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

darfix/gui/{binningWidget.py → binning_widget.py}

@@ -4,7 +4,6 @@ from silx.gui.plot.StackView import StackViewMainWindow
 
 import darfix
 from darfix import dtypes
-from darfix.core.state_of_operation import Operation
 from darfix.gui.utils.custom_doublespinbox import createCustomDoubleSpinBox
 from darfix.gui.utils.message import missing_dataset_msg
 
@@ -29,8 +28,6 @@ class BinningWidget(qt.QMainWindow):
     def __init__(self, parent=None):
         qt.QMainWindow.__init__(self, parent)
 
-        self._display_tooltip_msg = True
-
         widget = qt.QWidget()
         layout = qt.QGridLayout()
 
@@ -38,11 +35,9 @@ class BinningWidget(qt.QMainWindow):
         # original dataset, the one treated. Keep it to be able to re-apply modifications
         self._update_dataset = None
         # dataset with applied modifications. This is the one displayed
-        self.indices = None
-        self.bg_indices = None
         self.bg_dataset = None
 
-        self._scaleLE = createCustomDoubleSpinBox(1)
+        self._scaleLE = createCustomDoubleSpinBox(0.5)
         _buttons = qt.QDialogButtonBox(parent=self)
         self._okB = _buttons.addButton(_buttons.Ok)
         self._applyB = _buttons.addButton(_buttons.Apply)
@@ -63,7 +58,7 @@ class BinningWidget(qt.QMainWindow):
                 normalization=darfix.config.DEFAULT_COLORMAP_NORM,
             )
         )
-        layout.addWidget(qt.QLabel("Scale: "), 0, 0)
+        layout.addWidget(qt.QLabel("Binning factor: "), 0, 0)
         layout.addWidget(self._scaleLE, 0, 1)
         layout.addWidget(self._sv, 1, 0, 1, 2)
         layout.addWidget(_buttons, 2, 0, 1, 2)
@@ -93,26 +88,8 @@ class BinningWidget(qt.QMainWindow):
     def setDataset(self, dataset: dtypes.Dataset):
         self._dataset = dataset.dataset
         self._update_dataset = dataset.dataset
-        self.indices = dataset.indices
-        self.bg_indices = dataset.bg_indices
         self.bg_dataset = dataset.bg_dataset
         self.setStack()
-        if self._display_tooltip_msg:
-            self.display_tooltip_msg()
-
-    def display_tooltip_msg(self):
-        msg = qt.QMessageBox()
-        msg.setIcon(qt.QMessageBox.Information)
-        msg.setText(
-            "Binning can be used to reduce the computation time of the operations in the workflow.\n"
-            + "The scale is the factor to which the images will be rescaled.\n"
-            + "After the correct parameters are found, you can remove the binning widget from the workflow"
-            + " and execute it either with the GUI or using ewoks.\nBinning should be applied after any"
-            + " ROI to have original images size and not the binned one.\n"
-        )
-        msg.setWindowTitle("Fit succeeded!")
-        msg.setStandardButtons(qt.QMessageBox.Ok)
-        msg.exec()
 
     def setStack(self, dataset=None):
         """
@@ -144,10 +121,6 @@ class BinningWidget(qt.QMainWindow):
         self._startComputation()
         self.sigApply.emit()
 
-    def abort(self):
-        self._abortB.setEnabled(False)
-        self._update_dataset.stop_operation(Operation.BINNING)
-
     def apply(self):
         self.sigComputed.emit()
 

darfix/gui/{blindSourceSeparationWidget.py → blind_source_separation_widget.py}

@@ -6,10 +6,10 @@ import numpy
 from silx.gui import qt
 
 from darfix import dtypes
-from darfix.tasks.blindsourceseparation import Method
+from darfix.tasks.blind_source_separation import Method
 
-from .displayComponentsWidget import DisplayComponentsWidget
-from .operationThread import OperationThread
+from .display_components_widget import DisplayComponentsWidget
+from .parallel.operation_thread import OperationThread
 
 
 class BSSWidget(qt.QMainWindow):
@@ -104,8 +104,6 @@ class BSSWidget(qt.QMainWindow):
 
     def setDataset(self, dataset: dtypes.Dataset):
         self.dataset = dataset.dataset
-        self.indices = dataset.indices
-        self.bg_indices = dataset.bg_indices
         self.bg_dataset = dataset.bg_dataset
         self.computeButton.setEnabled(True)
         self.detectButton.setEnabled(True)
@@ -113,13 +111,9 @@ class BSSWidget(qt.QMainWindow):
     def _nbComponentEdited(self, *args, **kwargs):
         self.sigNbComponentsChanged.emit(int(self.nComponentsLE.text()))
 
