feat: allow editing pixel size in props dock widget

cellacdc/gui.py

@@ -2061,7 +2061,7 @@ def gui_createRegionPropsDockWidget(self, side=Qt.LeftDockWidgetArea):
         self.propsDockWidget.setAllowedAreas(
             Qt.LeftDockWidgetArea | Qt.RightDockWidgetArea
         )
-
+        
         self.addDockWidget(side, self.propsDockWidget)
         self.propsDockWidget.hide()
 
@@ -5714,8 +5714,11 @@ def updatePropsWidget(self, ID, fromHover=False):
 
         propsQGBox.cellAreaPxlSB.setValue(area_pxl)
 
-        PhysicalSizeY = posData.PhysicalSizeY
-        PhysicalSizeX = posData.PhysicalSizeX
+        pixelSizeQGBox = self.guiTabControl.pixelSizeQGBox
+        PhysicalSizeX = pixelSizeQGBox.pixelWidthWidget.value()
+        PhysicalSizeY = pixelSizeQGBox.pixelHeightWidget.value()
+        PhysicalSizeZ = pixelSizeQGBox.voxelDepthWidget.value()
+
         yx_pxl_to_um2 = PhysicalSizeY*PhysicalSizeX
 
         area_um2 = area_pxl*yx_pxl_to_um2
@@ -8182,6 +8185,10 @@ def ruler_cb(self, checked):
             self.ax1_rulerPlotItem.setData([], [])
             self.ax1_rulerAnchorsItem.setData([], [])
 
+    def updatePixelSize(self):
+        posData = self.data[self.pos_i]
+        ...
+
     def editImgProperties(self, checked=True):
         posData = self.data[self.pos_i]
         posData.askInputMetadata(
@@ -8192,6 +8199,7 @@ def editImgProperties(self, checked=True):
             save=True, singlePos=True,
             askSegm3D=False
         )
+        self.updatePixelSize()
 
     def setHoverToolSymbolData(self, xx, yy, ScatterItems, size=None):
         if not xx:
@@ -15405,6 +15413,7 @@ def loadingDataCompleted(self):
         self.updateImageValueFormatter()
         self.checkManageVersions()
         self.initManualBackgroundImage()
+        self.initPixelSizePropsDockWidget()
 
         self.setWindowTitle(f'Cell-ACDC - GUI - "{posData.exp_path}"')
 
@@ -16046,9 +16055,11 @@ def onZsliceSpinboxValueChange(self, value):
     def update_z_slice(self, z):
         posData = self.data[self.pos_i]
         idx = (posData.filename, posData.frame_i)
+        fn = posData.filename
+        i = posData.frame_i
         if self.switchPlaneCombobox.depthAxes() == 'z': 
             try:
-                posData.segmInfo_df.loc[idx:, 'z_slice_used_gui'] = z
+                posData.segmInfo_df.loc[fn].loc[i:, 'z_slice_used_gui'] = z
             except Exception as err:
                 printl(posData.segmInfo_df)
                 printl(idx)
@@ -22331,7 +22342,7 @@ def openNewWindow(self):
         )
         win.run()
         self.newWindows.append(win)
-        
+
     def helpNewFile(self):
         msg = widgets.myMessageBox(showCentered=False)
         href = f'<a href="{user_manual_url}">user manual</a>'
@@ -24758,9 +24769,31 @@ def onEscape(self):
         except Exception as e:
             pass
 
+    def askCloseAllWindows(self):
+        txt = html_utils.paragraph("""
+            There are other open windows that were created from this window.
+            <br><br>
+            If you proceed, the <b>other windows will be closed too.<br>
+        """)
+        msg = widgets.myMessageBox(wrapText=False)
+        msg.warning(
+            self, 'Open windows', txt, 
+            buttonsTexts=('Cancel', 'Ok, close now')
+        )
+        return msg.cancel
+
     def closeEvent(self, event):
         self.onEscape()
         self.saveWindowGeometry()
+
+        if self.newWindows:
+            cancel = self.askCloseAllWindows()
+            if cancel:
+                event.ignore()
+                return
+
+            for window in self.newWindows:
+                window.close()
 
         if self.slideshowWin is not None:
             self.slideshowWin.close()
@@ -24769,6 +24802,7 @@ def closeEvent(self, event):
 
         proceed = self.askSaveOnClosing(event)
         if not proceed:
+            event.ignore()
             return
 
         self.autoSaveClose()
@@ -24834,6 +24868,15 @@ def storeDefaultAndCustomColors(self):
         self.defaultToolBarButtonColor = c
         self.doublePressKeyButtonColor = '#fa693b'
 
+    def initPixelSizePropsDockWidget(self):
+        posData = self.data[self.pos_i]
+        PhysicalSizeX = posData.PhysicalSizeX
+        PhysicalSizeY = posData.PhysicalSizeY
+        PhysicalSizeZ = posData.PhysicalSizeZ
+        self.guiTabControl.initPixelSize(
+            PhysicalSizeX, PhysicalSizeY, PhysicalSizeZ
+        )
+
     def showPropsDockWidget(self, checked=False):
         if self.showPropsDockButton.isExpand:
             self.propsDockWidget.setVisible(False)

cellacdc/widgets.py

@@ -4109,6 +4109,61 @@ def checkFavouriteFuncs(self):
             groupbox.checkFavouriteFuncs()
         self.doNotWarn = False
 
