GEOPY-2771: backport - high runtime and memory for GeoImage.copy_by_extent#858
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sebhmg merged 2 commits intoMiraGeoscience:hotfix/gi-4.3from Mar 16, 2026
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GEOPY-2540: Copy from extent GeoImage takes forever. (cherry picked from commit 9fb75bc)
sebhmg
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sebhmg
changed the title
Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## hotfix/gi-4.3 #858 +/- ##
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+ Coverage 90.91% 91.12% +0.21%
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Files 113 114 +1
Lines 9869 10067 +198
Branches 1836 1867 +31
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+ Hits 8972 9174 +202
+ Misses 485 477 -8
- Partials 412 416 +4
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Pull request overview
Addresses GEOPY-2540 by reworking GeoImage.copy_from_extent to avoid expensive Grid2D round-trips and introducing shared geometry helpers to compute extent/plane intersections more directly.
Changes:
- Added a new
Planemodel + polygon/box intersection utilities to compute crop extents in UV space. - Updated
GeoImage.copy_from_extentto crop via PIL using the computed pixel rectangle instead of converting to Grid2D. - Expanded/adjusted test coverage around GeoImage extent-copying, rotations/dips, and new cut-by-extent helpers.
Reviewed changes
Copilot reviewed 7 out of 7 changed files in this pull request and generated 13 comments.
Show a summary per file
| File | Description |
|---|---|
geoh5py/objects/geo_image.py |
Reimplements copy_from_extent, adjusts tag handling, and tweaks dip/rotation logic and image loading behavior. |
geoh5py/shared/cut_by_extent.py |
New Plane/geometry module used to compute intersections and pixel crop extents. |
geoh5py/shared/utils.py |
Adds extent-cleaning and vector/polygon helper validators used by new geometry logic; updates mask_by_extent. |
geoh5py/shared/conversion/geo_image.py |
Uses GeoImage-derived u_count/v_count and cell sizes for Grid2D conversion. |
tests/geo_image_test.py |
Adds/updates tests for tags/vertices, rotation/dip, and copy-from-extent behavior. |
tests/shared_utils_test.py |
Adjusts expectations around mask_by_extent input validation. |
tests/cut_by_extent_test.py |
New tests for Plane validation and extent_from_vertices_and_box input checks. |
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| if not isinstance(extent, np.ndarray) or extent.shape not in [(2, 3), (2, 2)]: | ||
| raise ValueError( | ||
| "extent must be a numpy array of shape (2, 3)." |
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| old_limit = Image.MAX_IMAGE_PIXELS | ||
| Image.MAX_IMAGE_PIXELS = None | ||
| try: | ||
| im = Image.open(BytesIO(self.image_data.file_bytes)) | ||
| finally: | ||
| Image.MAX_IMAGE_PIXELS = old_limit |
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| if len(xyz) != 4: | ||
| raise ValueError("Array of 'vertices' must be of shape (4, 3).") | ||
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| self._vertices = xyz | ||
| self._tag = None | ||
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| if self.on_file: | ||
| self.workspace.update_attribute(self, "vertices") |
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| # Create with image so we get past the image check, then remove vertices | ||
| image = Image.fromarray(np.arange(16, dtype="uint8").reshape(4, 4), "L") |
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| if extent.shape[1] == 2 or np.all(extent[:, 2] == 0): | ||
| z_coordinates = locations[:, 2] | ||
| z_min, z_max = float(z_coordinates.min()), float(z_coordinates.max()) | ||
| z_bounds = np.array([[z_min - 1], [z_max + 1]], dtype=np.float64) | ||
| extent = np.column_stack([extent.astype(np.float64), z_bounds]) |
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| print(geoimage3.dip, geoimage3.rotation) | ||
| np.testing.assert_array_almost_equal(geoimage3.dip, 44) | ||
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| geoimage4 = GeoImage.create( | ||
| workspace, name="test_area", image=image, dip=44, rotation=66 | ||
| ) | ||
| print(geoimage4.dip, geoimage4.rotation) |
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| warn("Skipping comparison due to one method returning None") | ||
| return |
| ValueError, match=re.escape("Input 'extent' must be a 2D array-like.") | ||
| ): | ||
| mask_by_extent(points, 1.0) | ||
| with pytest.raises(ValueError, match="Input 'extent' must be a 2D array-like."): |
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| raise ValueError( | ||
| "Input 'extent' must be a 2D array-like with 2 points and 2 or 3 columns" | ||
| ) |
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| f"Got {type(vertices)} with shape {vertices.shape}." | ||
| ) | ||
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| if not isinstance(extent, np.ndarray) or extent.shape not in [(2, 3), (2, 2)]: | ||
| raise ValueError( | ||
| "extent must be a numpy array of shape (2, 3)." | ||
| f"Got {type(extent)} with shape {extent.shape}." |
domfournier
approved these changes
Mar 16, 2026
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GEOPY-2771 - backport - high runtime and memory allocation for GeoImage.copy_by_extent
GEOPY-2540: Copy from extent GeoImage takes forever. (cherry picked from commit 9fb75bc)