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The laboratory technician calibrates the system when needed by adjusting camera settings and analyzing an imaged Xrite XRite Color Checker Standard (MacBeth card) or a QP 101 V4 Color Standard. The current light system 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 brass led mount should be set between 2 and 4cm from the image surface. For uneven hard rock cores the height can be set higher but illumination intensity will drop, exposure times lengthen, f-stop opened and scanning speed reduced. 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 Understanding the SHIL Calibration for further reading. Maintain temperature of the lights at 30-35 °C during calibration.
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- These lights can get hot if the cooling fans are not used (cooling fans work automatically when lights come one). The temperature is shown on the LED read out above the camera and is maintained at set to maintain a temperature of 30 °C. During a section scan, the temperature will range between 30 and 35 °C. If Temperature goes above 50°C an alarm will sound. Notify a technician if alarm sounds. Caution is needed when technicians perform during the calibration process because the lights are stationary and you must be conscious of the temperature of the lightsremain on for much longer (during calibration the user controls Lights On/Lights Off). You can use the manual power switch to turn the lights on and off or the buttons in the software (the calibration procedure below uses the buttons in software). Use the heat resistant grey silicone mat for the shading and pixel corrections. Do not use the plastic Gray card. Make sure the temperature is maintained between 30 and 35°C for calibration (to match temperature of lights during imaging of a section).
- Never look at the LEDs directly. Even the reflected light can be painful. When working under the track make sure that the power is off.
- NOTE: if you are concerned with the heat dissipation on the core surface, you can use our FLIR cameras to confirm that the temperature is ok.
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White Balance: a camera setting that adjusts the color balance of light the you’re shooting in so that it appears a neutral white, and it’s it is used to counteract the orange/yellow color of artificial light.
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- Note which version of standard you are using. Each color standard values vary based on the version and the manufacturer of the standard. The X-Rite XRite Colorchecker (MacBeth standard, Figure 20) 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 MacBeth standard the RGB values of white is 243 and black is 52. For the QP 101 v4 card, the RGB values are 235, 111, and 80 (Figure 21). All SHIL calibration standards are found in drawer PP-2B.
- Obtain the 3D standard (Figure 20), the gray silicone mat standardand standard and the lens cap from PP-2B.
- Set camera f/stop to either F/16 or F/22 (Figure 22). The manufacturer suggested F/22 as the preferred for scanning with the current 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 is 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.
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Figure 22: Setting the F Stop on the Camera. Note that F/22 was recommended by the camera manufacturer but this that value is debated. F/16 is the preferred value by the imaging specialists onboard. Darker cores may need F/22.
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3. Compare the current scan rate (Speed) to the requested rate. The Speed (Figure 23) of the camera will be in the first box. If the values need to be changed to match the requested values by the science party, please proceed to the calibration section below as you will need to do a full calibration. If the values match, close the ‘Image Scan Setup’ window and proceed with the following checks. Speed of 8 to 10 is the most common value and must be less than the scan speed value calculated in the JAI Camera Setup utility.
Figure 23: Checking the Image Scan Speed.
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2. Turn the lights off IMMEDIATELY by clicking Lights OFF. Remember the lights produce a lot of heat and can cause damage to anything underneath them if they remain stationary for too longwe want to maintain the calibration at temperatures between 30-35 °C.
3. Click Rates and Exposure tab (Figure 24).
4. Check that the Max Image Scan Speed is equal to, or slightly more than the designated scan rate (Speed, Figure 23). The Max Image Scan Speed is usually between 8 to 10.
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10. Draw another ROI box around the Color Checker squares and this time making sure to only have XRite MacBeth colorchecker 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.
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Check TIFF and JPEG Corrections
Here we check and can adjust, if needed, our TIFF and JPEG Corrections. You may find you only need to slightly tweak the values and the calibration is good. 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, 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.
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4. In the Tiff Correction tab adjust the LUT polynomial order values for the Red, Green, and Blue channels (Figure 29-5). Adjust these values to create the lowest residual error with the smoothest curve in the Uncorrected Image tab. Poly values should be around 4. Make sure that the curve does not wave about. If it does, the order values need to be lowered. Also check that the corrected ROI and MacBeth values should be very close. Make sure that the white does not exceed the MacBeth value (243). If you are unable to produce a reasonable correction curve, it is necessary to redo your white balance correction in the Calibration section below.
