auto-options-python 0.1.4__py3-none-any.whl

auto_options_python-0.1.4.dist-info/METADATA

@@ -0,0 +1,58 @@
+Metadata-Version: 2.4
+Name: auto-options-python
+Version: 0.1.4
+Summary: Mange command options in python and create QWidgets for them.
+Author: Volker Baecker
+Author-email: volker.baecker@mri.cnrs.fr
+License: MIT License
+        
+        Copyright (c) 2025 Montpellier Ressources Imagerie
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
+Project-URL: Bug Tracker, https://github.com/MontpellierRessourcesImagerie/auto-options-python/issues
+Project-URL: Documentation, https://montpellierressourcesimagerie.github.io/auto-options-python/
+Project-URL: Source Code, https://github.com/MontpellierRessourcesImagerie/auto-options-python
+Project-URL: User Support, https://github.com/MontpellierRessourcesImagerie/auto-options-python/issues
+Classifier: Development Status :: 4 - Beta
+Classifier: Framework :: napari
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: appdirs
+Requires-Dist: pyqt5
+Requires-Dist: qtpy
+Requires-Dist: napari
+Requires-Dist: pyperclip
+Requires-Dist: matplotlib
+Dynamic: license-file
+
+# auto-options-python
+Mange command options in python and create QWidgets for them.

auto_options_python-0.1.4.dist-info/RECORD

@@ -0,0 +1,19 @@
+auto_options_python-0.1.4.dist-info/licenses/LICENSE,sha256=V8dHxj3sXeWgZfNq_3nAXemaXxbfmQvLHKy4jBBV-eQ,1088
+autooptions/__init__.py,sha256=oW5bTiKfFmjiMLcgreBwwL6FOWSHLwasxckp50y_UdU,233
+autooptions/_version.py,sha256=dCmqTphVTtnLNv5-BupgeR8iw0z5iLBjWjRFRXqOyso,520
+autooptions/array_util.py,sha256=ZHgfTbxu-hc_rxJg8_sg1YfMyOHHykhHm0N4uNvEhjQ,1533
+autooptions/napari_util.py,sha256=S-9v9Q_YHAD3EBqB6Y8w2xN9_7jKNuvNVS27RmXk4Hs,4496
+autooptions/options.py,sha256=Ya9Nx6haj4dgtRFJD_T1quDhQj1L4bPgzAAD2GMw61o,13951
+autooptions/qtutil.py,sha256=uEM_KJSnpvqb7bNCk6tMUXxvDcptdeJNJTpIfT_T4m0,9252
+autooptions/widget.py,sha256=GdjkoDry-55mbKUgIbcDXwmZr2W4Ci4yCIplRTH29Y4,13929
+autooptions/_tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+autooptions/_tests/test_array_util.py,sha256=enGGtzk1uXBMOtcgaCVhJz1zyRK7_pXOSIg1E69LQXQ,557
+autooptions/_tests/test_napari_util.py,sha256=ja4cMcWx4AoIPX3PJfSd50HdJuYLDJLMMNLXb8lVyRs,4578
+autooptions/_tests/test_options.py,sha256=4Y2fMfobqlSd2f4ahOypswQinqLMlDXg5hP5Wpmw9WI,6554
+autooptions/_tests/test_qtutil.py,sha256=YQ2L_e5ju_umAYaC9x_aUWwUI9XcwrHZVJthnzRY73g,8875
+autooptions/_tests/test_widget.py,sha256=Jtdb2uKceAe4YBfHdK1sE9YYBvhni512Fx3MFx_SQKQ,5154
+scratch/options.py,sha256=lsmQ8zwzmyyR0iqxkRmpduqUdsdndHx4oShDmVrxHfg,1332
+auto_options_python-0.1.4.dist-info/METADATA,sha256=oobt8KbF2FiZh2D4xRCMtxyBEldK4qLSbgPK2MsbMS4,2832
+auto_options_python-0.1.4.dist-info/WHEEL,sha256=aeYiig01lYGDzBgS8HxWXOg3uV61G9ijOsup-k9o1sk,91
+auto_options_python-0.1.4.dist-info/top_level.txt,sha256=7hs1Zw5d4qriyx2pJbx7RLv2UgRAnvR9X-TqCCIzYPg,20
+auto_options_python-0.1.4.dist-info/RECORD,,

auto_options_python-0.1.4.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (82.0.1)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

auto_options_python-0.1.4.dist-info/licenses/LICENSE

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+MIT License
+
+Copyright (c) 2025 Montpellier Ressources Imagerie
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

