CLAIM IS BASED THE RESONON GROUP S COLLECTI VE LIABILITY UNDER THIS AGREEMENT WILL NOT EXCEED THE GREATER OF 500 FIVE HUNDRED U S DOLLARS AND THE FEES PAID BY YOU UNDER THIS LICENSE IF ANY SOME JURISDICTIONS DO NOT ALLOW THE EXCLUSION OR LIMITATION OF INCI DENTAL CONSEQUENTIAL OR SPECIAL DAMAGES SO THIS EXCLUSION AND LIMITATION MAY NOT APPLY TO YOU 9 MISCELLANEOUS a This Agreement constitutes the entire agreement between Resonon and you concerning the subject matter hereof and it may only be modified by a written amendment signed by an authorized executive of Resonon b Except to the extent applicable law if any provides otherwise this Agreement will be governed by the laws of the State of Montana U S A excluding its conflict of law provisions and in respect of any dispute which may arise hereunder you consent to the jurisdiction of the federal and state courts sitting in the State of Montana c This Agreement will not be governed by the United Nations Convention on Contracts for the International Sale of Goods d If any part of this Agreement is held invalid or unenforceable that part will be construe
12. al Imaging or imaging spectroscopy refers to the creation of a digital image containing very high spectral color resolution Each spatial point pixel in a hyperspectral image represents a continuous curve of incoming light intensity versus wavelength The data can also be interpreted as a stack of images with each layer in the stack representing the scene at a different wavelength 9000 8000 7000 600 700 800 900 Wavelength nm Hyperspectral imaging has a long heritage as a remote sensing tool operating from satellites and airplanes In this capacity it has proven itself as a useful tool for scene discrimination the Pika series imaging spectrometers provide this powerful capability in a cost effective compact package Requirements Windows XP Service Pack 2 512 of RAM 1 Gig or more recommended Intel amp Pentium 4 2 0GHZ or compatible processors AGP video card with 64 MB video memory 32 bit standard PCI slot for IEEE 1394 card Firewire 800 port with Texas Instruments OHCI Compliant IEEE 1394b Host Controller Installation This chapter covers e Installing the Hardware Installing the Software Installing the Hardware The Pika series spectrometers are inescanning instruments meaning that they collects one line of image data per frame In order to collect a 2D image a Pika imaging spectrometer or the object to be imaged must be physically moved or scanned Resonon sells two options for scann
13. as rs ues ste An 21 Advanced Data Manipulation and 1 22 S w 22 D n ZZ Spectral Correction E E EE SEES E I 23 Radidlc COLT OCI OU ina a a E E EE E E E E E E 23 Cube M oro dao NN 23 The Spectral Angle Map cube tool sse 23 Advanced Seit Illo S 0099922522452 Vau Doa EEEE Pun Va 26 PEENI AA T EE diua AA ERA EMEN NNNM MESSEN E M BEI NEUE 26 26 I TITIUS Tnww0 wwn n 0 n H 26 Dpoonrlm ee 26 EVIDENCE 26 Kecording UT isciani nieren i e aiaiai aeann i ie ri iniii 26 Slope and Intercept CallDration ceti te N E eat Da AONE 2 T T QM ay SEPS PET F PAME EEEE e UM MU 27 ISCCONHUS PEOR S O 27 A a e A EA I AE A A A O E A A E AA E 2i Fi
14. d to reflect the parties original intent and the remaining portions will remain in full force and effect e A waiver by either party of any term or condition of this Agreement or any breach thereof in any one instance will not waive such term or condition or any subsequent breach thereof f Except as required by law the controlling language of this Agreement is English g You may assign your rights under this Agreement to any party that consents to and agrees to be bound by its terms Resonon may assign its rights under this Agreement without condition h This Agreement will be binding upon and will inure to the benefit of the parties their successors and permitted assigns End Spectronon EULA The Python Imaging Library PIL is Copyright 1997 2006 by Secret Labs AB Copyright 1995 2006 by Fredrik Lundh By obtaining using and or copying this software and or its associated documentation you agree that you have read understood and will comply with the following terms and conditions Permission to use copy modify and distribute this software and its associated documentation for any purpose and without fee is hereby granted provided that the above copyright notice appears in all copies and that both that copyright notice and this permission notice appear in supporting documentation and that the name of Secret Labs AB or the author not be used in advertising or publicity pertaining to distribution of the software with
