Geometry debug function by viktormai · Pull Request #4012 · openmc-dev/openmc

viktormai · 2026-07-12T17:00:05Z

This PR adds a 3D geometry debugging utility to Model for identifying overlap and undefined regions within an OpenMC geometry by sampling a user-defined bounding box.

Main changes

Added Model.geometry_debug():

Samples a 3D region using a stack of 2D slices obtained through openmc.lib.slice_data.
Detects both overlap regions (using the overlap sentinel) and internal undefined regions, returning a summary containing the total number of overlap and undefined samples and example coordinates for each type of geometry issue.
Optionally prints a human-readable summary.

Added _classify_undefined_regions() helper:

Separates undefined pixels into boundary-connected ("outside") undefined regions and internal undefined regions enclosed within the geometry.
Uses a breadth-first search starting from the image boundary to identify boundary-connected undefined pixels.
Issues a warning when undefined regions exist but none are connected to the sampled slice boundary, indicating a potentially enclosed undefined region or insufficient sampling resolution.

This pair of functions provides a simple way to locate common geometry construction problems—particularly overlaps and enclosed undefined regions—by returning representative coordinates that users can inspect directly, rather than relying solely on transport failures or visual inspection. These sample points can also be leveraged by AI agents to easily fix geometry issues in the model. Reusable undefined-region classification logic that can be leveraged by future plotting and geometry diagnostics for plotting undefined regions is also established.

Checklist

I have performed a self-review of my own code
I have run clang-format (version 18) on any C++ source files (if applicable)
I have followed the style guidelines for Python source files (if applicable)
I have made corresponding changes to the documentation (if applicable)
I have added tests that prove my fix is effective or that my feature works (if applicable)

paulromano

Thanks for the initial shot at this! Here are my initial thoughts:

viktormai · 2026-07-22T15:10:29Z

Thanks for checking it out @paulromano. I have added some updates for the bounding box idea for both overlapping and undefined regions, including a warning if undefined regions are under-resolved. Let me know what you think.

paulromano

Thanks for the updates @viktormai! Here is another round of comments:

paulromano

Thanks for the updates @viktormai! This is getting closer. Now that it is looking better, you should also add some unit tests for the capability to ensure it works properly.

paulromano · 2026-08-13T20:51:12Z

+ result : dict
+ Dictionary summarizing the sampled geometry.


This doesn't really tell the user how to interpret the dict that's returned. There should be a description of the (key, value) pairs in the dictionary.

paulromano · 2026-08-13T20:54:33Z

+ xc = x0 + (pix[:, 1] + 0.5) * (x1 - x0) / nx
+ yc = y1 - (pix[:, 0] + 0.5) * (y1 - y0) / ny


This looks like it just uses the pixel centers. I think it would be more conservative to use the bounds of the pixel itself rather than just its center (if I'm interpreting it correctly, this is already how it works for the undefined pixels?).

paulromano · 2026-08-13T20:55:43Z

+ for box in overlap_boxes + undefined_boxes:
+ bbox = box["bbox"]
+ bbox.lower_left = np.round(bbox.lower_left, 4)
+ bbox.upper_right = np.round(bbox.upper_right, 4)


While it's OK to round numbers in the output if print_summary=True (looks like that's already the case), I wouldn't modify the data that is actually returned in the dictionary

paulromano · 2026-08-13T20:56:18Z

+ "n_overlaps": len(overlap_boxes),
+ "n_undefined_regions": len(undefined_boxes),


These are easily inspectable from the data itself and can be removed IMO

… into geometry-debug-function

viktormai · 2026-07-12T17:00:05Z

This PR adds a 3D geometry debugging utility to Model for identifying overlap and undefined regions within an OpenMC geometry by sampling a user-defined bounding box.

Main changes

Added Model.geometry_debug():

Samples a 3D region using a stack of 2D slices obtained through openmc.lib.slice_data.
Detects both overlap regions (using the overlap sentinel) and internal undefined regions, returning a summary containing the total number of overlap and undefined samples and example coordinates for each type of geometry issue.
Optionally prints a human-readable summary.

Added _classify_undefined_regions() helper:

Separates undefined pixels into boundary-connected ("outside") undefined regions and internal undefined regions enclosed within the geometry.
Uses a breadth-first search starting from the image boundary to identify boundary-connected undefined pixels.
Issues a warning when undefined regions exist but none are connected to the sampled slice boundary, indicating a potentially enclosed undefined region or insufficient sampling resolution.

This pair of functions provides a simple way to locate common geometry construction problems—particularly overlaps and enclosed undefined regions—by returning representative coordinates that users can inspect directly, rather than relying solely on transport failures or visual inspection. These sample points can also be leveraged by AI agents to easily fix geometry issues in the model. Reusable undefined-region classification logic that can be leveraged by future plotting and geometry diagnostics for plotting undefined regions is also established.

Checklist

I have performed a self-review of my own code
I have run clang-format (version 18) on any C++ source files (if applicable)
I have followed the style guidelines for Python source files (if applicable)
I have made corresponding changes to the documentation (if applicable)
I have added tests that prove my fix is effective or that my feature works (if applicable)

paulromano

Thanks for the initial shot at this! Here are my initial thoughts:

viktormai · 2026-07-22T15:10:29Z

Thanks for checking it out @paulromano. I have added some updates for the bounding box idea for both overlapping and undefined regions, including a warning if undefined regions are under-resolved. Let me know what you think.

paulromano

Thanks for the updates @viktormai! Here is another round of comments:

paulromano

Thanks for the updates @viktormai! This is getting closer. Now that it is looking better, you should also add some unit tests for the capability to ensure it works properly.

paulromano · 2026-08-13T20:51:12Z

+ result : dict
+ Dictionary summarizing the sampled geometry.