-    def _displayComponents(
-        self, dataset: dtypes.ImageDataset, indices, bg_indices, comp, W
-    ):
+    def _displayComponents(self, dataset: dtypes.ImageDataset, comp, W):
         """
         :param dataset: dataset for which we want to display the components
-        :param indices: dataset indices
-        :param bg_indices: background indices
         :param comp: components
         :param W: Matrix with the rocking curves values
         """
@@ -143,12 +137,6 @@ class BSSWidget(qt.QMainWindow):
         self.computeButton.setEnabled(True)
         self.nComponentsLE.setEnabled(True)
         self.detectButton.setEnabled(True)
-        if bg_indices is not None:
-            # If filter data is activated, the matrix W has reduced dimensionality, so reshaping is not possible
-            # Create empty array with shape the total number of frames
-            W = numpy.zeros((dataset.nframes, n_comp))
-            # Set actual values of W where threshold of filter is True
-            W[indices] = W
         self._displayComponentsWidget.setComponents(
             comp,
             W,

darfix/gui/{chooseDimensions.py → choose_dimensions.py}

@@ -2,7 +2,7 @@ from __future__ import annotations
 
 from typing import Callable
 
-from ewoksorange.gui.parameterform import block_signals
+from ewoksorange.gui.widgets.parameter_form import block_signals
 from silx.gui import qt
 
 from darfix.core.dimension import AcquisitionDims

darfix/gui/concatenate_scans.py

@@ -4,15 +4,15 @@ import logging
 import os
 
 import h5py
-from ewoksorange.gui.parameterform import block_signals
+from ewoksorange.gui.widgets.parameter_form import block_signals
 from silx.gui import qt
 
-from darfix.core.datapathfinder import DETECTOR_KEYWORD
-from darfix.core.datapathfinder import SCAN_KEYWORD
+from darfix.core.data_path_finder import DETECTOR_KEYWORD
+from darfix.core.data_path_finder import SCAN_KEYWORD
 from darfix.gui.configuration.action import AdvancedConfigurationAction
 from darfix.gui.configuration.action import RequiredConfigurationAction
 from darfix.gui.configuration.level import ConfigurationLevel
-from darfix.gui.data_selection.hdf5_data_selection_widgets import (
+from darfix.gui.data_selection.hdf5_dataset_selection_widget import (
     HDF5DatasetSelectionWidget,
 )
 from darfix.gui.utils.fileselection import FileSelector

darfix/gui/data_selection/{hdf5_data_selection_widgets.py → hdf5_dataset_selection_widget.py}

@@ -3,9 +3,9 @@ from __future__ import annotations
 import h5py
 from silx.gui import qt
 
-from darfix.core.datapathfinder import DETECTOR_KEYWORD
-from darfix.core.datapathfinder import FIRST_SCAN_KEYWORD
-from darfix.core.datapathfinder import LAST_SCAN_KEYWORD
+from darfix.core.data_path_finder import DETECTOR_KEYWORD
+from darfix.core.data_path_finder import FIRST_SCAN_KEYWORD
+from darfix.core.data_path_finder import LAST_SCAN_KEYWORD
 from darfix.gui.utils.data_path_selection import DataPathSelection
 from darfix.gui.utils.fileselection import FileSelector
 from darfix.tasks.hdf5_scans_concatenation import ConcatenateHDF5Scans
@@ -96,56 +96,3 @@ class HDF5DatasetSelectionWidget(qt.QWidget):
 
