diff --git a/.github/workflows/mypy-type-check.yml b/.github/workflows/mypy-type-check.yml
index e87cf1c28..a22f339c5 100644
--- a/.github/workflows/mypy-type-check.yml
+++ b/.github/workflows/mypy-type-check.yml
@@ -39,4 +39,9 @@ jobs:
tiatoolbox/__main__.py \
tiatoolbox/typing.py \
tiatoolbox/tiatoolbox.py \
- tiatoolbox/utils/*.py
+ tiatoolbox/utils/*.py \
+ tiatoolbox/tools/__init__.py \
+ tiatoolbox/tools/stainextract.py \
+ tiatoolbox/tools/pyramid.py \
+ tiatoolbox/tools/tissuemask.py \
+ tiatoolbox/tools/graph.py
diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 4ce2bf445..0ef67b49e 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -30,7 +30,7 @@ jobs:
sudo apt update
sudo apt-get install -y libopenslide-dev openslide-tools libopenjp2-7 libopenjp2-tools
python -m pip install --upgrade pip
- python -m pip install ruff==0.1.13 pytest pytest-cov pytest-runner
+ python -m pip install ruff==0.2.1 pytest pytest-cov pytest-runner
pip install -r requirements/requirements.txt
- name: Cache tiatoolbox static assets
uses: actions/cache@v3
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index bc0650353..935cf209b 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -68,7 +68,7 @@ repos:
language: python
- repo: https://github.com/astral-sh/ruff-pre-commit
# Ruff version.
- rev: v0.1.14
+ rev: v0.2.1
hooks:
- id: ruff
args: [--fix, --exit-non-zero-on-fix]
diff --git a/benchmarks/annotation_nquery.ipynb b/benchmarks/annotation_nquery.ipynb
index 458ecbb22..64a58794a 100644
--- a/benchmarks/annotation_nquery.ipynb
+++ b/benchmarks/annotation_nquery.ipynb
@@ -71,7 +71,7 @@
"from shapely.geometry import Polygon\n",
"\n",
"sys.path.append(\"..\") # If running locally without pypi installed tiatoolbox\n",
- "from tiatoolbox.annotation.storage import ( # noqa: E402\n",
+ "from tiatoolbox.annotation.storage import (\n",
" Annotation,\n",
" AnnotationStore,\n",
" DictionaryStore,\n",
diff --git a/benchmarks/annotation_store.ipynb b/benchmarks/annotation_store.ipynb
index 128ad387c..6c8b83d65 100644
--- a/benchmarks/annotation_store.ipynb
+++ b/benchmarks/annotation_store.ipynb
@@ -207,8 +207,8 @@
"\n",
"sys.path.append(\"..\") # If running locally without pypi installed tiatoolbox\n",
"\n",
- "from tiatoolbox import logger # noqa: E402\n",
- "from tiatoolbox.annotation.storage import ( # noqa: E402\n",
+ "from tiatoolbox import logger\n",
+ "from tiatoolbox.annotation.storage import (\n",
" Annotation,\n",
" DictionaryStore,\n",
" SQLiteStore,\n",
diff --git a/benchmarks/annotation_store_alloc.py b/benchmarks/annotation_store_alloc.py
index 41b85043f..d5b6df9cb 100644
--- a/benchmarks/annotation_store_alloc.py
+++ b/benchmarks/annotation_store_alloc.py
@@ -139,12 +139,12 @@ def __exit__(self: memray, *args: object) -> None:
# Intentionally blank.
-import numpy as np # noqa: E402
-import psutil # noqa: E402
-from shapely.geometry import Polygon # noqa: E402
-from tqdm import tqdm # noqa: E402
+import numpy as np
+import psutil
+from shapely.geometry import Polygon
+from tqdm import tqdm
-from tiatoolbox.annotation.storage import ( # noqa: E402
+from tiatoolbox.annotation.storage import (
Annotation,
DictionaryStore,
SQLiteStore,
diff --git a/examples/full-pipelines/slide-graph.ipynb b/examples/full-pipelines/slide-graph.ipynb
index de6f2b60f..54d1cdbde 100644
--- a/examples/full-pipelines/slide-graph.ipynb
+++ b/examples/full-pipelines/slide-graph.ipynb
@@ -397,7 +397,7 @@
"# https://docs.gdc.cancer.gov/Encyclopedia/pages/TCGA_Barcode/\n",
"wsi_patient_codes = np.array([\"-\".join(v.split(\"-\")[:3]) for v in wsi_names])\n",
"wsi_labels = np.array(\n",
- " [clinical_info[v] if v in clinical_info else np.nan for v in wsi_patient_codes],\n",
+ " [clinical_info.get(v, np.nan) for v in wsi_patient_codes],\n",
")\n",
"\n",
"# * Filter the WSIs and paths that do not have labels\n",
diff --git a/pyproject.toml b/pyproject.toml
index dbf71f456..05463efe8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -72,7 +72,7 @@ search = 'TOOLBOX_VER: {current_version}'
replace = 'TOOLBOX_VER: {new_version}'
[tool.ruff]
-select = [
+lint.select = [
"A", # flake8-builtins
"B", # flake8-bugbear
"D", # pydocstyle, need to enable for docstrings check.
