I. Introduction

The section half image logger (SHIL) takes digital images of the flat face of split cores using a line scan camera and generates RGB data. All 'Archive' section halves are imaged on the SHIL. Sediment cores are imaged as soon as possible after splitting and scraping to minimize color changes that occur through oxidation and drying. The SHIL can also be used to image the outside of a whole round hard rock section (see section 360° Imaging Hard Rock for details).

Theory of Operation

The track system is composed of two slaved linear actuators and a linear encoder that provides precise triggering pulses to a gantry-mounted JAI color line scan camera. The line scan interval is 20 lines/mm (50 microns) and the camera height is adjusted so that image pixels will be square. Light is provided by a number of Advanced Illumination high-current focused light emitting diode (LED) line lights adjusted to precise angles relative to the lens axis in order to evenly illuminate an uneven surface. Motion control is performed using Galil software and hardware coupled to the linear actuators.

Line Scan Camera

Unlike a "normal" distal photo sensor with a square sensor array, similar to a postage stamp, a line scan camera's array consists of a single line of pixels. Whereas a normal camera captures frames, the line scan camera sees only a single line at a time and sends this line image to a capture card on a dedicated computer. Line by line, the computer compiles the final image.
In some applications, the photographic subject may move in front of the camera on a conveyor belt at a specific combination of object speed and shutter speed. In the case of the SHIL, the camera moves across the sample via a motorized gantry. The combination of gantry travel speed and camera shutter speed is critical and is explained in the Camera Configuration Advanced User Guide.
The line scan camera images only one line of pixels rather than an area and therefore what happens outside the line of view is of no consequence. The line scan camera effectively masks everything other than the single line of pixels being imaged. This fact is key to the effectiveness of the line lights in providing even illumination at different distances from the lens.
The camera lens on the imaging track, Nikon 60 mm macro, does not have 1/2 or 1/3 stops, only whole F/stops: 5.6, 6.3, 8, 11, 16, 22, and 32. F/16 is the minimum aperture needed to achieve the required depth of field to image the subject at varying heights.

II. Procedures

A. Preparing the Instrument

1. Double-click the MUT icon on the desktop (Figure 1a) and login using ship credentials. For more information on data uploading see the "Uploading Data to LIMS" section below.
2. Double-click the IMS icon (Figure 1b). IMS initializes the instrument. Once initialized, the logger is ready to measure the first section.

Figure 1. (a) MUT Icon. (b) IMS Icon.

At launch, IMS begins an initialization process:

• Testing instrument communications
• Reloading configuration values
• Homing the pusher arm of the motion control system.

After successful initialization, the IMS Control and Instruments' windows appear (Figure 2).

Figure 2. IMS Control window (left) and Instrument' windows (right).

The IMS Control panel (Figure 3): Provides access to utilities/editors via drop-down menus.

Figure 3. Control Panel Drop Down menus.

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 06 Dec 2021 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 .

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 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.

Calibration is conducted in the following steps. 

1. Physically set the camera at the correct height and focus .  See Camera Height and Focusing.
2. Set the saturation range for each channel of the CCD while maintaining the white balance between these channels for neutral colors (white, greys and black). See Setting Exposures and Setting Gains.
3. Correct for uneven lighting, dark noise and pixel flatness. See Pixel Black, Shading and Flat Corrections.
4. Calibrate and create a correction LUT for each RGB channel. See Image Calibration.

The first three steps are done using the JAI Camera Setup Utility, the 4th step is done using Image Correction Utility.  Before opening the utility you must disable Motion Control so that you can move the camera by hand.

Disable Drive:

1. In the IMS control panel select Motion and then Drive Disable from the dropdown menu (Figure 19). You will have to move the camera by hand for the calibration, disabling the motor allows manual movement of the camera on the track.

Figure 19. IMS commands to disable the drive.

2. Open JAI Camera Setup utility: In the IMS control panel click Instruments > JAI Camera Settings (Figure 20). The lights turn on automatically when the JAI Camera Setup window opens.

Figure 20. Selecting JAI Camera Setup

3. Click Lights OFF (Figure 21) IMMEDIATELY. Remember we want to keep the temperature below 40 °C. Use the LED read out of the light's temperature located above the camera. 