This doesn't really tell the user how to interpret the dict that's returned. There should be a description of the (key, value) pairs in the dictionary.

paulromano · 2026-08-13T20:54:33Z

+ xc = x0 + (pix[:, 1] + 0.5) * (x1 - x0) / nx
+ yc = y1 - (pix[:, 0] + 0.5) * (y1 - y0) / ny


This looks like it just uses the pixel centers. I think it would be more conservative to use the bounds of the pixel itself rather than just its center (if I'm interpreting it correctly, this is already how it works for the undefined pixels?).

paulromano · 2026-08-13T20:55:43Z

+ for box in overlap_boxes + undefined_boxes:
+ bbox = box["bbox"]
+ bbox.lower_left = np.round(bbox.lower_left, 4)
+ bbox.upper_right = np.round(bbox.upper_right, 4)


While it's OK to round numbers in the output if print_summary=True (looks like that's already the case), I wouldn't modify the data that is actually returned in the dictionary

paulromano · 2026-08-13T20:56:18Z

+ "n_overlaps": len(overlap_boxes),
+ "n_undefined_regions": len(undefined_boxes),


These are easily inspectable from the data itself and can be removed IMO

… into geometry-debug-function

viktormai · 2026-07-12T17:00:05Z

This PR adds a 3D geometry debugging utility to Model for identifying overlap and undefined regions within an OpenMC geometry by sampling a user-defined bounding box.

Main changes

Added Model.geometry_debug():

Samples a 3D region using a stack of 2D slices obtained through openmc.lib.slice_data.
Detects both overlap regions (using the overlap sentinel) and internal undefined regions, returning a summary containing the total number of overlap and undefined samples and example coordinates for each type of geometry issue.
Optionally prints a human-readable summary.

Added _classify_undefined_regions() helper:

Separates undefined pixels into boundary-connected ("outside") undefined regions and internal undefined regions enclosed within the geometry.
Uses a breadth-first search starting from the image boundary to identify boundary-connected undefined pixels.
Issues a warning when undefined regions exist but none are connected to the sampled slice boundary, indicating a potentially enclosed undefined region or insufficient sampling resolution.

This pair of functions provides a simple way to locate common geometry construction problems—particularly overlaps and enclosed undefined regions—by returning representative coordinates that users can inspect directly, rather than relying solely on transport failures or visual inspection. These sample points can also be leveraged by AI agents to easily fix geometry issues in the model. Reusable undefined-region classification logic that can be leveraged by future plotting and geometry diagnostics for plotting undefined regions is also established.

Checklist

I have performed a self-review of my own code
I have run clang-format (version 18) on any C++ source files (if applicable)
I have followed the style guidelines for Python source files (if applicable)
I have made corresponding changes to the documentation (if applicable)
I have added tests that prove my fix is effective or that my feature works (if applicable)

paulromano

Thanks for the initial shot at this! Here are my initial thoughts:

viktormai · 2026-07-22T15:10:29Z

Thanks for checking it out @paulromano. I have added some updates for the bounding box idea for both overlapping and undefined regions, including a warning if undefined regions are under-resolved. Let me know what you think.

paulromano

Thanks for the updates @viktormai! Here is another round of comments:

paulromano

Thanks for the updates @viktormai! This is getting closer. Now that it is looking better, you should also add some unit tests for the capability to ensure it works properly.

paulromano · 2026-08-13T20:51:12Z

+ result : dict
+ Dictionary summarizing the sampled geometry.


This doesn't really tell the user how to interpret the dict that's returned. There should be a description of the (key, value) pairs in the dictionary.

paulromano · 2026-08-13T20:54:33Z

+ xc = x0 + (pix[:, 1] + 0.5) * (x1 - x0) / nx
+ yc = y1 - (pix[:, 0] + 0.5) * (y1 - y0) / ny


This looks like it just uses the pixel centers. I think it would be more conservative to use the bounds of the pixel itself rather than just its center (if I'm interpreting it correctly, this is already how it works for the undefined pixels?).

paulromano · 2026-08-13T20:55:43Z

+ for box in overlap_boxes + undefined_boxes:
+ bbox = box["bbox"]
+ bbox.lower_left = np.round(bbox.lower_left, 4)
+ bbox.upper_right = np.round(bbox.upper_right, 4)


While it's OK to round numbers in the output if print_summary=True (looks like that's already the case), I wouldn't modify the data that is actually returned in the dictionary

paulromano · 2026-08-13T20:56:18Z

+ "n_overlaps": len(overlap_boxes),
+ "n_undefined_regions": len(undefined_boxes),


These are easily inspectable from the data itself and can be removed IMO

… into geometry-debug-function

viktormai · 2026-07-12T17:00:05Z

This PR adds a 3D geometry debugging utility to Model for identifying overlap and undefined regions within an OpenMC geometry by sampling a user-defined bounding box.

Main changes

Added Model.geometry_debug():

Samples a 3D region using a stack of 2D slices obtained through openmc.lib.slice_data.
Detects both overlap regions (using the overlap sentinel) and internal undefined regions, returning a summary containing the total number of overlap and undefined samples and example coordinates for each type of geometry issue.
Optionally prints a human-readable summary.

Added _classify_undefined_regions() helper:

Separates undefined pixels into boundary-connected ("outside") undefined regions and internal undefined regions enclosed within the geometry.
Uses a breadth-first search starting from the image boundary to identify boundary-connected undefined pixels.
Issues a warning when undefined regions exist but none are connected to the sampled slice boundary, indicating a potentially enclosed undefined region or insufficient sampling resolution.

This pair of functions provides a simple way to locate common geometry construction problems—particularly overlaps and enclosed undefined regions—by returning representative coordinates that users can inspect directly, rather than relying solely on transport failures or visual inspection. These sample points can also be leveraged by AI agents to easily fix geometry issues in the model. Reusable undefined-region classification logic that can be leveraged by future plotting and geometry diagnostics for plotting undefined regions is also established.

Checklist

I have performed a self-review of my own code
I have run clang-format (version 18) on any C++ source files (if applicable)
I have followed the style guidelines for Python source files (if applicable)
I have made corresponding changes to the documentation (if applicable)
I have added tests that prove my fix is effective or that my feature works (if applicable)

paulromano

Thanks for the initial shot at this! Here are my initial thoughts:

viktormai · 2026-07-22T15:10:29Z

Thanks for checking it out @paulromano. I have added some updates for the bounding box idea for both overlapping and undefined regions, including a warning if undefined regions are under-resolved. Let me know what you think.

paulromano

Thanks for the updates @viktormai! Here is another round of comments:

paulromano

Thanks for the updates @viktormai! This is getting closer. Now that it is looking better, you should also add some unit tests for the capability to ensure it works properly.

paulromano · 2026-08-13T20:51:12Z

+ result : dict
+ Dictionary summarizing the sampled geometry.


