Allow creating new position folders data struct, see #750

cellacdc/acdc_bioio_bioformats/_read_metadata.py

@@ -28,8 +28,6 @@
     metadataXML = bioformats.get_omexml_metadata(raw_filepath)
     metadata = bioformats.OMEXML().init_from_metadata(metadataXML)
 
-    print(metadata)
-
     os.makedirs(bioio_sample_data_folderpath, exist_ok=True)
     metadataXML_filepath = os.path.join(
         bioio_sample_data_folderpath, 'metadataXML.txt'

cellacdc/apps.py

@@ -3052,10 +3052,11 @@ def __init__(
         label = QLabel(txt)
         entriesLayout.addWidget(label, row, 0, alignment=Qt.AlignRight)
         entriesLayout.addWidget(self.SizeS_SB, row, 1)
-        self.SizeS_SB.valueChanged.connect(self.SizeSvalueChanged)
-
+
         if rawDataStruct == 0:
             row += 1
+            self.SizeS_SB.setValue(1)
+            self.SizeS_SB.setDisabled(True)
             self.posSelector = widgets.ExpandableListBox()
             positions = ['All positions']
             positions.extend([f'Position_{i+1}' for i in range(SizeS)])
@@ -3064,6 +3065,7 @@ def __init__(
             label = QLabel(txt)
             entriesLayout.addWidget(label, row, 0, alignment=Qt.AlignRight)
             entriesLayout.addWidget(self.posSelector, row, 1)
+            self.SizeS_SB.valueChanged.connect(self.SizeSvalueChanged)
 
         row += 1
         self.LensNA_DSB = QDoubleSpinBox()

cellacdc/dataStruct.py

@@ -73,7 +73,6 @@ class bioFormatsWorker(QObject):
     progressPbar = Signal(int)
     initPbar = Signal(int)
     criticalError = Signal(str, str, str)
-    filesExisting = Signal(str)
     confirmMetadata = Signal(
         str, float, int, int, int, int,
         float, str, float, float, float,
@@ -86,7 +85,9 @@ def __init__(
             self, raw_src_path, rawFilenames, exp_dst_path,
             mutex, waitCond, rawDataStruct, 
             bioformats_backend: Literal['bioio', 'python-bioformats'],
-            lazy_load=True, move_raw_microscopy_files=True
+            lazy_load=True, move_raw_microscopy_files=True,
+            overwrite=False, add_files=False, create_new=False,
+            start_pos_n=1
         ):
         QObject.__init__(self)
         self.raw_src_path = raw_src_path
@@ -98,9 +99,11 @@ def __init__(
         self.overWriteMetadata = False
         self.trustMetadataReader = False
         self.rawDataStruct = rawDataStruct
-        self.overwritePos = False
-        self.addFiles = False
+        self.overwritePos = overwrite
+        self.addFiles = add_files
+        self.createNew = create_new
         self.cancel = False
+        self.start_pos_n = start_pos_n
         self.bioformats_backend = bioformats_backend
         self.lazy_load = lazy_load
         self.move_raw_microscopy_files = move_raw_microscopy_files
@@ -505,7 +508,7 @@ def readMetadata(self, raw_src_path, filename):
             self.PhysicalSizeZ = PhysicalSizeZ
             # self.chNames = chNames
             self.emWavelens = emWavelens
-            return
+            return False
 
         sampleImgData = None
         while True:
@@ -563,42 +566,42 @@ def readMetadata(self, raw_src_path, filename):
         self.saveChannels = self.metadataWin.saveChannels
         self.emWavelens = self.metadataWin.emWavelens
         self.addImageName = self.metadataWin.addImageName
+
+        return False
 
     def saveToPosFolder(
-            self, p, raw_src_path, exp_dst_path, filename, series, p_idx=0
+            self, p, raw_src_path, exp_dst_path, filename, series, pos_n,
+            p_idx=0,
         ):
         rawFilePath = os.path.join(raw_src_path, filename)
 
         if os.path.basename(raw_src_path) == 'raw_microscopy_files':
             raw_src_path = os.path.dirname(raw_src_path)
-        
-        pos_name = f'Position_{p+1}'
+
+        in_file_pos_name = f'Position_{p+1}'
         savePos = (
-            'All Positions' in self.selectedPos or pos_name in self.selectedPos
+            'All Positions' in self.selectedPos 
+            or in_file_pos_name in self.selectedPos
         )
         if not savePos:
             return False
 
-        pos_path = os.path.join(exp_dst_path, f'Position_{p+1}')
+        pos_path = os.path.join(exp_dst_path, f'Position_{pos_n}')
         images_path = os.path.join(pos_path, 'Images')
 
