IMS-X-ray Image Logger User Guide

March 2019

I. Introduction

II. Procedures

A. Preparing the Instrument

B. Instrument Calibration

C. Set Measurement Parameters

D. Preparing Sections// Preparing Samples

E. Making a Measurement

F. Evaluating your Measurement

G. IMS Utilities

III. Uploading Data to LIMS

A. Data Upload Procedure

B. View and Verify Data

C. Retrieve Data from LIMS

IV. Important Notes

V. Appendix

A.1 Health, Safety & Environment

A.2 Maintenance and Troubleshooting

B.1 IMS Program Structure

a) IMS Program Structure

b) Communication and Control Setup

B.2 Motion Control Setup

C.1 Hardware

VI. Credits

VII. Archived Versions

Introduction

This guide describes the standard operating procedures for the x-ray imager (XMSL).  The system is capable of collecting 2-D x-radiographs on whole round and section half cores.

Theory of Operation

Users should review the X-ray Imager.pptx powerpoint from LeVay, 2019 for background on x-ray radiograph acquisition before operating the system.

Hardware

The IODP x-ray system is composed of a 120 kV, 1 mA constant potential x-ray source and a detector unit.  The source is a Teledyne ICM CP120B portable x-ray generator with a 0.8 by 0.5 mm focal spot.  The beam angle is 50 by 50 degrees generating a directional cone onto the detector, which is distanced 65 cm from the source.  The detector is a Go-Scan 1510 HR unit composed of an array of CMOS sensors with an active area of 102 by 153 mm and a resolution of 99 microns.

Manual Configuration

You must manually configure Teledyne ICM CP120B prior to closing the shielding.  This needs to be done whenever you replace the source. From the control panel on the source do:

1. Insert Key and turn on power.  Wait for system to initialize.
2. Press Menu
3. Press either the plus or minus buttons unit you see "Settings"
4. Press Enter and then press the plus key once for each configuration
   • Auto Config = Manual Mode
   • Keep Alive = Disabled
   • English (don't care)
   • Fil(iment) Always On = Enable
   • Bluetooth = some code (ignore)
   • Trig(ger) = Security Enable
   • Com Status = Enable
   • Baud Rate = 9600
   • Long Time = Enable
   • Menu Step = Quick (don't care)
   • Factory = Disabled
   • Back Light = Enable (don't care)
   • External Trig = Disabled
   • Start Button = Disabled
   • Pre-warning = 0 sec
5. Press Escape

Shielding

The shielding consists of four sections as shown in Figure 1.  The Source Shield houses the x-ray source and detector. It is constructed with 6-mm of lead with an internal baffle on the unload side of the box.  The exterior corners are covered with 6-mm lead strips and lead vinyl (½-mm) covering the sides. The GRA-MS shield section is constructed with 2-mm of lead with an internal baffle on the load side.

The starboard load end of the track and the port unload end of the track are shielded by  lead vinyl (½-mm) (Figure 2).  Take care when handling the load and unload doors, they are heavy.  On the load side, we have counterweighted the door to hold it open and to take some of the weight.  On the unload door we have mounted magnets to hold it open.  Keep in mind that the vinyl lead shielding is held in place with Velcro and can be dislodge compromising the shielding.

 Figure 1 X-ray Image Logger Shielding 

Figure 2- X-ray Image Logger from starboard (left) and port (right).

Safety Systems

The x-ray imager has multiple safety systems in place to ensure a user does not operate the system in an unsafe configuration. Never attempt to operate the x-ray source without the proper shielding in place! The safety systems include:

1)      Visual Light Indications

2)      Door Switches

3)      Active Area Monitor

4)      Emergency Stop Switch

These switches and monitors are wired into one fail safe circuit.

Failsafe Circuit

In order to generate x-rays, a series of safety switches must be closed to complete the circuit between the CP160’s ground (pin 2) and x-ray trigger (pin 4) of the 6-pin external connector.

In addition, the following  CP160 parameters must be set using the menu keyboard on the CP160:

• Settings = SafeySys.Mode
• Trigger = Security

Figure 3 shows the failsafe circuit and the safety switches involved.  All switches must be closed before the command from the software to generate x-rays will be performed.

Figure 3- Fail safe circuit diagram. 

Visual Indicators

A tri-color tower light mounted on the lead shielded x-ray box acts as a visual indicator of the x-ray source status.

• Amber light is lit when the x-ray source is connected to power.

• Green light is lit when the load and unload doors are closed, FPD access door is closed, and the emergency shut off switch is not engaged. ( amber must be lit before the green is illuminated)

• Red light is lit when x-rays are generated.  The light will blink quickly as it powers on and then slowly once the kV and mA are stable.

• When both the amber and green lights are lit, the system is powered and ready to generate x-rays.

• When all three lights are lit, X-rays are on!

Figure 4- Tri-color tower light mounted on the lead shielded x-ray box.  This light acts as a visual indicator of the x-ray source status

Door Switches

Mechanical door switches have been installed on both the port and starboard doors, as well as on the small hatch in the lead lined box (Figure 5).  If any of these switches are open, the communications with the source will be interrupted and the source will not be able to generate x-rays.

Figure 5- Safety switch inside the port door (left), starboard door (middle), and the hatch where the third mechanical switch is located (right).

Active Area Monitor

The purpose of the Active Area Monitor is to provide an independent means of insuring the system’s overall safety.  The monitor consist of two scintillators mounted at either end of the track so that they view the shielding except for the top and bottom (Figure 6).

Two alarms levels can be set.  The low-level alarm will sound a warning beep while the high-level will trigger the strobe light and shut down the x-rays as part of the failsafe circuit. The alarm levels are set as follows:

Low-level: 1-kcps (1000-cps) above background

High-level: 1.2-kcps (1200-cps) above background

Background radiation levels will change with latitude!

The goal is to set the alarms high enough so that it does not go off during normal operations with shielding in place; but low enough to immediately sound if the shielding is compromised. The JR X-Ray Imaging System Safety Inspection and Radiation Survey Forms provides the procedures for setting and testing the area monitor alarm level.

Figure 6- Active area monitor display (left), high level alarm warning light and port side scintillator (middle), starboard scintillator (right).