@@ -126,13 +126,13 @@ select = [
"SLOT", # flake8-slots
"ASYNC", # flake8-async
]
-ignore = []
+lint.ignore = []
# Allow Ruff to discover `*.ipynb` files.
include = ["*.py", "*.pyi", "**/pyproject.toml", "*.ipynb"]
# Allow autofix for all enabled rules (when `--fix`) is provided.
-fixable = ["A", "B", "C", "D", "E", "F", "G", "I", "N", "Q", "S", "T", "W", "ANN", "ARG", "BLE", "COM", "DJ", "DTZ", "EM", "ERA", "EXE", "FBT", "ICN", "INP", "ISC", "NPY", "PD", "PGH", "PIE", "PL", "PT", "PTH", "PYI", "RET", "RSE", "RUF", "SIM", "SLF", "TCH", "TID", "TRY", "UP", "YTT"]
-unfixable = []
+lint.fixable = ["A", "B", "C", "D", "E", "F", "G", "I", "N", "Q", "S", "T", "W", "ANN", "ARG", "BLE", "COM", "DJ", "DTZ", "EM", "ERA", "EXE", "FBT", "ICN", "INP", "ISC", "NPY", "PD", "PGH", "PIE", "PL", "PT", "PTH", "PYI", "RET", "RSE", "RUF", "SIM", "SLF", "TCH", "TID", "TRY", "UP", "YTT"]
+lint.unfixable = []
# Exclude a variety of commonly ignored directories.
exclude = [
@@ -149,27 +149,27 @@ exclude = [
]
# Ignore `F401` (import violations) in all `__init__.py` files.
-per-file-ignores = {"__init__.py" = ["F401"], "tests/*" = ["T201", "PGH001", "SLF001", "S101", "PLR2004"], "benchmarks/*" = ["T201", "INP001"], "pre-commit/*" = ["T201", "INP001"], "tiatoolbox/cli/*" = ["PLR0913"]}
+lint.per-file-ignores = {"__init__.py" = ["F401"], "tests/*" = ["T201", "PGH001", "SLF001", "S101", "PLR2004"], "benchmarks/*" = ["T201", "INP001"], "pre-commit/*" = ["T201", "INP001"], "tiatoolbox/cli/*" = ["PLR0913"]}
# Same as Black.
line-length = 88
# Allow unused variables when underscore-prefixed.
-dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
+lint.dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
# Minimum Python version 3.8.
target-version = "py38"
-[tool.ruff.mccabe]
+[tool.ruff.lint.mccabe]
# Unlike Flake8, default to a complexity level of 10.
max-complexity = 14
# need to enable for docstrings check.
-[tool.ruff.pydocstyle]
+[tool.ruff.lint.pydocstyle]
# Use Google-style docstrings.
convention = "google"
-[tool.ruff.pylint]
+[tool.ruff.lint.pylint]
max-args = 10
[tool.mypy]
diff --git a/requirements/requirements_dev.txt b/requirements/requirements_dev.txt
index 6911165c5..7c58e0703 100644
--- a/requirements/requirements_dev.txt
+++ b/requirements/requirements_dev.txt
@@ -12,7 +12,7 @@ pytest>=7.2.0
pytest-cov>=4.0.0
pytest-runner>=6.0
pytest-xdist[psutil]
-ruff==0.1.13 # This will be updated by pre-commit bot to latest version
+ruff==0.2.1 # This will be updated by pre-commit bot to latest version
toml>=0.10.2
twine>=4.0.1
wheel>=0.37.1
diff --git a/tests/test_dsl.py b/tests/test_dsl.py
index e09753556..ad811ac6e 100644
--- a/tests/test_dsl.py
+++ b/tests/test_dsl.py
@@ -101,7 +101,7 @@ class TestSQLite:
@staticmethod
def test_prop_or_prop() -> None:
"""Test OR operator between two prop accesses."""
