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IR Vista - FLIR Systems

1. 5 1 1 HARDWARE AND SOFTWARE REQUIREMENTS 5 1 2 INSTALLING IRVISTA 2 51 5 1 3 IRVISTA 2 51 OVERVIEW 6 CHAPTER 2 GETTING STARTED 7 2 1 INITIALIZATION 7 2 2 IRVISTA 2 51 TUTORIAL 8 2 2 1 AN OVERVIEW OF THE IRVISTA 2 51 WINDOW 8 2 2 2 GUIDED TOUR 9 2 2 3 SOFTWARE SETTINGS TUTORIAL 29 2 2 4 CAMERA CALIBRATION TUTORIAL 33 2 2 5 CRI VARISPEC TUNABLE FILTER CONTROL
2. 74 5 4 LOW LEVEL CAMERA CONTROL FOR ALPHA NIR CAMERAS 75 5 5 SUMMARY 77 IRvista 2 51 User s Manual 321 0028 10 04 08 03 5 Chapter 1 Introduction IRvista 2 51 is a real time image acquisition and analysis application that provides the user with acquisition storage retrieval display processing and analysis of still images and video in a flexible convenient Windows interface Control of your Indigo Systems cameras is also available through IRvista 2 51 IRvista 2 51 is an upgrade of IRvista 2 4 1 1 Hardware and Software requirements To install IRvista 2 51 you will need the following 1 1 1 IBM compatible Pentium based computer Pentium IV 1 5 GHz or better recommended 1 1 2 XGA 1024 x 768 or better screen resolution 1 1 3 Windows NT or Windows 2000 operating system 1 1 4 1 G of available hard drive space 2 G or more recommended 1 1 5 512 MB RAM 1 1 6 National Instruments PCI 1422 Frame Grabber Card 1 1 7 Indigo Systems Alpha NIR Phoenix or Merlin Camera 1 1 8 National Instruments cable for Indigo Alpha NIR Phoenix or Merlin Camera 1 1 9 RS232 Cable for Indigo Camera 1 1 10 National Instruments Measurement and Automation Explorer software not required for IRvista 2 51 installation but needed to allow full functio
3. Exit Exits the IRvista 2 51 application 3 2 2 Setup The Setup menu allows enabling of video processing features setting camera parameters and setting application preferences The Setup menu has five items Compression Enables disables image data compression in the form of intensity windowing Not available from tool bar NUC Enables disables Non Uniformity correction routine that multiplies each raw pixel value by a gain correction and then adds an offset correction BPR Enables disables Bad Pixel Replacement BPR which replaces the bad pixels from the camera with pixels whose value is determined through interpolation Preferences Opens an Application Preferences settings dialog box 3 2 3 Mode The Mode menu allows switching between the four video display modes Button controls for changing operating mode live burst disk filter are available beneath the image rather than on the toolbar The Mode menu has four items Live Selects the video source as camera and displays a continuous real time video This also removes the display of the VCR controls IRvista 2 51 User s Manual 321 0028 10 04 08 03 56 Burst Selects the video source as camera records a fixed number of frames burst and displays the recorded video This also enables the display of the VCR controls if not already displayed Disk Selects the video source as a file opens and displays the recorded saved video
4. 40 CHAPTER 3 IRVISTA 2 51 REFERENCE 44 3 1 MAIN WINDOW 44 3 2 MENU BAR 54 3 2 1 FILE 54 3 2 2 SETUP 55 3 2 3 MODE 55 3 2 4 TOOLS 56 3 2 5 CAMERA 58 CHAPTER 4 TECHNICAL INFORMATION 58 4 1 NON UNIFORMITY CORRECTION AND BAD PIXEL REPLACEMENT 59 4 2 STRUCTURE OF IMAGE SEQUENCE AND SETTINGS FILES 61
5. 2 MB per second To prevent inadvertently writing excessively long image sequence files to disk maximum acquisition time and maximum frames settings controls are provided If either limit is exceeded acquisition will stop and a notice will be posted to the screen Operating system limitations prevent acquisition of video files exceeding 2GB Acquisitions exceeding 2GB will be divided into multipart files The characters _xyz will be appended to each partial file To facilitate long term monitoring the minimum time between frames can be set up to 1 000 000 seconds The actual delay between frames will be slightly longer due to image processing and analysis time with the extra duration depending on the system configuration This will normally be noticeable only when the delay between frames is short Note that the maximum acquisition time and maximum frames limits are applied independent of the delay between frames Press the timestamp button Press record again and name the file firsttimestamp or something similar The image file now being recorded will include a timestamp for each image During record the timestamp button will disappear user cannot change during record phase Deselect record We will use this file again later Switch to burst mode by pressing the burst button A window will pop up informing the user that a burst is being acquired with a delay of 1 ms between frames The burst will probably have forty images unless system mem
6. Hit the save mask button Navigate to a suitable location and enter the file name firstmask As usual bin will be added automatically The mask that was contained in the NUC and BPM portion of the image sequence file disposable bin has now been saved as a separate file named firstmask bin You can now load and display this mask We will now create a new mask The gains from the sequence disposable bin should now be displayed as image A If not load this sequence and extract the gains again When the gains from disposable bin are displayed as image A find the histogram of control below the masking histogram Set the source to A and hit go You will see a histogram of the image A data Now set the red cursors to exclude some of the pixels as illustrated below and hit create mask A mask will be created The white regions represent image pixels whose intensity is outside the limits set by the cursor You may recall that you set limits on the acceptable range of gain correction coefficients each time you calibrated your camera We have now set the limits differently and have created a new bad gains mask IRvista 2 51 User s Manual 321 0028 10 04 08 03 72 Adjust the limits and create another mask Note that the gain map in the figure above is simulated for purposes of illustration and has far more bad pixels would be found in an Indigo camera Next we will AND the mask we have created with the original sequence mask The resulting mask will label as
7. IRvista 2 51 User s Manual 321 0028 10 04 08 03 61 4 2 Structure of Image Sequence and Settings Files An image sequence or camera settings file is a LabVIEW standard I16 data file and has the extension bin It consists of three sections the header the NUC and BPR tables and the images along with optional wavelength and timestamp data A camera settings file is simply an image sequence file with zero viewable images and thus we do not distinguish between images sequences and camera settings file in the discussion that follows Each of the three sections of the file is described briefly in the figure and then in more detail in the following paragraphs The header portion of the sequence file contains the software and hardware settings in use at the time the image sequence was acquired Header elements and comments each element is a 16 bit or 2 byte integer 0 major software version number 1 minor software version number 2 number of elements in header Allows for future expansion of the header file while maintaining compatibility with older sequence and settings files 3 columns in each image 4 rows in each image 5 images lsb or least significant byte 6 images msb or most significant byte IRvista 2 51 User s Manual 321 0028 10 04 08 03 62 The number of images is header 6 2 16 header 5 7 NUC BPR elements lsb 8 NUC BPR elements msb The number of elements in the NUC BPR tables is header 8 2 16
8. IT is entered a pop up window will notify the user that the old IT is being retained For Phoenix cameras the integration time is set using separate software Contact Indigo Systems Corp for more information 2 2 2 4 Image Intensity Windowing In the lower right corner of the application window find the intensity histogram Image compression controls are located to the left of the histogram and below the histogram It is often useful to apply a data compression routine to the image pixels as follows For 12 bit images with 0 I 4095 A pixel with intensity below Imin is replaced by 0 A pixel with intensity above Imax is replaced by 255 A pixel with intensity Imin I Imax is replaced by I I Imin 255 Imax Imin For 14 bit images with 0 I 16 383 A pixel with intensity below Imin is replaced by 0 A pixel with intensity above Imax is replaced by 255 A pixel with intensity Imin I Imax is replaced by I I Imin 255 Imax Imin This data compression algorithm can enhance small differences in pixel intensity that would otherwise not be obvious and is sometimes called intensity windowing IRvista 2 51 User s Manual 321 0028 10 04 08 03 19 Imin and Imax can be selected from the histogram controls The histogram a graph of the number of pixels with intensity I versus I features two cursors The lower cursor gives the value of Imin and the upper cursor gives the value of Imax These cu
9. bad any pixel that we excluded in the last step any that were found to have bad gains during the calibration and any that were found to fluctuate during the calibration Hit the AND Masks button IRvista 2 51 User s Manual 321 0028 10 04 08 03 73 Set the Mask A selector to current mask and hit load Set the Mask B selector to from disk and hit load Navigate to fistmask bin and load Hit A AND B The resulting mask is displayed at right Hit go for make this current mask Hit Return We will now insert our new mask into the image sequence file Hit Insert Mask and navigate to disposable bin Select disposable bin and open You will be prompted to decide whether to replace the file disposable bin Hit replace This image sequence now contains the new mask If it is opened in Indigo IRvista 2 51 the pixels labeled bad in the new mask will be replaced via the bad pixel replacement algorithm WARNING Insertion of a new mask bad pixel map into an image sequence file or a settings file is an irreversible process Users are strongly advised to make back up copies of settings files and image sequence files before altering the imbedded masks bad pixel maps Alteration of the bad pixel maps in the settings files supplied with the camera will void the software warranty WARNING If a settings file is altered by insertion of a new mask the changes will not take effect until the IRvista 2 51 software is restarted We will now use the mask we have crea
10. can be viewed in Internet Explorer and other applications The print button prints the application window to the default printer selected via Windows Open save frame save image save panel print and exit are all accessible from the file menu Use the menu to access at least one of these functions Press the preferences button A window appears that allows the user to change various software and hardware settings including camera integration time the number of images to acquire in burst mode the file type for image and panel snap shots and the location of the non uniformity correction and bad pixel replacement tables Use of these controls will be discussed in the Software Settings Tutorial below For now press the OK button without making changes IRvista 2 51 User s Manual 321 0028 10 04 08 03 22 The NUC button turns on off non uniformity correction The software launches with NUC turned on Press the button to turn off the NUC The image will probably show flaws Turn the NUC on again by pressing the NUC button a second time When image streams are saved to disk in either continuous or burst mode the NUC tables are saved in the file When the file is recalled the NUC tables are recalled as well and thus the images are subjected to the same correction that was used when they were originally collected Note that the Merlin Uncooled camera offers the option of using an internal NUC routine or the software NUC routines The BPR button
11. file This also enables the display of the VCR controls if not already displayed Filter Operates the VariSpec Tunable Filter from Cambridge Research amp Instrumentation Corporation in conjunction with IRvista 2 51 This mode allows acquisition of an image sequence in which each image is acquired with a different range of wavelengths This mode will be enabled only if a VariSpec filter is present in the system 3 2 4 Tools The Tools menu allows selecting the video analysis tools and zooming The Tools menu has eleven items ROI Enables disables the selecting of a Region of Interest ROI for analysis or zooming Zoom ROI Zooms Unzooms according to the ROI selected Zoom X2 Zooms Unzooms image by a factor of 2 Centroid Enables disables the analysis and display of the Intensity Centroid of the displayed image or user defined ROI This also disables the Spot Intensity Area Stats or Line Profile tools if enabled IRvista 2 51 User s Manual 321 0028 10 04 08 03 57 Area Stats Enables disables the display of statistical information including min max mean and standard deviation for an entire image or a region of interest within an image Provides display of crosshairs on min and max pixels Only one crosshair appears if multiple pixels have the same value This also disables the Line Profile Centroid or Spot Intensity tools if enabled Note Due to software constraints
12. for 12 bit cameras Alpha NIR and Merlin In other words an entry of 2059 in the offset table represents an offset of 11 For 14 bit Phoenix cameras 8096 is added to each offset This allows the gains and offsets to be stored as 16 bit unsigned integers In the bad pixel map bad pixels are ones and good pixels are zeros IRvista 2 51 User s Manual 321 0028 10 04 08 03 63 During operation the image data is corrected as follows Pij corrected Gij Pij Oij where Pij is the column i row j pixel Gij refers to gains and Oij refers to offsets The viewable images are stored sequentially following the NUC and BPR tables each occupying M x N x 2 bytes If a tunable filter is in use the wavelength at which each image is acquired is stored as a single 16 bit element that precedes each image If timestamp is enabled the date and time at which each image was acquired is stored as a set of four 16 bit elements following the wavelength Details of Data Format Actual 2D image data whether viewable or part of the NUC BPR portion of the file is written as a long string of bytes using the standard LabVIEW Write I16 file command The data is written as r0 c0 r0 c1 r0 cM r1 c0 r1 c1 r1 cM rN cM where r0 refers to row 0 and c1 refers to column 1 If the data is read back using the standard LabVIEW read characters function that data will appear in this order in hex format Note that a common source of confusion with LabVIEW data files