Emergency Stop Switch

An emergency stop switch is located over the starboard side shielding (Figure 7).  When activated, this switch will interrupt the power to the source and stop the source from generating x-rays as part of the fail safe circuit.

Figure 7-X-ray logger Emergency Shut Off Switch. 

Thermal Management

With continuous running, the CP160 can overheat.  The CP160 will shut itself down when the internal tank temperature reaches 55°C.  The IMS software continuously monitors the CP160 temperature and displays on the main acquisition screen.  If the x-ray source temperature exceeds 45°C the x-rays are shut off and the Cool Down Wait… window (Figure 8) is displayed until the temperature drops below 35°C.  Once reaching 35°C the X-ray Start command will be given and acquisition will resume.  The user may abort at any time by clicking the ABORT button.

Figure 8- Cool Down Wait window.  This window will appear if the IMS software detects an x-ray source temperature of 45 degrees C or higher.

Launching the IMS X-ray Imager application

The IMS XMSL software can be launched from the Windows Start menu or from the desktop icon (Figure 9).

Figure 9- XMSL Desktop Icon

At launch, the program begins the following initialization process:

• Testing instrument communications
• Homing the pusher arm of the motion control system
• Verifying Dark and Light Calibration images.  If the calibration images are not found, the program will ask the user to run a calibration.

After successful initialization, the main IMS-XMSL window will appear (Figure 10).

Figure 10- XMSL IMS Main Window

A Quick Introduction to the IMS Program Structure

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

• INST plug-in: code for each of the instruments
• MOTION plug-in: code for the motion control system
• DAQ Engine: code that organizes INST and MOTION plug-ins into a track system

The XMSL system, specifically, is built with one INST module (XMSL), one MOTION module, and one DAQ Engine module.

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

Each module manages a configuration file that opens the IMS program at the same state it was when previously closed and provides utilities for the user to edit or modify the configuration data and calibration routines.

The four buttons on the IMS-UI window provide access to utilities/editors via dropdown menus as shown in Figure 11.

Figure 11- IMS Control Panel Drop down Menus

Initial Instrument Setup

XMSL Configuration

Configuration values should be set during initial setup and configuration by the technician or scientist(s).  There should be no need to change these values unless the configuration file is corrupted or the hardware setup is changed.

XMSL Instrument General Setup

To open the XMSL instrument setup window (Figure 12), select Instruments > Camera: General Setup from the IMS panel menu (Figure 11).  These settings are related to the detector only.

1. Ensure the values in the window are set as shown in Figure 12.
   1. The instrument X-offset is measured from the home switch to the center pixel of the detector (Figure 13).
   2. This value must be updated should the detector position change or if the home switch on the track is modified.

2)      Click ACCEPT to save the changes and write them to the configuration file.  Click Cancel to revert to previous values.

Figure 12- XMSL Parameters Window

Figure 13- Position of detector center from the track's home switch

XMSL DAQ Parameters

Prior to collecting x-radiographs on whole rounds or section halves in the XMSL, the user must set the imaging parameters (voltage, exposure, current).  For explanation on how to test exposure parameters prior to imaging, see the Image Utility section. For explanation on how to test image processing parameters, see the Image Process Utility section.

To open the Measurement Editor (Figure 14), select DAQ > Measurement Editor from the IMS panel menu (Figure 11).  This window allows the user to view and adjust the XMSL DAQ parameters.

• Interval: Number of centimeters the core will move between each image.  This value is hardcoded in the IMS software and cannot be changed in this window.  This interval guarantees image overlap, but maximizes system efficiency.
• Width: This is the fixed length of the image produced.  This value is dependent on the detector and hardware setup.  Each image is 15 cm in length, but due to projection, we see less than 15 cm of the core section in the image. For example, with 12 cm of motion, we are seeing 12 cm of core in a 15 cm image.
• Stack: The number of x-radiographs to take at each position.  These images are stacked and averaged to produce the final raw image.  Twenty images is the standard as stacking more images does not appear to improve the image quality further. See Image Stacking section for more explanation.
• Exposure Time: The duration of each exposure in milliseconds.
• X-Ray on Time: Time needed to image a full section keeping the x-rays on between images. Recommended: 300 ms. This time helps to avoid black images.
• kV: X-ray tube voltage.  Maximum voltage for the source is 120 kV. Lowering the voltage while maintaining the number of x-rays penetrating the core (longer exposure or higher current) will increase image contrast.
• mA: X-ray tube current.  Maximum current for the source is 1 mA.   Increasing the current will increase contrast if voltage is kept constant.

Each of the stacked images is taken with the exposure time, kV, and mA set in this window.  To estimate the length of time it takes for each image at specific settings, multiply the exposure time by the number of stacked images.

Figure 14- XMSL Measurement Editor Window

Starting Measurements

Prior to imaging cores, especially at the start of an expedition, the user must:

1. Perform a detector calibration.  (Detector Calibration Section)
2. Test the exposure parameters in the imaging utility (Imaging Utility Section)
3. Set the exposure parameters in the Measurement Editor (XMSL DAQ Parameters section)
4. Adjust the automatic image processing settings. (Image Processing Section)

Note: Recalibrate the detector if the detector grid pattern becomes visible in the images.

Once these steps are complete, the user may begin imagin.

Sample Information Window

Click START on the IMS panel (Figure 10) to open the sample information window (Figures 15). This is where the user enters the sample ID for a section and initiates the measurement. There are three tabs available on the sample information screen.  Each provides a different method for entering the sample ID information.

Sample Entry Tabs

• Scanner: Scan the IODP barcode to enter the sample’s Text ID and Label ID values.
• LIMS: Select expedition, site, hole, core, and section values from a series of list boxes that are populated with data from the LIMS database.
• Manual: Manually enter the sample’s Text ID and Label ID values and a length. The name fields will accept any name, so the user must be careful to enter the name properly. If the name is incorrect a file will be created, but it may not upload properly. User the section ID for whole round images and the section half ID for section half images.

Figure 15- Sample Information Window- Scanner entry (left), LIMS entry (middle), and Manual Entry (right).

