...
- 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 Setting 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.
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Camera Height and Focusing
Setting
...
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.
When you adjust the Line Trigger Interval you will notice that the Max Image Scan Speed value changes. If you scan faster than this, you dropped lines but you can scan slower with affecting the calibration. When you click Save in this Utility the value in the Image Scan Setup window will be updated but you are allowed to change this value but should always be lower not higher. As a general rule we want to stay at 8-cm/s or higher to maintain core flow in the lab.
After you done a few calibrations you will develop a feel for what is possible with current set up but if you just stating we recommend setting the line rate to emulate a scan speed of 8-cm/s.
Now you are ready to start setting the exposures for the RGB channels.
- Turn on the lights
- Click the START GRAB button
- Move the camera over the white square on the ColoChecker standard.
- Use the mouse and draw a ROI (Region of Interest) square with only the white square inside. The RGB values and Ratio values will only be calculated for the pixels inside the ROI.
- Go to the Gains-Black-Shades-Flat tab and click the Clear All Gains and click Clear Black Gains
- Go to the Rates and Exposure tab and set the Green Lock to Off
At this point look at the intensity graph and determine which channel is the weakest (lower).
- Start with this channel and increase the exposure time until its value is between 240-245. For the current lighting this is the red channel and well use this for these instructions but this could vary if the lights are changed.
- Adjust the green exposure until the red/green ratio is 1.000 +/-0.005.
- Adjust the blue exposure until the blue/green ratio is 1.000 +/-0.005.
Lets say in the above example you could not get the red to to 240 you have several options:
- Lower the lights for increased intensity
- Open up the f-stop for more light
- Increase the line rate (slower scan speeds) so that you can increase the exposure period
- Use gains to amplify the signals.
Using gains is generally the simplest choose because the other choices are not practical. The down side of using gains is they amplify both signal and electrical noise, so use with alight touch. In the next section will discuss how to use the gains but remember you will likely move back forth between setting exposures and gains to optimize the camera. It is an iterative process.
Open the Gains-Black-Shades-Flat tab. Keeping with the scenario that we cannot obtain 240 on the red channel , the first thing we'll do is adjust the Master Gain until the red is in the 240-245 range. If the Green and Blue are two high you can apply negative gains to those channel until get the ratios to 1 or go back to the exposures and the their exposure levels. The later method is preferred.
Using exposures and gains you have now balanced the White ColorCheck square in the 240-245 range it is time to set the dark response of the camera
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 RGB values of White and Black are listed here for various illuminants. For illuminant D65 White RGBs are 242, 242 and 236 and and Black RGBs are 49, 49, 50 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.
Figure 5. 3D standard with Xrite Color checker (MacBeth Color) standard on the left.
Figure 6. QP card 101 v4 grey scale standard.
Figure 7. Setting the f/stop on the Camera. F/16 is the preferred value by the imaging specialists onboard. Darker cores may need a larger f/stop of F/22.
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.
b) Calibration (JAI Camera Setup and Image Corrections)
Camera and Track Setup
Resetting Gains and Corrections
1. Click the Gains-Black-Shade-Flat tab (Figure 19).
Figure 19. JAI Camera Setup Window showing the Gains-Black-Shade-Flat tab. The Gains-Black-Shade-Flat tab is outlined in red.
2. Click the Clear All Gains, Clear Black Gains, Remove Pixel Black Correction, Remove Shading Correction, and Remove Pixel Gain Correction (Figure 20). You will notice all values in the Master and Black gains go to zero.
Figure 20. Remove the corrections and clear gains.
4. In Master Black field, enter 40. That is a good starting point. We have found the value Master Black of 60 works best for our system's set up.
Color Balancing the Camera
Color Balancing should be done with the Xrite color checker mini classic standard version 2019. The grey standard on the top of the track should be the QP card 101 v4 gray scale card. Be sure to use new color standards as some where damaged (faded). The calibration using the Xrite color checker standard card is described below (note: the QP card v.4 101 method that was implemented in 2020 due to the high temperature of lights is described at end of this User Guide if you need to reference that method).