15. deo Update SCG T H 2 Pow PEE 28 Introduction Resonon s Pika imaging spectrometers are compact high fidelity digital instruments for industrial and scientific applications Spectronon is a powerful hyperspectral data collection and analysis software package Spectronon s data collection tools are highly integrated with the Pika imaging spectrometers to streamline the collection of spectral images Spectronon s data viewing and analysis functions can also be used without a Pika imaging spectrometer For data viewing and analysis Spectronon is easy to learn offers efficient workflow and is highly extensible by the user for custom applications This User Manual covers the installation and use of Pika series imaging spectrometers and Spectronon software Due to the tight integration between the Pika series imaging spectrometers and Spectronon both topics are covered together Users of Spectronon without Pika can skip sections specific to the Pika 1 Topics covered in this manual e Introduction to Hyperspectral Imaging Setting up the Imaging Spectrometer and Additional hardware Installing Spectronon Software e Collecting Hyperspectral Data e Viewing and manipulating Data e Advanced Features of Spectronon Software e Advanced Data Manipulation and Analysis Brief Introduction to Hyperspectral Data Hyperspectr
16. e and select Process to New Cube gt Utilities Correct from Spectrum or select menu item Cube Process to New Cube gt Utilities Correct from Spectrum In the resulting dialog select the Spectrum you created before and press OK The entire cube will be corrected Radiance Correction This procedure is used to correct a datacube for the response of the instrument and leave the data in terms of relative radiance To perform this procedure select the Correct from Cube tool from the Process to New Utilities menu item Select the correction datacube and input the blackbody temperature of the correction cube A new corrected cube will be generated For more information on obtaining a correction cube for use in this procedure please contact Resonon Cube Tools Example The Spectral Angle Map cube tool The Spectral Angle Map SAM function is a powerful analysis tool for computing the similarity between two spectra SAM returns an n dimensional angle that represents the similarity of the spectra of a pixel in a datacube to a reference spectrum where n the number of spectral bands in the datacube This technique is relatively insensitive to the intensity of the compared spectra it is comparing the shape of the spectra instead To use SAM first create a Region Of Interest ROI to define the reference spectrum To do this use the Lasso tool to encircle a small area of the red center vein of the leaf small b
17. e focus of the microscope while viewing the focusing object through the microscope s eyepieces Then adjust the focus on the camera port of your microscope until the instrument is focused simultaneously Cables Before installation of the software please connect the USB Stage Controller and the Pika II via the provided Firewire 800 cable to your computer Lighting Proper lighting is very important to collecting high fidelity data A brief introduction to lighting techniques is covered in Chapter 3 Installing the Software Resonon s hyperspectral data collection and analysis software Spectronon provides the user interface for collecting data from Pika spectrometers The software also includes data viewing and manipulation functionality which can be used without a Pika spectrometer on any hyperspectral data of the proper format bil bip or bsq with an ENVIO formatted header file To use the software for data acquisition the Pika imaging spectrometer and scanning stage controller must be plugged in before the installation process begins If Spectronon has been installed previously without the Pika or scanning stage controller plugged in the software must be reinstalled with those units plugged in before they can be used Once installed Spectronon can be run with or without the hardware attached First download Spectronon software from www resonon com downloadPro A username and password are included with your spectrom
18. esonon for support for the current patch Collecting Data This chapter covers Lighting Fundamentals e Using the Autoexposure feature Focusing the Pika Il e Dark Current and Response Correction e Collecting and Saving Data e Adjusting the Scanning Stage settings Lighting Fundamentals Proper lighting is essential in the process of collecting high fidelity hyperspectral data The three most important factors for lighting are 1 Stable spectral stability and intensity stability 2 Diffuse 3 Spectrally Continuous not fluorescent or discharge Halogen lights are good inexpensive sources Incandescent lamps are also acceptable but are not as bright as halogen Fluorescent or discharge lamps contain sharp spectral features of high intensity at some wavelengths and low intensity at other wavelengths These lamps are not recommended as they do not provide sufficient illumination at many of the wavelengths of interest If the blue and UV spectral regions are of particular importance a high color temperature gt 4500 K or Daylight halogen bulb should be used as most conventional halogen bulbs do not emit much light in the low blue UV region To improve the stability of halogen or incandescent lights let the lights warm up for at least 5 minutes prior to collecting data Additionally a regulated power supply for the lights is highly recommended To diffuse the light sources ground glass plates or plastic diffu
