Fix: add option to keep analysis results after computation

Author: PierreRaybaut

cdl/computation/base.py

@@ -17,7 +17,7 @@
 import guidata.dataset as gds
 import numpy as np
 
-from cdl.config import _
+from cdl.config import Conf, _
 from cdl.obj import ResultProperties, create_signal
 
 if TYPE_CHECKING:
@@ -200,7 +200,8 @@ def dst_11(
     if suffix:  # suffix may be None or an empty string
         title += suffix
     dst = src.copy(title=title)
-    dst.delete_results()  # Remove any previous results
+    if not Conf.proc.keep_results.get():
+        dst.delete_results()  # Remove any previous results
     return dst
 
 
@@ -228,7 +229,8 @@ def dst_n1n(
     if suffix is not None:
         title += "|" + suffix
     dst = src1.copy(title=title)
-    dst.delete_results()  # Remove any previous results
+    if not Conf.proc.keep_results.get():
+        dst.delete_results()  # Remove any previous results
     return dst
 
 

cdl/computation/image/__init__.py

@@ -45,7 +45,7 @@
     dst_n1n,
     new_signal_result,
 )
-from cdl.config import _
+from cdl.config import Conf, _
 from cdl.obj import (
     BaseProcParam,
     ImageObj,
@@ -60,21 +60,26 @@
 
 
 def restore_data_outside_roi(dst: ImageObj, src: ImageObj) -> None:
-    """Restore data outside the Region Of Interest (ROI) of the input image after a
-    computation, only if the input image has a ROI, if the data types are compatible,
+    """Restore data outside the Region Of Interest (ROI) of the input image
+    after a computation, only if the input image has a ROI,
+    and if the output image has the same ROI as the input image,
+    and if the data types are compatible,
     and if the shapes are the same.
     Otherwise, do nothing.
 
     Args:
         dst: output image object
         src: input image object
     """
-    if (
-        src.maskdata is not None
-        and (dst.data.dtype == src.data.dtype or not is_integer_dtype(dst.data.dtype))
-        and dst.data.shape == src.data.shape
-    ):
-        dst.data[src.maskdata] = src.data[src.maskdata]
+    if src.maskdata is not None and dst.maskdata is not None:
+        if (
+            np.array_equal(src.maskdata, dst.maskdata)
+            and (
+                dst.data.dtype == src.data.dtype or not is_integer_dtype(dst.data.dtype)
+            )
+            and dst.data.shape == src.data.shape
+        ):
+            dst.data[src.maskdata] = src.data[src.maskdata]
 
 
 class Wrap11Func:
@@ -289,7 +294,8 @@ def compute_arithmetic(src1: ImageObj, src2: ImageObj, p: ArithmeticParam) -> Im
     initial_dtype = src1.data.dtype
     title = p.operation.replace("obj1", src1.short_id).replace("obj2", src2.short_id)
     dst = src1.copy(title=title)
-    dst.delete_results()  # Remove any previous results
+    if not Conf.proc.keep_results.get():
+        dst.delete_results()  # Remove any previous results
     o, a, b = p.operator, p.factor, p.constant
     # Apply operator
     if o in ("×", "/") and a == 0.0:

cdl/computation/signal.py

@@ -39,27 +39,31 @@
     dst_n1n,
     new_signal_result,
 )
-from cdl.config import _
+from cdl.config import Conf, _
 from cdl.obj import ResultProperties, ResultShape, ROI1DParam, SignalObj
 
 VALID_DTYPES_STRLIST = SignalObj.get_valid_dtypenames()
 
 
 def restore_data_outside_roi(dst: SignalObj, src: SignalObj) -> None:
-    """Restore data outside the region of interest, after a computation, only if the
-    source signal has a ROI, if the data types are the same and if the shapes are the
-    same. Otherwise, do nothing.
+    """Restore data outside the Region Of Interest (ROI) of the input signal
+    after a computation, only if the input signal has a ROI,
+    and if the output signal has the same ROI as the input signal,
+    and if the data types are the same,
+    and if the shapes are the same.
+    Otherwise, do nothing.
 
     Args:
         dst: destination signal object
         src: source signal object
     """
-    if (
-        src.maskdata is not None
-        and dst.xydata.dtype == src.xydata.dtype
-        and dst.xydata.shape == src.xydata.shape
-    ):
-        dst.xydata[src.maskdata] = src.xydata[src.maskdata]
+    if src.maskdata is not None and dst.maskdata is not None:
+        if (
+            np.array_equal(src.maskdata, dst.maskdata)
+            and dst.xydata.dtype == src.xydata.dtype
+            and dst.xydata.shape == src.xydata.shape
+        ):
+            dst.xydata[src.maskdata] = src.xydata[src.maskdata]
 
 
 class Wrap11Func:
@@ -251,7 +255,8 @@ def compute_arithmetic(
     initial_dtype = src1.xydata.dtype
     title = p.operation.replace("obj1", src1.short_id).replace("obj2", src2.short_id)
     dst = src1.copy(title=title)
-    dst.delete_results()  # Remove any previous results
+    if not Conf.proc.keep_results.get():
+        dst.delete_results()  # Remove any previous results
     o, a, b = p.operator, p.factor, p.constant
     if o in ("×", "/") and a == 0.0:
         dst.y = np.ones_like(src1.y) * b

cdl/config.py

@@ -161,6 +161,11 @@ class ProcSection(conf.Section, metaclass=conf.SectionMeta):
     # - False: extract each ROI in a separate signal or image
     extract_roi_singleobj = conf.Option()
 
