darfix 4.2.0__py3-none-any.whl → 4.3.0__py3-none-any.whl

darfix/tests/orange/test_ewoks.py

@@ -6,17 +6,17 @@ import pytest
 from ewoks import load_graph
 from ewoks import save_graph
 from ewokscore import execute_graph
-from ewoksorange.bindings import ows_to_ewoks
+from ewoksorange.gui.workflows.owscheme import ows_to_ewoks
 
 from darfix.core.moment_types import MomentType
-from darfix.tasks.blindsourceseparation import BlindSourceSeparation
-from darfix.tasks.blindsourceseparation import Method
-from darfix.tasks.dimensiondefinition import DimensionDefinition
-from darfix.tasks.grainplot import GrainPlot
+from darfix.tasks.blind_source_separation import BlindSourceSeparation
+from darfix.tasks.blind_source_separation import Method
+from darfix.tasks.dimension_definition import DimensionDefinition
+from darfix.tasks.grain_plot import GrainPlot
 from darfix.tasks.hdf5_data_selection import HDF5DataSelection
-from darfix.tasks.noiseremoval import NoiseRemoval
+from darfix.tasks.noise_removal import NoiseRemoval
 from darfix.tasks.roi import RoiSelection
-from darfix.tasks.shiftcorrection import ShiftCorrection
+from darfix.tasks.shift_correction import ShiftCorrection
 
 try:
     from importlib.resources import files as resource_files
@@ -122,7 +122,9 @@ def test_example_workflow1(tmpdir, silx_resources):
                     )
 
             numpy.testing.assert_allclose(
-                ref_entry["Mosaicity/Mosaicity"], output_entry["Mosaicity/Mosaicity"]
+                ref_entry["Mosaicity/Mosaicity"],
+                output_entry["Mosaicity/Mosaicity"],
+                atol=0.002,
             )
             numpy.testing.assert_allclose(
                 ref_entry["Orientation distribution/key/image"],
@@ -175,7 +177,9 @@ def test_example_workflow2(tmpdir, load_from_json, silx_resources):
                     )
 
             numpy.testing.assert_allclose(
-                ref_entry["Mosaicity/Mosaicity"], output_entry["Mosaicity/Mosaicity"]
+                ref_entry["Mosaicity/Mosaicity"],
+                output_entry["Mosaicity/Mosaicity"],
+                atol=0.002,
             )
             numpy.testing.assert_allclose(
                 ref_entry["Orientation distribution/key/image"],

darfix/tests/orange/widgets/test_hdf5_data_selection.py

@@ -1,4 +1,5 @@
 import os
+from unittest import mock
 
 import h5py
 import numpy
@@ -58,3 +59,95 @@ def test_HDF5DataSelectionWidgetOW(tmp_path, qtapp):  # noqa F811
 