19. ess to New Cube gt Utilities Bin Cube This is followed by a dialog box requesting the Binning parameters Spectral binning reduces the spectral resolution of the data Sample binning reduces the spatial resolution of the data in the X axis unless the data has been rotated on screen and Line binning reduces the Y axis Spatial dimension The Float Mode check box allows the data to be returned as a floating point datacube For more information on Float Mode vs Integer Mode please see Chapter 5 Advanced Settings gt Float Mode After selecting OK in the Binning parameter dialog box the binned datacube will be returned to the Resource Tree 27 Spectral Correction The Spectral Correction cube tool is used to correct a datacube for the response function of the imager and the spectral component of the illumination source in situations where the reflectance reference does not cover the entire field of view of the imager To use this tool the datacube must contain a reflectance reference It is also required that the aperture of the imager be set at f 4 or higher First create a Spectrum object in the Resource Tree from the reflectance reference in the datacube To do this choose the appropriate ROI Tool select the reflectance reference in the image and right click to Make ROI and Mean The mean spectra from your selected ROI will be added to the Spectra list in the Resource Tree Right click on the datacube to correct in the Resource Tre
20. eter or contact Resonon if you have lost your username and password To install Spectronon double click Setup exe and follow the screens below Spectronon Setup Installation Folder E Setup will install Spectronon in Ehe Following Folder install in a different Ms Folder click Browse and select another Folder Click Next Eo continue lestination Folder C Program Files Spectronon Browse Space required 21 3 Space available 3 256 Cancel Click Next shortcuts az Accessories ActiveState Visual Python Administrative Tools Adobe Adobe Acrobat 4 0 Atmel AVR Tools Autot AD 2000 AVAMTES Software Data Batch zip Toolkit ll Syst Click Install Hardware Installation The software you are installing for this hardware Hesonan Scanning Stage has not passed Windows Logo testing to verify its compatibility with Windows Tell me why this testing Is important Continuing your installation of this software may impair or destabilize the correct operation of your system either immediately or in the future Microsoft strongly recommends that you stop this installation now and contact the hardware vendor for software that has passed Windows Logo testing Lontinve Angway STOP Installation Click Continue Anyway Hardware Installation The software vou installing For this hardware CMU 1344 Digital Camera D
21. evice has not passed Windows Logo testing bo verify compatibility with Windows XP Tell me why this testing iz important Continuing your installation of this software may impair or destabilize the correct operation of your system either immediately or in the future Microsoft strongly recommends that you stop this installation now and contact the hardware vendor for software that has passed Windows Logo testing Continue Anyway STOP Installation Click Continue Anyway Once finished please restart your computer Spectronon software is now installed Calibration Before using your new Pika spectrometer you will need to put in the calibration values for your spectrometer These values are included on a sheet with your spectrometer If you have lost your calibration values please contact Resonon To install the calibration values for your Pika Spectrometer Window gt Preferences gt Imager gt Advanced This will bring up the window below Preferences Rendering IImager Advanced Warnings Plotters Imager Advanced Interface Slope Intercept Type in the Slope and Intercept values for your Pika spectrometer and click the set buttons for each Note Windows XP Service Pack 2 contains a bug that limits to maximum bandwidth of Firewire 800 In Spectronon this bug limits the maximum framerate of the Pika Il to 7 5 FPS Patches are available but change frequently Please contact R
