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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 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 MacBeth standard the RGB values of White and Black are listed here. White RGBs are 242, 242 and 236 and black RGBs are 49, 49, 50. For the QP 101 v4 card, the RGB values are 235 (light grey), 111 (medium grey), and 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 and the lens cap 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 for f/stop for scanning with the current our light set up however we have found F/16 works well for our section halves and is the most used Ff/stop for calibration and scanning sections. For hard rock cruises, where 360° whole round scanning is required, a larger Ff/stop number is 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.
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Figure 6. QP card 101 v4 grey scale standard.
Figure 7. Setting the F Stop f/stop on the Camera. Note that F/22 was recommended by the camera manufacturer but that value is debated. 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
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3. Compare the current scan rate (Speed) to the requested rate. The Speed (Figure 8) 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 values and the speed must be less than the scan speed value calculated in the JAI Camera Setup utility (see info below). Note that the speed rarely changes between expeditions.
Figure 8. 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 we want to maintain the calibration at temperatures between 30-35 39 °C.
3. Click Rates and Exposure tab (Figure 9).
4. Check that the Max Image Scan Speed is equal to, or slightly more than the designated scan rate (Speed, Figure 8). The Max Image Scan Speed is usually between 8 to 10.
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Prepare the scan to assess the current image correction 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 (Calibration section).
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.
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Figure 12. Image Correction command selection.
NOTE: The main Image Correction screen has been updated as of Nov 25th 2021. We are in discussion with Lab Working Group on utilizing the new window. The main difference is that we can use colors other than the White, grey and Black to make any corrections.
The main Image Correction window displays three main areas: window displays three main areas:
A. Graph panel: Main graphical viewing area on the left side of the screen.
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7. Select Open Test Image and select the image you just took (Figure 13-1), located in C:/DATA/IN/IMAGE. It does not matter if the JPEG or TIFF file is loadedThe program prompts you to select the TIFF file as soon as the Image Correction window opens. The image loads into both the Original and Corrected windows.
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Figure 13. Image Correction Window. Steps are indicated in the figure. (New image correction window vi to be ADDED).
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 (These steps need to be updated to reflect new user interface)
1. Click TIFF Correction Mode (Figure 13-2).
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4. In the Tiff Correction tab adjust the LUT polynomial order values for the Red, Green, and Blue channels (Figure 13-5). 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 about 3. Make sure that the curve does not wave about. If it does, the values need to be lowered. Also check that the corrected ROI and MacBeth values should be Xrite color checker values are very close. Make sure that the white does not exceed the MacBeth Xrite values (RGB = 242. , 242. , 236). 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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Figure 13. 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. (INSERT NEW FIGUREHERE)
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 14-4).
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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 14-4).
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3. Click JPEG Corrections tab (Figure 14-3). 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 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. (see JPEG corrections cheat sheet in SHIL lab notebook, to be added). The Applied Corrections Graph should be The Applied Corrections Graph should be a straight line and the ROI Corrected Box should have values near the RGB values of 242, 242, 236. 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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Figure 14. 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. (INSERT NEW FIGURE)
4. 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 section and complete the calibration instructions listed in the Calibration section below.
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Camera and Track Setup
1. Confirm the camera F-f/stop is set to F/16 or F/22 (Figure 15). F/22 is preferred by the camera manufacturer for scanning with the current light set up however the reasoning behind that is unclear. The imaging specialists onboard have been using F/16 and are confident F/16 works for our set up. For hard rock cruises, where 360° whole round scanning is required, a larger F-stop number is maybe required (ie. F/22).
Figure 15. Setting the F Stop on the Camera.
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4. In Master Black field, enter 40. That is a good starting point. The Note for tech: the last value used on the Master Black was 60, so you may want to try 60 now (Why?).
Color Balancing the Camera
Color Balancing should be done with the Xrite color checker mini classic (MacBeth) 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) by the high temperature of the previous light set up. 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).
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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.
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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 35 °C 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).
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7. Move the camera over the Macbeth 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).
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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 close to 242.
10. Adjust the Green Exposure Interval value until the RED/GREEN value is as close to 1 as you can achieve. (Red is 242, Green is 242, ratio = 1)
11. Adjust the Blue Exposure Interval value until the BLUE/GREEN value is near 1 (actual ratio 0.98, Blue is 236, Green is 242). You just completed the White Balance of the upper limit of the camera.
12. 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.
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3. Adjust the Master Black gain until the GREEN value is around 15 (Figure 43???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. Remember to turn off the lights regularly!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 (actual ratio 1.02, Blue is 50, Green is 49).
6. Keep an eye on the histogram graph on the bottom left corner (Figure 2326). 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. Adjusting the gain Important Note: adjusting those gains likely changed the RGB values in the White square of the MacBeth Xrite Color checker. Move the camera back over the white square. Draw an ROI box in the White white square. If the values aren't near 242 go back to the Rates and Exposure tab and adjust the the values until you hit 242 (RGB 242, 242, 236). 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 White reads near 242 (RGB 242, 242, 236). This is a balancing act and can be tedious. Remember do not let the temperature to go about 35 °C39°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 , 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)
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Pixel Black Auto Correction
1. Take the lens cap (Figure 26) and place on lens (Figure 27). The lens cap is located in drawer PP-2B. The new light set up makes adding a lens cap difficult and so it has been noted determined that added the lens may not be needed if the pixel black auto correct can be done without the cap (Figure 27). Ensure the lights are off but I have yet to test that.
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Figure 27. Lens Cap being put on camera - note the lens cap is not needed. Ensure the lights are off.
2. Click With lights off click Pixel Black Auto Correction. The RGB lines in the Profile graph should be uniform (Figure 28).