     def getInputFile(self) -> str | None:
         return self._inputFileSelector.getFilePath()
-
-
-class HDF5RawDatasetSelectionWidget(HDF5DatasetSelectionWidget):
-    """Same as the 'HDF5DatasetSelectionWidget' but adds an option to keep data on disk and to provide the title"""
-
-    sigKeepDataOnDiskChanged = qt.Signal(bool)
-    sigTitleChanged = qt.Signal(str)
-
-    def __init__(self, parent: qt.QWidget | None = None) -> None:
-        super().__init__(parent)
-        self._keepDataOnDisk = qt.QCheckBox("Keep data on disk")
-        self.layout().addWidget(self._keepDataOnDisk, 1, 3, 2, 2)
-
-        self._titleLabel = qt.QLabel("Workflow title")
-        self.layout().addWidget(self._titleLabel, 3, 0, 1, 1)
-        self._title = qt.QLineEdit("")
-        self.layout().addWidget(self._title, 3, 1, 1, 4)
-
-        # redefine layout because we want to display 'title' just after the file path selection
-        self.layout().addWidget(self._detectorDataPath, 4, 0, 1, 5)
-        self.layout().addWidget(self._positionerDataPath, 5, 0, 1, 5)
-
-        # connect signal / slot
-        self._keepDataOnDisk.toggled.connect(self.sigKeepDataOnDiskChanged)
-        self._title.editingFinished.connect(self._titleChanged)
-
-    def isKeepingDataOnDisk(self) -> bool:
-        return self._keepDataOnDisk.isChecked()
-
-    def setKeepDataOnDisk(self, value: bool):
-        self._keepDataOnDisk.setChecked(value)
-
-    def getWorkflowTitle(self) -> str:
-        return self._title.text()
-
-    def setWorkflowTitle(self, title: str):
-        self._title.setText(title)
-        self._titleChanged()
-
-    def _titleChanged(self, *args, **kwargs):
-        self.sigTitleChanged.emit(self._title.text())
-
-
-class HDF5DarkDatasetSelectionWidget(HDF5DatasetSelectionWidget):
-    """Same as the 'HDF5DatasetSelectionWidget' but hide metadata selection that is unused for dark"""
-
-    def __init__(self, parent: qt.QWidget | None = None) -> None:
-        super().__init__(parent)
-        # no positioner possible for dark so hide the selection
-        self._positionerDataPath.hide()
-
-    def getMetadataPathSelection(self) -> None:
-        return None

darfix/gui/data_selection/line_edits.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import h5py
 from silx.gui import qt
 from silx.gui.dialog.DatasetDialog import DatasetDialog
 from silx.gui.dialog.GroupDialog import GroupDialog
@@ -15,52 +16,84 @@ class _BaseLineEdit(qt.QWidget):
     dialogSelected = qt.Signal(str)
     editingFinished = qt.Signal()
 
+    _ERROR_LINE_EDIT_STYLE_SHEET = "border: 2px solid red"
+    _INVALID_INPUT_TXT = "Invalid input."
+
     def __init__(self, parent: qt.QWidget | None = None, **kwargs) -> None:
         super().__init__(parent, **kwargs)
 
         self._lineEdit = qt.QLineEdit()
+        self._defaultLineEditStyle = self._lineEdit.styleSheet()
+        self._errorMsgLabel = qt.QLabel()
+        self._errorMsgLabel.setStyleSheet("color : red")
+        self._errorMsgLabel.setText(self._INVALID_INPUT_TXT)
+        self._errorMsgLabel.hide()
         browseButton = qt.QPushButton("Browse...")
 
         layout = qt.QHBoxLayout(self)
         layout.setContentsMargins(0, 0, 0, 0)
         layout.addWidget(self._lineEdit)
         layout.addWidget(browseButton)
+        layout.addWidget(self._errorMsgLabel)
 
         browseButton.clicked.connect(self._openDialog)
-        self._lineEdit.editingFinished.connect(self.editingFinished)
+        self._lineEdit.editingFinished.connect(self._onEditFinished)
 
     def _getDialogResult(self) -> str | None:
         raise NotImplementedError()
 