Figure 21. Software commands to turn the Lights on or off.

Camera Height and Focusing

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 22).  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 22. QP 101 card showing centimeter marks for pixel pitch calibration.

2. On the screen you will see the cm lines and vertical peaks on the Profile graph (Figure 23).

Figure 23. Example of the QP-101 marks and the profile graph.

3. On the Profile graph, drag the purple and yellow cursors to the center of two adjacent peaks near the center of the image.  These peaks are the centimeter lines in the QP card.

4. Use the graph controls and expand (zoom) the graph horizontally (Figure 24).

Figure 24. Cursor placement on the QP 101's centimeter marks in Profile graph. 

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 25).

Figure 25. Cursor pixel values and span. 

Setting Exposures

BEFORE YOU START

1)  Click the Gains-Black-Shade-Flat tab (Figure 26).

Figure 26. 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 26). You will notice all values in the Master and Black gains go to zero.

Figure 26. Remove the corrections and clear gains.

3) Check the camera's f/stop which should either f/16 or f/22 (see Figure 27).  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 mean longer exposures - which means slow track speeds for scanning - which could impact core flow in the lab.  So on a low recovery expeditions 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.      

Figure 27. Setting the F Stop on the Camera.

4) Place the 3D Calibration Standard in the track. The color square must be oriented as shown in Figure 28.

Figure 28. Calibration 3D standard with the xrite color checker mini.

CHANGING EXPOSURE VALUES

Now you are ready to start setting the exposures for the RGB channels.

1) Turn on the lights

2) Click the START GRAB button

Figure 28. Start Grab

3) Move the camera over the white square on the ColorChecker standard. 

4) Use the mouse and draw a ROI (Region of Interest) with only the white square inside (Figure 28).  The RGB values and Ratio values will only be calculated for the pixels inside the ROI (Figure 30).

Figure 29.

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 30. RGB and Ratio values calculated from the pixels in the ROI.

5) Go to the Gains-Black-Shades-Flat tab and click the Clear All Gains and click Clear Black Gains if not already done.

6) Go to the Rates and Exposure tab and set the Green Lock to Off 

Figure 31. Set Green Lock off.

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). 

3) Adjust the blue exposure until the blue/green ratio is near 1.000 (+/-0.005). 

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 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.

Setting Gains

Working with the White Side

1) Open the Gains-Black-Shades-Flat tab. 

2) Adjust the Master Gain until the the weak channel is in the 240-245 range. 

3) If the other channels are two high, you can apply negative gains to those channel until the ratios back to 1 or you can re-adjust the exposures .  The later method is preferred. 

Once you have initially roughed in the RGB channels for the White ColorCheck square, its time to look at the dark side .

Figure 32. Pixel Black Auto Correction

Working With the Dark Side

1) Turn on the lights

2) Click the START GRAB button

3) Move the camera over the black square on the ColorChecker standard. 

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.

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

Finalizing Exposure and Gain Settings.

You will need go back and repeat the process starting at the section  "CHANGING EXPOSURE VALUES" to achieve balanced neutral colors from white to black. But before you do so, this is a good point to first correct Pixel Shading and Pixel Flat.

This is a balancing act and can be tedious!

Pixel Black, Shading and Flat Corrections

We apply three corrections Pixel Black, Shading and Pixel Flat (gain). Only do the corrections after you have finished the first "rough in" adjustment of the RGB exposure and gains. 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 (dark noise) 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 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: 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: Each pixel has a different response to a fixed light source. To correct for this non-uniformity a couple lines of data are calculated 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). 

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.

2) With lights off click Pixel Black Auto Correction. The RGB lines in the Profile graph should be uniform (Figure 34). 

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.

2) Place the heat resistant gray silicone mat on the track. Make sure that it is level and perpendicular to the camera’s axis.

3) Click Lights On, and move the camera over the gray mat.

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)

Before we can begin the calibration process, an uncorrected image of ColorChecker standard must be taken.

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.

2. Open IMS and Click Start.

3. Scan the STND Color barcode label (Figure 39b). Check the ColorChecker Standard box (Figure 39a). With this box selected no corrections are applied to the image so we are able to assess the raw image quality.