- query = eval( # skipcq: PYL-W0123 # noqa: S307
+ query = eval( # skipcq: PYL-W0123
"(props['int'] == 2) | (props['int'] == 3)",
SQL_GLOBALS,
{},
@@ -143,7 +143,7 @@ def test_number_binary_operations(
"""Check that binary operations between ints does not error."""
for op in BINARY_OP_STRINGS:
query = f"2 {op} 2"
- result = eval( # skipcq: PYL-W0123 # noqa: S307
+ result = eval( # skipcq: PYL-W0123
query,
eval_globals,
eval_locals,
@@ -159,7 +159,7 @@ def test_property_binary_operations(
"""Check that binary operations between properties does not error."""
for op in BINARY_OP_STRINGS:
query = f"props['int'] {op} props['int']"
- result = eval( # skipcq: PYL-W0123 # noqa: S307
+ result = eval( # skipcq: PYL-W0123
query,
eval_globals,
eval_locals,
@@ -175,7 +175,7 @@ def test_r_binary_operations(
"""Test right hand binary operations between numbers and properties."""
for op in BINARY_OP_STRINGS:
query = f"2 {op} props['int']"
- result = eval( # skipcq: PYL-W0123 # noqa: S307
+ result = eval( # skipcq: PYL-W0123
query,
eval_globals,
eval_locals,
@@ -191,7 +191,7 @@ def test_number_prefix_operations(
"""Test prefix operations on numbers."""
for op in PREFIX_OP_STRINGS:
query = f"{op}1"
- result = eval( # skipcq: PYL-W0123 # noqa: S307
+ result = eval( # skipcq: PYL-W0123
query,
eval_globals,
eval_locals,
@@ -207,7 +207,7 @@ def test_property_prefix_operations(
"""Test prefix operations on properties."""
for op in PREFIX_OP_STRINGS:
query = f"{op}props['int']"
- result = eval( # skipcq: PYL-W0123 # noqa: S307
+ result = eval( # skipcq: PYL-W0123
query,
eval_globals,
eval_locals,
@@ -222,7 +222,7 @@ def test_regex_nested_props(
) -> None:
"""Test regex on nested properties."""
query = "props['nesting']['fib'][4]"
- result = eval( # skipcq: PYL-W0123 # noqa: S307
+ result = eval( # skipcq: PYL-W0123
query,
eval_globals,
eval_locals,
@@ -237,7 +237,7 @@ def test_regex_str_props(
) -> None:
"""Test regex on string properties."""
query = "regexp('Hello', props['string'])"
- result = eval( # skipcq: PYL-W0123 # noqa: S307
+ result = eval( # skipcq: PYL-W0123
query,
eval_globals,
eval_locals,
@@ -252,7 +252,7 @@ def test_regex_str_str(
) -> None:
"""Test regex on string and string."""
query = "regexp('Hello', 'Hello world!')"
- result = eval( # skipcq: PYL-W0123 # noqa: S307
+ result = eval( # skipcq: PYL-W0123
query,
eval_globals,
eval_locals,
@@ -267,7 +267,7 @@ def test_regex_props_str(
) -> None:
"""Test regex on property and string."""
query = "regexp(props['string'], 'Hello world!')"
- result = eval( # skipcq: PYL-W0123 # noqa: S307
+ result = eval( # skipcq: PYL-W0123
query,
eval_globals,
eval_locals,
@@ -282,7 +282,7 @@ def test_regex_ignore_case(
) -> None:
"""Test regex with ignorecase flag."""
query = "regexp('hello', props['string'], re.IGNORECASE)"
- result = eval( # skipcq: PYL-W0123 # noqa: S307
+ result = eval( # skipcq: PYL-W0123
query,
eval_globals,
eval_locals,
@@ -297,7 +297,7 @@ def test_regex_no_match(
) -> None:
"""Test regex with no match."""
query = "regexp('Yello', props['string'])"
- result = eval( # skipcq: PYL-W0123 # noqa: S307
+ result = eval( # skipcq: PYL-W0123
query,
eval_globals,
eval_locals,
@@ -312,7 +312,7 @@ def test_has_key(
) -> None:
"""Test has_key function."""
query = "has_key(props, 'foo')"
- result = eval( # skipcq: PYL-W0123 # noqa: S307
+ result = eval( # skipcq: PYL-W0123
query,
eval_globals,
eval_locals,
@@ -327,7 +327,7 @@ def test_is_none(
) -> None:
"""Test is_none function."""
query = "is_none(props['null'])"
- result = eval( # skipcq: PYL-W0123 # noqa: S307
+ result = eval( # skipcq: PYL-W0123
query,
eval_globals,
eval_locals,
@@ -342,7 +342,7 @@ def test_is_not_none(
) -> None:
"""Test is_not_none function."""
query = "is_not_none(props['int'])"
- result = eval( # skipcq: PYL-W0123 # noqa: S307
+ result = eval( # skipcq: PYL-W0123
query,
eval_globals,
eval_locals,
@@ -357,7 +357,7 @@ def test_nested_has_key(
) -> None:
"""Test nested has_key function."""
query = "has_key(props['dict'], 'a')"
- result = eval( # skipcq: PYL-W0123 # noqa: S307
+ result = eval( # skipcq: PYL-W0123
query,
eval_globals,
eval_locals,
@@ -372,7 +372,7 @@ def test_list_sum(
) -> None:
"""Test sum function on a list."""
