Add unit tests for arcade collection convert tasks (#80)

* Bump scikit-image (0.19.3 -> 0.24.0)

* Add Python 3.11 to workflows

* Add Python 3.11 to tox

* Start adding unit tests and documentation for convert to simularium task

* Finish adding unit tests and docstrings for convert to simularium tasks

* Fix linting issues

* Move build tar instance to test utilities module

* Add docstrings and unit tests for convert to contours task

* Add docstrings and unit tests for convert to images task

* Remove test return values

* Add docstrings and unit tests for convert to meshes task

* Rename to locations tar for clarity

* Add ignore to pyproject

* Apply linting suggestions for convert to meshes task

* Update convert to images task to support TFE format

* Add docstrings and unit tests for convert to colorizer task

* Rename colorizer to TFE

* Add docstrings to convert to projection task

.github/workflows/build.yml

@@ -8,14 +8,15 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ["3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11"]
 
     steps:
 
     - name: Checkout the repo
       uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
+      id: setup-python
       uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
@@ -31,7 +32,7 @@ jobs:
       uses: actions/cache@v4
       with:
         path: .venv
-        key: ${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
+        key: ${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}
 
     - name: Install dependencies
       if: steps.cached-dependencies.outputs.cache-hit != 'true'

.github/workflows/documentation.yml

@@ -15,6 +15,7 @@ jobs:
       uses: actions/checkout@v4
 
     - name: Set up Python 3.9
+      id: setup-python
       uses: actions/setup-python@v5
       with:
         python-version: 3.9
@@ -30,7 +31,7 @@ jobs:
       uses: actions/cache@v4
       with:
         path: .venv
-        key: ${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
+        key: ${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}
 
     - name: Install dependencies
       if: steps.cached-dependencies.outputs.cache-hit != 'true'

.github/workflows/lint.yml

@@ -12,6 +12,7 @@ jobs:
       uses: actions/checkout@v4
 
     - name: Set up Python 3.9
+      id: setup-python
       uses: actions/setup-python@v5
       with:
         python-version: 3.9
@@ -27,7 +28,7 @@ jobs:
       uses: actions/cache@v4
       with:
         path: .venv
-        key: ${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
+        key: ${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}
 
     - name: Install dependencies
       if: steps.cached-dependencies.outputs.cache-hit != 'true'

pyproject.toml

@@ -13,7 +13,7 @@ python = "^3.9"
 prefect = "^2.14.3"
 numpy = "^1.24.2"
 pandas = "^1.5.3"
-scikit-image = "^0.19.3"
+scikit-image = "^0.24.0"
 simulariumio = "^1.7.0"
 matplotlib = "^3.7.2"
 
@@ -43,7 +43,7 @@ build-backend = "poetry.core.masonry.api"
 disable = [
     "missing-module-docstring",
 ]
-good-names = ["i", "j", "k", "x", "y", "z", "u", "v", "w", "ds", "dt", "ax"]
+good-names = ["i", "j", "k", "x", "y", "z", "u", "v", "w", "ds", "dt", "dx", "dy", "dz", "ax"]
 
 [tool.pylint.design]
 max-args = 10 # maximum number of arguments for function / method
@@ -95,6 +95,9 @@ max-args = 10
     "INP001", # implicit-namespace-package
     "ANN201", # missing-return-type-undocumented-public-function
     "S311",   # suspicious-non-cryptographic-random-usage
+    "ANN001", # missing-type-function-argument
+    "ANN003", # missing-type-kwargs
+    "ANN202", # missing-type-args
 ]
 
 [tool.coverage.report]
@@ -107,7 +110,7 @@ exclude_lines = [
 legacy_tox_ini = """
 [tox]
 isolated_build = True
-envlist = py{39,310}, format, lint, typecheck
+envlist = py{39,310,311}, format, lint, typecheck
 skipsdist=True
 
 [testenv]

src/arcade_collection/convert/__init__.py

@@ -2,20 +2,20 @@
 
 from prefect import task
 
-from .convert_to_colorizer import convert_to_colorizer
 from .convert_to_contours import convert_to_contours
 from .convert_to_images import convert_to_images
 from .convert_to_meshes import convert_to_meshes
 from .convert_to_projection import convert_to_projection
 from .convert_to_simularium import convert_to_simularium
 from .convert_to_simularium_objects import convert_to_simularium_objects
 from .convert_to_simularium_shapes import convert_to_simularium_shapes
+from .convert_to_tfe import convert_to_tfe
 
-convert_to_colorizer = task(convert_to_colorizer)
 convert_to_contours = task(convert_to_contours)
 convert_to_images = task(convert_to_images)
 convert_to_meshes = task(convert_to_meshes)
 convert_to_projection = task(convert_to_projection)
 convert_to_simularium = task(convert_to_simularium)
 convert_to_simularium_objects = task(convert_to_simularium_objects)
 convert_to_simularium_shapes = task(convert_to_simularium_shapes)
+convert_to_tfe = task(convert_to_tfe)

src/arcade_collection/convert/convert_to_contours.py

@@ -11,33 +11,64 @@
     "side1": (0, 2, 1),
     "side2": (2, 1, 0),
 }
+"""Axis rotations for different contour views."""
 
 
 def convert_to_contours(
     series_key: str,
-    data_tar: tarfile.TarFile,
+    locations_tar: tarfile.TarFile,
     frame: int,
     regions: list[str],
     box: tuple[int, int, int],
     indices: dict[str, list[int]],
 ) -> dict[str, dict[str, dict[int, list]]]:
-    locations = extract_tick_json(data_tar, series_key, frame, "LOCATIONS")
+    """
+    Convert data to iso-valued contours.
+
+    Contours are calculated using "marching squares" method. Note that these
+    contours follow the iso-values, which means that a single "square" voxel
+    will produce a diamond-shaped contour. For the exact outline of a set of
+    voxels, consider using ``extract_voxel_contours`` from the
+    ``abm_shape_collection`` package.
+
+    Parameters
+    ----------
+    series_key
+        Simulation series key.
+    locations_tar
+        Archive of location data.
+    frame
+        Frame number.
+    regions
+        List of regions.
+    box
+        Size of bounding box.
+    indices
+        Map of view to slice indices.
+
+    Returns
+    -------
+    :
+        Map of region, view, and index to contours.
+    """
+
+    locations = extract_tick_json(locations_tar, series_key, frame, "LOCATIONS")
 
     contours: dict[str, dict[str, dict[int, list]]] = {
-        region: {view: {} for view in indices.keys()} for region in regions
+        region: {view: {} for view in indices} for region in regions
     }
 
     for location in locations:
         for region in regions:
             array = np.zeros(box)
-            voxels = get_location_voxels(location, region)
+            voxels = get_location_voxels(location, region if region != "DEFAULT" else None)
 
             if len(voxels) == 0:
                 continue
 
             array[tuple(np.transpose(voxels))] = 1
 
-            for view in indices.keys():
+            for view in indices:
                 array_rotated = np.moveaxis(array, [0, 1, 2], ROTATIONS[view])
 
                 for index in indices[view]:
@@ -49,6 +80,9 @@ def convert_to_contours(
                     if index not in contours[region][view]:
                         contours[region][view][index] = []
 
-                    contours[region][view][index].extend(measure.find_contours(array_slice))
+                    array_contours = [
+                        contour.tolist() for contour in measure.find_contours(array_slice)
+                    ]
+                    contours[region][view][index].extend(array_contours)
 
     return contours