...
Pixel Black Auto Correction
1. )The new light set up makes adding a lens cap difficult so it has been decided and tested that the pixel black auto correct can be done without the cap (Figure 33). But Ensure the lights are off.
...
Figure 33. Lens Cap being put on camera - note the lens cap is not needed. Ensure the lights are off.
2. ) With lights off click Pixel Black Auto Correction. The RGB lines in the Profile graph should be uniform (Figure 34).
...
Figure 34. Pixel Black Correction applied.
Shading Correction
1. ) Take the heat resistant gray silicone mat and wooden board from the SHIL calibration drawer. Clean off any dust with a piece of tape (Figure 35). Dust will cause unwanted artifacts in the image. The mat must be clean and flat on the track.
2. ) Place the heat resistant gray silicone mat on the track. Make sure that it is level and perpendicular to the camera’s axis.
3. ) Click Lights On, and move the camera over the gray mat.
4. ) Note for Tech: previously we defocused the lens to preform the Shading correction. That is no longer needed because the silicone mat is even in color/texture.
...
Figure 35. The Gray silicone mat being cleaned with tape.
5. ) The RGB lines should first appear “bowed” evenly across profile and centered in the image (Figure 36). If not check the orientation of the gray mat, it needs to be flat and perpendicular to the camera. This very important. A wooden holder was designed to hold the mat, it should be in the SHIL calibration drawer.
...
Figure 36. Grayscale card corresponding RGB Profile visible.
6. ) Click the Shading Correction - Flat Method button. This can take a few seconds, don’t click anything else until it is done. The RGB lines should now be flat (Figure 37).
...
Figure 37. Image grab and profile after the Shading Correction has been applied.
7. ) Click Lights OFF and wait for temperature to decrease below 35 °C.
Pixel Gain Correction
1. ) Make sure gray silicone mat is flat.
3 2) Click Lights ON
2. 3) Click the Pixel Gain Correction - Flat Method button and move the camera slowly back and forth. 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. When its done the RGB lines should still be flat and the individual RGB the same, but may not be equal to each other.
a) Calibration Check using Image Correction
The following calibration check is designed for technicians to check the SHIL’s calibration. The calibration check is required to be done at the start of every expedition prior to receiving the first core. If adjustments to the calibration are needed, please see the Calibration section below.
Figure 9. Checking the Max Image Scan Speed.
Assess the SHIL scan
Prepare the scan to assess the current Image Correction values. If you can achieve a good image by either adjusting, or better yet, keeping the same, values in the following steps you will not need to adjust any of the camera settings in the JAI Camera Set-up window in the calibration instructions below.
NOTE: The Image Correction screen has been updated as of . We are in discussion with Lab Working Group on utilizing the new user interface. The main difference is that we can use colors other than the white, shades of grey and black to determine corrections. For now, continue to select the white, shades of greys and black for image correction calibrations. This user guide is in the process of being updated to reflect the new user interface.
Take an Image
1. Place the 3D calibration standard on track as shown (Figure 10). Be sure to use the XRite Color checker 2019. The color squares must be oriented as pictured below, butted against the red reflection bar.
Figure 10. Color standard in track in correct orientation.
2. Open IMS and Click Start.
3. Scan the STND Color barcode label (Figure 11b). Check the ColorChecker Standard box (Figure 11a). With this box selected no corrections are applied to the image so we are able to assess the raw image quality.
4. Click Take A Picture.
5. When the image has finished click Crop and then Save. We use the uncropped image so the crop here is not important.
Figure 11. a) sample information screen with ColorChecker box checked, b) standard barcode being scanned.
6. On the main IMS panel select Instruments and Camera: Image Correction (Figure 12).
Figure 12. Image Correction command selection.
The main Image Correction window displays three main areas (Figure 13):
A. Graph panel: Main graphical viewing area on the left side of the screen.
Uncorrected Image Tab: Shows the measured red, green, and blue values of the gray scale color squares.
Applied Corrections Tab: Applies polynomial fit corrections to the RGB lines.
Compare: Shows a visual and RGB values of the Original color square before corrections, the Xrite Color checker standard and of the color after corrections are applied.
B. Image Viewing Panels: Area in upper right portion of the screen that displays the original and corrected test image and Xrite color checker.
Original: Displays the uploaded tiff.
Corrected: Displays the uploaded tiff with corrections applied.
Color Checker: Displays the known values of the Xrite Color Checker.
C. Correction Panel: Panel in the lower right portion of the screen that allows user to apply corrections to the image
TIFF Correction: Shows tiff red, green, and blue polynomial fit.
JPEG Correction: Shows brightness, contrast, and gamma settings.
Figure 13: Image Correction user interface.
7. On opening of the Image correction window the program prompts you to select the TIFF file of the color standard you took. The image loads into both the Original and Corrected windows.
8. Draw a ROI box loosely around the color checker in the Original box (Figure 14-1)
9. Click Crop (Figure 14-2).
10. Draw another ROI box around the Color Checker squares and this time making sure to only have XRite color checker in the box. White squares will appear inside each square. Adjust the box to get those white squares close to the center of the color squares. Do not click Crop again.