13. header 7 9 12 Camera PN 13 16 Camera SN 17 20 Camera VN 21 24 Camera options 25 26 Case Temp 27 28 FPA Temp 29 30 FPA Mode 31 Long Int Mode 32 Ext Int time 33 34 Int Time 35 Short Int Time 36 37 VDetCom 38 61 not in use 62 Integration time us lsb 63 Integration time us msb The integration time in microseconds is header 63 2 16 header 62 64 Filter present 65 Include wavelengths 1 0 1 16 bit element per image 66 Include time stamp 1 0 4 16 bit elements per image 67 Starting wavelength 68 Maximum pixel value 69 Offset correction 70 Video is NUC corrected 71 Video is BPR corrected 72 Sync Mode 0 Internal 1 External The next section contains the NUC and BPR tables The data is stored as a set of three image arrays The first one is the gains table then the offsets and then the bad pixel map The tables are identical in size and format to viewable images If the image has M columns and N rows it will have M x N elements each two bytes For example if the image is 316 x 252 pixels then each image occupies 79632 elements or 159264 bytes Thus the first 130 bytes of the settings file are the header the next 159264 bytes are gains then 159264 bytes of offsets then 159264 bytes of bad pixels map The gains are all multiplied by 1000 In other words an entry in the gain table of 1050 represents a gain factor of 1 05 Similarly 2048 is added to each offset
14. is that data is stored backwards as bigendian numbers This is because LabVIEW was originally written for Mac OS LabVIEW BIG ENDIAN 00000001 00000000 00000001 Byte4 Byte3 Byte2 Byte1 Win C LITTLE ENDIAN 00000001 00000001 00000000 Byte1 Byte2 Byte3 Byte4 IRvista 2 51 User s Manual 321 0028 10 04 08 03 64 4 3 Support Files This section of the manual describes support files included with IRvista 2 51 software Some of these files can be viewed using text editors others cannot 4 3 1 Settings files There are three settings files associated with IRvista 2 51 software The first is a general software settings file with the name IndigoSettings txt This file can be viewed with a text editor It contains information such as the type of camera the default image file types color of ROI tools and a variety of other parameters When users make changes to the software preferences the information is saved to this file IndigoSettings txt also contains a file path to another file the camera settings file that contains camera settings as opposed to software settings As was discussed in the previous section the camera settings file contains a header with camera settings and NUC and BPR tables It is simply an image sequence file with no viewable images Camera settings files have the extension bin For example the file default bin contains factory default camera settings and NUC and BPR tables spec
15. located at C program files IRvista Indigo Data data TtxPalsExample def Select one of the color palettes and return 2 2 2 2 Operating modes Beneath the color palette selector are the operating mode buttons IRvista 2 51 software can be operated in three distinct modes with an optional fourth mode if your system includes a tunable filter If a camera is present the application is in live mode In live mode images are acquired from the camera and displayed immediately at a rate that will be system dependent and will change as analysis features are turned on explained below An instantaneous frame rate display appears in the upper right corner of the IRvista panel Since this is an instantaneous frame rate updated per image acquired it may fluctuate But a typical display rate would be 13 15 frames per second slowing somewhat if multiple analysis features are in use If no camera is connected please skip to the disk mode section below If a camera is present please continue IRvista 2 51 User s Manual 321 0028 10 04 08 03 11 Press the freeze button When freeze is selected the system continues to acquire images but the display is not updated Analysis tools will operate on the frozen image Deselect freeze Press the record button When the pop up file dialog appears navigate to a suitable location for IRvista 2 51 files Enter the filename video1 The extension bin will be added automatically A file will be created and frames w
16. offsets that tend to be more sensitive to image conditions than gains This requires updating the offsets while the camera is presented with a uniform view with medium brightness The exact value of the medium brightness is not important but uniformity is However as we have just seen it is also possible to use this feature to create a background in the image Exit IRvista 2 51 and relaunch The background image is gone The Camera Control button launches a pop up window that allows the user to control the camera directly Press this button IRvista 2 51 will automatically launch the correct window for your camera Examples are presented in the figures 2 4 2 6 below for various Indigo Systems cameras IRvista 2 51 User s Manual 321 0028 10 04 08 03 27 If you are using an Alpha NIR camera notice that the pop up window includes integration time Vdetcom skmming image orientation gain settings sync mode and test patterns Pressing the status panel button will launch a window that displays information from the camera s status and FPA registers Note Do not enter external sync mode unless this feature is supported by your camera and you have a trigger signal connected If you are using a Merlin or Phoenix camera a smaller set of commands is available In either case a live image is provided so that users can observe the effects of settings changes Note that the image here may appear different from the image in the IRvista 2 51 win
17. sequence a graph of spot intensity versus wavelength will be presented in the upper right section of the IRvista 2 51 window IRvista 2 51 User s Manual 321 0028 10 04 08 03 44 Chapter 3 IRvista 2 51 Reference This chapter contains an overview of the application window tool bar and menu bar and is intended to serve as a reference rather than a substitute for the tutorial in chapter 2 3 1 Main Window The main window contains the image window and related controls and indicator needed to control and analyze the image It has many sections and functions The appearance of the main window depends on the Display Mode that is selected The three display modes are Continuous Burst and Disk The IRvista 2 51 main window in live burst disk and filter mode is shown in figures 3 1 3 5 Figure 3 1 IRvista 2 51 panel in Live Mode with no filter present The image in this figure was acquired using an Alpha NIR camera IRvista 2 51 User s Manual 321 0028 10 04 08 03 45 Figure 3 2 IRvista 2 51 panel in Burst Mode The image in this figure was acquired using a Merlin Uncooled camera IRvista 2 51 User s Manual 321 0028 10 04 08 03 46 Figure 3 3 IRvista 2 51 panel in Disk Mode The image in this figure was acquired using a Phoenix camera IRvista 2 51 User s Manual 321 0028 10 04 08 03 47 Figure 3 4 IRvista 2 51 panel in Live Mode with optional tunable filter Notice the wavelength control beneath the image The im
18. turns on off the bad pixel replacement algorithm The software launches with BPR turned on Press the button to turn off BPR Bad pixels may appear in the image as either dark spots white spots or flickering spots Press the BPR button a second time to turn the BPR algorithm back on The bad pixel replacement algorithm replaces the bad pixels from the camera with a value determined through interpolation of nearby pixel values When image streams are saved to disk in either continuous or burst mode the Bad Pixel Mask BPM is saved in the file When the file is recalled the Bad Pixel Map is recalled as well and thus the images are subjected to the Bad Pixel Replacement algorithm for display Note that the Merlin Uncooled camera offers the option of using internal an BPR routine or the software BPR routine Note that the images saved to disk in either continuous or burst mode are saved in raw form uncorrected for non uniformity or bad pixels However the bad pixel map and non uniformity correction data applied to the image at the time of acquisition is saved in the file When a data file is loaded from disk the NUC and BPM are loaded and applied to the image This strategy offers the user the powerful option of changing the NUC and BPM applied to data long after acquisition and also assures that no information is lost when video is saved to disk The current NUC and BPM data are saved in the file even if these features are turned off during acquisition Th
19. 04 08 03 IRvista 2 51 User Manual 321 0028 10 IRvista 2 51 is a trademark of Indigo Systems Corp WinSoft is a trademark of WinSoft Corp IRvista 2 51 User s Manual 321 0028 10 04 08 03 2 If You Need Help Technical Support If you need help at any time with the installation or use of IRvista 2 51 please call IRvista 2 51 Technical Support at WinSoft Corp 714 444 4844 or email us at support winsoft com Disclaimer In no event shall WinSoft or its representatives be liable for any consequential damages whatsoever including without limitation damages for loss of business profits business interruption loss of business information or other loss arising out of the use of or inability to use IRvista 2 51 Even if WinSoft has been advised of the possibility for such damages Copyright Trademarks and Version Copyright 2002 WinSoft Corp All rights reserved No part of this document may be reproduced stored in a retrieval system or transmitted in any form or by any means electronic mechanical photocopying recording or otherwise without prior written consent of WinSoft Corp This manual was updated to IRvista 2 51 IRvista 2 51 is a registered trademark of Indigo Systems Corporation WinSoft is a registered trademark of WinSoft Corp IRvista 2 51 User s Manual 321 0028 10 04 08 03 3 CHAPTER 1 INTRODUCTION
20. 4 3 SUPPORT FILES 64 4 3 1 SETTINGS FILES 64 4 3 2 THERMOTEKNIX PALETTES 64 4 3 3 OTHER SUPPORT FILES 64 CHAPTER 5 ADVANCED FEATURES 65 5 1 OVERVIEW 65 5 2 THE IMAGE STATISTICS WINDOW 65 5 3 IMAGE STATISTICS TUTORIAL 67 5 3 1 ARITHMETIC OPERATIONS ON IMAGES 67 5 3 2 MASKING SEQUENCES AND SETTINGS FILES 69 IRvista 2 51 User s Manual 321 0028 10 04 08 03 4 5 3 3 EXAMPLE PROBLEMS
21. Burst Mode Disk Mode or Filter Mode only Allows user to save an entire sequence or only the portion between the VCR limits Save as Disk Mode only Allows the user to save a sequence with a different name Open Disk Mode only Allows the user to open an existing sequence file Pressing the open button is equivalent to pushing the open button on the tool bar Export Disk Mode only Allows user to export all or part of a sequence in tif or fts format These files can be opened with suitable applications Centroid Indicator Displays the X and Y location of the Intensity Centroid of displayed image or user defined ROI IRvista 2 51 User s Manual 321 0028 10 04 08 03 51 Centroid ROI Button Switches the Centroid function between displaying Centroid of displayed image and displaying Centroid of user defined ROI Area Stats Indicators Display the min max average and standard deviation of the entire image or a region of interest selected by the user via the Area Stats ROI Button Area Stats Min Max Buttons Put crosshairs on the locations of the minimum and maximum pixels in the image or region of interest If multiple pixels have the same minimum or maximum value only one min and one max will be labeled with a crosshair Area Stats ROI Button Switches the area stats function between displaying statistics for the entire image and displaying statistics for user defined ROI Spot Intensity Indicator Displays of the Average Int
22. TICS package to measure the average and standard deviation of the low intensity regions of the beam Write an outline of how this would be done and then compare to the solution on the next page 2 Senior Technician Jones wants to display a map and study statistics of portions of the beam that fluctuate He has acquired a sequence of beam images Write an outline of how this would be done and then compare to the solution on the next page IRvista 2 51 User s Manual 321 0028 10 04 08 03 75 Solution to example 1 1 Using IMAGE STATISTICS load the sequence of beam images 2 Write the sequence average to A 3 Using the masking tools display a histogram of A 4 Set the low limit cursor to zero and set the high limit cursor to exclude saturated pixels or to some appropriate upper limit 5 Hit create mask 6 In the controls for image A hit apply mask The statistics displayed for image A do not include saturated pixels Solution to example 2 1 Using IMAGE STATISTICS load the sequence of beam images 2 Write the sequence standard deviation to A 3 Using the masking tools display a histogram of A 4 Set the low limit cursor above zero to exclude pixels that are not fluctuating Set the high limit cursor to 4095 5 Hit create mask 6 In the controls for image A hit apply mask The statistics displayed for image A do not include pixels that are stable 5 4 Low Level Camera Control for Alpha NIR Cameras If you are using an Alph
23. a NIR camera please continue If you are using a Merlin please skip this chapter Hit the exit button on IMAGE STATISTICS to return to IRvista 2 51 Low level camera control To access the low level camera control hit the camera control button IRvista 2 51 User s Manual 321 0028 10 04 08 03 76 Hit the low level camera control button A pop up panel appears as below IRvista 2 51 User s Manual 321 0028 10 04 08 03 77 Caution study the documentation that came with the Alpha NIR camera before attempting to use this panel To use this panel select a function from the function control at left For example select read info The panel will now display the camera part number serial number and camera firmware version number Select FPA mode The panel will display a number of camera settings as shown below These settings can be changed by hitting the corresponding buttons For example hitting the Invert button will put the camera in a mode in which it inverts the image Hit the display raw data button The panel will also display bytes acquired directly from the camera in the process of reading and writing from and to the camera Consult the camera documentation for use of the various functions Optional Use of External Sync Caution Do not put your camera into external sync mode until you verify that the camera has external sync capability and you have prepared and external sync signal If the camera is put into external sync mo
