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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. 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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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.
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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 28). 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 28. Color standard in track in correct orientation.
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2. Adjust the Brightness, Contrast, and Gamma levels (Figure 35-1) 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 35-2, 35-3) 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.
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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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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
- 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 60).
Figure 60. Select VCDS Setup
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.
- Accept: Saves any modifications to parameters.
Cancel: Does not save parameter modifications and reverts back to prior settings.
Editing Scratch Sheet in LabVIEW
- Navigate to C: > IMS-10 > Resources > Templates and double-click a VI to open it in LabVIEW.
- 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!
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
Navigate to the 'View' button on the toolbar. Select the 'Tools Palette' Option (Figure 61).
Figure 61. 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. LIMS Component Tables
The following LIMS component tables are included under the Section Half Imaging Logger (SHIL):
- LSIMG - linescan imaging of the section half
- RGB - red/green/blue analysis of the LSIMG TIF, usually in 2 cm wide (Y-axis) x 0.5 cm deep (Z-axis) bins at the Y-axis center of the section
- WRLS - linescan imaging of the individual 90-degree quadrants for whole-round imaging of the outside of a hard rock section
- WRLSC - component for the collection of the final 90-degree quadrant images as well as the 360-degree composite image
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B.3 LIMS Component Tables
The following LIMS component tables are included under the Section Half Imaging Logger (SHIL):
- LSIMG - linescan imaging of the section half
- RGB - red/green/blue analysis of the LSIMG TIF, usually in 2 cm wide (Y-axis) x 0.5 cm deep (Z-axis) bins at the Y-axis center of the section
- WRLS - linescan imaging of the individual 90-degree quadrants for whole-round imaging of the outside of a hard rock section
- WRLSC - component for the collection of the final 90-degree quadrant images as well as the 360-degree composite image
| ANALYSIS | TABLE | NAME | ABOUT TEXT |
| LSIMG | SAMPLE | Exp | Exp: expedition number |
| LSIMG | SAMPLE | Site | Site: site number |
| LSIMG | SAMPLE | Hole | Hole: hole number |
| LSIMG | SAMPLE | Core | Core: core number |
| LSIMG | SAMPLE | Type | Type: type indicates the coring tool used to recover the core (typical types are F, H, R, X). |
| LSIMG | SAMPLE | Sect | Sect: section number |
| LSIMG | SAMPLE | A/W | A/W: archive (A) or working (W) section half. |
| LSIMG | SAMPLE | text_id | Text_ID: automatically generated database identifier for a sample, also carried on the printed labels. This identifier is guaranteed to be unique across all samples. |
| LSIMG | SAMPLE | sample_number | Sample Number: automatically generated database identifier for a sample. This is the primary key of the SAMPLE table. |
| LSIMG | SAMPLE | label_id | Label identifier: automatically generated, human readable name for a sample that is printed on labels. This name is not guaranteed unique across all samples. |
| LSIMG | SAMPLE | sample_name | Sample name: short name that may be specified for a sample. You can use an advanced filter to narrow your search by this parameter. |
| LSIMG | SAMPLE | x_sample_state | Sample state: Single-character identifier always set to "W" for samples; standards can vary. |
| LSIMG | SAMPLE | x_project | Project: similar in scope to the expedition number, the difference being that the project is the current cruise, whereas expedition could refer to material/results obtained on previous cruises |
| LSIMG | SAMPLE | x_capt_loc | Captured location: "captured location," this field is usually null and is unnecessary because any sample captured on the JR has a sample_number ending in 1, and GCR ending in 2 |
| LSIMG | SAMPLE | location | Location: location that sample was taken; this field is usually null and is unnecessary because any sample captured on the JR has a sample_number ending in 1, and GCR ending in 2 |
| LSIMG | SAMPLE | x_sampling_tool | Sampling tool: sampling tool used to take the sample (e.g., syringe, spatula) |
| LSIMG | SAMPLE | changed_by | Changed by: username of account used to make a change to a sample record |
