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START button will allow the user to begin measurements. Section Information window (Figure 4) will pop up.
Figure 4. Section Information window.Change for SHIL Image
B. Camera Setup and Calibration
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 7). 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 8). The lights turn on automatically when the JAI Camera Setup window opens.
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1. Move the camera so that it is scanning just the centimeter marks on the QP 101 card (Figure 10). Also, it is important that the QP 101 card is mounted straight so that the scale lines are parallel to the direction of motion.
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2. On the screen you will see the cm lines and vertical peaks on the Profile graph (Figure 11).
Figure 11. 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 12).
Figure 12. 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 13).
Figure 13. Cursor pixel values and span.
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1. Click the Gains-Black-Shade-Flat tab (Figure 14).
Figure 14. 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 15). You will notice all values in the Master and Black gains go to zero.
Figure 15. Remove the corrections and clear gains.
3. Check the camera's f/stop which should either f/16 or f/22 (see Figure 16). 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 levels mean longer exposures - which means slow track speeds for scanning - which could impact core flow in the lab. So on a low recovery expedition 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 of the time needed for scanning sections.
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4. Place the 3D Calibration Standard in the track. The color square must be oriented as shown in Figure 17.
Figure 17. Calibration 3D standard with the 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 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 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 starting we recommend setting the line rate to emulate a scan speed of 8 cm/s. |
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2. Click the START GRAB button (Figure 18).
Figure 18. Start Grab.
3. Move the camera over the White square on the Xrite Color Checker standard.
4. Use the mouse and draw a ROI (Region of Interest) with only the white square inside (Figure 19). The RGB values and Ratio values will only be calculated for the pixels inside the ROI (Figure 20). 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 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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6. Go to the Rates and Exposure tab and set the Green Lock to Off. That step allows you to adjust the exposure intervals (Figure 21).
Figure 21. Set Green Lock off.
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1. Open the Gains-Black-Shades-Flat tab (Figure 22).
2. Increase the Master Gain until the the Blue value near 240.
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Once you have initially roughed in the RGB channels for the White Color Checker square, it is time to look at the black (dark) corrections.
Figure 22. Adjusting Master Gain to bring the Blue values up to 240.
Setting the Black (Dark) Values
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4. Use the mouse and draw a ROI (Region of Interest) with only the black square inside. The RGB values and Ratio values will only be calculated for the pixels inside the ROI (Figure 23).
5. Adjust the Master Black value unit the Green value is near 15. 40 is a good starting value for and we increasing to 60 works best.
6. Adjust the Red Black and Blue Black Gains until the ratio are close to 1.000 +/- 0.05. The RGB values of the Black square is balanced (R=50, G=50, B=50) so achieving a ratio of 1.000 is best.
Keep an eye on the histogram graph on the bottom left corner (Figure 2223). 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.
Figure 23. Adjusting Master Black, RedBlack and BlueBlack to reach RGB values of 15 for black square.
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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 24. Pixel Black Correction applied.
Shading Correction
- 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 25). Dust will cause unwanted artifacts in the image. The mat must be clean and flat on the track.
- Place the heat resistant gray silicone mat on the track. Make sure that it is level and perpendicular to the camera’s axis.
- Click Lights On, and move the camera over the gray mat.
- 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 25. 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 26). 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 26. 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 27).
Figure 27. Image grab and profile after the Shading Correction has been applied.
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 1028). 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 3828. Color standard in track in correct orientation.
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3. Scan the STND Color barcode label (Figure 39b). Check the ColorChecker Standard box (Figure 39a29a). With this box selected no corrections are applied to the image so we are able to assess the raw image quality.
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5. When the image has finished click Crop and then Save. We use the uncropped tif image so the crop here is not important.
Figure 3929. a) sample information screen with ColorChecker box checked, b) standard barcode being scanned.
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6. On the main IMS panel select Instruments and Camera: Image Correction (Figure 4030).
Figure 4030. Image Correction command selection.
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The main Image Correction window displays three main areas (Figure 4131):
A. Graph panel: Main graphical viewing area on the left side of the screen.
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JPEG Correction: Shows brightness, contrast, and gamma settings.
Figure 4131: Image Correction user interface.
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8. Draw a ROI box loosely around the color checker in the Original box (Figure 4232-1)
9. Click Crop (Figure 4232-2).
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 2432-3). As of use only the white, shades of grey and the black.
Figure 4232. Image Correction Window.
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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>5), 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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1. Click TIFF Correction tab (Figure 4333-1).
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 4333-1). 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 4434). Make sure that the white does not exceed the Xrite values (RGB = 242240, 242, 236235). 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 4333. 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 44-134).
