feat: allow drawing and clearing objects in a freehand region

Author: ElpadoCan

cellacdc/docs/source/tooltips.rst

@@ -237,6 +237,12 @@
     :height: 16px
     :width: 16px
 
+.. |drawClearRegionAction| image:: https://raw.githubusercontent.com/SchmollerLab/Cell_ACDC/3dcf5611281c35e3cf8b7676ca7c00c9b17ee8e7/cellacdc/resources/icons/clear_freehand_region.svg
+    :target: https://github.com/SchmollerLab/Cell_ACDC/blob/main/cellacdc/resources/icons/clear_freehand_region.svg
+    :alt: drawClearRegionAction icon
+    :height: 16px
+    :width: 16px
+
 .. |addDelPolyLineRoiAction| image:: https://raw.githubusercontent.com/SchmollerLab/Cell_ACDC/3dcf5611281c35e3cf8b7676ca7c00c9b17ee8e7/cellacdc/resources/icons/addDelPolyLineRoi.svg
     :target: https://github.com/SchmollerLab/Cell_ACDC/blob/main/cellacdc/resources/icons/addDelPolyLineRoi.svg
     :alt: addDelPolyLineRoiAction icon
@@ -431,6 +437,7 @@ Edit tools: Segmentation and tracking
     * Add custom poly-line deletion ROI. Every ID touched by the ROI will be automatically deleted.
     * Moving and reshaping the ROI will restore deleted IDs if they are not touched by it anymore. 
     * To delete the ROI ``right-click on it --> remove``.
+* **Clear freehand region (** |drawClearRegionAction| **):** Draw a freehand region and clear all objects present in the region. Once activated, additional options will appear in a new toolbar.
 * **Delete bordering objects (** |delBorderObjAction| **):** Remove segmented objects touching the border of the image.
 * **Repeat tracking (** |repeatTrackingAction| **"Shift+T"):** Repeat tracking on current frame. Tracking method can be changed in ``Tracking --> Select real-time tracking algorithm``
 * **Manual tracking (** |manualTrackingButton| **"T"):** Select ID to track and right-click on an object to assign that ID.

cellacdc/gui.py

@@ -2067,6 +2067,10 @@ def gui_createToolBars(self):
         )
         self.addDelPolyLineRoiAction.roiType = 'polyline'
 
+        self.drawClearRegionAction = editToolBar.addWidget(
+            self.drawClearRegionButton
+        )
+        
         editToolBar.addAction(self.delBorderObjAction)
 
         self.addDelRoiAction.toolbar = editToolBar
@@ -2896,6 +2900,15 @@ def gui_createControlsToolbar(self):
         self.copyLostObjToolbar.setVisible(False)
         self.controlToolBars.append(self.copyLostObjToolbar)
 
+        # Copy lost object contour toolbar
+        self.drawClearRegionToolbar = widgets.DrawClearRegionToolbar(
+            "Draw freehand region and clear objects controls", self
+        )
+        
+        self.addToolBar(Qt.TopToolBarArea, self.drawClearRegionToolbar)
+        self.drawClearRegionToolbar.setVisible(False)
+        self.controlToolBars.append(self.drawClearRegionToolbar)
+        
         # Empty toolbar to avoid weird ranges on image when showing the 
         # other toolbars --> placeholder
         placeHolderToolbar = widgets.ToolBar("Place holder", self)
@@ -3396,15 +3409,20 @@ def gui_createActions(self):
         self.addDelRoiAction.roiType = 'rect'
         self.addDelRoiAction.setIcon(QIcon(":addDelRoi.svg"))
 
-        
         self.addDelPolyLineRoiButton = QToolButton(self)
         self.addDelPolyLineRoiButton.setCheckable(True)
         self.addDelPolyLineRoiButton.setIcon(QIcon(":addDelPolyLineRoi.svg"))
 
         self.checkableButtons.append(self.addDelPolyLineRoiButton)
         self.LeftClickButtons.append(self.addDelPolyLineRoiButton)
+        
+        self.drawClearRegionButton = QToolButton(self)
+        self.drawClearRegionButton.setCheckable(True)
+        self.drawClearRegionButton.setIcon(QIcon(":clear_freehand_region.svg"))
+        
+        self.checkableButtons.append(self.drawClearRegionButton)
+        self.LeftClickButtons.append(self.drawClearRegionButton)
 
-
         self.delBorderObjAction = QAction(self)
         self.delBorderObjAction.setIcon(QIcon(":delBorderObj.svg"))
 
