tomwer 1.3.26__py3-none-any.whl → 1.4.0__py3-none-any.whl

tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_singletomoobj.py

@@ -0,0 +1,40 @@
+import gc
+import os
+import pickle
+import shutil
+import tempfile
+
+import numpy
+from orangecanvas.scheme.readwrite import literal_dumps
+from silx.gui import qt
+from silx.gui.utils.testutils import TestCaseQt
+
+from orangecontrib.tomwer.widgets.control.SingleTomoObjOW import SingleTomoObjOW
+from tomwer.core.volume.hdf5volume import HDF5Volume
+
+
+class TestSingleTomoObjOW(TestCaseQt):
+    def setUp(self):
+        super().setUp()
+        self.window = SingleTomoObjOW()
+        self.folder = tempfile.mkdtemp()
+        self.volume_1 = HDF5Volume(
+            file_path=os.path.join(self.folder, "vol_file.hdf5"),
+            data_path="entry0000",
+            data=numpy.linspace(0, 10, 100 * 100 * 3).reshape(3, 100, 100),
+        )
+        self.volume_1.save()
+
+    def tearDown(self):
+        self.window.setAttribute(qt.Qt.WA_DeleteOnClose)
+        self.window.close()
+        self.window = None
+        shutil.rmtree(self.folder)
+        gc.collect()
+
+    def test(self):
+        self.window.show()
+        self.window.widget.setTomoObject(self.volume_1)
+        # test serialization
+        pickle.dumps(self.window._tomo_obj_setting)
+        literal_dumps(self.window._tomo_obj_setting)

tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_timerow.py

@@ -0,0 +1,25 @@
+# coding: utf-8
+from __future__ import annotations
+
+
+import gc
+
+from silx.gui import qt
+from silx.gui.utils.testutils import TestCaseQt
+
+from orangecontrib.tomwer.widgets.control.TimerOW import TimerOW
+
+
+class TestTimerOW(TestCaseQt):
+    def setUp(self):
+        super().setUp()
+        self.widget = TimerOW()
+
+    def tearDown(self):
+        self.widget.setAttribute(qt.Qt.WA_DeleteOnClose)
+        self.widget.close()
+        self.widget = None
+        gc.collect()
+
+    def test(self):
+        self.widget.show()

tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_tomoobj_series.py

@@ -0,0 +1,96 @@
+import gc
+import os
+import shutil
+import tempfile
+
+import numpy
+from silx.gui import qt
+from silx.gui.utils.testutils import SignalListener, TestCaseQt
+
+from orangecontrib.tomwer.widgets.control.TomoObjSeriesOW import TomoObjSeriesOW
+from tomwer.core.utils.scanutils import HDF5MockContext
+from tomwer.core.volume.hdf5volume import HDF5Volume
+
+
+class TestTomoObjSeriesOW(TestCaseQt):
+    """
+    Test the TomoObjSeriesOW orange widget
+    """
+
+    def setUp(self):
+        super().setUp()
+        self.window = TomoObjSeriesOW()
+        self.folder = tempfile.mkdtemp()
+
+        # connect to the series created signal
+        self._listener = SignalListener()
+        self.window._widget.sigSeriesSelected.connect(self._listener)
+
+    def tearDown(self):
+        self.window.setAttribute(qt.Qt.WA_DeleteOnClose)
+        self.window.close()
+        self.window = None
+        self._listener = None
+        shutil.rmtree(self.folder)
+        gc.collect()
+
+    def test_with_volumes(self):
+        """test the TomoObjSeriesOW with volumes"""
+        volume_1 = HDF5Volume(
+            file_path=os.path.join(self.folder, "vol_file.hdf5"),
+            data_path="entry0000",
+            data=numpy.linspace(0, 10, 100 * 100 * 3).reshape(3, 100, 100),
+        )
+        volume_1.save()
+        volume_2 = HDF5Volume(
+            file_path=os.path.join(self.folder, "vol_file2.hdf5"),
+            data_path="entry0001",
+            data=numpy.linspace(60, 120, 100 * 100 * 5).reshape(5, 100, 100),
+        )
+        volume_2.save()
+
+        assert self._listener.callCount() == 0
+        assert len(self.window._widget._widget.getSelectedSeries()) == 0
+        # add the volume to the possible objects to be added
+        self.window.addTomoObj(volume_1)
+        self.window.addTomoObj(volume_2)
+        assert len(self.window._widget._widget.getSelectedSeries()) == 0
+
+        # add volume to the series defined
+        newSerieWidget = (
+            self.window._widget._widget._seriesDefinitionWidget._manualDefWidget._newSeriesWidget
+        )
+        newSerieWidget.addTomoObjToCurrentSeries(volume_1)
+        assert len(self.window._widget._widget.getSelectedSeries()) == 1
+        newSerieWidget.addTomoObjToCurrentSeries(
+            volume_1
+        )  # try adding twice the same object
+        assert len(self.window._widget._widget.getSelectedSeries()) == 1
+        newSerieWidget.addTomoObjToCurrentSeries(volume_2)
+        assert len(self.window._widget._widget.getSelectedSeries()) == 2
+        assert self._listener.callCount() == 0
+        self.window._widget._selectButton.released.emit()
+        self.qapp.processEvents()
+        assert self._listener.callCount() == 1
+
+    def test_with_scans(self):
+        """test the TomoObjSeriesOW with scans"""
+        with HDF5MockContext(
+            scan_path=os.path.join(self.folder, "test", "scan"), n_proj=100
+        ) as scan:
+            assert self._listener.callCount() == 0
+
+            # add the scan to possible objects to be added
+            self.window.addTomoObj(scan)
+            assert len(self.window._widget._widget.getSelectedSeries()) == 0
+
+            # add scan to the series defined
+            newSerieWidget = (
+                self.window._widget._widget._seriesDefinitionWidget._manualDefWidget._newSeriesWidget
+            )
+            newSerieWidget.addTomoObjToCurrentSeries(scan)
+
+            assert len(self.window._widget._widget.getSelectedSeries()) == 1
+            self.window._widget._selectButton.released.emit()
+            self.qapp.processEvents()
+            assert self._listener.callCount() == 1

