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

darfix/tasks/hdf5_data_selection.py

@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import logging
-import os.path
 
 from ewokscore import Task
 from ewokscore.missing_data import MISSING_DATA
@@ -12,6 +11,7 @@ from pydantic import Field
 from silx.io.url import DataUrl
 
 from .. import dtypes
+from ..core.data_selection import get_default_output_directory
 from ..core.data_selection import load_process_data
 
 _logger = logging.getLogger(__file__)
@@ -87,15 +87,11 @@ class HDF5DataSelection(
             bg_data_url = None
 
         treated_data_dir = self.get_input_value("treated_data_dir", None)
-        # Move output folder to 'PROCESSED_DATA' instead of 'RAW_DATA' when possible
-        # but ONLY if it was not set by the user
-        if treated_data_dir is None and "RAW_DATA" in raw_data_url.file_path():
-            treated_data_dir = os.path.dirname(raw_data_url.file_path()).replace(
-                "RAW_DATA", "PROCESSED_DATA"
-            )
-            _logger.warning(f"Treated data will be saved in {treated_data_dir}")
+        if treated_data_dir is None:
+            treated_data_dir = get_default_output_directory(raw_data_url.file_path())
+        _logger.info(f"Output directory is {treated_data_dir}.")
 
-        dataset, indices, bg_indices, bg_dataset = load_process_data(
+        dataset, bg_dataset = load_process_data(
             detector_url=raw_data_url.path(),
             root_dir=treated_data_dir,
             dark_detector_url=bg_data_url,
@@ -105,7 +101,5 @@ class HDF5DataSelection(
 
         self.outputs.dataset = dtypes.Dataset(
             dataset=dataset,
-            indices=indices,
-            bg_indices=bg_indices,
             bg_dataset=bg_dataset,
         )

darfix/tasks/hdf5_scans_concatenation.py

@@ -16,10 +16,10 @@ from pydantic import ConfigDict
 from pydantic import Field
 from silx.io.dictdump import dicttoh5
 
-from darfix.core.datapathfinder import DETECTOR_KEYWORD
-from darfix.core.datapathfinder import SCAN_KEYWORD
-from darfix.core.datapathfinder import DataPathFinder
-from darfix.core.datapathfinder import sort_bliss_scan_entries
+from darfix.core.data_path_finder import DETECTOR_KEYWORD
+from darfix.core.data_path_finder import SCAN_KEYWORD
+from darfix.core.data_path_finder import DataPathFinder
+from darfix.core.data_path_finder import sort_bliss_scan_entries
 from darfix.core.settings import PROCESSED_DATA
 from darfix.core.settings import RAW_DATA
 