query = "sum(props['list'])"
- result = eval( # skipcq: PYL-W0123 # noqa: S307
+ result = eval( # skipcq: PYL-W0123
query,
eval_globals,
eval_locals,
@@ -387,7 +387,7 @@ def test_abs(
) -> None:
"""Test abs function."""
query = "abs(props['neg'])"
- result = eval( # skipcq: PYL-W0123 # noqa: S307
+ result = eval( # skipcq: PYL-W0123
query,
eval_globals,
eval_locals,
@@ -402,7 +402,7 @@ def test_not(
) -> None:
"""Test not operator."""
query = "not props['bool']"
- result = eval( # skipcq: PYL-W0123 # noqa: S307
+ result = eval( # skipcq: PYL-W0123
query,
eval_globals,
eval_locals,
@@ -417,7 +417,7 @@ def test_props_int_keys(
) -> None:
"""Test props with int keys."""
query = "props['list'][1]"
- result = eval( # skipcq: PYL-W0123 # noqa: S307
+ result = eval( # skipcq: PYL-W0123
query,
eval_globals,
eval_locals,
@@ -432,7 +432,7 @@ def test_props_get(
) -> None:
"""Test props.get function."""
query = "is_none(props.get('foo'))"
- result = eval( # skipcq: PYL-W0123 # noqa: S307
+ result = eval( # skipcq: PYL-W0123
query,
eval_globals,
eval_locals,
@@ -447,7 +447,7 @@ def test_props_get_default(
) -> None:
"""Test props.get function with default."""
query = "props.get('foo', 42)"
- result = eval( # skipcq: PYL-W0123 # noqa: S307
+ result = eval( # skipcq: PYL-W0123
query,
eval_globals,
eval_locals,
@@ -462,7 +462,7 @@ def test_in_list(
) -> None:
"""Test in operator for list."""
query = "1 in props.get('list')"
- result = eval( # skipcq: PYL-W0123 # noqa: S307
+ result = eval( # skipcq: PYL-W0123
query,
eval_globals,
eval_locals,
@@ -478,7 +478,7 @@ def test_has_key_exception(
"""Test has_key function with exception."""
query = "has_key(1, 'a')"
with pytest.raises(TypeError, match="(not iterable)|(Unsupported type)"):
- _ = eval( # skipcq: PYL-W0123 # noqa: S307
+ _ = eval( # skipcq: PYL-W0123
query,
eval_globals,
eval_locals,
@@ -492,7 +492,7 @@ def test_logical_and(
) -> None:
"""Test logical and operator."""
query = "props['bool'] & is_none(props['null'])"
- result = eval( # skipcq: PYL-W0123 # noqa: S307
+ result = eval( # skipcq: PYL-W0123
query,
eval_globals,
eval_locals,
@@ -507,7 +507,7 @@ def test_logical_or(
) -> None:
"""Test logical or operator."""
query = "props['bool'] | (props['int'] < 2)"
- result = eval( # skipcq: PYL-W0123 # noqa: S307
+ result = eval( # skipcq: PYL-W0123
query,
eval_globals,
eval_locals,
@@ -522,7 +522,7 @@ def test_nested_logic(
) -> None:
"""Test nested logical operators."""
query = "(props['bool'] | (props['int'] < 2)) & abs(props['neg'])"
- result = eval( # skipcq: PYL-W0123 # noqa: S307
+ result = eval( # skipcq: PYL-W0123
query,
eval_globals,
eval_locals,
@@ -537,7 +537,7 @@ def test_contains_list(
) -> None:
"""Test contains operator for list."""
query = "1 in props['list']"
- result = eval( # skipcq: PYL-W0123 # noqa: S307
+ result = eval( # skipcq: PYL-W0123
query,
eval_globals,
eval_locals,
@@ -552,7 +552,7 @@ def test_contains_dict(
) -> None:
"""Test contains operator for dict."""
query = "'a' in props['dict']"
- result = eval( # skipcq: PYL-W0123 # noqa: S307
+ result = eval( # skipcq: PYL-W0123
query,
eval_globals,
eval_locals,
@@ -567,7 +567,7 @@ def test_contains_str(
) -> None:
"""Test contains operator for str."""
query = "'Hello' in props['string']"
- result = eval( # skipcq: PYL-W0123 # noqa: S307
+ result = eval( # skipcq: PYL-W0123
query,
eval_globals,
eval_locals,
@@ -582,7 +582,7 @@ def test_key_with_period(
) -> None:
"""Test key with period."""