| LSIMG | SAMPLE | changed_on | Changed on: date/time stamp for change made to a sample record |
| LSIMG | SAMPLE | sample_type | Sample type: type of sample from a predefined list (e.g., HOLE, CORE, LIQ) |
| LSIMG | SAMPLE | x_offset | Offset (m): top offset of sample from top of parent sample, expressed in meters. |
| LSIMG | SAMPLE | x_offset_cm | Offset (cm): top offset of sample from top of parent sample, expressed in centimeters. This is a calculated field (offset, converted to cm) |
| LSIMG | SAMPLE | x_bottom_offset_cm | Bottom offset (cm): bottom offset of sample from top of parent sample, expressed in centimeters. This is a calculated field (offset + length, converted to cm) |
| LSIMG | SAMPLE | x_diameter | Diameter (cm): diameter of sample, usually applied only to CORE, SECT, SHLF, and WRND samples; however this field is null on both Exp. 390 and 393, so it is no longer populated by Sample Master |
| LSIMG | SAMPLE | x_orig_len | Original length (m): field for the original length of a sample; not always (or reliably) populated |
| LSIMG | SAMPLE | x_length | Length (m): field for the length of a sample [as entered upon creation] |
| LSIMG | SAMPLE | x_length_cm | Length (cm): field for the length of a sample. This is a calculated field (length, converted to cm). |
| LSIMG | SAMPLE | status | Status: single-character code for the current status of a sample (e.g., active, canceled) |
| LSIMG | SAMPLE | old_status | Old status: single-character code for the previous status of a sample; used by the LIME program to restore a canceled sample |
| LSIMG | SAMPLE | original_sample | Original sample: field tying a sample below the CORE level to its parent HOLE sample |
| LSIMG | SAMPLE | parent_sample | Parent sample: the sample from which this sample was taken (e.g., for PWDR samples, this might be a SHLF or possibly another PWDR) |
| LSIMG | SAMPLE | standard | Standard: T/F field to differentiate between samples (standard=F) and QAQC standards (standard=T) |
| LSIMG | SAMPLE | login_by | Login by: username of account used to create the sample (can be the LIMS itself [e.g., SHLFs created when a SECT is created]) |
| LSIMG | SAMPLE | login_date | Login date: creation date of the sample |
| LSIMG | SAMPLE | legacy | Legacy flag: T/F indicator for when a sample is from a previous expedition and is locked/uneditable on this expedition |
| LSIMG | TEST | test changed_on | TEST changed on: date/time stamp for a change to a test record. |
| LSIMG | TEST | test status | TEST status: single-character code for the current status of a test (e.g., active, in process, canceled) |
| LSIMG | TEST | test old_status | TEST old status: single-character code for the previous status of a test; used by the LIME program to restore a canceled test |
| LSIMG | TEST | test test_number | TEST test number: automatically generated database identifier for a test record. This is the primary key of the TEST table. |
| LSIMG | TEST | test date_received | TEST date received: date/time stamp for the creation of the test record. |
| LSIMG | TEST | test instrument | TEST instrument [instrument group]: field that describes the instrument group (most often this applies to loggers with multiple sensors); often obscure (e.g., user_input) |
| LSIMG | TEST | test analysis | TEST analysis: analysis code associated with this test (foreign key to the ANALYSIS table) |
| LSIMG | TEST | test x_project | TEST project: similar in scope to the expedition number, the difference being that the project is the current cruise, whereas expedition could refer to material/results obtained on previous cruises |
| LSIMG |
| TEST |
| test sample_number | TEST sample number: the sample_number of the sample to which this test record is attached; a foreign key to the SAMPLE table | ||
| LSIMG | TEST | test x_display | TEST display flag: T/F field to indicate whether an image is the display image |
| LSIMG | TEST | test legacy | TEST legacy: T/F indicator for when a test from a previous expedition and is locked/uneditable on this expedition |
| LSIMG | CALCULATED | Top depth CSF-A (m) | Top depth CSF-A (m): position of observation expressed relative to the top of the hole. |
| LSIMG | CALCULATED | Bottom depth CSF-A (m) | Bottom depth CSF-A (m): position of observation expressed relative to the top of the hole. |
| LSIMG | CALCULATED | Top depth CSF-B (m) | Top depth [other] (m): position of observation expressed relative to the top of the hole. The location is presented in a scale selected by the science party or the report user. |
| LSIMG | CALCULATED | Bottom depth CSF-B (m) | Bottom depth [other] (m): position of observation expressed relative to the top of the hole. The location is presented in a scale selected by the science party or the report user. |
| LSIMG | RESULT | config_asman_id | RESULT configuration file ASMAN_ID: serial number of the ASMAN link for the configuration file |
