feat: crop frames in dataprep

cellacdc/acdc_bioio_bioformats/reader.py

@@ -1,5 +1,6 @@
 import os
 
+from .. import printl
 from . import install, EXTENSION_PACKAGE_MAPPER
 
 def set_reader(image_filepath, **kwargs):

cellacdc/apps.py

@@ -5629,8 +5629,8 @@ def __init__(
         self.lowerZscrollbar.label = QLabel(f'{s}/{SizeZ}')
 
         self.upperZscrollbar = QScrollBar(Qt.Horizontal)
-        self.upperZscrollbar.setValue(SizeZ-1)
         self.upperZscrollbar.setMaximum(SizeZ-1)
+        self.upperZscrollbar.setValue(SizeZ-1)
         self.upperZscrollbar.label = QLabel(f'{SizeZ}/{SizeZ}')
 
         cancelButton = widgets.cancelPushButton('Cancel')
@@ -16429,3 +16429,114 @@ def steps(self, return_keepInputDataType=False):
 
         keep_input_dtype = self.keepInputDataTypeToggle.isChecked()
         return steps, keep_input_dtype # why does this not work???s 
+
+class QCropTrangeTool(QBaseDialog):
+    sigClose = Signal()
+    sigTvalueChanged = Signal(int)
+    sigReset = Signal()
+    sigCrop = Signal(int, int)
+
+    def __init__(
+            self, SizeT, 
+            cropButtonText='Apply crop', 
+            parent=None, 
+            addDoNotShowAgain=False, 
+            title='Select frames range'
+        ):
+        super().__init__(parent)
+
+        self.cancel = True
+
+        self.setWindowFlags(Qt.Tool | Qt.WindowStaysOnTopHint)
+
+        self.SizeT = SizeT
+        self.numDigits = len(str(self.SizeT))
+
+        self.setWindowTitle(title)
+
+        layout = QGridLayout()
+        buttonsLayout = QHBoxLayout()
+
+        self.startFrameScrollbar = QScrollBar(Qt.Horizontal)
+        self.startFrameScrollbar.setMaximum(SizeT-1)
+        t = str(1).zfill(self.numDigits)
+        self.startFrameScrollbar.label = QLabel(f'{t}/{SizeT}')
+
+        self.endFrameScrollbar = QScrollBar(Qt.Horizontal)
+        self.endFrameScrollbar.setMaximum(SizeT-1)
+        self.endFrameScrollbar.setValue(SizeT-1)
+        self.endFrameScrollbar.label = QLabel(f'{SizeT}/{SizeT}')
+
+        cancelButton = widgets.cancelPushButton('Cancel')
+        cropButton = widgets.okPushButton(cropButtonText)
+        buttonsLayout.addWidget(cropButton)
+        buttonsLayout.addWidget(cancelButton)
+
+        row = 0
+        layout.addWidget(
+            QLabel('Start frame n.  '), row, 0, alignment=Qt.AlignRight
+        )
+        layout.addWidget(
+            self.startFrameScrollbar.label, row, 1, alignment=Qt.AlignRight
+        )
+        layout.addWidget(self.startFrameScrollbar, row, 2)
+
+        row += 1
+        layout.setRowStretch(row, 5)
+
+        row += 1
+        layout.addWidget(
+            QLabel('Stop frame n. '), row, 0, alignment=Qt.AlignRight
+        )
+        layout.addWidget(
+            self.endFrameScrollbar.label, row, 1, alignment=Qt.AlignRight
+        )
+        layout.addWidget(self.endFrameScrollbar, row, 2)
+
+        row += 1
+        if addDoNotShowAgain:
+            self.doNotShowAgainCheckbox = QCheckBox('Do not ask again')
+            layout.addWidget(
+                self.doNotShowAgainCheckbox, row, 2, alignment=Qt.AlignLeft
+            )
+            row += 1
+
+        layout.addLayout(buttonsLayout, row, 2, alignment=Qt.AlignRight)
+
+        layout.setColumnStretch(0, 0)
+        layout.setColumnStretch(1, 0)
+        layout.setColumnStretch(2, 10)
+
+        self.setLayout(layout)
+
+        # resetButton.clicked.connect(self.emitReset)
+        cropButton.clicked.connect(self.emitCrop)
+        cancelButton.clicked.connect(self.close)
+        self.startFrameScrollbar.valueChanged.connect(self.TvalueChanged)
+        self.endFrameScrollbar.valueChanged.connect(self.TvalueChanged)
+
+    def emitReset(self):
+        self.sigReset.emit()
+
+    def emitCrop(self):
+        self.cancel = False
+        low_z = self.startFrameScrollbar.value()
+        high_z = self.endFrameScrollbar.value()
+        self.sigCrop.emit(low_z, high_z)
+        self.close()
+
+    def updateScrollbars(self, start_frame_i, lower_frame_i):
+        self.startFrameScrollbar.setValue(start_frame_i)
+        self.endFrameScrollbar.setValue(lower_frame_i)
+
+    def TvalueChanged(self, value):
+        t = str(value+1).zfill(self.numDigits)
+        self.sender().label.setText(f'{t}/{self.SizeT}')
+        self.sigTvalueChanged.emit(value)
+
+    def showEvent(self, event):
+        self.resize(int(self.width()*1.5), self.height())
+
+    def closeEvent(self, event):
+        super().closeEvent(event)
+        self.sigClose.emit()