24. age in this figure was acquired using an Alpha NIR camera and compatible filter IRvista 2 51 User s Manual 321 0028 10 04 08 03 48 Figure 3 5 IRvista 2 51 panel in optional Filter Mode that is available only when a supported tunable filter is present The image in this figure was acquired using an Alpha NIR camera and a compatible filter Details of the IRvista 2 51 panel Some controls are visible only in certain modes or under certain circumstances Image Window Displays the video as an image or zoomed image The resolution depends on the type of camera in use For example Alpha NIR images are 252x316 but images from other cameras are often 256x320 Images from large format cameras such as the Phoenix will be reduced to fit into the image display portion of the panel ROI images will be zoomed to roughly fill the image display portion of the panel The image is compressed to 8 bit gray scale for display Palette Control Allows selection of various color palettes to use when displaying the image Palette Invert Button Inverts the assignment of intensity colors selected in the from the palette control i e the bright color becomes the dark color and visa versa IRvista 2 51 User s Manual 321 0028 10 04 08 03 49 Thermoteknix Button Loads a color palette from a Thermoteknix palette Live Button Selects the video source as camera and displays a continuous real time video This also removes the display of the VCR controls Bu
25. am has been saved to disk it has a definite number of frames and is displayed in the same way that a burst is displayed The VCR limits will reflect the number of frames in the video stream Observe that the VCR controls and color palette controls work as before The limits control allows the user the save the entire image sequence or only the portion between the VCR limits This setting applies to both the save as function and the export function Set the VCR limits to display some fraction of the sequence Select between VCR limits only and push the save as button Select a name for the sequence such as partial bin Press the open button and load the partial sequence Observe that is contains only the selected frames Press the open file button again and open the timestamp file probably named firsttimestamp bin Note that an indicator appears that gives the date and time at which each image was acquired The Export button allows the user to save all or part of the current sequence in industry standard tif fts mpg and avi formats Press the Export button The window below will pop up IRvista 2 51 User s Manual 321 0028 10 04 08 03 16 Select a format you can open with other image applications you use Both avi and mpg can be viewed from a variety of applications so select one of these if you are unsure There are several features of the export function that may require special attention These are described in the italicized notes b
26. and BPR tables as well as camera settings to factory defaults The camera integration time can also be set in the preferences window If the settings are saved to the software settings file the camera will launch with the preferred integration time Camera serial communications can be disabled in the settings window but this will make a substantial portion of IRvista s functionality unavailable Software Preferences Page IRvista 2 51 User s Manual 321 0028 10 04 08 03 32 The second page of the preferences window allows the user to customize certain aspects of the appearance of the software In particular the color of ROI tools can be set along with the size of crosshairs that appear in various analysis tools and the default color palette Image File Preferences Page The third page of the settings panel is associated with file paths for image and panel snap shots As explained above in the tool bar and analysis features section of the tutorial image snap shots and panel snap shots can be saved in jpg tif png or bmp formats The first time an image snap shot is saved during a session the user will be prompted for a file name Subsequent images will be saved with the default names filename2 jpg filename3 jpg and so on The filename can be changed by pressing the file icon next to the file path box for each type of snap shot IRvista 2 51 User s Manual 321 0028 10 04 08 03 33 Filter Preferences Page The filter preferences are d
27. complete the tutorial in chapter 2 before attempting to operate the software independently Chapters 3 4 and 5 contain reference material technical information and discussion of advanced features The first mention of a panel control or new concept is in italicized bold Figures that show an entire panel are generally numbered in the format chapter figure but figures showing a single control or small portion of a panel are generally not numbered IRvista 2 51 User s Manual 321 0028 10 04 08 03 7 Chapter 2 Getting Started 2 1 Initialization Make sure your NI Frame Grabber Board and Indigo Systems camera are installed If you are using a Phoenix or Merlin camera make sure the serial cable is connected securely to the camera and the computer Power on the camera For cooled focal plane cameras it will be necessary to wait for a few minutes Launch the IRvista 2 51 application by double clicking the IRvista 2 51 icon The IRvista 2 51 window will be displayed and the application will automatically attempt to communicate with camera and begin video display If the software and camera are properly installed an image will appear in the upper left corner of the IRvista 2 51 window If no camera is available the application will inform the user and ask if the user wants to display a video from disk If the user chooses to display video from disk a file dialog box will appear prompting the user to select a video file to display Example vi
28. crosshairs are always displayed at the upper left corner of the selected pixel Multiple Spots Enables disables a pop up display of the image enlarged by a factor of two Basic statistics can be monitored for up to four spots or ROIs simultaneously Spot Intensity Enables disables the analysis and display of the Average Intensity within a user defined spot or a user defined ROI User defined ROI s can be elliptical or rectangular If the standard square spot is selected the spot size can be 1x1 5x5 10x10 or 50x50 Spots that enclose a single pixel will be marked on the image with a crosshair Larger spots will be marked with a square box or in the case of a user defined ROI a rectangle or ellipse This feature disables the Centroid Area Stats or Line Profile tools if enabled Note Due to software constraints crosshairs are always displayed at the upper left corner of the selected pixel Line Profile Enables disables the analysis and display of the Intensity Line Profile of a user defined pixel line within the displayed image The thickness of the line is selectable Selecting a thicker line averages over small spatial fluctuations in the pixel intensity This tool disables the Centroid Area Stats or Spot Intensity tools if enabled 3D Graph Enables disables display of a 3D graph intensity versus location in the image The graph can be resized but slows acquisition substantially if the graph is large Can be used in conjunction
29. dark average but the medium standard deviation should still be small represented as a relatively dark image Again following the instructions in the message box present the camera with a uniform bright source Such a source can be approximated by again placing a white sheet of paper in front of the camera and opening the iris further Adjust the scene and or iris until a fairly tight distribution of intensities is observed somewhere around 3500 or so for Merlin or Alpha or 14000 for Phoenix Again the exact brightness of the source is not important But avoid having a large number of pixels pegged out at the maximum intensity of 4095 Merlin Alpha or 16363 Phoenix When the results are satisfactory hit the Go button A sequence of 64 images has been acquired The average over the 64 frames has been written to the top left section of the panel and the standard deviation over the 64 frames has been written to the top center right section of the panel as below IRvista 2 51 User s Manual 321 0028 10 04 08 03 37 The bright average should be nearly white but the bright standard deviation should be relatively dark You are now ready to continue with the calibration procedure A panel will pop up displaying a map of pixels with gain outside of the acceptable range represented by white and pixels with gains in the acceptable range represented by black See below You can change the acceptable range by typing in new minimum and maximum al
30. de accidentally it may be necessary to power down the camera and restart If your Alpha NIR camera is equipped with an external sync function prepare an external sync signal for your camera It is recommended that you check the sync signal with a scope before connecting Once the external sync signal has been connected switch to external sync mode One image will be acquired per external trigger provided the trigger rate is not too fast 5 5 Summary Operating the Indigo Systems IRvista 2 51 software in advanced mode gives the advanced user access to a range of powerful tools for analyzing images modifying camera settings files and operating the Alpha NIR camera via low level commands The user must exercise care when the software is operated in advanced mode Concluding Remarks Indigo IRvista 2 51 is a powerful integrated solution that can be used to acquire record and analyze images in many applications Upgrades and add ons are available from Indigo Systems to further increase the power and versatility of this software
31. deos are included with the software Navigate to the Indigo Systems folder and open Find the Example Bursts folder and open Select Example1 bin If IRvista is unable to communicate with the camera via the serial interface a message notifying the user of the problem will appear It is possible to operate the software without serial communications but a substantial portion of IRvista s functionality will be lost A camera settings file with calibration data specific to your camera serial number specific has probably been installed in the factory If not you may wish to launch the preferences window and install the file now or wait until later in the tutorial where the preferences window is discussed In either case Please follow the directions provided with the camera settings file If the serial number specific settings file is not in use blank camera settings files will be used and the image quality will be substantially reduced The IRvista 2 51 window during operation with a camera will look like figure 2 1a below If the application is displaying example1 bin the appearance will be somewhat different The image may not appear as you would expect at this moment Many camera and software settings can affect the image Adjustment of these settings is explained later in this manual IRvista 2 51 User s Manual 321 0028 10 04 08 03 8 Figure 2 1a The IRvista 2 51 application window in live mode The image in this figure was acquired using a
32. different settings file causes the camera to be configured as it was during the calibration procedure use to produce that settings file 2 2 5 CRI VariSpec Tunable Filter Control This section of the manual discusses use of the optional CRI VariSpec Tunable Filter If your system includes a tunable filter please exit from IRvista 2 51 install the hardware and optics install the camera settings file that came with the filter and launch IRvista 2 51 Notice that a new control appears on the panel beneath the image in live mode The center of the filter bandwidth can be set using this control Set the wavelength control to various values near the center of the filter range and near the edge Notice that the image is essentially black Since the filter transmits only a narrow range of wavelengths the total intensity of light entering the camera aperture is quite small Press the preferences button In the camera preferences page use the camera settings path control to navigate to the camera settings file that came with the filter Press the apply but don t save button Applying this camera settings file puts the camera in high gain mode sets the wavelength to 1530 nm where the filter transparency is high and sets the camera integration time higher This will allow the camera to acquire a viewable image with the filter present Exit from the preferences window and observe the image It should be bright enough to see clearly Some focus adjustment ma
33. displayed at the upper left corner of the selected pixel Fun with ROI Tools The ROI can be dragged across the image by clicking near the center and dragging the mouse while holding down the left button Try this The shape of the ROI can be changed by dragging an edge or corner Clicking on a new spot on the image starts a new ROI In the center panel above the integration time control find the ROI shape selector Set to ellipse and repeat the previous steps with the centroid ROI functions These ROI functions work with all of the analysis tools that support ROIs Deselect centroid The image area stats button turns on display of image statistics for the entire image or a region of interest Press the button The statistics include the mean standard deviation min and max Press the min button and observe that a crosshair marks the position of the minimum intensity pixel in the region If there are multiple pixels with the same minimum value only one will be marked Push the max button and observe the results Note that the maker for the maximum pixel is larger than the marker for the minimum pixel Press the ROI button and select an ROI The statistics of the ROI will now be displayed Either rectangular or elliptical ROIs can be selected Deselect image area stats The spot intensity button turns on the algorithm that finds the average pixel intensity enclosed in a region of selectable size Press this button The spot intensity display comes to
34. dow because the image displayed on the camera control panels is acquired directly from the camera Image intensity windowing software NUC and software BPR have not been applied If you are using a Merlin or Phoenix camera and internal NUC and BPR are enabled then corrected image data will be displayed Figure 2 4 The Alpha NIR Camera Control Window IRvista 2 51 User s Manual 321 0028 10 04 08 03 28 Figure 2 5 The Merlin camera control panel IRvista 2 51 User s Manual 321 0028 10 04 08 03 29 Figures 2 6 The Phoenix control panel The exit button or menu function under file exits the IRvista 2 51 application 2 2 3 Software Settings Tutorial The software features described below are designed for more experienced users It is recommended that the user become comfortable with the basic software features before proceeding with the settings and calibration tutorials below With the application running in live mode press the preferences button A window appears as below IRvista 2 51 User s Manual 321 0028 10 04 08 03 30 This preferences panel enables the user to change certain hardware and software settings These new settings can be applied for the duration of the session only by pressing the Apply Preferences but Don t Save button or they can be written to the settings file IndigoSettings txt by pressing the Apply and Save Preferences button If the settings are written to the settings file IRvista 2 51 w