Figure 4434. 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 4535).
1. Click JPEG Correction tab (Figure 4535-1)
2. Adjust the Brightness, Contrast, and Gamma levels (Figure 4535-1) 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 4535-2, 4535-3) 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 4535. JPEG Correction using Brightness, Contrast and Gamma.
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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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- DAQ > Image Capture Motion Setup (Figure 4236)
Figure 4236. Image Scan Setup window
2. Instruments > Camera: General Setup (Figure 4337).
Figure 4337. General Camera Setup window
3. Instruments > Camera: JAI Camera Setup (Figure 4438).
Figure 4438. General Camera Setup fixed Settings
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1.Go to Instruments > Camera: General Setup (Figure 4539). The JAI Camera Setup Parameters window will appear (Figure 4639).
Figure 4539. Select JAI Camera Setup Parameters window
2. Adjust values in the 'RGB Data' setting controls (Figure 40).
- Stripe Width: Centered in the middle of the core, this determines the width across the core that will be used to calculate RGB data. This is typically set to 2cm. While the value can be changed higher or lower it is commonly at 2 cm. The advantage is this width provides enough material to not exaggerate small disturbances but rather provides RGB data representative of the bulk lithology.
- Decimate Interval: The interval that sets the recorded offset along the length of the core. This value can be set between 1 - 2.9 cm
- Mean or Midpoint: Can choose how RGB is calculated for the interval. Interval mean calculates the mean RGB values over the interval. Interval Midpoint uses the RGB value at the center of the interval. This is typically set to Interval Mean.
Figure 4640. JAI Camera Setup Parameters window
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- Go to DAQ > Image Capture Motion Setup (Figure 4741).
Figure 4741. Select Image Scan Setup window
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1. Click the green Start button in the IMS Control panel (Figure 4842).
2.The SHIL Section Information window will pop up.
Figure 4842. Select SHIL Section Information window
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4. There are three ways to enter sample information into IMS (Figure 43):
- Barcode (most common): Put cursor in the 'Scan' box. Use the bar-code scanner to scan the label on the end-cap. The sample information will parse into the 'Sample ID', 'LIMS ID', and Length fields.
- LIMS Entry: Select the 'LIMS' tab at the top of the window. Navigate through the hierarchy to select the correct, expedition, site, hole, core, and section. Length information will automatically populate when the section is selected.
- Manual Entry: Select the 'Manual' tab at the top of the window. Click in the box and manually type sample information into the box.
By default the instrument is set for imaging the archive half and will not allow you to scan a working label. If you want to take a picture of a working half you need to go to the MANUAL tab and select W (working) into the Section Half label (Figure 4943). Once you have selected W (working), you will not be able to scan an archive half; in order to do that you need to go back into the MANUAL tab and re-select A (archive).
Figure 4943. SHIL MANUAL Section Information window
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7. The Image Crop window (Figure 5044) pops up. An image should be cropped to include all material and the inner edge of the end-cap. RGB data will exclude data outside of the Crop area. The green box is the IMS estimation of the crop area. Click and drag the green lines to adjust the cropped area at the top, bottom, and sides of the image. Tools in this window include:
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10. The 'Image CROP' window will go away and the 'SHIL Section Information' window will appear again.
Figure 5044. Image CROP window
b) 360 Imaging Hard Rock
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2. Place the split liner section with the whole round core on the tray below the SHIL and align the top with the 0 cm on the ruler on the tray (Figure 5145).
Figure 5145. Whole round core correctly placed on the split liner section.
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4. Attach the not 0° aluminum strip and rotate the tray so that the 0° position is up, facing the camera (Figure 5246).
Figure 5246. Whole round core correctly placed on the aluminum tray
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1. Click START and the SHIL Section Information screen will appear (Figure 5347).
2. Scan the section barcode from the endcap
3. Select the 360 Imaging on Image Type and the default quadrant will be 0 Degrees. Select Dry-Hard Rock. Click TAKE A PICTURE
Figure 5347. SHIL Section Information window for 360 Hard Rock Imaging
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- On the desktop click the MUT icon on the bottom task bar (Figure 5448) and login with ship credentials. The LIMS Uploader window will appear (Figure 5549).
- Once activated, the list of files from the C:\DATA\IN directory is displayed. Files are marked ready for upload by a green check mark.
Figure 5448. MUT icon
Figure 5549. LIMS Uploader window
3. To manually upload files, check each file individually and clip upload. To automatically upload files, click on the Automatic Upload checkbox. The window can be minimized and MUT will be running in the background.