4. Click Take A Picture.

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 39.  a) sample information screen with ColorChecker box checked, b) standard barcode being scanned.

6. On the main IMS panel select Instruments and Camera: Image Correction (Figure 40).

Figure 40. Image Correction command selection.

The main Image Correction window displays three main areas (Figure 41):

A. Graph panel: Main graphical viewing area on the left side of the screen. 

Uncorrected Image Tab: Shows the measured red, green, and blue values of the gray scale color squares.

Applied Corrections Tab: Applies polynomial fit corrections to the RGB lines.

Compare: Shows a visual and RGB values of the Original color square before corrections, the Xrite Color checker standard and of the color after corrections are applied.

B. Image Viewing Panels: Area in upper right portion of the screen that displays the original and corrected test image and Xrite color checker.

Original: Displays the uploaded tiff.

Corrected: Displays the uploaded tiff with corrections applied.

Color Checker: Displays the known values of the Xrite Color Checker.

C. Correction Panel: Panel in the lower right portion of the screen that allows user to apply corrections to the image

TIFF Correction: Shows tiff red, green, and blue polynomial fit.

JPEG Correction: Shows brightness, contrast, and gamma settings.

Figure 41: Image Correction user interface. 

7. On opening of the Image correction window the program prompts you to select the TIFF file of the color standard you took. The image loads into both the Original and Corrected windows. 

8.  Draw a ROI box loosely around the color checker in the Original box (Figure 42-1)

9. Click Crop (Figure 42-2).

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 24-3). As of 24 Nov 2021 use only the white, shades of grey and the black.

Figure 42. Image Correction Window. 

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

1. Click TIFF Correction tab (Figure 43-1).

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 43-1). 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 44).  Make sure that the white does not exceed the Xrite values (RGB = 242, 242, 236).  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 43. 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 44-1).

Figure 44. 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 45).

1.  Click JPEG Correction tab (Figure 45-1)

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. 

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 45. JPEG Correction using Brightness, Contrast and Gamma. 

Image Check on Calibrated Monitor

Check the final scan:

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

3. Copy the image to a shared network folder to view on a calibrated computer screen in the Imaging Office. Images located in the C:/DATA/IN/IMAGE folder.

4. Open the TIFF and JPEG in Photoshop in the Imaging Office (calibrated computer).

5. Visually examine each file you just preformed to ensure the colors, neutrals, mid-tone and contrast are true to the real values, and that the scan is free from artifacts. Use the eyedropper tool in photoshop to see the values of pixels (Fig. ## Figure needs to be added).

C. Set Measurement Parameters

a) Instrument Setup

1. DAQ > Image Capture Motion Setup (Figure 42)

Figure 42. Image Scan Setup window

 2. Instruments > Camera: General Setup (Figure 43).

Figure 43. General Camera Setup window

3. Instruments > Camera: JAI Camera Setup (Figure 44).

Figure 44. General Camera Setup fixed Settings

b) Set Measurement Parameters

Adjust measurement parameters before beginning measurements. Users can adjust the RGB settings and camera speed.

RGB

Users can adjust three RGB parameters: decimate interval, stripe width, and whether to use the mean or midpoint RGB value. For more information regarding how RGB data is calculated please see Appendix A: RGB Calculation.

Adjust RGB Settings

1.Go to Instruments > Camera: General Setup (Figure 45). The JAI Camera Setup Parameters window will appear (Figure 46).

Figure 45. Select JAI Camera Setup Parameters window

2. Adjust values in the 'RGB Data' setting controls.

• 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 46. JAI Camera Setup Parameters window

The 'General' and 'Dropped Lines Warning Threshold' should not need to be adjusted. If something needs to be altered talk to the programmers and ALOs.

3. Click 'Accept' to save values. If select 'Cancel' the values will revert back to prior settings and the window will close. 

Camera Speed

Camera Speed is calculated during the calibration procedure. The camera speed set must be lower than the speed determined by the calibration or else the camera will start 'dropping lines'. Dropped lines means the camera is moving too quickly to calculate the RGB and offsets at the bottom of the core will return values of '0'.