Taking X-radiographs

1. Select START on the IMS panel (Figure 11) to open the sample information window (Figure 15).
2. Enter the Sample ID Information

• Scanner mode: Place cursor in the scan box; scan the IODP barcode from the whole round or the section half label from the end cap.
• LIMS mode: Select a section using the hierarchy columns.
• Manual entry mode: Type in the sample label ID (i.e., 362-U1480A-1H-1-A) and LIMS Text ID (i.e., SHLF7851761) and length of section. Use the whole round id when imaging whole rounds.

- Any entry will be accepted, but that does not guarantee the data will upload. The Text ID information must match an actual section in order for the data to upload.
- Select USE ME to update the IDs and enable the MEASURE button.

3. Ensure the Core Status (left side of window) is set to match the type of core being imaged

1. 1. Full= Whole round
   2. Half= Section half

4. Ensure the section half is inside the load end door and that all doors are closed.

1. 1. The green and yellow light on top of the lead box should be illuminated

5. Select MEASURE

1. 1. The motion control pusher will move until the section breaks the top of core switch beam.
   2. The x-ray source will ramp up and a window with the x-ray source status will appear (Figure 16). Once the mA and kV are stable, the window will close and image acquisition will begin.  The user may abort at any time by clicking the Abort button.
      1. Once the top of core is located, the pusher will automatically move the section to the proper location over the detector and begin imaging.  The user interface will have a display as shown in Figure 17.
      2. The system will automatically take images along the section until the actuator reaches its limit switch, at which time it will return to the home position and the source will ramp down.

Figure 16- X-ray Status Window (left). As the source ramps up, the measured values will update.  X-ray system not ready window (right).  If the source is not ready to ramp up this window will be displayed. Normally, this indicates that a door is open. If the doors are not open, look at the values in the status displays and refer to the vendor’s manual to determine the issue.  As soon as the issue is cleared, this window will close and the x-ray start process will resume.

Figure 17- IMS Display During Imaging.  Main features of this window include: Abort button, raw image display, imaging parameters display, X-ray source temperature graph, histogram of pixel value and displays of the pixel values along the length and width of the image.

6. The Sample ID information window will reappear on the screen (Figure 18).

1. 1. Place the Pusher section onto the track.
      1.  The pusher should be an empty liner with tape along the top and bottom edges, not the water core from the WRMSL track. 
      2. Close the load end door.
      3. Select Pusher end sequence in the Sample ID window.  The source will ramp back up and the motion control system will continue to push the section through the x-ray system.

Figure 18- Sample Information Window- Pusher End Sequence View

When the imaging is complete, IMS will automatically process the raw images and output them to the AUX_DATA folder.  These are not the primary processed images, but are available for quick image evaluation.  For more information on IMS image processing, see the Automatic Image Processing section.

X-Rays OFF

Figure 19 will be displayed when the X-ray Off command is sent to the CP120.  The window will be displayed until the kV has been confirmed to be at zero.

You will also see this window flash on during X-Ray START when the CP120 fails to respond to the start command.  The X-ray off will reset communications with the CP160 and bring it to a known state which will clear any communication issue.

Figure 19- X-ray Off Status Window

NOTE: During imaging, the user can use the software abort button to end the imaging process and ramp down the source.  The abort button is available when the x-ray source is ramping up and during the imaging process.

If the abort button is used, a dialog window will appear (Figure 20). Once pressed, imaging will end and the user will need to start imaging the section from the beginning.  Dialog window options are:

Return to Load Position: Actuator returns to the home position. User will need to manually remove core

Stop and Do Nothing:  Actuator will remain in place.  Use this option if the section had jammed in the XMSL or is there is a hardware issue.

Figure 20- Dialog when after user selects abort during imaging.  The x-ray source will automatically ramp down once abort is selected.  The section in the imager will need to be restarted from the beginning once abort is selected.

Detector Calibration

Detector calibration should be done at the beginning of the expedition and whenever the exposure settings are changed significantly (integration time especially).  If the detector grid becomes visible in any images, calibrate the detector and reimage the core.

To calibrate the detector select Instruments> Camera: FPD Calibration from the main IMS menu (Figure 11).  The flat panel detector (FPD) calibration utility window will open (Figure 21). The purpose of this utility is to collect images that will be used to perform offset and gain corrections for all images acquired with the FPD.  The calibration process requires two images: Dark (Offset) and White (Gain).

Figure 21- Detector Calibration user interface window.  From this utility a user may take necessary calibration images and test the corrections prior to applying them to images.

The offset and gain correction are applied to the raw image according to this formula:

Calibrating the Detector

Dark Image Calibration

The DARK image is normally made with the x-rays off to capture the electrical background noise of the detector.  Material used in the detector’s construction causes a grid to imprint on the images (Figure 22); therefore, it is necessary to take the dark image with the x-rays on at minimal level to capture the imprint.

Figure 22 Example of detector grid appearing in image.  If this is noted in an image, immediately stop imaging and recalibrate the detector.

To capture the DARK image:

1.  Select the tab labeled DARK-1 (Figure 21).
   1. The default exposure values are automatically displayed and are the recommend values, but you may set other values. Be aware that the dark saturation (image intensity saturation) must be 7% or lower and you need to capture at least 100 images for stacking. 
   2. Default values are Image stack: 100, kV: 80, mA: 0.7, Integration Time: 1 ms
2. Click the Take DARK Image button.
   1. The X-Ray Image Acquisition window will open (Figure 23).  During acquisition, the image window appears black but you will see values in the histogram and in the image line profile.

Once acquisition is completed, you will be return the FPD Calibration Utility window.

3. Check the saturation value and confirm that is less than 7% (Figure 21). If not, adjust the exposure values and repeat.

The Dark Max value is used during normal acquisition to warn the user that additional exposure is needed.  Ignoring this warning means that image acquired will have some data clipped at zero.

Figure 23-Dark Image Acquisition Window

White Image Calibration

The WHITE image is used for the gain correction after the offset correction with the dark image is completed. 

To capture the WHITE image:

1. Select the tab labeled WHITE-2 (Figure 24). 
   1. The default exposure values are automatically displayed and are the recommend values, but you may set other values. Just be aware that the maximum intensity cannot exceed 99%. 
   2. Default values are Image stack: 20,  kV: 112, mA: 1.0, Integration Time: 120 ms
2. Click the Take WHITE Image button.
   1. The X-Ray Image Acquisition window will open (Figure 25).
   2. During acquisition, the image window appears white shading to darker grey on the left and right edges.