| LSIMG | RESULT | config_filename | RESULT configuration filename: file name of the configuration file |
| LSIMG | RESULT | consumer_image_asman_id | RESULT consumer image ASMAN_ID: serial number of the ASMAN link for the uncropped JPG image file |
| LSIMG | RESULT | consumer_image_filename | RESULT consumer image filename: file name of the uncropped JPG image file |
| LSIMG | RESULT | correction | RESULT correction: summary of corrections applied to the TIF file and JPG file (contrast, gamma, and brightness only) |
| LSIMG | RESULT | cropped_image_asman_id | RESULT cropped image ASMAN_ID: serial number of the ASMAN link for the cropped JPG image file |
| LSIMG | RESULT | cropped_image_filename | RESULT cropped image filename: file name of the cropped JPG image file |
| LSIMG | RESULT | cropped_image_length | RESULT cropped image length (cm): length of the cropped image as calculated from the total lines x 50 micron pixels |
| LSIMG | RESULT | image_description | RESULT image description: archaic field for "Pristine" or other choices |
| LSIMG | RESULT | image_purpose | RESULT image purpose: field for what the target is (e.g., soft sediment, dry hard rock) |
| LSIMG | RESULT | instrument | RESULT instrument: which sensor is used for this result; for LSIMG it is currently JAI SW-2001T-CL-F camera |
| LSIMG | RESULT | observed_length | RESULT observed length (cm): length of the core section as entered by the operator |
| LSIMG | RESULT | original_image_asman_id | RESULT original image ASMAN_ID: serial number of the ASMAn link for the uncropped TIF file (also not adjusted for contrast, gamma, or brightness) |
| LSIMG | RESULT | original_image_filename | RESULT original image filename: file name of the uncropped TIF file |
| LSIMG | RESULT | roi_left_edge | RESULT region of interest left edge (pixels): position of the left edge of the cropped image in pixels |
| LSIMG | RESULT | roi_lower_edge | RESULT region of interest lower edge (pixels): position of the lower edge of the cropped image in pixels |
| LSIMG | RESULT | roi_right_edge | RESULT region of interest right edge (pixels): position of the right edge of the cropped image in pixels |
| LSIMG | RESULT | roi_upper_edge | RESULT region of interest upper edge (pixels): position of the upper edge of the cropped image in pixels |
| LSIMG | RESULT | run_asman_id | RESULT run file ASMAN_ID: serial number of the ASMAN link for the run (.ROI) file |
| LSIMG | RESULT | run_filename | RESULT run filename: file name for the run (.ROI) file |
| LSIMG | SAMPLE | sample description | SAMPLE comment: contents of the SAMPLE.description field, usually shown on reports as "Sample comments" |
| LSIMG | TEST | test test_comment | TEST comment: contents of the TEST.comment field, usually shown on reports as "Test comments" |
| LSIMG | RESULT | result comments | RESULT comment: contents of a result parameter with name = "comment," usually shown on reports as "Result comments" |
| ANALYSIS | TABLE | NAME | ABOUT TEXT |
| RGB | SAMPLE | Exp | Exp: expedition number |
| RGB | SAMPLE | Site | Site: site number |
| RGB | SAMPLE | Hole | Hole: hole number |
| RGB | SAMPLE | Core | Core: core number |
| RGB | SAMPLE | Type | Type: type indicates the coring tool used to recover the core (typical types are F, H, R, X). |
| RGB | SAMPLE | Sect | Sect: section number |
| RGB | SAMPLE | A/W | A/W: archive (A) or working (W) section half. |
| RGB | SAMPLE | text_id | Text_ID: automatically generated database identifier for a sample, also carried on the printed labels. This identifier is guaranteed to be unique across all samples. |
| RGB | SAMPLE | sample_number | Sample Number: automatically generated database identifier for a sample. This is the primary key of the SAMPLE table. |
| RGB | SAMPLE | label_id | Label identifier: automatically generated, human readable name for a sample that is printed on labels. This name is not guaranteed unique across all samples. |
| RGB | SAMPLE | sample_name | Sample name: short name that may be specified for a sample. You can use an advanced filter to narrow your search by this parameter. |
| RGB | SAMPLE | x_sample_state | Sample state: Single-character identifier always set to "W" for samples; standards can vary. |
| RGB | SAMPLE | x_project | Project: similar in scope to the expedition number, the difference being that the project is the current cruise, whereas expedition could refer to material/results obtained on previous cruises |
| RGB | SAMPLE | x_capt_loc | Captured location: "captured location," this field is usually null and is unnecessary because any sample captured on the JR has a sample_number ending in 1, and GCR ending in 2 |
| RGB | SAMPLE | location | Location: location that sample was taken; this field is usually null and is unnecessary because any sample captured on the JR has a sample_number ending in 1, and GCR ending in 2 |