Adjust Camera Speed

1. Go to DAQ > Image Capture Motion Setup (Figure 47).
   

Figure 47. Select Image Scan Setup window

2. The Image Scan Setup window appears. There are four settings in this window:

• Speed: This is the speed in cm/sec the camera moves while measuring the section. This speed must be set lower or equal to the speed determined by the Camera Calibration.
• Acceleration: The rate in cm/sec the camera ramps up to when not measuring a section.
• Deccelaration: The rate in cm/sec the camera will slow down when not measuring a section.
• Start Position: This is the position the imaging begins. Note it will be a negative number. The top of the core starts at 0 cm in order to image the standard gray-scale card in front of the core, that location will be negative.

D. Preparing Sections

Sediment

The surface of the archive half generally needs to be scraped after splitting to clean the sections and better reveal layering and structures. Sediment cores should be imaged as soon as possible after splitting and scraping are completed to minimize color change through oxidation and drying.

Hard Rock

Rock pieces should be dry and individually rotated such that the split face is approximately perpendicular to the axis of the camera. The lights and lens aperture are configured to give consistent illumination and focus to effectively image rubble bins.
For 360 Imaging of hard rock cores refer to the section 360 Imaging Hard Rock.

Loading Section

1. Pick up section half and place in the track loading area with the blue end cap forward against the color block. Make sure the section is pushed all the way against the block so the end cap is lined up with 0 cm on the ruler.
2. Bring the endcap for the section to the SHIL workstation for entering sample information.
3. If the section has a whole round sample taken, denoted by a yellow bottom endcap, place a split styrofoam spacer at the end of the section. Cut the styrofoam to same length of the sample taken and write letters on the styrofoam to indicate the type of the sample taken. For example a 5 cm Interstitial Water whole round sample taken. A 5 cm styrofoam spacer with 'IW' written on it would be placed at the bottom. Once a spacer has been made it can be used over the course of the expedition for applicable section halves.

E. Making a Measurement

NOTE: Before taking images make sure the lights and camera are set up and calibrated properly.

a) Sediment

1. Click the green Start button in the IMS Control panel (Figure 48).

2.The SHIL Section Information window will pop up.

Figure 48. Select SHIL Section Information window

3. The area on the left has four fields to define the condition of the sample measurement:

1. 1. Image Type: 'Section Imaging' or '360 Imaging'. For instructions on the 360 imaging refer to 360 Imaging Hard Rock section.
   2. Wet/Dry: Indicates the type of the material being image
   3. Condition: 'Pristine' or 'Sampled-Altered'. Sampled-Altered could include imaging the working half or a highly disturbed section. Most instances should be Pristine.
   4. 360 Imaging: This area is grayed out unless '360 Imaging' Image Type is selected. For instructions on the 360 imaging refer to 360 Imaging Hard Rock section.

        Select the conditions appropriate for the section half.

4. There are three ways to enter sample information into IMS:

• 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 49). 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 49. SHIL MANUAL Section Information window

5. Click Take a Picture. The lights will turn on and start moving down the length of the core. In the IMS interface the sample information will go away revealing the measurement windows. The image and RGB data is displayed and updates as the measurement progresses. 

6. When the measurement is complete, the camera lights will turn off and move back to the home position on the track.

7. The Image Crop window (Figure 50) 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:

• Show Bottom of Image: Takes image down to illustrate the bottom of the image and crop box.
• Show Top of Image: Brings image up to show the top of the image and crop box.
• Crop Image: Crops the image to show only image inside of the green box.                   
• Uncrop Image: Will undo a crop and allow user to re-adjust the green crop box.
• Save Image: Saves the image, RGB data, and writes the upload files
• Discard Image: Does not save the image or RGB data.

The Image crop restricts users to limit adjustments to 2cm or less. The message box will indicate if the crop has exceeded allowable limits and the 'WRND Info' message box indicates if and where any whole round samples were taken from the section. If the image needs to cropped by more than 2cm check the correct section/end cap is being uses, a styrofoam spacer is not missing, and the curated length. Cores can expand so if the curated length is incorrect, talk to the curator on shift to correct the length. Note this will also create a need for the curator to re-calcuate depth of the hole. If the error is in the curated length of the core a user can check the 'override crop restriction' button to crop the image and upload the data.