darfix/tasks/noise_removal.py

@@ -0,0 +1,88 @@
+from __future__ import annotations
+
+import copy
+import logging
+import threading
+from typing import Any
+
+from ewokscore import TaskWithProgress
+from ewokscore.missing_data import MissingData
+from ewokscore.model import BaseInputModel
+from pydantic import ConfigDict
+from pydantic import Field
+
+from darfix.core.noise_removal_type import NoiseRemovalType
+from darfix.dtypes import Dataset
+
+from ..core.noise_removal import add_background_data_into_operation
+from ..core.noise_removal import apply_noise_removal_operations
+
+_logger = logging.getLogger(__name__)
+
+
+class Inputs(BaseInputModel):
+    model_config = ConfigDict(use_attribute_docstrings=True)
+    dataset: Dataset
+    """ Input dataset containing a stack of images """
+    operations: list[dict[str, Any]] | MissingData = Field(
+        default=[],
+        examples=[
+            [
+                {"type": "THRESHOLD", "parameters": {"bottom": 10.0, "top": 1000.0}},
+                {"type": "HP", "parameters": {"kernel_size": 3}},
+            ]
+        ],
+        description="""List of noise removal operations to apply to the dataset. Empty list if not provided."
+
+        Available operations :
+
+        - 'Operation.THRESHOLD': Threshold operation. Parameters: 'bottom' (float) and 'top' (float). Keep value only if it is between bottom and top.
+        - 'Operation.HP': Hot Pixel removal using median filter operation. Parameters: 'kernel_size' (int).
+        - 'Operation.BS': Background subtraction operation. Parameters: 'method' ("mean" | "median") and 'background_type' ("Data" | "Unused data (after partition)" | "Dark data").
+        - 'Operation.MASK': Mask removal operation. Parameters: 'mask' (numpy.ndarray 2D containing 0 and 1 where 0 indicates the pixels to be removed).
+        """,
+    )
+    copy_dataset: bool = False
+    """If `True`, operations are applied on a copy of the input dataset. Else, operations are applied directly on the input dataset"""
+
+
+class NoiseRemoval(
+    TaskWithProgress,
+    input_model=Inputs,
+    output_names=["dataset"],
+):
+    """Apply a list of noise removal operations on a Darfix dataset."""
+
+    def run(self):
+
+        self.cancelEvent = threading.Event()
+
+        inputs = Inputs(**self.get_input_values())
+
+        input_dataset: Dataset = inputs.dataset
+
+        if inputs.copy_dataset:
+            input_dataset = copy.deepcopy(input_dataset)
+
+        for operation in inputs.operations:
+            if operation["type"] is NoiseRemovalType.BS:
+                _logger.info("Computing background...")
+                add_background_data_into_operation(input_dataset, operation)
+
+        apply_noise_removal_operations(
+            input_dataset.dataset.as_array3d(),
+            inputs.operations,
+            self._is_cancelled,
+            self._set_progress,
+        )
+
+        self.outputs.dataset = input_dataset
+
+    def cancel(self) -> None:
+        self.cancelEvent.set()
+
+    def _is_cancelled(self) -> bool:
+        return self.cancelEvent.is_set()
+
+    def _set_progress(self, progress: int):
+        self.progress = progress

darfix/tasks/noiseremoval.py

@@ -1,88 +1,10 @@
-from __future__ import annotations
+import warnings
 
-import copy
-import logging
-import threading
-from typing import Any
+from .noise_removal import NoiseRemoval  # noqa: F401
 
-from ewokscore import TaskWithProgress
-from ewokscore.missing_data import MissingData
-from ewokscore.model import BaseInputModel
-from pydantic import ConfigDict
-from pydantic import Field
-
-from darfix.core.state_of_operation import Operation
-from darfix.dtypes import Dataset
-
-from ..core.noiseremoval import add_background_data_into_operation
-from ..core.noiseremoval import apply_noise_removal_operations
-
-_logger = logging.getLogger(__name__)
-
-
-class Inputs(BaseInputModel):
-    model_config = ConfigDict(use_attribute_docstrings=True)
-    dataset: Dataset
-    """ Input dataset containing a stack of images """
-    operations: list[dict[str, Any]] | MissingData = Field(
-        default=[],
-        examples=[
-            [
-                {"type": "THRESHOLD", "parameters": {"bottom": 10.0, "top": 1000.0}},
-                {"type": "HP", "parameters": {"kernel_size": 3}},
-            ]
-        ],
-        description="""List of noise removal operations to apply to the dataset. Empty list if not provided."
-
-        Available operations :
-
-        - 'Operation.THRESHOLD': Threshold operation. Parameters: 'bottom' (float) and 'top' (float). Keep value only if it is between bottom and top.
-        - 'Operation.HP': Hot Pixel removal using median filter operation. Parameters: 'kernel_size' (int).
-        - 'Operation.BS': Background subtraction operation. Parameters: 'method' ("mean" | "median") and 'background_type' ("Data" | "Unused data (after partition)" | "Dark data").
-        - 'Operation.MASK': Mask removal operation. Parameters: 'mask' (numpy.ndarray 2D containing 0 and 1 where 0 indicates the pixels to be removed).
-        """,
-    )
-    copy_dataset: bool = False
-    """If `True`, operations are applied on a copy of the input dataset. Else, operations are applied directly on the input dataset"""
-
-
-class NoiseRemoval(
-    TaskWithProgress,
-    input_model=Inputs,
-    output_names=["dataset"],
-):
-    """Apply a list of noise removal operations on a Darfix dataset."""
-
-    def run(self):
-
-        self.cancelEvent = threading.Event()
-
-        inputs = Inputs(**self.get_input_values())
-
-        input_dataset: Dataset = inputs.dataset
-
-        if inputs.copy_dataset:
-            input_dataset = copy.deepcopy(input_dataset)
-
-        for operation in inputs.operations:
-            if operation["type"] is Operation.BS:
-                _logger.info("Computing background...")
-                add_background_data_into_operation(input_dataset, operation)
-
-        apply_noise_removal_operations(
-            input_dataset.dataset.as_array3d(input_dataset.indices),
-            inputs.operations,
-            self._is_cancelled,
-            self._set_progress,
-        )
-
-        self.outputs.dataset = input_dataset
-
-    def cancel(self) -> None:
-        self.cancelEvent.set()
-
-    def _is_cancelled(self) -> bool:
-        return self.cancelEvent.is_set()
-
-    def _set_progress(self, progress: int):
-        self.progress = progress
+warnings.warn(
+    f"The '{__name__}' module is deprecated and will be removed in a future release. "
+    "Please replace module name `noiseremoval` by `noise_removal`",
+    DeprecationWarning,
+    stacklevel=2,
+)