-        if os.path.exists(images_path) and self.askReplacePosFiles:
-            self.askReplacePosFiles = False
-            self.mutex.lock()
-            self.filesExisting.emit(pos_path)
-            self.waitCond.wait(self.mutex)
-            self.mutex.unlock()
-            if self.cancel:
-                return True
-
         if os.path.exists(images_path) and self.overwritePos:
             shutil.rmtree(images_path)
 
+        if os.path.exists(images_path) and self.createNew:
+            images_path = re.sub(
+                r'Position_\d+', f'Position_{pos_n}', images_path
+            )
+
         if not os.path.exists(images_path):
             os.makedirs(images_path, exist_ok=True)
-
+        
         self.saveData(
-            images_path, rawFilePath, filename, p, series, p_idx=p_idx
+            images_path, rawFilePath, filename, p, series, pos_n, p_idx=p_idx,
         )
 
         return False
@@ -776,16 +779,19 @@ def saveImgDataChannel(
             shutil.move(tempFilepath, filePath)
             shutil.rmtree(tempDir)
 
-    def saveData(self, images_path, rawFilePath, filename, p, series, p_idx=0):
+    def saveData(
+            self, images_path, rawFilePath, filename, p, series, pos_n,
+            p_idx=0
+        ):
         if self.bioformats_backend == 'bioio':
             from cellacdc import acdc_bioio_bioformats as bioformats
         else:
             import javabridge
             from cellacdc import bioformats
-            
-        s0p = str(p+1).zfill(self.numPosDigits)
+
+        s0p = str(pos_n).zfill(self.numPosDigits)
         self.progress.emit(
-            f'Position {p+1}/{self.numPos}: saving data to {images_path}...'
+            f'Position {pos_n}/{self.numPos}: saving data to {images_path}...'
         )
         filenameNOext, ext = os.path.splitext(filename)
 
@@ -920,7 +926,7 @@ def saveData(self, images_path, rawFilePath, filename, p, series, p_idx=0):
                 if not saveCh:
                     continue
 
-                rawFilename = f'{basename}{p+1}_{chName}'
+                rawFilename = f'{basename}{pos_n}_{chName}'
                 pos_rawFilenames.append(rawFilename)
                 raw_src_path = os.path.dirname(rawFilePath)
                 rawFilePath = [
@@ -981,7 +987,7 @@ def saveData(self, images_path, rawFilePath, filename, p, series, p_idx=0):
             if self.moveOtherFiles or self.copyOtherFiles:
                 # Move the other files present in the folder if they
                 # contain "otherFilename" in the name
-                otherFilename = f'{basename}{p+1}'
+                otherFilename = f'{basename}{pos_n}'
                 rawFilePath = set()
                 for f in myutils.listdir(raw_src_path):
                     notRawFile = all(
@@ -1027,39 +1033,42 @@ def run(self):
         self.cancelled = False
         self.isCriticalError = False
         for p, filename in enumerate(self.rawFilenames):
+            pos_n = p + self.start_pos_n
             if self.rawDataStruct == 0:
                 if not self.overWriteMetadata:
-                    abort = self.readMetadata(raw_src_path, filename)
-                    if abort:
+                    cancel = self.readMetadata(raw_src_path, filename)
+                    if cancel:
                         self.cancelled = True
                         break
 
                 self.numPos = self.SizeS
                 self.numPosDigits = len(str(self.numPos))
                 if p == 0:
                     self.initPbar.emit(self.numPos*self.SizeC)
-                for p in range(self.SizeS):
-                    abort = self.saveToPosFolder(
-                        p, raw_src_path, exp_dst_path, filename, p
+
+                for in_file_p in range(self.SizeS):
+                    cancel = self.saveToPosFolder(
+                        in_file_p, raw_src_path, exp_dst_path, filename, 
+                        in_file_p, pos_n
                     )
-                    if abort:
+                    if cancel:
                         self.cancelled = True
                         break
 
             elif self.rawDataStruct == 1:
                 if not self.overWriteMetadata:
-                    abort = self.readMetadata(raw_src_path, filename)
-                    if abort:
+                    cancel = self.readMetadata(raw_src_path, filename)
+                    if cancel:
                         self.cancelled = True
                         break
                 self.numPos = len(self.rawFilenames)
                 self.numPosDigits = len(str(self.numPos))
                 if p == 0:
                     self.initPbar.emit(self.numPos*self.SizeC)
-                abort = self.saveToPosFolder(
-                    p, raw_src_path, exp_dst_path, filename, 0
+                cancel = self.saveToPosFolder(
+                    p, raw_src_path, exp_dst_path, filename, 0, pos_n
                 )
-                if abort:
+                if cancel:
                     self.cancelled = True
                     break
 