| RGB | SAMPLE | x_sampling_tool | Sampling tool: sampling tool used to take the sample (e.g., syringe, spatula) |
| RGB | SAMPLE | changed_by | Changed by: username of account used to make a change to a sample record |
| RGB | SAMPLE | changed_on | Changed on: date/time stamp for change made to a sample record |
| RGB | SAMPLE | sample_type | Sample type: type of sample from a predefined list (e.g., HOLE, CORE, LIQ) |
| RGB | SAMPLE | x_offset | Offset (m): top offset of sample from top of parent sample, expressed in meters. |
| RGB | SAMPLE | x_offset_cm | Offset (cm): top offset of sample from top of parent sample, expressed in centimeters. This is a calculated field (offset, converted to cm) |
| RGB | SAMPLE | x_bottom_offset_cm | Bottom offset (cm): bottom offset of sample from top of parent sample, expressed in centimeters. This is a calculated field (offset + length, converted to cm) |
| RGB | SAMPLE | x_diameter | Diameter (cm): diameter of sample, usually applied only to CORE, SECT, SHLF, and WRND samples; however this field is null on both Exp. 390 and 393, so it is no longer populated by Sample Master |
| RGB | SAMPLE | x_orig_len | Original length (m): field for the original length of a sample; not always (or reliably) populated |
| RGB | SAMPLE | x_length | Length (m): field for the length of a sample [as entered upon creation] |
| RGB | SAMPLE | x_length_cm | Length (cm): field for the length of a sample. This is a calculated field (length, converted to cm). |
| RGB | SAMPLE | status | Status: single-character code for the current status of a sample (e.g., active, canceled) |
| RGB | SAMPLE | old_status | Old status: single-character code for the previous status of a sample; used by the LIME program to restore a canceled sample |
| RGB | SAMPLE | original_sample | Original sample: field tying a sample below the CORE level to its parent HOLE sample |
| RGB | SAMPLE | parent_sample | Parent sample: the sample from which this sample was taken (e.g., for PWDR samples, this might be a SHLF or possibly another PWDR) |
| RGB | SAMPLE | standard | Standard: T/F field to differentiate between samples (standard=F) and QAQC standards (standard=T) |
| RGB | SAMPLE | login_by | Login by: username of account used to create the sample (can be the LIMS itself [e.g., SHLFs created when a SECT is created]) |
| RGB | SAMPLE | login_date | Login date: creation date of the sample |
| RGB | SAMPLE | legacy | Legacy flag: T/F indicator for when a sample is from a previous expedition and is locked/uneditable on this expedition |
| RGB | TEST | test changed_on | TEST changed on: date/time stamp for a change to a test record. |
| RGB | TEST | test status | TEST status: single-character code for the current status of a test (e.g., active, in process, canceled) |
| RGB | TEST | test old_status | TEST old status: single-character code for the previous status of a test; used by the LIME program to restore a canceled test |
| RGB | TEST | test test_number | TEST test number: automatically generated database identifier for a test record. This is the primary key of the TEST table. |
| RGB | TEST | test date_received | TEST date received: date/time stamp for the creation of the test record. |
| RGB | TEST | test instrument | TEST instrument [instrument group]: field that describes the instrument group (most often this applies to loggers with multiple sensors); often obscure (e.g., user_input) |
| RGB | TEST | test analysis | TEST analysis: analysis code associated with this test (foreign key to the ANALYSIS table) |
| RGB | TEST | test x_project | TEST project: similar in scope to the expedition number, the difference being that the project is the current cruise, whereas expedition could refer to material/results obtained on previous cruises |
| RGB |
| TEST |
| test sample_number | TEST sample number: the sample_number of the sample to which this test record is attached; a foreign key to the SAMPLE table | ||
| RGB | CALCULATED | Depth CSF-A (m) | Depth CSF-A (m): position of observation expressed relative to the top of the hole. |
| RGB | CALCULATED | Depth CSF-B (m) | Depth [other] (m): position of observation expressed relative to the top of the hole. The location is presented in a scale selected by the science party or the report user. |
| RGB | RESULT | red | RESULT red (R) channel: average of digitized red (R) channel over a user-defined rectangle along the core section. Values range from 0 to 255 (8-bit color digitization). |
| RGB | RESULT | green | RESULT green (G) channel: average of digitized green (G) channel over a user-defined rectangle along the core section. Values range from 0 to 255 (8-bit color digitization). |
| RGB | RESULT | blue | RESULT blue (B) channel: average of digitized blue (B) channel over a user-defined rectangle along the core section. Values range from 0 to 255 (8-bit color digitization). |