     dataset = window.get_task_output_value("dataset")
     assert isinstance(dataset, Dataset)
+
+
+def test_bad_file_selection(qtapp):  # noqa F811
+
+    window = HDF5DataSelectionWidgetOW()
+    window._rawDataSelection.setFilePath("file_with_bad_name")
+
+    # Border color is red
+    assert (
+        window._rawDataSelection._fileLineEdit._lineEdit.styleSheet()
+        == window._rawDataSelection._fileLineEdit._ERROR_LINE_EDIT_STYLE_SHEET
+    )
+
+    with mock.patch(
+        "orangecontrib.darfix.widgets.hdf5dataselection.show_error_msg"
+    ) as mock_error_msg:
+
+        window._executeTask()
+        # Should pop an error message because file path does not exist
+        mock_error_msg.assert_called_once()
+
+
+def test_file_with_unexpected_format(tmp_path, qtapp):  # noqa F811
+    raw_data_dir = tmp_path / "raw_data"
+    raw_data_dir.mkdir()
+
+    raw_data_file = os.path.join(raw_data_dir, "raw.hdf5")
+    with h5py.File(raw_data_file, mode="w") as h5f:
+        detector = h5f.create_group("/my_detector/")
+        detector.create_dataset("dataset", (10, 100, 100), numpy.uint16)
+        h5f.create_group("/my_positioners/")
+
+    window = HDF5DataSelectionWidgetOW()
+
+    fileLineEdit = window._rawDataSelection._fileLineEdit
+    detectorLineEdit = window._rawDataSelection._detectorLineEdit
+    positionerLineEdit = window._rawDataSelection._positionersLineEdit
+
+    fileLineEdit._lineEdit.setText(raw_data_file)
+    fileLineEdit._lineEdit.editingFinished.emit()
+
+    # Border color is red
+    assert (
+        detectorLineEdit._lineEdit.styleSheet()
+        == detectorLineEdit._ERROR_LINE_EDIT_STYLE_SHEET
+    )
+
+    # Border color is red
+    assert (
+        positionerLineEdit._lineEdit.styleSheet()
+        == positionerLineEdit._ERROR_LINE_EDIT_STYLE_SHEET
+    )
+
+    with mock.patch(
+        "orangecontrib.darfix.widgets.hdf5dataselection.show_error_msg"
+    ) as mock_error_msg:
+
+        window._executeTask()
+        # Should pop an error message because positioners and detector paths are bad
+        mock_error_msg.assert_called_once()
+
+    window._rawDataSelection.setDetectorPath("/my_detector/dataset")
+
+    # Border recover normal stylesheet
+    assert (
+        detectorLineEdit._lineEdit.styleSheet()
+        == detectorLineEdit._defaultLineEditStyle
+    )
+
+    with mock.patch(
+        "orangecontrib.darfix.widgets.hdf5dataselection.show_error_msg"
+    ) as mock_error_msg:
+
+        window._executeTask()
+        # Should pop an error message because positioners path is bad
+        mock_error_msg.assert_called_once()
+
+    window._rawDataSelection.setPositionersPath("/my_positioners")
+
+    # Border recover normal stylesheet
+    assert (
+        positionerLineEdit._lineEdit.styleSheet()
+        == positionerLineEdit._defaultLineEditStyle
+    )
+
+    with mock.patch(
+        "orangecontrib.darfix.widgets.hdf5dataselection.show_error_msg"
+    ) as mock_error_msg:
+
+        window._executeTask()
+        # No error message as all field are valid now
+        mock_error_msg.assert_not_called()

darfix/tests/tasks/test_data_copy.py

@@ -8,11 +8,9 @@ from darfix.tests.utils import createDataset
 def test_data_copy():
     dataset = Dataset(
         dataset=createDataset(data=numpy.linspace(1, 10, 100).reshape(10, 5, 2)),
-        indices=None,
         bg_dataset=numpy.ones(
             100,
         ).reshape(10, 5, 2),
-        bg_indices=None,
     )
 
     task = DataCopy(

darfix/tests/tasks/{test_dimensiondefinition.py → test_dimension_definition.py}

@@ -6,7 +6,7 @@ import pytest
 from ewokscore.missing_data import MISSING_DATA
 
 from darfix import dtypes
-from darfix.tasks.dimensiondefinition import DimensionDefinition
+from darfix.tasks.dimension_definition import DimensionDefinition
 from darfix.tests.utils import create_3_motors_metadata
 from darfix.tests.utils import createDataset
 

darfix/tests/tasks/test_weak_beam.py

@@ -0,0 +1,9 @@
+from darfix.dtypes import Dataset
+from darfix.tasks.weak_beam import WeakBeam
+
+
+def test_weakbeam(input_dataset, tmp_path):
+    input_dataset.find_dimensions()
+    input_dataset.reshape_data()
+    task = WeakBeam(inputs={"dataset": Dataset(input_dataset), "nvalue": 1})
+    task.execute()

darfix/tests/test_components_matching.py

@@ -3,8 +3,8 @@ import pytest
 from silx.opencl.common import ocl
 from skimage import data
 
-from darfix.core.componentsMatching import ComponentsMatching
-from darfix.core.componentsMatching import Method
+from darfix.core.components_matching import ComponentsMatching
+from darfix.core.components_matching import Method
 
 
 @pytest.fixture(scope="module")

darfix/tests/test_dataset.py

@@ -37,9 +37,8 @@ class _BaseDatasetTest:
         result = numpy.sum(self.dataset.as_array3d(), axis=0)
         numpy.testing.assert_array_equal(zsum, result)
 
