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The laboratory technician calibrates the system when needed by adjusting camera settings and analyzing an imaged 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. While these to 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 Advanced SHIL Calibration (in developement).
Note: the following instructions are devided into 2 sections. Calibration Check and Calibration.
*Method based on Instructions sent by Bill Mills. BILL and SARAH please review, correct, and update. Any questions are highlighted with an inline comment or marked in red.
For more detailed information on the theory behind the calibration please refer to the Advanced SHIL Calibration.
Safety Concerns
- These lights get hot and can damage or burn surfaces if left stationary and on for over 20secs. This is not an issue during normal imaging operations and will not heat the core surface at all. Bus during calibration process when the lights are stationary you must be aware of the length of time the lights are on. You can use the manual power switch to turn the lights on and off or the buttons in the software. Use the heat resistant grey silicone mat for the shading and pixel corrections. Do not use the plastic Gray card. (testing needs to be completed on which color silicone mat is best to use)
- 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, you can use our FLIR cameras to confirm that the temperature is ok.
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- Color Standard values vary based on the standard and the manufacturer of the standard. Verify the values of the MacBeth Color Standard (multi color squares on the 3D standard, Fig ##) before starting (How do we do this?). Check the grayscale card to determine what the percentage of gray. The target calibration values will vary based on the percentage of gray because the target values depend on the percent grayscale card. Max RGB value is 255. If using a 50% grayscale card, target red and green value is 127, a 25% grayscale card target value is 64, etc. For our QP 101 v4 card, the RGB values are 235, 111, and 80 (Fig. ##). All SHIL calibration standards are found in drawer PP-2B.
- Set camera f/stop to 22 (Fig. ##). F/22 is preferred for standard scanning with the current light set up; F/16 is also acceptable. 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.
Figure ##: 3D standard with MacBeth Color standard.
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Calibration Check
The following three steps in Calibration Check are designed for technicians to check the SHIL’s calibration and to determine if it needs to be adjusted. 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 full SHIL Calibration section below.Step 1:
Determine the scan rate for the expedition
1. Talk to your science party to determine what scanning parameters (scan rate) they wish to use. A typically scan rate has been between 8-10 cm per second. Note, with the new, brighter LED lighting system, faster scan rates can be achieved compared to expeditions prior to Expedition 390C.
2. Compare the current scan rate to the requested rate.
a. Launch ‘IMS’ IMS on the SHIL computer, click on the ‘DAQ’ tab and open the
b. Click on DAQ and click Image Capture Motion Setup window.
b. The speed (Fig. ##) 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 full SHIL Calibration guide 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.
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- Click on Instruments and open the JAI Camera Set-up window.
- Turn the lights off IMMEDIATLY by clicking Lights OFF (Fig. ##). Remember the lights produce a lot of heat and can cause damage to anything underneath them if they remain stationary for too long.
- Click Rates and Exposure tab (Fig. ##)
- Check that the Max Image Scan Speed is equal to, or slightly less than the designated Scan Rate.
- Again, if the values need to be changed to match the requested values by the science party, please proceed to the full SHIL Calibration calibration section below. If the values match, close the JAI Camera Set-up window and proceed.
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Figure ##: Checking the Max Image Scan Speed.
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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 full SHIL Calibrationcalibration instructions below (Calibration section).
Take an Image
1. Place the 3D calibration standard on track as shown (Fig. ##). The color squares must be oriented as pictured below, butted against the red reflection bar.
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Figure 23: Image Correction Window. Steps are indicated in the screenfigure.
8. Draw a ROI box loosely around the color checker in the Original box as illustrated above, then click Crop. Draw another ROI box around the Color Checker squares and this time making sure to only have squares 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 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. For more detail on the graphs and values in the Image Correction window please see Create Correction Curve section below.
TIFF Correction Check (Fig. ##)
1. Select Click TIFF Correction Mode
2. Click Uncorrected Image tab. This graph shows the measured red, green, and blue values of the gray scale color squares.
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4. Adjust the Red, Green, and Blue polynomial orders to create the lowest residual error with the smoothest curve in the UNCORRECTED IMAGE Uncorrected Image tab. Values should be around 3 or 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. If you are unable to produce a reasonable correction curve, it is necessary to redo your white balance correction in the full Calibration discussed section below. (see TIFF corrections cheat sheet in SHIL lab notebook, to be added).
