Proof of principle napari workflows mock

pyproject.toml

@@ -35,12 +35,13 @@ scikit-image = { version = ">=0.19", optional = true }
 napari-segment-blobs-and-things-with-membranes = { version = "^0.3.3", optional = true }
 napari-workflows = { version = "^0.2.8", optional = true }
 napari-skimage-regionprops = { version = "^0.8.1", optional = true }
+napari-skimage-regionprops-mock = { file="tests/data/napari_workflows/mock_package/dist/napari_skimage_regionprops_mock-9.9.9-py3-none-any.whl", optional = true }
 napari-tools-menu = { version = "^0.1.19", optional = true }
 cellpose = { version = "~2.2", optional = true }
 torch = { version = "<=2.0.0", optional = true }
 
 [tool.poetry.extras]
-fractal-tasks = ["Pillow", "imageio-ffmpeg", "scikit-image", "llvmlite", "napari-segment-blobs-and-things-with-membranes", "napari-workflows", "napari-skimage-regionprops", "napari-tools-menu", "cellpose", "torch"]
+fractal-tasks = ["Pillow", "imageio-ffmpeg", "scikit-image", "llvmlite", "napari-segment-blobs-and-things-with-membranes", "napari-workflows", "napari-skimage-regionprops", "napari-skimage-regionprops-mock", "napari-tools-menu", "cellpose", "torch"]
 
 [tool.poetry.group.dev]
 optional = true

tests/data/napari_workflows/mock_package/.gitignore

@@ -0,0 +1,82 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+.napari_cache
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask instance folder
+instance/
+
+# Sphinx documentation
+docs/_build/
+
+# MkDocs documentation
+/site/
+
+# PyBuilder
+target/
+
+# IPython Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# OS
+.DS_Store
+
+# written by setuptools_scm
+*/_version.py
+/.idea/
+/venv/
+test.csv

tests/data/napari_workflows/mock_package/LICENSE

@@ -0,0 +1,34 @@
+This folder is a mock of the original
+https://github.com/haesleinhuepf/napari-skimage-regionprops/ package. The
+original copyright notice is reported below:
+
+-------------------------------------------------------------------------------
+
+
+Copyright (c) 2021, Robert Haase, Physics of Life, TU Dresden
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of napari-skimage-regionprops nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

tests/data/napari_workflows/mock_package/MANIFEST.in

@@ -0,0 +1,6 @@
+include requirements.txt
+
+recursive-exclude * __pycache__
+recursive-exclude demo *
+recursive-exclude images *
+recursive-exclude * *.py[co]

tests/data/napari_workflows/mock_package/README.md

@@ -0,0 +1,4 @@
+Build command:
+```
+poetry run python -m build --wheel
+```

tests/data/napari_workflows/mock_package/napari_skimage_regionprops_mock/__init__.py

@@ -0,0 +1,15 @@
+import logging
+
+from napari_plugin_engine import napari_hook_implementation
+
+from ._regionprops import regionprops_table  # , regionprops_table_all_frames
+
+logging.critical(
+    "WARNING: THIS IS A MOCK OF THE ACTUAL "
+    "'napari_skimage_regionprops' PACKAGE"
+)
+
+
+@napari_hook_implementation
+def napari_experimental_provide_function():
+    return [regionprops_table]

tests/data/napari_workflows/mock_package/napari_skimage_regionprops_mock/_regionprops.py

@@ -0,0 +1,41 @@
+import warnings
+
+import numpy as np
+import pandas
+
+try:
+    import napari
+except Exception as e:
+    warnings.warn(str(e))
+
+from napari_tools_menu import register_function
+
+
+@register_function(menu="Measurement tables > Regionprops (scikit-image, nsr)")
+def regionprops_table(
+    image: "napari.types.ImageData",
+    labels: "napari.types.LabelsData",
+    size: bool = True,
+    intensity: bool = True,
+    perimeter: bool = False,
+    shape: bool = False,
+    position: bool = False,
+    moments: bool = False,
+    napari_viewer: "napari.Viewer" = None,
+) -> "pandas.DataFrame":
+    """
+    MOCK OF THE ORIGINAL FUNCTION
+    """
+
+    num_labels = len(np.unique(labels))
+    int_values = np.arange(num_labels)
+    float_values = np.arange(num_labels) + 0.5
+    table = dict(
+        label=int_values,
+        area=float_values,
+        bbox_area=float_values,
+        equivalent_diameter=float_values,
+        convex_area=float_values,
+    )
+    df = pandas.DataFrame(table)
+    return df

tests/data/napari_workflows/mock_package/requirements.txt

@@ -0,0 +1,5 @@
+napari-plugin-engine>=0.1.4
+numpy
+pandas
+napari-tools-menu>=0.1.19
+napari-workflows

tests/data/napari_workflows/mock_package/setup.py

@@ -0,0 +1,34 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+import codecs
+import os
+
+from setuptools import setup
+
+
+def read(fname):
+    file_path = os.path.join(os.path.dirname(__file__), fname)
+    return codecs.open(file_path, encoding="utf-8").read()
+
+
+# Add your dependencies in requirements.txt
+# Note: you can add test-specific requirements in tox.ini
+requirements = []
+with open("requirements.txt") as f:
+    for line in f:
+        stripped = line.split("#")[0].strip()
+        if len(stripped) > 0:
+            requirements.append(stripped)
+
+
+setup(
+    name="napari-skimage-regionprops-mock",
+    author="Marcelo Zoccoler, Robert Haase",
+    author_email="[email protected]",
+    license="BSD-3",
+    description='MOCK OF "A regionprops table widget plugin for napari"',
+    python_requires=">=3.8",
+    install_requires=requirements,
+    version="9.9.9",
+    setup_requires=["setuptools_scm"],
+)

