Section Half Imaging Logger: User Guide
Manual Information
Author(s): | M. Hastedt |
Reviewer(s): | Crawford, Fulton, Beck |
Supervisor Approval (Name, Title, Date): | |
Audience: | Scientists and Technical Staff |
Current Version: | V383P | Draft 11/01/08 LLP |
Revised: | Draft 6/17/2019 |
Domain: | Physics |
Analysis: | Section Half Imaging |
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9. When the colors all seem well balanced you can move on to the next step. How long the lights have been will affect the color balance. If the lights have gotten quite warm and everything looks even, then when the lights are 'cold' the blue channel will be lower than the others.
Apply Corrections
We apply three corrections. Only do the corrections after you have finished adjusting the exposure and gain. Find information regarding each correction below:
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After discussion with JAI we learned the order of corrections should be Pixel Black, Shading, and Pixel Gain. Previously our order was Shading, Pixel Gain, and Pixel Black. The order has been updated here. We were also to told to do all exposure and gain adjustments before doing these three camera corrections. This manual has been updated to reflect those changes.
Black Gain Correction
1.Turn off the lights.
2. Take the lens cap (Figure 29) and place on lens (Figure 30). The lens cap is located in drawer PP-2B.
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Figure 31: Grab and Profile after the Pixel Black Correction applied.
Shading Correction
- Place the gray card silicone mat on the tray make sure that it is level and perpendicular to the camera’s axis. The card mat should be positioned at the height of the core surface. This is an important step. If the card mat is placed closer to the camera your calibration will be off.
- Turn on the lights, with the same method used to turn off the lights, and move the camera over the gray cardmat.
- Unfocus the lens on the camera just a little bit (Figure 25). Look at the Profile graph and rotate the lens’ focus until the RGB lines are smooth. de-focus the lens until the RGB line on the Profile graph just become smooth and no more (but still variable)
Figure 25: The lens being unfocused.
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4. Now move the camera over the gray card and make sure to de-focus the lens until the RGB line on the Profile graph just become smooth and no more (but still variable) (Figure 26). The RGB lines should appear “bowed” evenly across profile and centered in the image. If not check the orientation of the grayscale card. This very important!
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Figure 27: Grab and profile after the Shading Correction has been applied.
Pixel Gain Correction
1.The camera’s lens should still be de-focused and grayscale gray silicone mat card flat and illuminated.
2. Click the Pixel Gain Correction - Flat Method button . and move the camera very slowly back and forth over the mat. This averages the pixels and helps eliminate streaking in the image. This will take several seconds, don’t click anything else until it is done. The When its done the RGB lines should still be flat and the individual RGB are the same (may not be equal to each other) (Figure 28).
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Figure 28: Grab and Profile after the Pixel Gain Correction has been applied.
Create Correction Curve
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3. Refocus the lens.
4. Click
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Save.
Create Correction Curve
Take New Picture
1.Go to Motion > Drive Enable, to re-enable the motor (Figure 38).
Figure 38: Drive enable control highighted.
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2. Go to IMS Main Panel Select DAQ > Image Capture Motion Setup (Figure 39). In this window confirm that speed is set lower than the speed calculated by the Line Trigger Interval
Figure 39: Image Scan Setup Window.
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3. Click Start
4. Scan the STND Color label on the aluminum track behind the monitor (Figure
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Figure 40: Standard barcode.
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XX). Check the
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ColorChecker Standard box
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. With this box selected no corrections are applied to the image so we are able to assess the raw image quality.
5. Click Take A Picture.
6.
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Figure 42: Image Correction selection highlighted.
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When the image has finished click Crop and then Save. We user the uncropped image so the crop here is not important.
7. On the main IMS panel select Instruments and Camera: Image Correction
8. The main window opens. On the right side of the screen select Open Test Image. Open the image just taken (Figures ). It has been mentioned that it doesn't matter if you load in the jpeg or tiff, not tested yet
Figure 45: Open Test Image Window with all images displayed.
Tiff Correction
The main Image Correction window opens (Figure 43). Note the three main areas in the window:
Figure 43: Image Correction Window.
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Instructions: Shows instructions to follow in this window.
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1.Make sure TIFF Correction Mode is selected in the upper right corner and the TIFF Corrections tab is selected in the bottom right corner (Figure 44).
Figure 44: Tiff correction Mode button and Tiff Correction tab both highlighted in red.
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2.
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In the
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Figure 45: Open Test Image Window with all images displayed.
Figure 46: The tiff image loaded into the Original Window.
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ORIGINAL image control create a selection rectangle (right-click drag) of the MacBeth card and click CROP (Figure 47). Repeat as necessary until the card fills the entire image.
Figure 47: Green crop square drawn around the color squares.
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3. Again create another selection rectangle over the image but do not release the mouse. Move the lower corner of the rectangle until small white boxes appear over the color squares. Make sure the boxes are in the center of the squares. Release the mouse. The pixels in the squares will be averaged and used for the RGB values in the calibration (Figure 48). (not quite how it works right now, white squares don't show up until mouse is released, error reported in confluence).
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Figure 48: Final crop square drawn around color squares.
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4. Look in the TIFF Correction tab and set the LUT polynomial order values for the RGB channels. Adjust these values to create the lowest residual error with the smoothest curve in the UNCORRECTED image tab. Should be around 4. Make sure that the curve does not wave about if it does the order values need to be lowered. Also check the corrected ROI and MacBeth values should be very close. Make sure that the white does not exceed the MacBeth value. If you are unable to produce a reasonable correction curve, it may be necessary to redo your white balance correction and start over.
