Rename sigima.computation to sigima.proc

Author: PierreRaybaut

datalab/gui/processor/__init__.py

@@ -6,7 +6,7 @@
 for signals and images.
 
 Processor objects are the bridge between the computation modules
-(in :mod:`sigima.computation`) and the GUI modules (in :mod:`datalab.gui`).
+(in :mod:`sigima.proc`) and the GUI modules (in :mod:`datalab.gui`).
 They are used to call the computation functions and to update the GUI from inside
 the data panel objects.
 
@@ -15,7 +15,7 @@
 - Add an action in the :mod:`datalab.gui.actionhandler` module to trigger the
   processing feature from the GUI (e.g. a menu item or a toolbar button).
 
-- Implement the computation function in the :mod:`sigima.computation` module
+- Implement the computation function in the :mod:`sigima.proc` module
   (that would eventually call the algorithm from the :mod:`sigima.tools` module).
 
 - Implement the processor object method in this package to call the computation

datalab/gui/processor/base.py

@@ -23,9 +23,9 @@
 from guidata.widgets.arrayeditor import ArrayEditor
 from qtpy import QtCore as QC
 from qtpy import QtWidgets as QW
-from sigima.computation import is_computation_function
 from sigima.config import options as sigima_options
 from sigima.objects import ImageObj, SignalObj, TypeROI, TypeROIParam
+from sigima.proc import is_computation_function
 
 from datalab import env
 from datalab.config import Conf, _
@@ -1216,7 +1216,7 @@ def run_feature(
 
         .. code-block:: python
 
-            import sigima.computation.signal as sigima_signal
+            import sigima.proc.signal as sigima_signal
             import sigima.params
 
             # For patterns `1_to_1`, `1_to_0`, `n_to_1`:
@@ -1312,8 +1312,8 @@ def run_feature(
     def compute_roi_extraction(self, roi: TypeROI | None = None) -> None:
         """Extract Region Of Interest (ROI) from data with:
 
-        - :py:func:`sigima.computation.image.compute_extract_roi` for single ROI
-        - :py:func:`sigima.computation.image.compute_extract_rois` for multiple ROIs"""
+        - :py:func:`sigima.proc.image.compute_extract_roi` for single ROI
+        - :py:func:`sigima.proc.image.compute_extract_rois` for multiple ROIs"""
         # Expected behavior:
         # -----------------
         # * If `roi` is not None or not empty, skip the ROI dialog

datalab/gui/processor/image.py

@@ -9,9 +9,9 @@
 from __future__ import annotations
 
 import numpy as np
-import sigima.computation.base as sigima_base
-import sigima.computation.image as sigima_image
 import sigima.params
+import sigima.proc.base as sigima_base
+import sigima.proc.image as sigima_image
 from guidata.qthelpers import exec_dialog
 from plotpy.widgets.resizedialog import ResizeDialog
 from qtpy import QtWidgets as QW
@@ -480,7 +480,7 @@ def register_computations(self) -> None:
 
     @qt_try_except()
     def compute_resize(self, param: sigima.params.ResizeParam | None = None) -> None:
-        """Resize image with :py:func:`sigima.computation.image.resize`"""
+        """Resize image with :py:func:`sigima.proc.image.resize`"""
         obj0 = self.panel.objview.get_sel_objects(include_groups=True)[0]
         for obj in self.panel.objview.get_sel_objects():
             if obj.data.shape != obj0.data.shape:
@@ -507,7 +507,7 @@ def compute_resize(self, param: sigima.params.ResizeParam | None = None) -> None
 