22. ing a Rotation Stage which is a tripod based unit intended for outdoor use and a Linear Stage which is intended for scanning objects under controlled lighting Rotation Stage First attach the Rotation Stage mounting bracket to the bottom of the Pika imaging spectrometer using the provided screws low head 1 8 4 20 as shown below oecond attach the Pika imaging spectrometer to the Rotation Stage and tighten the set screw in the Rotation Stage mounting bracket ESONON Translation Stage To use the translation stage attach mounting posts to the mounting holes in the base of the Pika imaging spectrometer then insert the mounting posts to the post holders on the stage frame Microscope Option First screw in the C Mount Microscope adapter into the threads on the front of the Pika imaging spectrometer Note If your Pika spectrometer was purchased with an objective lens as well as a C Mount Microscope adapter you will have to remove the objective lens before you can attach the Microscope adapter This should be done in a low dust environment to decrease the chances of getting particulate contamination in the slit This is shown below i i uL a a EEUU MN C Mougt Microscope Adaptere Second mount the Pika 1 on the camera port of your microscope and lock down the set screw in the C Mount Microscope adapter Adjust th
23. ions please contact Resonon for more information The lower the framerate the more integration time the imager has increasing the signal to noise ratio SNR but also increasing the amount of time necessary to collect data To adjust the Framerate of the imager go to Window in the menu bar then Preferences gt Scanner Gain and Shutter The gain and shutter settings of the imager are determined automatically during the AutoExposure mode To override or adjust these settings go the Window gt Preferences Scanner It is necessary to re record Dark Correction and Response Correct cubes after adjusting these settings Binning Binning of the datacube increases the SNR of the data decreases its size but decreases the spectral or spatial resolution of the data To adjust the binning select Window gt Preferences gt Scanner Calibration Cube Sizes The size of the calibration cubes used in the data correction may be adjusted at Window gt Preferences Scanner The size of the Dark Correction cube does normally not need to be adjusted It may be necessary to increase the size of the Response Correction cube if the reflection standard shows obvious spatial variability Recording Modes Four options for recording data are available To change these options see Window gt Preferences gt Imager The options are reviewed below 26 Buffer Mode The Buffer Mode is the method of buffering data as it streams from the imager In Memor
24. ip image you may want to zoom in first as shown below 23 Right click inside the selected area and select Make ROI and Mean Now right click on the eaf small bip in the Resource Tree and select Process to new Cube gt Classification 2 SAM In the Member count dialog input the number of Member Spectra you wish to classify In this case this number is one Next in the Member Spectrum O dropdown select the leaf small spec O spectrum that you created and click OK The controls for this Render will show up on the right side of Spectronon as shown below luti 5AM Member Count EH 3 Member 0 spec 0 Thresh D o 1000 Jg Member 1 v Thresh 1 00000 3 Member Z l Thresh 2 0 0000 2 Stretch Enter 0 1 for a Threshold Now press update The resulting render will appear To see the raw data from the SAM algorithm use the Inspector tool and the X or Y Plotter window shown 24 e O H 2 leaf small True Color leaf small Spectral Angle Map Spectral Plot plotter vplotter Plotter Target lea small spec 0 Spectrum 1 red Target w Spectrum 2 green Target Y Spectrum 3 You may select a Live Update to interactively select a threshold This opti
25. is notice SPECTRONON END USER SOFTWARE LICENSE AGREEMENT Version 1 1 April 2007 The executable code version of Spectronon or SpectrononPro and all related media printed material electronic documentation and other documentation collectively the Software is made available to you under the terms of this RESONON END USER SOFTWARE LICENSE AGREEMENT AGREEMENT BY INSTALLING COPYING OR OTHERWISE USING THE SOFTWARE YOU ARE CONSENTING TO BE BOUND BY THIS AGREEMENT IF YOU DO NOT AGREE TO THE TERMS AND CONDITIONS OF THIS AGREEMENT DO NOT INSTALL OR USE ANY PART OF THE SOFTWARE DURING THE SOFTWARE INSTALLATION PROCESS AND AT LATER TIMES YOU MAY BE GIVEN THE OPTION OF INSTALLING ADDITIONAL COMPONENTS FROM THIRD PARTY SOFTWARE PROVIDERS THE INSTALLATI ON AND USE OF THOSE THIRD PARTY COMPONENTS MAY BE GOVERNED BY ADDITIONAL LICENSE AGREEMENTS 1 LICENSE GRANT Resonon Inc a Montana business corporation Resonon grants you a non exclusive license to use the executable code version of the Software This Agreement will also govern any software upgrades provided by Resonon that replace and or supplement the original Software unless such upgrades are accompanied by a separate license in which case the terms of that license will govern 2 DESCRIPTION OF OTHER RIGHTS AND LIMITATIONS Maintenance of Proprietary Notices You may not remove or alter any trademark logo copyright or other proprietary notice in or on the Software This licen