+class PixelSizeGroupbox(QGroupBox):
+    sigValueChanged = Signal(float, float, float)
+    sigReset = Signal()
+
+    def __init__(self, parent=None):
+        super().__init__('Pixel size', parent)
+
+        mainLayout = QGridLayout()
+
+        row = 0
+        label = QLabel('Pixel width (μm): ')
+        self.pixelWidthWidget = FloatLineEdit(initial=1.0)
+        mainLayout.addWidget(label, row, 0)
+        mainLayout.addWidget(self.pixelWidthWidget, row, 1)
+
+        row += 1
+        label = QLabel('Pixel height (μm): ')
+        self.pixelHeightWidget = FloatLineEdit(initial=1.0)
+        mainLayout.addWidget(label, row, 0)
+        mainLayout.addWidget(self.pixelHeightWidget, row, 1)
+
+        row += 1
+        label = QLabel('Voxel depth (μm): ')
+        self.voxelDepthWidget = FloatLineEdit(initial=1.0)
+        mainLayout.addWidget(label, row, 0)
+        mainLayout.addWidget(self.voxelDepthWidget, row, 1)
+
+        row += 1
+        resetButton = reloadPushButton('Reset')
+        mainLayout.addWidget(
+            resetButton, row, 1, alignment=Qt.AlignRight
+        )
+
+        row += 1
+        mainLayout.addWidget(QHLine(), row, 0, 1, 2)
+
+        mainLayout.setColumnStretch(0, 0)
+        mainLayout.setColumnStretch(1, 1)
+
+        self.setLayout(mainLayout)
+
+        self.pixelWidthWidget.valueChanged.connect(self.emitValueChanged)
+        self.pixelHeightWidget.valueChanged.connect(self.emitValueChanged)
+        self.voxelDepthWidget.valueChanged.connect(self.emitValueChanged)
+        resetButton.clicked.connect(self.emitReset)
+
+    def emitReset(self):
+        self.sigReset.emit()
+
+    def emitValueChanged(self, value):
+        PhysicalSizeX = self.pixelWidthWidget.value()
+        PhysicalSizeY = self.pixelHeightWidget.value()
+        PhysicalSizeZ = self.voxelDepthWidget.value()
+        self.sigValueChanged.emit(PhysicalSizeX, PhysicalSizeY, PhysicalSizeZ)
+
 class objPropsQGBox(QGroupBox):
     def __init__(self, parent=None):
         QGroupBox.__init__(self, 'Properties', parent)
@@ -4285,11 +4340,14 @@ class guiTabControl(QTabWidget):
     def __init__(self, *args):
         super().__init__(args[0])
 
+        self._defaultPixelSize = None
+
         self.propsTab = QScrollArea(self)
 
         container = QWidget()
         layout = QVBoxLayout()
 
+        self.pixelSizeQGBox = PixelSizeGroupbox(parent=self.propsTab)
         self.propsQGBox = objPropsQGBox(parent=self.propsTab)
         self.intensMeasurQGBox = objIntesityMeasurQGBox(parent=self.propsTab)
 
@@ -4307,6 +4365,7 @@ def __init__(self, *args):
         highlightLayout.addWidget(self.highlightSearchedCheckbox)
 
         layout.addLayout(highlightLayout)
+        layout.addWidget(self.pixelSizeQGBox)
         layout.addWidget(self.propsQGBox)
         layout.addWidget(self.intensMeasurQGBox)  
         layout.addStretch(1)     
@@ -4315,9 +4374,43 @@ def __init__(self, *args):
         self.propsTab.setWidgetResizable(True)
         self.propsTab.setWidget(container)
         self.addTab(self.propsTab, 'Measurements')
-
+
+        self.pixelSizeQGBox.sigValueChanged.connect(self.pixelSizeChanged)
+        self.pixelSizeQGBox.sigReset.connect(self.resetPixelSize)
+
     def addChannels(self, channels):
         self.intensMeasurQGBox.addChannels(channels)
+
+    def resetPixelSize(self):
+        if self._defaultPixelSize is None:
+            return
+
+        self.initPixelSize(*self._defaultPixelSize)
+
+    def initPixelSize(self, PhysicalSizeX, PhysicalSizeY, PhysicalSizeZ):
+        self.pixelSizeQGBox.pixelWidthWidget.setValue(PhysicalSizeX)
+        self.pixelSizeQGBox.pixelHeightWidget.setValue(PhysicalSizeY)
+        self.pixelSizeQGBox.voxelDepthWidget.setValue(PhysicalSizeZ)
+        self._defaultPixelSize = (PhysicalSizeX, PhysicalSizeY, PhysicalSizeZ)
+
+    def pixelSizeChanged(self, PhysicalSizeX, PhysicalSizeY, PhysicalSizeZ):
+        propsQGBox = self.propsQGBox
+        yx_pxl_to_um2 = PhysicalSizeY*PhysicalSizeX
+        vox_rot_to_fl = float(PhysicalSizeY)*pow(float(PhysicalSizeX), 2)
+        vox_3D_to_fl = PhysicalSizeZ*PhysicalSizeY*PhysicalSizeX
+
+        area_pxl = propsQGBox.cellAreaPxlSB.value()
+        area_um2 = area_pxl*yx_pxl_to_um2
+        propsQGBox.cellAreaUm2DSB.setValue(area_um2)
+
+        vol_rot_vox = propsQGBox.cellVolVoxSB.value()
+        vol_rot_fl = vol_rot_vox*vox_rot_to_fl
+        propsQGBox.cellVolFlDSB.setValue(vol_rot_fl)
+
+        vol_3D_vox = propsQGBox.cellVolVox3D_SB.value()
+        vol_3D_fl = vol_3D_vox*vox_3D_to_fl
+        propsQGBox.cellVolFl3D_DSB.setValue(vol_3D_fl)
+
 
 class expandCollapseButton(PushButton):
     sigClicked = Signal()