8. Click Crop Image when satisfied the green box will capture the entire image.

9. If satisfied with the image click Save Image. If the image needs to be re-imaged click 'Discard Image' and re-start the measuring process.

10. The 'Image CROP' window will go away and the 'SHIL Section Information' window will appear again.

Figure 50. Image CROP window

b) 360 Imaging Hard Rock

The SHIL can be used to image the external surface of whole round hard rock cores in order to assemble a 360° composite image of the whole round. Oriented rock pieces are imaged after they have been binned and the structural scientist has marked the split lines on the pieces. Using the custom whole round scanning tray, the whole round core surface is imaged four times at the 0°, 90°, 180°, and 270° orientation from the splitting line.  The Imaging Specialist will download the images and assemble a composite image from the four scans and upload the composite separately.

Sample Preparation

1.  Remove the section half scanning tray from the SHIL and replace it with the whole round scanning tray making sure to align the blocks correctly.  Note that the rotating section of the tray has 0°, 90°, 180°, and 270° markings on each end and that the rotating section will click and lock into each orientation.

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 51).

Figure 51. Whole round core correctly placed on the split liner section.

3. Remove the 0° aluminum strip and another aluminum strip on either side of 0°. Move the dry, oriented pieces into the tray, keeping the pieces at the correct offsets and aligning the split line with the 0° orientation.

4. Attach the not 0° aluminum strip and rotate the tray so that the 0° position is up, facing the camera (Figure 52).

Figure 52. Whole round core correctly placed on the aluminum tray

Take Image

1. Click START and the SHIL Section Information screen will appear (Figure 53).

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 53. SHIL Section Information window for 360 Hard Rock Imaging

4. When the scan is finished, the Image CROP window will open. Crop the image and Save it.

5. The SHIL Section Information window for whole round will open and the rotation angle will default to the next quadrant, in this case 90 Degrees.

6. Replace the aluminum strip and rotate the tray to the next position, remove the aluminum strip facing up.  Ensure that the rotation angle setting in the window is that same as on the tray.  Click TAKE A PICTURE.

7. Continue the cropping, rotating and scanning process until all quadrants are complete.  Once the images are uploaded to the database, the Imaging Specialist will create the 360 composite image and upload it to the database. If an image needs to be discarded, the software returns to the main screen and the user will need to start over, however, the user can select which quadrant to start on.

III. Uploading Data to LIMS

A. Data Upload Procedure

To upload the images into the database (LIMS) MegaUploadaTron (MUT) program must be running in background.

If not already started do the following:

1. On the desktop click the MUT icon on the bottom task bar (Figure 54) and login with ship credentials. The LIMS Uploader window will appear (Figure 55).
2. 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 54. MUT icon

Figure 55. 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.

4. If files are marked by a purple question mark or red and white X icons, please contact a technician.
    Purple question mark: Cannot identify the file.

    Red and white X icons: Contains file errors.

5. Upon upload, data is moved to C:\DATA\Archive. If upload is unsuccessful, data is automatically moved to C:\DATA\Error. Please contact the PP technician is this occurs.

MUT Configuration

File Path

The file path MUT should look for files to upload is C: > data > IN. IMS writes upload files to C: > data > IN, so ensure the file path is set correctly. Note the uploaded files are written directly into the 'IN' folder. Images are not directly uploaded and are written to C: > data > IN > Images

Active Analyses

In MUT the 'active analyses' (Figure 56) 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 56. Select Set active analyses on MUT

Data File Formats

Two files are uploaded to LORE via MegaUploadaTron (MUT):

1. .roi file : Contains callouts to the uncropped TIFF , uncropped JPEG, and cropped JPEG images. The images are linked files in LORE as Images > Core Closeup (LSIMG).
2. .RGB file : Contains the red, green, and blue values calculated for each offset. The information is in LORE under Physical Properties > RGB Channels (RGB).

The files are independent of each other, both do not need to be present in order to upload, and often appear in MUT at different times.