darfix/tasks/pca.py

@@ -35,7 +35,7 @@ class PCA(
             )
         num_components = self.get_input_value("num_components")
 
-        pca_kwargs = {"return_vals": True, "indices": dataset.indices}
+        pca_kwargs = {"return_vals": True}
         if not is_missing_data(num_components):
             pca_kwargs["num_components"] = num_components
 
@@ -44,7 +44,5 @@ class PCA(
         self.outputs.vals = vals
         self.outputs.dataset = Dataset(
             dataset=dataset.dataset,
-            indices=dataset.indices,
             bg_dataset=dataset.bg_dataset,
-            bg_indices=dataset.bg_indices,
         )

darfix/tasks/projection.py

@@ -32,16 +32,11 @@ class Projection(Task, input_model=Inputs, output_names=["dataset"]):
             raise DatasetTypeError(dataset)
 
         darfix_dataset = dataset.dataset
-        indices = dataset.indices
         dimension: Sequence[int] = self.inputs.dimension
 
-        darfix_dataset = darfix_dataset.project_data(
-            dimension=dimension, indices=indices
-        )
+        darfix_dataset = darfix_dataset.project_data(dimension=dimension)
 
         self.outputs.dataset = Dataset(
             dataset=darfix_dataset,
-            indices=indices,
-            bg_indices=dataset.bg_indices,
             bg_dataset=dataset.bg_dataset,
         )

darfix/tasks/rocking_curves.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 import os.path
+import threading
 from pathlib import Path
 from typing import Literal
 
@@ -33,6 +34,8 @@ class RockingCurves(Task, input_model=Inputs, output_names=["dataset", "maps"]):
     """
 
     def run(self):
+        self.cancelEvent = threading.Event()
+
         inputs = Inputs(**self.get_input_values())
 
         output_filename = inputs.output_filename
@@ -43,23 +46,25 @@ class RockingCurves(Task, input_model=Inputs, output_names=["dataset", "maps"]):
             )
 
         dataset = inputs.dataset.dataset
-        indices = inputs.dataset.indices
         new_image_dataset, maps = dataset.apply_fit(
-            indices=indices, int_thresh=inputs.int_thresh, method=inputs.method
+            int_thresh=inputs.int_thresh,
+            method=inputs.method,
+            abort_event=self.cancelEvent,
         )
 
         if output_filename is not None:
             nxdict = generate_rocking_curves_nxdict(
                 new_image_dataset,
                 maps,
-                residuals=compute_residuals(new_image_dataset, dataset, indices),
+                residuals=compute_residuals(new_image_dataset, dataset),
             )
             dicttonx(nxdict, output_filename)
 