Once acquisition is completed, you will be return to the FPD Calibration Utility window.

3. Check the saturation value and confirm that it is in the target range of 94-98%. If not, adjust the exposure values and repeat (Figure 24).

Figure 24- White Image tab in the detector calibration window

Figure 25- White Image Acquisition Window

Validating the Calibration

To confirm that the offset and gain calibration have been done correctly, follow this procedure.  Note that this is an optional step, but is a good practice to ensure quality x-radiographs will be produced when imaging core.

1. Select tab TEST-3 (Figure 26)

2. Place a core over the detector and take an image.

a. Adjust the exposure for the material being imaged

3. Once the exposure is completed, you’ll be returned to the FPD Calibration Utility window (Figure 26).

4. Select tab CORRECTED-4 (Figure 27). 

a. The image shown is the raw image with the gain and offset correction applied. 

b. The background on either side of the core should appear as a flat white area. 

c. The shading seen in the WHITE image should be nearly gone.

5. Select the DIFF-5 tab to view the DIFFERENCE image (Figure 28)

a. This image includes the image mask

b. Everything in the image should be black, except the core

c. If the core itself is covered by the mask, then there is an issue with the calibration

6. Select the PROCESSED-6 tab to review the automatically processed image (Figure 29).

a. Evaluate the images.  Do they appear flat grey? Are the images highly eroded?

b, If there is an issue with the processed image, return to the Image Processing utility and adjust the processing parameters.  Then return to the Calibration Utility.

7.  If the Calibration is determined to be acceptable, select Save Calibration Images

Figure 26- Test Image Tab after selecting take test image

Figure 27- Corrected Image Tab

Figure 28- Difference Image Tab

Figure 29- Processed Image Tab

Saving the Calibration Images

When you have completed acquiring both images and validating the calibration, click Save Calibration Images. These images will be automatically applied to the images. Or select Cancel and revert to the previous calibration images.   The filenames of the DARK and WHITE image files are stored in the I_PI_GOSCAN.ini configuration file.  When the IMS program is initiated, these images are opened and the data is extracted.  If these files are missing you will be notified and will have to complete the calibration process before any images can be acquired.

Other Utility Features

• Saving individual images:  Images shown in the tabs can be saved as TIF image files by selecting Save Image.  A file dialog box will open and the user is promted to select the location and name of the file.  This does not update the calibration information.
• Source temperature: A graphical temperature display is provided to monitor the temperature of the X-rays source. 

Comments

• During and after acquisition of a new DARK image, the DARK image display will be black. But when the utility first opens and displays the previous image, it appears brighter.  We have confirmed that the data in the image has not been altered from its initial acquisition and have no explanation as to why the display has been lightened.
• Never alter the DARK and WHITE image with other programs.
• The grid pattern is not fully eliminated from the image but is suppressed by the DARK image subtraction.  Under certain conditions and processing parameters it may still be detected in the images.

Image Utility

The image utility can be found under Instruments > Camera: Image Utility (Figure 11).  This utility is useful for determining the proper voltage, current, and integration (exposure) time for imaging cores.  User can also review the processed images in this utility.

1. Adjust the integration time, number of images to stack, kV, and mA on the right side of the window (Figure 30).
   1. REMEMBER: Lower voltage with a longer exposure time may increase image contrast.  High voltage does not equal better images.
2. Select Take TEST Image
3. Wait for the x-ray source to ramp up and collect x-radiographs
4. Review the test images
5.  Repeat process until image is acceptable
6. Note the settings.  For these settings to be used, the user needs enter them under DAQ > Measurement Editor
7. Select Close to return to the main IMS window.

Figure 30- General Image Utility User Interface Window.  This utility is used test exposure settings before imaging a section.  The histogram (upper left) will be displayed when the ROI box tool is used and the line profile (lower left) is displayed when the ROI line tool is used.

Image Processing

The raw .tif IMS images are automatically saved during image collection.  IODP provides two methods for processing the raw images.

1. Automatic Image Processing: A program written in LabVIEW.  Processing is automatically completed by the software after images are collected.  User is able to make adjustments using the Image Process Utility under the Instruments menu.  The processed image is given a scale bar with the correct offset and the core identification information is overlaid at the top of each image.
2. Manual Image Processing: A program written in “GO”.  User must initiate and control the image processing settings.  Scale bar provided is 1 cm black and white lines along the left side of the image.  A stitching guide is also provided on the processed image.

Image Processing Utility (Automatic Image Processing)

This utility has the following purpose:

1. It allows the user to experiment with the processing parameters to determine the correct setting for the desired processed results.  The values can then be saved and use for all subsequent in-line image processing.
2. The utility can be used to mass reprocess images.

Select Instruments > Image Process Utility from the IMS panel menu (Figure 11). The user interface will open (Figure 31).

Figure 31- Image Processing User Interface Window. There screen is divided into 4 main sections. The user may test image processing settings and apply them to any previously collected images or subsequent images. 

Note this is the display after an image has been selected.  If no raw image has been selected or acquired, this window will by blank.

User Interface Layout

The user interface window is divided into four areas.

1. On the left is a window that will contain the raw source image for the process testing.  This can be load from an existing raw image (click Open Raw Image) or a new acquired image using the x-ray source (click Acquire Image).  The raw image used should be an image taken with the planned exposure parameters.  (Figure 31)
2. On the right-hand side is a tab control that will display either the masked image or the final processed image. 
   1. All three image displays will allow you to draw a profile line across the image using the ROI image tools. (Figure 32 and 33)
   2. Any line drawn on one image display will be shown on the others but the content of line profile will only be from the image where the line was drawn.
   3. In the center top of the user interface window is a tab control which allows the user to view the line profile, histogram of the difference image, or the expanded histogram of the processed image.
   4. In the bottom center of the user interface window are the controls for image processing. The software provides for two process variable groups.  The APC parameters are applied to core types “H” and “F” and ROTARY is applied to all other core types.  The Light%, Dark%, Anchor Type and Anchor At controls apply to the histogram expansion and will apply to the images immediately as their values are changed.  The other control values apply to the smoothing process and require that you click either Process APC or Process ROTARY buttons to apply the changes to the processed image displayed.  You’ll to set process variables for both types when drilling an APC/XCB hole. How the process parameters work will be discussed later in this document.

