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Note: The following instructions are divided into 2 sections: Calibration Check and full Calibration.
Calibrartion
Before Starting:
Calibration is conducted in the following steps.
- Physically set the camera at the correct height and focus . See Camera Height and Focusing.
- Next we want to set the saturation range for each channel of the CCD while maintaining the white balance between these channels for neutral colors. See Setting Exposures and Gains
- Correct for uneven lighting and pixel flatness. See Shading and Pixel Flat Corrections.
- Calibrate and create a correction LUT for each RGB channel. See Image Calibration.
The first three steps are done using the JAI Camera Setup Utility. Before opening the utility it is best to disable Motion Cotrol so that you can move the camera by hand or open the Motion Widget to control motion with the program. User's choice.
In the IMS control panel select Motion and then Drive Disable from the dropdown menu (Figure 19). You will have to move the camera by hand for the calibration, disabling the motor allows manual movement of the camera on the track.
3. In the IMS control panel click Instruments > JAI Camera Settings (Figure 20). The lights turn on automatically when the JAI Camera Setup window opens.
Camera Height and Focusing
Setting Exposures and Gains
1) First you need to check the camera's f/stop which should either f/16 or f/22 (see Figure 18). Remember that the higher the f-stop the greater the depth of focus. The down side is that a higher f-stops means less light and low light level mean longer exposures - which means slow track speeds for scanning - which could impact core flow in the lab. So on a low recovery expeditions you can afford the longer scan time, so go for f/22 otherwise f/16. If you are doing 360-imaging f/22 is a must. Check with the LO and EPM if you are unsure.
Figure 18. Setting the F Stop on the Camera.
2) When the camera moves it will receive trigger pulses from the linear encoder that will start exposure the cycle. The encoder will provide 200 pulses for every centimeter of movement; therefore, the speed of the track controls the time between pulse which controls the maximum potential exposure period. The individual exposure periods for the RGB channels must be completed in this time or lines will be dropped.
When setting up the JAI camera we are not moving and not receiving trigger pulses. In this mode we use the line rate trigger (free run) to simulate the encoder trigger period.
Before Starting:
- Note which version of standard you are using. Each color standard values vary based on the version and the manufacturer of the standard. The XRite Colorchecker 2019 (MacBeth standard, Figure 5) is the preferred card to use for calibration. The program is set up to use the White and Black squares on the XRite Colorchecker (MacBeth standard). On the Xrite color checker standard the Note which version of standard you are using. Each color standard values vary based on the version and the manufacturer of the standard. The XRite Colorchecker 2019 (MacBeth standard, Figure 5) is the preferred card to use for calibration. The program is set up to use the White and Black squares on the XRite Colorchecker (MacBeth standard). On the Xrite color checker standard the RGB values of White and Black are listed here for various illuminants. White RGBs are 242, 242 and 236 and and black RGBs are 49, 49, 50 (those values are calculated using illuminant D65), as of there is discussion that we will use RGBs calculated under illuminant A as it better matches our LED lights. Using illuminant A the RGBs for white is 240, 242, 235 and black is 50, 50, 50. For the QP 101 v4 card, the RGB values are 235, 235, 235 (light grey), 111, 111, 111 (medium grey), and 80, 80, 80 (dark grey) (Figure 6). All SHIL calibration standards are found in drawer PP-2B.
- Obtain the 3D standard (Figure 5) and the gray silicone mat standard from PP-2B.
- Set camera f/stop to either F/16 or F/22 (Figure 7). The camera manufacturer suggested F/22 as the preferred f/stop for scanning with the our light set up however we have found F/16 works well for our section halves and is the most used f/stop for calibration and scanning sections. For hard rock cruises, where 360° whole round scanning is required, a larger f/stop number maybe required.
- If you haven’t set the camera’s height, now is the time to do so! See the section Camera Height Adjustment at the end of the calibration section. The camera height should not need to change between expeditions.
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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.
b) Calibration (JAI Camera Setup and Image Corrections)
Camera and Track Setup
1. Confirm the camera f/stop is set to F/16 or F/22 (Figure 18). F/22 is preferred by the camera manufacturer for scanning with the current light set up however the reasoning behind that is unclear. The imaging specialists onboard have been using F/16 and are confident F/16 works for our set up. For hard rock cruises, where 360° whole round scanning is required, a larger F-stop number maybe required (ie. F/22).
Figure 18. Setting the F Stop on the Camera.
2. In the IMS control panel select Motion and then Drive Disable from the dropdown menu (Figure 19). You will have to move the camera by hand for the calibration, disabling the motor allows manual movement of the camera on the track.
3. In the IMS control panel click Instruments > JAI Camera Settings (Figure 20). The lights turn on automatically when the JAI Camera Setup window opens.
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, 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.
b) Calibration (JAI Camera Setup and Image Corrections)
Camera and Track Setup
Resetting Gains and Corrections
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