MUT and .ini file

Be aware uploaded files have a callout for the .ini file. There is only one .ini file and the files will callout the .ini file currently present at the moment of uploading to LORE. If changes are made to settings that will alter the .ini and there are files piled up that have not uploaded to LORE, those files will upload the current .ini file, not the .ini file settings used for measurement. This implies files could have incorrect .ini files if rapid changes are made and users are not being careful.

Auxillary data Produced

The SHIL has the capability to produce two additional file types at the scientist's request:

1. Hi RES RGB
2. VCD-S

These files appear in separate folders in C: > data > in

Hi RES RGB: This file default is turned off and can be turned on in Instruments > Camera: General Setup (Figure 57). 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 57) . 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 57. Select to preserve a digital copy of VCD-S

B. View and Verify Data

Data Available in LIVE

The data measured on each instrument can be viewed in real time on the LIMS information viewer (LIVE).

Choose the appropriate template (Ex: IMAGES_All), Expedition, Site, Hole or the needed restrictions and click View Data. The requested data will be displayed. You can travel in them by clicking on each of each core or section, which will enlarge the image.

Data Available in LORE

Each data set is written to a file by section. These reports are found under the Images heading and include: Core composites (COREPHOTO), core sections (LSIMG) and whole-round sections (WRLSC). The expanded reports include the linked original data files and more detailed information regarding the measurement.

Sample and Analysis Components

C. Retrieve Data from LIMS

Expedition data can be downloaded from the database using the instrument Expanded Report on Download LIMS core data (LORE).

IV. Important Notes

Glossary of Terms

Gain: a digital camera setting that controls the amplification of the signal from the camera sensor. It should be noted that this amplifies the whole signal, including any associated background noise.

Gamma: a digital camera setting that controls the grayscale reproduced on the image. An image gamma of unity indicates that the camera sensor is precisely reproducing the object gray scale (linear response). A gamma setting much greater than unity results in a silhouetted image in black and white.

White Balance: a camera setting that adjusts the color balance of light so that it appears a neutral white, and it is used to counteract the orange/yellow color of artificial light.

V. Appendix

A.1 Health, Safety & Environment

Safety

• 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 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. Caution is needed during the calibration process because the lights are stationary and remain 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.
• Do not put your hands in or near the moving equipment. The actuators will torque out when impeded but injury could occur before that happens. Hardware abort buttons are located at both ends of the system for an emergency stop.
• Take care when working inside the electronics enclosure to avoid shocks from the power supply terminals.

Pollution Prevention

This procedure does not generate heat or gases and requires no containment equipment.

A.2 Maintenance and Troubleshooting

Troubleshooting

Common problems encountered when using the core imager and their possible causes and solutions:

Maintenance

B.1 IMS Program Structure

a) IMS Program Structure

IMS is a modular program. Individual modules are as follows:

• Config Files: Unique for each track. Used for initialize the track and set up default parameters.
• Documents: Important Information related with configuration setup.
• Error: IMS error file.
• FRIENDS: Systems that use IMS but don't use DAQ Engine.
• IMS Common: Programs that are used by different instruments.
• PLUG-INS: Code for each of the instruments. 
• Projects: Main IMS libraries.
• Resources: Other information and programs needed to run IMS.
• UI: User Interface
• X-CONFIG: .ini files, specifics for each instrument.
• MOTION plug-in: Codes for the motion control system.
• DAQ Engine: Code that organizes INST and MOTION plug-ins into a track system.

The IMS Main User Interface (IMS-UI) calls these modules, instructs them to initialize, and provides a user interface to their functionality.

b) Communication and Control Setup

Data communication and control is USB based and managed via National Instrument’s Measurement & Automation Explorer (NI-MAX). When you open NI-MAX and expand the Device and Interface section.  The correct communications setup can be found at /wiki/spaces/LN/pages/7338174611.

B.2 Motion Control Setup

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 58) 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.

At IMS launch, a series of commands are sent to place the motor into a known state and then to search for the home switch and zero the encoder's position out put.