35. e frame Run forward and loop continuously default To last frame Grab the Scrub Bar control and drag to the left or right This control allows the user to move quickly to another portion of the sequence It is also possible to type a frame number into the control above the scrub bar and go directly to that frame Playback operations in use prior to operation of the scrub bar controls will continue when the scrub bar is released Adjust the Frame Delay This allows the user to view the video in slow motion with a limit of 1 second per frame Adjust the VCR limits This allows the user to display any portion of a longer video stream Switch to disk mode by pressing the disk button in the operating mode selection region of the application window A dialog window will pop up asking the user to locate the file to be displayed Select a burst that was saved earlier such as burst1 bin If no camera is available navigate to the Indigo Systems folder and find the folder examples Load video1 bin You may be prompted with a message informing you that the sequence you are trying to open was collected with different camera settings You will then have the option of applying the file settings to the camera or retaining current settings For now retain current settings Note If user selects the first part of a multi part file file name does not contain any numbers and other files contain the same filename with _ where is 002 003 etc then t
36. e settings file with a descriptive name Finally a pop up window will ask the user what should be done with the new settings file See below IRvista 2 51 User s Manual 321 0028 10 04 08 03 40 Don t apply leaves the newly created and saved settings file unused for the time being Apply now but don t change default settings file applies the new settings file to the camera during this session but next time the software is launched the previous settings file will be used Finally apply and change the default settings file will cause the new settings file to be applied during this session and will also cause the new settings file to become the default used when launching the software The right portion of the camera calibration panel now contains statistical summaries of the calibration data The corrected medium sigma provides at a glance diagnostics This number which measures the standard deviation of the pixels in the uniform medium image after correction should be about one or less When you are finished reviewing the calibration statistics hit the continue button to return to the Indigo IRvista 2 51 application Change the camera integration time from the IRvista 2 51 panel from the settings panel or from the menu all three options are equivalent Repeat the calibration procedure creating a new settings file Now use the settings panel to switch back and forth between settings files and observe the effect Note that selecting a
37. elow Note If you select mpg it may be necessary to download additional software from the web In this case you will see the following message Codec not installed Please go to http www divx digest com software mpeg4codec html and follow instructions Note Not all image viewing applications support 12 bit TIF format If you export a 12 bit TIF file and try to view it in an application that does not support this format you may see a badly distorted image Note Due to operating system limitations the maximum file size that can be saved or exported is 2 gigabytes GB Therefore if the user tries to save a multi part file that is greater than 2GB the software will advise the user to reduce the number of frames to get a file less than 2 GB IRvista 2 51 User s Manual 321 0028 10 04 08 03 17 Figure 2 3 The IRvista 2 51 application window in disk mode with the filename visible below the VCR controls The image of electronic components warming during operation in this figure was acquired using a Phoenix camera Note that images from the Phoenix 640 x 512 camera are reduced by a factor of two in size so that they can be displayed in the IRvista GUI without covering other controls Image sequence files contain the entire 640 x 512 image The mode controls are also accessible from the menu bar Under the mode menu find the continuous burst and disk selections Under the file menu find the open item This is equivalent to pushing the open b
38. ensity axis scale can be adjusted by highlighting and changing the largest or smallest number on the intensity axis Experiment with this The stats button at the right of the line profile graph enables display of parameters including the mean standard deviation min and max of pixels in the line The save button on the line profile graph allows the user to save the histogram data as a two column spreadsheet file that can be opened with Excel Push this button and enter a file name With IRvista 2 51 running launch Excel and view the data Excel probably runs slowly and acquisition will probably slow in IRvista 2 51 IRvista 2 51 is a processor and memory intensive application that will slow operation of other applications The multiple spot meters feature calls a pop up window that enables the user to get basic information about several regions of the image simultaneously Press this button Observe the enlarged image displayed on the pop up window as shown below IRvista 2 51 User s Manual 321 0028 10 04 08 03 25 Press the select button next to the spot one indicator Define a rectangular or elliptical ROI in the image and push the select button again Stats for the selected portion of the image will be displayed Now press the select button next to the spot two indicator Deselect ROI Point at a spot on the image and set the spot size selector to 5x5 Press the select button again Statistics for both spot one and spot two will now be dis
39. ensity within a user defined spot or a user defined ROI spot The user defined spot size is selectable and can be 1x1 5x5 10x10 or 50x50 The X and Y location of the spot is also displayed Spot Intensity Size Control Allows selecting the spot size for user defined spots The user defined spot sizes available are 1x1 5x5 10x10 and 50x50 Spot ROI Button Switches the Spot Intensity function between displaying Spot Intensity of user defined spot and displaying Spot Intensity of user defined ROI spot ROI Selector Button Selects the shape of the user defined Region of Interest ROI Can be elliptical or rectangular Note that ROIs can be resized by dragging an edge or moved by clicking on the center of the ROI and dragging The number of pixels in the ROI is displayed below the shape selector Integration Time Control Controls the camera integration time Select with number and type in a new value or click on the up down arrows to change the IT Note that various cameras support different ranges of integration time according to customer specifications If the user requests an integration time that is not in the allowed range a warning is posted to the screen and the previous IT is retained IRvista 2 51 User s Manual 321 0028 10 04 08 03 52 Line Profile Graph Displays the Intensity Line Profile of a user defined pixel line within the displayed image The Y axis units are raw binary Intensity units and Y axis range is 0 to 4095 corres
40. er the min cursor or the max cursor which appear on the intensity histogram graph The selected and unlocked cursor can be dragged with the mouse or moved by pressing the diamond shaped cursor control located below the cursor palette The cursors are used to determine the range of the intensity windowing function applied to the displayed image This intensity windowing function is applied when the Compression button is pressed Cursors AGC s Switch Allows switching intensity histogram cursor control between user controlled Cursors position and Automatic Gain Controlled AGC s position If Automatic Gain Controlled the cursors are set to a fixed number of standard deviations from the mean That fixed number of standard deviations is determined by the AGC s numeric control located to the right of the Cursors AGC s switch The cursors are used to determine the range of the intensity windowing function applied to the displayed image This intensity windowing function is applied when the Compression button is pressed IRvista 2 51 User s Manual 321 0028 10 04 08 03 54 AGC s Numeric Control When the Cursors AGC s switch is in the AGC s position the AGC s numeric control determines the number of standard deviations from the mean which to position the cursors The cursors are used to determine the range of the intensity windowing function applied to the displayed image This intensity windowing function is applied
41. erations on images such as addition subtraction multiplication division etc Image sequences can be opened and viewed and non uniformity correction tables and bad pixel maps can be modified IRvista 2 51 User s Manual 321 0028 10 04 08 03 66 The IMAGE STATISTICS window is divided into four regions The top section presents the user with tools for arithmetic manipulations of individual images The bottom left section offers the user tools for manipulating and modifying masks such as bad pixel maps and offers the user the option of inserting modified masks into existing settings files The bottom right section is for displaying and manipulating image sequences The bottom center section is the display for both sequences and masks IRvista 2 51 User s Manual 321 0028 10 04 08 03 67 5 3 IMAGE STATISTICS Tutorial This tutorial offers a guided tour of the IMAGE STATISTICS window and shows an example application Our tutorial begins at the upper right corner of the IMAGE STATISTICS window Press the image size button This determines the size of the test images that we will create in the following steps It is suggested that you select an image size that matches your camera but this is not essential Similarly we can set the pixel depth for images to be created in the Image Statistics window If IRvista software is running with a camera the bit depth will automatically default to the value appropriate for the camera Users ha
42. etrieved at the full gray scale bit depth produced by the camera Alpha NIR and Merlin are 12 bit cameras while Phoenix cameras produce 14 bit images Note that some Indigo Systems cameras can be reconfigured by the user to produce 8 bit data Most of the features in IRvista 2 51 software are independent of the type of Indigo Systems camera in use but a few features are specific to a particular model Control of your Indigo Systems camera is also accessible through the application s easy to use graphical user interface Camera control features allow user to quickly and conveniently set commonly changed camera parameters during acquisition Video processing Video processing features include non uniform pixel correction bad pixel correction and pixel intensity windowing Non uniformity correction NUC and bad pixel replacement BPR are based on camera calibration tables that are provided with the camera but users can also make their own camera calibration tables by accessing the Camera Calibration window in the IRvista 2 51 software Video analysis Video analysis features include flexible zooming to a region of interest ROI and enlarging of an image or ROI intensity centroid of displayed image or region of interest ROI integrated intensity of a spot or ROI image area statistics intensity profile of a user defined line of pixels intensity histogram of displayed image and other tools About this manual It is strongly recommended that users
43. front of the camera to verify that this is a live image Note if the integration time is short or the scene presented to the camera is dark it may be difficult to observe changes in the live image At center bottom find the intensity histogram This is a display of number of pixels with a particular intensity versus pixel intensity The mean and standard deviation of the histogram are displayed beneath the histogram At the bottom right find the Frames to Acquire control This sets the number of frames to be acquired in for the dark medium and bright sequences The default is 64 Depending on system resources it may be useful to reduce the number of frames to be acquired when calibrating a large format camera such as the Phoenix 640 x 512 Following the instructions in the message box present the camera with a uniform dark source Such a source can be roughly approximated by placing a white sheet of paper in front of the camera and almost closing the iris or by reducing the illumination of the paper Adjust the scene and or iris until a fairly tight distribution of intensities is observed somewhere around 500 or so The calibration procedure is not very sensitive to the actual value but the image should appear to be as uniform as possible Avoid having a large number of pixels that read zero intensity IRvista 2 51 User s Manual 321 0028 10 04 08 03 35 When the results are satisfactory hit the Go button A sequence of 64 images has been acqu
44. hat bad pixel replacement and non uniformity are not applied to sequences and images displayed in the IMAGE STATISTICS window since one of the primary uses of this window is manipulation and modification of the NUC and BPM tables Hit the play button again to stop playing Select image 1 in the image box set the destination selector to A and hit go Notice that the first image in the sequence is displayed as image A set the destination selector for Sequence Average to A and hit go The average of all of the images in the sequence is displayed as image A In other words the pixel Ai j is the average of the N values of Pij in the sequence with N frames Set the destination selector for Sequence Standard Deviation to B and hit go The standard deviation of the N images in the sequence is displayed as image B In other words Bi j is the standard deviation of the N values of Pi j in the sequence Set the destination selector for Sequence Gains to A and hit go The gain correction factors stored in the sequence file are displayed as image A Note that the gain correction factors are all near 1 so they are multiplied by 1000 for storage in the form of an image array The average of the gains displayed below image A should be near 1000 The standard deviation indicates how widely varied the gain corrections are from one pixel to another The average and standard deviation of the gain correction factors will vary from camera to camera and even for the same ca