Color Balancing Camera - Xrite Color Checker Classic 2019 Card
Make sure the lens is focused. Use the cm marks on the QP 101 V4 card to focus the lens. If the camera has been moved you will need to adjust the height of the camera using the method described below in Camera Height Adjustment. There should be no reason to adjust the height of the camera between expeditions.
1. Put the 3D Calibration Standard in the track. The color square must be oriented as pictured Figure 21.
Figure 21. Color standard in track in correct orientation.
2. Select the tab RATES and EXPOSURE (Figure 22).
Figure 22. Rates and Exposure window, the tab is highlighted in red.
3. On the Green Lock control select OFF (Figure 23). The other exposures are now adjustable.
Figure 23. Green Lock control highlighted in red and set to off.
4. Set the Line Trigger Interval until the Max Image Scan Speed is between 8 and 10, 8.06 was used . Adjust values by clicking in the light trigger Interval field and typing values.
5. Turn on lights. Remember if the Temperature goes above 39°C you must turn the lights off and wait until the temperature drops before proceeding. This is to insure the calibration is done at the same temperature as scanning the sections.
6. Click the Start Grab (Figure 24).
Figure 24. Start Grab button highlighted in red.
7. Move the camera over the Xrite color standard until you see the white, dark blue, orange and brown color bars in the image. Place the cursor in the white square, right-click and draw a rectangle by dragging diagonally. Release the mouse when you have selected most of the white bar. The rectangle (marked in green) should only have the white color and nothing else inside (Figure 25).
Figure 25. The grab window is highlighted in red. A green square is drawn in the white color square of the appropriate row.
8. Above the image you will see values for the average RED, GREEN and BLUE (RGB) for all of the pixels within the green selected rectangle (White square). You will also see the ratio values for RED/GREEN and BLUE/GREEN.
9. Adjust the Green Exposure Interval value until the Green value is close to 242.
10. Adjust the Red Exposure Interval value until the RED/GREEN value is near 1.
11. Adjust the Blue Exposure Interval value until the BLUE/GREEN value is near 1.
12. Don't worry about getting an exact value of 1, the TIFF/JPEG correction will correct those values.
13. Turn lights off by clicking Lights Off.
Adjust Gains
Master gain changes the whites/high RGB values. You can use positive or negative values. Master black changes black/low RGB values. You can only input positive values for Master Black. Without changing the gain values, the SHIL gives you a raw image with too high of a contrast. That is, whites are too bright, and blacks are too dark. You need to adjust the mid-tone and black level to achieve a good calibration. To do this, it is recommended to at least raise the master black. Lowering the master gain will help achieve a more ideal mid-tone, but be careful, because color can start to lose saturation when you do. (Figure 26).
1. Select the tab GAINS-BLACK-SHADE-FLAT tab.
2. Turn Lights On by clicking Lights On. Remember if the Temperature goes above 39°C you must turn the lights off and wait until the temperature drops before proceeding.
2. Move the camera over the Macbeth color standard until you see the black, blue, gold and cyan color bars in the image.
3. Place the cursor in the black square, right-click and draw a rectangle by dragging diagonally. Release the mouse when you have select most of the black bar.
3. Adjust the Master Black gain until the GREEN value is around 15 (Figure 26, RED GREEN and BLUE boxes in the image grab window). Qualitatively, this is what's been found to produce a nice image. Please note that the RGB value of the black square is about 50, but this will be corrected for in the TIFF/JPEG correction. Turn off the lights if temp is getting above 39°C.