query = "props['dot.key']"
- result = eval( # skipcq: PYL-W0123 # noqa: S307
+ result = eval( # skipcq: PYL-W0123
query,
eval_globals,
eval_locals,
diff --git a/tests/test_wsireader.py b/tests/test_wsireader.py
index 390751b5d..76a5d3861 100644
--- a/tests/test_wsireader.py
+++ b/tests/test_wsireader.py
@@ -204,7 +204,7 @@ def read_bounds_level_consistency(wsi: WSIReader, bounds: IntBounds) -> None:
# from interpolation when calculating the downsampled levels. This
# adds some tolerance for the comparison.
blurred = [cv2.GaussianBlur(img, (5, 5), cv2.BORDER_REFLECT) for img in resized]
- as_float = [img.astype(np.float_) for img in blurred]
+ as_float = [img.astype(np.float64) for img in blurred]
# Pair-wise check resolutions for mean squared error
for i, a in enumerate(as_float):
@@ -2646,7 +2646,7 @@ def test_read_rect_level_consistency(wsi: WSIReader) -> None:
# from interpolation when calculating the downsampled levels. This
# adds some tolerance for the comparison.
blurred = [cv2.GaussianBlur(img, (5, 5), cv2.BORDER_REFLECT) for img in resized]
- as_float = [img.astype(np.float_) for img in blurred]
+ as_float = [img.astype(np.float64) for img in blurred]
# Pair-wise check resolutions for mean squared error
for i, a in enumerate(as_float):
diff --git a/tiatoolbox/annotation/storage.py b/tiatoolbox/annotation/storage.py
index 429beee80..19e3f959f 100644
--- a/tiatoolbox/annotation/storage.py
+++ b/tiatoolbox/annotation/storage.py
@@ -2028,7 +2028,9 @@ def transform(
transformed_geoms = {
key: transform(annotation.geometry) for key, annotation in self.items()
}
- self.patch_many(transformed_geoms.keys(), transformed_geoms.values())
+ _keys = transformed_geoms.keys()
+ _values = transformed_geoms.values()
+ self.patch_many(_keys, _values)
def __del__(self: AnnotationStore) -> None:
"""Implements destructor method.
diff --git a/tiatoolbox/tools/graph.py b/tiatoolbox/tools/graph.py
index 6114b9b48..c3b138ddd 100644
--- a/tiatoolbox/tools/graph.py
+++ b/tiatoolbox/tools/graph.py
@@ -18,7 +18,7 @@
from numpy.typing import ArrayLike
-def delaunay_adjacency(points: ArrayLike, dthresh: Number) -> list:
+def delaunay_adjacency(points: ArrayLike, dthresh: float) -> list:
"""Create an adjacency matrix via Delaunay triangulation from a list of coordinates.
Points which are further apart than dthresh will not be connected.
@@ -28,7 +28,7 @@ def delaunay_adjacency(points: ArrayLike, dthresh: Number) -> list:
Args:
points (ArrayLike):
An nxm list of coordinates.
- dthresh (int):
+ dthresh (float):
Distance threshold for triangulation.
Returns:
@@ -57,6 +57,7 @@ def delaunay_adjacency(points: ArrayLike, dthresh: Number) -> list:
tessellation = Delaunay(points)
# Find all connected neighbours for each point in the set of
# triangles. Starting with an empty dictionary.
+ triangle_neighbours: defaultdict
triangle_neighbours = defaultdict(set)
# Iterate over each triplet of point indexes which denotes a
# triangle within the tessellation.
@@ -157,7 +158,7 @@ def edge_index_to_triangles(edge_index: ArrayLike) -> ArrayLike:
def affinity_to_edge_index(
affinity_matrix: torch.Tensor | ArrayLike,
- threshold: Number = 0.5,
+ threshold: float = 0.5,
) -> torch.tensor | ArrayLike:
"""Convert an affinity matrix (similarity matrix) to an edge index.
@@ -233,12 +234,12 @@ def _umap_reducer(graph: dict[str, ArrayLike]) -> ArrayLike:
def build(
points: ArrayLike,
features: ArrayLike,
- lambda_d: Number = 3.0e-3,
- lambda_f: Number = 1.0e-3,
- lambda_h: Number = 0.8,
- connectivity_distance: Number = 4000,
- neighbour_search_radius: Number = 2000,
- feature_range_thresh: Number | None = 1e-4,
+ lambda_d: float = 3.0e-3,
+ lambda_f: float = 1.0e-3,
+ lambda_h: float = 0.8,
+ connectivity_distance: int = 4000,
+ neighbour_search_radius: int = 2000,
+ feature_range_thresh: float | None = 1e-4,
) -> dict[str, ArrayLike]:
"""Build a graph via hybrid clustering in spatial and feature space.