45. he user will be asked whether or not they would like to work with all the parts or just the first part IRvista 2 51 User s Manual 321 0028 10 04 08 03 15 The application window changes appearance only slightly as shown in 2 3 In particular the burst controls disappear and a filename appears in the file path box beneath the VRC controls An open file button appears in the upper left corner of the application window on the tool bar and an open button with identical functionality appears in the image control portion of the GUI for convenience The save as control allows the user to save the image sequence under another name Press the open file button on the tool bar or beneath the image A file dialog window will pop up Select the first continuous video stream that was saved earlier or one of the examples in the Indigo Systems Examples folder You may be prompted with a message informing you that the sequence you are trying to open was collected with different camera settings You will then have the option of applying the file settings to the camera or retaining current settings Try opening a few files and try applying the settings in at least one case Observe the effect integration time and other camera settings will change automatically When you switch to live mode the file settings will apply This facilitates comparison of image sequences acquired under related circumstances Notice that the VCR controls remain visible Once the video stre
46. ific to your camera A third settings file ImageFileNames txt is created the first time the software launches It contains information about the filenames for the image and panel snap shots created from the toolbar 4 3 2 Thermoteknix palettes Color palettes false color schemes applied to gray scale images developed by Thermoteknix Corporation are provided with IRvista 2 51 These files have the extension def The file TtxPalsExample def can be viewed with a text editor 4 3 3 Other support files IRvista_Spash bmp is a graphics file that is used as a splash screen when the software launches If your system includes a tunable filter then the file CRIfilter txt will be included This file contains serial number specific calibration data for your filter IRvista 2 51 User s Manual 321 0028 10 04 08 03 65 Chapter 5 Advanced Features 5 1 Overview Prior to IRvista 2 51 these advanced technical features were password protected Now IRvista 2 51 gives all users the opportunity to mathematically alter images and control Alpha NIR cameras at a lower level We will now explore the advanced technical features of IRvista 2 51 Section 2 describes use of the IMAGE STATISTICS window and section 3 describes use of advanced camera control functions for Alpha NIR cameras 5 2 The IMAGE STATISTICS WINDOW Press the IMAGE STATISTICS button and observe the IMAGE STATISTICS window This window allows the user to perform a variety of op
47. ill be appended to the file as 12 bit or 14 bit gray scale images depending on the camera type All Alpha files are 12 bit Merlin files are generally 12 bit but the Merlin camera can be set to produce 8 bit data Phoenix files are generally14 bit but the Phoenix can be set to produce 8 bit data Press the record button Figure 2 1b and note that the software continues to operate as before but you may notice a decrease in the acquisition rate This decrease will be system dependent Analysis tools described below will continue to function while video is streaming to disk The freeze button turns into a Pause button when recording Pressing Pause will stop recording of images to file and Pause will start to blink Pressing Pause again will stop the blinking and start recording images to file After a few seconds deselect record The rate at which images are acquired and written to disk can be increased substantially by turning off analysis features compression NUC and BPR these functions are explained in detail later in the manual Even if these features are disabled while recording to disk they can be enabled again when reviewing the saved image sequence Figure 2 1b The IRvista 2 51 application window in live mode and recording The image in this figure was acquired using an Alpha NIR camera IRvista 2 51 User s Manual 321 0028 10 04 08 03 12 Warning recording a continuous stream of video to disk fills disk space at the rate of about 1
48. ill launch with the new settings in the future Notes Concerning Settings Files IRvista 2 51 User s Manual 321 0028 10 04 08 03 31 There are two settings files associated with IRvista 2 51 software The first is a general software settings file with the name IndigoSettings txt This file can be viewed with a text editor It contains information such as the type of camera the default image file types color of ROI tools and a variety of other parameters IndigoSettings txt also contains a file path to another file the camera settings file that contains camera settings as opposed to software settings The camera settings file contains a header that includes the software version and a variety of camera parameters It also contains NUC and BPR tables that are appropriate for use with the camera with the settings included in the header Camera settings files have the extension bin which is the same as the extension for IRvista 2 51 image sequence files In fact a settings file is simply an image sequence file with no viewable images Thus users wishing to repeat an experiment with identical camera settings can use a previously acquired image sequence as the camera settings file Preferences Panel The preferences panel is divided into pages accessible via tabs on the top of the preferences window The first page is associated with controlling camera settings The default values for limits on the size of sequences recorded in live mode and burst
49. ired The average over the 64 frames is written to the top left section of the panel with the label Dark Average and the standard deviation over the 64 frames has been written to the top center right section of the panel with the label Dark Standard Deviation as below Note that the dark standard deviation should be small represented by a dark image since the standard deviation of the pixels over the 64 frames represents the degree to which the response of the camera pixels fluctuates when presented with a uniform source There may be a few bright pixels in the otherwise dark image Again following the instructions in the message box present the camera with a uniform medium source Such a source can be approximated by again placing a white sheet of paper in front of the camera and opening the iris slightly Adjust the scene and or iris until a fairly tight distribution of intensities is observed somewhere around 2000 or so for Merlin or Alpha or 8000 for Phoenix Again the exact brightness of the source is not important When the results are satisfactory hit the Go button A sequence of 64 images has been acquired The average over the 64 frames has been written to the top left section of the panel and the standard deviation over the 64 frames has been written to the top center right section of the panel as below IRvista 2 51 User s Manual 321 0028 10 04 08 03 36 Note that the medium average should be substantially brighter than the
50. is capability is discussed in more detail in the preferences section of the tutorial and in the appendix Non uniformity correction and bad pixel replacement algorithms can also be turned on and off from the menus Find the NUC and BPR items in the setup menu Deselect and select each and observe the results The centroid button turns on the algorithm that finds the intensity centroid of the entire image or of a region of interest ROI analogous to the center of mass for a material body Press the button The centroid display in the analysis tools section of the application window comes to life A crosshair appears on the image showing the location of the centroid graphically and the x y coordinates are shown in the centroid display The origin for this coordinate system is the upper left corner of the image If a light source is used to make a bright source in the camera s field of view the centroid will be seen to shift toward the bright spot in the image Press the ROI button in the centroid display Point at a spot on the image and press the left mouse button Drag the mouse while holding down the left mouse button to select a rectangular region of interest in the image The centroid algorithm will now calculate the intensity centroid of only the region of interest with the origin again being the upper left corner of the image IRvista 2 51 User s Manual 321 0028 10 04 08 03 23 Note Due to software constraints crosshairs are always
51. iscussed in section 2 2 5 in conjunction with discussion of the use of the tunable filter in IRvista 2 51 2 2 4 Camera Calibration Tutorial This camera calibration tutorial will take you through the calibration process in the end producing a new settings file with custom NUC and BPM tables Expect this process to take about one hour to complete You will need three uniform light sources A low intensity dark source medium intensity medium source and a high intensity bright source If uniform sources are not available a white sheet of paper that can be illuminated from a distance ideally with a with a halogen lamp will serve for purposes of illustration However the quality of the calibration depends directly on the uniformity of the dark medium and bright sources Some Indigo Systems cameras have the option of using internal NUC and BPR correction and or automatic gain control AGC It is strongly recommended that the user turn off internal NUC BPR and AGC before proceeding Depending on the camera model this may require using other software supplied by Indigo Calibration procedure overview The camera calibration procedure is based on acquiring a set of three image sequences one with a uniform dark light source a second with a uniform medium light source and a third with a uniform bright light source The IRvista 2 51 software will use these sequences to calculate a gain correction and offset for each camera pixel so that the c
52. istogram Bins Adjusts the number of bins in the histogram Defaults to 256 but can be set to larger or smaller values For a 12 bit image 4096 bins would assign each possible intensity to its own bin With 256 bins each bin contains a range of 16 different intensities Increasing the number of bins can result in larger statistical fluctuations in the histogram values IRvista 2 51 User s Manual 321 0028 10 04 08 03 53 Intensity Histogram Update Adjusts the rate at which the histogram is updated If the update delay is set to one the histogram updates per frame If it is set to ten then the histogram updates every tenth frame An update delay of zero disables the histogram update entirely However the most recent value of the min and max intensities are used to apply intensity windowing to each incoming frame regardless of the update rate Intensity Histogram Full Scale Sets the range of the editable horizontal axis to the full range of intensities for the type of image being acquired usually 0 4095 for a 12 bit image Intensity Histogram Zoom Sets the range of the editable horizontal axis to the cursor values Thus the histogram displays counts only for pixel intensities between the black limit min cursor and white limit max cursor Intensity Histogram Save Saves the current histogram data to an Excel file with the usual xls extension Intensity Histogram Cursors The cursor palette allows selecting and locking unlocking eith
53. lengths from 1000 to 1600 nm in steps of 50 nm The fill and append can be used independently In other words a ramp can be appended to an existing list or additional wavelengths can be appended to a ramp Filter palette files Filter palette files can be saved and retrieved using the file buttons on the toolbar Press the save palette button and navigate to a suitable location The file will be saved with the extension pal Acquiring a Cube On the next panel press the autoIT button This will cause the camera integration time to adjust to approximately compensate for variations in the transmission of the filter The initial integration time displayed on the IRvista 2 51panel will be used for wavelengths where the filter s transparency is at a maximum and the integration time will be adjusted upward to compensate for lower transparency at other wavelengths Press the run button on the toolbar IRvista 2 51 User s Manual 321 0028 10 04 08 03 43 When the sequence has been acquired a flashing done message will appear Press the exit button to return to the main IRvista 2 51 window Analyzing a Cube Notice that most of the analysis tools are still present but their meaning will be different in this operating mode However the line profile is no longer available Instead a graph appears that will work in conjunction with the spot meter Press the spot meter button and select a spot on the image After IRvista 2 51 loops through the entire
54. lication window there is a line profile display This is described in detail below 2 2 2 Guided Tour This tutorial will take the user on a guided tour of the IRvista 2 51 application illustrating the function of each control This tutorial takes several hours to complete To start the tour launch IRvista 2 51 if it is not already running 2 2 2 1 Color palettes IRvista 2 51 User s Manual 321 0028 10 04 08 03 10 Immediately beneath the image on the left side find the color palette selector and the color palette inverter The default color palette is Gray Scale white is high black is low intensity Switch to Sepia High intensity pixels will appear yellow to white and dark pixels will appear brown to black Push the invert button High intensity pixels will now appear brown to black while low intensity pixels will appear yellow to white Push the invert button again to turn off image intensity inversion Click on the selector controls to the left of the color palette display and try various false color schemes with inversion on and off The Tx button allows the user to load a color palette from a Thermoteknix palette file Additional information on Thermoteknix palettes is available at the Thermoteknix web page but an example file was provided with your copy of IRvista 2 51 Push the Tx button and navigate to the Thermoteknix def file that was installed with your software If you selected the default installation the file should be
