1

CT, µCT and FIB-SEM / Re: Histogram of Grayscale Values for Material(s) Post Segmentation

« on: Today at 04:12:00 PM »

Hello Jack,

If I understand correctly, you're currently using the Spatial Intensity Histogram within Compute Metrics. Unfortunately, this function does not meet your requirements, as it generates a histogram of all gray values combined and only displays the probability - separate histograms for each material cannot be obtained this way.

To generate the histogram you need, I recommend following the approach using Python scripting previously outlined by my colleague Janine:

Hello Jack,

there are many options to analyze volume fields with the Compute Metrics command, as described here: https://geodict-userguide.math2market.de/2025/geodict_computemetrics.html

For example, you can compute the mean value and standard deviation for a specific material with it. However, the option to compute the histogram for only one material is not included yet.

But if needed, you can use Python to create your own custom histogram GeoApp.

For example, you get a 3D numpy array of your structure using the command gd.getStructure() as described here:
https://geodict-userguide.math2market.de/2025/automation_api_structure.html?anchor=getstructure

and for your volume field using gd.getVolumefield(volume field index), as described here:
https://geodict-userguide.math2market.de/2025/automation_api-results.html?anchor=getvolumefield

Then, you can for example use numpy methods to get a histogram for only one material ID.
https://numpy.org/doc/stable/index.html

Best regards,
Janine

Best regards,
Jonas

2

Air- and Liquid Filtration / MOVED: Add Description to Resultfile with python macro

« on: Today at 01:09:57 PM »

This topic has been moved to Automation.

https://forum.math2market.de/index.php?topic=124.0

3

CT, µCT and FIB-SEM / Re: Histogram of Grayscale Values for Material(s) Post Segmentation

« on: May 06, 2025, 04:21:12 PM »

Hello Jack,

from your description, it sounds like you're currently viewing the segmented structure with three materials, rather than the original gray value volume field.

Let me walk you through the full workflow I use, which might help clarify things:

1. Import the dataset via ImportGeo-Vol. Enter all necessary parameters (like voxel size), then click on Image Processing.

2. This opens the 3D Image Processing dialog, where you can process the images (e.g., crop, rotate, or filter), and then segment them into different materials. At this point, the gray value data is also loaded into the main GeoDict window as a Volume Field.
[attachimg=1]

3. Segment the structure using tools like Global Thresholding or AI Segmentation. After clicking Create Segmentation, the segmented structure is loaded into GeoDict and visible alongside the gray value volume field.
[attachimg=2]

4. With both the segmented structure and gray value data loaded, you can now compute gray value statistics for each material using Compute Metrics. To do this, right-click the Gray Value volume field in the Project Status section and select Compute Metrics.
[attachimg=3]

5. In the dialog, ensure the Gray Value field is selected. Choose which metrics to compute (e.g., Minimum, Maximum, Mean Value, Standard Deviation and Variance), then under Values for, select Chosen Material IDs and specify the material of interest. Click Run to generate the statistics for the gray values of belonging to this material only.
[attachimg=4]
 
Let me know if anything remains unclear or if you need help with a specific step.

Best regards,
Jonas

4

CT, µCT and FIB-SEM / Re: Histogram of Grayscale Values for Material(s) Post Segmentation

« on: April 28, 2025, 10:33:14 AM »

Hello Jack,

thank you for the clarification. Could you please specify how exactly you created the Gray Values volume field?
From what you describe, it seems that your volume field might be empty and does not actually contain any values.

The easiest way to obtain the Gray Values volume field is by importing your dataset using ImportGeo-Vol.
This automatically loads the dataset into the import dialog and, at the same time, into the main GeoDict GUI as a volume field containing the gray values for each voxel.

Let me know if this helps or if you run into any issues!

Best regards,
Jonas

5

CT, µCT and FIB-SEM / Re: Histogram of Grayscale Values for Material(s) Post Segmentation

« on: April 25, 2025, 01:38:24 PM »

Hi Jack,

Thanks for your message - great to hear the previous response was helpful!

Regarding the issue you're seeing, could you specify your workflow and settings for using Compute Metrics on your gray-value dataset?

As an example, I applied Compute Metrics to one of the gray-value datasets that we deliver with GeoDict (Long Fiber Composite):

First, I loaded the dataset and segmented it into solid fibers and pore space using Global Thresholding with the Otsu method.
[attachimg=1]

Now with both the segmented structure and Gray Values volume field loaded, I selected Compute Metrics on this volume field.
[attachimg=2]

In the Compute Metrics dialog I chose to compute the Minimum, Maximum, Mean Value, Standard Deviation and Variance. I computed three cases:

• For All Materials
• For Chosen Material IDs -> 0 to get the metrics only for the pore space gray values
• For Chosen Material IDs -> 1 to get the metrics only for the fiber gray values

This gave me the following results:
[attachimg=3]

You can see the difference, e.g. between the mean gray values for pore space (16.776), fibers (82.6702), and the complete dataset (27.5684).

Please let me know if this explanation helped you or if you have any questions.

Best regards,
Jonas

6

Simulation & Prediction / Re: Boundary conditions in FlowDict

« on: January 17, 2025, 12:21:50 PM »

Hi Danny,

the Boundary Conditions in Flow Direction define how the flow enters and leaves your structure depending on the chosen flow directions.

The Periodic boundary condition repeats the structure periodically before the inflow and after the outflow plane. In the example shown below this option does not work since there is no connected flow path. This option works best for periodic structures and structures with high porosity. We recommend using periodic boundary condition when possible, as the computational memory requirements are comparatively low leading to shorter runtimes.
[attachimg=1]

The Symmetric boundary condition mirrors the structure at the inflow and outflow plane. This option works well for low porosity structures because the pores remain connected due to the mirroring.
[attachimg=2]

The Velocity inlet, Pressure outlet boundary conditions apply a constant flow velocity in the inlet and a constant pressure drop in the outlet.
[attachimg=3]

All the options described above do not change the thickness of your model. The option Add implicit region adds voxel before the inflow plane and after the outflow plane. This option changes the thickness of the structure and influences the final simulation result.
[attachimg=4]

I hope this clarifies your question.
Please let me know if anything is unclear or if you have any further questions.

Kind regards,
Jonas