-        indices = [0, 1]
-        zsum = self.dataset.zsum(indices)
-        result = numpy.sum(self.dataset.as_array3d(indices), axis=0)
+        zsum = self.dataset.zsum()
+        result = numpy.sum(self.dataset.as_array3d(), axis=0)
         numpy.testing.assert_array_equal(zsum, result)
 
     def test_filter_data(self):
@@ -66,10 +65,6 @@ class _BaseDatasetTest:
 
         self.assertEqual(len(shift), 2)
 
-        shift = self.dataset.find_shift(indices=[0, 1])
-
-        self.assertEqual(len(shift), 2)
-
     def test_pca(self):
 
         H, W = self.dataset.pca()
@@ -79,13 +74,6 @@ class _BaseDatasetTest:
         )
         self.assertEqual(W.shape, (self.dataset.nframes, self.dataset.nframes))
 
-        n_components = 1
-        indices = [1, 2]
-        H, W = self.dataset.pca(num_components=n_components, indices=indices)
-
-        self.assertEqual(H.shape, (n_components, len(self.dataset.data[0].flatten())))
-        self.assertEqual(W.shape, (2, n_components))
-
     def test_nmf(self):
 
         num_components = 2
@@ -94,13 +82,6 @@ class _BaseDatasetTest:
         self.assertEqual(H.shape, (num_components, len(self.dataset.data[0].flatten())))
         self.assertEqual(W.shape, (self.dataset.nframes, num_components))
 
-        num_components = 1
-        indices = [1, 2]
-        H, W = self.dataset.nmf(num_components=num_components, indices=indices)
-
-        self.assertEqual(H.shape, (num_components, len(self.dataset.data[0].flatten())))
-        self.assertEqual(W.shape, (2, num_components))
-
     def test_nica(self):
 
         num_components = 2
@@ -109,13 +90,6 @@ class _BaseDatasetTest:
         self.assertEqual(H.shape, (num_components, len(self.dataset.data[0].flatten())))
         self.assertEqual(W.shape, (self.dataset.nframes, num_components))
 
-        num_components = 1
-        indices = [1, 2]
-        H, W = self.dataset.nica(num_components=num_components, indices=indices)
-
-        self.assertEqual(H.shape, (num_components, len(self.dataset.data[0].flatten())))
-        self.assertEqual(W.shape, (2, num_components))
-
 
 class TestHDF5Dataset(_BaseDatasetTest, unittest.TestCase):
     def setUp(self):

darfix/tests/test_dimension.py

@@ -10,7 +10,7 @@ from darfix.core.dataset import ImageDataset
 from darfix.core.dimension import AcquisitionDims
 from darfix.core.dimension import Dimension
 from darfix.dtypes import Dataset
-from darfix.tasks.dimensiondefinition import get_dimensions_error
+from darfix.tasks.dimension_definition import get_dimensions_error
 from darfix.tests.utils import createHDF5Dataset
 
 

darfix/tests/test_generate_grain_maps_nxdict.py

@@ -5,8 +5,8 @@ import numpy
 from silx.io.dictdump import dicttonx
 from silx.io.nxdata import NXdata
 
+from darfix.core.grainplot import GrainPlotData
 from darfix.core.grainplot import MultiDimMomentType
-from darfix.core.grainplot import OrientationDistData
 from darfix.core.grainplot import generate_grain_maps_nxdict
 from darfix.core.moment_types import MomentType
 
@@ -19,7 +19,7 @@ def test_generate_grain_maps_nxdict_1d():
     dset = createHDF5Dataset1D(numpy.random.rand(10, 10, 10))
     dset.find_dimensions()
     dset.apply_moments()
-    nxdict = generate_grain_maps_nxdict(dset, None, None)
+    nxdict = generate_grain_maps_nxdict(dset, None)
 
     for moment_type in MomentType:
         assert moment_type.value in nxdict["entry"]
@@ -33,10 +33,9 @@ def test_generate_grain_maps_nxdict_3d():
     dset = createHDF5Dataset3D(numpy.random.rand(5, 5, 5, 6, 6))
     dset.find_dimensions()
     dset.apply_moments()
-    orientation_dist_data = OrientationDistData(dset, 0, 1, [0, 1], [0, 1], dset.zsum())
-    mosa = numpy.zeros((10, 10))
+    orientation_dist_data = GrainPlotData(dset, 0, 1, [0, 1], [0, 1], dset.zsum())
 
