August 2006 Version 1.1
Table of Contents Section Page 1 Hardware... 1 2 Mounting Procedure... 2 3 CCD Alignment... 6 4 Software... 7 5 Wiring Diagram... 19
1 HARDWARE While it is not necessary to have a comprehensive understanding of the Hyperscan hardware to collect spectral data, a low-level understanding of the components will help the user better understand how the system operates. The numbered items seen in Figure 1 represent the main components of the Hyperscan system. A description of each of these components is found in Table 1. (1) (4) (2) (3) (12) (5) (6) (11) (10) (8) (9) (7) # 1 2 3 4 5 6 7 8 9 10 11 12 Figure 1. System Components. Table 1. Component Description. Component Function Mounting Plate #1 Attach system to mounting surface Power Supply Provide power to system components Spectrograph Create spectral data Mounting Plate #2 Attach system to mounting surface Shutter Controller Trigger shutter Firewire Hub Provide external power to firewire camera Firewire Camera Capture image data Lens Focus light onto spectrograph s slit Shutter Allow dark field collection Scanning Mirror Reflect light into the focusing lens Stepper Motor Move mirror to change the field of view Stepper Motor Controller Convert control logic into current pulses A laptop computer with the Hyperscan software already installed has been shipped with the system. The specifications of the laptop are shown in Figure 2. 1
Figure 2. Computer Specifications. 2 MOUNTING PROCEDURE The Hyperscan system has been designed so that it can be mounted on its side or from the top. Both mounting orientations allow for easy attachment to standard optical breadboards with ¼ - 20 tapped holes on one inch centers. 2.1 Side Mounting In order to allow the system to be mounted on its side, the Hyperscan system comes equipped with a removable balance plate. The balance plate, which is visible in Figure 3, is not needed when mounting the system from the top. 2
1 Balance Plate Side Mounting Holes 6 1 2.1 Top Mounting Figure 3. Hole Pattern for Side Mounting. To hold the Hyperscan system from the top, two mounting plates have been provided. These plates have a combination of ¼ - 20 clearance and tapped holes. The top mounting configuration is further explained by Figure 4. Upon delivery of the Hyperscan unit, it will be necessary to remove the shutter controller (labeled 5 in Figure 1) in order to access the bottom of mounting plate number 2. Removing the shutter controller is very straightforward. First, remove the four screws holding the controller s box together using a small Phillips screwdriver. Be sure not to remove the two cap screws oriented diagonally from one and other. The screw removal process is illustrated in Figure 5. 3
1 1 9 ¼ - 20 Tapped/Clearance Figure 4. Top Mounting Bolt Pattern. Top View Don t Remove Remove Don t Remove Figure 5. Screw Removal. 4
Once the four Phillips screws have been removed, unplug the cable from the control box and remove the shutter controller. The controller is shown removed in Figure 6. Notice that all of the electronic hardware has come off with the cover. There is no need to remove any wires. Figure 6. Shutter Controller After Removal. With the shutter controller removed, the next step is to remove the back of the controller s box. This is done by removing two M6 bolts. These bolts are covered with black electrical tape to prevent them for shorting any of the shutter s electronics. The shutter back removal process is shown in Figure 7. Figure 7. Shutter Box Removal. Once the back of the shutter box has been removed, it is possible to access the mounting holes from below. This is shown in Figure 8. 5
Figure 8. Mounting Hole Access. After the Hyperscan unit is mounted, reassemble the shutter box and plug in the D-sub cable. Be sure to remember to cover the bolts holding the back cover with electrical tape. 3 CCD ALIGNMENT Before shipment of the Hyperscan system, performs a rigorous alignment to assure that the CCD is positioned correctly with respect to the spectrograph. However, if the system goes out of alignment a series of screws can be adjusted in order to bring the system components back into their correct positions. The CCD imager is attached to the spectrograph via a 4 degree-of-freedom fixture. Specifically, tip, tilt, rotation, and z (distance between spectrograph and CCD focal plane) positions can be manipulated via the mount. These manipulations are facilitated by adjusting the position of the 5 screws shown in Figure 9. Adjusting the rotation of the CCD imager via the two rotation screws assures that the pixel array is square with the image formed by the spectrograph. In order for the Hyperscan system to produce meaningful data, it is essential that the CCD is oriented correctly with the spectrograph. Therefore, note the original orientation of the camera before detaching it to prevent it from being mounted 180 out of position. Adjustment of the camera s pan, tilt, and z positions is facilitated by adjusting three screw assemblies labeled Alignment Screws in Figure 9. Using the special tool shipped with the Hyperscan unit, the outer ring of the screw assemblies is adjusted to set the gap between plates 1 and 2. Once adjusted, the center cap screw is used to lock the plates into place. 6