     @qt_try_except()
     def compute_binning(self, param: sigima.params.BinningParam | None = None) -> None:
-        """Binning image with :py:func:`sigima.computation.image.binning`"""
+        """Binning image with :py:func:`sigima.proc.image.binning`"""
         edit = param is None
         obj0 = self.panel.objview.get_sel_objects(include_groups=True)[0]
         input_dtype_str = str(obj0.data.dtype)
@@ -524,7 +524,7 @@ def compute_line_profile(
         self, param: sigima.params.LineProfileParam | None = None
     ) -> None:
         """Compute profile along a vertical or horizontal line
-        with :py:func:`sigima.computation.image.line_profile`"""
+        with :py:func:`sigima.proc.image.line_profile`"""
         title = _("Profile")
         add_initial_shape = self.has_param_defaults(sigima.params.LineProfileParam)
         edit, param = self.init_param(param, sigima_image.LineProfileParam, title)
@@ -544,7 +544,7 @@ def compute_segment_profile(
         self, param: sigima.params.SegmentProfileParam | None = None
     ):
         """Compute profile along a segment
-        with :py:func:`sigima.computation.image.segment_profile`"""
+        with :py:func:`sigima.proc.image.segment_profile`"""
         title = _("Profile")
         add_initial_shape = self.has_param_defaults(sigima.params.SegmentProfileParam)
         edit, param = self.init_param(param, sigima_image.SegmentProfileParam, title)
@@ -564,7 +564,7 @@ def compute_average_profile(
         self, param: sigima.params.AverageProfileParam | None = None
     ) -> None:
         """Compute average profile
-        with :py:func:`sigima.computation.image.average_profile`"""
+        with :py:func:`sigima.proc.image.average_profile`"""
         title = _("Average profile")
         add_initial_shape = self.has_param_defaults(sigima.params.AverageProfileParam)
         edit, param = self.init_param(param, sigima_image.AverageProfileParam, title)
@@ -584,7 +584,7 @@ def compute_radial_profile(
         self, param: sigima.params.RadialProfileParam | None = None
     ) -> None:
         """Compute radial profile
-        with :py:func:`sigima.computation.image.radial_profile`"""
+        with :py:func:`sigima.proc.image.radial_profile`"""
         title = _("Radial profile")
         edit, param = self.init_param(param, sigima_image.RadialProfileParam, title)
         if edit:
@@ -669,7 +669,7 @@ def translate_coords(obj, orig, coords):
     @qt_try_except()
     def compute_offset_correction(self, param: ROI2DParam | None = None) -> None:
         """Compute offset correction
-        with :py:func:`sigima.computation.image.offset_correction`"""
+        with :py:func:`sigima.proc.image.offset_correction`"""
         obj = self.panel.objview.get_sel_objects(include_groups=True)[0]
         if param is None:
             dlg = imagebackground.ImageBackgroundDialog(obj, parent=self.panel.parent())
@@ -686,13 +686,13 @@ def compute_all_threshold(self) -> None:
         """Compute all threshold algorithms
         using the following functions:
 
-        - :py:func:`sigima.computation.image.threshold.threshold_isodata`
-        - :py:func:`sigima.computation.image.threshold.threshold_li`
-        - :py:func:`sigima.computation.image.threshold.threshold_mean`
-        - :py:func:`sigima.computation.image.threshold.threshold_minimum`
-        - :py:func:`sigima.computation.image.threshold.threshold_otsu`
-        - :py:func:`sigima.computation.image.threshold.threshold_triangle`
-        - :py:func:`sigima.computation.image.threshold.threshold_yen`
+        - :py:func:`sigima.proc.image.threshold.threshold_isodata`
+        - :py:func:`sigima.proc.image.threshold.threshold_li`
+        - :py:func:`sigima.proc.image.threshold.threshold_mean`
+        - :py:func:`sigima.proc.image.threshold.threshold_minimum`
+        - :py:func:`sigima.proc.image.threshold.threshold_otsu`
+        - :py:func:`sigima.proc.image.threshold.threshold_triangle`
+        - :py:func:`sigima.proc.image.threshold.threshold_yen`
         """
         self.compute_multiple_1_to_1(
             [
@@ -714,10 +714,10 @@ def compute_all_denoise(self, params: list | None = None) -> None:
         """Compute all denoising filters
         using the following functions:
 
-        - :py:func:`sigima.computation.image.restoration.denoise_tv`
-        - :py:func:`sigima.computation.image.restoration.denoise_bilateral`
-        - :py:func:`sigima.computation.image.restoration.denoise_wavelet`
-        - :py:func:`sigima.computation.image.restoration.denoise_tophat`
+        - :py:func:`sigima.proc.image.restoration.denoise_tv`
+        - :py:func:`sigima.proc.image.restoration.denoise_bilateral`
+        - :py:func:`sigima.proc.image.restoration.denoise_wavelet`
+        - :py:func:`sigima.proc.image.restoration.denoise_tophat`
         """
         if params is not None:
             assert len(params) == 4, "Wrong number of parameters (4 expected)"
@@ -748,12 +748,12 @@ def compute_all_morphology(
         """Compute all morphology filters
         using the following functions:
 
-        - :py:func:`sigima.computation.image.morphology.white_tophat`
-        - :py:func:`sigima.computation.image.morphology.black_tophat`
-        - :py:func:`sigima.computation.image.morphology.erosion`
-        - :py:func:`sigima.computation.image.morphology.dilation`
-        - :py:func:`sigima.computation.image.morphology.opening`
-        - :py:func:`sigima.computation.image.morphology.closing`
+        - :py:func:`sigima.proc.image.morphology.white_tophat`
+        - :py:func:`sigima.proc.image.morphology.black_tophat`
+        - :py:func:`sigima.proc.image.morphology.erosion`
+        - :py:func:`sigima.proc.image.morphology.dilation`
+        - :py:func:`sigima.proc.image.morphology.opening`
+        - :py:func:`sigima.proc.image.morphology.closing`
         """
         if param is None:
             param = sigima_image.MorphologyParam()
@@ -774,20 +774,20 @@ def compute_all_edges(self) -> None:
         """Compute all edges filters
         using the following functions:
 