-    nxdict = generate_grain_maps_nxdict(dset, mosa, orientation_dist_data)
+    nxdict = generate_grain_maps_nxdict(dset, orientation_dist_data)
 
     for motor in ("motor1", "motor2", "motor3"):
         for moment_type in MomentType:

darfix/tests/test_image_operations.py

@@ -1,7 +1,7 @@
 import numpy
 import pytest
 
-from darfix.processing import imageOperations
+from darfix.processing import image_operations
 
 
 @pytest.fixture
@@ -45,7 +45,7 @@ def test_background_subtraction(data, dark):
         dtype=numpy.uint16,
     )
 
-    imageOperations.background_subtraction(data, dark)
+    image_operations.background_subtraction(data, dark)
     numpy.testing.assert_array_equal(expected, data)
 
 
@@ -62,7 +62,7 @@ def test_hot_pixel_removal(data):
         dtype=numpy.uint16,
     )
 
-    imageOperations.hot_pixel_removal(data)
+    image_operations.hot_pixel_removal(data)
     numpy.testing.assert_array_equal(expected, data)
 
 
@@ -80,6 +80,6 @@ def test_threshold_removal(data):
         dtype=numpy.uint16,
     )
 
-    imageOperations.threshold_removal(data, 2, 4)
+    image_operations.threshold_removal(data, 2, 4)
 
     numpy.testing.assert_array_equal(expected, data)

darfix/tests/test_image_registration.py

@@ -6,7 +6,7 @@ try:
 except ImportError:
     scipy = None
 
-from darfix.core import imageRegistration
+from darfix.core import image_registration
 from darfix.tests import utils
 
 
@@ -63,8 +63,8 @@ def test_find_shift(data):
     shift = (-1.4, 1.32)
     for img in data:
         # The shift corresponds to the pixel offset relative to the reference image
-        offset_image = imageRegistration._opencv_fft_shift(img, shift[1], shift[0])
-        computed_shift = imageRegistration.find_shift(img, offset_image, 100)
+        offset_image = image_registration._opencv_fft_shift(img, shift[1], shift[0])
+        computed_shift = image_registration.find_shift(img, offset_image, 100)
         numpy.testing.assert_allclose(shift, -computed_shift, rtol=1e-04)
 
 
@@ -72,10 +72,10 @@ def test_apply_shift(data):
     """Tests the correct apply of the shift"""
     shift = (0, 0)
     for img in data:
-        shifted_image = imageRegistration.apply_opencv_shift(img, shift)
+        shifted_image = image_registration.apply_opencv_shift(img, shift)
         numpy.testing.assert_allclose(img, shifted_image, rtol=1e-04)
     for img in data:
-        shifted_image = imageRegistration.apply_opencv_shift(
+        shifted_image = image_registration.apply_opencv_shift(
             img, shift, shift_approach="linear"
         )
         numpy.testing.assert_allclose(img, shifted_image, rtol=1e-04)
@@ -83,11 +83,11 @@ def test_apply_shift(data):
 
 def test_improve_shift(data):
     """Tests the shift improvement"""
-    h = imageRegistration.improve_linear_shift(
+    h = image_registration.improve_linear_shift(
         data, [1, 1], 0.1, 0.1, 1, shift_approach="fft"
     )
     numpy.testing.assert_allclose(h, 0.0)
-    h = imageRegistration.improve_linear_shift(
+    h = image_registration.improve_linear_shift(
         data, [1, 1], 0.1, 0.1, 1, shift_approach="linear"
     )
     numpy.testing.assert_allclose(h, 0.0)
@@ -108,7 +108,7 @@ def test_shift_detection10(rstate):
             ).real
         ]
     data = numpy.asanyarray(data, dtype=numpy.int16)
-    optimal_shift = imageRegistration.shift_detection(data, 100, shift_approach="fft")
+    optimal_shift = image_registration.shift_detection(data, 100, shift_approach="fft")
 
     shift = [-1, 0]
 
