darfix 4.3.0__tar.gz → 4.3.2__tar.gz

{darfix-4.3.0/src/darfix.egg-info → darfix-4.3.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: darfix
-Version: 4.3.0
+Version: 4.3.2
 Summary: Computer vision software for the interpretation of diffraction images
 Author-email: ESRF <dau-pydev@esrf.fr>
 License: The MIT license follows:

{darfix-4.3.0 → darfix-4.3.2}/pyproject.toml

@@ -8,7 +8,7 @@ addopts = "--import-mode=importlib" # for all pytest versions, pytest-cov needs
 
 [project]
 name = "darfix"
-version = "4.3.0"
+version = "4.3.2"
 keywords = ["orange3 add-on","ewoks"]
 authors = [{name = "ESRF", email = "dau-pydev@esrf.fr"}]
 description = "Computer vision software for the interpretation of diffraction images"

{darfix-4.3.0 → darfix-4.3.2}/src/darfix/gui/dimensions_widget.py

@@ -83,8 +83,6 @@ class DimensionTable(qt.QTableWidget):
             assert isinstance(dim, Dimension)
             self._addDim(axis, dim, decimals)
 
-        self.sigUpdateDims.emit()
-
     def onRemoveDim(self, iRow: int):
         """
         Remove dimension.
@@ -298,11 +296,13 @@ class DimensionItem(qt.QWidget):
         # start
         self._startWidget = qt.QDoubleSpinBox(self)
         self._startWidget.setMinimum(float("-inf"))
+        self._startWidget.setMaximum(float("+inf"))
         self._startWidget.setDecimals(5)
         self._startWidget.valueChanged.connect(self.sigDimChanged)
         # end
         self._stopWidget = qt.QDoubleSpinBox(self)
         self._stopWidget.setMinimum(float("-inf"))
+        self._stopWidget.setMaximum(float("+inf"))
         self._stopWidget.setDecimals(5)
         self._stopWidget.valueChanged.connect(self.sigDimChanged)
         # rm button

{darfix-4.3.0 → darfix-4.3.2}/src/darfix/gui/grain_plot/grain_plot_widget.py

@@ -124,7 +124,6 @@ class GrainPlotWidget(qt.QMainWindow):
 
         return generate_grain_maps_nxdict(
             self._grainPlotMaps,
-            self._mosaicity_widget.getMosaicity(),
             orientation_dist_data,
         )
 

{darfix-4.3.0 → darfix-4.3.2}/src/darfix/gui/noise_removal/noise_removal_widget.py

@@ -138,7 +138,7 @@ class NoiseRemovalWidget(qt.QWidget):
         self._dataset = dataset
 
         if self._imgDataset.title != "":
-            self._plot.setTitleCallback(lambda idx: self._imgDataset.title)
+            self._plot.setGraphTitle(self._imgDataset.title)
 
         self._initPlot()
 

{darfix-4.3.0 → darfix-4.3.2}/src/darfix/gui/rocking_curves/rocking_curves_plot.py

@@ -245,7 +245,7 @@ class RockingCurvesPlot(qt.QWidget):
             y_gauss = bivariate_gaussian(x_values, *pars)
 
         except (TypeError, RuntimeError):
-            _logger.warning("Cannot fit", exc_info=True)
+            _logger.error("Cannot fit", exc_info=True)
             y_gauss = numpy.full_like(rocking_curve, numpy.nan)
         else:
             self._lastFitParamsLabel.setText(

{darfix-4.3.0 → darfix-4.3.2}/src/darfix/processing/rocking_curves.py

@@ -17,9 +17,6 @@ from ..math import trivariate_gaussian
 
 FitMethod = Literal["trf", "lm", "dogbox"]
 
-_ZERO_SUM_RELATIVE_TOLERANCE = 1e-3
-""" Relative tolerance used to check if the sum of values equals 0. Skips fit if it is the case."""
-
 _BOUNDS_TOLERANCE = 1e-3
 """ Absolute tolerance for to set bounds of fit parameters. The bounds will be set to (min - tol, max + tol) whenever possible."""
 