It is assumed that the hardware has been installed correctly and powered up. On the very first launch, a set of default values will be loaded that should get the track safely running. BUT BE READY to kill the motion using the Emergency-Stop button. Generally, a run-off is caused by incorrect scaling factors for the gear ratio, screw pitch, and or encoder counts per revolution. Setting these up correctly usually correct the issue.

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 58. Interface board for motion control.

MDrive Setup

Select Setup from the Motion menu bar for MDrive Motion control window (Figure 59).

Figure 59. MDrive Motion Control window.

Track Options

Click Motor and Track Options to open the Track Motor Setup (Figure 60). Here is where the relationship between motor revolutions and linear motion of the track is defined.

Select Axis: In the case of the WRMSL and STMSL, it is always X.

Encoder Pulses/rev: Defined by the manufacturer of the MDrive as 2048.

Screw Pitch: Defined by the NSK actuator manufacturer as 2 cm/screw revolution.

Gear Ratio: In the current configuration, this is 4 to 1 but it can be changed.

Direction: The WRMSL is a right-hand track and a CCW rotation moves the pusher in a positive (from home to end of track) direction. The STMSL is a left-hand track so this value is set to CW. Now both are set as CCW.

Click Motion Utility to test these settings.
Click Accept to save the values or Cancel to return to the previous values.

Figure 60. Track Motor Setup window.

Fixed Positions

Click Fixed Positions to open the Track Configuration window (Figure 61). In this window, define fixed track locations (Figure 61) used by IMS and enable the top of section (TOS) switch and the runout switch (ROS).

Figure 61. Track Configuration window.

Select Axis: In the case of the WRMSL and STMSL it is always X.
Max Section Length: Maximum length of section that can be placed in the track and still expect the track to handle and measure correctly. This value is set to 160 cm.
Track length: Distance in cm between the limit switches. Use the motion Utility to determine this value. This value is set to 200 cm.
Load and Unload: Offset in cm where the track will stop when ready to load a new section of core. In the case of both the WRMSL and STMSL, this the same as the home switch.
Top-of-Section Switch: THIS MUST ALWAYS BE enabled! The IMS software uses this switch to determine the physical length of the section, which is critical to the calculations that move the cores through the sensor. Without a TOS switch, the track is not functional.
Top-of-Section Switch Offset: Distance in cm from the home switch to the TOS switch. There is a utility under the DAQ > Find Top-of-Section Switch menu that will determine this value based on the current DAQ Move motion parameters (discussed in this section). ANY change in the motion profile requires that this utility be run because the final position (where the pusher bar stops) changes.
Push Past: The offset from the TOS where the pusher should stop. This value set the maximum measurement interval but MUST be several centimeters less than the distance from the TOS to the limit switch.
Fast Past: Distance the pusher will move at a higher speed before slowing down to find the TOS switch. This value MUST be several centimeters less than the distance from the TOS to the maximum section length with the pusher arm in the home position.
Run Out Switch: Switch at the end of the track that when enabled pauses the motion, preventing the section from being pushed onto the floor.

Click Motion Utility to test these settings. Click Accept to save the values or Cancel to return to the previous values.

Figure 62. Schematic of fixed positions.

Limit and Home Switches

Click Limit and Home Switches to open Limit & Home Switches window (Figure 63).

Figure 63. Limit & Home Switches window.

Select Axis: In the case of the WRMSL and STMSL it is always X.

The MDrive can be used with either a dedicated Home switch or a limit switch as a home switch. These tracks use the dedicated Home switch. Select the appropriate setup for the track in use. Use the Utilities to execute the Home command and verify the correct setting. If the home switch position of detection edge changes, verify the instrument offsets and relocate the TOS switch are still correct. Setting the edge from CW to CCW will change the offset by a least 1 cm.

Click Motion Utility to test these settings.
Click Accept to save the values or Cancel to return to the previous values.

Motion Profiles

Click Motion Profiles to open Motion Profiles window (Figure 64).  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 64. 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.

Click Motion Utility to test these settings.
Click Accept to save the values or Cancel to return to the previous values.

The following table shows the motion profile settings for the SHIL.