This correction is applied to both the TIFF and JPEG image but for the JPEG image you can also apply a Brightness, Contrast and Gamma correction. This is done at the photographer’s discretion. With better balanced leds on the new light system I did not use the correction and left the values at their mid-points.
Camera Height Adjustment
JPEG Correction
Situations may arise where a JPEG correction should be applied. In the instance of very white or very dark cores, the TIFF images may look good but the JPEG images may look washed out or too dark to view details. JPEG corrections do not alter TIFF image settings. To apply a JPEG Correction follow the steps below:
1. Select JPEG Correction Mode (Figure 56).
2. In the BCG Correction Window, select JPEG Correction. Adjust the Brightness, Contrast, and Gamma Settings. The Corrected color squares will update as the settings are changed.
3. The Applied Corrections Graph should be a straight line and the ROI Corrected Box should have values near 250. These may change depending on the instance of extreme colors, extremely white or extremely dark cores, in which the settings may have be tweaked more to get a user friendly consumer image.
Camera Height Adjustment
- Move the camera so it is just on the edge of the grayscale card at the end on the tray. On this card are mm and cm marks on the edge.
- Click the GRAB button and watch the image as you make slow camera position adjustments until the centimeter lines show up on the image graph as sharp spikes.
- The graph as two cursors, use the mouse and drag one cursor aligning it with the spike. Take the second cursor and do the same with an adjacent spike. Just above the Profile graph there is a control labelled Pixel Delta this value should be between 198 and 202 pixels. If not, adjust the camera
- Move the camera so it is just on the edge of the grayscale card at the end on the tray. On this card are mm and cm marks on the edge.
- Click the GRAB button and watch the image as you make slow camera position adjustments until the centimeter lines show up on the image graph as sharp spikes.
- The graph as two cursors, use the mouse and drag one cursor aligning it with the spike. Take the second cursor and do the same with an adjacent spike. Just above the Profile graph there is a control labelled Pixel Delta this value should be between 198 and 202 pixels. If not, adjust the camera (not lights up and down refocusing after every move until you get within the range. Warning this can be very tedious!
Check on Calibrated Computer
1.Take, crop, and save another test image now that all corrections have been applied. Use the same procedure to take an image as described in the section: Take an Image
2. Copy the image to a shared network folder to view on a calibrated computer screen in the Imaging Office.
Adjusting JPEG Correction
Situations may arise where a JPEG correction should be applied. In the instance of very white or very dark cores, the TIFF images may look good but the JPEG images may look washed out or too dark to view details. JPEG corrections do not alter TIFF image settings. To apply a JPEG Correction follow the steps below:
1. Take the MacBeth Color Checker Standard and place on SHIL Imaging Track
2. Click Start in IMS (Figure 49).
Figure 49. Sample Information Window
3. In the Sample Information window, check the box for Color Checker Standard (Figure 50). Checking this box produces an uncorrected image. Click back in the Sample Information bar and scan the Color Checker Label mounted on the track behind the computer.
Figure 50. Color Checker box outlined in red and selected
4. Click Take an Picture
5. Adjust green crop box as necessary. When satisfied select Crop Image and then Save Image (Figure 51)
Figure 51. Crop and Save Window
6. Close out of the Sample Information Window. In the IMS start area go to Instruments > JPEG Correction (Figure 52)
7. The main window opens (Figure 53).
Figure 53. Main Image Correction Window
8. On the right side of the screen select Open Test Image. The IMAGE folder will appear. Select the Image just taken. Make sure to select the .tif image and not the .jpg. With the mouse, hoover over the file and check the extension is .tif. Select the appropriate file and click Open (Figure 54). As of writing this, keep TIFF Corection selected while opening Test Image, will receive an IMS error message if select JPEG Correction and then try to load in test image
Figure 54. Selecting Appropriate test image. Callouts to button and .tif image
9. The image loads into main window in the Original section (Figure 55)
Figure 55. Test Image loaded into Original window
10. Now select JPEG Correction Mode (Figure 56).
Figure 56. JPEG Correction selected
11. With the square tool selected draw a box around the color squares (Figure 57). This creates a crop area to focus in on the color boxes. Select crop when the box looks about right. For now the box can be approximate.
Figure 57. Crop Box drawn around test image
12. With the square tool still selected, draw another box around the squares (Figure 48). This time get the green box very close to the edge of the colored squares. Small white boxes will appear in the color squares. Adjust the green rectangle so the white boxes are approximately in the center of the squares.
Figure 58. Crop box drawn with white boxes centered in color squares
13. In the BCG Correction Window, make sure JPEG Correction is selected. Adjust the Brightness, Contrast, and Gamma Settings. The Corrected color squares will update as the settings are changed.
Check on Calibrated Computer
1.Take, crop, and save another test image now that all corrections have been applied. Use the same procedure to take an image as described in the section: Take an Image
2. Copy the image to a shared network folder to view on a calibrated computer screen in the Imaging Office.14. The Applied Corrections Graph should be a straight line and the ROI Corrected Box should have values near 250. These may change depending on the instance of extreme colors, extremely white or extremely dark cores, in which the settings may have be tweaked more to get a user friendly consumer image.
Color Balacing Camera - Old Method MacBeth Color Checker Card
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