         self.outputs.dataset = Dataset(
             dataset=new_image_dataset,
-            indices=indices,
-            bg_indices=inputs.dataset.bg_indices,
             bg_dataset=inputs.dataset.bg_dataset,
         )
         self.outputs.maps = maps
+
+    def cancel(self):
+        self.cancelEvent.set()

darfix/tasks/roi.py

@@ -58,7 +58,5 @@ class RoiSelection(
 
         self.outputs.dataset = Dataset(
             dataset=dataset,
-            indices=input_dataset.indices,
-            bg_indices=input_dataset.bg_indices,
             bg_dataset=bg_dataset,
         )

darfix/tasks/shift_correction.py

@@ -0,0 +1,45 @@
+from __future__ import annotations
+
+import copy
+from typing import Sequence
+
+from ewokscore import Task
+from ewokscore.model import BaseInputModel
+from pydantic import ConfigDict
+
+from darfix.core.shift_correction import apply_shift
+from darfix.dtypes import Dataset
+
+
+class Inputs(BaseInputModel):
+    model_config = ConfigDict(use_attribute_docstrings=True)
+    dataset: Dataset
+    """ Input dataset containing a stack of images """
+    shift: Sequence[float] | Sequence[Sequence[float]] | None = None
+    """Shift to apply to the images. If not provided, dataset will be unchanged."""
+    selected_axis: int | None = None
+    """Selected dimension axis. If not None. We considere a linear shift along this dimension.  Darfix convention is : dimension with axis 0 is the fast motor."""
+    copy_dataset: bool = False
+    """If `True`, operations are applied on a copy of the input dataset. Else, operations are applied directly on the input dataset"""
+
+
+class ShiftCorrection(
+    Task,
+    input_model=Inputs,
+    output_names=["dataset"],
+):
+    def run(self):
+        inputs = Inputs(**self.get_input_values())
+
+        if inputs.shift is None:
+            self.outputs.dataset = inputs.dataset
+            return
+
+        input_dataset: Dataset = inputs.dataset
+
+        if inputs.copy_dataset:
+            input_dataset = copy.deepcopy(input_dataset)
+
+        apply_shift(input_dataset, inputs.shift, inputs.selected_axis)
+
+        self.outputs.dataset = input_dataset

darfix/tasks/shiftcorrection.py

@@ -1,45 +1,10 @@
-from __future__ import annotations
+import warnings
 
-import copy
-from typing import Sequence
+from .shift_correction import ShiftCorrection  # noqa: F401
 
-from ewokscore import Task
-from ewokscore.model import BaseInputModel
-from pydantic import ConfigDict
-
-from darfix.core.shiftcorrection import apply_shift
-from darfix.dtypes import Dataset
-
-
-class Inputs(BaseInputModel):
-    model_config = ConfigDict(use_attribute_docstrings=True)
-    dataset: Dataset
-    """ Input dataset containing a stack of images """
-    shift: Sequence[float] | Sequence[Sequence[float]] | None = None
-    """Shift to apply to the images. If not provided, dataset will be unchanged."""
-    selected_axis: int | None = None
-    """Selected dimension axis. If not None. We considere a linear shift along this dimension.  Darfix convention is : dimension with axis 0 is the fast motor."""
-    copy_dataset: bool = False
-    """If `True`, operations are applied on a copy of the input dataset. Else, operations are applied directly on the input dataset"""
-
-
-class ShiftCorrection(
-    Task,
-    input_model=Inputs,
-    output_names=["dataset"],
-):
-    def run(self):
-        inputs = Inputs(**self.get_input_values())
-
-        if inputs.shift is None:
-            self.outputs.dataset = inputs.dataset
-            return
-
-        input_dataset: Dataset = inputs.dataset
-
-        if inputs.copy_dataset:
-            input_dataset = copy.deepcopy(input_dataset)
-
-        apply_shift(input_dataset, inputs.shift, inputs.selected_axis)
-
-        self.outputs.dataset = input_dataset
+warnings.warn(
+    f"The '{__name__}' module is deprecated and will be removed in a future release. "
+    "Please replace module name `shiftcorrection` by `shift_correction`",
+    DeprecationWarning,
+    stacklevel=2,
+)

