Section Half Imaging Logger: User Guide

Manual Information

Contents

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.

System Operation

SHIL system operation involves a number of processes, some performed only once upon initial installation, some only when lighting or camera equipment is replaced, and some on a routine basis at the beginning of each expedition or at the beginning of each batch of samples. The following procedures are covered in this manual:

• Installing and calibrating light array (see Light Array User Guide).
• Setting black and white saturation gain levels (see Maximum Dynamic Sensor Range).
• Setting color balance Author: Where is this covered?
• Making camera corrections (see Routine Camera Adjustments).
• Setting track velocity (see Track Speed Example).
• Adjusting knee slope, if needed (see Procedure: Iterative Adjustment).
• Performing QA/QC to confirm camera settings (see Quality Assurance/Quality Control).

Apparatus

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)
• Light system
  • High-current line lights: Advanced Illumination model LL068
  • Power supply: 24 V/6 A
  • Current source: model CS420-0103 constant (modified)
• 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

Software

Operates with LabVIEW 10.0 application.

Maintenance

Before taking images make sure the lights and camera are calibrated properly. See section Light Array Setup and Camera Calibration for instructions on procedures.

Instrument Settings

Image Capture Motion Setup

General Camera Setup

General Camera Setup fixed Settings

Sample Preparation & Imaging

Sample Preparation and Loading

Sediment

If the surface of the archive half is rough use a flat spatula to provide a "clean" surface for imaging to 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 of 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 the section is pushed all the way against the block so the end cap is lined up with 0cm 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 5cm Interstitial Water whole round sample taken. A 5cm 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.

Launch IMS Application

1. First open the IMS Application 'SHIL' on the desktop.(Figure X)

2. At launch, the program begins an initialization process:

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

3. After successful initialization, two windows will appear: The IMS Control Panel on the left and the measurement window along the top of the screen. FIGURE (XX)

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

• 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

• 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.
• 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.

Adjust RGB Settings

1.Go to Instruments > General Setup

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

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 than 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 0cm in order to image the standard gray-scale card in front of the core, that location will be negative

Start A Measurement

1.Click the green Start Button in the IMS Control panel.

2. The SHIL Section Information Window will pop up (FIGURE XX).

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 XXXXXX
   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 XXXXXX

        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.

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 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 'Sample Information' window will appear again.

Uploading data

Data Structure

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 eachother, 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.

How to Upload data

1. Open up MUT (FIG XX). Use LIMS Applications password to login.
2. Set 'Project' at the bottom of the screen to either the current expedition or '999' if performing tests.
3. Files with checkmarks in the right column will upload. A green arrow in the COLUMN XX indicates it is in process of upload. A purple question mark indicates the file is not recognized by MUT. This could be due to an incorrect sample name or only one file being in the 'IN' Folder.
4. Check 'Automatic Upload'. At the refresh interval the files will upload to LORE.
5. After files are successfully uploaded they move from 'data > in' to the 'data > archive' folder. When the files move they will not longer appear MUT. If a file was unable to upload it will move from 'data > in' to 'data > error' and two new buttons will appear in MUT saying 'Show Error' and 'Show Error Files'.

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 filepath 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' 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.

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 > General Setup (FIG XX). 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 "XXXXXXXX". Files are then written to C: data > in > VCD-S. These files are not uploaded to LORE 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.

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 0cm on the ruler on the tray.

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.

Take Image

1. Click START and the Sample Information screen will appear

2. Scan the section barcode from the endcap

3. Select the 360 Imaging type and the default quadrant will be 0°. Select Dry-Hard Rock. Click TAKE A PICTURE

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

5. The whole round rotation window will open and the rotation angle will default to the next quadrant, in this case, 90°

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.

Maintenance

Instrument Preparation

Preparing the track system for imaging cores requires adjusting the position of the lights and barcode imager for optimal quality and calibrating the system by adjusting camera settings. The position of the lights and barcode imager, once set, should be stable throughout an expedition. The technical staff will calibrate the camera settings (SHIL: Camera Configuration AUG) and light array (SHIL: Light Array AUG) whenever the camera or light sources have been repositioned or changed.

Setting up the Lights

Initial light installation and fine adjustment procedures are described in the SHIL: Light Array AUG. For routine operation, follow these steps:

1. Rotate the lights to the desired rough angle to the camera (usually ~30° to the camera axis for sediment cores). Fine-tune the light position by observing the camera output using MAX.
2. Manually turn on one line light at a time to full power by pressing the "+" button on the light controller until you reach 100%.
3. Loosen the brackets on both sides of the light mounts and make small position adjustments until the brightest image is achieved.
4. Turn off the light by pressing the "–" button and press Select to enable the other light.
5. Repeat Steps 2–4 for the second light.

Calibration

The laboratory technician calibrates the system when needed by adjusting camera settings and analyzing an imaged Kodak Q13 grayscale standard.
Calibration adjustments are performed using an iterative process of imaging a ruler placed crosswise on the track then counting the pixels between millimeter marks, moving the camera up or down, and repeating. See <LINK> [Author: Where is this procedure documented?] for details on this procedure.

LIMS Integration

Sample and Analysis Components

Troubleshooting

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

Scheduled Maintenance

Standard Replacement Parts/Spares

Spares are available for the following parts:

• camera
• camera lens
• frame grabber card
• linear encoder head
• lights power supply

Non-camera-specific items are part of the shared spares pool for all the track systems. See a technician for the location of the shared spares.

Health, Safety, and Environment

Safety

• Avoid staring into the line lights, as they produce 90,000 lux each at full power. This is roughly equivalent to staring directly into the sun.
• 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.

Vendor Information

Galil Motion Control

270 Technology Way Rocklin, CA 95765 800-377-6329 galil@galilmc.com www.galilmc.com

JAI Inc., USA

625 River Oaks Parkway San Jose, CA 95134 800-445-5444 www.pulnix.com

Microscan

800-251-7711 helpdesk@microscan.com www.microscan.com/index.htm

Advanced Illumination, Inc.

24 Peavine Drive Rochester, VT 05767 800-767-3830 info@advancedillumination.com www.advancedillumination.com/

NSK Corporation

4200 Goss Road Ann Arbor, MI 48105 800-521-0605 www.npa.nsk.com/public/enu/1001_102.asp

Newall Electronics, Inc.

1778 Dividend Drive Columbus, OH 43228 800-229-4376 www.newall.com/LEDs/leds.htm

Digi-Key

www.digikey.com is a good source for small quantities of AMP hardware

Related Documentation/Links

The following documents contain more detailed information on the logger system components:

• LabVIEW: NI-IMAQ3_error_codes.xls
• JAI camera: CV-107CL manual.pdf
• Microscan barcode imager: MS4manual.pdf
• Advanced Illumination
  • Controller: AIcontroller.pdf
  • Lights: LL068.pdf
• Galil
• Motors: Blm_n23.pdf
• Software: wsdk.pdf
• Controllers: man19540.pdf
• Amplifiers: man18x-6.pdf
• Newall
  • Linear encoder: Newall_linear_encoder.pdf
  • Wiring diagram: Encoder_Connections.xls
  • ImCheck manual: Imcheck_Guide_V1.pdf

APPENDIX A: RGB Calculation

APPENDIX B: 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

IMS Configuration

1. To access the scratch sheet configuration options, click the Instruments button and follow the menu down to VCDS Setup (fig. 1).
2. The parameter screen will then display (fig. 2). Several configurable options appear:
   • 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.
   • Save Values: 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 (fig. 4). 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 XX)

   

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