4. Adjust the Red Black gain until the RED/GREEN value is near 1.
5. Adjust the Blue Black gain until the BLUE/GREEN value is near 1.
6. Keep an eye on the histogram graph on the bottom left corner (Figure 26). We want all the colors to overlay each other pretty closely. Adjusting the RedGain and BlueGain will move the colors (histograms) in the graph in the lower left, move until they are over lapping.
7. Important Note: adjusting those gains likely changed the RGB values in the White square of the Xrite Color checker. Move the camera back over the white square. Draw an ROI box in the white square. If the values aren't near 240 and ratios of R/G and B/G are not near 1, go back to the Rates and Exposure tab and adjust the the values until you hit near 240 or a ratio of 1.. Check back in the Black square and see its still about 15. Adjust the gains and/or exposure intervals until the Black reads near 15 and the R/G, and B/G ratios are near 1. This is a balancing act and can be tedious. Remember do not let the temperature to go about 39°C white doing the balancing. If all fails use the values in the Figure 43, they should be close to an acceptable color balance.
8 Click Lights Off.
Figure 26. Adjusting the Master Black and Red Black and Blue Black to reach RGB values of about 15 for the Black square.
Apply Corrections
We apply three corrections Pixel Black, Shading and Pixel Gain. Only do the corrections after you have finished adjusting the RGB exposure and Gain. Obtain the heat resistant silicone gray mat from the drawer PP-2B. The heat resistant silicon mat is homogenous in color which is helpful for the corrections (no mottling as seen in the old grey cardboard card).
Pixel Black Auto Correction: The pixel black level represents extra energy in the camera independent of a light source and is a consistent pattern in the sensor. To correct for this the light source must be turned off and the camera internal correction circuit collects a few lines of data. An average is taken across the line, and pixels are either added to or subtracted from in order for each pixel to have the average value. (Vendor Manual Reference)
Shading Correction - Flat Method: Shading effects can come from an uneven distribution of light and along the outer edge of the camera lens. Shading is corrected for by averaging the signal across a group of eight pixels to represent the line.
Pixel Gain Correction - Flat Method: Each pixel has a different response to a fixed light source. To correct for this non-uniformity a couple lines of data are calculated and the average response of the pixels are calculated. Then each pixel has a correction factor applied to bring all pixels to the average level. The Pixel Gain Correction also corrects for some shading effects and should be done after the shading correction (Note: the order of pixel gain and shading correction is debated, it is suggested to do it in the order above). If color streaking is evident in the image, this correction is needed to remove the unwanted streaking.
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 27). But Ensure the lights are off.
Figure 27. 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 28).
Figure 28. 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 29). 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.
...
the across image pixel pitch requires a lot of patience.
Move the camera so that it is scanning just the centimeter marks on the QP 101. Also, it is important that the QP 101 card is mounted straight so that the scale lines are parallel to the direction of motion.
On the screen you will see this..
On the Profile graph, drag the purple and yellow cursors to the center of two adjacent peaks near the center of the image. These peaks are the centimeter lines in the QP card.
Use the graph controls and expand (zoom) the graph horizontally and you should see this…
In the expanded view, adjust the cursors so that the are centered in the peak's width (not necessarily the max value).
Checking the focus can be done by obtaining the maximum peak height in the Profile Graph. Adjust the focus back and forth and you notice that the peak rises and falls as you cross the focus point. So after every height adjustment repeat this process for maximum peak height, adjust the cursors and check the Pixel Delta value.
You are ready to begin obtain an in focused pixel pitch of 200-pixels/cm (+/- 1px). You will be repeating the following steps until you reach this goal.
- Change camera height
- Focus
- Adjust cursors
- Check Pixel Delta
A word of caution. Be careful how you tighten the clamps holding the camera to the T- Slot. Make sure to tighten with even pressure, if you don't the camera can be offsetand you will see the image in the Grab window shift. The camera attachment method is not ideal and should be replace.
After performing this process you need to check the home position. When at the home position the camera should be scanning the edge of the tray where the section top sets against. If not, you will need to adjust the home switch on the track until it does. An improperly set home switch will affect the placement of the crop window and potentially the offsets assigned to the RGB values.