| RGB | RESULT | config_asman_id | RESULT config file ASMAN_ID: serial number of the ASMAN link for the configuration file |
| RGB | RESULT | config_filename | RESULT config filename: file name of the configuration file |
| RGB | RESULT | observed_length (cm) | RESULT observed length (cm): length of the section as recorded by the core logger track |
| RGB | RESULT | offset (cm) | RESULT offset (cm): position of the observation made, measured relative to the top of a section half. |
| RGB | RESULT | run_asman_id | RESULT run file ASMAN_ID: serial number of the ASMAN link for the run (.RGB) file |
| RGB | RESULT | run_filename | RESULT run filename: file name of the run (.RGB) file |
| RGB | RESULT | rgb_high_res_asman_id | RESULT high res RGB ASMAN_ID: serial number of the ASMAN link for the high resolution RGB (.DAT) file |
| RGB | RESULT | rgb_high_res_filename | RESULT high res RGB filename: filename for the high resolution RGB (.DAT) file |
| RGB | SAMPLE | sample description | SAMPLE comment: contents of the SAMPLE.description field, usually shown on reports as "Sample comments" |
| RGB | TEST | test test_comment | TEST comment: contents of the TEST.comment field, usually shown on reports as "Test comments" |
| RGB | RESULT | result comments | RESULT comment: contents of a result parameter with name = "comment," usually shown on reports as "Result comments" |
| ANALYSIS | TABLE | NAME | ABOUT TEXT |
| WRLS | SAMPLE | Exp | Exp: expedition number |
| WRLS | SAMPLE | Site | Site: site number |
| WRLS | SAMPLE | Hole | Hole: hole number |
| WRLS | SAMPLE | Core | Core: core number |
| WRLS | SAMPLE | Type | Type: type indicates the coring tool used to recover the core (typical types are F, H, R, X). |
| WRLS | SAMPLE | Sect | Sect: section number |
| WRLS | SAMPLE | text_id | Text_ID: automatically generated database identifier for a sample, also carried on the printed labels. This identifier is guaranteed to be unique across all samples. |
| WRLS | SAMPLE | sample_number | Sample Number: automatically generated database identifier for a sample. This is the primary key of the SAMPLE table. |
| WRLS | SAMPLE | label_id | Label identifier: automatically generated, human readable name for a sample that is printed on labels. This name is not guaranteed unique across all samples. |
| WRLS | SAMPLE | sample_name | Sample name: short name that may be specified for a sample. You can use an advanced filter to narrow your search by this parameter. |
| WRLS | SAMPLE | x_sample_state | Sample state: Single-character identifier always set to "W" for samples; standards can vary. |
| WRLS | SAMPLE | x_project | Project: similar in scope to the expedition number, the difference being that the project is the current cruise, whereas expedition could refer to material/results obtained on previous cruises |
| WRLS |
| SAMPLE | x_capt_loc | Captured location: "captured location," this field is usually null and is unnecessary because any sample captured on the JR has a sample_number ending in 1, and GCR ending in 2 | |
| WRLS | SAMPLE | location | Location: location that sample was taken; this field is usually null and is unnecessary because any sample captured on the JR has a sample_number ending in 1, and GCR ending in 2 |
| WRLS | SAMPLE | x_sampling_tool | Sampling tool: sampling tool used to take the sample (e.g., syringe, spatula) |
| WRLS | SAMPLE | changed_by | Changed by: username of account used to make a change to a sample record |
| WRLS | SAMPLE | changed_on | Changed on: date/time stamp for change made to a sample record |
| WRLS | SAMPLE | sample_type | Sample type: type of sample from a predefined list (e.g., HOLE, CORE, LIQ) |
| WRLS | SAMPLE | x_offset | Offset (m): top offset of sample from top of parent sample, expressed in meters. |
| WRLS | SAMPLE | x_offset_cm | Offset (cm): top offset of sample from top of parent sample, expressed in centimeters. This is a calculated field (offset, converted to cm) |
| WRLS | SAMPLE | x_bottom_offset_cm | Bottom offset (cm): bottom offset of sample from top of parent sample, expressed in centimeters. This is a calculated field (offset + length, converted to cm) |
| WRLS | SAMPLE | x_diameter | Diameter (cm): diameter of sample, usually applied only to CORE, SECT, SHLF, and WRND samples; however this field is null on both Exp. 390 and 393, so it is no longer populated by Sample Master |
| WRLS | SAMPLE | x_orig_len | Original length (m): field for the original length of a sample; not always (or reliably) populated |
| WRLS | SAMPLE | x_length | Length (m): field for the length of a sample [as entered upon creation] |
| WRLS | SAMPLE | x_length_cm | Length (cm): field for the length of a sample. This is a calculated field (length, converted to cm). |
| WRLS | SAMPLE | status | Status: single-character code for the current status of a sample (e.g., active, canceled) |
