Merge branch 'dicom-update' of https://github.com/TissueImageAnalytic…

…s/tiatoolbox into faster-patch-dataset

pyproject.toml

@@ -1,3 +1,6 @@
+[tool.pytest.ini_options]
+  collect_ignore = ["setup.py", "benchmark/"]
+
 [tool.black]
   exclude = '''
   /(
@@ -34,3 +37,17 @@
   ]
   ignore_errors = true
   omit = ['tests/*', 'tiatoolbox/__main__.py', '*/utils/env_detection.py']
+
+[tool.isort]
+  profile = "black"
+  multi_line_output = 3
+  line_length = 88
+  filter_files = "True"
+  skip = [".gitignore", "benchmarks/*"]
+
+[build-system]
+  requires = ["setuptools"]
+  build-backend = "setuptools.build_meta"
+
+[tool.distutils.bdist_wheel]
+  universal = true

setup.cfg

@@ -19,9 +19,6 @@ replace = version: {new_version}  # TIAToolbox version
 search = TOOLBOX_VER: {current_version}
 replace = TOOLBOX_VER: {new_version}
 
-[bdist_wheel]
-universal = 1
-
 [flake8]
 exclude = docs, *__init__*, setup.py
 max-line-length = 88
@@ -30,16 +27,3 @@ spellcheck-targets = comments
 dictionaries = en_US,python,technical
 max-cognitive-complexity = 14
 max-expression-complexity = 7
-
-[aliases]
-test = pytest
-
-[tool:pytest]
-collect_ignore = ['setup.py', 'benchmark/']
-
-[isort]
-profile = black
-multi_line_output = 3
-skip_gitignore = True
-line_length = 88
-filter_files = True

tests/test_wsireader.py

@@ -2118,7 +2118,7 @@ def test_ngff_omero_below_min_version(tmp_path):
         wsireader.WSIReader.open(sample_copy)
 
 
-def test_ngff_omero_above_max_version(tmp_path):
+def test_ngff_omero_above_max_version(tmp_path, caplog):
     """Test for FileNotSupported when omero version is above maximum."""
     sample = _fetch_remote_sample("ngff-1")
     # Create a copy of the sample
@@ -2130,8 +2130,10 @@ def test_ngff_omero_above_max_version(tmp_path):
     zattrs["omero"]["version"] = "10.0"
     with open(sample_copy / ".zattrs", "w") as fh:
         json.dump(zattrs, fh, indent=2)
-    with pytest.raises(FileNotSupported):
+    # Check that the warning is logged
+    with caplog.at_level(logging.WARNING):
         wsireader.WSIReader.open(sample_copy)
+    assert "maximum supported version" in caplog.text
 
 
 def test_ngff_multiscales_below_min_version(tmp_path):
@@ -2150,7 +2152,7 @@ def test_ngff_multiscales_below_min_version(tmp_path):
         wsireader.WSIReader.open(sample_copy)
 
 
-def test_ngff_multiscales_above_max_version(tmp_path):
+def test_ngff_multiscales_above_max_version(tmp_path, caplog):
     """Test for FileNotSupported when multiscales version is above maximum."""
     sample = _fetch_remote_sample("ngff-1")
     # Create a copy of the sample
@@ -2162,8 +2164,10 @@ def test_ngff_multiscales_above_max_version(tmp_path):
     zattrs["multiscales"][0]["version"] = "10.0"
     with open(sample_copy / ".zattrs", "w") as fh:
         json.dump(zattrs, fh, indent=2)
-    with pytest.raises(FileNotSupported):
+    # Check that the warning is logged
+    with caplog.at_level(logging.WARNING):
         wsireader.WSIReader.open(sample_copy)
+    assert "maximum supported version" in caplog.text
 
 
 def test_ngff_non_numeric_version(tmp_path, monkeypatch):

tiatoolbox/wsicore/wsireader.py

@@ -165,7 +165,7 @@ def is_ngff(
                 max_version,
                 multiscales_versions,
             )
-            return False
+            return True
 
     if len(multiscales_versions) > 1:
         logger.warning(
@@ -189,7 +189,7 @@ def is_ngff(
             max_version,
             multiscales_versions,
         )
-        return False
+        return True
 
     return is_zarr(path)
 
@@ -3881,7 +3881,7 @@ def _info(self) -> WSIMeta:
             )
             for level in self.wsi.levels
         ]
-        dataset = self.wsi.base_level.datasets[0]
+        dataset = self.wsi.levels.base_level.datasets[0]
         # Get pixel spacing in mm from DICOM file and convert to um/px (mpp)
         mm_per_pixel = dataset.pixel_spacing
         mpp = (mm_per_pixel.width * 1e3, mm_per_pixel.height * 1e3)