Setting Exposures
Before you start..
1. Click the Gains-Black-Shade-Flat tab (Figure 19).
Figure 19. JAI Camera Setup Window showing the Gains-Black-Shade-Flat tab. The Gains-Black-Shade-Flat tab is outlined in red.
2) Click the Clear All Gains, Clear Black Gains, Remove Pixel Black Correction, Remove Shading Correction, and Remove Pixel Gain Correction (Figure 20). You will notice all values in the Master and Black gains go to zero.
Figure 20. Remove the corrections and clear gains.
3) 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.
Understanding triggers and exposure
When the camera moves it will receive trigger pulses from the linear encoder. Each trigger pulse 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.
When you adjust the Line Trigger Interval you will notice that the Max Image Scan Speed value changes. If you scan faster than this, you will drop lines but you can scan slower with affecting the calibration. When you click Save in the value in the Image Scan Setup window will be updated but you are allowed to change this value but should always be lower not higher. As a general rule we want to stay at 8-cm/s or higher value to maintain core flow in the lab.
After you done a few calibrations you will develop a feel for what is possible with current camera set up but if you just stating we recommend setting the line rate to emulate a scan speed of 8-cm/s.
Now you are ready to start setting the exposures for the RGB channels.
- Turn on the lights
- Click the START GRAB button
- Move the camera over the white square on the ColorChecker standard.
- Use the mouse and draw a ROI (Region of Interest) square with only the white square inside. The RGB values and Ratio values will only be calculated for the pixels inside the ROI.
- Go to the Gains-Black-Shades-Flat tab and click the Clear All Gains and click Clear Black Gains
- Go to the Rates and Exposure tab and set the Green Lock to Off
It is helpful to know which RGB channel has the lowest intensity because this channel will be the limiting factor. To find this out remove all gains and set identical exposure values for the RGB channels. The intensities will look like this...
In this case it is the blue channel,
- Start with the blue channel, increase the exposure time until its value is between 240-245.
- Adjust the green exposure until the red/green ratio is 1.000 +/-0.005.
- Adjust the blue exposure until the blue/green ratio is 1.000 +/-0.005.
If cannot get the blue channel tp 240, you have several correction options:
- Lower the lights for increased illumination intensity
- Open up the f-stop for more light
- Increase the line rate (slower scan speeds) so that you can increase the exposure period
- Use gains to amplify the signals.
Using gains is generally the simplest choose because the other choices are not practical or desirable. The down side of using gains is that they amplify both signal and electrical noise. Amplifiing noise isnot good so use gains sapringly as necessary. In the next section will discuss how to use the gains but remember you will likely move back forth between setting exposures and gains to optimize the camera. It is an iterative process.
Setting Gains
Open the Gains-Black-Shades-Flat tab. Adjust the Master Gain until the the weak channel is in the 240-245 range. If the other channels are two high, you can apply negative gains to those channel until get the ratios back to 1 or re-adjust the exposures . The later method is preferred.
Once you have initially roughed in the RGB channels for the White ColorCheck square, it time to look at the dark side.
Still in the Gains-Black-Shades-Flat tab, turn off the lights and click Pixel Black Auto Correction. To be honest we are not quite sure what this does and there appears to be no harm if this step is skipped.
Using exposures and gains you have now balanced the White ColorCheck square in the 240-245 range it is time to set the dark response of the camera
b) Calibration (JAI Camera Setup and Image Corrections)
Camera and Track Setup
Resetting Gains and Corrections
1. Click the Gains-Black-Shade-Flat tab (Figure 19).
Figure 19. JAI Camera Setup Window showing the Gains-Black-Shade-Flat tab. The Gains-Black-Shade-Flat tab is outlined in red.
