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The laboratory technician calibrates the system when needed by adjusting camera settings and analyzing an imaged Xrite Color Checker Mini standard (MacBeth card). Be sure to use a 2014 or newer version of the Xrite Color checker because the RGB values used for correction uses the values from the newer standard. The RGB values on the standard are calculated from the L*ab values provided by Xrite. As of we are using RGB values calculated under an illuminant A. The excel spreadsheet of RGB values of the Xrite color checker using varying illuminants and can be found here. The white square has R=240, G=242, B=235 and the black square R=50, G=50, B=50. A 3-D standard that holds the Xrite color checker and a grey silicon mat is in the SHIL calibration drawer, PP-2B (Figure 5).
Figure 5. 3D standard with Xrite color checker standard.
The current light system (Figure 6) obtains nearly uniform illumination intensity from the core’s surface (half or whole round) to the bottom of the liner by a combination of high intensity, overlapping large diameter light source, close coupling to the imaged surface and the “line” image plane. The bottom edge of the led mount should be set between 2 and 4cm from the image surface. Note, any height change to the lights requires re-calibration. Heat is removed from the LEDs and transferred to the surrounding air via the copper heat pipes and is cooled with mini fans. While the copper rods can get hot they are not a burn hazard. However they are very delicate and bend at the slightest touch, so use care when working with the camera lens. For more detailed information on the theory behind the calibration please refer to the /wiki/spaces/LN/pages/7338174348 for further reading. Maintain temperature of the lights at 30-40 °C during calibration. LED's of temperature is located above the camera. During a section scan the temperature ranges between 30-36 °C.
Figure 6. SHIL Camera and Lights set up.
Calibration is conducted in the following steps.
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1. In the IMS control panel select Motion and then Drive Disable from the dropdown menu (Figure 197). You will have to move the camera by hand for the calibration, disabling the motor allows manual movement of the camera on the track.
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2. Open JAI Camera Setup utility: In the IMS control panel click Instruments > JAI Camera Settings (Figure 208). The lights turn on automatically when the JAI Camera Setup window opens.
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In practice the camera height rarely changes and this step is not necessary to perform for every calibration but it should be checked at the beginning of each expedition. |
The goal is to set the across image pixel pitch with a focused camera. Warning this can be tedious and requires two people.
1. Move the camera so that it is scanning just the centimeter marks on the QP 101 card (Figure 2210). Also, it is important that the QP 101 card is mounted straight so that the scale lines are parallel to the direction of motion.
Figure 2210. QP 101 card showing centimeter marks for pixel pitch calibration.
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2. On the screen you will see the cm lines and vertical peaks on the Profile graph (Figure 2311).
Figure 2311. Example of the QP-101 marks and the profile graph.
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4. Use the graph controls and expand (zoom) the graph horizontally (Figure 2412).
Figure 2412. Cursor placement on the QP 101's centimeter marks in Profile graph.
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5. In the expanded view, adjust the cursors so that the are centered in the peak's width (not necessarily the max value). You want to achieve a Pixel Delta of 200 pixels/cm (+/-1px) (Figure 2513).
Figure 2513. Cursor pixel values and span.
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Be careful how you tighten the clamps holding the camera to the T-Slot. Make sure to tighten with even pressure on both sides, if you don't the camera can be offset and 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 is placed against (red strip). 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
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1) . Click the Gains-Black-Shade-Flat tab (Figure 2614).
Figure 2614. 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 2615). You will notice all values in the Master and Black gains go to zero.
Figure 2615. Remove the corrections and clear gains.
3) . Check the camera's f/stop which should either f/16 or f/22 (see Figure 2716). 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 levels mean longer exposures - which means slow track speeds for scanning - which could impact core flow in the lab. So on a low recovery expeditions expedition you can afford the longer scan time, so go for f/22 otherwise otherwise f/16. If you are doing 360-imaging f/22 is a must. Check with the LO and EPM if you are unsure of the time needed for scanning sections.
Figure 2716. Setting the F Stop on the Camera.
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Although the figure says f/22 is recommended (recommended by the manufacturer) onboard we found f/16 works best for our scanning needs.
4. Place the 3D Calibration Standard in the track. The color square must be oriented as shown in Figure 2817.
Figure 2817. Calibration 3D standard with the xrite Xrite color checker mini.
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When the camera moves it will receive trigger pulses from the linear encoder. Each trigger pulse will start an exposure in 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 allowable 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 (yellow slider in above figure) 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 without affecting the calibration. You can adjust scan speed in the Image Scan Setup window as well (figure below). When you click Save in the Image Scan Setup window the value will be updated. The Speed in the Image Scan Setup window will be updated but you are allowed to change this value but should always be lower, not higher, than the Max Image Scan Speed calculated by the Line Trigger Interval. 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 are just stating starting we recommend setting the line rate to emulate a scan speed of 8 - cm/s. |
CHANGING EXPOSURE VALUES
Now you are ready to start setting the exposures for the RGB channels.
