Updates to CI

examples/annotations_to_mask.py

@@ -1,108 +1,26 @@
 # Copyright (c) dlup contributors
 """This code provides an example of how to convert annotations to a mask."""
-import json
 from pathlib import Path
 
-import numpy as np
 import PIL.Image
 
 from dlup.annotations_experimental import SlideAnnotations
 
-d_fn = Path("TCGA-E9-A1R4-01Z-00-DX1.B04D5A22-8CE5-49FD-8510-14444F46894D.json")
 
-Z_INDICES = {
-    "tissue (area)": 0,
-    "artefact mechanical expansion (area)": 1,
-    "artefact out of focus (area)": 2,
-    "artefact edge margin ink (area)": 3,
-    "artefact mechanical compression (area)": 3,
-    "artefact other (area)": 4,
-    "artefact air bubble (area)": 5,
-    "artefact foreign object (area)": 5,
-    "artefact coverslip (area)": 6,
-    "artefact pen marking (area)": 7,
-}
+def convert_annotations_to_mask() -> None:
+    scaling = 0.02
+    annotations = SlideAnnotations.from_dlup_xml(Path(__file__).parent / "files" / "dlup_annotation_test.xml")
 
-index_map = {
-    "tissue (area)": 1,
-    "artefact air bubble (area)": 2,
-    "artefact mechanical expansion (area)": 3,
-    "artefact mechanical compression (area)": 4,
-    "artefact out of focus (area)": 5,
-    "artefact pen marking (area)": 6,
-}
-annotations = SlideAnnotations.from_darwin_json(d_fn, z_indices=Z_INDICES, sorting="Z_INDEX")
-scaling = 0.02
+    bbox = annotations.bounding_box_at_scaling(scaling)
 
-bbox = annotations.bounding_box_at_scaling(scaling)
-annotations.reindex_polygons(index_map)
-region = annotations.read_region((0, 0), scaling, bbox[1])
-LUT = annotations.color_lut
-import time
+    region = annotations.read_region((0, 0), scaling, bbox[1])
+    LUT = annotations.color_lut
 
-start_time = time.time()
-curr_mask = region.polygons_eager.to_mask()
-print(f"Time to compute mask eagerly: {time.time() - start_time}")
+    bbox = annotations.bounding_box_at_scaling(scaling)
 
+    curr_mask = region.polygons.to_mask().numpy()
+    print(curr_mask.shape)
+    PIL.Image.fromarray(LUT[curr_mask]).save("output.png")
 
-print(region, "region")
-print(region.polygons, "region.polygons")  # This should be lazy
 
-# for polygon in region.polygons.get_geometries():
-#     print(polygon)
-polys = region.polygons.get_geometries()  # This should start computing
-
-import time
-
-start_time = time.time()
-curr_mask = region.polygons.to_mask().numpy()
-print(f"Time to compute mask lazily: {time.time() - start_time}")
-
-
-print(curr_mask)
-print(np.asarray(curr_mask).shape)
-
-mask_itself = region.polygons.to_mask().numpy()
-
-mask = LUT[mask_itself]
-
-PIL.Image.fromarray(mask).save("mask.png")
-from dlup.geometry import Box, GeometryCollection
-
-collection = GeometryCollection()
-polygon = Box((1, 1), (4, 4)).as_polygon()
-polygon.index = 2
-collection.add_polygon(polygon)
-
-region = collection.read_region((0, 0), 1.0, (5, 5))
-
-print("Python: Getting geometries")
-# region.polygons.get_geometries()
-print("Python: got geometries")
-print("Python: Computing mask")
-mask = np.asarray(region.polygons.to_mask())
-print("Python: Got mask")
-# print(mask)
-# assert mask.sum() == 16 * 2
-print("Python: Done")
-mask = np.asarray(region.polygons.to_mask())
-
-
-# print("Getting geometries")
-
-# # for polygon in region.polygons.get_geometries():
-# #     print(polygon)
-
-# with open("test.xml", "w") as f:
-#     f.write(annotations.as_dlup_xml())
-
-
-# with open("test.geojson", "w") as f:
-#     f.write(json.dumps(annotations.as_geojson(), indent=2))
-
-# annotations2 = SlideAnnotations.from_dlup_xml("test.xml")
-# region2 = annotations2.read_region((0, 0), scaling, bbox[1])
-# LUT = annotations2.color_lut
-
-# mask = LUT[region.polygons.to_mask().numpy()]
-# PIL.Image.fromarray(mask).save("mask2.png")
+convert_annotations_to_mask()

meson.build

@@ -4,14 +4,8 @@ project('dlup', 'cpp', 'cython',
 
 ninja = find_program('ninja', required : true)
 
-# Import Python module
-
 py_mod = import('python')
-if host_machine.system() == 'darwin'
-    py = py_mod.find_installation(pure: false)
-else
-    py = py_mod.find_installation()
-endif
+py = py_mod.find_installation(pure: false)
 py_dep = py.dependency()
 
 # Base compiler and linker arguments

tests/test_slide_annotations.py

@@ -225,15 +225,17 @@ def test_conversion_halo_geojson(self):
 
     def test_halo_annotations(self):
         halo_annotations = self.halo_annotations.copy()
-        offset, _ = halo_annotations.bounding_box
-        assert halo_annotations.bounding_box[0] == (-29349.0, 50000.55808864343)
+        bounding_box = halo_annotations.bounding_box
+        assert bounding_box[0] == (-29349.0, 50000.55808864343)
         halo_annotations.set_offset((29349.0, -50000.55808864343))
         assert halo_annotations.bounding_box[0] == (0, 0)
+
         for polygon in halo_annotations.layers.polygons:
             polygon.index = 1
-        halo_mask = halo_annotations.read_region((0, 0), 0.01, (522, 374)).polygons.to_mask()
-        output_color_mask = halo_annotations.color_lut[halo_mask]
-        assert halo_mask.sum() == 87709
+
+        new_bbox = halo_annotations.bounding_box_at_scaling(0.01)
+        region = halo_annotations.read_region(new_bbox[0], 0.01, new_bbox[1])
+        output_color_mask = halo_annotations.color_lut[region.polygons.to_mask().numpy()]
         assert output_color_mask.sum() == 51485183
 
     def test_reexpert_dlup_xml(self):

third_party/meson.build

@@ -1,11 +1,7 @@
 ### third_party/meson.build ###
 
 py_mod = import('python')
-if host_machine.system() == 'darwin'
-    py = py_mod.find_installation(pure: false)
-else
-    py = py_mod.find_installation()
-endif
+py = py_mod.find_installation(pure: false)
 py_dep = py.dependency()
 
 python_path = run_command(py, ['-c', 'import sys; print(sys.executable)'], check: true).stdout().strip()