| WRLS | SAMPLE | old_status | Old status: single-character code for the previous status of a sample; used by the LIME program to restore a canceled sample |
| WRLS | SAMPLE | original_sample | Original sample: field tying a sample below the CORE level to its parent HOLE sample |
| WRLS | SAMPLE | parent_sample | Parent sample: the sample from which this sample was taken (e.g., for PWDR samples, this might be a SHLF or possibly another PWDR) |
| WRLS | SAMPLE | standard | Standard: T/F field to differentiate between samples (standard=F) and QAQC standards (standard=T) |
| WRLS | SAMPLE | login_by | Login by: username of account used to create the sample (can be the LIMS itself [e.g., SHLFs created when a SECT is created]) |
| WRLS | SAMPLE | login_date | Login date: creation date of the sample |
| WRLS | SAMPLE | legacy | Legacy flag: T/F indicator for when a sample is from a previous expedition and is locked/uneditable on this expedition |
| WRLS | TEST | test changed_on | TEST changed on: date/time stamp for a change to a test record. |
| WRLS | TEST | test status | TEST status: single-character code for the current status of a test (e.g., active, in process, canceled) |
| WRLS | TEST | test old_status | TEST old status: single-character code for the previous status of a test; used by the LIME program to restore a canceled test |
| WRLS | TEST | test test_number | TEST test number: automatically generated database identifier for a test record. This is the primary key of the TEST table. |
| WRLS | TEST | test date_received | TEST date received: date/time stamp for the creation of the test record. |
| WRLS | TEST | test instrument | TEST instrument [instrument group]: field that describes the instrument group (most often this applies to loggers with multiple sensors); often obscure (e.g., user_input) |
| WRLS | TEST | test analysis | TEST analysis: analysis code associated with this test (foreign key to the ANALYSIS table) |
| WRLS | TEST | test x_project | TEST project: similar in scope to the expedition number, the difference being that the project is the current cruise, whereas expedition could refer to material/results obtained on previous cruises |
| WRLS |
| TEST |
| test sample_number | TEST sample number: the sample_number of the sample to which this test record is attached; a foreign key to the SAMPLE table | ||
| WRLS | TEST | test x_display | TEST display flag: T/F field to indicate whether an image is the display image |
| WRLS | TEST | test legacy | TEST legacy: T/F indicator for when a test from a previous expedition and is locked/uneditable on this expedition |
| WRLS | CALCULATED | Top depth CSF-A (m) | Top depth CSF-A (m): position of observation expressed relative to the top of the hole. |
| WRLS | CALCULATED | Bottom depth CSF-A (m) | Bottom depth CSF-A (m): position of observation expressed relative to the top of the hole. |
| WRLS | CALCULATED | Top depth CSF-B (m) | Top depth [other] (m): position of observation expressed relative to the top of the hole. The location is presented in a scale selected by the science party or the report user. |
| WRLS | CALCULATED | Bottom depth CSF-B (m) | Bottom depth [other] (m): position of observation expressed relative to the top of the hole. The location is presented in a scale selected by the science party or the report user. |
| WRLS | RESULT | quadrant | RESULT quadrant: which 90-degree quadrant was captured in this image |
| WRLS | RESULT | quadrant_tif_asman_id | RESULT quadrant TIF ASMAN_ID: serial number of the ASMAN link for the quadrant TIF/TIFF image |
| WRLS | RESULT | quadrant_tif_filename | RESULT quadrant TIF filename: file name of the quadrant TIF/TIFF image |
| WRLS | RESULT | quadrant_jpg_asman_id | RESULT quadrant JPG ASMAN_ID: serial number of the ASMAN link for the quadrant JPG/JPEG image |
| WRLS | RESULT | quadrant_jpg_filename | RESULT quadrant JPG filename: file name of the quadrant JPG/JPEG image |
| WRLS | RESULT | run_asman_id | RESULT run file ASMAN_ID: serial number of the ASMAN link for the run (.WRLS) file |
| WRLS | RESULT | run_filename | RESULT run filename: file name of the run (.WRLS) file |
| WRLS | SAMPLE | sample description | SAMPLE comment: contents of the SAMPLE.description field, usually shown on reports as "Sample comments" |
| WRLS | TEST | test test_comment | TEST comment: contents of the TEST.comment field, usually shown on reports as "Test comments" |
| WRLS | RESULT | result comments | RESULT comment: contents of a result parameter with name = "comment," usually shown on reports as "Result comments" |
| ANALYSIS | TABLE | NAME | ABOUT TEXT |
| WRLSC | SAMPLE | Exp | Exp: expedition number |
| WRLSC | SAMPLE | Site | Site: site number |
| WRLSC | SAMPLE | Hole | Hole: hole number |
| WRLSC | SAMPLE | Core | Core: core number |
| WRLSC | SAMPLE | Type | Type: type indicates the coring tool used to recover the core (typical types are F, H, R, X). |