tests/data/napari_workflows/wf_4_mock.yaml

@@ -0,0 +1,12 @@
+!!python/object:napari_workflows._workflow.Workflow
+_tasks:
+  regionprops_DAPI: !!python/tuple
+  - !!python/name:napari_skimage_regionprops_mock._regionprops.regionprops_table ''
+  - dapi_img
+  - dapi_label_img
+  - true
+  - false
+  - false
+  - false
+  - false
+  - false

tests/tasks/test_workflows_napari_workflows.py

@@ -32,6 +32,14 @@
     napari_workflows_wrapper,
 )
 
+try:
+    import napari_skimage_regionprops_mock
+
+    has_napari_skimage_regionprops_mock = True
+    print(napari_skimage_regionprops_mock)
+except ModuleNotFoundError:
+    has_napari_skimage_regionprops_mock = False
+
 
 def test_napari_workflow(
     tmp_path: Path,
@@ -365,35 +373,6 @@ def test_relabeling(
         )
     debug(metadata)
 
-    # Re-run with overwrite=True
-    for component in metadata["image"]:
-        napari_workflows_wrapper(
-            input_paths=[str(zarr_path)],
-            output_path=str(zarr_path),
-            metadata=metadata,
-            component=component,
-            input_specs=input_specs,
-            output_specs=output_specs,
-            workflow_file=workflow_file,
-            input_ROI_table="FOV_ROI_table",
-            overwrite=True,
-        )
-
-    # Re-run with overwrite=False
-    with pytest.raises(OverwriteNotAllowedError):
-        for component in metadata["image"]:
-            napari_workflows_wrapper(
-                input_paths=[str(zarr_path)],
-                output_path=str(zarr_path),
-                metadata=metadata,
-                component=component,
-                input_specs=input_specs,
-                output_specs=output_specs,
-                workflow_file=workflow_file,
-                input_ROI_table="FOV_ROI_table",
-                overwrite=False,
-            )
-
     # Check output
     image_zarr = Path(zarr_path / metadata["image"][0])
     validate_labels_and_measurements(
@@ -781,3 +760,77 @@ def test_napari_workflow_CYX_wrong_dimensions(
                 level=2,
             )
         debug(e.value)
+
+
+@pytest.mark.skipif(
+    not has_napari_skimage_regionprops_mock,
+    reason="napari_skimage_regionprops_mock not available",
+)
+def test_napari_workflow_mock(
+    tmp_path: Path,
+    testdata_path: Path,
+    zenodo_zarr: list[str],
+    zenodo_zarr_metadata: list[dict[str, Any]],
+):
+
+    # Init
+    zarr_path = tmp_path / "tmp_out/"
+    metadata = prepare_3D_zarr(
+        str(zarr_path), zenodo_zarr, zenodo_zarr_metadata
+    )
+    debug(zarr_path)
+    debug(metadata)
+
+    # Prepare parameters for first napari-workflows task (labeling)
+    workflow_file = str(testdata_path / "napari_workflows/wf_1.yaml")
+    input_specs: dict[str, NapariWorkflowsInput] = {
+        "input": {"type": "image", "channel": {"wavelength_id": "A01_C01"}},  # type: ignore # noqa
+    }
+    output_specs: dict[str, NapariWorkflowsOutput] = {
+        "Result of Expand labels (scikit-image, nsbatwm)": {  # type: ignore # noqa
+            "type": "label",
+            "label_name": "label_DAPI",
+        },
+    }
+
+    # Run once
+    for component in metadata["image"]:
+        napari_workflows_wrapper(
+            input_paths=[str(zarr_path)],
+            output_path=str(zarr_path),
+            metadata=metadata,
+            component=component,
+            input_specs=input_specs,
+            output_specs=output_specs,
+            workflow_file=workflow_file,
+            input_ROI_table="FOV_ROI_table",
+            level=2,
+        )
+    debug(metadata)
+
+    # Prepare parameters for second napari-workflows task (measurement)
+    workflow_file = str(testdata_path / "napari_workflows/wf_4_mock.yaml")
+    input_specs = {
+        "dapi_img": {"type": "image", "channel": {"wavelength_id": "A01_C01"}},  # type: ignore # noqa
+        "dapi_label_img": {"type": "label", "label_name": "label_DAPI"},  # type: ignore # noqa
+    }
+    output_specs = {
+        "regionprops_DAPI": {  # type: ignore # noqa
+            "type": "dataframe",
+            "table_name": "regionprops_DAPI",
+        },
+    }
+
+    # Run once
+    for component in metadata["image"]:
+        napari_workflows_wrapper(
+            input_paths=[str(zarr_path)],
+            output_path=str(zarr_path),
+            metadata=metadata,
+            component=component,
+            input_specs=input_specs,
+            output_specs=output_specs,
+            workflow_file=workflow_file,
+            input_ROI_table="FOV_ROI_table",
+        )
+    debug(metadata)