auto_options_python-0.1.4.dist-info/top_level.txt

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+autooptions
+scratch

autooptions/__init__.py

@@ -0,0 +1,16 @@
+try:
+    from ._version import version as __version__
+except ImportError:
+    __version__ = "unknown"
+
+from .options import (
+    Options
+)
+
+from .widget import (
+    OptionsWidget,
+)
+__all__ = (
+    "Options",
+    "OptionsWidget",
+)

autooptions/_tests/test_array_util.py

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+import numpy as np
+from autooptions.array_util import ArrayUtil
+
+
+def testStripZeroRowsAndColumns():
+
+    testData = np.array([
+        [1, 0, 3],
+        [0, 0, 0],
+        [5, 0, 6]
+    ])
+
+    data, columns, rows = ArrayUtil.stripZeroRowsAndColumns(testData)
+    assert data.shape == (2,2)
+    assert data[0 ,0] == 1
+    assert data[0, 1] == 3
+    assert data[1, 0] == 5
+    assert data[1, 1] == 6
+    assert len(columns) == 2
+    assert columns[0] == 0
+    assert columns[1] == 2
+    assert len(rows) == 2
+    assert rows[0] == 0
+    assert rows[1] == 2

autooptions/_tests/test_napari_util.py

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+import pytest
+import numpy as np
+from napari.layers import Labels, Image, Points
+from autooptions.napari_util import NapariUtil
+
+class Layer:
+    pass
+
+
+
+@pytest.fixture
+def layers():
+    layers = [Image(np.zeros(shape=(3, 3), dtype=np.uint8), name="toad", metadata={'fft': 'fft'}),
+              Image(np.zeros(shape=(3, 3), dtype=np.uint8), name="frog", scale=(1, 3), units="nm"),
+              Points(np.zeros((3, 3)), name="ant"), Labels(np.zeros(shape=(4, 4), dtype=np.uint8), name="oak"),
+              Points(np.zeros((2, 3)), name="bee"), Image(np.zeros(shape=(3, 3), dtype=np.uint8), name="bird")]
+    yield layers
+
+
+
+def test_constructor(make_napari_viewer_proxy):
+    viewer = make_napari_viewer_proxy()
+    napariUtil = NapariUtil(viewer)
+    assert napariUtil.viewer == viewer
+
+
+def testGetImageLayers(make_napari_viewer_proxy, layers):
+    viewer = make_napari_viewer_proxy()
+    napariUtil = NapariUtil(viewer)
+    for layer in layers:
+        viewer.add_layer(layer)
+
+    assert len(napariUtil.getImageLayers()) == 3
+    assert napariUtil.getImageLayers()[0] == "toad"
+    assert napariUtil.getImageLayers()[1] == "frog"
+    assert napariUtil.getImageLayers()[2] == "bird"
+
+
+def testGetFFTLayers(make_napari_viewer_proxy, layers):
+    viewer = make_napari_viewer_proxy()
+    napariUtil = NapariUtil(viewer)
+    for layer in layers:
+        viewer.add_layer(layer)
+
+    fftLayers = napariUtil.getFFTLayers()
+    assert len(fftLayers) == 1
+    assert fftLayers[0] == 'toad'
+
+
+def testGetLabelLayers(make_napari_viewer_proxy, layers):
+    viewer = make_napari_viewer_proxy()
+    napariUtil = NapariUtil(viewer)
+    for layer in layers:
+        viewer.add_layer(layer)
+
+    labelLayers = napariUtil.getLabelLayers()