darfix/tasks/transformation.py

@@ -76,7 +76,5 @@ class TransformationMatrixComputation(
 
         self.outputs.dataset = Dataset(
             dataset=dataset,
-            indices=input_dataset.indices,
-            bg_indices=input_dataset.bg_indices,
             bg_dataset=input_dataset.bg_dataset,
         )

darfix/tasks/weak_beam.py

@@ -0,0 +1,71 @@
+from __future__ import annotations
+
+import copy
+import os
+import string
+
+import h5py
+import numpy
+from ewokscore import Task
+from ewokscore.missing_data import MISSING_DATA
+from ewokscore.missing_data import MissingData
+from ewokscore.model import BaseInputModel
+from pydantic import ConfigDict
+
+from darfix import dtypes
+from darfix.core.moment_types import MomentType
+
+
+class Inputs(BaseInputModel):
+    model_config = ConfigDict(use_attribute_docstrings=True)
+    dataset: dtypes.Dataset
+    """Input dataset containing a stack of images."""
+    nvalue: float | MissingData = MISSING_DATA
+    """Increase or decrease the top threshold (threshold = `nvalue` * std)"""
+    title: str | MissingData = MISSING_DATA
+    """Title for the output file. If not provided, title is empty."""
+    copy_dataset: bool = False
+    """If `True`, operations are applied on a copy of the input dataset. Else, operations are applied directly on the input dataset"""
+
+
+class WeakBeam(
+    Task,
+    input_model=Inputs,
+    output_names=["dataset"],
+):
+    """
+    Obtain dataset with filtered weak beam and recover its Center of Mass.
+    Save file with this COM for further processing.
+    """
+
+    def run(self):
+        inputs = Inputs(**self.get_input_values())
+
+        dataset = inputs.dataset
+
+        if inputs.copy_dataset:
+            dataset = copy.deepcopy(dataset)
+
+        nvalue = inputs.nvalue
+
+        img_dataset = dataset.dataset
+
+        img_dataset.recover_weak_beam(nvalue)
+        com = img_dataset.apply_moments()[0][MomentType.COM]
+        os.makedirs(img_dataset.dir, exist_ok=True)
+        filename = os.path.join(img_dataset.dir, "weakbeam_{}.hdf5".format(nvalue))
+
+        title = self.get_input_value("title", "")
+        # title can be set to None, MISSING_DATA or an empty string. So safer to use the following line
+        title = title or self.get_random_title()
+        with h5py.File(filename, "a") as _file:
+            _file[title] = com
+
+        self.outputs.dataset = dtypes.Dataset(
+            dataset=img_dataset,
+        )
+
+    @staticmethod
+    def get_random_title() -> str:
+        letters = string.ascii_lowercase
+        return "".join(numpy.random.choice(list(letters)) for i in range(6))