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. Turn on the lights.
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. Click the START GRAB button (Figure 18).
Figure 2818. Start Grab.
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. Move the camera over the
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White square on the
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Xrite Color Checker standard.
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. Use the mouse and draw a ROI (Region of Interest) with only the white square inside (Figure
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19). The RGB values and Ratio values will only be calculated for the pixels inside the ROI (Figure
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20)
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Place the cursor in the white square, right-click and draw a rectangle by dragging diagonally. Release the mouse when you
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have selected most of the white bar. The rectangle (marked in green) should only have the white color and nothing else
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inside.
Figure 19. Selecting the ROI of the White square.
Figure 20. RGB and Ratio values calculated from the pixels in the ROI.
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. Go to the Gains-Black-Shades-Flat tab and click the Clear All Gains and click Clear Black Gains if not already done.
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. Go to the Rates and Exposure tab and set the Green Lock
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to Off. That step allows you to adjust the exposure intervals (Figure 21).
Figure 21. Set Green Lock off.
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It is helpful to know which RGB channel has the lowest intensity because this channel will be the limiting factor when setting exposures. To find this out which channel is the weakest remove all gains and set identical exposure values for the RGB channels. The intensities will look like Figure XX. If you already know which channel you can skip this step.
In this case, it is the blue channel that has the lowest intensity. |
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Make sure to keep an eye on the light temperature. You want stay within 30 to 39-deg C. Shut the lights off as necessary and let them cool down. |
For simplicity well use the blue channel as the weakest.
1) Start with the blue channel, increase the exposure time until its value is between 240-245.
2) Adjust the green exposure until the red/green ratio is near 1.000 (+/-0.005).
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the figure below. Onboard our weakest channel is Blue.
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7. Start with the blue channel (the weakest channel), increase the Exposure Interval time until its value is near 240.
8. Adjust the green exposure interval until the blue/green ratio is near 1.000 (+/-0.005).
9. Adjust the red exposure interval until the red/green ratio is near 1.000 (+/-0.005).
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It is important to note that the RGB values for the White square are R=240, G=242 and B=235 for the 2019 Xrite color checker standard. Thus the ratios for B/G and R/G are not 1.000 (as we say to achieve in steps 8 and 9 above). B/G = 0.97, R/G = 0.99 (Xrite color checker v. 2019) Previous color standards used onboard had balanced RGB values, meaning the R, G and B were equal, hence achieving B/G and R/G rations of near 1.000 was the goal. With the 2019 Xrite color checker these values are not balanced for white so achieving 1.000 may not be the ideal ratio for color balancing. What ratio is best to use needs to be tested. It may not make any difference, but when time allows we should test update this User Guide if improvement is found in the calibration curve. |
If you cannot get the blue channel to 240, you have several correction options:
1) Lower the lights for increased illumination.
2) Open up the f-stop for more light.
3) Increase the line rate (slower scan speeds) so that you can increase the exposure period.
4) Use gains to amplify the signals.
Using gains to amplify the signal is generally the simplest choice because the other options are often not practical or desirable. The down side of using gains is that they amplify both signal and electrical noise. Amplifying noise is not good so use gains sparingly. 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.
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5) Adjust the Master Back value unit the Green value is near 15. 40 is a good starting point.
6) Adjust the Red Black and Blue Black Gains until the ratio are close to 1 +/- 0.05
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Image striking is caused when used a non-uniform standard for the Pixel Gain Correction correction or just from dirt. Until we found the silicone sheets we would have to defocus the lens to mitigate this issues. If see streaks chack your target material and repeat this correction. |
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 correction can be done without the cap. But Ensure the lights are off.
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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.
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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.
2) Click Lights ON
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.
IMAGE Calibration (Correction)
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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 38. Color standard in track in correct orientation.
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2. Adjust the Brightness, Contrast, and Gamma levels (Figure 45-1) 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 45-2, 45-3) 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.
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1. To double check your calibration under the same scanning conditions as the scientists see, scan an image of the 3D standard without the color checker box selected.
2. Click Crop and Click Save
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C.2 ColorChecker RGB Values
A link to the Excel Spreadsheet of RGB values calculated from L*a*b* for the Xrite Mini Color Checker is here. L*a*b* was obtained from xrite.com.
C.3 VCD-S Configuration
"Scratch sheets" are printouts of section half images produced by SHIL. The sheet is a LabVIEW VI with embedded images that can print automatically when a user 'saves' an image. The VI is scaled to print SHIL images correctly on 11x17" paper in portrait orientation. The scratch sheet can be customized to include various columns to capture descriptions or drawings on paper. The goal of this guide is to instruct how to use and customize scratch sheets.
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