Table: Motion Profile X-Axis for SHIL

C.1 Hardware

The core imaging track system includes the following hardware components:

• Camera
  • 3CCD (charge-coupled device) line scan camera: JAI model CV107CL
  • Macro lens: AF micro Nikkor 60 mm (1:2.8)
• LED Light system
  • 6 Cree XLamp CXB3590 LEDs
• Linear encoder: Newall 2 µm/72 in. model SHG-TT
• Motor system
  • Motors: Galil model BLM-N23-50-100
  • PCI controller card: model DMC-1846
  • Motor amplifier: model AMP-19520
  • Breakout board: ICB-90044-M 44-pin
  • Power supply: CPS 56V/12A
  • Connectors for motor extension cords: AMP 4-pin connectors (172167-1 male, 172159-1 female)
• Robot modules: NSK 2-meter model XY-HRS200-F06246
• PC Workstation
  • NI frame grabber card model PCIe-1429
  • NI camera link I/O extension board.

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.

Data Structure

Each scratch sheet template is it's own VI. Each VI has to have the same root name "VCDS_SHLF". You may add any additional naming after this root name as long as the root remains unmodified.

• Files must be located in C: > IMS10 > RESOURCES > VCD-S_TEMPLATE on the SHIL computer. Do not alter this file path, it is currently hard-coded in the software.
• To temporarily temporarily disable a scratch sheet version, simply put some characters in front of the root name. These files can be moved to C: > IMS10 > Resources > Templates Old

Configuration

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 65).

Figure 65. Select VCDS Setup

Several configurable options appear:

1. • Format: Choose between Side by Side or Section Half scratch pages.
   • Expedition ID: Enter the name of the Current Expedition. This prints on the scratch sheet.
   • SHLF Form Folder: Currently hard-coded to C:\IMS10\RESOURCES\VCD-S_TEMPLATE.
   • Print VCDS: Enables or disables automatic printing of the scratch sheet. When the button says 'enable auto print' scratch sheets will automatically print when an image is saved.
   • Archive File: Button enables disables saving scratch pages to the hard drive. All files are saved in .PNG format. If button says 'Do not save file to archive' files will not be saved.
   • Section ID: Insert your expeditions name here which will appear in the top right corner of every scratch sheet along with the Text ID of the section half.
   • Test Image and Test Print: Allows prints of images already on the computer or in the database to see the scratch sheet. Use the folder icon to the right of 'Test Image' to browse to a section half image of your choice. This image will be embedded into your chosen scratch page mode. Click the 'Test Print' button to send it to the printer.
   • Accept: Saves any modifications to parameters.

   • Cancel: Does not save parameter modifications and reverts back to prior settings.

Editing Scratch Sheet in LabVIEW

1. Navigate to C: > IMS-10 > Resources > Templates and double-click a VI to open it in LabVIEW.
2. The front panel will open. Edits can be made to the objects on the white space. Editing the white or gray areas could affect scaling of the image, ruler, or print layout
   • The main layout consists of an outermost borderless white box that indicates the printable area that is available.
   • The leftmost gray column is a control for the section-half image and the ruler; do not make alterations in this area. There are two additional controls that feed the scratch page titles on the top left and right sides. These are not immediately visible when editing the layout on the front panel though. If you are not very familiar with LabVIEW please see a developer for help. The title controls can be moved, but it is up to you to remember where you put them!

3. All other column widths and headers are available for editing/resizing. If you need more columns simply select one, then copy/paste as you would in any standard graphics program and resize things to fit within the outermost white box. Maintain the vertical scaling of all columns to match that of the ruler/image column on the left. Header blocks are just boxes that can be copied and resized as well.

How to Make Edits

1. Navigate to the 'View' button on the toolbar. Select the 'Tools Palette' Option (Figure 66).

   
   

   

Figure 66. Select Tools Palette on LabVIEW

2. The Tools Palette window will appear (Figure 67). This allows you to select objects.

Figure 67. Tools Palette window

VI. Credits

All improvements to the Quick Start Guides and User Guides are a communal effort, with honorable mention to the group of LOs, ALOs, and technicians who have helped.

VII. Archived Versions

LMUG-SHILUserGuide-020320-1516-374.pdf

SHIL User Guide 2021.pdf