Figure 24##: Steps for Tiff Correction illustrated on image. 1. Redraw box on color squares. 2. Select Tiff Correction Mode. 3. Put graph on Uncorrected Image. 4. Select Tiff Correction to view polynomial order. 5. Adjust polynomial order. 6. Check graph for linear relationship.
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JPEG Correction Check (
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Fig.##)
In JPEG correction you will check and adjust if necessary the brightness, contrast and gamma (BCG) of the image.
1. Click JPEG Correction Mode
2. Click Applied Corrections tab
3. Click JPEG Corrections tab. Adjust the Brightness, Contrast, and Gamma levels to achieve a straight line in the Applied Corrections tab and the ROI Corrected box should have values near 250 for the white square (is this correct or should they be 235). We want a linear relationship between the measured and given values.
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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 250. 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.
Figure 25: Steps for JPEG Correction illustrated on image. 1. Select JPEG Correction Mode. 2. Select Applied Corrections tab on graph. 3. Select JPEG Correction to see Brightness, Contrast, and Gamma Corrections. 4. Adjust Brightness, Contrast, and Gamma corrections. 6. Check graph for Linear Relationship. 7. Check the boxes in the Color Checker and compare to RGB values in corrected image.
34. If the values all look 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 it the doesn't look good, click cancel Cancel and you can proceed to the following section and calibrate.
Setup the Track and Camera
complete the calibration instructions listed in the Calibration section below.
Calibration
Track Setup
1. Confirm the camera F-stop is set to 22 (Fig. ##). F/22 is preferred for standard scanning with the current light set up; F/16 is also acceptable. For hard rock cruises, where 360°whole round scanning is required, a larger F-stop number is required. See the Advanced SHIL Calibration (in developement) for further information on F-stop.
Figure ##: Setting the F Stop on the Camera.
21.Disable the motor that moves the camera. In the IMS control panel select Motion and then Drive Disable from the dropdown menu (Figure 26). The user can now manually move the camera to the desired spotFig. ##). You will have to move the camera by hand for the calibration, disabling the motor allows manual movement of the camera on the track.
23. Back in In the IMS control panel go to click Instruments > JAI Camera Settings (Figure 27Fig. ##). The lights turn on automatically when the JAI Camera Setup window opens
4. Click Lights OFF (Fig. ##) IMMEADIATELY. You can also turn the lights off with the physical power switch located behind the monitor (Fig. ##). Note if the lights are turned off by the hardware switch, the lights cannot then be turned on the software command.
3. Confirm the camera f-stop is set to 16. If not, change it to 16.
4. The lights will turn on when the JAI Camera Window opens. Due to the intensity and heat produced by the LEDs it is best to turn off the lights until ready. Turn off the lights in the software window (Figure 28) or with the physical power switch located behind the monitor (Figure 29). Note if the lights are turned off by the hardware switch, the lights cannot then be turned on the software command.
Figure 28: Software commands to turn the Lights On or Off.
Color Balance the Camera
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Reseting Gains and Corrections
1.Select Click the Gains-Black-Shade-Flat tab (Figure Fig. 30).
Figure 30: JAI Camera Setup Window showing the Gains-Black-Shade-Flat tab. The Gains-Black-Shade-Flat tab is outlined in red.
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2. Click the Clear All Gains, Clear Black Gains, Remove Pixel Black Correction, Remove Shading Correction, and Remove Pixel Gain Correction (Figure 31Fig. ##). You will notice all values in the Master and Black gains to zero.
Figure 31: The five clear and remove buttons of interest are outlined in red.
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Remove the corrections and clear gains.
4. In Master Black field, enter 40. (Why? - to raise the sensitivity of the camera's sensors to pick up dark values?)
Color Balancing the Camera
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Color Balancing is currently being done using the QP101 QP card 101 v4 gray scale card. The MacBeth Color standard cards on board have all been damaged by the LED lights, changing the RGB values ont he cards. The MacBeth Method is still retained in a below section Color Balacing Camera - Old Method MacBeth Color Checker Card section below. We have carry a lot large stock of QP Cards 101 cards on board, they are more heat resistant than the MacBeth card, and much cheaper to replace.