@@ -246,6 +243,24 @@ def _gaussian_p0(com: list[float], fwhm: list[float], ptp_y: float):
     ]
 
 
+def _filter_contiguous_zeros(arr) -> numpy.ndarray:
+    """
+    Mask is FALSE if value == 0 AND its left neighbor == 0 AND its right neighbor == 0.
+
+    :param arr: 1D array
+
+    :return: 1D mask
+    """
+    is_zero = arr == 0
+
+    left_neighbor_zero = numpy.concatenate(([True], is_zero[:-1]))
+
+    right_neighbor_zero = numpy.concatenate((is_zero[1:], [True]))
+
+    mask = is_zero & left_neighbor_zero & right_neighbor_zero
+    return ~mask
+
+
 def _fit_xd_rocking_curve(
     len_maps: int,
     gaussian_function: Callable,
@@ -273,38 +288,42 @@ def _fit_xd_rocking_curve(
     if thresh is None:
         thresh = 15.0
 
-    com, fwhm = compute_com_fwhm(x_values, y_values)
-
     ptp_y = numpy.ptp(y_values)
 
+    y_not_zero_mask = _filter_contiguous_zeros(y_values)
+    x_not_zero_values = x_values[:, y_not_zero_mask]
+    y_not_zero_values = y_values[y_not_zero_mask]
     y_zeros = numpy.zeros_like(y_values)
 
+    com, fwhm = compute_com_fwhm(x_not_zero_values, y_not_zero_values)
+
     if ptp_y <= thresh:
         # Ptp under threshold
         return y_zeros, numpy.full(len_maps, numpy.nan)
 
-    if len(y_values) < len_maps:
-        return y_zeros, numpy.full(len_maps, numpy.nan)
-
     p0 = p0_function(com, fwhm, ptp_y)
 
+    if x_not_zero_values.shape[1] < len_maps:
+        # Cannot fit if there is less points than the number of parameters.
+        # Return `p0` for gaussian parameters is enough when there only a few points.
+        y_fitted = y_zeros
+        y_fitted[y_not_zero_mask] = gaussian_function(x_not_zero_values, *p0)
+        return y_fitted, p0
+
     vmax = max(y_values.max(), ptp_y)
 
     bounds = bounds_function(
         method,
-        x_values,
+        x_not_zero_values,
         min_y=thresh,
         max_y=vmax,
     )
 
-    y_not_zero_mask = y_values > 0
-    x_values_masked = x_values[:, y_not_zero_mask]
-
     try:
         fit_params, cov = curve_fit(
             f=gaussian_function,
-            xdata=x_values_masked,
-            ydata=y_values[y_not_zero_mask],
+            xdata=x_not_zero_values,
+            ydata=y_not_zero_values,
             p0=p0,
             method=method,
             bounds=bounds,
@@ -317,7 +336,7 @@ def _fit_xd_rocking_curve(
         return y_zeros, numpy.full(len_maps, numpy.nan)
 
     y_fitted = y_zeros
-    y_fitted[y_not_zero_mask] = gaussian_function(x_values_masked, *fit_params)
+    y_fitted[y_not_zero_mask] = gaussian_function(x_not_zero_values, *fit_params)
 
     return y_fitted, fit_params
 

{darfix-4.3.0 → darfix-4.3.2}/src/darfix/tasks/rocking_curves.py

@@ -25,6 +25,8 @@ class Inputs(BaseInputModel):
     """Method to use for the rocking curves fit"""
     output_filename: str | Path | None = None
     """Output filename to save the rocking curves results. Results are not saved if not provided"""
+    save_maps: bool = True
+    """Whether to save the maps to file. Default is True."""
 
 
 class RockingCurves(Task, input_model=Inputs, output_names=["dataset", "maps"]):
@@ -38,13 +40,6 @@ class RockingCurves(Task, input_model=Inputs, output_names=["dataset", "maps"]):
 
         inputs = Inputs(**self.get_input_values())
 
-        output_filename = inputs.output_filename
-        if output_filename and os.path.isfile(output_filename):
-            raise FileExistsError(
-                f"""Cannot launch rocking curves fit: saving destination {output_filename} already exists.
-                Change the `output_filename` input or set it to None to disable saving."""
-            )
-
         dataset = inputs.dataset.dataset
         new_image_dataset, maps = dataset.apply_fit(
             int_thresh=inputs.int_thresh,
@@ -52,13 +47,14 @@ class RockingCurves(Task, input_model=Inputs, output_names=["dataset", "maps"]):
             abort_event=self.cancelEvent,
         )
 
-        if output_filename is not None:
+        if inputs.save_maps:
+
             nxdict = generate_rocking_curves_nxdict(
                 new_image_dataset,
                 maps,
                 residuals=compute_residuals(new_image_dataset, dataset),
             )
-            dicttonx(nxdict, output_filename)
+            dicttonx(nxdict, _get_output_path(inputs.output_filename, dataset.dir))
 
         self.outputs.dataset = Dataset(
             dataset=new_image_dataset,
@@ -68,3 +64,17 @@ class RockingCurves(Task, input_model=Inputs, output_names=["dataset", "maps"]):
 
     def cancel(self):
         self.cancelEvent.set()
+
+
+def _get_output_path(output_path: str | None, output_directory: str) -> str:
+    """
+    :return: Default output path or output path specified by user.
+    """
+    if output_path is None:
+        output_path = str(Path(output_directory) / "rocking_curve_maps.h5")
+    if os.path.isfile(output_path):
+        raise FileExistsError(
+            f"""Cannot launch rocking curves fit: saving destination {output_path} already exists.
+                Change the `output_filename` input or set `save_maps` input to False to disable saving."""
+        )
+    return output_path