@@ -1088,7 +1097,7 @@ def run(self):
             for p_idx, pos in enumerate(self.posNums):
                 p = pos-1
                 abort = self.saveToPosFolder(
-                    p, raw_src_path, exp_dst_path, self.basename,
+                    p, raw_src_path, exp_dst_path, self.basename, pos_n,
                     0, p_idx=p_idx
                 )
                 if abort:
@@ -1565,7 +1574,14 @@ def main(self):
         if not exp_dst_path:
             self.close()
             return
+
+        out = self.askPosFoldersExisting(exp_dst_path)
+        if out is None:
+            self.close()
+            return
 
+        overwrite, add_files, create_new, start_pos_n = out
+
         self.log('Instructing to move raw data...')
         loadEntirePosIntoRam = self.askHowToLoadData()
         if loadEntirePosIntoRam is None:
@@ -1599,7 +1615,11 @@ def main(self):
             self.mutex, self.waitCond, rawDataStruct, 
             self.bioformats_backend, 
             lazy_load=not self.loadEntirePosIntoRam,
-            move_raw_microscopy_files=move_raw_microscopy_files
+            move_raw_microscopy_files=move_raw_microscopy_files,
+            overwrite=overwrite,
+            add_files=add_files,
+            create_new=create_new,
+            start_pos_n=start_pos_n,
         )
         if self.rawDataStruct == 2:
             self.worker.basename = self.basename
@@ -1621,7 +1641,6 @@ def main(self):
         self.worker.critical.connect(self.workerCritical)
         self.worker.criticalError.connect(self.criticalBioFormats)
         self.worker.confirmMetadata.connect(self.askConfirmMetadata)
-        self.worker.filesExisting.connect(self.askReplacePos)
         self.thread.started.connect(self.worker.run)
 
         self.thread.start()
@@ -2016,6 +2035,7 @@ def warnMultipleFiles(self, files):
             return []
         else:
             files = [win.selectedItemText]
+            return files
 
     def attemptSeparateMultiChannel(self, rawFilenames):
         self.chNames = set()
@@ -2130,25 +2150,41 @@ def askConfirmMetadata(
         self.worker.metadataWin = self.metadataWin
         self.waitCond.wakeAll()
 
-    def askReplacePos(self, pos_path):
-        msg = widgets.myMessageBox()
+    def askPosFoldersExisting(self, exp_dst_path):
+        pos_foldernames = myutils.get_pos_foldernames(exp_dst_path)
+        if not pos_foldernames:
+            return False, False, False, 1
+
+        msg = widgets.myMessageBox(wrapText=False)
         txt = html_utils.paragraph(
-            f'The following folder <b>already exists</b>.<br><br>'
-            f'<code>{pos_path}</code><br><br>'
-            'Do you want to <b>overwrite</b> all of its content or '
-            '<b>add files</b> to it?'
+            'The selected destination folder <b>already contains Position folders</b>.<br><br>'
+            'Do you want to <b>overwrite</b> all of its content, '
+            '<b>add files</b> to the existing Position folders,<br>'
+            'or <b>create new</b> Position folders?'
         )
-        cancelButton, overwriteButton, addFilesButton = msg.warning(
-           self, 'Replace files?', txt,
-           buttonsTexts=('Cancel', 'Overwrite', 'Add files')
+        _, overwriteButton, addFilesButton, createNewButton = msg.warning(
+           self, 'Warning: existing Position folders detected!', txt,
+           buttonsTexts=(
+               'Cancel', 
+               'Overwrite', 
+               'Add files', 
+               widgets.newFilePushButton('Create new'),
+            ),
+           path_to_browse=exp_dst_path
         )
         if msg.cancel:
-            self.worker.cancel = True
-        elif overwriteButton == msg.clickedButton:
-            self.worker.overwritePos = True
-        elif addFilesButton == msg.clickedButton:
-            self.worker.addFiles = True
-        self.waitCond.wakeAll()
+            return 
+
+        overwrite = overwriteButton == msg.clickedButton
+        add_files = addFilesButton == msg.clickedButton
+        create_new = createNewButton == msg.clickedButton
+
+        start_pos_n = 1
+        if create_new:
+            pos_ns = [int(pos.split('_')[-1]) for pos in pos_foldernames]
+            start_pos_n = max(pos_ns) + 1
+
+        return overwrite, add_files, create_new, start_pos_n
 
     def closeEvent(self, event):
         self.logger.info('Closing data structure logger...')