26. lect Make New Rendering gt Tri Band gt Color Infrared This can also be accessed by the menu item Cube gt Make New Render gt Tri Band gt Color Infrared 20 Resource Tree Cubes leaf small True Color Save Cube Save Cube As Cube Get Info Make Mew Rendering True Color Process ta new Cube Color Infrared Single Band k Tri Band Euclidian Distance Frame Number ht The Color Infrared render will appear with the default Two Percent filter To switch filters click on Rendering button on the toolbar and select Change Filter from the pull down menu Choose from rendering options given You should see the view of the render change slightly The Two Percent filter is a contrast enhancement where the brightest 2 of pixels are set to 1 0 brightness white and the darkest 2 pixels set to 0 0 brightness black The middle 96 of the pixels are then scaled from O to 1 0 brightness A Linear filter is similar but sets the brightest and darkest pixels to 1 0 and 0 0 respectively This could be thought of as a 0 stretch The Stretch Filter also available in the filter menu allows the user to interactively set the upper and lower stretch percentages Note that these functions do not change the data just its rendering your screen Another example of using Renders and Filters is covered in Chapter 5 Saving Spectra Plots and Renders
27. on is processor intensive and is only recommended on higher performance computers Note for scanned datacubes that have not yet been saved the Live Update feature may not be available under default settings See Chapter 6 Advanced Settings Disk Memory Mode for more information Next we will render the SAM data in a grey scale Right click on the MultiSam cube in the Resource Tree Select Make New Rendering gt Single Band gt By Band Number This will produce a rendering where the dark pixels are very similar in spectra to your Member spectra and the light pixels are quite dissimilar Generally one would like the reverse rendering This can be obtained by checking the Inverse box which will yield a rendering similar to that shown below leaf small True Color leaf small Spectral Angle Spectral Plot plotter plotter Platter 1 00 0 75 0 25 0 00 Pixel Number Spectral Angle Map Target leaf small spec 23 Advanced Settings This chapter provides an explanation of the advanced settings of Spectronon Imager Settings e Stage Settings Imager Settings Framerate By default the framerate of the imager is set to 30 frames per second FPS The framerate can be set as high as 60 FPS at normal detector settings and as low as 1 875 FPS The imager can be set at higher frames rates for specialty applicat
28. out specific written prior permission SECRET LABS AB AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS IN NO EVENT SHALL SECRET LABS AB OR THE AUTHOR BE LIABLE FOR ANY SPECIAL INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE DATA OR PROFITS WHETHER IN AN ACTION OF CONTRACT NEGLIGENCE OR OTHER TORTIOUS ACTION ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE Contacts and Support Customer support forum www spectronon com bb Online Documentation www spectronon com Table of Contents GIL O Pt c 1 Bet Introduction to Hyperspectral MOANA 4 4 atta uA ans dais Dueb AR 1 PRS EUs TAN 2 NTS CA AUTO cesses cu M 3 Wins the Te Ay ANG as ors 3 on oes Oe 6 ev HIR 10 Lien a Tondamenal NN TERT 10 Preparing Tor Data n perte 11 dor AAE TEA 11 Unio a ce reper et cass digs pts dena idu dui ua ita duct NE UNES Iu S 12 Adjusting the Aperture OTT I3 ISS E E N EE A E A NEE E ee 13 E EE E E
29. s used to adjust the time delay in between steps while positioning the stage It should normally be set to 0 0 as a non zero setting will limit the line rate of the system Interface Video Update Speed On lower performance computers the responsiveness and line rate of Spectronon may be increased by lowering the update rate of the data display To adjust this setting go to Window Preferences Interface 21 Problem Resolutions If you have questions or are experiencing problems regarding your Pika imaging spectrometer or Spectronon please start your inquiry at http www spectronon com The FAQ section may have the answer you or looking for Also the solutions to many problems might also be found at the Forum section at http www spectronon com bb If you do not see the answer to your question post your question and a Resonon support member will answer it as soon as possible 28