tomwer/tests/orangecontrib/tomwer/widgets/control/tests/test_volume_selector.py

@@ -0,0 +1,69 @@
+import gc
+import os
+import pickle
+import shutil
+import tempfile
+
+import numpy
+from orangecanvas.scheme.readwrite import literal_dumps
+from silx.gui import qt
+from silx.gui.utils.testutils import TestCaseQt
+
+from orangecontrib.tomwer.widgets.control.VolumeSelector import VolumeSelectorOW
+from tomwer.core.volume.hdf5volume import HDF5Volume
+
+
+class TestVolumeSelectorOW(TestCaseQt):
+    def setUp(self):
+        super().setUp()
+        self.window = VolumeSelectorOW()
+        self.folder = tempfile.mkdtemp()
+        self.volume_1 = HDF5Volume(
+            file_path=os.path.join(self.folder, "vol_file.hdf5"),
+            data_path="entry0000",
+            data=numpy.linspace(0, 10, 100 * 100 * 3).reshape(3, 100, 100),
+        )
+        self.volume_1.save()
+        self.volume_2 = HDF5Volume(
+            file_path=os.path.join(self.folder, "vol_file2.hdf5"),
+            data_path="entry0001",
+            data=numpy.linspace(60, 120, 100 * 100 * 5).reshape(5, 100, 100),
+        )
+        self.volume_2.save()
+
+    def tearDown(self):
+        self.window.setAttribute(qt.Qt.WA_DeleteOnClose)
+        self.window.close()
+        self.window = None
+        shutil.rmtree(self.folder)
+        gc.collect()
+
+    def test(self):
+        self.window.show()
+        # check adding one volume
+        self.window.addVolume(self.volume_1)
+        assert self.window.widget.dataList.n_data() == 1
+        # check behavior adding the same volume
+        self.window.addVolume(self.volume_1)
+        assert self.window.widget.dataList.n_data() == 1
+        # check adding another volume
+        self.window.addVolume(self.volume_2)
+        assert self.window.widget.dataList.n_data() == 2
+        # check removing volume(s)
+        self.window.removeVolume(self.volume_1)
+        assert self.window.widget.dataList.n_data() == 1
+        self.window.removeVolume(self.volume_1)
+        assert self.window.widget.dataList.n_data() == 1
+        self.window.removeVolume(self.volume_2)
+        assert self.window.widget.dataList.n_data() == 0
+
+        # and adding them back
+        self.window.addVolume(self.volume_1)
+        self.window.addVolume(self.volume_2)
+        assert self.window.widget.dataList.n_data() == 2
+
+        # test serialization
+        self.window._updateSettings()
+        assert len(self.window._scanIDs) == 2
+        pickle.dumps(self.window._scanIDs)
+        literal_dumps(self.window._scanIDs)

orangecontrib/tomwer/widgets/edit/test/test_image_key_editor.py → tomwer/tests/orangecontrib/tomwer/widgets/debugtools/tests/test_dataset_generator.py