55. life Click with the left mouse button on a spot on the image and observe the results A 5 x 5 pixel square box will appear and the intensity will appear in Ienclosed Use the selector box to change the spot size The spot size defaults to 5 x 5 each time spot intensity is selected Notice that the box is replaced by a crosshair for a 1 x 1 spot Push the ROI button in the spot intensity display You can now select a region of interest with a rectangular or elliptical shape and display the average pixel intensity in that region The X and Y coordinates displayed here are the coordinates of the center of the ROI Deselect spot intensity Note Due to software constraints crosshairs are always displayed at the upper left corner of the selected pixel IRvista 2 51 User s Manual 321 0028 10 04 08 03 24 The line profile button turns on the line profile algorithm Press this button Left click the mouse at a spot on the image and drag while holding the mouse button down A line will appear across the image and a graph of pixel intensity along the line will appear in the line profile display Try several lines that stretch across the image in various directions Adjust the line thickness control to three or five pixels This averages three or five adjacent parallel lines to give a better indication of the line profile of a noisy image The autoscale button adjusts the scale of the intensity axis to the range of data If the autoscale is turned off the int
56. lowed gains Note that the minimum and maximum allowed gains are defined in terms of the mean gain of all of the pixels For example if the minimum allowed gain is 0 5 then pixels with gain less than 50 of the mean gain of all pixels will be labeled bad Adjust the limits and observe the behavior When the results are satisfactory hit the accept button Note the warning indicator that will light if there are more than ten adjacent bad pixels in a row or column In the event that the settings produce more than ten adjacent bad pixels in a row or column a message will flash warning the user that the use of the settings file may cause unexpected behavior in IRvista IRvista 2 51 User s Manual 321 0028 10 04 08 03 38 A second pop up panel will now display a map of pixels which fluctuated during the medium sequence acquisition by more than the acceptable amount Again the ranges of acceptable standard deviation can be changed The default minimum standard deviation is 0 1 times the mean of the standard deviations of all of the pixels Adjust the limits and hit accept when the results are satisfactory See below Again the warning indicator and message will be activated if there are more than ten adjacent bad pixels in a row or column IRvista 2 51 User s Manual 321 0028 10 04 08 03 39 Saving and using the settings file A dialog box will now pop up asking for a name for the new settings file Navigate to a suitable location and save th
57. ly diminish the quality of the displayed image Chapter 4 Technical Information This chapter contains technical information about IRvista 2 51 and associated support and image sequence files Most users will not need to use the information in this chapter directly IRvista 2 51 User s Manual 321 0028 10 04 08 03 59 4 1 Non Uniformity Correction and Bad Pixel Replacement This section of the manual describes the use of Non Uniformity Correction NUC and Bad Pixel Replacement BPR routines contained in IRvista 2 51 The NUC and BPR algorithms are contained in dll s called by the VIs provided with IRvista 2 51 Non Uniformity Correction NUC Pixels in a focal plane typically have a range of gains and offsets Indigo Systems IRvista 2 51 software includes a utility that allows the user to measure the gain and offset of each pixel in the focal plane and then construct a settings file that contains a gain and offset correction for each pixel Many Indigo cameras are supplied with one or more settings files Corrected pixel values are then calculated according to corrected ij ij ij ij P G P O Note that Gij and Oij are not the measured gains and offsets of the pixels but rather correction terms to make the gains and offsets uniform across the focal plane Calculating Gij and Oij The gain and offset coefficients are calculated so as to make the focal plane response uniform In other words each pixel in a calibrated focal
58. mera these numbers will vary with integration time and other camera settings Set the destination selector for Sequence Offsets to B and hit go The offset corrections stored in the image sequence file are displayed as image B Offset corrections are typically numbers of magnitude ranging up to a few hundred and they can be positive or negative For storage in the image sequence file 2048 is added to each pixel offset for 12 bit cameras and 8096 is added for 14 bit images Thus the average of the offsets should be about 2000 to 3000 or 8000 9000 The standard deviation of the offsets indicated how widely the offsets vary from one pixel to another Before we leave this section of the tutorial write the gains in the sequence to image A Masking A mask is an image that contains 1 s and 0 s A mask is typically used in conjunction with another image to exclude certain pixels from the calculation In particular if the average pixel value of an image is calculated with a mask applied pixels represented by 1 s in the mask are excluded from the average The bad pixel maps in image sequence files and settings files are stored in the form of masks with 0 s representing good pixels and 1 s representing bad pixels IRvista 2 51 User s Manual 321 0028 10 04 08 03 71 In the lower left portion of the IMAGE STATISTICS window locate the masking tools Hit the extract mask button and navigate to disposable bin The mask will be displayed to the right
59. mode can be set here but these are only the defaults that can be changed in the main IRvista 2 51 window in the live and disk acquisition modes Camera Preferences Page Some camera settings file controls are provided in the preferences window It is recommended that users delay use of these controls until a basic familiarity with IRvista 2 51 has been developed but an overview is provided here A different existing camera settings file can be selected by navigating to the file This will apply different NUC and BPR tables and will change camera settings Pressing the create new NUC BPR file button will generate a new camera settings file using the current NUC and BPR tables and the current camera settings if an Alpha NIR camera is in use Camera settings for other Indigo Systems cameras are saved in the settings files if the camera is in external NUC and BPR mode When the camera is in internal NUC mode blank NUC tables with gains of 1 and offsets of 0 are stored in the settings file Similarly setting the camera to internal BPR mode causes the settings files to contain bad pixel maps with no bad pixels This feature is useful for repeating experiments under identical circumstances When the desired camera configuration and NUC BPR tables are in use press this button and save a settings file Simply reload this settings file by pressing the file dialog button to return to the same conditions Pressing the Set to Factory Defaults button will reset the NUC
60. n Alpha NIR camera 2 2 IRvista 2 51 Tutorial 2 2 1 An overview of the IRvista 2 51 window IRvista 2 51 User s Manual 321 0028 10 04 08 03 9 The IRvista 2 51 window is divided into several regions In the tour that follows we will explore each region in detail The menu bar is located across the top of the application window The tool bar is located directly beneath the menu bar Most application features are accessible from both the menus and the tool bar The exit button is at the right end of the tool bar near the Indigo Systems logo but exiting is also possible under the file menu as usual in Windows applications Video and still images are displayed on the left portion of the panel beneath the toolbar For large format cameras such as the Phoenix 640 x 512 the image is reduced by a factor of two so that it can be displayed on the IRvista GUI without covering other controls However the entire 640 x 512 image is recorded to disk and the entire image is used in all image analysis routines The color palette selector and the color palette inverter are located beneath the image display window Displays associated with certain analysis tools are visible in the top of the center section of the application window Controls for the intensity histogram and intensity windowing are located beneath the analysis tool displays This histogram is located to the right of the histogram controls Above the histogram on the right portion of the app
61. n a single image We will now perform some arithmetic operations on this image Set the operation selector below A to and type 1000 in the number box adjacent to the operation selector Note do not use the operation selector that is located between images A and B We will learn how to use that later Hit the C button and observe the results IRvista 2 51 User s Manual 321 0028 10 04 08 03 69 Notice that the image written to the C image display is the A image with 1000 added to each pixel Again notice that the average and standard deviation of C are calculated and displayed below the image Try some other operations on A For example try multiplying A by 100 In this case all of the pixel values will be larger than the 12 bit image maximum of 4095 and the 14 bit image maximum of 16383 and are thus mapped to the appropriate maximum and displayed as white Save image C as image1 bin by pressing the Save C button Hit the Load A button Select the file image1 bin Again perform some operations and observe the results Try to open an image sequence with the using the Load A button In this case the first image in the sequence is displayed We will see later that there is a way to extract any image from a sequence and display it Binary image operations Now hit the create A button again and create an image with an average of 1000 and a standard deviation of 100 Hit the create B button and create an image with an average of 1000 and a s
62. n record mode Maximum Time Control Live Mode only Sets the maximum time for acquisition of frames in record mode IRvista 2 51 User s Manual 321 0028 10 04 08 03 50 Minimum Delay Control Live or Burst Mode only Sets the minimum delay between frames in record mode This allows long term monitoring of a scene The actual delay between frames will be slightly longer due to acquisition processing and disk writing time The additional delay will be system dependent VCR Controls Burst Mode Disk Mode or Filter Mode only Nine buttons that allow typical VCR type controls The nine buttons are rewind to first frame fast rewind single step rewind rewind pause play single step play fast forward forward to last frame Frame Indicator Burst Mode Disk Mode or Filter Mode only Indicates the current frame of the recorded video displayed VCR Limits Control Burst Mode Disk Mode or Filter mode only Sets the range of recorded video frames to display and indicates the number of frames available in the recorded video Frame Delay Control Burst Mode Disk Mode or Filter mode only Sets the frame delay in milliseconds for the display of the recorded video New Burst Button Burst Mode only Records a new video of a fixed number of frames burst and displays the new burst Save Burst Button Burst Mode only Saves the current recorded burst to disk A file dialog prompts the user for path and filename Save Portion Control
63. nality of the IRvista 2 51 application 1 2 Installing IRvista 2 51 IRvista 2 51 is provided on a CD To install IRvista 2 51 Insert CD into the CD drive From the Desktop double click the My Computer icon Within the My Computer Folder double click the CD Drive icon Open the READ ME FIRST file on the CCD and follow the setup instructions You can now start IRvista 2 51 by double clicking the applications icon located in the installation directory IRvista 2 51 User s Manual 321 0028 10 04 08 03 6 1 3 IRvista 2 51 Overview IRvista 2 51 is a real time image acquisition and analysis application that provides the user with acquisition storage retrieval display processing and analysis of still images and video in a flexible convenient Windows interface Video acquisition and camera control Video acquisition via the National Instruments PCI 1422 Card is automatic and transparent to the user Live video images can be displayed in a continuous stream from the acquisition system at about ten frames per second or bursts with a fixed number of frames can be acquired at a higher camera rate and can subsequently be reviewed with convenient VCR style controls The video is displayed as an 8 bit gray scale mage with color palette selection and zoom features available Bursts and live image streams can be saved to disk and later retrieved While the image is compressed to 8 bit gray scale for display the video is saved analyzed and r
64. nd is engaged and you can turn on and off expand when zoom is engaged Try some of these combinations Deselect expand and zoom when finished The zoom and expand image features can also be selected or deselected from the menu Under the tools menu select ROI Define a region of interest and then push the zoom button The ROI zoom feature can now be selected or deselected from the menu Under the tools menu select zoom X 2 and observe Deselect zoom X 2 The Image Statistics panel allows user to use addition subtraction multiplication division and other mathematical operations on images This tool is further discussed in Chapter 5 0 Advanced Features The NUC and BPR routine is used to calibrate the camera by generating new non uniformity and bad pixel replacement tables This operation has the potential to make a new camera settings file to replace the one that come with your camera A calibration tutorial is included later in this manual The update pixel offsets routine temporarily updates the offsets table used in the non uniformity correction routines This routine does not affect the camera settings file and the update will be lost once the software is restarted Press this button When the prompt appears present any view to the camera and proceed When the new offsets table is generated and applied observe the effects The intended use for the update pixel offsets routine is improvement of camera calibration by adjusting the pixel