@@ -130,7 +130,7 @@ def test_shift_detection01(rstate):
             ).real
         ]
     data = numpy.asanyarray(data, dtype=numpy.int16)
-    optimal_shift = imageRegistration.shift_detection(data, 100, shift_approach="fft")
+    optimal_shift = image_registration.shift_detection(data, 100, shift_approach="fft")
 
     shift = [0, -1]
 
@@ -153,7 +153,7 @@ def test_shift_detection11(rstate):
         ]
     data = numpy.asanyarray(data, dtype=numpy.int16)
 
-    optimal_shift = imageRegistration.shift_detection(data, 100)
+    optimal_shift = image_registration.shift_detection(data, 100)
 
     shift = [-1, -1]
 
@@ -175,7 +175,7 @@ def test_shift_detection_float(rstate):
             ).real
         ]
     data = numpy.asanyarray(data, dtype=numpy.int16)
-    optimal_shift = imageRegistration.shift_detection(data, 100)
+    optimal_shift = image_registration.shift_detection(data, 100)
     shift = [-0.5, -0.2]
 
     numpy.testing.assert_allclose(shift, numpy.round(optimal_shift, 1))
@@ -184,7 +184,7 @@ def test_shift_detection_float(rstate):
 def test_shift_correction00(data):
     """Tests the shift correction of a [0,0] shift."""
 
-    data = imageRegistration.shift_correction(
+    data = image_registration.shift_correction(
         data, numpy.outer([0, 0], numpy.arange(3))
     )
     numpy.testing.assert_allclose(data, data, rtol=1e-03)
@@ -219,7 +219,7 @@ def test_shift_correction01(data):
         ]
     )
 
-    new_data = imageRegistration.shift_correction(
+    new_data = image_registration.shift_correction(
         data, numpy.outer([1, 0], numpy.arange(3))
     )
     numpy.testing.assert_allclose(new_data, expected, rtol=1e-03)
@@ -254,7 +254,7 @@ def test_shift_correction10(data):
         ]
     )
 
-    new_data = imageRegistration.shift_correction(
+    new_data = image_registration.shift_correction(
         data, numpy.outer([0, 1], numpy.arange(3))
     )
     numpy.testing.assert_allclose(new_data, expected, rtol=1e-05)
@@ -288,7 +288,7 @@ def test_shift_correction11(data):
             ],
         ]
     )
-    new_data = imageRegistration.shift_correction(
+    new_data = image_registration.shift_correction(
         data, numpy.outer([1, 1], numpy.arange(3))
     )
     numpy.testing.assert_allclose(new_data, expected, rtol=1e-05)
@@ -321,7 +321,7 @@ def test_shift_correction_float(data):
         ],
     ]
 
-    new_data = imageRegistration.shift_correction(
+    new_data = image_registration.shift_correction(
         data, numpy.outer([0.25, 0.1], numpy.arange(3))
     )
     numpy.testing.assert_allclose(new_data, expected, rtol=1e-05)
@@ -411,4 +411,4 @@ def test_shift_correction0(tmpdir, first_frame, metadata_dict):
 
     for frame in dataset.data.take(0, 0):
         # Check if the difference between the shifted frames and the sample frame is small enough
-        numpy.testing.assert_allclose(dataset.as_array3d(0), frame, atol=6)
+        numpy.testing.assert_allclose(dataset.as_array3d()[0], frame, atol=6)

darfix/tests/test_image_stack.py

@@ -1,8 +1,8 @@
 import numpy
 import pytest
 
-from darfix.core.imageStack import FixedDimension
-from darfix.core.imageStack import ImageStack
+from darfix.core.image_stack import FixedDimension
+from darfix.core.image_stack import ImageStack
 
 
 def flatten_scans(data: numpy.ndarray):
@@ -100,10 +100,6 @@ def test_filter_indices(image_stack: ImageStack):
 def test_get_filtered_data(image_stack: ImageStack):
     # Should give the same result as old ImageDataset::get_data
 