2. Click the Clear All Gains, Clear Black Gains, Remove Pixel Black Correction, Remove Shading Correction, and Remove Pixel Gain Correction (Figure 20). You will notice all values in the Master and Black gains go to zero.
Figure 20. Remove the corrections and clear gains.
4. In Master Black field, enter 40. That is a good starting point. We have found the value Master Black of 60 works best for our system's set up.
Color Balancing the Camera
Color Balancing should be done with the Xrite color checker mini classic standard version 2019. The grey standard on the top of the track should be the QP card 101 v4 gray scale card. Be sure to use new color standards as some where damaged (faded). The calibration using the Xrite color checker standard card is described below (note: the QP card v.4 101 method that was implemented in 2020 due to the high temperature of lights is described at end of this User Guide if you need to reference that method).
Color Balancing Camera - Xrite Color Checker Classic 2019 Card
Make sure the lens is focused. Use the cm marks on the QP 101 V4 card to focus the lens. If the camera has been moved you will need to adjust the height of the camera using the method described below in Camera Height Adjustment. There should be no reason to adjust the height of the camera between expeditions.
1. Put the 3D Calibration Standard in the track. The color square must be oriented as pictured Figure 21.
Figure 21. Color standard in track in correct orientation.
2. Select the tab RATES and EXPOSURE (Figure 22).
Figure 22. Rates and Exposure window, the tab is highlighted in red.
3. On the Green Lock control select OFF (Figure 23). The other exposures are now adjustable.
Figure 23. Green Lock control highlighted in red and set to off.
4. Set the Line Trigger Interval until the Max Image Scan Speed is between 8 and 10, 8.06 was used . Adjust values by clicking in the light trigger Interval field and typing values.
5. Turn on lights. Remember if the Temperature goes above 39°C you must turn the lights off and wait until the temperature drops before proceeding. This is to insure the calibration is done at the same temperature as scanning the sections.
6. Click the Start Grab (Figure 24).
Figure 24. Start Grab button highlighted in red.
7. Move the camera over the Xrite color standard until you see the white, dark blue, orange and brown color bars in the image. Place the cursor in the white square, right-click and draw a rectangle by dragging diagonally. Release the mouse when you have selected most of the white bar. The rectangle (marked in green) should only have the white color and nothing else inside (Figure 25).
Figure 25. The grab window is highlighted in red. A green square is drawn in the white color square of the appropriate row.
8. Above the image you will see values for the average RED, GREEN and BLUE (RGB) for all of the pixels within the green selected rectangle (White square). You will also see the ratio values for RED/GREEN and BLUE/GREEN.
9. Adjust the Green Exposure Interval value until the Green value is close to 242.
10. Adjust the Red Exposure Interval value until the RED/GREEN value is near 1.
11. Adjust the Blue Exposure Interval value until the BLUE/GREEN value is near 1.
12. Don't worry about getting an exact value of 1, the TIFF/JPEG correction will correct those values.
13. Turn lights off by clicking Lights Off.
Adjust Gains
Master gain changes the whites/high RGB values. You can use positive or negative values. Master black changes black/low RGB values. You can only input positive values for Master Black. Without changing the gain values, the SHIL gives you a raw image with too high of a contrast. That is, whites are too bright, and blacks are too dark. You need to adjust the mid-tone and black level to achieve a good calibration. To do this, it is recommended to at least raise the master black. Lowering the master gain will help achieve a more ideal mid-tone, but be careful, because color can start to lose saturation when you do. (Figure 26).
1. Select the tab GAINS-BLACK-SHADE-FLAT tab.
2. Turn Lights On by clicking Lights On. Remember if the Temperature goes above 39°C you must turn the lights off and wait until the temperature drops before proceeding.
2. Move the camera over the Macbeth color standard until you see the black, blue, gold and cyan color bars in the image.
3. Place the cursor in the black square, right-click and draw a rectangle by dragging diagonally. Release the mouse when you have select most of the black bar.