65. nter disk mode and recall SingleFrame bin Observe the display of the single frame of video All analysis and ROI tools discussed below can be applied to this frame of video Return to live mode Hover near the save image button The tip saves current image as bmp tif png or jpg file will appear Press this button A file dialog window pops up asking the user to enter a file path A snapshot of the current image will be saved as username1 bmp username1 jpg etc Pressing the button again will cause the current image to be saved as username2 bmp or jpg and so on unless the user enters a new name Press the button and save with a suitable name Press the button again The snap shots can be viewed in Internet Explorer and other applications Note that the saved image will be identical to the image displayed on the screen In other words the saved image will have the same resolution color palette and analysis tools as the image displayed on the screen In particular images acquired with large format cameras will be saved at lower than native resolution using this function Use the export function discussed below to save images in other formats Hover near save panel button and observe the tool tip Press the save panel button and enter a file name Operation of the save panel feature is very similar to operation of the save image feature except that the save panel feature saves snap shots of the entire application window These snap shots
66. ol window but reverting in the camera control window affects NUC and BPR The toolbar revert does not but the user may notice a slight reduction in frame rate when the toolbar revert is used Deselect image reversal The analysis tools we have just toured are available via the menu Under the tools menu select and deselect one or two of the analysis features such as spot intensity area stats line profile etc and The define ROI for zoom button left allows the user to select a region of interest to zoom into Press the button and select an ROI as above For this first attempt select an ROI that is perhaps 1 3 as wide and 1 3 as tall as the entire image Press the zoom button right The application will now display an enlarged image of the ROI that roughly fills the image viewing area If the define ROI for zoom button is pushed a second time selection of an ROI will be cancelled The ROI selection times out after 5 seconds with a warning that no ROI has been selected Try selecting and displaying some different ROIs IRvista 2 51 User s Manual 321 0028 10 04 08 03 26 The expand image button enlarges by a factor of two the image or ROI if zoom is selected This will cause some of the controls and displays to be covered Press the button and observe Press the expand button again to deselect ROI Zoom and expand operate independently You can select an ROI for zoom when the expand is engaged you can turn on and off zoom while expa
67. orrected pixel intensities will be described by P ij Gij Pij Oij Where P ij are the corrected pixel intensities Gij are the gain corrections Pij are the uncorrected pixel intensities and Oij are the pixel offsets The details of this calculation are described in Chapter 4 Pixels with gains outside of an acceptable range defined by the user during calibration will be labeled bad pixels Pixels which fluctuate too much during the 64 frame sequences acquired for calibration will also be labeled bad During operation the IRvista 2 51 software will replace bad pixels intensities by values obtained from a bi linear interpolation of adjacent pixel intensities The details of this calculation are described in Chapter 4 Camera Calibration When ready press the camera calibration button You will immediately be prompted for a file name Note the flashing message box at the bottom of the window This box will contain directions for each step in the calibration process Navigate to a suitable location and type in a file name Hit save A folder with this name will be created for files associated with the camera calibration procedure Alternately you can navigate to an existing folder and hit Select Cur Dir IRvista 2 51 User s Manual 321 0028 10 04 08 03 34 You should now see the following window The panel is divided into five sections At the bottom left the current live image is displayed Move the camera or move your hand in
68. ory is very limited IRvista dynamically sets the maximum number of images in a burst according to available system memory The acquisition will take about seven seconds The number of frames to be acquired in burst mode can be set from the front panel using the control Later we will use the settings window to change the number of images to be acquired in a burst and other burst parameters Once the burst has been acquired the application window will change appearance In particular VCR controls and burst controls will appear as shown in figure 2 2 IRvista 2 51 User s Manual 321 0028 10 04 08 03 13 Figure 2 2 The IRvista 2 51 application window in burst mode The image in this figure was acquired using a Merlin camera Beneath the VCR controls find the burst controls Press new burst A new 64 frame burst will be acquired and displayed Press save burst A file dialog will pop up Save the video as burst1 Set the minimum frame delay to 10 000 ms and acquire a sequence with 5 frames The pop up burst acquisition window displays an image acquisition counter for sequences that are expected to take longer than five seconds to acquire Press the various VCR controls and observe their behavior From left to right they are To frame 1 IRvista 2 51 User s Manual 321 0028 10 04 08 03 14 Run backwards and loop continuously Back one frame Run backwards and stop at frame 1 Pause Run forward and stop at last frame Forward on
69. plane should produce exactly the same readings when the camera is presented with a perfectly uniform view plus or minus about one count due to noise This calibration proceeds as follows First a sequence of 64 frames is obtained for a bright source Bij a medium source Mij and a dark source Dij The average of all 64 frames is calculated in each case The result is three images one for a dark source one for a medium source and one for a bright source These three images are used in the next step with the caveat that bad pixels are excluded from the calculation This will be explained below The difference between the bright and dark readings is measured per pixel and is called the response of the pixels Rij The spatial average lt Rij gt of Rij is calculated by averaging over all the pixels in the image and the pixel gain correction factors are then defined as Gij lt Rij gt Rij To the extent that the gain of each pixel is constant over the range from the dark intensity to the bright intensity the application of these gain correction coefficients thus assures that a change in brightness will cause the same change in reading for all pixels in this range The offset corrections are then calculated to ensure that the reading for each pixel will be the same at the medium brightness This is done as follows Taking the raw medium pixel readings Mij and multiplying by the gain correction factors yields the gain corrected medium intensity pixel
70. played Stats for up to four spots can be displayed simultaneously The color of the overlay marking each region can be changed using the ROI color controls Make the color of each overlay different and observe the results The 3D Graph feature calls a pop up window that displays a 3D graph with intensity on the z axis This operation is computationally intensive and slows the frame rate noticeably Press the button and observe the graph The graph can be resized by dragging a corner in the usual way Increase the size of the graph and observe that the slowing of the frame rate is more severe If the 3D graph is too large it may not be possible to display the entire graph The limitations on the size of the graph will be system dependent Close the 3D graph either from the menu or by pressing the 3D graph button on the toolbar again The invert image feature inverts the image top to bottom Press the button and observe the results If your system includes an Indigo Alpha NIR camera the image can also be inverted in the camera control window but inverting in the camera control window affects NUC and BPR The toolbar invert does not but the user may notice a slight reduction in frame rate when the toolbar invert is used Deselect image inversion The revert image feature reverses the image from left to right Press the button and observe the results If your system in includes an Indigo Alpha NIR camera the image can also be reverted in the camera contr
71. ponding to the 12 bit intensity data of the image The X axis units are pixel number and correspond to the pixels included in the user defined line Line Profile Line Thickness Selects the thickness of the line from which the statistics are calculated A line thickness of three for example averages the statistics for three adjacent lines Thicker lines reduce statistical fluctuations in the profile Line Profile Autoscale Autoscales the horizontal axis of the line profile graph When autoscaling is turned off the axis scale can be edited by selecting the largest or smallest label and typing in a new value Line Profile Save Button Saves the current line profile data as an Excel spreadsheet file with extension xls Line Profile Stats Button Turns on calculation and display of statistics for pixels along the selected line Intensity Histogram Graph Displays an Histogram of pixel intensities for the pixel displayed in the image window The Y axis units are number of pixels in a particular intensity bin and the X axis units are the Intensity bins ranging from 0 to 4095 for the 12 bit image Right mouse on the graph to enable autoscaling and to define new axis parameters Intensity Histogram Stats Turns on calculation and display of statistics for the image pixels used in the histogram calculation Usually this is the entire image but if ROI Zoom is in use then the histogram will contain only data for pixels in the region of interest Intensity H
72. rsors can operate in either of two modes If automatic gain control AGC is turned on then mean and standard deviation of the histogram is measured and the cursors and thus the intensity limits are set to mean n where n is set by the selector to the right of the cursors AGC switch Set the Cursors AGC switch to AGC and adjust the number of standard deviations to include in the intensity window Observe the effect on the image Set the cursors AGC switch to cursors The cursors can now be moved with the mouse Grab the lower cursor and move it Repeat with the upper cursor Note what happens if the upper cursor is set just above the lower cursor In this case most of the pixels in the image are either above Imax or below Imin and are mapped to black or white thus the image appears mostly black or white The cursor positions can be changed in small steps using the arrows to the left of the histogram The number of bins in the histogram is normally set at 256 With a 12 bit image there are 4096 possible values of the intensity 14 bit has 16384 possible values and thus each bin in the histogram contains the number of pixels with 16 different intensity values The number of bins can be adjusted For example if the number of bins is set to 4096 then the number of pixels with each possible intensity in the 12 bit image will be reported Setting the number of bins larger than 256 slows acquisition and also results in larger statistical fluctuations in his
73. rst Button Selects the video source as camera records a fixed number of frames burst and displays the recorded video This also enables the display of the VCR controls if not already displayed Disk Button Selects the video source as a file opens and displays the recorded saved video file This also enables the display of the VCR controls if not already displayed Filter Button Puts IRvista 2 51 into tunable filter mode This button is disabled and grayed out if no filter is present File Path Indicator Disk Mode only Displays the file path of the recorded video file currently displayed Freeze Pause Button Live Mode only Freezes the video display During recording this button becomes a Pause button Pressing Pause during recording stops the recording of images to file Record Button Live Mode only Records the video to disk The user is prompted with a file dialog before recording begins File size is set in the Preferences Panel The maximum single file size is 2 GB Larger image sequences will be divided into multipart files with the characters _001 _002 appended to the individual partial files Timestamp button Adds a timestamp to the file for each acquired image Disappears during recording phase Time date display Displays time and date at which images were acquired if timestamp was selected during acquisition Maximum Frames Control Live Mode only Sets the maximum number of frames that can be recorded to disk i
74. s readings GijMij The average gain corrected medium intensity pixel reading lt GijMij gt is calculated by averaging over all the pixels The offset corrections Oij are then calculated by requiring that the gain and offset corrected pixels all have the same reading when presented with a uniform medium intensity source so that GijMij Oij lt GijMij gt IRvista 2 51 User s Manual 321 0028 10 04 08 03 60 The average gain correction factor is by construction 1 0 and the average offset correction factor is by construction 0 0 Bad Pixel Replacement BPR Most focal planes contain a few defective pixels that cannot be corrected by the NUC routines These bad pixels are identified in two ways The first step of the NUC routine above involves acquiring 64 frames while the camera is presented with a bright medium and dim source The response for each pixel are then calculated as Rij Bij Dij Pixels with response too far from the average are labeled bad and are not used in the remainder of the calculations In particular they are not used in computing lt Rij gt In addition the temporal fluctuation of the readings for the medium intensity source are measured as the standard deviation of the values of each pixel Pij over the 64 frames in the medium intensity sequence Pixels which fluctuate too much are labeled bad and are not used in the remainder of the calculations The bad pixel maps produced in each step are anded
75. so that only pixels that pass both tests are labeled good In the IRvista 2 51 calibration routine the user is able to set limits for the average response and acceptable fluctuations The data from bad pixels are typically replaced by data from one or more nearby pixels The algorithm employed in the IRvista 2 51 averages the nearest good pixel in each of four directions x x y y to replace the data from the bad pixel For example in the partial image below the pixels marked with X s are defective while the rest are good In this example pixels 3 4 and 3 5 are bad Pixel 3 4 would be replaced by the average of pixel 3 3 3 6 2 4 4 4 Similarly pixel 3 5 would be replaced by the average of pixels 3 3 2 5 4 5 3 6 Note that replacement pixels can be at most ten pixels away from the bad pixel NUC and BPR data is specific to a particular focal plane and to specific camera settings such as high low gain image orientation other settings and particularly integration time During manufacture by Indigo Systems each focal plane is carefully calibrated against uniform sources of known intensity under well defined conditions The results of the calibration include a gain and offset for good each pixel in the focal plane as well as a map of the bad pixels These are provided in the form of a camera settings file that is serial number specific We now turn to the structure of image sequence and camera settings files