-    numpy.testing.assert_array_equal(
-        image_stack.get_filtered_data([0, 1, 2]),
-        legacy_get_data(image_stack, [0, 1, 2]),
-    )
     numpy.testing.assert_array_equal(
         image_stack.get_filtered_data(None), legacy_get_data(image_stack, None)
     )
@@ -120,10 +116,3 @@ def test_get_filtered_data(image_stack: ImageStack):
         image_stack.get_filtered_data(fixed_dimension=FixedDimension(2, 1)),
         legacy_get_data(image_stack, dimension=[[2], [1]]),
     )
-
-    numpy.testing.assert_array_equal(
-        image_stack.get_filtered_data(
-            fixed_dimension=FixedDimension(2, 1), indices=numpy.arange(0, 18)
-        ),
-        legacy_get_data(image_stack, dimension=[[2], [1]], indices=numpy.arange(0, 18)),
-    )

darfix/tests/test_mask.py

@@ -1,6 +1,6 @@
 import numpy
 
-from darfix.processing.imageOperations import mask_removal
+from darfix.processing.image_operations import mask_removal
 
 from .utils import create_1d_dataset
 

darfix/tests/test_moments.py

@@ -7,10 +7,10 @@ from darfix.core.utils import NoDimensionsError
 def test_apply_moments(dataset):
 
     with pytest.raises(NoDimensionsError):
-        dataset.apply_moments(indices=[1, 2, 3, 4])
+        dataset.apply_moments()
 
     dataset.find_dimensions()
     dataset.reshape_data()
-    moments = dataset.apply_moments(indices=[1, 2, 3, 4])
+    moments = dataset.apply_moments()
     assert moments[0][MomentType.COM].shape == dataset.frame_shape
     assert moments[1][MomentType.SKEWNESS].shape == dataset.frame_shape

darfix/tests/test_rocking_curves.py

@@ -54,13 +54,11 @@ def test_apply_fit_on_2d_dataset():
     with pytest.raises(NoDimensionsError):
         fit_dataset, maps = dataset.apply_fit()
     dataset.find_dimensions()
-    indices = [0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-    fit_dataset, maps = dataset.apply_fit(indices=indices)
+    fit_dataset, maps = dataset.apply_fit()
 
     assert dataset.dims.ndim == 2
     assert len(maps) == 7
     assert fit_dataset.nframes == dataset.nframes
-    numpy.testing.assert_equal(fit_dataset.as_array3d(10), dataset.as_array3d(10))
 
 
 def test_apply_fit_on_3d_dataset():

darfix/tests/test_shift.py

@@ -1,7 +1,7 @@
 import numpy
 import pytest
 
-from darfix.core.imageRegistration import apply_opencv_shift
+from darfix.core.image_registration import apply_opencv_shift
 from darfix.tests.utils import createHDF5Dataset2D
 
 
@@ -15,7 +15,7 @@ def two_motors_dataset():
 
 
 def test_find_shift(two_motors_dataset):
-    """Tests the shift detection with dimensions and indices"""
+    """Tests the shift detection"""
     dataset = two_motors_dataset
 
     dataset.find_dimensions()
@@ -39,7 +39,7 @@ def test_find_shift(two_motors_dataset):
 
 
 def test_apply_shift(two_motors_dataset):
-    """Tests the shift correction with dimensions and indices"""
+    """Tests the shift correction"""
     dataset = two_motors_dataset
 
     dataset.find_dimensions()
@@ -50,7 +50,7 @@ def test_apply_shift(two_motors_dataset):
     # Axis 1 : dim size is 10
     assert dataset.dims[1].size == 10
 
-    input_img = dataset.as_array3d(4).copy()
+    input_img = dataset.as_array3d()[4].copy()
     # Check fit is well applied at index 4
     result_idx4 = apply_opencv_shift(input_img, shift=(0.5 * 4, 0.5 * 4))
 