| WRLSC | SAMPLE | Sect | Sect: section number |
| WRLSC | SAMPLE | text_id | Text_ID: automatically generated database identifier for a sample, also carried on the printed labels. This identifier is guaranteed to be unique across all samples. |
| WRLSC | SAMPLE | sample_number | Sample Number: automatically generated database identifier for a sample. This is the primary key of the SAMPLE table. |
| WRLSC | SAMPLE | label_id | Label identifier: automatically generated, human readable name for a sample that is printed on labels. This name is not guaranteed unique across all samples. |
| WRLSC | SAMPLE | sample_name | Sample name: short name that may be specified for a sample. You can use an advanced filter to narrow your search by this parameter. |
| WRLSC | SAMPLE | x_sample_state | Sample state: Single-character identifier always set to "W" for samples; standards can vary. |
| WRLSC | SAMPLE | x_project | Project: similar in scope to the expedition number, the difference being that the project is the current cruise, whereas expedition could refer to material/results obtained on previous cruises |
| WRLSC |
| SAMPLE | x_capt_loc | Captured location: "captured location," this field is usually null and is unnecessary because any sample captured on the JR has a sample_number ending in 1, and GCR ending in 2 | |
| WRLSC | SAMPLE | location | Location: location that sample was taken; this field is usually null and is unnecessary because any sample captured on the JR has a sample_number ending in 1, and GCR ending in 2 |
| WRLSC | SAMPLE | x_sampling_tool | Sampling tool: sampling tool used to take the sample (e.g., syringe, spatula) |
| WRLSC | SAMPLE | changed_by | Changed by: username of account used to make a change to a sample record |
| WRLSC | SAMPLE | changed_on | Changed on: date/time stamp for change made to a sample record |
| WRLSC | SAMPLE | sample_type | Sample type: type of sample from a predefined list (e.g., HOLE, CORE, LIQ) |
| WRLSC | SAMPLE | x_offset | Offset (m): top offset of sample from top of parent sample, expressed in meters. |
| WRLSC | SAMPLE | x_offset_cm | Offset (cm): top offset of sample from top of parent sample, expressed in centimeters. This is a calculated field (offset, converted to cm) |
| WRLSC | SAMPLE | x_bottom_offset_cm | Bottom offset (cm): bottom offset of sample from top of parent sample, expressed in centimeters. This is a calculated field (offset + length, converted to cm) |
| WRLSC | SAMPLE | x_diameter | Diameter (cm): diameter of sample, usually applied only to CORE, SECT, SHLF, and WRND samples; however this field is null on both Exp. 390 and 393, so it is no longer populated by Sample Master |
| WRLSC | SAMPLE | x_orig_len | Original length (m): field for the original length of a sample; not always (or reliably) populated |
| WRLSC | SAMPLE | x_length | Length (m): field for the length of a sample [as entered upon creation] |
| WRLSC | SAMPLE | x_length_cm | Length (cm): field for the length of a sample. This is a calculated field (length, converted to cm). |
| WRLSC | SAMPLE | status | Status: single-character code for the current status of a sample (e.g., active, canceled) |
| WRLSC | SAMPLE | old_status | Old status: single-character code for the previous status of a sample; used by the LIME program to restore a canceled sample |
| WRLSC | SAMPLE | original_sample | Original sample: field tying a sample below the CORE level to its parent HOLE sample |
| WRLSC | SAMPLE | parent_sample | Parent sample: the sample from which this sample was taken (e.g., for PWDR samples, this might be a SHLF or possibly another PWDR) |
| WRLSC | SAMPLE | standard | Standard: T/F field to differentiate between samples (standard=F) and QAQC standards (standard=T) |
| WRLSC | SAMPLE | login_by | Login by: username of account used to create the sample (can be the LIMS itself [e.g., SHLFs created when a SECT is created]) |
| WRLSC | SAMPLE | login_date | Login date: creation date of the sample |
| WRLSC | SAMPLE | legacy | Legacy flag: T/F indicator for when a sample is from a previous expedition and is locked/uneditable on this expedition |
| WRLSC | TEST | test changed_on | TEST changed on: date/time stamp for a change to a test record. |
| WRLSC | TEST | test status | TEST status: single-character code for the current status of a test (e.g., active, in process, canceled) |
| WRLSC | TEST | test old_status | TEST old status: single-character code for the previous status of a test; used by the LIME program to restore a canceled test |
| WRLSC | TEST | test test_number | TEST test number: automatically generated database identifier for a test record. This is the primary key of the TEST table. |
| WRLSC | TEST | test date_received | TEST date received: date/time stamp for the creation of the test record. |
| WRLSC | TEST | test instrument | TEST instrument [instrument group]: field that describes the instrument group (most often this applies to loggers with multiple sensors); often obscure (e.g., user_input) |