+    # Keep analysis results after processing:
+    # - True: keep analysis results (dangerous because results may not be valid anymore)
+    # - False: do not keep analysis results (default)
+    keep_results = conf.Option()
+
     # FFT shift enabled state for signal/image processing:
     # - True: FFT shift is enabled (default)
     # - False: FFT shift is disabled
@@ -309,6 +314,7 @@ def initialize():
     Conf.proc.operation_mode.get("single")
     Conf.proc.fft_shift_enabled.get(True)
     Conf.proc.extract_roi_singleobj.get(False)
+    Conf.proc.keep_results.get(False)
     Conf.proc.ignore_warnings.get(False)
     # View section
     tb_pos = Conf.view.plot_toolbar_position.get("left")

cdl/core/gui/panel/base.py

@@ -34,6 +34,8 @@
 from cdl.core.gui import actionhandler, objectmodel, objectview
 from cdl.core.gui.roieditor import TypeROIEditor
 from cdl.core.model.base import (
+    ANN_KEY,
+    ROI_KEY,
     ResultProperties,
     ResultShape,
     TypeObj,
@@ -247,6 +249,18 @@ def create_resultdata_dict(objs: list[SignalObj | ImageObj]) -> dict[str, Result
     return rdatadict
 
 
+class PasteMetadataParam(gds.DataSet):
+    """Paste metadata parameters"""
+
+    keep_roi = gds.BoolItem(_("Regions of interest"), default=True)
+    keep_resultshapes = gds.BoolItem(_("Result shapes"), default=False).set_pos(col=1)
+    keep_annotations = gds.BoolItem(_("Annotations"), default=True)
+    keep_resultproperties = gds.BoolItem(_("Result properties"), default=False).set_pos(
+        col=1
+    )
+    keep_other = gds.BoolItem(_("Other metadata"), default=True)
+
+
 class BaseDataPanel(AbstractPanel, Generic[TypeObj, TypeROI, TypeROIEditor]):
     """Object handling the item list, the selected item properties and plot"""
 
@@ -535,15 +549,60 @@ def duplicate_object(self) -> None:
 
     def copy_metadata(self) -> None:
         """Copy object metadata"""
-        obj_cpy = self.objview.get_sel_objects()[0].copy()
-        obj_cpy.delete_results()  # Remove all object-specific analysis results
-        self.__metadata_clipboard = obj_cpy.metadata
-
-    def paste_metadata(self) -> None:
+        obj = self.objview.get_sel_objects()[0]
+        self.__metadata_clipboard = obj.metadata.copy()
+        new_pref = obj.short_id + "_"
+        for key, value in obj.metadata.items():
+            if ResultShape.match(key, value):
+                mshape = ResultShape.from_metadata_entry(key, value)
+                if not re.match(obj.PREFIX + r"[0-9]{3}[\s]*", mshape.title):
+                    # Handling additional result (e.g. diameter)
+                    for a_key, a_value in obj.metadata.items():
+                        if isinstance(a_key, str) and a_key.startswith(mshape.title):
+                            self.__metadata_clipboard.pop(a_key)
+                            self.__metadata_clipboard[new_pref + a_key] = a_value
+                    mshape.title = new_pref + mshape.title
+                    # Handling result shape
+                    self.__metadata_clipboard.pop(key)
+                    self.__metadata_clipboard[mshape.key] = value
+
+    def paste_metadata(self, param: PasteMetadataParam | None = None) -> None:
         """Paste metadata to selected object(s)"""
+        if param is None:
+            param = PasteMetadataParam(
+                _("Paste metadata"),
+                comment=_(
+                    "Select what to keep from the clipboard.<br><br>"
+                    "Result shapes and annotations, if kept, will be merged with "
+                    "existing ones. <u>All other metadata will be replaced</u>."
+                ),
+            )
+            if not param.edit(parent=self.parent()):
+                return
+        metadata = {}
+        if param.keep_roi and ROI_KEY in self.__metadata_clipboard:
+            metadata[ROI_KEY] = self.__metadata_clipboard[ROI_KEY]
+        if param.keep_annotations and ANN_KEY in self.__metadata_clipboard:
+            metadata[ANN_KEY] = self.__metadata_clipboard[ANN_KEY]
+        if param.keep_resultshapes:
+            for key, value in self.__metadata_clipboard.items():
+                if ResultShape.match(key, value):
+                    metadata[key] = value
+        if param.keep_resultproperties:
+            for key, value in self.__metadata_clipboard.items():
+                if ResultProperties.match(key, value):
+                    metadata[key] = value
+        if param.keep_other:
+            for key, value in self.__metadata_clipboard.items():
+                if (
+                    not ResultShape.match(key, value)
+                    and not ResultProperties.match(key, value)
+                    and key not in (ROI_KEY, ANN_KEY)
+                ):
+                    metadata[key] = value
         sel_objects = self.objview.get_sel_objects(include_groups=True)
         for obj in sorted(sel_objects, key=lambda obj: obj.short_id, reverse=True):
-            obj.metadata.update(self.__metadata_clipboard)
+            obj.update_metadata_from(metadata)
         # We have to do a manual refresh in order to force the plot handler to update
         # all plot items, even the ones that are not visible (otherwise, image masks
         # would not be updated after pasting the metadata: see issue #123)
@@ -1324,8 +1383,8 @@ class PlotResultParam(gds.DataSet):
                                     x.append(index)
                                 else:
                                     i_xaxis = rdata.xlabels.index(param.xaxis)
-                                    x.append(float(result.shown_array[mask, i_xaxis]))
-                                y.append(float(result.shown_array[mask, i_yaxis]))
+                                    x.append(result.shown_array[mask, i_xaxis][0])
+                                y.append(result.shown_array[mask, i_yaxis][0])
                             self.__add_result_signal(
                                 x, y, f"{title}{roi_suffix}", param.xaxis, param.yaxis
                             )