This doesn't really tell the user how to interpret the dict that's returned. There should be a description of the (key, value) pairs in the dictionary.

paulromano · 2026-08-13T20:54:33Z

+ xc = x0 + (pix[:, 1] + 0.5) * (x1 - x0) / nx
+ yc = y1 - (pix[:, 0] + 0.5) * (y1 - y0) / ny


This looks like it just uses the pixel centers. I think it would be more conservative to use the bounds of the pixel itself rather than just its center (if I'm interpreting it correctly, this is already how it works for the undefined pixels?).

paulromano · 2026-08-13T20:55:43Z

+ for box in overlap_boxes + undefined_boxes:
+ bbox = box["bbox"]
+ bbox.lower_left = np.round(bbox.lower_left, 4)
+ bbox.upper_right = np.round(bbox.upper_right, 4)


While it's OK to round numbers in the output if print_summary=True (looks like that's already the case), I wouldn't modify the data that is actually returned in the dictionary

paulromano · 2026-08-13T20:56:18Z

+ "n_overlaps": len(overlap_boxes),
+ "n_undefined_regions": len(undefined_boxes),


These are easily inspectable from the data itself and can be removed IMO

… into geometry-debug-function

viktormai · 2026-07-12T17:00:05Z

This PR adds a 3D geometry debugging utility to Model for identifying overlap and undefined regions within an OpenMC geometry by sampling a user-defined bounding box.

Main changes

Added Model.geometry_debug():

Samples a 3D region using a stack of 2D slices obtained through openmc.lib.slice_data.
Detects both overlap regions (using the overlap sentinel) and internal undefined regions, returning a summary containing the total number of overlap and undefined samples and example coordinates for each type of geometry issue.
Optionally prints a human-readable summary.

Added _classify_undefined_regions() helper:

Separates undefined pixels into boundary-connected ("outside") undefined regions and internal undefined regions enclosed within the geometry.
Uses a breadth-first search starting from the image boundary to identify boundary-connected undefined pixels.
Issues a warning when undefined regions exist but none are connected to the sampled slice boundary, indicating a potentially enclosed undefined region or insufficient sampling resolution.

This pair of functions provides a simple way to locate common geometry construction problems—particularly overlaps and enclosed undefined regions—by returning representative coordinates that users can inspect directly, rather than relying solely on transport failures or visual inspection. These sample points can also be leveraged by AI agents to easily fix geometry issues in the model. Reusable undefined-region classification logic that can be leveraged by future plotting and geometry diagnostics for plotting undefined regions is also established.

Checklist

I have performed a self-review of my own code
I have run clang-format (version 18) on any C++ source files (if applicable)
I have followed the style guidelines for Python source files (if applicable)
I have made corresponding changes to the documentation (if applicable)
I have added tests that prove my fix is effective or that my feature works (if applicable)

paulromano

Thanks for the initial shot at this! Here are my initial thoughts:

viktormai · 2026-07-22T15:10:29Z

Thanks for checking it out @paulromano. I have added some updates for the bounding box idea for both overlapping and undefined regions, including a warning if undefined regions are under-resolved. Let me know what you think.

paulromano

Thanks for the updates @viktormai! Here is another round of comments:

paulromano

Thanks for the updates @viktormai! This is getting closer. Now that it is looking better, you should also add some unit tests for the capability to ensure it works properly.

paulromano · 2026-08-13T20:51:12Z

+ result : dict
+ Dictionary summarizing the sampled geometry.


This doesn't really tell the user how to interpret the dict that's returned. There should be a description of the (key, value) pairs in the dictionary.

paulromano · 2026-08-13T20:54:33Z

+ xc = x0 + (pix[:, 1] + 0.5) * (x1 - x0) / nx
+ yc = y1 - (pix[:, 0] + 0.5) * (y1 - y0) / ny


This looks like it just uses the pixel centers. I think it would be more conservative to use the bounds of the pixel itself rather than just its center (if I'm interpreting it correctly, this is already how it works for the undefined pixels?).

paulromano · 2026-08-13T20:55:43Z

+ for box in overlap_boxes + undefined_boxes:
+ bbox = box["bbox"]
+ bbox.lower_left = np.round(bbox.lower_left, 4)
+ bbox.upper_right = np.round(bbox.upper_right, 4)


While it's OK to round numbers in the output if print_summary=True (looks like that's already the case), I wouldn't modify the data that is actually returned in the dictionary

paulromano · 2026-08-13T20:56:18Z

+ "n_overlaps": len(overlap_boxes),
+ "n_undefined_regions": len(undefined_boxes),


These are easily inspectable from the data itself and can be removed IMO

… into geometry-debug-function

viktormai · 2026-07-12T17:00:05Z

This PR adds a 3D geometry debugging utility to Model for identifying overlap and undefined regions within an OpenMC geometry by sampling a user-defined bounding box.

Main changes

Added Model.geometry_debug():

Samples a 3D region using a stack of 2D slices obtained through openmc.lib.slice_data.
Detects both overlap regions (using the overlap sentinel) and internal undefined regions, returning a summary containing the total number of overlap and undefined samples and example coordinates for each type of geometry issue.
Optionally prints a human-readable summary.

Added _classify_undefined_regions() helper:

Separates undefined pixels into boundary-connected ("outside") undefined regions and internal undefined regions enclosed within the geometry.
Uses a breadth-first search starting from the image boundary to identify boundary-connected undefined pixels.
Issues a warning when undefined regions exist but none are connected to the sampled slice boundary, indicating a potentially enclosed undefined region or insufficient sampling resolution.

This pair of functions provides a simple way to locate common geometry construction problems—particularly overlaps and enclosed undefined regions—by returning representative coordinates that users can inspect directly, rather than relying solely on transport failures or visual inspection. These sample points can also be leveraged by AI agents to easily fix geometry issues in the model. Reusable undefined-region classification logic that can be leveraged by future plotting and geometry diagnostics for plotting undefined regions is also established.