If you wish to safe a copy of either source or processed image, there is a Save Image button just above the display you can click.

Once you are satisfied with the processing outcome, you may apply these to an existing set of raw images by clicking Mass Reprocess Files.  A file dialog box will open where you will select a folder that contains images.  All images found in the folder will be processed.  The reprocessed files will be saved to C:\Reprocessed_timestamp.  You will be given the option of retaining the original file timestamp or a current timestamp in the file names.  If you plan to replace existing processed files in LIMS, then you should use the original timestamp.  Use the current timestamp to create duplicates.

If you want save the process parameters and use them on newly acquired images, click Save Process Values; otherwise click Cancel Changes to revert to the existing values.

Figure 31 Image Processing Utility User interface.  The user may test image processing settings and apply them to any previously collected images or subsequent images.  Note this is the display after an image has been selected.  If no raw image has been selected or acquired, this window will by blank.

Figure 32- ROI tool available in the image processing utility.  The histogram or line profile will be displayed when the ROI tool is used.  A line will produced a line profile.  A box will produce a histogram.

Figure 33- Example of ROI tool used on a raw image and the resulting intensity profile.

Getting An Image

Before you can begin experimenting with the settings, you need to open an existing image or acquire a new image. If you are opening an existing image make sure that it is a “raw” image.  If you are acquiring an image make sure that the FPD calibration has been done and the exposure parameters set appropriately.  Click either the Open Raw Image or the Acquire Image button.

Processing Parameters

The processing parameters can be set in any order after completing the “Getting An Image” steps. But the Mask Threshold value must be valid; otherwise subsequent processing steps may fail or produce undesirable results. Also, keep in mind not all combinations of parameters will work.

MASK threshold. 

The image mask is used to isolate the core image from the empty detector’s background, which normally is made up of overexposed pixels that we do not want to process (Figure 34).   The mask is very dependent on the exposure settings, so any time the exposure values (kV, mA or integration time) change, the Mask Threshold value needs to be reviewed.

We create an image mask by setting pixel intensity to zero where their values lie in the upper range based on a user selected percentage. The formula is as follows:

Where MaxPX and MinPx determined from the entire image ignoring values equal to 65534 (oversaturated pixels) and n is the user set percentage.

Figure 34- Example image before the mask is applied (left) and after (right)

Image ROI

Using the mask, we locate the right, left, top and bottom edges of the core in the image (Figure 35).  Using these values we center the core left-to-right and crop the bottom and top as necessary. This is repeated for the original mask, as well.

Figure 35- Selecting the region of interest to exclude the blank detector

Image Smoothing: Flattening                                    

The best way to understand the image smoothing process is to look at the pixel intensity profile across the core (Figure 36). The black line is the profile of the original image. The variation due to the core thickness is greater than the variation due to internal sedimentary structure/particles.  The red line is the same profile after smoothing.

Figure 36- Pixel intensity profile across the core (black line).  Note that the variation due to core thickness is larger than the variation due to sedimentary structure.  The red line is the smoothed profile.

Subtracting the smoothed intensities from the original intensities will produce a difference image that ranges across zero with the resulting profile shown in Figure 37, removing the effects of the core’s thickness on the image.

Figure 37- Difference Image profile

Next, the difference image is offset by subtracting its minimal value.  This step is necessary to insure that we are working with only positive values.  The above profile shifts as shown in Figure 38.

Figure 38- Difference Image profile offset to positive values.

The following is description of the image processing in detail:

1. The masked image is cast to a 2-dimensional array of floating-point values.
2. The array is indexed to process each column first, which is the parallel to the core’s Z-axis (along core).  Each column of pixels is processed by using the Savitzky-Golay FIR or Median smoothing filter.  Different methods may be used for the row (X) and column (Z) smoothing passes.

• Savitzky-Golay FIR smoothing:
  • o Side-point divider: The length of the row or column is divided by this value to determine the length of the side points used by the smoothing operation.  A large value means shorter side point length. Note, using values below 3 for the Z axis will significantly increase the processing time!
  • o Polynomial: Determines how close the smooth curve fits the original data.  For the X-axis this should be set high to conform to the whole or half-round attenuation pattern.  Low values will cause “ripples’ on the side edges.  For APC cores, the Z-axis value should be set near two. For rotary cores, the Z-axis value should be set closer to seven.  The value will depends on how disturbed the core is and experimentation is needed to get good results.
• Median Filter:  Rank is the length of values used in the filter operations.  Small rank values are more responsive to shape changes but will cause fine details to disappear.

3. The resulting array is then processed by row using the values set for the X-axis settings. This results in an array of “smoothed” values.

4. This array is then subtracted from the original and offset into positive values by subtracting the minimal value of the entire array.

5. The resulting 2D array is cast back to U16 image (Unsigned 16 bit format), referred to as the difference image.

Trim to Black

This effects how the smoothing operators (above) are applied. If this value is set false, then the above process is applied to the entire mask image including the mask. If it is set to true, then the mask is not processed.  This is important for rotary cores where the edges are irregular and core gaps are common. 

Image Contrast Expansion:

• The difference image is unusable as the final processed image. The contrast range is very small, its histogram is narrow and the image is nearly uniform gray (Figure 39). To create a usable image, the contrast must be expanded.
• U16 images have an intensity range of 0 to 65354 and we will expand the contrast into a 5000 to 60354 intensity interval. 
• All of the information is contained in a narrow band of intensities.  To locate this band, we need to determine 3 points in the histogram:  the first two points are the indices the histogram values exceed a user specified percentage of the maximum intensity.  These indices are found by searching from the dark side of the histogram (blue cursor) and then the light side (red cursor). The user sets these values using the Dark% and Light % controls (Figure 31).
• The third point is either the index of the histogram maximum or the index of the mid-point between the dark and light indices as selected by the user using the Anchor Type control.
• The user then selects the new intensity value to anchor 3^rd point too in the histogram using the Anchor At. The dark side intensities are expanded from this value to 5000 and light side expanded up to the 60353 values.
• Intensity values below and above the threshold percentage will be compressed into the 0-5000 and 60354-65354 ranges respectively.