-        - :py:func:`sigima.computation.image.edges.roberts`
-        - :py:func:`sigima.computation.image.edges.prewitt`
-        - :py:func:`sigima.computation.image.edges.prewitt_h`
-        - :py:func:`sigima.computation.image.edges.prewitt_v`
-        - :py:func:`sigima.computation.image.edges.sobel`
-        - :py:func:`sigima.computation.image.edges.sobel_h`
-        - :py:func:`sigima.computation.image.edges.sobel_v`
-        - :py:func:`sigima.computation.image.edges.scharr`
-        - :py:func:`sigima.computation.image.edges.scharr_h`
-        - :py:func:`sigima.computation.image.edges.scharr_v`
-        - :py:func:`sigima.computation.image.edges.farid`
-        - :py:func:`sigima.computation.image.edges.farid_h`
-        - :py:func:`sigima.computation.image.edges.farid_v`
-        - :py:func:`sigima.computation.image.edges.laplace`
+        - :py:func:`sigima.proc.image.edges.roberts`
+        - :py:func:`sigima.proc.image.edges.prewitt`
+        - :py:func:`sigima.proc.image.edges.prewitt_h`
+        - :py:func:`sigima.proc.image.edges.prewitt_v`
+        - :py:func:`sigima.proc.image.edges.sobel`
+        - :py:func:`sigima.proc.image.edges.sobel_h`
+        - :py:func:`sigima.proc.image.edges.sobel_v`
+        - :py:func:`sigima.proc.image.edges.scharr`
+        - :py:func:`sigima.proc.image.edges.scharr_h`
+        - :py:func:`sigima.proc.image.edges.scharr_v`
+        - :py:func:`sigima.proc.image.edges.farid`
+        - :py:func:`sigima.proc.image.edges.farid_h`
+        - :py:func:`sigima.proc.image.edges.farid_v`
+        - :py:func:`sigima.proc.image.edges.laplace`
         """
         funcs = [
             sigima_image.roberts,
@@ -824,7 +824,7 @@ def compute_peak_detection(
         self, param: sigima.params.Peak2DDetectionParam | None = None
     ) -> dict[str, ResultShape]:
         """Compute 2D peak detection
-        with :py:func:`sigima.computation.image.peak_detection`"""
+        with :py:func:`sigima.proc.image.peak_detection`"""
         edit, param = self.init_param(
             param, sigima_image.Peak2DDetectionParam, _("Peak detection")
         )

datalab/gui/processor/signal.py

@@ -12,9 +12,9 @@
 from collections.abc import Callable
 
 import numpy as np
-import sigima.computation.base as sigima_base
-import sigima.computation.signal as sigima_signal
 import sigima.params
+import sigima.proc.base as sigima_base
+import sigima.proc.signal as sigima_signal
 from guidata.qthelpers import exec_dialog
 from sigima.objects import (
     ResultProperties,
@@ -465,7 +465,7 @@ def register_computations(self) -> None:
     @qt_try_except()
     def compute_offset_correction(self, param: ROI1DParam | None = None) -> None:
         """Compute offset correction
-        with :py:func:`sigima.computation.signal.offset_correction`"""
+        with :py:func:`sigima.proc.signal.offset_correction`"""
         obj = self.panel.objview.get_sel_objects(include_groups=True)[0]
         if param is None:
             dlg = signalbaseline.SignalBaselineDialog(obj, parent=self.panel.parent())
@@ -483,13 +483,13 @@ def compute_all_stability(
         """Compute all stability analysis features
         using the following functions:
 