Checklist

I have performed a self-review of my own code
I have run clang-format (version 18) on any C++ source files (if applicable)
I have followed the style guidelines for Python source files (if applicable)
I have made corresponding changes to the documentation (if applicable)
I have added tests that prove my fix is effective or that my feature works (if applicable)

paulromano

Thanks for the initial shot at this! Here are my initial thoughts:

viktormai · 2026-07-22T15:10:29Z

Thanks for checking it out @paulromano. I have added some updates for the bounding box idea for both overlapping and undefined regions, including a warning if undefined regions are under-resolved. Let me know what you think.

paulromano

Thanks for the updates @viktormai! Here is another round of comments:

paulromano

Thanks for the updates @viktormai! This is getting closer. Now that it is looking better, you should also add some unit tests for the capability to ensure it works properly.

paulromano · 2026-08-13T20:51:12Z

+ result : dict
+ Dictionary summarizing the sampled geometry.


This doesn't really tell the user how to interpret the dict that's returned. There should be a description of the (key, value) pairs in the dictionary.

paulromano · 2026-08-13T20:54:33Z

+ xc = x0 + (pix[:, 1] + 0.5) * (x1 - x0) / nx
+ yc = y1 - (pix[:, 0] + 0.5) * (y1 - y0) / ny


This looks like it just uses the pixel centers. I think it would be more conservative to use the bounds of the pixel itself rather than just its center (if I'm interpreting it correctly, this is already how it works for the undefined pixels?).

paulromano · 2026-08-13T20:55:43Z

+ for box in overlap_boxes + undefined_boxes:
+ bbox = box["bbox"]
+ bbox.lower_left = np.round(bbox.lower_left, 4)
+ bbox.upper_right = np.round(bbox.upper_right, 4)


While it's OK to round numbers in the output if print_summary=True (looks like that's already the case), I wouldn't modify the data that is actually returned in the dictionary

paulromano · 2026-08-13T20:56:18Z

+ "n_overlaps": len(overlap_boxes),
+ "n_undefined_regions": len(undefined_boxes),


These are easily inspectable from the data itself and can be removed IMO

… into geometry-debug-function

viktormai · 2026-07-12T17:00:05Z

This PR adds a 3D geometry debugging utility to Model for identifying overlap and undefined regions within an OpenMC geometry by sampling a user-defined bounding box.

Main changes

Added Model.geometry_debug():

Samples a 3D region using a stack of 2D slices obtained through openmc.lib.slice_data.
Detects both overlap regions (using the overlap sentinel) and internal undefined regions, returning a summary containing the total number of overlap and undefined samples and example coordinates for each type of geometry issue.
Optionally prints a human-readable summary.

Added _classify_undefined_regions() helper:

Separates undefined pixels into boundary-connected ("outside") undefined regions and internal undefined regions enclosed within the geometry.
Uses a breadth-first search starting from the image boundary to identify boundary-connected undefined pixels.
Issues a warning when undefined regions exist but none are connected to the sampled slice boundary, indicating a potentially enclosed undefined region or insufficient sampling resolution.

This pair of functions provides a simple way to locate common geometry construction problems—particularly overlaps and enclosed undefined regions—by returning representative coordinates that users can inspect directly, rather than relying solely on transport failures or visual inspection. These sample points can also be leveraged by AI agents to easily fix geometry issues in the model. Reusable undefined-region classification logic that can be leveraged by future plotting and geometry diagnostics for plotting undefined regions is also established.

Checklist

I have performed a self-review of my own code
I have run clang-format (version 18) on any C++ source files (if applicable)
I have followed the style guidelines for Python source files (if applicable)
I have made corresponding changes to the documentation (if applicable)
I have added tests that prove my fix is effective or that my feature works (if applicable)

paulromano

Thanks for the initial shot at this! Here are my initial thoughts:

viktormai · 2026-07-22T15:10:29Z

Thanks for checking it out @paulromano. I have added some updates for the bounding box idea for both overlapping and undefined regions, including a warning if undefined regions are under-resolved. Let me know what you think.

paulromano

Thanks for the updates @viktormai! Here is another round of comments:

paulromano

Thanks for the updates @viktormai! This is getting closer. Now that it is looking better, you should also add some unit tests for the capability to ensure it works properly.

paulromano · 2026-08-13T20:51:12Z

+ result : dict
+ Dictionary summarizing the sampled geometry.


This doesn't really tell the user how to interpret the dict that's returned. There should be a description of the (key, value) pairs in the dictionary.

paulromano · 2026-08-13T20:54:33Z

+ xc = x0 + (pix[:, 1] + 0.5) * (x1 - x0) / nx
+ yc = y1 - (pix[:, 0] + 0.5) * (y1 - y0) / ny


This looks like it just uses the pixel centers. I think it would be more conservative to use the bounds of the pixel itself rather than just its center (if I'm interpreting it correctly, this is already how it works for the undefined pixels?).

paulromano · 2026-08-13T20:55:43Z

+ for box in overlap_boxes + undefined_boxes:
+ bbox = box["bbox"]
+ bbox.lower_left = np.round(bbox.lower_left, 4)
+ bbox.upper_right = np.round(bbox.upper_right, 4)


While it's OK to round numbers in the output if print_summary=True (looks like that's already the case), I wouldn't modify the data that is actually returned in the dictionary

paulromano · 2026-08-13T20:56:18Z

+ "n_overlaps": len(overlap_boxes),
+ "n_undefined_regions": len(undefined_boxes),


These are easily inspectable from the data itself and can be removed IMO

… into geometry-debug-function

viktormai · 2026-07-12T17:00:05Z

This PR adds a 3D geometry debugging utility to Model for identifying overlap and undefined regions within an OpenMC geometry by sampling a user-defined bounding box.

Main changes

Added Model.geometry_debug():

Samples a 3D region using a stack of 2D slices obtained through openmc.lib.slice_data.
Detects both overlap regions (using the overlap sentinel) and internal undefined regions, returning a summary containing the total number of overlap and undefined samples and example coordinates for each type of geometry issue.
Optionally prints a human-readable summary.

Added _classify_undefined_regions() helper:

Separates undefined pixels into boundary-connected ("outside") undefined regions and internal undefined regions enclosed within the geometry.
Uses a breadth-first search starting from the image boundary to identify boundary-connected undefined pixels.
Issues a warning when undefined regions exist but none are connected to the sampled slice boundary, indicating a potentially enclosed undefined region or insufficient sampling resolution.