Figure 39- Image Contrast Expansion example.  The top image is the difference image prior to the expansion.  Note the overall grey raw image.  In the lower image, the contrast range has been expanded.  The sedimentary structures are now visible within the image.

With the expanded histogram the same cross-core profile shown in Figure 38 will now look like Figure 40. Example images of the processing steps are shown in Figure 41.

 Figure 40- Cross core profile after expanding the histogram

Figure 41- Original image (left), difference image (raw-smooth) (middle), and the difference (flattened) (right) image with the expanded histogram.

Final Touches

Before saving the image, a scale is generated based on the image center offset and a scaling factor of 109.6 pixels/cm is added to the left-hand side of the image.  A header is then added to the top of the image with the label id, text id and the exposure parameters (kV, mA, integration time and number of images stacked) (Figure 42).  Processed images are saved to the C:/AUX_DATA folder on the host computer.

Figure 42- Final processed image with header and scale

Considerations:

This process does not require geometry of the system but is based solely on the content of the image to produce a processed image.  This technique is very good at showing fine scale changes in the image.  That means it very good at showing noise and the irregular surface of rotary cores! To produce a good image you need to consider the following:

Image Stacking:  You must take a sufficient number of images to suppress the random noise that is common to X-ray images.  It is recommended that you stack at least 20 image.

Offset and Gain Calibration:  Seeing a grid pattern or fine streaks in the image?  This indicates that the gain and offset calibration was not done or done incorrectly.  Remember that the dark image is not truly “dark” but “dark grey”.  Use minimal exposure to capture the grid pattern and the thermal noise of the detector.  Also, make sure that the “white” image is not oversaturated.

Exposure Setting:  As lithology changes, you will need to properly adjust the kV, mA of the source and the integration time of the detector.  As this is a new system, we have no hard guidelines yet, so it is necessary to experiment with different setting using the Image General Utility.  Your goals are to capture an image where: 1)the minimal intensity value is greater than 5,000 and 2)there is enough contrast between the core edge and the empty detector so that the masking process can identify the core boundaries in the image. The core liner should nearly disappear in the raw image without eroding the edges of the core.

Rotary Cores:  XCB and rotary cores are often damaged by the coring process.  The rough surfaces will be seen in the images and will often obscure sedimentary structures.  There is also cuttings and other muck between the core and liner that will degrade the image.  Imaging the section-half instead of the whole-round sections may improve the image.  Also, keep in mind that the values used in the processing are selected to produce the best APC core images where the core material fills the entire liner.  Rubble and pieces will often show halos (areas of dark) around the edges.

Greyscale Changes:  Each image is processed alone based on its content and this will result in greyscale shifts between images.  This will be noticed if you attempt to splice the images together.

Scale:  The scale in the final image is only as accurate as the information used to create it.

1. The axis of the source’s x-ray beam must centered on the detector and perpendicular to its surface.
2. The pixel to centimeter scaling factor must be determined.  As of X379 this value was determined to be 109.6px/cm when measured at the half-core height. A grid standard is available for use to repeat the measurement
3. In IMS, you must set the instrument offset to the center row of pixels of the detector.

Manual Image Processing

The raw .tif IMS images are automatically saved during image collection.  IODP provides two methods for processing the raw images.

1. Manual Image Processing: A program written in “GO”.  User must initiate and control the image processing settings.  Scale bar provided is 1 cm black and white lines along the left side of the image.  A stitching guide is also provided on the processed image.
2. Automatic Image Processing: A program written in LabVIEW.  Processing is automatically completed by the software after images are collected.  User is able to make adjustments using the Image Process Utility under the Instruments menu.  The processed image is given a scale bar with the correct offset and the core identification information is overlaid at the top of each image.

Manual Image Processing

The IODP processing algorithm is available in a Linux and PC version and can easily be placed on any work station.   This program allows the user to adjust the contrast and change settings related to instrument setup and geometry.  The processing software files (Figure 11) must be placed in a directory above the location of the images to ensure file navigation will work.

These instructions will work for Sherlock (vendor proprietary software for collecting images) or IMS collected .tif images as long as the program is properly configured.  If you are switching between software packages, beware!  The raw images are not identical and settings must be adjusted.  For a more in depth explanation of the math behind this program, follow the Math Documentation link once the program is open in a web browser.  For ease of processing, it is best to have the raw files sorted into the groups that you wish to process together (whole core, single section, etc).

Prior to processing, ensure that the xrayImgProcessing_1.0.1 executable, the static folder, and the setup.cfg are in a folder one level above the location of the images to be processed (Figure 43).  It is recommended that the processing software be placed in the Data folder, (C:\Data). The images will be saved to the C:\Data\In folder.

Figure 43- X-ray image processing software files needed for image processing

Process a raw image

1. Open xrayImgProcessing_windows_1.0.1.exe on a PC (or Linux version on a MAC)
   1. This will trigger a command window to open (Figure 44).  This command window will display the program status as images are processed. Refer to this screen to review what the processing software is doing or to check for any errors.

Figure 44- IODP processing X-ray Imager software command window

2. Open an internet browser window and enter/copy the local host address, http://localhost:8080/, from the X-ray imager command window

a. The X-ray image processing window should open (Figure 45).

Figure 45- IODP X-ray imager processing window

3. Select the Processing Settings link under the Navigation heading.  This step is only necessary when first configuring the program or when changing file types.

a. The settings window will open (Figure 46).

Figure 46- Processing Settings Window

4. Set Instrument Geometry values (Figure 46):

a. Source height: 65 cm, value will only change if source height is changed physically

b. Core height above detector: 0.4 cm, value will only change if detector position is changed physically

c. Motion of core between images: 12 cm, value will only change if software is manually changed

5. Set Detector Settings (Figure 46):

a. If processing IMS raw images:

i. Pixel Height of detector:  1549

ii. Number of bits used to store raw data: 16

b. If processing Sherlock raw images:

  i. Pixel Height of detector:  1550

  ii.  Number of bits used to store raw data: 14

c. For IMS and Sherlock raw images:

i. Pixel Width of Detector:1032, value will change if a different detector is installed

ii. Size of each pixel: 0.0099, value will change if a different detector is installed

6. Set Histogram and Core Axis settings (Optional!)

a. See Figure 47 for default values

b. User can adjust these values, but these settings should not need to be altered in normal operation.