{darfix-4.3.0 → darfix-4.3.2}/src/darfix/tests/tasks/test_rocking_curves.py

@@ -2,7 +2,9 @@ import warnings
 from pathlib import Path
 
 import h5py
+import hdf5plugin  # noqa: F401
 import numpy
+import pytest
 from scipy.optimize import OptimizeWarning
 
 from darfix.core.rocking_curves_map import Maps_2D
@@ -10,8 +12,16 @@ from darfix.dtypes import Dataset
 from darfix.tasks.rocking_curves import RockingCurves
 
 
-def test_rocking_curves(input_dataset, tmp_path):
-    output_filename = tmp_path / "rocking_curves.h5"
+@pytest.mark.parametrize("test_default_value", (True, False))
+def test_rocking_curves(input_dataset, tmp_path, test_default_value):
+
+    if test_default_value:
+        output_filename = None
+        expected_output_filename = tmp_path / "rocking_curve_maps.h5"
+    else:
+        output_filename = tmp_path / "file_name_defined_by_user.h5"
+        expected_output_filename = output_filename
+
     input_dataset.find_dimensions()
     input_dataset.reshape_data()
     task = RockingCurves(
@@ -22,6 +32,7 @@ def test_rocking_curves(input_dataset, tmp_path):
             "int_thresh": 15,
         }
     )
+
     with warnings.catch_warnings():
         warnings.simplefilter("always", RuntimeWarning)
         warnings.simplefilter("always", OptimizeWarning)
@@ -29,8 +40,8 @@ def test_rocking_curves(input_dataset, tmp_path):
 
     assert isinstance(task.get_output_value("maps"), numpy.ndarray)
     assert isinstance(task.get_output_value("dataset"), Dataset)
-    assert output_filename.is_file()
-    with h5py.File(output_filename, "r") as output_file:
+    assert expected_output_filename.is_file()
+    with h5py.File(expected_output_filename, "r") as output_file:
         output_entry = output_file["entry"]
         for map_type in Maps_2D:
             assert map_type.value in output_entry

{darfix-4.3.0 → darfix-4.3.2/src/darfix.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: darfix
-Version: 4.3.0
+Version: 4.3.2
 Summary: Computer vision software for the interpretation of diffraction images
 Author-email: ESRF <dau-pydev@esrf.fr>
 License: The MIT license follows:

{darfix-4.3.0 → darfix-4.3.2}/src/orangecontrib/darfix/widgets/dimensions.py

@@ -108,6 +108,7 @@ class DimensionWidgetOW(DatasetWidgetBase, ewokstaskclass=DimensionDefinition):
                 )
                 # Disable inputs only when the dim rows are added
                 self._widget.setEnableInputs(False)
+                self.buttons.button(qt.QDialogButtonBox.Ok).setEnabled(True)
             else:
                 self._widget.setEnableInputs(True)
                 _logger.error(
@@ -142,8 +143,7 @@ class DimensionWidgetOW(DatasetWidgetBase, ewokstaskclass=DimensionDefinition):
             raw_dims = self.get_task_input_value("dims")
             if not is_missing_data(raw_dims):
                 dims = convert_dim_from_dict_to_Dimension(raw_dims)
-                with block_signals(self._widget):
-                    self._widget.setDims(dims)
+                self._widget.setDims(dims)
             self._widget.setZigzagMode(self.get_task_input_value("is_zigzag", False))
             self._widget.setEnableInputs(False)
         except ValueError as e:

{darfix-4.3.0 → darfix-4.3.2}/src/orangecontrib/darfix/widgets/rockingcurves.py

@@ -52,6 +52,7 @@ class RockingCurvesWidgetOW(DatasetWidgetBase, ewokstaskclass=RockingCurves):
             self._widget.updateDataset(dataset.dataset, maps)
 
     def _launch_fit(self):
+        self.set_dynamic_input("save_maps", False)
         self.set_default_input("int_thresh", self._widget.getIntensityThreshold())
         self.set_default_input("method", self._widget.getFitMethod())
         self.execute_ewoks_task()