| WRLSC | TEST | test analysis | TEST analysis: analysis code associated with this test (foreign key to the ANALYSIS table) |
| WRLSC | TEST | test x_project | TEST project: similar in scope to the expedition number, the difference being that the project is the current cruise, whereas expedition could refer to material/results obtained on previous cruises |
| WRLSC |
| TEST |
| test sample_number | TEST sample number: the sample_number of the sample to which this test record is attached; a foreign key to the SAMPLE table | ||
| WRLSC | TEST | test x_display | TEST display flag: T/F field to indicate whether an image is the display image |
| WRLSC | TEST | test legacy | TEST legacy: T/F indicator for when a test from a previous expedition and is locked/uneditable on this expedition |
| WRLSC | CALCULATED | Top depth CSF-A (m) | Top depth CSF-A (m): position of observation expressed relative to the top of the hole. |
| WRLSC | CALCULATED | Bottom depth CSF-A (m) | Bottom depth CSF-A (m): position of observation expressed relative to the top of the hole. |
| WRLSC | CALCULATED | Top depth CSF-B (m) | Top depth [other] (m): position of observation expressed relative to the top of the hole. The location is presented in a scale selected by the science party or the report user. |
| WRLSC | CALCULATED | Bottom depth CSF-B (m) | Bottom depth [other] (m): position of observation expressed relative to the top of the hole. The location is presented in a scale selected by the science party or the report user. |
| WRLSC | RESULT | jpg0_asman_id | RESULT 0 degree JPG ASMAN_ID: serial number of the ASMAN link for the 0-degree quadrant JPG/JPEG image |
| WRLSC | RESULT | jpg90_asman_id | RESULT 90 degree JPG ASMAN_ID: serial number of the ASMAN link for the 90-degree quadrant JPG/JPEG image |
| WRLSC | RESULT | jpg180_asman_id | RESULT 180 degree JPG ASMAN_ID: serial number of the ASMAN link for the 180-degree quadrant JPG/JPEG image |
| WRLSC | RESULT | jpg270_asman_id | RESULT 270 degree JPG ASMAN_ID: serial number of the ASMAN link for the 270-degree quadrant JPG/JPEG image |
| WRLSC | RESULT | jpg360_asman_id | RESULT 360 degree image JPG ASMAN_ID: serial number of the composite 360-degree image JPG/JPEG image |
| WRLSC | RESULT | jpg360_filename | RESULT 360 degree JPG filename: file name of the composite 360-degree JPG/JPEG image (a filename exists for each quadrant, but name is similar enough it was omitted from expanded report) |
| WRLSC | RESULT | tif0_asman_id | RESULT 0 degree TIF ASMAN_ID: serial number of the ASMAN link for the 0-degree quadrant TIF/TIFF image |
| WRLSC | RESULT | tif90_asman_id | RESULT 90 degree TIF ASMAN_ID: serial number of the ASMAN link for the 90-degree quadrant TIF/TIFF image |
| WRLSC | RESULT | tif180_asman_id | RESULT 180 degree TIF ASMAN_ID: serial number of the ASMAN link for the 180-degree quadrant TIF/TIFF image |
| WRLSC | RESULT | tif270_asman_id | RESULT 270 degree TIF ASMAN_ID: serial number of the ASMAN link for the 270-degree quadrant TIF/TIFF image |
| WRLSC | RESULT | tif360_asman_id | RESULT 360 degree image TIF ASMAN_ID: serial number of the composite 360-degree image TIF/TIFF image |
| WRLSC | RESULT | tif360_filename | RESULT 360 degree TIF filename: file name of the composite 360-degree JPG/JPEG image (a filename exists for each quadrant, but name is similar enough it was omitted from expanded report) |
| WRLSC | RESULT | timestamp | RESULT timestamp: time/date stamp when the composite was made by the Imaging Specialist (not always filled in) |
| WRLSC | SAMPLE | sample description | SAMPLE comment: contents of the SAMPLE.description field, usually shown on reports as "Sample comments" |
| WRLSC | TEST | test test_comment | TEST comment: contents of the TEST.comment field, usually shown on reports as "Test comments" |
| WRLSC | RESULT | result comments | RESULT comment: contents of a result parameter with name = "comment," usually shown on reports as "Result comments" |
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
- 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 60).
Figure 60. Select VCDS Setup
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.
- Accept: Saves any modifications to parameters.
Cancel: Does not save parameter modifications and reverts back to prior settings.
Editing Scratch Sheet in LabVIEW
- Navigate to C: > IMS-10 > Resources > Templates and double-click a VI to open it in LabVIEW.
- 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!
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
Navigate to the 'View' button on the toolbar. Select the 'Tools Palette' Option (Figure 61).
Figure 61. 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.
VIII. Archived Versions
SHIL User Guide - 27Sept2022
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