+    assert len(labelLayers) == 1
+    assert 'oak' == labelLayers[0]
+
+
+def testGetPointLayers(make_napari_viewer_proxy, layers):
+    viewer = make_napari_viewer_proxy()
+    napariUtil = NapariUtil(viewer)
+    for layer in layers:
+        viewer.add_layer(layer)
+
+    pointLayers = napariUtil.getPointsLayers()
+    assert len(pointLayers) == 2
+    assert pointLayers[0] == 'ant'
+    assert pointLayers[1] == 'bee'
+
+
+def testGetLayersOfType(make_napari_viewer_proxy, layers):
+    viewer = make_napari_viewer_proxy()
+    napariUtil = NapariUtil(viewer)
+    for layer in layers:
+        viewer.add_layer(layer)
+
+    labelLayers = napariUtil.getLayersOfType(Labels)
+    assert len(labelLayers) == 1
+    assert labelLayers[0] == 'oak'
+
+
+def testGetDataOfLayerWithName(make_napari_viewer_proxy, layers):
+    viewer = make_napari_viewer_proxy()
+    napariUtil = NapariUtil(viewer)
+    for layer in layers:
+        viewer.add_layer(layer)
+
+    data = napariUtil.getDataOfLayerWithName("oak")
+    assert data.shape == (4,4)
+    data = napariUtil.getDataOfLayerWithName("marsupilami")
+    assert data is None
+
+
+def testGetLayerWithName(make_napari_viewer_proxy, layers):
+    viewer = make_napari_viewer_proxy()
+    napariUtil = NapariUtil(viewer)
+    for layer in layers:
+        viewer.add_layer(layer)
+
+    layer = napariUtil.getLayerWithName("bee")
+    assert layer.name == "bee"
+    layer = napariUtil.getLayerWithName("marsupilami")
+    assert layer is None
+
+
+def testGetDataAndScaleOfLayerWithName(make_napari_viewer_proxy, layers):
+    viewer = make_napari_viewer_proxy()
+    napariUtil = NapariUtil(viewer)
+    for layer in layers:
+        viewer.add_layer(layer)
+
+    data, scale, unit = napariUtil.getDataAndScaleOfLayerWithName('frog')
+    assert data.shape == (3,3)
+    assert scale[0] == 1
+    assert scale[1] == 3
+    assert unit == "nanometer"
+
+
+def testGetOriginalPath(make_napari_viewer_proxy, layers):
+    viewer = make_napari_viewer_proxy()
+    napariUtil = NapariUtil(viewer)
+    for layer in layers:
+        viewer.add_layer(layer)
+    toad = napariUtil.getLayerWithName('toad')
+    toad.metadata['original_path'] = "d/e/f"
+    assert napariUtil.getOriginalPath(napariUtil.getLayerWithName('bee')) is None
+    layer = Layer()
+    layer.source = Layer()
+    layer.source.path = "a/b/c"
+    layer.metadata = {}
+    assert napariUtil.getOriginalPath(layer)
+    assert napariUtil.getOriginalPath(toad) == 'd/e/f'
+
+
+def testCopOriginalPath(make_napari_viewer_proxy, layers):
+    viewer = make_napari_viewer_proxy()
+    napariUtil = NapariUtil(viewer)
+    for layer in layers:
+        viewer.add_layer(layer)
+    toad = napariUtil.getLayerWithName('toad')
+    toad.metadata['original_path'] = "d/e/f"
+    frog = napariUtil.getLayerWithName('frog')
+    napariUtil.copyOriginalPath(toad, frog)
+    assert napariUtil.getOriginalPath(frog) == "d/e/f"