This pair of functions provides a simple way to locate common geometry construction problems—particularly overlaps and enclosed undefined regions—by returning representative coordinates that users can inspect directly, rather than relying solely on transport failures or visual inspection. These sample points can also be leveraged by AI agents to easily fix geometry issues in the model. Reusable undefined-region classification logic that can be leveraged by future plotting and geometry diagnostics for plotting undefined regions is also established.

Checklist

I have performed a self-review of my own code
I have run clang-format (version 18) on any C++ source files (if applicable)
I have followed the style guidelines for Python source files (if applicable)
I have made corresponding changes to the documentation (if applicable)
I have added tests that prove my fix is effective or that my feature works (if applicable)

paulromano

Thanks for the initial shot at this! Here are my initial thoughts:

viktormai · 2026-07-22T15:10:29Z

Thanks for checking it out @paulromano. I have added some updates for the bounding box idea for both overlapping and undefined regions, including a warning if undefined regions are under-resolved. Let me know what you think.

paulromano

Thanks for the updates @viktormai! Here is another round of comments:

paulromano

Thanks for the updates @viktormai! This is getting closer. Now that it is looking better, you should also add some unit tests for the capability to ensure it works properly.

paulromano · 2026-08-13T20:51:12Z

+ result : dict
+ Dictionary summarizing the sampled geometry.


This doesn't really tell the user how to interpret the dict that's returned. There should be a description of the (key, value) pairs in the dictionary.

paulromano · 2026-08-13T20:54:33Z

+ xc = x0 + (pix[:, 1] + 0.5) * (x1 - x0) / nx
+ yc = y1 - (pix[:, 0] + 0.5) * (y1 - y0) / ny


This looks like it just uses the pixel centers. I think it would be more conservative to use the bounds of the pixel itself rather than just its center (if I'm interpreting it correctly, this is already how it works for the undefined pixels?).

paulromano · 2026-08-13T20:55:43Z

+ for box in overlap_boxes + undefined_boxes:
+ bbox = box["bbox"]
+ bbox.lower_left = np.round(bbox.lower_left, 4)
+ bbox.upper_right = np.round(bbox.upper_right, 4)


While it's OK to round numbers in the output if print_summary=True (looks like that's already the case), I wouldn't modify the data that is actually returned in the dictionary

paulromano · 2026-08-13T20:56:18Z

+ "n_overlaps": len(overlap_boxes),
+ "n_undefined_regions": len(undefined_boxes),


These are easily inspectable from the data itself and can be removed IMO

… into geometry-debug-function

paulromanoand others added 30 commits February 9, 2026 23:11

Add filter_get_bins interface (not efficient for plotter)
c547b57

Combine filter index search with id_map
7f668bc

Implement new openmc_raster_plot function
2287926

Avoid duplicated code in get_raster_map
b12b92e

Remove get_plot_bins for Filter
e86c060

Add tests for raster_plot
2e81cb0

Small doc fix
d80198b

Initial shot at arbitrary orientation slice plots
3db1e54

Remove 'axes' and reorder arguments in lib.raster_plot
adf7ad3

Support u_span and v_span in Model.raster_plot
fceb98c

Rename raster -> slice for consistency
ac0e900

Merge branch 'develop' into slice-plot-api
4d6c610

Restore original (arbitrary) direction for slice plotting
6533034

Revert changes to comments
4824efa

Merge branch 'develop' into slice-plot-api
1485504

Merge branch 'develop' into slice-plot-api
447efcc

Initial overlap checking support using new slice plot API
4e225e2

Added unit test for 2 cell and 3 cell overlap returns
064e68f

Fixed overlap logic to be based off slice_data name
e5a8b14

Merged main branch with overlap changes
5d0bd24

Fixed show_overlaps_ syntax
54017c1

Fixed _dll bindings bug
943478d

Added test file
a0f5a6f

Clang format
99f74be

Remove unwanted test files
d4757f4

Fixed clang format 2
25a68b6

geometry_debug button for 3D
ba4fad4

Fixed geometry_debug with temporary session
532189c

geometry_debug() cleanup and added test file
4856b59

Merged with current upstream
18b38c5

viktormai added 2 commits July 12, 2026 11:32

Updated with upstream
7e3c718

Modified for new overlap changes
f885b65

paulromano requested changes Jul 14, 2026
View reviewed changes

Comment threadopenmc/model/model.py
Comment threadopenmc/model/model.py Outdated
Comment threadopenmc/model/model.py

viktormai added 4 commits July 20, 2026 10:54

Improved internal/external grouping
3381c65

Region separation updates
a7791fc

Improved geometry_debug workflow
1adf056

Removed erosion for overlaps
bc96c3d

viktormai marked this pull request as ready for review July 22, 2026 15:10

paulromano requested changes Jul 22, 2026
View reviewed changes

viktormaiand others added 4 commits July 24, 2026 09:27

Used BoundingBox class, cleaned up
b648c61

Added return section
57457cd

Small edits
96e09d1

Docstring fixes
2ad13e7

paulromano requested changes Aug 13, 2026
View reviewed changes

viktormai added 2 commits August 26, 2026 09:58

Cleaned up rounding
5ac0e93

Merge branch 'geometry-debug-function' of github.com:viktormai/openmc…
e821265
… into geometry-debug-function