+    def _isValid(self, result: str) -> bool:
+        raise NotImplementedError()
+
     def _openDialog(self):
         result = self._getDialogResult()
         if not result:
             return
 
         self._lineEdit.setText(result)
-        self.dialogSelected.emit(result)
+
+        if self.validateLineEdit():
+            self.dialogSelected.emit(result)
+
+    def _onEditFinished(self):
+        if self.validateLineEdit():
+            self.editingFinished.emit()
+
+    def validateLineEdit(self) -> bool:
+        isValid = self._isValid(self._lineEdit.text())
+        if isValid:
+            self._lineEdit.setStyleSheet(self._defaultLineEditStyle)
+            self._errorMsgLabel.hide()
+        else:
+            self._lineEdit.setStyleSheet(self._ERROR_LINE_EDIT_STYLE_SHEET)
+            self._errorMsgLabel.show()
+
+        return isValid
 
     def setText(self, text: str):
         self._lineEdit.setText(text)
+        self._onEditFinished()
 
     def getText(self) -> str:
         return self._lineEdit.text()
 
 
-class FileLineEdit(_BaseLineEdit):
+class H5FileLineEdit(_BaseLineEdit):
     """A line edit for file paths that can filled via a file selection dialog"""
 
-    dialogSelected = qt.Signal(str)
-    editingFinished = qt.Signal()
+    _INVALID_INPUT_TXT = "File does not exist or is not a valid H5 file."
 
     def _getDialogResult(self) -> None | str:
-        dialog = qt.QFileDialog()
+        dialog = qt.QFileDialog(filter="h5 file (*.h5 *.hdf *.hdf5 *.nx *.nxs)")
         result = dialog.exec()
 
         if not result:
             return None
         return dialog.selectedFiles()[0]
 
+    def _isValid(self, result: str) -> bool:
+        return h5py.is_hdf5(result)
+
 
 class DatasetLineEdit(_BaseLineEdit):
     """
@@ -68,8 +101,7 @@ class DatasetLineEdit(_BaseLineEdit):
     The file needs to be set beforehand with `setFile`
     """
 
-    dialogSelected = qt.Signal(str)
-    editingFinished = qt.Signal()
+    _INVALID_INPUT_TXT = "Not a valid H5 dataset."
 
     def __init__(self, parent: qt.QWidget | None = None, **kwargs) -> None:
         super().__init__(parent, **kwargs)
@@ -91,6 +123,12 @@ class DatasetLineEdit(_BaseLineEdit):
         url = dialog.getSelectedDataUrl()
         return url.data_path() if url else None
 
+    def _isValid(self, result: str) -> bool:
+        if not h5py.is_hdf5(self._file):
+            return False
+        with h5py.File(self._file) as f:
+            return isinstance(f.get(result), h5py.Dataset)
+
 
 class GroupLineEdit(_BaseLineEdit):
     """
@@ -98,6 +136,8 @@ class GroupLineEdit(_BaseLineEdit):
     The file needs to be set beforehand with `setFile`
     """
 
+    _INVALID_INPUT_TXT = "Not a valid H5 group."
+
     dialogSelected = qt.Signal(str)
     editingFinished = qt.Signal()
 
@@ -120,3 +160,9 @@ class GroupLineEdit(_BaseLineEdit):
 
         url = dialog.getSelectedDataUrl()
         return url.data_path() if url else None
+
+    def _isValid(self, result: str) -> bool:
+        if not h5py.is_hdf5(self._file):
+            return False
+        with h5py.File(self._file) as f:
+            return isinstance(f.get(result), h5py.Group)

darfix/gui/data_selection/scan_selection_widgets.py

@@ -1,19 +1,17 @@
 from __future__ import annotations
 
 import logging
-import os
 
 import silx.io
-from ewoksorange.gui.qtsignals import block_signals
+from ewoksorange.gui.widgets.parameter_form import block_signals
 from silx.gui import qt
 
 from darfix.gui.data_selection.utils import find_detector_name
 from darfix.gui.data_selection.utils import find_scan_names
-from darfix.gui.utils.message import show_error_msg
 
 from .line_edits import DatasetLineEdit
-from .line_edits import FileLineEdit
 from .line_edits import GroupLineEdit
+from .line_edits import H5FileLineEdit
 
 _logger = logging.getLogger(__file__)
 
@@ -25,10 +23,12 @@ class ScanSelectionWidget(qt.QWidget):
     Autofills the detector path when the scan is updated.
     """
 
+    sigNewFileSelected = qt.Signal()
+
     def __init__(self, parent: qt.QWidget | None = None, **kwargs) -> None:
         super().__init__(parent=parent, **kwargs)
 