cdl/core/gui/processor/base.py

@@ -624,7 +624,8 @@ def compute_n1(
                     src_dtype = src_obj1.data.dtype
                     dst_dtype = complex if is_complex_dtype(src_dtype) else float
                     dst_obj = src_obj1.copy(dtype=dst_dtype)
-                    dst_obj.delete_results()  # Remove any previous results
+                    if not Conf.proc.keep_results.get():
+                        dst_obj.delete_results()  # Remove any previous results
                     src_objs_pair = [src_obj1]
                     for src_gid in src_gids[1:]:
                         src_obj = src_objs[src_gid][i_pair]
@@ -641,12 +642,15 @@ def compute_n1(
                         )
                         if dst_obj is None:
                             break
-                        dst_obj.update_resultshapes_from(src_obj)
+                        if Conf.proc.keep_results.get():
+                            dst_obj.update_resultshapes_from(src_obj)
                         if src_obj.roi is not None:
                             if dst_obj.roi is None:
                                 dst_obj.roi = src_obj.roi.copy()
                             else:
-                                dst_obj.roi.add_roi(src_obj.roi)
+                                roi = dst_obj.roi
+                                roi.add_roi(src_obj.roi)
+                                dst_obj.roi = roi
                     if func_objs is not None:
                         func_objs(dst_obj, src_objs_pair)
                     short_ids = [obj.short_id for obj in src_objs_pair]
@@ -673,7 +677,8 @@ def compute_n1(
                         src_dtypes[src_gid] = src_dtype = src_obj.data.dtype
                         dst_dtype = complex if is_complex_dtype(src_dtype) else float
                         dst_objs[src_gid] = dst_obj = src_obj.copy(dtype=dst_dtype)
-                        dst_obj.delete_results()  # Remove any previous results
+                        if not Conf.proc.keep_results.get():
+                            dst_obj.delete_results()  # Remove any previous results
                         dst_obj.roi = None
                         src_objs[src_gid] = [src_obj]
                     else:
@@ -691,12 +696,15 @@ def compute_n1(
                         if dst_obj is None:
                             break
                         dst_objs[src_gid] = dst_obj
-                        dst_obj.update_resultshapes_from(src_obj)
+                        if Conf.proc.keep_results.get():
+                            dst_obj.update_resultshapes_from(src_obj)
                     if src_obj.roi is not None:
                         if dst_obj.roi is None:
                             dst_obj.roi = src_obj.roi.copy()
                         else:
-                            dst_obj.roi.add_roi(src_obj.roi)
+                            roi = dst_obj.roi
+                            roi.add_roi(src_obj.roi)
+                            dst_obj.roi = roi
 
             grps = self.panel.objview.get_sel_groups()
             if grps:

cdl/core/gui/settings.py

@@ -110,6 +110,7 @@ class ProcSettings(gds.DataSet):
     )
     fft_shift_enabled = gds.BoolItem("", _("FFT shift"))
     extract_roi_singleobj = gds.BoolItem("", _("Extract ROI in single object"))
+    keep_results = gds.BoolItem("", _("Keep results after computation"))
     ignore_warnings = gds.BoolItem("", _("Ignore warnings"))
     _g0 = gds.EndGroup("")