30. se does not grant you any right to use the trademarks service marks or logos of Resonon or its licensors Distribution You may not distribute copies of the Software to third parties Transfer You may permanently transfer all of your rights under this Agreement provided the recipient agrees to the terms of this Agreement You may not rent lease loan or sublicense the Software Prohibition on Modification etc Except as permitted by applicable law notwithstanding this Agreement you may not modify translate or create derivative works from the Software Compliance with Law You must comply with all applicable laws regarding use of the Software 3 PROPRIETARY RIGHTS Resonon for itself and on behalf of its licensors hereby reserves all intellectual property rights including but not limited to copyrights in the Software except for the rights expressly granted in this Agreement 4 TERMINATION If you breach this Agreement your right to use the Software will terminate immediately and without notice but all provisions of this Agreement except the License Grant Paragraph 1 will survive termination and continue in effect Upon termination you must destroy all copies of the Software 5 EXPORT CONTROLS This license is subject to all applicable export restrictions You must comply with all export import laws and restrictions and regulations of any United States or foreign agency or authority relating to the Software and its use
31. sers are recommended Integrating spheres are ideal but expensive and often impractical Diffusers should be positioned between the light sources in a manner to maximize the uniformity of the illumination on the object 10 Preparing for Data Collection To begin the data collection process ensure that the imager and scanning stage are plugged in and that the lights are on and properly warmed up Launch Spectronon The imager and stage controls should be active not grayed as shown below Bec Focusing Place the Spectralon or Teflon sheet in the field of view of the imager in place of the object to be imaged Press the AutoExposure button shown below 3 This function will automatically set the exposure time and gain setting of the imager It is helpful to do this before focusing to make sure the camera settings are adjusted such than you can see the object under your lighting conditions Once the AutoExposure is complete press the Focuser button This function shows live data from the imager It is used to focus the imager and also to place the Spectralon or Teflon in the proper location for collecting correction data By waving your hand under the imager near the white reference you should see movement in the main Spectronon window Place the object to scan in the field of view of the instrument using the data window for feedback Unscrew the lock ring on the objective lens of the imager as
32. shown below 11 Screw the main body of the objective lens in or out until the lines in the data window begin to sharpen For assistance in focusing click on the Inspector tool and then click on the data screen over the sharpest spatial features Then click on the YPlotter tab on the right side of the Spectronon window Your screen should look like the screencapture below REF semis o s 3 Fons Last Frame 7 Spara Plot plotter HoStreiclh When Focuser is running the YPlotter graph shows the Y cross section of the live data opatial features of the object show up as dips or rises in the cross section Focus the imager to maximize the contrast steepness of these features You may use the Zoom and Pan tools on the toolbar to zoom in and navigate the features in the graph For objects without fine spatial features to use for focusing it is recommended that graph paper or another suitable target with sharply contrasted features be placed on top of the object Using AutoExposure Position the Spectralon or Teflon watching the data window to fill the entire field of view of the imager Because of its high reflectance the white reference will look much brighter in the data window than its surroundings Interpreting the live data is an acquired skill but is learned quickly Once the white reference fills the field of view of the imager press the AutoExposure button again to properly set
33. te Reflectance of the scene is desired Because all light sources including halogen lamps and the sun have spectral structure it is necessary to remove the spectral component of the light source from the collected data Additionally spectral imagers have non uniform spectral and spatial response which also must be removed from the data In order to do this data from a uniform reference is collected A flat sheet of TeflonO is an inexpensive reference with a nearly flat spectral reflection near 95 95 However for high fidelity applications it is recommended to use a Spectralon www labsphere com panel instead The first step in collecting Reflectance data is to set the exposure using Autoexposure as described in the preceding section Next a Dark Current Correction Cube is necessary Press the Dark Current button i 13 You will be instructed to cover the lens of the to block all incoming light This is best done with the included lens cap Once the lens is covered select OK After recording this data the Dark Current button will show a red checkmark indicating that the dark current noise of the imager will be automatically removed from the data g Next a Response Correction Cube must be collected Users of the Rotation stage for which the white reference does not fill the entire field of view Skip this step Correcting the data in this case is explained in Chapter 5 Once the collection of the Dark current