Rotation Screws Alignment Screws Figure 9. Alignment/Rotation Screws. 4 SOFTWARE The Graphical User Interface (GUI) used to control the Hyperscan system is shown in Figure 10. Inspection of Figure 10 shows the GUI divided into 5 sections. Each of these sections are discussed in detail below. 4.1 GUI Section 1 - Lab Setup The section of the GUI with the heading Lab Setup is used in conjunction with the Mirror Control section to control the field of view of the Hyperscan system. Each of the controls found in the Lab Setup section are described in Table 2. Figures 11 and 12 have also been added to further explain the Lab Setup parameters. 7
1 2 3 4 Figure 10. Graphical User Interface. 5 Figure 11. Lab Setup. 8
Label CCD Pixel Size Focal Length Object Distance GSD (Ground Sampling Dist.) Start Distance End Distance Number of Lines Table 2. Lab Setup Parameter Description. Description CCD s pixel size is 13.7 µm 13.7 µm Focal length of the collecting lens Distance between ground and lens Size of a single pixel at the object distance The distance, with respect to the reference point, to start the scan The distance, with respect to the reference point, to end the scan Number of frames captured to complete the scan Adjustable NO YES YES NO YES YES NO Figure 12. Hyperscan System Schematic. 4.2 GUI Section 2 - Mirror Control The Mirror Control section is used to manually adjust the position of mirror and set the reference point. Figure 13 and Table 3 describe the Mirror Control parameters in greater detail. 9
Button << < > >> - Stop + Set Reference Go to Reference Figure 13. Mirror Control. Table 3. Mirror Control Parameter Description. Function Moves the mirror towards the limit switch at high speed Moves the mirror towards the limit switch at low speed Moves the mirror away from the limit switch at low speed (scan direction) Moves the mirror away from the limit switch at high speed (scan direction) Moves the mirror one scan line* towards the limit switch Stops all mirror movement Moves the mirror one scan line* away from the limit switch (scan direction) Changes the reference point to the current mirror position Moves the mirror to the reference point 4.3 GUI Section 3 - Camera Setup *Scan line refers to the distance between subsequent frame captures The third section of the GUI is shown in Figure 14. The first button, which is label Cam Setup, is used to control the camera s capture parameters. When this button is pushed, a screen appears that gives the user additional controls. This screen is shown in Figure 15. Figure 14. Section 3 of the GUI. 10
Figure 15. Camera Setup Screen. The Camera Setup screen shown in Figure 15 has been divided into 4 sections. The first section contains an image histogram and the controls used to change the way the histogram is displayed. Table 4 describes the contents of Section 1 in detail. Label Y Min Y Max X Min X Max Auto Axis Manual Axis Threshold Table 4. Histogram Parameters. Description Sets the minimum value of the histogram s Y axis Sets the maximum value of the histogram s Y axis Sets the minimum value of the histogram s X axis Sets the maximum value of the histogram s X axis Automatically sets the min and max axis values Allows the user to manually set the min and max axis values Set the pixel count used to control the image display Adjustment Y* Y* Y* Y* On/Off On/Off Y * Manual axis control must be selected 11
The threshold control shown in Section 1 is used for image display purposes only. Specifically, the threshold value can be adjusted to set the slope and intercept of the line used to map the captured image (12 bits) to an image that can be displayed on the screen (8 bits). Figure 16 further explains how the threshold number affects bit mapping. Figure 16. Bit Mapping. From Figure 16 it can be seen that a threshold of 10 causes an intersection at X 1 and X 2. In order to display the image that corresponds Figure 16 s histogram, the Hyperscan software sets all pixels values less than X 1 to 0 (black) and all values greater than X 2 to 255 (white). Pixel values between X 1 and X 2 are remapped in a linear fashion. Section 2 of the Cam Setup screen holds the controls for integration time, gain, and offset. The Default buttons located next to the integration, gain, and offset sliders are used to replace the existing values with a hard coded value. Table 5 gives additional information regarding the controls in Section 2. Label Close Integration Time Gain Offset Table 5. Section 2 Control Parameters. Description Max Value Min Value Closes the Cam Setup Screen - - Controls Integration 17.9 min 0.01 ms Controls Gain 45 1 Controls Offset 2,047-2,048 Default Value - 10 ms 1 0 12