Figure 47- Histogram and Core Axis settings default values

7. Adjust Thickness Compensation settings and scale bar settings (Optional!)

a. See Figure 48 for default values

b. Thickness compensation:

i. Minimum Core Thickness Used for Compensation: Set at 0.5 as default. Adjust these values to change how the software corrects for core thickness.  XCB and RCB cores are narrower and may require different compensation values than APC and HLAPC cores.  Larger values exclude more of the image from the correction (Figure 48).

                       ii. Maximum Core Thickness Used to Define the Edges: Adjust this value to change the thickness of the black bars indicating the edges of core diameter.  Set to zero to remove these lines from the processed images.

c. Scale Bar Settings: Adjust these settings to change how the scale bar is projected on the processed image.

Figure 48- Thickness Compensation and Scale Bar Settings Default values

Figure 49- Minimum Core Thickness Compensation Example images.  The compensation values for these images are 0.5 cm (left) and 5 cm (right).  Notice the narrowed corrected image on the right.

8. Scroll to the bottom of the page and select SAVE under the update settings header (Figure 48).

9.  Return to the top of the page and select the Main Page link.  This will return you to the main image processing window (Figure 46).

10. Under the File Explorer heading, navigate to the location of your files (Figure 45).

a. The initial address displayed will be the location of the executable file used to open the command window. Ie if you place the xrayImgProcessing_windows_1.0.1.exe and associated files (Figure 43) in C:\Data, you will only be able to navigate to files that are also stored in the Data folder.

b. Use single clicks when selecting a folder

c. Use the arrow at the left side of the screen next to the address to go back a folder.

11. Select the raw .tif files you wish to process

a. Use the Select All check box if you wish to process everything within the folder

12. Select Get Histogram below the Image Histogram header (Figure 50).

a. See Troubleshooting section of manual if the histogram appears abnormal (small, bars far apart, etc.)

13. Use the sliders below the histogram to adjust how the image will be processed.

a. The left edge slider will make the image darker the further you go to the right.  Place this near or at the left edge of the histogram

b. Place the Peak Position slider under the main peak of the histogram.

c. The right edge slider does not need to be adjusted, but it may help image quality

d. This process may need to be done multiple times to find the best settings.

Figure 50- Image Histogram from x-ray image processing software

14. Adjust the settings under the Process Images header to match with the image setup (Figure 51).

a. Core Dimensions: Select if the images are for a section half or whole round core

b. Diameter of the Core: This setting determines how wide of an area of the image is used in the corrections.  If this is too wide (includes blank detector) or too narrow (excludes parts of core) the corrections will not work appropriately.

i. Set to 7.0 cm for APC cores that fill the liner

ii. Use values as close to the core diameter as possible, this may take some experimenting.

iii. If wide core (7.0 cm) and narrow core (4.0 cm) are in the same image, the processing will need to be done twice, possibly with the images separated into narrow vs wide batches (Figure 52).

c. Axis Determination: Used to correct for core not being centered over the detector or not being parallel with the sides of the detector when imaged.

i. Use the default Auto Detect Core Axis in most cases

ii. If Auto Detect does not produce satisfactory images, use the Set Core Axis option and experiment with settings.

    Figure 51- X-ray image processing screen.  Adjust the core settings and folder name before processing images

Figure 52- Core diameter adjustment example images. This section of core contained full liner with narrowed sediments in between. The left and middle image were processed with the entire section, whereas the image on the right was processed individually. The diameter of the core is set at 7.0 cm in the left image and is set to 6.0 cm in the middle image and right image. Note that in the individually processed image, some smaller clasts are visible.

15. Under the File Name header:

a. Input the Name of the output folder.  Recommended name is processed_core# core type-section #, ie processed 2H 2

i. The folder will be placed in the same location as the raw files

b. Optional: Enter a string to append to the end of each processed file

16. Select Process Files under the Process header. 

17. Navigate to the location of the processed files and review the images.

a. If the images are not satisfactory, return to the histogram and make adjustments. Simply select Process Files and the original processed files will be overwritten in the folder.

Troubleshooting:

1. Image edges are dark after manual processing (Figure 53): The value entered for core diameter is too narrow.  Increase the core diameter value and reprocess the images.

Figure 53- Example of manual processing when the core diameter is set too narrow.

2. No images appear after selecting Process Images: The bit size or pixel length are not set correctly.  Check the command window for error messages and check the settings in the processing settings window.

File Formats and File Uploading

IMS automatically outputs the raw and processed images.  Both file types are .tif images.

Raw file name: 379-U1533A-1H-1_0-140_SECT9762671_20190225104523_k110_a1_t3_n20_RAW.tif

Raw file location (section halves): C:\Data\In\SHLF\Site\Hole\Core\Section

Raw file location (whole rounds): C:\Data\In\SECT\Site\Hole\Core\Section

Processed file name:

379-U1533A-1H-1_0-140_SECT9762671_20190225104523_k110_a1_t3_n20_RAW_processed.tif

Processed file location (section halves): C:\Aux_Data\Flat Images\SHLF\Site\Hole\Core\Section

Processed file location (whole rounds): C:\Aux_Data\Flat Images\SECT\Site\Hole\Core\Section

Calibration Images (Dark and Light): C:\IMS-10\CONFIG_XMSL\XIMG CALB

DARK and WHITE image files are stored in the I_PI_GOSCAN.ini configuration file.

A unique time stamp is appended to each image.

Motion Control Setup:

Motion control should be set during initial setup and further changes should not be necessary. Motion control setup can be accessed by selecting Motion > Setup from the IMS panel menu (Figure 11). The M-Drive Motion Setup control panel will open (Figure 54).

The user may select between four setup panels from this window.

• Motor and Track Options
• Fixed Positions
• Limit and Home Switches
• Motion Profiles

Figure 54 - M-Drive Motion Setup

Motor and Track Options menu

Once these values have been properly set, they should not change. This panel is only for initial setup.

Make sure to use the values shown for the XMSL (Figure 55).