@@ -1,7 +1,7 @@
 # coding: utf-8
 # /*##########################################################################
 #
-# Copyright (c) 2017-2019 European Synchrotron Radiation Facility
+# Copyright (c) 2017-2021 European Synchrotron Radiation Facility
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -22,35 +22,36 @@
 # THE SOFTWARE.
 #
 # ###########################################################################*/
+
 __authors__ = ["H. Payno"]
 __license__ = "MIT"
-__date__ = "10/12/2021"
+__date__ = "21/06/2021"
 
 
 import gc
+import shutil
+import tempfile
 
-import pytest
 from silx.gui import qt
 from silx.gui.utils.testutils import TestCaseQt
 
-from orangecontrib.tomwer.widgets.edit.ImageKeyEditorOW import ImageKeyEditorOW
-from tomwer.tests.utils import skip_gui_test
-
+from orangecontrib.tomwer.widgets.debugtools.DatasetGeneratorOW import (
+    DatasetGeneratorOW,
+)
 
-@pytest.mark.skipif(skip_gui_test(), reason="skip gui test")
-class TestImageKeyEditor(TestCaseQt):
-    """Test that the ImageKeyEditorOW widget work correctly (at least launched)"""
 
+class TestDatasetGeneratorOW(TestCaseQt):
     def setUp(self):
-        super().setUp()
-        self._window = ImageKeyEditorOW()
+        self.tmp_dir = tempfile.mkdtemp()
+        self.widget = DatasetGeneratorOW()
+        self.widget.generatorGUI.mainWidget.setRootDir(self.tmp_dir)
 
     def tearDown(self):
-        self._window.setAttribute(qt.Qt.WA_DeleteOnClose)
-        self._window.close()
-        self._window = None
+        shutil.rmtree(self.tmp_dir)
+        self.widget.setAttribute(qt.Qt.WA_DeleteOnClose)
+        self.widget.close()
+        self.widget = None
         gc.collect()
 
     def test(self):
-        self._window.show()
-        self.qWaitForWindowExposed(self._window)
+        self.widget._generate().join()

tomwer/tests/orangecontrib/tomwer/widgets/debugtools/tests/test_object_inspector.py

@@ -0,0 +1,36 @@
+# coding: utf-8
+from __future__ import annotations
+
+
+import gc
+import os
+import shutil
+import tempfile
+
+from silx.gui import qt
+from silx.gui.utils.testutils import TestCaseQt
+
+from orangecontrib.tomwer.widgets.debugtools.ObjectInspectorOW import ObjectInspectorOW
+from tomwer.core.utils.scanutils import MockNXtomo
+
+
+class TestObjectInspectorOW(TestCaseQt):
+    def setUp(self):
+        super().setUp()
+        self.tmp_dir = tempfile.mkdtemp()
+        self.scan = MockNXtomo(
+            scan_path=os.path.join(self.tmp_dir, "myscan"),
+            n_proj=20,
+            n_ini_proj=20,
+            dim=10,
+        ).scan
+
+    def tearDown(self):
+        shutil.rmtree(self.tmp_dir)
+        gc.collect()
+
+    def test(self):
+        widget = ObjectInspectorOW()
+        widget.setObject(self.scan)
+        widget.setAttribute(qt.Qt.WA_DeleteOnClose)
+        widget.close()

{orangecontrib/tomwer/widgets/edit/test → tomwer/tests/orangecontrib/tomwer/widgets/edit/tests}/test_dark_flat_patch.py

