509 ignore blank patches

.github/workflows/mr_ci.yml

@@ -1,7 +1,10 @@
 ---
 name: Units Tests
 
-on: [push]
+on:
+  pull_request:
+    branches:
+      - main
 
 jobs:
 

.github/workflows/mr_ci_text_spotting.yml

@@ -1,7 +1,10 @@
 ---
 name: Units Tests - Text Spotting
 
-on: [push]
+on:
+  pull_request:
+    branches:
+      - main
 
 # Run linter with github actions for quick feedbacks.
 jobs:

.github/workflows/publish-to-conda-forge.yml

@@ -4,6 +4,8 @@ name: Publish to Conda Forge
 on:
   workflow_dispatch:
   push:
+    branches:
+      - main
     tags:
       - v*
 

.github/workflows/publish-to-pypi.yml

@@ -4,6 +4,8 @@ name: Publish Tagged Python 🐍 distributions 📦 to PyPI
 on:
   workflow_dispatch:
   push:
+    branches:
+      - main
     tags:
       - v*
 

CHANGELOG.md

@@ -17,6 +17,10 @@ The following table shows which versions of MapReader are compatible with which
 
 _Add new changes here_
 
+### Added
+
+- Added `skip_blank_patches` argument to `MapImages.patchify_all()` ([#540](https://github.com/maps-as-data/MapReader/pull/540))
+
 ## [v1.6.1](https://github.com/Living-with-machines/MapReader/releases/tag/v1.6.1) (2024-11-18)
 
 ### Added

docs/source/using-mapreader/step-by-step-guide/2-load.rst

@@ -211,6 +211,7 @@ This will create 1024 x 1024 pixel patches with 10% overlap between each patch.
     - ``square_cuts`` - This is a deprecated method and no longer recommended for use. By default, this is set to ``False`` and padding is added to patches at the edges of the parent image to ensure square patches. If you set ``square_cuts=True``, instead of padding, there will be some overlap between edge patches.
     - ``add_to_parent`` - By default, this is set to ``True`` so that each time you run ``patchify_all`` your patches are added to your ``MapImages`` object. Setting it to ``False`` (by specifying ``add_to_parent=False``) will mean your patches are created, but not added to your ``MapImages`` object. This can be useful for testing out different patch sizes.
     - ``rewrite`` - By default, this is set to ``False`` so that if your patches already exist they are not overwritten. Setting it to ``True`` (by specifying ``rewrite=True``) will mean already existing patches are recreated and overwritten.
+    - ``skip_blank_patches`` - By default, this is set to ``False``. Setting to ``True`` will omit any patches that only contain ``0`` values, which can speed up processing on irregularly shaped map images that have empty regions. The `Image.getbbox() <https://pillow.readthedocs.io/en/stable/reference/Image.html#PIL.Image.Image.getbbox>`_ method is used to determine if a patch is blank.
 
 If you would like to save your patches as geo-referenced tiffs (i.e. geotiffs), use:
 