@@ -416,7 +417,7 @@ def build(
@classmethod
def visualise(
- cls: SlideGraphConstructor,
+ cls: type[SlideGraphConstructor],
graph: dict[str, ArrayLike],
color: ArrayLike | str | Callable | None = None,
node_size: Number | ArrayLike | Callable = 25,
@@ -510,8 +511,8 @@ def visualise(
# Plot the nodes
plt.scatter(
*nodes.T,
- c=color(graph) if isinstance(color, Callable) else color,
- s=node_size(graph) if isinstance(node_size, Callable) else node_size,
+ c=color(graph) if callable(color) else color,
+ s=node_size(graph) if callable(node_size) else node_size,
zorder=2,
)
diff --git a/tiatoolbox/tools/pyramid.py b/tiatoolbox/tools/pyramid.py
index 1a797ebc3..a6506fb46 100644
--- a/tiatoolbox/tools/pyramid.py
+++ b/tiatoolbox/tools/pyramid.py
@@ -129,7 +129,7 @@ def level_count(self: TilePyramidGenerator) -> int:
total_level_count = super_level_count + 1 + self.sub_tile_level_count
return int(total_level_count)
- def get_thumb_tile(self: TilePyramidGenerator) -> Image:
+ def get_thumb_tile(self: TilePyramidGenerator) -> Image.Image:
"""Return a thumbnail which fits the whole slide in one tile.
The thumbnail output size has the longest edge equal to the tile
@@ -157,7 +157,7 @@ def get_tile(
pad_mode: str = "constant",
interpolation: str = "optimise",
transparent_value: int | None = None,
- ) -> Image:
+ ) -> Image.Image:
"""Get a tile at a given level and coordinate.
Note that levels are in the reverse order of those in WSIReader.
@@ -223,7 +223,7 @@ def get_tile(
)
output_size = np.repeat(output_size, 2).astype(int)
thumb = self.get_thumb_tile()
- thumb.thumbnail(output_size)
+ thumb.thumbnail((output_size[0], output_size[1]))
return thumb
slide_dimensions = np.array(self.wsi.info.slide_dimensions)
if all(slide_dimensions < [baseline_x, baseline_y]):
@@ -331,7 +331,7 @@ def save_tile(tile_path: Path, tile: Image.Image) -> None:
msg = "Unsupported compression for zip."
raise ValueError(msg)
- archive = zipfile.ZipFile(
+ zip_archive = zipfile.ZipFile(
path,
mode="w",
compression=compression2enum[compression],
@@ -343,7 +343,7 @@ def save_tile(tile_path: Path, tile: Image.Image) -> None:
tile.save(bio, format="jpeg")
bio.seek(0)
data = bio.read()
- archive.writestr(
+ zip_archive.writestr(
str(tile_path),
data,
compress_type=compression2enum[compression],
@@ -360,7 +360,7 @@ def save_tile(tile_path: Path, tile: Image.Image) -> None:
msg = "Unsupported compression for tar."
raise ValueError(msg)
- archive = tarfile.TarFile.open(path, mode=compression2mode[compression])
+ tar_archive = tarfile.TarFile.open(path, mode=compression2mode[compression])
def save_tile(tile_path: Path, tile: Image.Image) -> None:
"""Write the tile to the output zip."""
@@ -368,9 +368,9 @@ def save_tile(tile_path: Path, tile: Image.Image) -> None:
tile.save(bio, format="jpeg")
bio.seek(0)
tar_info = tarfile.TarInfo(name=str(tile_path))
- tar_info.mtime = time.time()
+ tar_info.mtime = int(time.time())
tar_info.size = bio.tell()
- archive.addfile(tarinfo=tar_info, fileobj=bio)
+ tar_archive.addfile(tarinfo=tar_info, fileobj=bio)
for level in range(self.level_count):
for x, y in np.ndindex(self.tile_grid_size(level)):
@@ -378,13 +378,17 @@ def save_tile(tile_path: Path, tile: Image.Image) -> None:
tile_path = self.tile_path(level, x, y)
save_tile(tile_path, tile)
- if container is not None:
- archive.close()
+ if container == "zip":
+ zip_archive.close()
+ if container == "tar":
+ tar_archive.close()
def __len__(self: TilePyramidGenerator) -> int:
"""Return length of instance attributes."""
- return sum(
- np.prod(self.tile_grid_size(level)) for level in range(self.level_count)
+ return int(
+ sum(
+ np.prod(self.tile_grid_size(level)) for level in range(self.level_count)
+ ),
)
def __iter__(self: TilePyramidGenerator) -> Iterator:
@@ -452,7 +456,7 @@ def tile_group(self: ZoomifyGenerator, level: int, x: int, y: int) -> int:
cumulative_sum = sum(np.prod(self.tile_grid_size(n)) for n in range(level))
index_in_level = np.ravel_multi_index((y, x), self.tile_grid_size(level)[::-1])
tile_index = cumulative_sum + index_in_level
- return tile_index // 256 # the tile group
+ return int(tile_index // 256) # the tile group
def tile_path(self: ZoomifyGenerator, level: int, x: int, y: int) -> Path:
"""Generate the Zoomify path for a specified tile.