11. Click the colors you want to use for the correction curve (Figure 14-3). As of use only the white, shades of grey and the black.
Figure 14. Image Correction Window.
Check TIFF and JPEG Corrections
Here we check and adjust, if needed, our TIFF and JPEG Corrections. You may find you only need to slightly tweak the values and the calibration is good. With the new lights we have found that no adjustments have been needed. However if the image appears streaky, a physical change has happened to the Camera or lights, the RGB values between corrected and expected are far off (>10), or the graphs of either the tiff or jpeg don't look good, you will need to re-calibrate following the full calibration discussed below.
TIFF Correction Check
1. Click TIFF Correction tab (Figure 15-1).
2. Click Uncorrected Image tab. This graph shows the measured red, green, and blue values of the color squares.
3. In the Tiff Correction tab adjust the LUT polynomial order values for the Red, Green, and Blue channels (Figure 15-1). Adjust these values to create the lowest residual error with the smoothest curve in the Uncorrected Image tab. Polynomial values should be about 3. Make sure that the curve does not wave about too much. If it does, the values need to be lowered.
4. In the Compare tab check that the corrected color square and Xrite color checker RGB values are very close (Figure 16). Make sure that the white does not exceed the Xrite values (RGB = 242, 242, 236). There is also a visual display so you can see the difference in color for the color checker and the corrected. If you are unable to produce a reasonable correction curve, it is necessary to redo your white balance correction described in the Calibration section below.
Figure 15. Tiff Correction
Note: the TIFF correction is applied to both the TIFF and JPEG image but for the JPEG image you can also apply a Brightness, Contrast and Gamma (BCG) correction (See JPEG Correction section below). This is done at the photographer’s discretion. With better balanced LEDs on the new light system you may not have to use the BCG corrections (leave the values at their mid-points. Figure 17-1).
Figure 16. Use the Compare tab to view the RGB values for the Xrite color checker and the corrected.
JPEG Correction Check
In JPEG correction you will check and adjust, if necessary, the brightness, contrast and gamma (BCG) of the image. Situations may also 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. As mentioned above, with the new lights the BCG values may not need to be adjusted and to be kept at the mid values (Figure 17).
1. Click JPEG Correction tab (Figure 17-1)
2. Adjust the Brightness, Contrast, and Gamma levels (Figure 17-1) to achieve a straight line in the Applied Corrections tab and the RGB Corrected values in the Compare tab should have values near 242 for the white square and near 50 for the black. We want a linear relationship between the measured and given values. Each BCG setting adjusts the line in different ways and there are many different ways to adjust the values to achieve a linear relationship. You want to achieve a good image with good brightness, where the image has good saturation and not too washed out. The Applied Corrections Graph should be a straight line and the ROI Corrected box for the color selected (Figure 17-2, 17-3) should have values near the RGB values of the Color Checker STND. 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.
3. If the values are good and there are no streaking issues in the images or other unwanted artifacts, you can click Save and no further adjustments are needed. However if you have determined the doesn't look good, click Cancel and you can proceed to the following Calibration section and complete the calibration instructions listed.
Figure 17. JPEG Correction using Brightness, Contrast and Gamma.
Figure 32. Grab and Profile after the Pixel Gain Correction has been applied.
3. Remove the gray mat. Confirm the Camera is in focus by moving it over the cm increments on the grey QP 101 V4 standard and focus the lens by turning it manually if needed.
4. Click Lights Off. At this point wait for lights to cool, turn lights back on and check the White square RGB values are near 242 and adjust the exposure intervals if needed.
4. Click Save. The lights will turn off and the window closes.
5. In the IMS Control panel click Motion and then Drive Enable (Figure 33). This allows the software to control the camera movement.
Figure 33. Drive enable control highlighted.
c) Image Corrections
Note: this section follows the same steps as listed in the Calibration Check section above. This needs to be completed after a Calibration.
The Image Correction screen has been updated as of . This is being discussed with Lab Working Group. The new interface allows the user to calibrate (image correct) with other colors on the Xrite color checker and provides a visual display of the colors calculated by the RGB values of the Xrite color checker and the corrected color. For now, continue to select the white, shades of greys and black for image correction calibrations.
Take New Picture
...
IMAGE Calibration (Correction)
Before we can begin the calibration process, an uncorrected image of ColorChecker standard must be taken.
1. Place the 3D calibration standard on track as shown (Figure 10). Be sure to use the XRite Color checker 2019. The color squares must be oriented as pictured below, butted against the red reflection bar.
Figure 3438. Color standard in track in correct orientation.
2. Open IMS and Click Start.
3. Scan the STND Color
...
barcode label (Figure
...
39b). Check the ColorChecker Standard box (Figure
...
39a). With this box selected no corrections are applied to the image so we are able to assess the raw image quality.
4. Click Take A Picture.
5. When the image has finished click Crop and then Save. We use the uncropped tif image so the crop here is not important.
Figure 3539. a) sample information screen with ColorChecker box checked, b) standard barcode being scanned.
6. On the main IMS panel select Instruments and Camera: Image Correction (Figure
...