Section 3 of the Cam Setup screen allows the user to specify a Region of Interest (ROI). A ROI is selected by specifying the upper-left and lower-right pixel coordinates of a rectangular box (applied to the frame display). Table 6 gives additional details about the ROI controls. Label Apply ROI Left (spatial) Top (spectral) Right (spatial) Bottom (spectral) Table 6. ROI Controls. Description Allows user to switch from full screen to ROI Used to select left-most coordinate of the ROI box Used to select the top-most coordinate of the ROI box Used to select the right-most coordinate of the ROI box Used to select the bottom-most coordinate of the ROI box The final section of the Cam Setup screen, Size Control, is used to set pixel binning. Pixel binning refers to a CCD s ability to clock multiple pixel charges, in both the horizontal and vertical directions, into a single larger charge or super pixel. The super pixel represents the area of all the individual pixels contributing to the charge. Binning of 1 1 means that an individual pixel is used as is. A binning of 2 2 means that an area of 4 adjacent pixels will be combined into one larger pixel, 3 3 uses 9 adjacent pixels, and so on. When 2 2 binning is used, the sensitivity to light has been increased by 4 (the 4 pixel contributions), but the resolution of the image has been cut in half. Figure 17 has been added to help illustrate the effects of pixel binning. Figure 17. Pixel Binning. The controls used to set the level of pixel binning are described further in Table 7. Label CCD Size, X (Spatial) CCD Size, Y (Spectral) Binning, X (Spatial) Binning, Y (Spectral) Data Size, X (Spatial) Data Size, Y (Spectral) 4.4 GUI Section 4 - Display Table 7. Size Control Parameters. Function Displays the number of spatial pixels available Displays the number of spectral pixels available Controls binning in the spatial direction Controls binning in the spectral direction Displays the number spatial super pixels after binning Displays the number of spectral super pixels after binning The section of the GUI with the heading Display is used to control the appearance of the displayed image. The Display section is shown in Figure 19. 13
Figure 19. Display Controls. The Hyperscan software offers two different image display modes. The first type of display is full frame. To view the full image frame, check the box labeled Frame Display. When Frame Display is selected, the Hyperscan software returns the entire image captured by the system s camera. Therefore, many different spectral bands and spatial locations are displayed simultaneously. Figure 20 shows a full frame image. Figure 20. Frame Display Image. The second visualization method is a waterfall display. In waterfall mode, the Hyperscan software builds up an image using the mirror s movement and a single spectral band of pixels. Waterfall mode is chosen by removing the check from the Frame Display control and selecting a spectral band by moving the slider labeled Mono. The final controls in the Display section of the GUI are the color sliders with labels R, G, and B for Red, Green and Blue respectively. The color sliders are used to change the color mapping when the Color Mode control has been checked. Specifically, these controls give the user the ability to designate the spectral bands to map to red, green, and blue. Therefore, by manipulating the color sliders the user can optimize the color mapping in the displayed image. 14
Table 8 summarizes the controls in the GUI s Display section. Label Mono Mode Color Mode Frame Display Mono R G B 4.5 GUI Section 5 - Capture Table 8. Display Controls. Description Displays image as grayscale when ON Displays the image in color when ON Full frame data displayed when checked; Waterfall display when unchecked. Used to select spectral band for waterfall display Used to select red band for color mapping Used to select green band for color mapping Used to select blue band for color mapping Control Type On/Off On/Off Check Box Slider Slider Slider Slider The fifth and final section of the GUI is labeled Capture. Figure 19 shows the Capture portion of the GUI. Figure 19. Display Controls. The controls found in the Capture section are used to control dark frame acquisition, scan start and stop, shutter open and close, and the destination for saved files. Table 9 describes the controls in more detail. Label Start Scan Abort Pre Dark Frames Post Dark Frames Shutter Close Destination and File Basename 4.6 ENVI Reflectance Program Table 9. Capture Parameters. Description Starts a scan Aborts an unfinished scan Controls the number of dark frames captured before scan begins Controls the number of dark frames captured after the scan ends Closes the shutter when checked Allows user to choose the name and destination of saved files An ENVI/IDL routine is shipped with the Hyperscan system to simplify the generation of reflectance cubes. For each line in a cube, the reflectance is calculated by subtracting off a dark field and then scaling by a corresponding bright field. This calculation can be described by the following equation: 15