@@ -537,7 +541,7 @@ def __init__(
mapper = {key: (*color, 1) for key, color in zip(types, colors)}
self.renderer.mapper = lambda x: mapper[x]
- def get_thumb_tile(self: AnnotationTileGenerator) -> Image:
+ def get_thumb_tile(self: AnnotationTileGenerator) -> Image.Image:
"""Return a thumbnail which fits the whole slide in one tile.
The thumbnail output size has the longest edge equal to the tile
@@ -587,7 +591,7 @@ def get_tile(
pad_mode: str | None = None,
interpolation: str | None = None,
transparent_value: int | None = None, # noqa: ARG002
- ) -> Image:
+ ) -> Image.Image:
"""Render a tile at a given level and coordinate.
Note that levels are in the reverse order of those in WSIReader.
@@ -646,20 +650,21 @@ def get_tile(
scale = self.level_downsample(level)
baseline_x = (x * self.tile_size * scale) - (self.overlap * scale)
baseline_y = (y * self.tile_size * scale) - (self.overlap * scale)
- coord = [baseline_x, baseline_y]
+ coord = (int(baseline_x), int(baseline_y))
if level < self.sub_tile_level_count:
output_size = self.output_tile_size // 2 ** (
self.sub_tile_level_count - level
)
output_size = np.repeat(output_size, 2).astype(int)
thumb = self.get_thumb_tile()
- thumb.thumbnail(output_size)
+ thumb.thumbnail((output_size[0], output_size[1]))
return thumb
slide_dimensions = np.array(self.info.slide_dimensions)
if all(slide_dimensions < [baseline_x, baseline_y]):
raise IndexError
- bounds = locsize2bounds(coord, [self.output_tile_size * scale] * 2)
+ size = [self.output_tile_size * scale] * 2
+ bounds = locsize2bounds(coord, (int(size[0]), int(size[1])))
tile = self.renderer.render_annotations(
self.store,
bounds,
diff --git a/tiatoolbox/tools/tissuemask.py b/tiatoolbox/tools/tissuemask.py
index ac99490d8..c2ea74d80 100644
--- a/tiatoolbox/tools/tissuemask.py
+++ b/tiatoolbox/tools/tissuemask.py
@@ -18,11 +18,6 @@ class TissueMasker(ABC):
"""
- def __init__(self: TissueMasker) -> None:
- """Initialize :class:`TissueMasker`."""
- super().__init__()
- self.fitted = False
-
@abstractmethod
def fit(
self: TissueMasker,
@@ -55,9 +50,6 @@ def transform(self: TissueMasker, images: np.ndarray) -> np.ndarray:
e.g. regions of tissue vs background.
"""
- if not self.fitted:
- msg = "Fit must be called before transform."
- raise SyntaxError(msg)
def fit_transform(
self: TissueMasker,
@@ -76,7 +68,7 @@ def fit_transform(
**kwargs (dict):
Other key word arguments passed to fit.
"""
- self.fit(images, **kwargs)
+ self.fit(images, masks=None, **kwargs)
return self.transform(images)
@@ -97,13 +89,15 @@ class OtsuTissueMasker(TissueMasker):
"""
- def __init__(self: TissueMasker) -> None:
+ def __init__(self: OtsuTissueMasker) -> None:
"""Initialize :class:`OtsuTissueMasker`."""
- super().__init__()
+ self.threshold: float | None
+ self.fitted: bool
self.threshold = None
+ self.fitted = False
def fit(
- self: TissueMasker,
+ self: OtsuTissueMasker,
images: np.ndarray,
masks: np.ndarray | None = None, # noqa: ARG002
) -> None:
@@ -141,7 +135,7 @@ def fit(
self.fitted = True
- def transform(self: TissueMasker, images: np.ndarray) -> np.ndarray:
+ def transform(self: OtsuTissueMasker, images: np.ndarray) -> np.ndarray:
"""Create masks using the threshold found during :func:`fit`.
Args:
@@ -155,7 +149,9 @@ def transform(self: TissueMasker, images: np.ndarray) -> np.ndarray:
channels).
"""
- super().transform(images)
+ if not self.fitted:
+ msg = "Fit must be called before transform."