-        self._fileLineEdit = FileLineEdit()
+        self._fileLineEdit = H5FileLineEdit()
         self._scanNameComboBox = qt.QComboBox()
         self._detectorLineEdit = DatasetLineEdit()
 
@@ -44,10 +44,7 @@ class ScanSelectionWidget(qt.QWidget):
 
     def _onNewFileEdit(self):
         path = self._fileLineEdit.getText()
-        if os.path.exists(path):
-            self._onNewFile(path)
-        else:
-            show_error_msg(f"File '{path}' does not exist")
+        self._onNewFile(path)
 
     def _onNewFile(self, filePath: str):
         self._detectorLineEdit.setFile(filePath)
@@ -61,6 +58,7 @@ class ScanSelectionWidget(qt.QWidget):
         with block_signals(self._scanNameComboBox):
             self._scanNameComboBox.clear()
         self._scanNameComboBox.addItems(scanNames)
+        self.sigNewFileSelected.emit()
 
     def _updateDetectorPath(self, scanNumber: str):
         scanUrl = f"{self._fileLineEdit.getText()}::/{scanNumber}"
@@ -69,10 +67,13 @@ class ScanSelectionWidget(qt.QWidget):
 
         if detectorName:
             self._detectorLineEdit.setText(f"/{scanNumber}/measurement/{detectorName}")
+        else:
+            self._detectorLineEdit.setText("")
+
+        self._detectorLineEdit.validateLineEdit()
 
     def setFilePath(self, file: str):
         self._fileLineEdit.setText(file)
-        self._onNewFile(file)
 
     def getFilePath(self) -> str:
         return self._fileLineEdit.getText()
@@ -86,6 +87,12 @@ class ScanSelectionWidget(qt.QWidget):
     def getDetectorPath(self) -> str:
         return self._detectorLineEdit.getText()
 
+    def validateSelection(self) -> bool:
+        return (
+            self._fileLineEdit.validateLineEdit()
+            and self._detectorLineEdit.validateLineEdit()
+        )
+
 
 class ScanSelectionWidgetWithPositioners(ScanSelectionWidget):
     """
@@ -103,14 +110,20 @@ class ScanSelectionWidgetWithPositioners(ScanSelectionWidget):
         self._scanNameComboBox.currentTextChanged.connect(self._updatePositionersPath)
 
     def _onNewFile(self, file_path: str):
-        super()._onNewFile(file_path)
         self._positionersLineEdit.setFile(file_path)
+        super()._onNewFile(file_path)
 
     def _updatePositionersPath(self, scan_number: str):
         self._positionersLineEdit.setText(f"/{scan_number}/instrument/positioners")
+        self._positionersLineEdit.validateLineEdit()
 
     def setPositionersPath(self, data_url: str):
         self._positionersLineEdit.setText(data_url)
 
     def getPositionersPath(self) -> str:
         return self._positionersLineEdit.getText()
+
+    def validateSelection(self) -> bool:
+        return (
+            super().validateSelection() and self._positionersLineEdit.validateLineEdit()
+        )

darfix/gui/data_selection/utils.py

@@ -39,6 +39,17 @@ def find_detector_name(scan: h5py.Group) -> str | None:
             # Found the LIMA detector
             return instrument_name
 
+    _logger.debug(
+        "Could not find a LIMA detector. Does this file have a NeXus Format ? Try to find any 3D dataset in measurement group."
+    )
+
+    # If nothing found, try at least to find a 3D dataset in measurement (Required for concatenate scans file as it does not have a Nexus Format).
+    for measurement_name, measurement in scan.get("measurement", {}).items():
+        if not isinstance(measurement, h5py.Dataset):
+            continue
+        if measurement.ndim == 3:
+            return measurement_name
+
     _logger.warning(
         f"Could not find valid detector in {scan.file}::{instrument_group.name} among {tuple(instrument_group.keys())}"
     )

darfix/gui/data_selection/{WorkingDirSelectionWidget.py → working_dir_selection_widget.py}

@@ -12,23 +12,23 @@ class WorkingDirSelectionWidget(qt.QWidget):
     Widget used to obtain a directory name
     """
 
-    dirChanged = qt.Signal()
-
     def __init__(self, parent=None):
         qt.QWidget.__init__(self, parent)
 