mapreader/load/images.py

@@ -1208,6 +1208,7 @@ def patchify_all(
         patch_size: int | None = 100,
         tree_level: str | None = "parent",
         path_save: str | None = None,
+        skip_blank_patches: bool = False,
         add_to_parents: bool | None = True,
         square_cuts: bool | None = False,
         resize_factor: bool | None = False,
@@ -1234,6 +1235,8 @@ def patchify_all(
             Directory to save the patches.
             If None, will be set as f"patches_{patch_size}_{method}" (e.g. "patches_100_pixel").
             By default None.
+        skip_blank_patches : bool
+            If True, any patch that only contains 0 values will be skipped, by default ``False``. Uses PIL.Image().get_bbox().
         add_to_parents : bool, optional
             If True, patches will be added to the MapImages instance's
             ``images`` dictionary, by default ``True``.
@@ -1313,6 +1316,7 @@ def patchify_all(
                     add_to_parents=add_to_parents,
                     resize_factor=resize_factor,
                     output_format=output_format,
+                    skip_blank_patches=skip_blank_patches,
                     rewrite=rewrite,
                     verbose=verbose,
                     overlap=overlap,
@@ -1326,6 +1330,7 @@ def _patchify_by_pixel(
         add_to_parents: bool | None = True,
         resize_factor: bool | None = False,
         output_format: str | None = "png",
+        skip_blank_patches: bool = False,
         rewrite: bool | None = False,
         verbose: bool | None = False,
         overlap: int | None = 0,
@@ -1347,6 +1352,8 @@ def _patchify_by_pixel(
             If True, resize the images before patchifying, by default ``False``.
         output_format : str, optional
             Format to use when writing image files, by default ``"png"``.
+        skip_blank_patches : bool
+            If True, any patch that only contains 0 values will be skipped, by default ``False``. Uses PIL.Image().get_bbox().
         rewrite : bool, optional
             If True, existing patches will be rewritten, by default ``False``.
         verbose : bool, optional
@@ -1370,6 +1377,7 @@ def _patchify_by_pixel(
             )
 
         height, width = img.height, img.width
+        overlap_pixels = int(patch_size * overlap)
 
         x = 0
         while x < width:
@@ -1389,6 +1397,15 @@ def _patchify_by_pixel(
 
                 else:
                     patch = img.crop((x, y, max_x, max_y))
+
+                    # skip if blank and don't add to parents
+                    if skip_blank_patches and patch.getbbox() is None:
+                        self._print_if_verbose(
+                            f"[INFO] Skipping empty patch: {patch_id}.", verbose
+                        )
+                        y = y + patch_size - overlap_pixels
+                        continue
+
                     if max_x == width:
                         patch = ImageOps.pad(
                             patch, (patch_size, patch.height), centering=(0, 0)
@@ -1416,7 +1433,6 @@ def _patchify_by_pixel(
                     self._add_patch_coords_id(patch_id)
                     self._add_patch_polygons_id(patch_id)
 
-                overlap_pixels = int(patch_size * overlap)
                 y = y + patch_size - overlap_pixels
             x = x + patch_size - overlap_pixels
 

tests/test_load/test_images.py

@@ -515,6 +515,26 @@ def test_patchify_pixels(sample_dir, image_id, tmp_path):
     assert os.path.isfile(f"{tmp_path}/patch-0-0-3-3-#{image_id}#.png")
 
 
+def test_patchify_pixels_skip_blank_rgb(sample_dir, tmp_path):
+    maps = MapImages(f"{sample_dir}/cropped_blank_corners_rgb.tif")
+    maps.patchify_all(patch_size=3, path_save=tmp_path, skip_blank_patches=True)
+    parent_list = maps.list_parents()
+    patch_list = maps.list_patches()
+    assert len(parent_list) == 1
+    assert len(patch_list) == 5
+    assert os.path.isfile(f"{tmp_path}/patch-0-3-3-6-#cropped_blank_corners_rgb.tif#.png")
+
+
+def test_patchify_pixels_skip_blank_rgba(sample_dir, tmp_path):
+    maps = MapImages(f"{sample_dir}/cropped_blank_corners_rgba.tif")
+    maps.patchify_all(patch_size=3, path_save=tmp_path, skip_blank_patches=True)
+    parent_list = maps.list_parents()
+    patch_list = maps.list_patches()
+    assert len(parent_list) == 1
+    assert len(patch_list) == 5
+    assert os.path.isfile(f"{tmp_path}/patch-0-3-3-6-#cropped_blank_corners_rgba.tif#.png")
+
+
 def test_patchify_pixels_square(sample_dir, image_id, tmp_path):
     maps = MapImages(f"{sample_dir}/{image_id}")
     maps.patchify_all(patch_size=5, path_save=f"{tmp_path}_square", square_cuts=True)