paulromanoand others added 30 commits February 9, 2026 23:11

Add filter_get_bins interface (not efficient for plotter)
c547b57

Combine filter index search with id_map
7f668bc

Implement new openmc_raster_plot function
2287926

Avoid duplicated code in get_raster_map
b12b92e

Remove get_plot_bins for Filter
e86c060

Add tests for raster_plot
2e81cb0

Small doc fix
d80198b

Initial shot at arbitrary orientation slice plots
3db1e54

Remove 'axes' and reorder arguments in lib.raster_plot
adf7ad3

Support u_span and v_span in Model.raster_plot
fceb98c

Rename raster -> slice for consistency
ac0e900

Merge branch 'develop' into slice-plot-api
4d6c610

Restore original (arbitrary) direction for slice plotting
6533034

Revert changes to comments
4824efa

Merge branch 'develop' into slice-plot-api
1485504

Merge branch 'develop' into slice-plot-api
447efcc

Initial overlap checking support using new slice plot API
4e225e2

Added unit test for 2 cell and 3 cell overlap returns
064e68f

Fixed overlap logic to be based off slice_data name
e5a8b14

Merged main branch with overlap changes
5d0bd24

Fixed show_overlaps_ syntax
54017c1

Fixed _dll bindings bug
943478d

Added test file
a0f5a6f

Clang format
99f74be

Remove unwanted test files
d4757f4

Fixed clang format 2
25a68b6

geometry_debug button for 3D
ba4fad4

Fixed geometry_debug with temporary session
532189c

geometry_debug() cleanup and added test file
4856b59

Merged with current upstream
18b38c5

viktormai added 2 commits July 12, 2026 11:32

Updated with upstream
7e3c718

Modified for new overlap changes
f885b65

paulromano requested changes Jul 14, 2026
View reviewed changes

Comment threadopenmc/model/model.py
Comment threadopenmc/model/model.py Outdated
Comment threadopenmc/model/model.py

viktormai added 4 commits July 20, 2026 10:54

Improved internal/external grouping
3381c65

Region separation updates
a7791fc

Improved geometry_debug workflow
1adf056

Removed erosion for overlaps
bc96c3d

viktormai marked this pull request as ready for review July 22, 2026 15:10

paulromano requested changes Jul 22, 2026
View reviewed changes

viktormaiand others added 4 commits July 24, 2026 09:27

Used BoundingBox class, cleaned up
b648c61

Added return section
57457cd

Small edits
96e09d1

Docstring fixes
2ad13e7

paulromano requested changes Aug 13, 2026
View reviewed changes

viktormai added 2 commits August 26, 2026 09:58

Cleaned up rounding
5ac0e93

Merge branch 'geometry-debug-function' of github.com:viktormai/openmc…
e821265
… into geometry-debug-function

paulromanoand others added 30 commits February 9, 2026 23:11

Add filter_get_bins interface (not efficient for plotter)
c547b57

Combine filter index search with id_map
7f668bc

Implement new openmc_raster_plot function
2287926

Avoid duplicated code in get_raster_map
b12b92e

Remove get_plot_bins for Filter
e86c060

Add tests for raster_plot
2e81cb0

Small doc fix
d80198b

Initial shot at arbitrary orientation slice plots
3db1e54

Remove 'axes' and reorder arguments in lib.raster_plot
adf7ad3

Support u_span and v_span in Model.raster_plot
fceb98c

Rename raster -> slice for consistency
ac0e900

Merge branch 'develop' into slice-plot-api
4d6c610

Restore original (arbitrary) direction for slice plotting
6533034

Revert changes to comments
4824efa

Merge branch 'develop' into slice-plot-api
1485504

Merge branch 'develop' into slice-plot-api
447efcc

Initial overlap checking support using new slice plot API
4e225e2

Added unit test for 2 cell and 3 cell overlap returns
064e68f

Fixed overlap logic to be based off slice_data name
e5a8b14

Merged main branch with overlap changes
5d0bd24

Fixed show_overlaps_ syntax
54017c1

Fixed _dll bindings bug
943478d

Added test file
a0f5a6f

Clang format
99f74be

Remove unwanted test files
d4757f4

Fixed clang format 2
25a68b6

geometry_debug button for 3D
ba4fad4

Fixed geometry_debug with temporary session
532189c

geometry_debug() cleanup and added test file
4856b59

Merged with current upstream
18b38c5

viktormai added 2 commits July 12, 2026 11:32

Updated with upstream
7e3c718

Modified for new overlap changes
f885b65

paulromano requested changes Jul 14, 2026
View reviewed changes

Comment threadopenmc/model/model.py
Comment threadopenmc/model/model.py Outdated
Comment threadopenmc/model/model.py

viktormai added 4 commits July 20, 2026 10:54

Improved internal/external grouping
3381c65

Region separation updates
a7791fc

Improved geometry_debug workflow
1adf056

Removed erosion for overlaps
bc96c3d

viktormai marked this pull request as ready for review July 22, 2026 15:10

paulromano requested changes Jul 22, 2026
View reviewed changes

viktormaiand others added 4 commits July 24, 2026 09:27

Used BoundingBox class, cleaned up
b648c61

Added return section
57457cd

Small edits
96e09d1

Docstring fixes
2ad13e7

paulromano requested changes Aug 13, 2026
View reviewed changes

viktormai added 2 commits August 26, 2026 09:58

Cleaned up rounding
5ac0e93

Merge branch 'geometry-debug-function' of github.com:viktormai/openmc…
e821265
… into geometry-debug-function

paulromanoand others added 30 commits February 9, 2026 23:11

Add filter_get_bins interface (not efficient for plotter)
c547b57

Combine filter index search with id_map
7f668bc

Implement new openmc_raster_plot function
2287926

Avoid duplicated code in get_raster_map
b12b92e

Remove get_plot_bins for Filter
e86c060

Add tests for raster_plot
2e81cb0

Small doc fix
d80198b

Initial shot at arbitrary orientation slice plots
3db1e54

Remove 'axes' and reorder arguments in lib.raster_plot
adf7ad3

Support u_span and v_span in Model.raster_plot
fceb98c

Rename raster -> slice for consistency
ac0e900

Merge branch 'develop' into slice-plot-api
4d6c610

Restore original (arbitrary) direction for slice plotting
6533034

Revert changes to comments
4824efa

Merge branch 'develop' into slice-plot-api
1485504

Merge branch 'develop' into slice-plot-api
447efcc

Initial overlap checking support using new slice plot API
4e225e2

Added unit test for 2 cell and 3 cell overlap returns
064e68f

Fixed overlap logic to be based off slice_data name
e5a8b14

Merged main branch with overlap changes
5d0bd24

Fixed show_overlaps_ syntax
54017c1

Fixed _dll bindings bug
943478d

Added test file
a0f5a6f

Clang format
99f74be

Remove unwanted test files
d4757f4

Fixed clang format 2
25a68b6

geometry_debug button for 3D
ba4fad4

Fixed geometry_debug with temporary session
532189c

geometry_debug() cleanup and added test file
4856b59

Merged with current upstream
18b38c5

viktormai added 2 commits July 12, 2026 11:32

Updated with upstream
7e3c718

Modified for new overlap changes
f885b65

paulromano requested changes Jul 14, 2026
View reviewed changes

Comment threadopenmc/model/model.py
Comment threadopenmc/model/model.py Outdated
Comment threadopenmc/model/model.py