The relationship between motor revolutions and linear motion of the track is defined in this window and is critical to both safe and accurate operation. User should be familiar with the M-Drive motor system prior to adjusting these settings.

• Select Axis: In the case of the XMSL it is always X.
• Encoder Pulses/rev: Defined by the manufacturer of the M-Drive as 2048.
• Screw Pitch: Set to 2.0 (the ratio of 2048 steps per revolution and chain displacement (cm) as a function of the drive gears diameter).
• Gear Ratio: Set to 4.0.
• Direction: Counter clockwise rotation moves the tray in a positive direction (from home to end of track).
• Click the Motion Utility button to open the Motion Utility window (Figure 56) and test the settings. Click Close to exit this window.

Click Accept to save the values or Cancel to return to previous values.

Figure 55 - XMSL Motor and Track Options Setup Window

Figure 56- Motion Utility Window

Fixed Positions menu

Once these values have been properly set, they should not change. This panel is only for initial setup.

In this window the user may define fixed track locations used by IMS motion control. For the XMSL, make sure to use these value unless there has been a physical change to the system (Figure 57).

• Select Axis: In the case of the XMSL it is always X.
• Max Section Length: Maximum length of section that can be placed in the track. This value is set to 160 cm.
• Track Length: Distance in cm between the limit switches. Use the Motion Utility (Figure) to determine this value by moving from limit switch to limit switch.  Currently the value is set at 200 cm.
• Load and Unload: For the XMSL set to 0. This will always bring the tray back to the sample load end after a measurement sequence.
• Top-of-Section Switch?: ON
• Top-of-Section Switch Offset: 158.85
• Push Past: 5.
• Fast Past: 5
• Run Out Switch?: ON.
• Click the Motion Utiilty button to open the Motion Utility window (Figure 57) and test the settings.
• Click Close to exit this window.
• Click Accept to save the settings. Click Cancel to return to previous values.

Note, these values along with the detector position set in the Camera: General Setup under instruments must be accurate for proper motion control. Take care in setting these values.

Figure 57 - XMSL Fixed Positions Window

Limit and Home Switches Window

Once these values have been properly set, they should not change. This panel is only for initial setup.

• This panel is used to define the orientation of the track system, limit switches, and the home switch (Figure 58). The MDrive can be used with either a dedicated Home switch or a limit switch as a home switch. In the case of the XMSL track we use a home switch.
• Select Axis: In the case of the XMSL it is always X.
• Select Track and Home Geometry: For the XMSL, select CW look @ CCW Edge
• Click the Motion Utility button to test the settings.
• Click Accept to save the settings. Click Cancel to return to previous values.

Figure 58- XMSL Limit and Home Switches Window

Motion Profiles

The motion profiles window can be used to adjust the speed and acceleration profiles used by the track (Figure 59) for various types of movements.

Setting the correct values for the motion profile takes a little experimentation to make the track run efficiently and safely. It is not usually necessary to adjust these values.

• DAQ Move: This profile controls moves between measurement positions. 
• Limit Seek: This profile finds the limit switch location. Do not exceed 3 cm/sec. Do not use a large acceleration value, but always use a large deceleration value.
• Home Final: This profile finds the final location of the home switch. Do not exceed 3 cm/sec. Do not use a large acceleration value, but always use a large deceleration value.
• Load/Unload: This profile is used for moving the actuator for general movements and moving out of the XMSL to the final position prior to ending a measurement.
• Push-Slow: This profile is used to move to the degauss start position
• Push-Fast: This profile is used to move the section/discrete samples from degauss stage position through the in line AF degauss coils for X, Y, and Z.
• User Defined: This profile is used for testing only in the Motion Utilities (Figure 56) program.

Click the Motion Utility button to open the Motion Utility (Figure 56) window and test the settings.

Click Accept to save the settings. Click Cancel to return to previous values.

Figure 59 - Motion Profiles Window

GOSCAN Hardware Setup for IMS

To use the GOSCAN Flat Panel Detector with IMS it is necessary to make the following hardware configuration in the Window’s Device Manger and in NIMAX.

Device Manager

1. Login as administrator
2. In the window, select the Intel 1350 Gigabit Network Connection (that is the NIC that the GOSCAN is connected to) (Figure 60).
3. Right click and select properties.
4. Click advance tab
5. Select Jumbo Packet and set value to 9014 Bytes.
6. Click OK

Figure 60- Device Manager window and jumbo packet setup

NI MAX Configuration:

1. Open NIMAX

2. Select Device and Interfaces>Network Devices> Teledyne DALSA GoScan 1510HR (Figure 61)

3. Select the Acquisition Attribute tab

4. Set the values as shown in Figure 62.

5. Make sure that Packet Size is 9004.  Should be able to set this value 9014 (Jumbo Packet Size).  From experience, this would cause instability in the acquisition.

6. Click Save.

Figure 61- NIMAX device manager

Figure 62- Acquisition Attributes window.  Set the packet size to 9004.

Programmer’s Note: the value “1727014677” is the alias name used by the LabVIEW code:

NIMAX summary

Most values shown are the default values.  Those highlight are critical to the IMS acquisition.

MAX Configuration Report

3/19/2019 6:12:21 PM

System Settings

System Resources

Settings

Attribute Categories

Attribute Tables

Transferring Images to Data 1

Images are transferred to Data 1 via a script on the XMSL host PC.  The script copies the output from the XMSL to data1 automatically and is executed via a task scheduler every 30 minutes.

The script:

• Connects to Data:\Data1\7.3 Petrophysics_XRAY directory
• Mirrors the Data and AUX_DATA directories on the host PC (currently XMSL is PC53236) to a "Mirror" directory via an Xray eDirectory user-account

This is a "one-way" mirror operation. Whatever changes are made to DATA and Aux_DATA directories on the host PC will be mirrored in the location in data1.  To make the files permanent in the Data1 folder, copy the mirror contents to the base folder periodically.  To make the script more efficient it is also recommended to remove the already copied files from the Data and AUX_ Data folders so they are not copied multiple times.

The script will hang if a user logs into the file servers while the script runs.  No one should log in to the servers on this computer unless absolutely necessary.  Task scheduler will kill the task if the script attempts to run for more than an hour and half.

Trouble Shooting

Archive Versions

• X-Ray Image Logger UG - 25022020