cellacdc/dataPrep.py

@@ -251,6 +251,20 @@ def gui_createActions(self):
         self.cropZaction.setEnabled(False)
         self.cropZaction.setCheckable(True)
 
+        self.cropTaction = QAction(
+            QIcon(":cropT.svg"), "Crop frames (time points)", self
+        )
+        self.cropTaction.setToolTip(
+            'Crop a specified time range.\n\n'
+            'If the button is disabled you need to click on the Start button '
+            'first.\n\n'
+            'USAGE: Click this button, adjust the start and end frame numbers '
+            'and click on "Apply crop" to activate the save button.\n\n'
+            'To save the cropped data click the Save button.'
+        )
+        self.cropTaction.setEnabled(False)
+        self.cropTaction.setCheckable(True)
+
         self.saveAction = QAction(
             QIcon(":file-save.svg"), "Crop and save", self)
         self.saveAction.setEnabled(False)
@@ -297,6 +311,7 @@ def gui_createToolBars(self):
         fileToolBar.addAction(self.startAction)
         fileToolBar.addAction(self.cropAction)
         fileToolBar.addAction(self.cropZaction)
+        fileToolBar.addAction(self.cropTaction)
         fileToolBar.addAction(self.saveAction)
 
         navigateToolbar = QToolBar("Navigate", self)
@@ -339,6 +354,7 @@ def gui_connectActions(self):
         self.cropAction.triggered.connect(self.applyCropYX)
         self.saveAction.triggered.connect(self.saveActionTriggered)
         self.cropZaction.toggled.connect(self.openCropZtool)
+        self.cropTaction.toggled.connect(self.openCropTtool)
         self.startAction.triggered.connect(self.prepData)
         self.interpAction.triggered.connect(self.interp_z)
         self.ZbackAction.triggered.connect(self.useSameZ_fromHereBack)
@@ -674,6 +690,8 @@ def init_attr(self):
         self.navigateScrollbar.valueChanged.connect(
             self.navigateScrollbarValueChanged
         )
+        self.startFrameIdxCrop = 0
+        self.endFrameIdxCrop = None
 
     def navigateScrollbarValueChanged(self, value):
         if self.num_pos > 1:
@@ -715,6 +733,12 @@ def crop(self, data, posData, cropROI):
             elif croppedData.ndim == 3:
                 croppedData = croppedData[lower_z:upper_z+1]
             SizeZ = (upper_z-lower_z)+1
+
+        if posData.SizeT > 1:
+            croppedData = croppedData[
+                self.startFrameIdxCrop:self.endFrameIdxCrop
+            ]
+
         return croppedData, SizeZ
 
     def saveBkgrROIs(self, posData):
@@ -1232,14 +1256,12 @@ def saveROIcoords(self, doCrop, posData):
     def openCropZtool(self, checked):
         posData = self.data[self.pos_i]
         if checked:
-            self.zSliceToRestore = self.zSliceScrollBar.value()
             self.cropZtool = apps.QCropZtool(posData.SizeZ, parent=self)
             self.cropZtool.sigClose.connect(self.cropZtoolClosed)
             self.cropZtool.sigZvalueChanged.connect(self.cropZtoolvalueChanged)
             self.cropZtool.sigCrop.connect(self.applyCropZslices)
             self.cropZtool.show()
         else:
-            self.zSliceToRestore = None
             self.cropZtool.close()
             self.cropZtool = None
             # Restore original z-slice
@@ -1248,6 +1270,18 @@ def openCropZtool(self, checked):
             z = posData.segmInfo_df.at[idx, 'z_slice_used_dataPrep']
             self.zSliceScrollBar.setValue(z)
 