-        self._dir = qt.QLineEdit("", parent=self)
-        self._dir.editingFinished.connect(self.dirChanged)
+        self._directoryLineEdit = qt.QLineEdit("", parent=self)
         self.completer = create_completer()
-        self._dir.setCompleter(self.completer)
+        self._directoryLineEdit.setCompleter(self.completer)
 
         self._addButton = qt.QPushButton("Select working directory", parent=self)
-        self._addButton.pressed.connect(self._selectWorkingDirectory)
         self.setLayout(qt.QHBoxLayout())
 
-        self.layout().addWidget(self._dir)
+        self.layout().addWidget(self._directoryLineEdit)
         self.layout().addWidget(self._addButton)
 
+        # Connect Signals / Slots
+
+        self._addButton.pressed.connect(self._selectWorkingDirectory)
+
     def _selectWorkingDirectory(self):
         """
         Select a folder to be used as working directory (task results will be saved at this location)
@@ -37,14 +37,15 @@ class WorkingDirSelectionWidget(qt.QWidget):
         fileDialog.setOption(qt.QFileDialog.ShowDirsOnly)
         fileDialog.setFileMode(qt.QFileDialog.Directory)
         if fileDialog.exec():
-            self._dir.setText(fileDialog.directory().absolutePath())
-            self.dirChanged.emit()
+            self._directoryLineEdit.setText(fileDialog.directory().absolutePath())
         else:
             _logger.warning("Could not open directory")
 
-    def getDir(self):
-        return str(self._dir.text())
+    def getDir(self) -> str:
+        return str(self._directoryLineEdit.text())
+
+    def setDir(self, working_directory: str):
+        self._directoryLineEdit.setText(str(working_directory))
 
-    def setDir(self, _dir):
-        self._dir.setText(str(_dir))
-        self.dirChanged.emit()
+    def setDefaultDir(self, default_dir: str):
+        self._directoryLineEdit.setPlaceholderText(default_dir + " (default)")

darfix/gui/{dimensionsWidget.py → dimensions_widget.py}

@@ -6,7 +6,7 @@ import numpy
 from silx.gui import qt
 
 from darfix.core.dimension import Dimension
-from darfix.tasks.dimensiondefinition import DimensionDefinition
+from darfix.tasks.dimension_definition import DimensionDefinition
 
 _logger = logging.getLogger(__file__)
 

darfix/gui/{displayComponentsWidget.py → display_components_widget.py}

@@ -13,7 +13,7 @@ from silx.gui.plot import StackView
 import darfix
 from darfix.io.utils import write_components
 
-from .chooseDimensions import ChooseDimensionDock
+from .choose_dimensions import ChooseDimensionDock
 from .utils.utils import select_output_hdf5_file_with_dialog
 
 

darfix/gui/{filterByDimension.py → filter_by_dimension.py}

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from ewoksorange.gui.parameterform import block_signals
+from ewoksorange.gui.widgets.parameter_form import block_signals
 from silx.gui import qt
 
 from darfix.core.dimension import AcquisitionDims

darfix/gui/{grainplot/dimensionRangeSlider2D.py → grain_plot/dimension_range_slider_2d.py}

@@ -2,12 +2,12 @@ from __future__ import annotations
 
 from functools import partial
 
-from ewoksorange.gui.parameterform import block_signals
+from ewoksorange.gui.widgets.parameter_form import block_signals
 from silx.gui import qt
 
 from darfix.core.dimension import AcquisitionDims
 from darfix.core.dimension import Dimension
-from darfix.gui.utils.rangeSlider import RangeSliderWithSpinBox
+from darfix.gui.utils.range_slider import RangeSliderWithSpinBox
 
 
 class _DimensionRangeSlider(qt.QWidget):

darfix/gui/{grainplot/grainPlotWidget.py → grain_plot/grain_plot_widget.py}

@@ -12,7 +12,7 @@ from darfix.core.moment_types import MomentType
 from ...core.grainplot import GrainPlotMaps
 from ...core.grainplot import generate_grain_maps_nxdict
 from ..utils.utils import select_output_hdf5_file_with_dialog
-from .mosaicityWidget import MosaicityWidget
+from .mosaicity_widget import MosaicityWidget
 from .utils import MapType
 from .utils import add_image_with_transformation