@@ -1,31 +1,5 @@
 # coding: utf-8
-# /*##########################################################################
-#
-# Copyright (c) 2017-2019 European Synchrotron Radiation Facility
-#
-# 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.
-#
-# ###########################################################################*/
-__authors__ = ["H. Payno"]
-__license__ = "MIT"
-__date__ = "10/12/2021"
-
+from __future__ import annotations
 
 import gc
 import os

tomwer/tests/orangecontrib/tomwer/widgets/edit/tests/test_image_key_editor.py

@@ -0,0 +1,30 @@
+# coding: utf-8
+from __future__ import annotations
+
+import gc
+
+import pytest
+from silx.gui import qt
+from silx.gui.utils.testutils import TestCaseQt
+
+from orangecontrib.tomwer.widgets.edit.ImageKeyEditorOW import ImageKeyEditorOW
+from tomwer.tests.utils import skip_gui_test
+
+
+@pytest.mark.skipif(skip_gui_test(), reason="skip gui test")
+class TestImageKeyEditor(TestCaseQt):
+    """Test that the ImageKeyEditorOW widget work correctly (at least launched)"""
+
+    def setUp(self):
+        super().setUp()
+        self._window = ImageKeyEditorOW()
+
+    def tearDown(self):
+        self._window.setAttribute(qt.Qt.WA_DeleteOnClose)
+        self._window.close()
+        self._window = None
+        gc.collect()
+
+    def test(self):
+        self._window.show()
+        self.qWaitForWindowExposed(self._window)

tomwer/tests/orangecontrib/tomwer/widgets/edit/tests/test_nxtomo_editor.py

@@ -0,0 +1,138 @@
+import os
+import pickle
+
+import numpy
+import pytest
+from nxtomomill.nexus.nxtomo import NXtomo
+from orangecanvas.scheme.readwrite import literal_dumps
+from silx.gui.utils.testutils import SignalListener
+from nxtomo.nxobject.nxdetector import ImageKey
+
+from orangecontrib.tomwer.widgets.edit.NXtomoEditorOW import NXtomoEditorOW
+from tomwer.core.process.edit.nxtomoeditor import NXtomoEditorKeys
+from tomwer.core.scan.nxtomoscan import NXtomoScan
+from tomwer.tests.utils import skip_gui_test
+from tomwer.gui.utils.qt_utils import QSignalSpy
+from tomwer.tests.conftest import qtapp  # noqa F401
+
+
+def getDefaultConfig() -> dict:
+    """return the configuration of the NXtomo editor. First value is the value of the field, second is: is the associated lock button locked or not"""
+    return {
+        NXtomoEditorKeys.ENERGY: (5.9, False),
+        NXtomoEditorKeys.SAMPLE_DETECTOR_DISTANCE: (2.4, True),
+        NXtomoEditorKeys.FIELD_OF_VIEW: ("Full", False),
+        NXtomoEditorKeys.X_PIXEL_SIZE: (0.023, True),
+        NXtomoEditorKeys.Y_PIXEL_SIZE: (0.025, True),
+        NXtomoEditorKeys.X_FLIPPED: (True, True),
+        NXtomoEditorKeys.Y_FLIPPED: (False, False),
+        NXtomoEditorKeys.X_TRANSLATION: (0.0,),
+        NXtomoEditorKeys.Z_TRANSLATION: (0.0,),
+    }
+
+
+@pytest.mark.skipif(skip_gui_test(), reason="skip gui test")
+def test_NXtomoEditorOW(
+    qtapp,  # noqa F811
+    tmp_path,
+):
+    window = NXtomoEditorOW()
+    # test serialization
+    window.setConfiguration(getDefaultConfig())
+    assert window.getConfiguration() == getDefaultConfig()
+    pickle.dumps(window.getConfiguration())
+
+    # test literal dumps
+    literal_dumps(window.getConfiguration())
+
+    # test widget automation
+    signal_listener = SignalListener()
+    window.sigScanReady.connect(signal_listener)
+    # set up the widget to define and lock distance, energy and x pixel size
+    distance_widget = window.widget.mainWidget._distanceMetricEntry
+    distance_widget.setValue(0.6)
+    distance_widget.setUnit("mm")
+    distance_locker = window.widget.mainWidget._distanceLB
+    distance_locker.setLock(True)
+    energy_widget = window.widget.mainWidget._energyEntry
+    energy_widget.setValue(88.058)
+    energy_locker = window.widget.mainWidget._energyLockerLB
+    energy_locker.setLock(True)
+    x_pixel_widget = window.widget.mainWidget._xPixelSizeMetricEntry
+    x_pixel_widget.setValue(45)
+    x_pixel_widget.setUnit("nm")
+    x_pixel_locker = window.widget.mainWidget._xPixelSizeLB