34. ted data is evident by flat topped spectra It is recommended to run AutoExposure again to solve this problem Bit overflow occurs when a reflectivity greater than 100 is reported Most likely this is caused by data noise while recording scenes of reflectivity near 100 where the noise pushes values over the 100 threshold It can also occur when faceted sample produces a glint from a non diffuse light source directly into the scanner or it may be caused by light source fluctuations or a poorly recorded Response Correction file It is recommended to record a new Response Correction file when bit overflow occurs 16 Adjusting the Scanning Stage Once data has been collected examine the image to determine if the aspect ratio the ratio of the X dimension scale to the Y dimension scale is correct If the image looks compressed in the direction of the scan the stage step size is too large If the image looks stretched in the direction of the scan the stage step size is too small To adjust the step size find Window in the Menu bar and select Preferences Find Stage in the tree and select it Change the Steps Per Frame setting until the aspect ratio is correct Scanning an image of a circle is often useful for setting the aspect ratio correctly 17 Viewing and Manipulating the Data This chapter includes the following topics Opening a Datacube Zoom Pan and Rotate Tools Selecting Regions of Interest Spectral Plot and XY Plo
35. tter Windows Renders and Filters Saving Spectra Cubes and Renders Opening a Datacube To open a datacube in Spectronon select the File gt Open menu item and select the datacube to open Spectronon can open any datacube with an ENVI formatted header Datacubes collected from a source other than a Resonon instrument need another parameter to be added into the header file for certain functions to operate If prompted for the Reflectance Scale Factor RSF enter that value now The RSF for an imaging spectrometer is the data value that corresponds to 100 reflectivity By default the data is opened with a True Color render of the data This render approximates the appearance of the object under normal lighting conditions by combining red green and blue bands from the datacube In general a Render is a 2D visualization of the datacube Renders and Filters will be covered in detail later in this chapter Zoom Pan Flip and Rotate Tools amp To Zoom into a specific area of the image click the Zoom In tool from the toolbar 18 By clicking in the Render the view will zoom in It is also possible to click and drag a window within the render to zoom into the windowed area To Zoom Out use the Zoom Out tool available on the toolbar The user may also Zoom In and Out using the mouse scroll wheel if available To Pan the image while Zoomed In select the Pan tool Click and Drag inside of the Render to pan cet qp e
36. y mode the data is placed in the computers Random Access Memory RAM This method is typically faster allowing higher speed operation of the imager but is limited to the amount of available RAM on the computer It is recommended for smaller datacubes where speed is a priority In Disk Mode data is buffered to the hard drive It is recommended for most applications Float Mode Data can be stored as Integers or Floats Float mode has the advantage of higher data fidelity in low signal applications because the dark current is removed more accurately and has the convenience that reflectance is scaled from 0 1 However it requires twice the space on disk as the integer mode and requires more time to load data Slope and Intercept Calibration The calibration of the imager is stored in see Window Preferences gt Advanced These settings should only be changed during the initial setup or under consultation from Resonon Stage Settings Steps Per Frame The Steps Per Frame setting changes the distance that the stage moves between frames This setting should be adjusted to maintain proper aspect ratio Go to Window Preferences Stage to change this setting If the image appears stretched in the direction of scan the Steps Per Frame setting is too low Similarly if the image is compressed in the direction of scan the setting is too high Seconds per Step This setting is found in Window Preferences Stage Advanced and i
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