R ijk = C ijk DC ik B ijk DB ik. R ijk is the reflectance for sample i, line j, band k, and C ijk and B ijk are the corresponding values in the input cube and the bright field. DC ik and DB ik are the dark fields for the input cube and the bright field respectively. These dark fields are automatically extracted for each cube when it is read in by averaging over lines that were taken with the shutter closed. These dark lines occur at the beginning and/or end of the cube, and the program knows the number of these dark lines from reading the information from the corresponding header file. To run the program select Calculate Reflectance from the ENVI menu bar under. Figure 20 shows the menu bar. j Figure 20. ENVI menu bar, showing routine. Next, select the bright field cube as illustrated by Figure 21. j Figure 21. Bright field selection dialog box. 16
After the bright field is selected, the user must choose the input cubes to be processed. Bright field selection is shown in Figure 22. In this step, the user has the option to process all of the cubes in the Input Folder by clicking the Choose button or manually selecting the cube(s) to be processed (the Ctrl or Shift buttons on the keyboard can be used to select multiple files). j Figure 22. Dialog for selecting input cubes. Next, the user specify the folder where the reflectance cubes will be saved. Figure 23 illustrates this process. By default, the Hyperscan software creates a new folder named Reflectance and locates it within the input folder. If a different folder is desired for the reflectance files, the user can click the Choose button and navigate to the desired folder (a new folder can not be created using the Choose button). For each input file processed, a reflectance cube is generated and saved with a file name that uses the name of the input file with a suffix appended to it. The default suffix is _Ref.cub. However, the suffix can be edited by the user in the text box shown in Figure 23. As an example, an input file named boogie.cub would be saved, by default, with the name boogie_ref.cub. j Figure 23. Dialog for output file. After the output file parameters have been specified, the program begins its calculations. Specifically, the program loops through the selected input cubes saving reflectance cubes as they are calculated. A dialog box shows the progress and the program can be aborted at any time by hitting the Cancel button. This process is illustrated in Figure 24. 17
j Figure 24. Progress bar. To install the program on another computer the folder must be copied. For this and also for ENVI upgrades the IDL path must edited to include the folder and the menu file (ENVI.men) must be edited to include the drop down menu. Please contact for instructions on how to do this. 4.7 Advanced User Options Each time the Hyperscan software is opened, it reads a series of values from a configuration file. These values are used to control a variety of parameters on a very low level. The configuration file, which is titled hyperscan.ini, is found in the Hyperscan folder and can be modified by a user that has a thorough understanding of the control parameters. Caution should be used when changing the values of the parameters in the.ini file because entering the wrong values could cause damage to the hardware or cause the software to function improperly. Table 10 shows the parameters that can be changed in the hyperscan.ini file. Parameter Slope Intercept MinExpFlag MinExp MaxExp SlideMode Rest Velocity MicroStepping Acc Initial Value -1.386 1062.1 1 0.01 1000 1 1 4000 256 1000 Table 10. Hyperscan.ini parameters. Description Sets the spectral dispersion Sets intercept (wavelength at unbinned pixel zero) Sets exposure time units (1=ms, 2=sec, 3=min) Sets the minimum exposure time Sets the maximum exposure time Sets the slider response (0=Linear, 1=Log Parabolic, 3=Log Linear) Sets the mirror delay between frame captures Sets the speed of the mirror (microsteps/sec) Sets the level of microstepping (64, 128, 256) (default:256) Sets the motor s acceleration (Range = 0-65000) (microsteps/sec^2) 18
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