autooptions/_tests/test_options.py

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+import os
+import pytest
+from autooptions.options import Options
+
+
+class TestOptions:
+
+
+    @pytest.fixture()
+    def options(self):
+        options = Options("Autooptions Test", "Magic Filter")
+        options.addImage('image', value=None, transient=True)
+        options.addInt('size xy', value=3, widget="input")
+        options.addInt('size z', value=1, widget="input")
+        options.addChoice('footprint', value=None, choices=["none", "cube", "ball", "octahedron"])
+        options.addInt('radius', value=1, widget="input")
+        yield options
+
+
+    def onSomething(self, value):
+        pass
+
+
+    def testConstructor(self):
+        options = Options("Autooptions Test", "Magic Filter")
+        assert options.applicationName == "Autooptions Test"
+        assert options.optionsName == "Magic Filter"
+        assert os.path.exists(os.path.dirname(options.optionsPath))
+
+
+    def testSetDefaultItems(self):
+        options = Options("Autooptions Test", "Magic Filter")
+        items = {'image': {'value': None, 'type': 'image', 'transient': True, 'position': 0, 'callback': None},
+            'size xy': {'type': 'int', 'value': 3, 'transient': False, 'position': 1, 'widget': 'input',
+                     'callback': 'onInputChanged'},
+         'size z': {'type': 'int', 'value': 1, 'transient': False, 'position': 2, 'widget': 'input', 'callback': None},
+         'footprint': {'name': 'footprint', 'value': None, 'type': 'choice',
+                       'choices': ['none', 'cube', 'ball', 'octahedron'], 'transient': False, 'position': None,
+                       'callback': None},
+         'radius': {'type': 'int', 'value': 1, 'transient': False, 'position': 4, 'widget': 'input', 'callback': None}}
+        options.setDefaultValues(items)
+        assert options.getItems() == items
+
+
+    def testGetItems(self, options):
+        items = options.getItems()
+        assert items['size xy']['value'] == 3
+        assert list(items.keys()) == ['image', 'size xy', 'size z', 'footprint', 'radius']
+
+
+    def testSaveAndLoad(self, options):
+        if os.path.exists(options.optionsPath):
+            os.remove(options.optionsPath)
+        oldItems = options.getItems().copy()
+        options.load()
+        self.items = None
+        options.load()
+        assert oldItems == options.getItems()
+
+
+    def testGet(self, options):
+        option = options.get("size xy")
+        assert option["value"] == 3
+
+
+    def testValue(self, options):
+        value = options.value("size xy")
+        assert value == 3
+
+
+    def testSet(self, options):
+        option = {'type': 'int', 'value': 1.365, 'transient': False, 'position': 5, 'widget': 'input', 'callback': None}
+        options.set("sigma", option)
+        optionRetrieved = options.get("sigma")
+        assert optionRetrieved == option
+
+
+
+    def testSetValue(self, options):
+        options.setValue("size xy", 8)
+        assert options.value("size xy") == 8
+
+
+    def testAddImage(self):
+        options = Options("Autooptions Test", "Magic Filter")
+        options.addImage('input image', value="img01", transient=True)
+        assert options.value("input image") == "img01"
+        options.addImage('mask', value="mask", transient=True)
+        assert options.value("mask") == "mask"
+        assert options.get("mask")["position"] == 2
+        assert options.get("mask")["type"] == "image"
+
+
+    def testAddLabels(self):
+        options = Options("Autooptions Test", "Magic Filter")
+        options.addLabels('labels', value="img01_seg", transient=True)
+        assert options.value("labels") == "img01_seg"
+        assert options.get("labels")["type"] == "labels"
+
+
+    def testAddPoints(self):
+        options = Options("Autooptions Test", "Magic Filter")
+        options.addPoints('centroids', value="centroids_layer", transient=True)
+        assert options.value("centroids") == "centroids_layer"
+        assert options.get("centroids")["type"] == "points"
+
+
+    def testAddFFT(self):
+        options = Options("Autooptions Test", "Magic Filter")
+        options.addFFT('fft1', value="img01_fft", transient=True)
+        assert options.value("fft1") == "img01_fft"
+        assert options.get("fft1")["type"] == "fft"
+
+
+    def testAddInt(self, options):
+        options.addInt('threshold', value=50, callback=self.onSomething)
+        assert options.get("threshold")["callback"] == "onSomething"
+        assert options.value("threshold") == 50
+        assert options.get("threshold")["type"] == "int"
+        assert options.get("threshold")["widget"] == "input"
+
+
+    def testAddFloat(self, options):
+        options.addFloat('sigma', value=1.3)
+        assert options.value("sigma") == 1.3
+        assert options.get("sigma")["type"] == "float"
+        assert options.get("sigma")["widget"] == "input"
+
+
+    def testAddChoice(self, options):
+        options.addChoice("no choice")
+        assert options.value("no choice") is None
+        assert options.get("no choice")["type"] == "choice"
+        assert options.get("no choice")["choices"] == []
+        options.addChoice("fruits", value="apple", choices=["orange", "banana", "apple"])
+        assert options.value("fruits") == "apple"
+        assert options.get("fruits")["type"] == "choice"
+        assert options.get("fruits")["choices"] == ["orange", "banana", "apple"]
+
+
+    def testAddStr(self, options):
+        options.addStr('experimenter', value="Albert")
+        assert options.value("experimenter") == "Albert"
+        assert options.get("experimenter")["type"] == "str"
+        assert options.get("experimenter")["widget"] == "input"
+
+
+    def testAddBool(self, options):
+        options.addBool('use gpu', value=True)
+        assert options.value("use gpu") == True
+        assert options.get("use gpu")["type"] == "bool"
+        assert options.get("use gpu")["widget"] == "checkbox"
+        options.addBool('remove background', value=False)
+        assert options.value("remove background") == False
+        assert options.get("remove background")["type"] == "bool"
+        assert options.get("remove background")["widget"] == "checkbox"
+
+
+    def testGetBaseOption(self, options):
+        option = options.getBaseOption(7, True, None, self.onSomething)
+        assert option["value"] == 7
+        assert option["transient"] == True
+        assert option["position"] == 6
+        assert option["callback"] == "onSomething"
+
+
+    def test_GetPosition(self, options):
+        position = options._getPosition(None)
+        assert position == 6
+        position = options._getPosition(3)
+        assert position == 3
+