-        - :py:func:`sigima.computation.signal.allan_variance`
-        - :py:func:`sigima.computation.signal.allan_deviation`
-        - :py:func:`sigima.computation.signal.overlapping_allan_variance`
-        - :py:func:`sigima.computation.signal.modified_allan_variance`
-        - :py:func:`sigima.computation.signal.hadamard_variance`
-        - :py:func:`sigima.computation.signal.total_variance`
-        - :py:func:`sigima.computation.signal.time_deviation`
+        - :py:func:`sigima.proc.signal.allan_variance`
+        - :py:func:`sigima.proc.signal.allan_deviation`
+        - :py:func:`sigima.proc.signal.overlapping_allan_variance`
+        - :py:func:`sigima.proc.signal.modified_allan_variance`
+        - :py:func:`sigima.proc.signal.hadamard_variance`
+        - :py:func:`sigima.proc.signal.total_variance`
+        - :py:func:`sigima.proc.signal.time_deviation`
         """
         if param is None:
             param = sigima_signal.AllanVarianceParam()
@@ -513,7 +513,7 @@ def compute_peak_detection(
         self, param: sigima.params.PeakDetectionParam | None = None
     ) -> None:
         """Detect peaks from data
-        with :py:func:`sigima.computation.signal.peak_detection`"""
+        with :py:func:`sigima.proc.signal.peak_detection`"""
         obj = self.panel.objview.get_sel_objects(include_groups=True)[0]
         edit, param = self.init_param(
             param, sigima_signal.PeakDetectionParam, _("Peak detection")
@@ -611,7 +611,7 @@ def compute_full_width_at_y(
         self, param: sigima.params.OrdinateParam | None = None
     ) -> dict[str, ResultShape] | None:
         """Compute full width at a given y
-        with :py:func:`sigima.computation.signal.full_width_at_y`"""
+        with :py:func:`sigima.proc.signal.full_width_at_y`"""
         if param is None:
             obj = self.panel.objview.get_sel_objects(include_groups=True)[0]
             dlg = signaldeltax.SignalDeltaXDialog(obj, parent=self.panel.parent())
@@ -626,7 +626,7 @@ def compute_full_width_at_y(
     def compute_x_at_y(
         self, param: sigima_signal.OrdinateParam | None = None
     ) -> dict[str, ResultProperties] | None:
-        """Compute x at y with :py:func:`sigima.computation.signal.x_at_y`."""
+        """Compute x at y with :py:func:`sigima.proc.signal.x_at_y`."""
         if param is None:
             obj = self.panel.objview.get_sel_objects(include_groups=True)[0]
             dlg = signalcursor.SignalCursorDialog(
@@ -643,7 +643,7 @@ def compute_x_at_y(
     def compute_y_at_x(
         self, param: sigima_signal.AbscissaParam | None = None
     ) -> dict[str, ResultProperties] | None:
-        """Compute y at x with :py:func:`sigima.computation.signal.y_at_x`."""
+        """Compute y at x with :py:func:`sigima.proc.signal.y_at_x`."""
         if param is None:
             obj = self.panel.objview.get_sel_objects(include_groups=True)[0]
             dlg = signalcursor.SignalCursorDialog(

datalab/plugins/datalab_testdata.py

@@ -9,8 +9,8 @@
 """
 
 import sigima.tests.data as test_data
-from sigima.computation.base import dst_1_to_1
 from sigima.objects import ImageObj, NormalRandomParam, SignalObj
+from sigima.proc.base import dst_1_to_1
 
 from datalab.config import _
 from datalab.plugins import PluginBase, PluginInfo

datalab/tests/backbone/main_app_test.py

@@ -12,8 +12,8 @@
 
 import os
 
-import sigima.computation.signal as sigima_signal
 import sigima.params
+import sigima.proc.signal as sigima_signal
 from sigima.tests.data import create_paracetamol_signal
 
 from datalab.env import execenv

datalab/tests/features/common/metadata_app_test.py

@@ -11,10 +11,10 @@
 # pylint: disable=invalid-name  # Allows short reference names like x, y, ...
 # guitest: show
 
-import sigima.computation.image as sigima_image
-import sigima.computation.signal as sigima_signal
 import sigima.objects
 import sigima.params
+import sigima.proc.image as sigima_image
+import sigima.proc.signal as sigima_signal
 from sigima.tests.data import create_paracetamol_signal
 
 from datalab.env import execenv

datalab/tests/features/common/misc_app_test.py

@@ -16,8 +16,8 @@
 import os.path as osp
 from typing import TYPE_CHECKING, Any
 
-import sigima.computation.signal as sigima_signal
 import sigima.params
+import sigima.proc.signal as sigima_signal
 from sigima.tests.data import (
     create_2dstep_image,
     create_paracetamol_signal,

datalab/tests/features/images/background_dialog_test.py

@@ -11,9 +11,9 @@
 from __future__ import annotations
 
 import numpy as np
-import sigima.computation.image as sigima_image
 import sigima.objects
 import sigima.params
+import sigima.proc.image as sigima_image
 from guidata.qthelpers import exec_dialog, qt_app_context
 from sigima.tests import vistools
 from sigima.tests.data import create_noisygauss_image

datalab/tests/features/images/flatfield_app_test.py

@@ -11,8 +11,8 @@
 
 # guitest: show
 
-from sigima.computation.image import FlatFieldParam
 from sigima.objects import Gauss2DParam, ImageTypes, NewImageParam, UniformRandomParam
+from sigima.proc.image import FlatFieldParam
 
 from datalab.config import _
 from datalab.tests import cdltest_app_context