+    def openCropTtool(self, checked):
+        posData = self.data[self.pos_i]
+        if checked:
+            self.cropTtool = apps.QCropTrangeTool(posData.SizeT, parent=self)
+            self.cropTtool.sigClose.connect(self.cropTtoolClosed)
+            self.cropTtool.sigTvalueChanged.connect(self.cropTtoolvalueChanged)
+            self.cropTtool.sigCrop.connect(self.applyCropTrange)
+            self.cropTtool.show()
+        else:
+            self.cropZtool.close()
+            self.cropZtool = None
+
     def cropZtoolvalueChanged(self, whichZ, z):
         self.zSliceScrollBar.valueChanged.disconnect()
         self.zSliceScrollBar.setValue(z)
@@ -1292,6 +1326,43 @@ def cropZtoolClosed(self):
         self.cropZaction.toggled.disconnect()
         self.cropZaction.setChecked(False)
         self.cropZaction.toggled.connect(self.openCropZtool)
+
+    def cropTtoolClosed(self):
+        self.cropTtool = None
+        self.cropTaction.toggled.disconnect()
+        self.cropTaction.setChecked(False)
+        self.cropTaction.toggled.connect(self.openCropTtool)
+
+    def cropTtoolvalueChanged(self, frame_i):
+        self.navigateScrollbar.setValue(frame_i+1)
+
+    def applyCropTrange(self, start_frame_i, end_frame_i):
+        self.startFrameIdxCrop = start_frame_i
+        self.endFrameIdxCrop = end_frame_i + 1
+        self.logger.info(
+            f'Previewing cropped frames ({start_frame_i+1},{end_frame_i+1})...'
+        )
+        for posData in self.data:
+            posData.img_data[:start_frame_i] = 0
+            posData.img_data[end_frame_i+1:] = 0
+
+        self.update_img()
+        note_text = (
+            f'Done. Frames outside of the range ({start_frame_i+1},{end_frame_i+1}) '
+            'will appear black now. To save cropped data, click on the "Save" '
+            'button on the top toolbar.'
+        )
+        self.logger.info(note_text)
+
+        txt = html_utils.paragraph(f"""
+            Cropping frames applied.<br><br>
+            Note that this is just a preview where the frames outside of the 
+            range ({start_frame_i+1},{end_frame_i+1}) will look black.<br><br>
+            <b>To save cropped data</b>, click on the <code>Save cropped data</code> 
+            button on the top toolbar.
+        """)
+        msg = widgets.myMessageBox(wrapText=False)
+        msg.information(self, 'Preview cropped frames', txt)
 
     def getCroppedData(self, askCropping=True):
         for p, posData in enumerate(self.data):
@@ -1484,12 +1555,17 @@ def setEnabledCropActions(self, enabled):
         self.cropAction.setEnabled(enabled)
         self.cropZaction.setEnabled(enabled)
         self.saveAction.setEnabled(enabled)
+        self.cropTaction.setEnabled(enabled)
+
         if not hasattr(self, 'data'):
             return
 
         posData = self.data[self.pos_i]
         if posData.SizeZ == 1:
             self.cropZaction.setEnabled(False)
+
+        if posData.SizeT == 1:
+            self.cropTaction.setEnabled(False)
 
     def removeAllHandles(self, roi):
         for handle in roi.handles:

cellacdc/dataStruct.py

@@ -630,10 +630,20 @@ def saveImgDataChannel(
         )
         filePath = os.path.join(images_path, filename)
         dimsIdx = {'c': ch_idx} 
+        numFrames = len(framesRange)
+        num_imgs = numFrames*SizeZ
+        pbar = tqdm(
+            total=num_imgs, 
+            ncols=100, 
+            desc=f'Reading image (z 0/{SizeZ}, t 0/{numFrames})'
+        )
         for t in framesRange:
             imgData_z = []
             dimsIdx['t'] = t
             for z in range(SizeZ):
+                pbar.set_description(
+                    f'Reading image (z {z+1}/{SizeZ}, t {t+1}/{numFrames})'
+                )
                 dimsIdx['z'] = z
                 if self.rawDataStruct != 2:
                     idx = self.getIndex(idxs, dimsIdx, self.DimensionOrder)
@@ -647,13 +657,15 @@ def saveImgDataChannel(
                     imgData_ch[t, z] = imgData
                 else:
                     imgData_z.append(imgData)
+
+                pbar.update()
 
             if not self.to_h5:
                 imgData_z = np.squeeze(np.array(imgData_z, dtype=imgData.dtype))
                 imgData_ch.append(imgData_z)
-
+        pbar.close()
+
         if not self.to_h5:
-
             imgData_ch = np.squeeze(np.array(imgData_ch, dtype=imgData.dtype))
             myutils.to_tiff(
                 filePath, imgData_ch, 

cellacdc/io.py

@@ -109,11 +109,11 @@ def save_image_data(filepath, img_data):
         myutils.to_tiff(filepath, img_data)
     return np.squeeze(img_data)
 
-def savez_compressed(filepath, data, safe=True):
+def savez_compressed(filepath, *args, safe=True, **kwargs):
     if not os.path.exists(filepath):
-        np.savez_compressed(filepath, data)
+        np.savez_compressed(filepath, *args, **kwargs)
         return
 
     temp_filepath = filepath.replace('.npz', '.new.npz')
-    np.savez_compressed(temp_filepath, data)
+    np.savez_compressed(temp_filepath, *args, **kwargs)
     os.replace(temp_filepath, filepath)