76. t is acquired from the camera except for non uniformity correction and bad pixel replacement more below Turn image compression back on and continue Note that the images saved to disk in either live or burst mode are saved in raw form The data saved on disk is not intensity windowed but recalled data will be intensity windowed for display in disk mode This allows the user to view a saved image stream with different intensity windowing settings and assures that no information is lost when the data is saved to disk 2 2 2 5 Tool bar and analysis features Press the live button in the mode selector portion of the application window This returns the software to the continuous operating mode The VCR controls will thus disappear Be sure record is deselected Find the tool bar near the top of the application window beneath the menu bar A pop up tool tip will appear when the mouse hovers near a button The open file button has disappeared It appears only when the application is in disk mode Pressing this button causes a new video file to be loaded IRvista 2 51 User s Manual 321 0028 10 04 08 03 21 Hover near the save frame button Pressing this button will cause the currently displayed frame to be saved as a IRvista 2 51 native sequence file with a single frame The structure of IRvista 2 51 sequence and settings files is discussed in detail later in the manual Press the save frame button and save a file with the name SingleFrame E
77. tandard deviation of 0 Set the binary operation selector between A and B to Hit the button between B and C and observe the results Hit the save C button Navigate to a suitable location and save the results of your calculation 5 3 2 Masking Sequences and Settings Files Before continuing with the tutorial we will need to learn more about the way that Indigo Systems IRvista 2 51 saves image sequences and settings files Detailed information about the file structure is presented in the Technical Information chapter in the IRvista 2 51 manual Please review this information before proceeding IRvista 2 51 User s Manual 321 0028 10 04 08 03 70 As is discussed in the Technical Information chapter in the IRvista 2 51 manual the settings files that you have created using the camera calibration routine are simply image sequence files with no images Thus settings files and image sequence files can be handled identically in most contexts We will now explore ways to modify these files directly using the IMAGE STATISTICS window Using Windows Explorer navigate to the examples folder or to your own data Make a disposable copy of one of the image sequence files and name it disposable bin In the lower right corner find the image sequence controls Hit the load button Navigate to the sequence disposable bin that you created in the last step Hit the play button to display the sequence Adjust the frame delay and observe the results Note t
78. ted Load the sequence disposable bin again and write image 1 to A Note the average and standard deviation Now hit the Apply Mask button and note that the statistics change The pixels labeled bad in the mask have been excluded from the statistics IRvista 2 51 User s Manual 321 0028 10 04 08 03 74 It is sometimes useful to create test image sequences analogous to the test images we created earlier In the image sequence controls section in the lower right portion of the Image Statistics window hit the create button A pop up window allows the user to create a sequence with an adjustable number of frames adjustable mean and adjustable sigma Set the average to 1000 12 bit or 4000 14 bit and set sigma to one fourth of the average Set the number of images to 25 When the created sequence is played a random shifting gravel like pattern appears It may be helpful to brighten the display by a factor of two The details of the appearance can be changed by adjusting the mean and standard deviation Send the sequence average to A and send the sequence standard deviation to B The numerical values in the discussion that follows assume a 14 bit image has been created If a 12 bit image has been created please divide all of the numbers by four First image A contains the image pixels averaged over the sequence and thus it is less grainy than any individual image in the sequence In particular notice that the average pixel value in the sequence a
79. togram values It is sometimes appropriate to update the histogram and ACG information less frequently Setting the update delay to 10 for example will cause the histogram to be updated every tenth frame If the update delay is set to zero the histogram will not update but intensity compression will continue to operate using the most recent cursor positions IRvista 2 51 User s Manual 321 0028 10 04 08 03 20 The range of histogram intensity axis horizontal axis can be adjusted by editing the markers For example select the 4100 Merlin Alpha or 16 400 Phoenix and type in 1000 Next push the zoom button Notice that the histogram intensity axis is adjusted so that only bins between the minimum and maximum intensity are displayed Push the full scale button and observe that the histogram intensity axis is adjusted to include the entire range of intensities The save button on the histogram allows the user to save the histogram data as a two column spreadsheet file that can be opened with Excel Push this button and enter a file name On the right side of the histogram find the stats button Press the button and observe that the mean standard deviation min and max of the intensity histogram are displayed Turn off display of histogram statistics Image compression is normally on but it can be turned off from the menu Find the compression on item in the setup menu and deselect compression The application is now displaying the image as i
80. utton on the tool bar Filter Mode If you purchased a tunable color filter with your Indigo Systems camera and it is connected a fourth operating mode will be available In this operating mode discussed in a later section it is possible to acquire a sequence of images in which each frame is acquired in a different band of wavelengths This is sometimes called an image cube Support for image cube acquisition and analysis is included in IRvista 2 51 2 2 2 3 Integration Time IRvista 2 51 User s Manual 321 0028 10 04 08 03 18 In the center section of the IRvista 2 51 panel below and to the right of the image find integration time IT control This control sets the camera integration time per frame Increasing the integration time is appropriate for dark fields of view while decreasing the integration time is appropriate for bright fields of view Valid integration times depend on the type of Indigo Systems camera present in your system Set the integration time to 5000 microseconds Alpha NIR or 45 us Merlin Uncooled by highlighting the entire number and typing in 5000 or 45 Unless the camera is presented with a dim field of view and or the shutter is nearly closed the histogram should show that nearly all of the pixels are pegged out at 4095 Try a few different values for integration time and observe the effects Note that the actual integration time may differ slightly from the requested integration time If an invalid
81. ve the option of changing the bit depth but it is recommended that users of Alpha and Merlin cameras work in 12 bit and Phoenix users work in 14 bit Note that the statistical tools will work correctly with all images and sequences created in IRvista independent of the bit depth setting for new images 5 3 1 Arithmetic Operations on Images We will create a noisy gray image and then perform some arithmetic operations on this image Hit the Create A button A pop up panel appears as below Set the average to 2000 and the standard deviation to 300 and hit return the exit button represented by a closing door IRvista 2 51 User s Manual 321 0028 10 04 08 03 68 The noisy gray image will now appear in the A image display section of the IMAGE STATISTICS window see below Notice that the average and standard deviation of the image are automatically calculated and displayed below the image Adjust the brighten control This brightens the display without changing the actual data Brighten the display by a factor of 2 and notice the results Image pixels can take values from 0 black to 4095 12 bit images or 16383 14 bit images When a calculation or brightening operation results in pixel values greater than or equal to 4095 or 16383 those pixels are set to the appropriate maximum and displayed as white When a calculation results in a pixel value of less than or equal to zero the pixel is mapped to zero and displayed as black Operations o
82. verage image A is very close to 4000 The standard deviation of the pixels in the sequence average image is about 200 This is expected since averaging noise reduces the sigma by a factor of square root of N where N is the number to trials Each pixel is averaged over 25 images so we expect the sigma to decrease by a factor of square root of 25 or 5 Thus the sigma of the pixels in the sequence average is 1000 5 200 Note that the sequence standard deviation which measures how much each pixel fluctuates from one frame to the next is about 1000 In other words each pixel fluctuates from frame to frame to the same degree that pixels within an image fluctuate Load the sequence gains to A and the sequence offsets to B Note that the gain corrections are all 1000 and the offsets are all 2048 12 bit or 8092 14 bit Recall from chapter 4 that gains are multiplied by 1000 for storage in the image sequence file so this means all of the gain corrections are 1 Similarly 2048 12 bit or 8092 14 bit is added to each offset for storage in the image sequence file so the offsets in this sequence are all zero 5 3 3 Example Problems 1 Senior Technician Smith is wants to study the low intensity portions of a laser beam She has used Indigo Systems IRvista 2 51 to acquire a sequence of images of the beam but studying the statistics of the many low intensity regions is tedious because they are spread throughout the image Smith can use the IMAGE STATIS
83. when the Compression button is pressed 3 2 Menu Bar The Menu Bar is the top item It has six drop down menus to select among the different functions and options File Setup Mode Tools Camera and About With few exceptions the functions in the menu are also accessible from the toolbar and vice versa In most cases users may thus choose to use the toolbar menus or both purely as a matter of taste and convenience In the following each of the functions in the menu is discussed An image of the toolbar button associated with each function is provided for convenience 3 2 1 File The File menu has seven items Open Opens an existing video file Save Image Saves the current image single frame of the video to disk in IRvista 2 51 native file format with a bin extension The bin file is a sequence file with a single image and contains the usual components of a IRvista 2 51 sequence file See chapter 4 for a detailed description of IRvista 2 51 sequence files Save Image Saves the current image single frame of the video to disk as a jpeg file Save Panel Saves the application window and the current image single frame of the video to disk as a jpeg file Page Setup Opens a dialog box for setting up printing options IRvista 2 51 User s Manual 321 0028 10 04 08 03 55 Print Panel Prints the application window and the current image single frame of the video
84. with other analysis tools IRvista 2 51 User s Manual 321 0028 10 04 08 03 58 Invert Enables disables inversion of the image from top to bottom Can be used in conjunction with other analysis tools Revert Enables disables reversion of the image from left to right Can be used in conjunction with other analysis tools Image Statistics Allows user to use addition subtraction multiplication division and other mathematical operations on images This tool is further discussed in Chapter 5 0 Advanced Features 3 2 5 Camera Calibrate Camera Launches a utility that helps users create new camera settings files including Non Uniformity Correction NUC tables and Bad Pixel Maps used in the Bad Pixel Replacement BPR routine These new tables can then be written to a new camera settings file The original camera settings files provided with the camera are not overwritten and can be restored to use if necessary Requires bright medium and dark uniform sources Recommended for expert users only Offset Update Similar to Calibrate Camera but only updates the offsets in the NUC tables This update is temporary and the information is lost when the application closes To make permanent changes use Calibrate Camera Camera Control Launches a camera control GUI that gives users access to most of the commonly used camera functions Warning some camera settings may be incompatible with NUC and BPR tables and may thus dramatical
85. y be necessary IRvista 2 51 User s Manual 321 0028 10 04 08 03 41 The filter mode button should now be available Press this button The software will enter the filter mode Notice that the line profile graph has been replaced by a graph of spot intensity versus wavelength but otherwise the main window looks similar to burst mode However acquisition has stopped We need to acquire a new burst with the filter present Press the new burst button A new window will appear as shown below This window is designed to help you set up and acquire an image cube An image cube is a set of images each taken with through a filter that passes only a narrow range of wavelengths IRvista 2 51 User s Manual 321 0028 10 04 08 03 42 When the window launches the minimum and maximum available filter settings are displayed We will need to construct a filter palette A filter palette is a set of wavelengths at which images will be acquired There are three tools to help the user construct a palette Appending wavelengths Type 1000 into the wavelength control beneath the append button Press the append button Notice that the first element in the palette is now 1000 nm Enter another wavelength and append Use of the fill command Press the clear button to clear out the palette Now set the start wavelength to 1000 nm the end wavelength to 1600 nm and the wavelength step to 50 nm Press the fill button Notice that the palette now has a ramp of wave

IR Vista - FLIR Systems

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