40).
Figure 3640. Image Correction command selection.
The main Image Correction window displays three main areas (Figure 3741):
A. Graph panel: Main graphical viewing area on the left side of the screen.
...
JPEG Correction: Shows brightness, contrast, and gamma settings.
Figure 3741: Image Correction user interface.
...
8. Draw a ROI box loosely around the color checker in the Original box (Figure 3842-1)
9. Click Crop (Figure 3842-2).
10. Draw another ROI box around the Color Checker squares and this time making sure to only have XRite color checker in the box. White squares will appear inside each square. Adjust the box to get those white squares close to the center of the color squares. Do not click Crop again.
11. Click the colors you want to use for the correction curve (Figure 3824-3). As of use only the white, shades of grey and the black.
Figure 3842. Image Correction Window.
...
Here we check and adjust, if needed, our TIFF and JPEG Corrections. You may find you only need to slightly tweak the values and the calibration is good. With the new lights we have found that no adjustments have been needed. However if the image appears streaky, a physical change has happened to the Camera or lights, the RGB values between corrected and expected are far off (>10), or the graphs of either the tiff or jpeg don't look good, you will need to re-calibrate following the full calibration discussed below.
TIFF Correction Check
1. Click TIFF Correction tab (Figure 3943-1).
2. Click Uncorrected Image tab. This graph shows the measured red, green, and blue values of the color squares.
3. In the Tiff Correction tab adjust the LUT polynomial order values for the Red, Green, and Blue channels (Figure 3943-1). Adjust these values to create the lowest residual error with the smoothest curve in the Uncorrected Image tab. Polynomial values should be about 3. Make sure that the curve does not wave about too much. If it does, the values need to be lowered.
4. In the Compare tab check that the corrected color square and Xrite color checker RGB values are very close (Figure 40). There 44). Make sure that the white does not exceed the Xrite values (RGB = 242, 242, 236). There is also a visual display so you can see the difference in color for the color checker and the corrected. If you are unable to produce a reasonable correction curve, it is necessary to redo your white balance correction described in the Calibration section below.
Figure 3943. Tiff Correction
Note: the TIFF correction is applied to both the TIFF and JPEG image but for the JPEG image you can also apply a Brightness, Contrast and Gamma (BCG) correction (See JPEG Correction section below). This is done at the photographer’s discretion. With better balanced LEDs on the new light system you may not have to use the BCG corrections (leave the values at their mid-points. Figure 4144-1).
Figure 4044. Use the Compare tab to view the RGB values for the Xrite color checker and the corrected.
...
In JPEG correction you will check and adjust, if necessary, the brightness, contrast and gamma (BCG) of the image. Situations may also 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. As mentioned above, with the new lights the BCG values may not need to be adjusted and to be kept at the mid values (Figure 4145).
1. Click JPEG Correction tab (Figure 4145-1)
2. Adjust the Brightness, Contrast, and Gamma levels (Figure 4145-1) to achieve a straight line in the Applied Corrections tab and the RGB Corrected values in the Compare tab should have values near 242 for the white square and near 50 for the black. We want a linear relationship between the measured and given values. Each BCG setting adjusts the line in different ways and there are many different ways to adjust the values to achieve a linear relationship. You want to achieve a good image with good brightness, where the image has good saturation and not too washed out. The Applied Corrections Graph should be a straight line and the ROI Corrected box for the color selected (Figure 4145-2, 4145-3) should have values near the RGB values of the Color Checker STND. 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.
3. If the values are good and there are no streaking issues in the images or other unwanted artifacts, you can click Save and no further adjustments are needed. However if you have determined the doesn't look good, click Cancel and you have can proceed to redo the following Calibration section and complete the Calibration calibration instructions listed.
Figure 4145. JPEG Correction using Brightness, Contrast and Gamma.
...
5. Visually examine each file you just preformed to ensure the colors, neutrals, mid-tone and contrast are true to the real values, and that the scan is free from artifacts. Use the eyedropper tool in photoshop to see the values of pixels (Fig. ## Figure needs to be added).
e) Camera Height Adjustment
1. 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.
2. 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.
a) Calibration Check using Image Correction
The following calibration check is designed for technicians to check the SHIL’s calibration. The calibration check is required to be done at the start of every expedition prior to receiving the first core. If adjustments to the calibration are needed, please see the Calibration section below.
Figure 9. Checking the Max Image Scan Speed.
Assess the SHIL scan
Prepare the scan to assess the current Image Correction values. If you can achieve a good image by either adjusting, or better yet, keeping the same, values in the following steps you will not need to adjust any of the camera settings in the JAI Camera Set-up window in the calibration instructions below.
NOTE: The Image Correction screen has been updated as of . We are in discussion with Lab Working Group on utilizing the new user interface. The main difference is that we can use colors other than the white, shades of grey and black to determine corrections. For now, continue to select the white, shades of greys and black for image correction calibrations. This user guide is in the process of being updated to reflect the new user interface.
Take an Image3. The graph has 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 up and down refocusing after every move until you get within the range. Warning this can be very tedious!
C. Set Measurement Parameters
...