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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 30-4).
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 settingsTIFF 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 30-4).
1. Click JPEG Correction Mode (Figure 30-1)
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3. Click JPEG Corrections tab (Figure 30-3). Adjust the Brightness, Contrast, and Gamma levels (Figure 54-4) to achieve a straight line in the Applied Corrections tab and the ROI Corrected box should have values near 250 243 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. (see JPEG corrections cheat sheet in SHIL lab notebook, to be added). The Applied Corrections Graph should be a straight line and the ROI Corrected Box should have values near 250243. 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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Color Balancing should be done with the Xrite color checker MacBeth standard. 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) by the high temperature of the previous light set up. The calibration using the MacBeth writewhite standard card is described below (note: the QP card v.4 101 method that was implemented in 2020 due to high temperature of lights is described at end of this User Guide if you need to reference that method).
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Make sure the lens is focused. Use the cm marks on the QP101 QP 101 V4 card to focus the lens.
1. Put the 3D Calibration Standard in the track (Figure 33). The color square must be oriented as pictured Figure 38.
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4. Set the Line Trigger Interval until the Max Image Scan Speed is about 8 ( between 8 and 10). Adjust values by clicking in the light trigger Interval field and typing values.
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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 Red Exposure Interval value until the RED value is 245243.
10. Adjust the Green Exposure Interval value until the RED/GREEN value is as close to 1 as you can achieve.
11. Adjust the Blue Exposure Interval value until the BLUE/GREEN value is is as close to 1 as you can achieve. You just completed the White Balance of the upper limit of the camera, but you are not done.
12. Turn lights off by clicking Lights Off.
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1. Select the tab GAINS-BLACK-SHADE-FLAT tab (Figure 39).
2. Turn Lights On by clicking Lights On. Remember if the Temperature goes above 35 °C you must turn the lights off and wait until the temperature drops before proceeding.
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3. Adjust the Master Black gain until the GREEN value is around 15 (Figure 43). Qualitatively, this is what's been found to produce a nice image. Please note that the RGB value of the black square is 52about 50, but this will be corrected for that value in the TIFF/JPEG correction. Remember to turn off the lights regularly!
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7. Adjusting the gain likely changed the RGB values in the White square of the MacBeth Color checker. Draw an ROI box in the White square. If the values aren't 243 go back to the Rates and Exposure tab and adjust the the values until you hit 243. Check back in the Black square and see its still about 15. Adjust the gains and/or exposure intervals until the Black reads 15 and White reads 243. This is a balancing act and can be tedious and remember to . Remember do not let the temperature to go about 35 °C.
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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 also homogenous in color which is helpful for the corrections (no mottling as seen in the old grey cardboard card).
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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 (with the lights at no more than 80% of max) 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.
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4. This step is no longer needed (info with strikethrough) because the silicone matting is homogenous. The previous material used had a mottle effect and thus defocusing was required to provide an even surface. If you find that defocusing is still valid please make a note here. Defocus the lens on the camera just a little bit (Figure 44). Look at the Profile graph and slightly rotate the lens’ focus until the RGB lines are smoother, but still have some variation.
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Figure 50: Grab and Profile after the Pixel Gain Correction has been applied.
3. Remove the gray mat. Move Camera Confirm the Camera is in focus by moving it over the mm 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 (243) again and adjust the exposure intervals if needed.
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4. In the Tiff Correction tab adjust the LUT polynomial order values for the Red, Green, and Blue channels (Figure 56-5). Adjust these values to create the lowest residual error with the smoothest curve in the Uncorrected Image tab. Values should be around 4. Make sure that the curve does not wave about. If it does the order values need to be lowered. Also check that the corrected ROI and MacBeth values should be very close. Make sure that the white does not exceed the MacBeth value (243). If you are unable to produce a reasonable correction curve, it is necessary to redo your White Balance by Shutter Correction in the Calibration section above.
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3. Click JPEG Corrections tab (Figure 57-3). Adjust the Brightness, Contrast, and Gamma levels (Figure 57-4) to achieve a straight line in the Applied Corrections tab and the ROI Corrected box should have values near 243 for the white square. 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 should have values near 250243. These The BCG 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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