+ raise SyntaxError(msg)
masks = []
for image in images:
@@ -165,7 +161,7 @@ def transform(self: TissueMasker, images: np.ndarray) -> np.ndarray:
mask = (grey < self.threshold).astype(bool)
masks.append(mask)
- return masks
+ return np.array(masks)
class MorphologicalMasker(OtsuTissueMasker):
@@ -206,7 +202,7 @@ class MorphologicalMasker(OtsuTissueMasker):
"""
def __init__(
- self: TissueMasker,
+ self: MorphologicalMasker,
*,
mpp: float | tuple[float, float] | None = None,
power: float | tuple[float, float] | None = None,
@@ -250,18 +246,19 @@ def __init__(
# Convert MPP to an integer kernel_size
if mpp is not None:
- mpp = np.array(mpp)
- if mpp.size != 2: # noqa: PLR2004
- mpp = mpp.repeat(2)
- kernel_size = np.max([32 / mpp, [1, 1]], axis=0)
+ mpp_array = np.array(mpp)
+ if mpp_array.size != 2: # noqa: PLR2004
+ mpp_array = mpp_array.repeat(2)
+ kernel_size = np.max([32 / mpp_array, [1, 1]], axis=0)
# Ensure kernel_size is a length 2 numpy array
- kernel_size = np.array(kernel_size)
- if kernel_size.size != 2: # noqa: PLR2004
- kernel_size = kernel_size.repeat(2)
+ kernel_size_array = np.array(kernel_size)
+ if kernel_size_array.size != 2: # noqa: PLR2004
+ kernel_size_array = kernel_size_array.repeat(2)
# Convert to an integer double/ pair
- self.kernel_size = tuple(np.round(kernel_size).astype(int))
+ self.kernel_size: tuple[int, int]
+ self.kernel_size = tuple(np.round(kernel_size_array).astype(int))
# Create structuring element for morphological operations
self.kernel = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, self.kernel_size)
@@ -270,7 +267,7 @@ def __init__(
if self.min_region_size is None:
self.min_region_size = np.sum(self.kernel)
- def transform(self: TissueMasker, images: np.ndarray) -> None:
+ def transform(self: MorphologicalMasker, images: np.ndarray) -> np.ndarray:
"""Create masks using the found threshold followed by morphological operations.
Args:
@@ -284,7 +281,9 @@ def transform(self: TissueMasker, images: np.ndarray) -> None:
channels).
"""
- super().transform(images)
+ if not self.fitted:
+ msg = "Fit must be called before transform."
+ raise SyntaxError(msg)
results = []
for image in images:
@@ -304,4 +303,4 @@ def transform(self: TissueMasker, images: np.ndarray) -> None:
mask = cv2.morphologyEx(mask, cv2.MORPH_DILATE, self.kernel)
results.append(mask.astype(bool))
- return results
+ return np.array(results)
diff --git a/tiatoolbox/utils/misc.py b/tiatoolbox/utils/misc.py
index 49ef21bad..4eb01b833 100644
--- a/tiatoolbox/utils/misc.py
+++ b/tiatoolbox/utils/misc.py
@@ -1308,7 +1308,7 @@ def dict_to_zarr(
compressor = (
kwargs["compressor"] if "compressor" in kwargs else numcodecs.Zstd(level=1)
)
- chunks = kwargs["chunks"] if "chunks" in kwargs else 10000
+ chunks = kwargs.get("chunks", 10000)
# ensure proper zarr extension
save_path = save_path.parent.absolute() / (save_path.stem + ".zarr")
diff --git a/tiatoolbox/utils/visualization.py b/tiatoolbox/utils/visualization.py
index 3e7c9da46..e75b7376c 100644
--- a/tiatoolbox/utils/visualization.py
+++ b/tiatoolbox/utils/visualization.py
@@ -633,6 +633,7 @@ def __init__( # noqa: PLR0913
self.secondary_cmap = secondary_cmap
self.blur_radius = blur_radius
self.function_mapper = function_mapper
+ self.blur: ImageFilter.GaussianBlur | None
if blur_radius > 0:
self.blur = ImageFilter.GaussianBlur(blur_radius)
self.edge_thickness = 0
diff --git a/tiatoolbox/visualization/bokeh_app/main.py b/tiatoolbox/visualization/bokeh_app/main.py
index 608dc23a9..0f29a4aea 100644
--- a/tiatoolbox/visualization/bokeh_app/main.py
+++ b/tiatoolbox/visualization/bokeh_app/main.py
@@ -64,14 +64,14 @@
# GitHub actions seems unable to find TIAToolbox unless this is here
sys.path.insert(0, str(Path(__file__).parent.parent.parent.parent))
-from tiatoolbox import logger # noqa: E402
-from tiatoolbox.models.engine.nucleus_instance_segmentor import ( # noqa: E402
+from tiatoolbox import logger
+from tiatoolbox.models.engine.nucleus_instance_segmentor import (
NucleusInstanceSegmentor,
)
-from tiatoolbox.tools.pyramid import ZoomifyGenerator # noqa: E402
-from tiatoolbox.utils.visualization import random_colors # noqa: E402
-from tiatoolbox.visualization.ui_utils import get_level_by_extent # noqa: E402
-from tiatoolbox.wsicore.wsireader import WSIReader # noqa: E402
+from tiatoolbox.tools.pyramid import ZoomifyGenerator
+from tiatoolbox.utils.visualization import random_colors
+from tiatoolbox.visualization.ui_utils import get_level_by_extent
+from tiatoolbox.wsicore.wsireader import WSIReader
if TYPE_CHECKING: # pragma: no cover
from bokeh.document import Document