Adjust Exposure
The exposure intervals we set relate to how long the camera can pick up values for each color band. Try not to keep the lights on for longer than ~ 20 seconds 20sec and then keep them off for ~ a minute~60 sec. As the lights warm up the RGB values change, particularly the blue value, and change most rapidly in the first minute of the lights warming up. Since the SHIL is often used after being off for a bit, we are trying to calibrate to represent the measuring conditions, as best we can. Right now we do not have a defined procedure for keeping the lights on/off during calibration and thus suggest 20 sec intervals.
1.
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Click the
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RATES and EXPOSURE
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tab (Fig. ##-2).
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Figure 32: Rates and Exposure tab with chronological steps on the screen.
2. On the Green Lock control select OFF (Figure Fig. 32-3). The other RGB exposures are now adjustable.
3. Set the Line Trigger Interval until the Max Image Scan Speed is 10 for now. Adjust (Fig. ##-4). Adjust values by clicking in the field and typing values or using the up and down arrow on the keyboard. The Line Trigger Value must be greater than the exposure intervals Exposure Intervals for red, green, and blue.
4. Move the camera carriage over about where the QP Card is card 101 on the track.
5. Click the Start Grab (Figure Fig. 32-5).
6. Turn on lights, but . Click Lights ON (Fig. ##-6). Remember to only keep them for ~20 seconds sec and then turn off for ~ 1 minute. 7. Move the Camera if necessary to ~60 sec while preforming the following. You should see the QP Card card 101 in the image live grab window.
7. Draw a green ROI box in the light gray (white) area. Now the Red, Green, and Blue values above the image grab window show the values inside your square. The RGB value of the QP Card card 101 v4 in the light gray (white) area is 235. Adjust the Red, Green, and Blue Exposure times until each value is 235. Remember to turn off the lights regularly!
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is 235.
8. Adjust the Red, Green, and Blue Exposure times until each value in the live grab window is 235. Remember to turn off the lights regularly!
Adjust Gains (Fig. ##)
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.
1. Select the Gains-Black-Shade-Flat tab.
2. Click Start Grab.
3. Click Lights ON. Turn the lights on Preform the following steps as quickly as possible. Try to do it in 20 sec intervals with 60 sec lights off break.
4. Draw the green ROI box on the dark darkest square.
5. Adjust the Master Black Value until the RGB values are ~40. Qualitatively, this is what's been found to produce a nice image. Please note that the RGB value of the QP Card 101 card v4 for this square is 80, but this will be corrected for that value in the tiffTIFF/jpeg JPEG correction. Remember to turn off the lights regularly!
6. You can also adjust the RedBlack and BlueBlack values to adjust those specific channels6. You can also adjust the RedBlack, BlueBlack, RedGain and BlueGain values to adjust those specific channels. Keep an eye on the histogram graph on the bottom left corner. We want all the colors to overlay each other pretty closely.
7. Adjusting the gain likely changed the RGB values in the light gray card. Draw an ROI box in the light gray (white) square. If the values aren't 235 go back to the Rates and Exposure tab and adjust the the values until you hit 235. Check back in the dark gray square and see its still around 40.
8. Keep an eye on the graph on the bottom left corner. We want all the colors to overlay each other pretty closely.
~40, adjust the gains to obtain RGB of ~40.
8. When the light grey (white) and the dark grey are 9. When the colors all seem well balanced you can move on to the next stepapplying corrections. How long the lights have been will affect the color balance. If the lights have gotten quite warm and everything looks even, then when the lights are 'cold' the blue channel will be lower than the others.
Figure ##: Adjusting Gains.
Apply Corrections
We apply three corrections Pixel Black, Shading and Pixel Gain. Only do the corrections after you have finished adjusting the exposure and gain. Find information regarding each correction below:
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, the lens cap put on, 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
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: 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
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: 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. If color streaking is evident in the image, this correction is needed to remove the unwated streaking.
After discussion with JAI we learned the order of corrections should be Pixel Black, Shading, and Pixel Gain. Previously our order was Shading, Pixel Gain, and Pixel Black. The order has been updated here. We were also to told to do all exposure and gain adjustments before doing these three camera corrections. This manual has been updated to reflect those changes.
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