@@ -3743,6 +3761,7 @@ def gui_connectEditActions(self):
         self.curvToolButton.toggled.connect(self.curvTool_cb)
         self.wandToolButton.toggled.connect(self.wand_cb)
         self.labelRoiButton.toggled.connect(self.labelRoi_cb)
+        self.drawClearRegionButton.toggled.connect(self.drawClearRegion_cb)
         self.reInitCcaAction.triggered.connect(self.reInitCca)
         self.moveLabelToolButton.toggled.connect(self.moveLabelButtonToggled)
         self.editCcaToolAction.triggered.connect(
@@ -6040,7 +6059,7 @@ def gui_mouseDragEventImg1(self, event):
         mode = str(self.modeComboBox.currentText())
         if mode == 'Viewer':
             return
-
+        
         posData = self.data[self.pos_i]
         Y, X = self.get_2Dlab(posData.lab).shape
         xdata, ydata = int(x), int(y)
@@ -6189,6 +6208,10 @@ def gui_mouseDragEventImg1(self, event):
                 self.labelRoiItem.setSize((w, h))
             elif self.labelRoiIsFreeHandRadioButton.isChecked():
                 self.freeRoiItem.addPoint(xdata, ydata)
+        
+        # Draw freehand clear region --> draw region
+        elif self.isMouseDragImg1 and self.drawClearRegionButton.isChecked():
+            self.freeRoiItem.addPoint(xdata, ydata)
 
     # @exec_time
     def fillHolesID(self, ID, sender='brush'):
@@ -7454,6 +7477,10 @@ def gui_mouseReleaseEventImg1(self, event):
 
             self.clickedOnBud = False
             self.BudMothTempLine.setData([], [])
+        
+        elif self.isMouseDragImg1 and self.drawClearRegionButton.isChecked():
+            self.freeRoiItem.closeCurve()
+            self.clearObjsFreehandRegion()
 
     def gui_clickedDelRoi(self, event, left_click, right_click):
         posData = self.data[self.pos_i]
@@ -7587,7 +7614,7 @@ def gui_mousePressEventImg1(self, event):
         )
         findNextMotherButtonON = self.findNextMotherButton.isChecked()
         unknownLineageButtonON = self.unknownLineageButton.isChecked()
-
+        drawClearRegionON = self.drawClearRegionButton.isChecked()
 
         # Check if right-click on segment of polyline roi to add segment
         segments = self.gui_getHoveredSegmentsPolyLineRoi()
@@ -7613,7 +7640,7 @@ def gui_mousePressEventImg1(self, event):
             and not curvToolON and not eraserON and not rulerON
             and not wandON and not polyLineRoiON and not labelRoiON
             and not middle_click and not keepObjON and not separateON
-            and not manualBackgroundON
+            and not manualBackgroundON and not drawClearRegionON
             and addPointsByClickingButton is None
         )
         if isPanImageClick:
@@ -7680,69 +7707,77 @@ def gui_mousePressEventImg1(self, event):
             and not brushON and not dragImgLeft and not eraserON
             and not polyLineRoiON and not labelRoiON
             and addPointsByClickingButton is None
-            and not manualBackgroundON
+            and not manualBackgroundON and not canDrawClearRegion
         )
         canBrush = (
             brushON and not curvToolON and not rulerON
             and not dragImgLeft and not eraserON and not wandON
             and not labelRoiON and not manualBackgroundON
-            and addPointsByClickingButton is None
+            and addPointsByClickingButton is None and not canDrawClearRegion
         )
         canErase = (
             eraserON and not curvToolON and not rulerON
             and not dragImgLeft and not brushON and not wandON
             and not polyLineRoiON and not labelRoiON
             and addPointsByClickingButton is None
-            and not manualBackgroundON
+            and not manualBackgroundON and not canDrawClearRegion
         )
         canRuler = (
             rulerON and not curvToolON and not brushON
             and not dragImgLeft and not brushON and not wandON
             and not polyLineRoiON and not labelRoiON
             and addPointsByClickingButton is None
-            and not manualBackgroundON
+            and not manualBackgroundON and not canDrawClearRegion
         )
         canWand = (
             wandON and not curvToolON and not brushON
             and not dragImgLeft and not brushON and not rulerON
             and not polyLineRoiON and not labelRoiON
             and addPointsByClickingButton is None
-            and not manualBackgroundON
+            and not manualBackgroundON and not canDrawClearRegion
         )
         canPolyLine = (
             polyLineRoiON and not wandON and not curvToolON and not brushON
             and not dragImgLeft and not brushON and not rulerON
             and not labelRoiON and not manualBackgroundON
             and addPointsByClickingButton is None
+            and not canDrawClearRegion
         )
         canLabelRoi = (
             labelRoiON and not wandON and not curvToolON and not brushON
             and not dragImgLeft and not brushON and not rulerON
             and not polyLineRoiON and not keepObjON
             and addPointsByClickingButton is None
-            and not manualBackgroundON
+            and not manualBackgroundON and not canDrawClearRegion
         )
         canKeep = (
             keepObjON and not wandON and not curvToolON and not brushON
             and not dragImgLeft and not brushON and not rulerON
             and not polyLineRoiON and not labelRoiON 
             and addPointsByClickingButton is None
-            and not manualBackgroundON
+            and not manualBackgroundON and not canDrawClearRegion
         )
         canAddPoint = (
             self.togglePointsLayerAction.isChecked()
             and addPointsByClickingButton is not None and not wandON 
             and not curvToolON and not brushON
             and not dragImgLeft and not brushON and not rulerON
             and not polyLineRoiON and not labelRoiON  and not keepObjON
-            and not manualBackgroundON
+            and not manualBackgroundON and not canDrawClearRegion
         )
         canAddManualBackgroundObj = (
             manualBackgroundON and not wandON and not curvToolON and not brushON
             and not dragImgLeft and not brushON and not rulerON
             and not polyLineRoiON and not labelRoiON 
             and addPointsByClickingButton is None
-            and not keepObjON
+            and not keepObjON and not canDrawClearRegion
+        )
+        canDrawClearRegion = (
+            drawClearRegionON and not wandON and not curvToolON and not brushON
+            and not dragImgLeft and not brushON and not rulerON
+            and not labelRoiON and not manualBackgroundON
+            and addPointsByClickingButton is None
+            and not polyLineRoiON 
         )
 