3. Adjust the Master Black gain until the GREEN value is around 15 (Figure 26, RED GREEN and BLUE boxes in the image grab window). Qualitatively, this is what's been found to produce a nice image. Please note that the RGB value of the black square is about 50, but this will be corrected for in the TIFF/JPEG correction. Turn off the lights if temp is getting above 39°C.
4. Adjust the Red Black gain until the RED/GREEN value is near 1.
5. Adjust the Blue Black gain until the BLUE/GREEN value is near 1.
6. Keep an eye on the histogram graph on the bottom left corner (Figure 26). We want all the colors to overlay each other pretty closely. Adjusting the RedGain and BlueGain will move the colors (histograms) in the graph in the lower left, move until they are over lapping.
7. Important Note: adjusting those gains likely changed the RGB values in the White square of the Xrite Color checker. Move the camera back over the white square. Draw an ROI box in the white square. If the values aren't near 240 and ratios of R/G and B/G are not near 1, go back to the Rates and Exposure tab and adjust the the values until you hit near 240 or a ratio of 1.. Check back in the Black square and see its still about 15. Adjust the gains and/or exposure intervals until the Black reads near 15 and the R/G, and B/G ratios are near 1. This is a balancing act and can be tedious. Remember do not let the temperature to go about 39°C white doing the balancing. If all fails use the values in the Figure 43, they should be close to an acceptable color balance.
8 Click Lights Off.
Figure 26. Adjusting the Master Black and Red Black and Blue Black to reach RGB values of about 15 for the Black square.
Apply Corrections
We apply three corrections Pixel Black, Shading and Pixel Gain. Only do the corrections after you have finished adjusting the RGB exposure and Gain. Obtain the heat resistant silicone gray mat from the drawer PP-2B. The heat resistant silicon mat is homogenous in color which is helpful for the corrections (no mottling as seen in the old grey cardboard card).
Pixel Black Auto Correction: The pixel black level represents extra energy in the camera independent of a light source and is a consistent pattern in the sensor. To correct for this the light source must be turned off and the camera internal correction circuit collects a few lines of data. An average is taken across the line, and pixels are either added to or subtracted from in order for each pixel to have the average value. (Vendor Manual Reference)
Shading Correction - Flat Method: Shading effects can come from an uneven distribution of light and along the outer edge of the camera lens. Shading is corrected for by averaging the signal across a group of eight pixels to represent the line.
Pixel Gain Correction - Flat Method: Each pixel has a different response to a fixed light source. To correct for this non-uniformity a couple lines of data are calculated and the average response of the pixels are calculated. Then each pixel has a correction factor applied to bring all pixels to the average level. The Pixel Gain Correction also corrects for some shading effects and should be done after the shading correction (Note: the order of pixel gain and shading correction is debated, it is suggested to do it in the order above). If color streaking is evident in the image, this correction is needed to remove the unwanted streaking.
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 27). But Ensure the lights are off.
Figure 27. 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 28).
Figure 28. 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 29). 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 29. 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 30). 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 30. 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 31).
Figure 31. 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.
2. Click Lights ON
2. 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 (Figure 32).
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 RGB values of White and Black are listed here for various illuminants. For illuminant D65 White RGBs are 242, 242 and 236 and and Black RGBs are 49, 49, 50 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.
Figure 5. 3D standard with Xrite Color checker (MacBeth Color) standard on the left.
Figure 6. QP card 101 v4 grey scale standard.
Figure 7. Setting the f/stop on the Camera. F/16 is the preferred value by the imaging specialists onboard. Darker cores may need a larger f/stop of F/22.
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.
5. The RGB lines should first appear “bowed” evenly across profile and centered in the image (Figure 30). 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 30. 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 31).
Figure 31. 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.
2. Click Lights ON
2. 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 (Figure 32).
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Figure 32. Grab and Profile after the Pixel Gain Correction has been applied.
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