viktormai added 4 commits July 20, 2026 10:54

Improved internal/external grouping
3381c65

Region separation updates
a7791fc

Improved geometry_debug workflow
1adf056

Removed erosion for overlaps
bc96c3d

viktormai marked this pull request as ready for review July 22, 2026 15:10

paulromano requested changes Jul 22, 2026
View reviewed changes

viktormaiand others added 4 commits July 24, 2026 09:27

Used BoundingBox class, cleaned up
b648c61

Added return section
57457cd

Small edits
96e09d1

Docstring fixes
2ad13e7

paulromano requested changes Aug 13, 2026
View reviewed changes

viktormai added 2 commits August 26, 2026 09:58

Cleaned up rounding
5ac0e93

Merge branch 'geometry-debug-function' of github.com:viktormai/openmc…
e821265
… into geometry-debug-function

paulromanoand others added 30 commits February 9, 2026 23:11

Add filter_get_bins interface (not efficient for plotter)
c547b57

Combine filter index search with id_map
7f668bc

Implement new openmc_raster_plot function
2287926

Avoid duplicated code in get_raster_map
b12b92e

Remove get_plot_bins for Filter
e86c060

Add tests for raster_plot
2e81cb0

Small doc fix
d80198b

Initial shot at arbitrary orientation slice plots
3db1e54

Remove 'axes' and reorder arguments in lib.raster_plot
adf7ad3

Support u_span and v_span in Model.raster_plot
fceb98c

Rename raster -> slice for consistency
ac0e900

Merge branch 'develop' into slice-plot-api
4d6c610

Restore original (arbitrary) direction for slice plotting
6533034

Revert changes to comments
4824efa

Merge branch 'develop' into slice-plot-api
1485504

Merge branch 'develop' into slice-plot-api
447efcc

Initial overlap checking support using new slice plot API
4e225e2

Added unit test for 2 cell and 3 cell overlap returns
064e68f

Fixed overlap logic to be based off slice_data name
e5a8b14

Merged main branch with overlap changes
5d0bd24

Fixed show_overlaps_ syntax
54017c1

Fixed _dll bindings bug
943478d

Added test file
a0f5a6f

Clang format
99f74be

Remove unwanted test files
d4757f4

Fixed clang format 2
25a68b6

geometry_debug button for 3D
ba4fad4

Fixed geometry_debug with temporary session
532189c

geometry_debug() cleanup and added test file
4856b59

Merged with current upstream
18b38c5

viktormai added 2 commits July 12, 2026 11:32

Updated with upstream
7e3c718

Modified for new overlap changes
f885b65

paulromano requested changes Jul 14, 2026
View reviewed changes

Comment threadopenmc/model/model.py
Comment threadopenmc/model/model.py Outdated
Comment threadopenmc/model/model.py

viktormai added 4 commits July 20, 2026 10:54

Improved internal/external grouping
3381c65

Region separation updates
a7791fc

Improved geometry_debug workflow
1adf056

Removed erosion for overlaps
bc96c3d

viktormai marked this pull request as ready for review July 22, 2026 15:10

paulromano requested changes Jul 22, 2026
View reviewed changes

viktormaiand others added 4 commits July 24, 2026 09:27

Used BoundingBox class, cleaned up
b648c61

Added return section
57457cd

Small edits
96e09d1

Docstring fixes
2ad13e7

paulromano requested changes Aug 13, 2026
View reviewed changes

viktormai added 2 commits August 26, 2026 09:58

Cleaned up rounding
5ac0e93

Merge branch 'geometry-debug-function' of github.com:viktormai/openmc…
e821265
… into geometry-debug-function

paulromanoand others added 30 commits February 9, 2026 23:11

Add filter_get_bins interface (not efficient for plotter)
c547b57

Combine filter index search with id_map
7f668bc

Implement new openmc_raster_plot function
2287926

Avoid duplicated code in get_raster_map
b12b92e

Remove get_plot_bins for Filter
e86c060

Add tests for raster_plot
2e81cb0

Small doc fix
d80198b

Initial shot at arbitrary orientation slice plots
3db1e54

Remove 'axes' and reorder arguments in lib.raster_plot
adf7ad3

Support u_span and v_span in Model.raster_plot
fceb98c

Rename raster -> slice for consistency
ac0e900

Merge branch 'develop' into slice-plot-api
4d6c610

Restore original (arbitrary) direction for slice plotting
6533034

Revert changes to comments
4824efa

Merge branch 'develop' into slice-plot-api
1485504

Merge branch 'develop' into slice-plot-api
447efcc

Initial overlap checking support using new slice plot API
4e225e2

Added unit test for 2 cell and 3 cell overlap returns
064e68f

Fixed overlap logic to be based off slice_data name
e5a8b14

Merged main branch with overlap changes
5d0bd24

Fixed show_overlaps_ syntax
54017c1

Fixed _dll bindings bug
943478d

Added test file
a0f5a6f

Clang format
99f74be

Remove unwanted test files
d4757f4

Fixed clang format 2
25a68b6

geometry_debug button for 3D
ba4fad4

Fixed geometry_debug with temporary session
532189c

geometry_debug() cleanup and added test file
4856b59

Merged with current upstream
18b38c5

viktormai added 2 commits July 12, 2026 11:32

Updated with upstream
7e3c718

Modified for new overlap changes
f885b65

paulromano requested changes Jul 14, 2026
View reviewed changes

Comment threadopenmc/model/model.py
Comment threadopenmc/model/model.py Outdated
Comment threadopenmc/model/model.py

viktormai added 4 commits July 20, 2026 10:54

Improved internal/external grouping
3381c65

Region separation updates
a7791fc

Improved geometry_debug workflow
1adf056

Removed erosion for overlaps
bc96c3d

viktormai marked this pull request as ready for review July 22, 2026 15:10

paulromano requested changes Jul 22, 2026
View reviewed changes

viktormaiand others added 4 commits July 24, 2026 09:27

Used BoundingBox class, cleaned up
b648c61

Added return section
57457cd

Small edits
96e09d1

Docstring fixes
2ad13e7

paulromano requested changes Aug 13, 2026
View reviewed changes

viktormai added 2 commits August 26, 2026 09:58

Cleaned up rounding
5ac0e93

Merge branch 'geometry-debug-function' of github.com:viktormai/openmc…
e821265
… into geometry-debug-function