@@ -60,9 +60,9 @@ def test_apply_shift(two_motors_dataset):
         AssertionError,
         numpy.testing.assert_array_equal,
         input_img,
-        dataset.as_array3d(4),
+        dataset.as_array3d()[4],
     )
-    numpy.testing.assert_allclose(result_idx4, dataset.as_array3d(4))
+    numpy.testing.assert_allclose(result_idx4, dataset.as_array3d()[4])
 
 
 def test_find_shift_along_dimension(two_motors_dataset):
@@ -79,7 +79,7 @@ def test_find_shift_along_dimension(two_motors_dataset):
 
 
 def test_apply_shift_along_dimension(two_motors_dataset):
-    """Tests the shift correction with dimensions and indices"""
+    """Tests the shift correction"""
     dataset = two_motors_dataset
 
     dataset.find_dimensions()

darfix/tests/test_workflow.py

@@ -7,7 +7,7 @@ except ImportError:
     pytest.skip("scipy is missing", allow_module_level=True)
 
 from darfix.core import roi
-from darfix.processing import imageOperations
+from darfix.processing import image_operations
 from darfix.tests import utils
 
 
@@ -61,15 +61,15 @@ def test_workflow0(dataset, dark_dataset):
     )
 
     # Background substraction of the data
-    imageOperations.background_subtraction(
-        data, imageOperations.compute_background(dark_frames, "median")
+    image_operations.background_subtraction(
+        data, image_operations.compute_background(dark_frames, "median")
     )
     # ROI of the data
     data = roi.apply_3D_ROI(
         data, size=[3, 1], center=(numpy.array(data[0].shape) / 2).astype(int)
     )
     # Threshold removal of the data
-    imageOperations.threshold_removal(data, 1, 20)
+    image_operations.threshold_removal(data, 1, 20)
     numpy.testing.assert_array_equal(data, expected)
 
 

darfix/tests/test_zsum.py

@@ -1,18 +1,15 @@
 import numpy
 
-from darfix.core.imageStack import FixedDimension
+from darfix.core.image_stack import FixedDimension
 
 
 def test_zsum(dataset):
-    indices = [1, 2, 3, 6]
 
     dataset.find_dimensions()
     dataset.reshape_data()
     result = numpy.sum(
-        dataset.get_filtered_data(
-            fixed_dimension=FixedDimension(0, 1), indices=indices
-        ),
+        dataset.get_filtered_data(fixed_dimension=FixedDimension(0, 1)),
         axis=0,
     )
-    zsum = dataset.zsum(indices=indices, dimension=FixedDimension(0, 1))
+    zsum = dataset.zsum(dimension=FixedDimension(0, 1))
     numpy.testing.assert_array_equal(zsum, result)

{darfix-4.2.0.dist-info → darfix-4.3.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: darfix
-Version: 4.2.0
+Version: 4.3.0
 Summary: Computer vision software for the interpretation of diffraction images
 Author-email: ESRF <dau-pydev@esrf.fr>
 License: The MIT license follows:
@@ -50,11 +50,13 @@ Requires-Dist: scikit-learn
 Requires-Dist: scipy
 Requires-Dist: tqdm
 Requires-Dist: joblib
+Requires-Dist: esrf-pathlib
+Requires-Dist: colorstamps
 Requires-Dist: eval_type_backport
 Provides-Extra: full-noqt
 Requires-Dist: opencv-python-headless>=4.3.0.36; extra == "full-noqt"
 Requires-Dist: scikit-image>=0.17.1; extra == "full-noqt"
-Requires-Dist: ewoksorange<3.0.0,>=2.1.0; extra == "full-noqt"
+Requires-Dist: ewoksorange>=3.0.0; extra == "full-noqt"
 Requires-Dist: hdf5plugin; extra == "full-noqt"
 Provides-Extra: full
 Requires-Dist: darfix[full_noqt]; extra == "full"
@@ -70,7 +72,7 @@ Requires-Dist: flake8_nb>=0.3.1; extra == "dev"
 Requires-Dist: isort; extra == "dev"
 Provides-Extra: doc
 Requires-Dist: darfix[test]; extra == "doc"
-Requires-Dist: sphinx>=4.5; extra == "doc"
+Requires-Dist: sphinx<9,>=7.2; extra == "doc"
 Requires-Dist: sphinx-autodoc-typehints>=1.16; extra == "doc"
 Requires-Dist: sphinxcontrib-video; extra == "doc"
 Requires-Dist: sphinx-copybutton; extra == "doc"