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In MUT the 'active analyses' (Figure 5650) should be set to Linescan Image, Processed RGB channels, and Whole-round Linescan. Linescan Image and Processed RGB Channels are for section half measurements. The Whole-Round Linescan Image is for 360 Imaging of hard rock cores. All three analyses should be set in the 'Active Uploaders' Column. Note it is ok for analyses to be in the 'Active Uploaders' even if MUT at that instrument host does not generate those files.
Figure 5650. Select Set active analyses on MUT
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Hi RES RGB: This file default is turned off and can be turned on in Instruments > Camera: General Setup (Figure 5751). The Hi-Res RGB file reports a Red, Green, and Blue value for each line of pixels down the length of the core. 1cm is 200 lines of pixels so a 150cm core will yield approximately 30,000 lines of data depending on the exact crop length. The file is not currently uploaded to the database and is instead copied to data1 at the end of the expedition. The files can be put on the server for scientist access to a convenient, shared location such as UserVol.
VCD-S: The SHIL can preserve a digital copy of the VCD-S that is printed out. If a scientist wants to keep a digital copy of the scratch sheet turn on the feature in Instruments > Camera: VCDS Setup (Figure 5751) . Files are then written to C: data > in > VCD-S. These files are not uploaded to LIMS and should be put in data1 at the end of the expedition. The files can be put on the server for scientist access to a convenient, shared location such as Uservol.
Figure 5751. Select to preserve a digital copy of VCD-S
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The track's push system consists of a NSK linear actuator driven by Schneider Electric stepping motor: MDrive23. The MDrive 23 is a high torque 1.8º integrated motor-driver-controller that connects to the PC via USB-RS485 cable. An IODP-built interface board (Figure 5852) provides power control, emergency, limit/home switches, specialty I/O connections, and status lights. With the exception of a built in "Home" function, the MDive's IMS motion software module provides direct control of the motor's functions. The motor can be installed directly out of the box without any special preparation.
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Note: If the motor fails to initialize or locate the home switch, then an error will be reported. At this point, access the motion control utilities for trouble shooting. The START button will not appear and measurements are prevented.
Figure 5852. Interface board for motion control.
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Select Setup from the Motion menu bar for MDrive Motion control window (Figure 5953).
Figure 5953. MDrive Motion Control window.
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Click Motor and Track Options to open the Track Motor Setup (Figure 6054). Here is where the relationship between motor revolutions and linear motion of the track is defined.
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Click Motion Utility to test these settings.
Click Accept to save the values or Cancel to return to the previous values.
Figure 6054. Track Motor Setup window.
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Click Fixed Positions to open the Track Configuration window (Figure 6156). In this window, define fixed track locations (Figure 6157) used by IMS and enable the top of section (TOS) switch and the runout switch (ROS).
Figure 6156. Track Configuration window.
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Click Motion Utility to test these settings. Click Accept to save the values or Cancel to return to the previous values.
Figure 6257. Schematic of fixed positions.
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Click Limit and Home Switches to open Limit & Home Switches window (Figure 6358).
Figure 6358. Limit & Home Switches window.
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Click Motion Profiles to open Motion Profiles window (Figure 6459). The profiles are used to set the speed and acceleration profiles used by the track.
Setting the correct values for the motion profile takes a little experimentation to make the track run efficiently and safely.
Figure 6459. Motion Profile window.
DAQ Move: This profile controls moves between measurement positions. Set this to a reasonable speed with gradual acceleration so the pusher does not bump the sections.
Limit Seek: This profile finds the limit switch locations. Do not exceed 5 cm/sec and use a large deceleration value or the core could overrun the limit switch and hit the mechanical stop.
Home Final: This profile finds the final location of the home switch. Do not exceed 1 cm/sec and use a large deceleration value.
Load/Unload: This profile moves the pusher back to the load position. Set this to a reasonable but high speed with gradual acceleration and deceleration values. Setting this too slow will waste time, but keep safety in mind.
Push-Slow: This profile allows the pusher to move the new section into contact with the previous section and to locate the top of section. Use a speed a little less than the DAQ Move speed with slightly lower acceleration and deceleration values.
Push-Fast: This profile allows the pusher to move quickly to the TOS switch. Typically, it is set the same as the Load/Unload values.
User Define: This profile is used for testing only in the Motion Utilities program.
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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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To access the scratch sheet configuration options, click the Instruments button and follow the menu down to Camera: VCDS Setup. The parameter screen will then display (Figure 6560).
Figure 6560. Select VCDS Setup
Several configurable options appear:
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Navigate to the 'View' button on the toolbar. Select the 'Tools Palette' Option (Figure 6661).
Figure 6661. Select Tools Palette on LabVIEW
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