paulromanoand others added 30 commits February 9, 2026 23:11

Add filter_get_bins interface (not efficient for plotter)
c547b57

Combine filter index search with id_map
7f668bc

Implement new openmc_raster_plot function
2287926

Avoid duplicated code in get_raster_map
b12b92e

Remove get_plot_bins for Filter
e86c060

Add tests for raster_plot
2e81cb0

Small doc fix
d80198b

Initial shot at arbitrary orientation slice plots
3db1e54

Remove 'axes' and reorder arguments in lib.raster_plot
adf7ad3

Support u_span and v_span in Model.raster_plot
fceb98c

Rename raster -> slice for consistency
ac0e900

Merge branch 'develop' into slice-plot-api
4d6c610

Restore original (arbitrary) direction for slice plotting
6533034

Revert changes to comments
4824efa

Merge branch 'develop' into slice-plot-api
1485504

Merge branch 'develop' into slice-plot-api
447efcc

Initial overlap checking support using new slice plot API
4e225e2

Added unit test for 2 cell and 3 cell overlap returns
064e68f

Fixed overlap logic to be based off slice_data name
e5a8b14

Merged main branch with overlap changes
5d0bd24

Fixed show_overlaps_ syntax
54017c1

Fixed _dll bindings bug
943478d

Added test file
a0f5a6f

Clang format
99f74be

Remove unwanted test files
d4757f4

Fixed clang format 2
25a68b6

geometry_debug button for 3D
ba4fad4

Fixed geometry_debug with temporary session
532189c

geometry_debug() cleanup and added test file
4856b59

Merged with current upstream
18b38c5

viktormai added 2 commits July 12, 2026 11:32

Updated with upstream
7e3c718

Modified for new overlap changes
f885b65

paulromano requested changes Jul 14, 2026
View reviewed changes

Comment threadopenmc/model/model.py
Comment threadopenmc/model/model.py Outdated
Comment threadopenmc/model/model.py

viktormai added 4 commits July 20, 2026 10:54

Improved internal/external grouping
3381c65

Region separation updates
a7791fc

Improved geometry_debug workflow
1adf056

Removed erosion for overlaps
bc96c3d

viktormai marked this pull request as ready for review July 22, 2026 15:10

paulromano requested changes Jul 22, 2026
View reviewed changes

viktormaiand others added 4 commits July 24, 2026 09:27

Used BoundingBox class, cleaned up
b648c61

Added return section
57457cd

Small edits
96e09d1

Docstring fixes
2ad13e7

paulromano requested changes Aug 13, 2026
View reviewed changes

viktormai added 2 commits August 26, 2026 09:58

Cleaned up rounding
5ac0e93

Merge branch 'geometry-debug-function' of github.com:viktormai/openmc…
e821265
… into geometry-debug-function

paulromanoand others added 30 commits February 9, 2026 23:11

Add filter_get_bins interface (not efficient for plotter)
c547b57

Combine filter index search with id_map
7f668bc

Implement new openmc_raster_plot function
2287926

Avoid duplicated code in get_raster_map
b12b92e

Remove get_plot_bins for Filter
e86c060

Add tests for raster_plot
2e81cb0

Small doc fix
d80198b

Initial shot at arbitrary orientation slice plots
3db1e54

Remove 'axes' and reorder arguments in lib.raster_plot
adf7ad3

Support u_span and v_span in Model.raster_plot
fceb98c

Rename raster -> slice for consistency
ac0e900

Merge branch 'develop' into slice-plot-api
4d6c610

Restore original (arbitrary) direction for slice plotting
6533034

Revert changes to comments
4824efa

Merge branch 'develop' into slice-plot-api
1485504

Merge branch 'develop' into slice-plot-api
447efcc

Initial overlap checking support using new slice plot API
4e225e2

Added unit test for 2 cell and 3 cell overlap returns
064e68f

Fixed overlap logic to be based off slice_data name
e5a8b14

Merged main branch with overlap changes
5d0bd24

Fixed show_overlaps_ syntax
54017c1

Fixed _dll bindings bug
943478d

Added test file
a0f5a6f

Clang format
99f74be

Remove unwanted test files
d4757f4

Fixed clang format 2
25a68b6

geometry_debug button for 3D
ba4fad4

Fixed geometry_debug with temporary session
532189c

geometry_debug() cleanup and added test file
4856b59

Merged with current upstream
18b38c5

viktormai added 2 commits July 12, 2026 11:32

Updated with upstream
7e3c718

Modified for new overlap changes
f885b65

paulromano requested changes Jul 14, 2026
View reviewed changes

Comment threadopenmc/model/model.py
Comment threadopenmc/model/model.py Outdated
Comment threadopenmc/model/model.py

viktormai added 4 commits July 20, 2026 10:54

Improved internal/external grouping
3381c65

Region separation updates
a7791fc

Improved geometry_debug workflow
1adf056

Removed erosion for overlaps
bc96c3d

viktormai marked this pull request as ready for review July 22, 2026 15:10

paulromano requested changes Jul 22, 2026
View reviewed changes

viktormaiand others added 4 commits July 24, 2026 09:27

Used BoundingBox class, cleaned up
b648c61

Added return section
57457cd

Small edits
96e09d1

Docstring fixes
2ad13e7

paulromano requested changes Aug 13, 2026
View reviewed changes

viktormai added 2 commits August 26, 2026 09:58

Cleaned up rounding
5ac0e93

Merge branch 'geometry-debug-function' of github.com:viktormai/openmc…
e821265
… into geometry-debug-function

		xc = x0 + (pix[:, 1] + 0.5) * (x1 - x0) / nx
		yc = y1 - (pix[:, 0] + 0.5) * (y1 - y0) / ny

		"n_overlaps": len(overlap_boxes),
		"n_undefined_regions": len(undefined_boxes),

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viktormai commented Jul 12, 2026

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viktormai commented Jul 12, 2026

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