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Sample and Analysis Components
| Analysis | Component | Definition |
|---|---|---|
LSIMG (Core Section) | Exp | expedition number |
| Site | site number | |
| Hole | hole number | |
| Core | core number | |
| Type | type indicates the coring tool used to recover the core (typical types are F, H, R, X) | |
| Sect | section number | |
| A/W | archive (A) or working (W) section half | |
| Top Depth CSF-A (m) | location of the upper edge of the section expressed relative to the top of the hole. | |
| Bottom Depth CSF-A (m) | location of the lower edge of the section expressed relative to the top of the hole. | |
| Top Depth (other) (m) | location of the upper edge of the section expressed relative to the top of the hole. The location is presented in a scale selected by the science party or the report user. | |
| Bottom depth (other) (m) | location of the lower edge of the section expressed relative to the top of the hole. The location is presented in a scale selected by the science party or the report user. | |
| Display Status (T/F) | "T" (true) indicates that this image has been selected as the core section image to display in core descriptions and core composites. "F" (false) indicates that this image will not be displayed. (All images prior to Expedition 349 are designated as display images.) | |
| Uncropped image (JPG) link | link to URL of JPG version of core section image that shows the ruler and external space at the top and bottom of the section. | |
| Uncropped image filename | filename of uncropped image provided for identification purposes. | |
| Cropped image (JPG) link | link to URL of JPG version of core section image with the ruler and external space at the top and bottom of the section cropped. | |
| Cropped image filename | filename of cropped image provided for identification purposes. | |
| Timestamp (UTC) | point in time at which an observation or set of observations were made. Precise meaning of the value varies between systems due to variation in capability and/or implementation. | |
| Instrument | line-scan camera (e.g., JAICV107CL). | |
| Instrument group | Section Half Imaging Logger (SHIL). | |
| Text ID | automatically generated unique database identifier for a sample, visible on printed labels. | |
| Test No | Unique number associated with the instrument measurement steps that produced these data. | |
| Comments | observer's notes about the sample. |
| Analysis | Component | Definition |
|---|---|---|
| RGB Channels (RGB) | Exp | expedition number |
| Site | site number | |
| Hole | hole number | |
| Core | core number | |
| Type | type indicates the coring tool used to recover the core (typical types are F, H, R, X). | |
| Sect | section number | |
| A/W | archive (A) or working (W) section half. | |
| Offset (cm) | position of the observation made, measured relative to the top of a section. | |
| Depth CSF-A (m) | location of the observation expressed relative to the top of a hole. | |
| Depth (other) (m) | location of the observation expressed relative to the top of a hole. The location is presented in a scale selected by the science party or the report user. | |
| R | average of digitized red (R) channel over a user-defined rectangle along the core section. Values range from 0 to 255 (8-bit color digitization). | |
| G | average of digitized green (G) channel over a user-defined rectangle along the core section. Values range from 0 to 255 (8-bit color digitization). | |
| B | average of digitized blue (B) channel over a user-defined rectangle along the core section. Values range from 0 to 255 (8-bit color digitization). | |
| Timestamp (UTC) | point in time at which an observation or set of observations was made on the logger. | |
| Instrument | line-scan camera (e.g., JAICV107CL). | |
| Instrument Group | Section Half Imaging Logger (SHIL). | |
| Text ID | automatically generated unique database identifier for a sample, visible on printed labels. | |
| Test No | Unique number associated with the instrument measurement steps that produced these data. | |
| Comments | observer's notes about a measurement, the sample, or the measurement process. |
C. Retrieve Data from LIMS
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Common problems encountered when using the core imager and their possible causes and solutions:
Issue | Possible Causes | Solution |
Actuator squeal | NA | Lightly tap the actuator housing to silence the noise |
Image too dark | Manual F-stop on the camera closed down | Have technician adjust F-stop aperture |
Exposure time is too low | Increase exposure time | |
Focused lights are not aimed at the correct spot | Adjust lights | |
Track is “stuck” | Run was aborted with the software abort switch | Reset software and run sample again |
Run was aborted with the hardware abort switch | Reset hardware and run sample again | |
Gantry flag has tripped the end-of-travel limit switch | Adjust gantry flag and run sample again | |
Current limit on motors was exceeded | Check the Galil AMP-19520 for LED error indicators. Call track technician or ET to reset the motor controller | |
Torque limit on motors was exceeded. <we need to check how Labview handles this!>[djh1] | ||
Image indicates that camera was triggered erratically OR no image acquired | Camera was left in Free Run mode in MAX | Set camera to Externally Triggered for normal operation |
Linear encoder head has failed | Call an ET to verify/repair | |
Lens cap is on | Remove cap and repeat image capture procedure. |
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Maintenance
Frequency | Task |
|---|---|
Daily | Ensure that the color standards, ruler, and barcode imager lens are free from dust, smudges, and crumbs. |
Weekly | Using a mirror, ensure that there are no fingerprints or smudges on the camera lens. Call the imaging specialist if the lens needs cleaning. Do not attempt to clean it yourself! |
Monthly | Check socket head cap screws in the camera and lights mounting plates for looseness. |
Every Expedition |
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Annually |
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B.1 IMS Program Structure
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The following table shows the motion profile settings for the SHIL.
Axis→ | X-Axis | ||
|---|---|---|---|
Profile↓ | Speed | Accel. | Decel. |
DAQ Move | 8.0 | 20.0 | 20.0 |
Limit Seek | 3.0 | 5.0 | 30.0 |
Home Final | 0.5 | 2.0 | 30.0 |
Load/Unload | 30.0 | 5.0 | 5.0 |
User Defined | 20.0 | 10.0 | 30.0 |
Table: Motion Profile X-Axis for SHIL
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