         # Enable dragging of the image window or the scalebar
@@ -7913,6 +7948,13 @@ def gui_mousePressEventImg1(self, event):
                 self.addClickedPoint(action, x, y, id)
             self.drawPointsLayers(computePointsLayers=False)
 
+        elif left_click and canDrawClearRegion:
+            x, y = event.pos().x(), event.pos().y()
+            xdata, ydata = int(x), int(y)
+            self.freeRoiItem.addPoint(xdata, ydata)
+            
+            self.isMouseDragImg1 = True
+        
         elif left_click and canRuler or canPolyLine:
             x, y = event.pos().x(), event.pos().y()
             xdata, ydata = int(x), int(y)
@@ -12638,6 +12680,7 @@ def connectLeftClickButtons(self):
         self.eraserButton.toggled.connect(self.Eraser_cb)
         self.wandToolButton.toggled.connect(self.wand_cb)
         self.labelRoiButton.toggled.connect(self.labelRoi_cb)
+        self.drawClearRegionButton.toggled.connect(self.drawClearRegion_cb)
         self.expandLabelToolButton.toggled.connect(self.expandLabelCallback)
         self.addDelPolyLineRoiButton.toggled.connect(self.addDelPolyLineRoi_cb)
         self.manualBackgroundButton.toggled.connect(self.manualBackground_cb)
@@ -12872,6 +12915,26 @@ def labelRoiTrangeCheckboxToggled(self, checked):
         self.labelRoiStartFrameNoSpinbox.setValue(posData.frame_i+1)
         self.labelRoiStopFrameNoSpinbox.setValue(posData.SizeT)
 
+    def drawClearRegion_cb(self, checked):
+        posData = self.data[self.pos_i]
+        if checked:
+            self.disconnectLeftClickButtons()
+            self.uncheckLeftClickButtons(self.drawClearRegionButton)
+            self.connectLeftClickButtons()
+
+        self.drawClearRegionToolbar.setVisible(checked)
+        
+        if not self.isSegm3D:
+            self.drawClearRegionToolbar.setZslicesControlEnabled(False)
+            return
+        
+        if not checked:
+            return
+        
+        self.drawClearRegionToolbar.setZslicesControlEnabled(
+            True, SizeZ=posData.SizeZ
+        )
+    
     def labelRoi_cb(self, checked):
         posData = self.data[self.pos_i]
         if checked:
@@ -12936,6 +12999,54 @@ def labelRoi_cb(self, checked):
             self.ax1.removeItem(self.labelRoiItem)
             self.updateLabelRoiCircularCursor(None, None, False)
 
+    def clearObjsFreehandRegion(self):
+        self.logger.info('Clearing objects inside freehand region...')
+        
+        # Store undo state before modifying stuff
+        self.storeUndoRedoStates(False, storeImage=False, storeOnlyZoom=True)
+        
+        posData = self.data[self.pos_i]
+        zRange = None
+        if self.isSegm3D:
+            z_slice = self.z_lab()
+            zRange = self.drawClearRegionToolbar.zRange(z_slice, posData.SizeZ)
+            
+        regionSlice = self.freeRoiItem.slice(zRange=zRange)
+        mask = self.freeRoiItem.mask()
+        
+        regionLab = posData.lab[..., *regionSlice].copy()
+        regionLab[..., ~mask] = 0
+        
+        clearBorders = (
+            self.drawClearRegionToolbar
+            .clearOnlyEnclosedObjsRadioButton
+            .isChecked()
+        )
+        if clearBorders:
+            regionLab = skimage.segmentation.clear_border(regionLab)
+        
+        regionRp = skimage.measure.regionprops(regionLab)
+        clearIDs = [obj.label for obj in regionRp]
+        
+        if not clearIDs:
+            if clearBorders:
+                self.logger.warning(
+                    'None of the objects in the freehand region are '
+                    'fully enclosed'
+                )
+            else:
+                self.logger.warning(
+                    'None of the objects are touching the freehand region'
+                )
+            return
+        
+        self.deleteIDmiddleClick(clearIDs, False, False)
+        self.update_cca_df_deletedIDs(posData, clearIDs)
+        
+        self.freeRoiItem.clear()
+        
+        self.updateAllImages()
+    
     def labelRoiWorkerFinished(self):
         self.logger.info('Magic labeller closed.')
         worker = self.labelRoiActiveWorkers.pop(-1)