Merge branch 'develop' into feature/env

Author: PierreRaybaut

.vscode/tasks.json

@@ -61,6 +61,7 @@
                 "-m",
                 "pylint",
                 "cdl",
+                "sigima_",
                 "--disable=duplicate-code",
                 "--disable=fixme",
                 "--disable=too-many-arguments",

cdl/gui/actionhandler.py

@@ -815,9 +815,9 @@ def cra_fit(title, fitdlgfunc, iconname, tip: str | None = None):
                         "related to Error function (erf)"
                     ),
                 )
-            self.action_for("windowing")
+            self.action_for("apply_window")
             self.action_for("detrending")
-            self.action_for("interpolation")
+            self.action_for("interpolate")
             self.action_for("resampling")
             with self.new_menu(_("Stability analysis"), icon_name="stability.svg"):
                 self.action_for("allan_variance")

cdl/gui/docks.py

@@ -61,7 +61,7 @@
 
 from cdl.config import APP_NAME, Conf, _
 from sigima_.algorithms.image import get_centroid_fourier
-from sigima_.algorithms.signal import fwhm
+from sigima_.algorithms.signal.pulse import fwhm
 from sigima_.obj import create_signal
 
 if TYPE_CHECKING:

cdl/gui/processor/base.py

@@ -1361,7 +1361,9 @@ def edit_regions_of_interest(self, extract: bool = False) -> TypeROI | None:
                     for obj_i in objs:
                         obj_i.roi = None
                 else:
-                    edited_roi = edited_roi.from_params(obj, params)
+                    edited_roi = edited_roi.__class__.from_params(
+                        obj, params, singleobj=edited_roi.singleobj
+                    )
                     if not extract:
                         for obj_i in objs:
                             obj_i.roi = edited_roi

cdl/gui/processor/signal.py

@@ -290,7 +290,7 @@ def register_computations(self) -> None:
         )
         # Other processing
         self.register_1_to_1(
-            sigima_signal.windowing,
+            sigima_signal.apply_window,
             _("Windowing"),
             paramclass=sigima_.param.WindowingParam,
             icon_name="windowing.svg",
@@ -305,7 +305,7 @@ def register_computations(self) -> None:
             icon_name="detrending.svg",
         )
         self.register_2_to_1(
-            sigima_signal.interpolation,
+            sigima_signal.interpolate,
             _("Interpolation"),
             paramclass=sigima_.param.InterpolationParam,
             obj2_name=_("signal for X values"),

cdl/gui/roieditor.py

@@ -221,7 +221,16 @@ class BaseROIEditor(
     Generic[TypeObj, TypeROI, TypePlotItem, TypeROIItem],  # type: ignore
     metaclass=BaseROIEditorMeta,
 ):
-    """ROI Editor"""
+    """ROI Editor
+
+    Args:
+        parent: Parent plot dialog
+        obj: Object to edit (:class:`sigima_.obj.SignalObj` or
+         :class:`sigima_.obj.ImageObj`)
+        extract: If True, the dialog is in "extract mode" (extracting ROIs)
+        item: Optional plot item to add to the plot (if None, a new item is created
+         from the object)
+    """
 
     ICON_NAME = None
     OBJ_NAME = None
@@ -247,6 +256,8 @@ def __init__(
         roi = obj.roi
         if roi is None:
             roi = self.get_obj_roi_class()()
+        if roi.singleobj is None:
+            roi.singleobj = Conf.proc.extract_roi_singleobj.get()
         self.__roi: TypeROI = roi
 
         fmt = create_adapter_from_object(obj).get_obj_option("format")
@@ -448,7 +459,16 @@ def get_text(self) -> str:
 
 
 class SignalROIEditor(BaseROIEditor[SignalObj, SignalROI, CurveItem, XRangeSelection]):
-    """Signal ROI Editor"""
+    """Signal ROI Editor
+
+    Args:
+        parent: Parent plot dialog
+        obj: Object to edit (:class:`sigima_.obj.SignalObj` or
+         :class:`sigima_.obj.ImageObj`)
+        extract: If True, the dialog is in "extract mode" (extracting ROIs)
+        item: Optional plot item to add to the plot (if None, a new item is created
+         from the object)
+    """
 
     ICON_NAME = "signal_roi.svg"
     OBJ_NAME = _("signal")
@@ -508,7 +528,16 @@ class ImageROIEditor(
         Union[AnnotatedPolygon, AnnotatedRectangle, AnnotatedCircle],
     ]
 ):
-    """Image ROI Editor"""
+    """Image ROI Editor
+
+    Args:
+        parent: Parent plot dialog
+        obj: Object to edit (:class:`sigima_.obj.SignalObj` or
+         :class:`sigima_.obj.ImageObj`)
+        extract: If True, the dialog is in "extract mode" (extracting ROIs)
+        item: Optional plot item to add to the plot (if None, a new item is created
+         from the object)
+    """
 
     ICON_NAME = "image_roi.svg"
     OBJ_NAME = _("image")

cdl/tests/features/signals/deltax_dialog_unit_test.py

@@ -11,7 +11,7 @@
 
 from cdl.tests.data import create_paracetamol_signal
 from cdl.widgets.signaldeltax import SignalDeltaXDialog
-from sigima_.algorithms.signal import full_width_at_y
+from sigima_.algorithms.signal.pulse import full_width_at_y
 
 
 def test_signal_delta_x_dialog():

cdl/tests/features/signals/fft1d_unit_test.py

@@ -16,13 +16,13 @@
 from guidata.qthelpers import qt_app_context
 
 import cdl.tests.data as ctd
-import sigima_.algorithms.signal as alg
 import sigima_.computation.signal as sigima_signal
 import sigima_.obj
 import sigima_.param
 from cdl.env import execenv
 from cdl.utils.tests import check_array_result, check_scalar_result
 from cdl.utils.vistools import view_curves
+from sigima_.algorithms.signal import fourier
 
 
 def test_signal_fft_interactive() -> None:
@@ -43,8 +43,8 @@ def test_signal_fft_interactive() -> None:
         extra_param = sigima_.obj.PeriodicParam()
         s1 = sigima_.obj.create_signal_from_param(newparam, extra_param=extra_param)
         t, y = s1.xydata
-        f, s = alg.fft1d(t, y)
-        t2, y2 = alg.ifft1d(f, s)
+        f, s = fourier.fft1d(t, y)
+        t2, y2 = fourier.ifft1d(f, s)
         execenv.print("Comparing original and FFT/iFFT signals...", end=" ")
         execenv.print("OK")
         check_array_result("Signal FFT/iFFT X data", t2, t)

cdl/tests/features/signals/fitdialog_unit_test.py

@@ -14,7 +14,7 @@
 from cdl.tests.data import GaussianNoiseParam, create_noisy_signal, get_test_signal
 from cdl.utils.tests import get_default_test_name
 from cdl.widgets import fitdialog as fdlg
-from sigima_.algorithms.signal import peak_indices
+from sigima_.algorithms.signal.peakdetection import peak_indices
 
 
 def test_fit_dialog():

cdl/tests/features/signals/select_xy_cursor_unit_test.py

@@ -16,7 +16,7 @@
 from cdl.env import execenv
 from cdl.tests.data import create_paracetamol_signal
 from cdl.widgets.signalcursor import SignalCursorDialog
-from sigima_.algorithms.signal import find_first_x_at_y_value
+from sigima_.algorithms.signal.features import find_first_x_at_y_value
 
 
 @pytest.mark.parametrize("cursor_orientation", ["horizontal", "vertical"])