Merge branch 'main' of github.com:qupath/qubalab

.github/workflows/tests.yml

@@ -3,6 +3,9 @@
 name: test
 
 on:
+  push:
+    branches:
+      main
   pull_request:
   workflow_dispatch:
 
@@ -16,9 +19,12 @@ jobs:
       - name: Set up python
         id: setup-python
         uses: actions/setup-python@v5
+
+      - name: Install Openslide
+        run: sudo apt install openslide-tools
 
       - name: Install
-        run: pip install .[test]
+        run: pip install .[test,openslide]
 
       - name: Run tests
         run: pytest

README.md

@@ -43,9 +43,9 @@ You can find the documentation on https://qupath.github.io/qubalab-docs/.
 This project contains the QuBaLab package in the `qubalab` folder.
 Take a look at the *Installation* section to install it.
 
-Some notebooks present in the `notebooks` folder show how to use the QuBaLab
-package. If you want to run them, you can take a look at the *Development* section.
-If you just want to go through them, look at the
+Some notebooks in the `notebooks` folder demonstrate how to use QuBaLab.
+If you want to run them, you can take a look at the *Development* section.
+If you just want to browse the content in them, look at the
 [documentation](https://qupath.github.io/qubalab/notebooks.html).
 
 ## Installation

qubalab/images/openslide_server.py

@@ -19,6 +19,8 @@ class OpenSlideServer(ImageServer):
     """
     An image server that relies on OpenSlide (https://openslide.org/) to read RGB images.
 
+    This server may only be able to detect the full resolution of a pyramidal image.
+
     OpenSlide provides some properties to define a rectangle bounding the non-empty region of the slide
     (see https://openslide.org/api/python/#standard-properties). If such properties are found, only this
     rectangle will be read (but note that this behaviour was not properly tested).

setup.cfg

@@ -18,8 +18,7 @@ packages =
 python_requires = >= 3.10
 install_requires =
     tiffslide ~= 2.4.0
-    aicsimageio ~= 4.13.0
-    dask[array] >= 2021.4.1
+    aicsimageio >= 4.10.0
     dask-image >= 0.6.0
     py4j ~= 0.10.9.7
     geojson ~= 3.1.0

tests/images/test_openslide_server.py

@@ -20,23 +20,12 @@ def test_image_shapes():
 
     shapes = openslide_server.metadata.shapes
 
-    assert shapes == multi_resolution_uint8_3channels.get_shapes()
+    # only the full resolution can be detected
+    assert shapes[0] == multi_resolution_uint8_3channels.get_shapes()[0]
 
     openslide_server.close()
 
 
-def test_image_pixel_calibration():
-    openslide_server = OpenSlideServer(multi_resolution_uint8_3channels.get_path())
-
-    pixel_calibration = openslide_server.metadata.pixel_calibration
-
-    assert pixel_calibration == PixelCalibration(
-        PixelLength.create_microns(multi_resolution_uint8_3channels.get_pixel_size_x_y_in_micrometers()),
-        PixelLength.create_microns(multi_resolution_uint8_3channels.get_pixel_size_x_y_in_micrometers())
-    )
-
-    openslide_server.close()
-
 
 def test_is_rgb():
     openslide_server = OpenSlideServer(multi_resolution_uint8_3channels.get_path())
@@ -93,7 +82,8 @@ def test_downsamples():
 
     downsamples = openslide_server.metadata.downsamples
 
-    assert downsamples == multi_resolution_uint8_3channels.get_downsamples()
+    # only the full resolution can be detected
+    assert downsamples[0] == multi_resolution_uint8_3channels.get_downsamples()[0]
 
     openslide_server.close()
 
@@ -119,26 +109,3 @@ def test_read_full_resolution_image():
     np.testing.assert_array_equal(image, expected_pixels)
 
     openslide_server.close()
-
-
-def test_read_lower_resolution_image():
-    level = len(multi_resolution_uint8_3channels.get_shapes()) - 1
-    lowest_resolution = multi_resolution_uint8_3channels.get_shapes()[level]
-    downsample = multi_resolution_uint8_3channels.get_downsamples()[level]
-    openslide_server = OpenSlideServer(multi_resolution_uint8_3channels.get_path())
-    expected_pixels = np.array(
-        [[[multi_resolution_uint8_3channels.get_pixel_value(downsample, x, y, c)
-            for x in range(lowest_resolution.x)]
-            for y in range(lowest_resolution.y)]
-            for c in range(lowest_resolution.c)],
-        multi_resolution_uint8_3channels.get_dtype()
-    )
-
-    image = openslide_server.read_region(
-        downsample,
-        Region2D(width=openslide_server.metadata.width, height=openslide_server.metadata.height)
-    )
-
-    np.testing.assert_array_equal(image, expected_pixels)
-
-    openslide_server.close()

tests/res/multi_resolution_uint8_3channels.py

@@ -78,7 +78,9 @@ def _write_image(pixels: np.array):
             metadata=metadata,
             subifds=number_of_subresolutions,
             resolution=(number_of_pixels_per_cm, number_of_pixels_per_cm),
-            resolutionunit=3    # indicate that the resolution above is in cm^-1
+            resolutionunit=3,    # indicate that the resolution above is in cm^-1,
+            photometric='rgb',
+            tile=(128, 128)
         )
 
         # Write sub resolutions
@@ -89,7 +91,9 @@ def _write_image(pixels: np.array):
                     metadata=metadata,
                     subfiletype=1,      # indicate that the image is part of a multi-page image
                     resolution=(number_of_pixels_per_cm / downsample, number_of_pixels_per_cm / downsample),
-                    resolutionunit=3
+                    resolutionunit=3,
+                    photometric='rgb', 
+                    tile=(128, 128)
                 )