+    x_pixel_locker.setLock(True)
+
+    # 1.0 create nx tomos with raw data
+    nx_tomo = NXtomo()
+    nx_tomo.instrument.detector.x_pixel_size = (
+        0.023  # should be overwrite by the configuration / lock buttons
+    )
+    nx_tomo.instrument.detector.y_pixel_size = (
+        0.025  # should be overwrite by the configuration / lock buttons
+    )
+    nx_tomo.instrument.detector.field_of_view = "full"
+    nx_tomo.instrument.detector.distance = (
+        2.4  # should be overwrite by the configuration / lock buttons
+    )
+    nx_tomo.instrument.detector.x_flipped = (
+        False  # should be overwrite by the configuration / lock buttons
+    )
+    nx_tomo.instrument.detector.y_flipped = True
+    nx_tomo.energy = 5.9
+    nx_tomo.instrument.detector.image_key_control = [ImageKey.PROJECTION.value] * 12
+    nx_tomo.instrument.detector.data = numpy.empty(shape=(12, 10, 10))
+    nx_tomo.sample.rotation_angle = numpy.linspace(0, 20, num=12)
+
+    file_path = os.path.join(tmp_path, "nxtomo.nx")
+    entry = "entry0000"
+    nx_tomo.save(
+        file_path=file_path,
+        data_path=entry,
+    )
+    # 2.0 set scan to the nxtomo-editor
+    scan = NXtomoScan(file_path, entry)
+    waiter = QSignalSpy(window.sigScanReady)
+    window.setScan(scan=scan)
+    # warning: avoid executing the ewoks task as this will be done
+    # automatically (has some field lock). This would create concurrency task
+    # and could bring some HDF5 concurrency error
+    waiter.wait(5000)
+    # 3.0 check results are as expected
+    # make sure the scan has been re-emitted
+    assert signal_listener.callCount() == 1
+    # make sure the edition of the parameters have been done and only those
+    overwrite_nx_tomo = NXtomo().load(
+        file_path=file_path,
+        data_path=entry,
+        detector_data_as="as_numpy_array",
+    )
+    numpy.testing.assert_almost_equal(
+        overwrite_nx_tomo.instrument.detector.x_pixel_size.si_value, 45e-9
+    )
+    assert (
+        overwrite_nx_tomo.instrument.detector.y_pixel_size.si_value
+        == nx_tomo.instrument.detector.y_pixel_size.si_value
+    )
+    assert (
+        overwrite_nx_tomo.instrument.detector.field_of_view
+        == nx_tomo.instrument.detector.field_of_view
+    )
+    numpy.testing.assert_almost_equal(
+        overwrite_nx_tomo.instrument.detector.distance.value, 6.0e-4
+    )
+    assert (
+        overwrite_nx_tomo.instrument.detector.x_flipped
+        == True  # is lock to True so should load the value and overwrite it
+    )
+
+    assert (
+        overwrite_nx_tomo.instrument.detector.y_flipped
+        == True  # is not locked and is initially set to False (should load it and ignore overwriting)
+    )
+    numpy.testing.assert_almost_equal(overwrite_nx_tomo.energy.value, 88.058)
+    numpy.testing.assert_array_almost_equal(
+        overwrite_nx_tomo.instrument.detector.data,
+        nx_tomo.instrument.detector.data,
+    )

tomwer/tests/orangecontrib/tomwer/widgets/other/tests/test_pythonscript.py

@@ -0,0 +1,31 @@
+import gc
+import logging
+
+from silx.gui import qt
+from silx.gui.utils.testutils import TestCaseQt
+
+from orangecontrib.tomwer.widgets.other.PythonScriptOW import OWPythonScript
+from tomwer.core.scan.nxtomoscan import NXtomoScan
+from tomwer.core.volume.hdf5volume import HDF5Volume
+
+logging.disable(logging.INFO)
+
+
+class TestEDFDarkRefWidget(TestCaseQt):
+    def setUp(self):
+        TestCaseQt.setUp(self)
+        self.widget = OWPythonScript()
+        self._scan = NXtomoScan("my_file.hdf5", entry="entry0000")
+        self._volume = HDF5Volume(file_path="my_volume.hdf5", data_path="volume")
+
+    def tearDown(self):
+        self.widget.setAttribute(qt.Qt.WA_DeleteOnClose)
+        self.widget.close()
+        self.widget = None
+        gc.collect()
+
+    def test_handle_data(self):
+        self.widget.handle_input(self._scan, (1,), "data")
+
+    def test_handle_volume(self):
+        self.widget.handle_input(self._volume, (1,), "volume")