darfix/tasks/weakbeam.py

@@ -1,69 +1,10 @@
-from __future__ import annotations
+import warnings
 
-import os
-import string
+from .weak_beam import WeakBeam  # noqa: F401
 
-import h5py
-import numpy
-from ewokscore import Task
-from ewokscore.missing_data import MISSING_DATA
-from ewokscore.missing_data import MissingData
-from ewokscore.model import BaseInputModel
-from pydantic import ConfigDict
-
-from darfix import dtypes
-
-
-class Inputs(BaseInputModel):
-    model_config = ConfigDict(use_attribute_docstrings=True)
-    dataset: dtypes.Dataset
-    """Input dataset containing a stack of images."""
-    nvalue: float | MissingData = MISSING_DATA
-    """Increase or decrease the top threshold by this fixed value."""
-    indices: list[int] | MissingData = MISSING_DATA
-    """Indices of the images to process. If not provided, all images will be processed."""
-    title: str | MissingData = MISSING_DATA
-    """Title for the output file. If not provided, title is empty."""
-
-
-class WeakBeam(
-    Task,
-    input_model=Inputs,
-    output_names=["dataset"],
-):
-    """
-    Obtain dataset with filtered weak beam and recover its Center of Mass.
-    Save file with this COM for further processing.
-    """
-
-    def run(self):
-        dataset = self.inputs.dataset
-        indices = self.get_input_value("indices", None)
-        if isinstance(dataset, dtypes.Dataset):
-            dataset = dataset.dataset
-        if not isinstance(dataset, dtypes.ImageDataset):
-            raise TypeError("dataset is expected to be an instance")
-
-        nvalue = self.inputs.nvalue
-        wb_dataset = dataset.recover_weak_beam(nvalue, indices=indices)
-        com = wb_dataset.apply_moments(indices=indices)[0][0]
-        os.makedirs(dataset.dir, exist_ok=True)
-        filename = os.path.join(dataset.dir, "weakbeam_{}.hdf5".format(nvalue))
-
-        title = self.get_input_value("title", "")
-        # title can be set to None, MISSING_DATA or an empty string. So safer to use the following line
-        title = title or self.get_random_title()
-        with h5py.File(filename, "a") as _file:
-            _file[title] = com
-
-        self.outputs.dataset = dtypes.Dataset(
-            dataset=dataset,
-            indices=indices,
-            bg_indices=self.inputs.dataset.bg_indices,
-            bg_dataset=self.inputs.dataset.bg_dataset,
-        )
-
-    @staticmethod
-    def get_random_title() -> str:
-        letters = string.ascii_lowercase
-        return "".join(numpy.random.choice(list(letters)) for i in range(6))
+warnings.warn(
+    f"The '{__name__}' module is deprecated and will be removed in a future release. "
+    "Please replace module name `weakbeam` by `weak_beam`",
+    DeprecationWarning,
+    stacklevel=2,
+)

darfix/tasks/zsum.py

@@ -21,7 +21,7 @@ class ZSum(
     input_model=Inputs,
     output_names=["zsum"],
 ):
-    """Sum all images of the dataset or images at specified indices along a given dimension."""
+    """Sum all images of the dataset or images along a given dimension."""
 
     def run(self):
         inputs = Inputs(**self.get_input_values())

darfix/tests/conftest.py

@@ -33,7 +33,7 @@ def input_dataset(tmp_path, silx_resources):
         file_path=input_filename, data_path="/2.1/instrument/positioners"
     )
 
-    dataset, _, _, _ = load_process_data(
+    dataset, _ = load_process_data(
         detector_url=detector_url,
         root_dir=tmp_path,
         title="input",

darfix/tests/gui/test_data_path_completer.py

@@ -3,10 +3,10 @@ import os
 import pytest
 from ewoksorange.tests.conftest import qtapp  # noqa F401
 
-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.datapathfinder import 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.core.data_path_finder import SCAN_KEYWORD
 from darfix.gui.utils.data_path_completer import DataPathLineEditWithCompleter
 from darfix.gui.utils.data_path_completer import DataPathModel
 from darfix.tests.utils import create_scans

darfix/tests/gui/test_dimension_range_slider_2d.py

@@ -7,8 +7,8 @@ from silx.gui.data.test.test_dataviewer import SignalListener
 
 from darfix.core.dimension import AcquisitionDims
 from darfix.core.dimension import Dimension
-from darfix.gui.grainplot.dimensionRangeSlider2D import DimensionRangeSlider2D
-from darfix.gui.grainplot.dimensionRangeSlider2D import _DimensionRangeSlider
+from darfix.gui.grain_plot.dimension_range_slider_2d import DimensionRangeSlider2D
+from darfix.gui.grain_plot.dimension_range_slider_2d import _DimensionRangeSlider
 
 
 @pytest.fixture

darfix/tests/gui/test_range_slider_with_spinboxes.py

@@ -7,7 +7,7 @@ from silx.gui import qt
 from silx.gui.data.test.test_dataviewer import SignalListener
 from silx.gui.widgets.RangeSlider import RangeSlider
 
-from darfix.gui.utils.rangeSlider import RangeSliderWithSpinBox
+from darfix.gui.utils.range_slider import RangeSliderWithSpinBox
 
 
 @pytest.fixture