Fiji macro for the separate channels option

cellacdc/apps.py

@@ -17395,9 +17395,13 @@ def __init__(self, parent=None):
         self.filesStructureCombobox = QComboBox()
         self.filesStructureCombobox.addItems([
             'Positions (aka "series") embedded in the file',
-            'Positions (aka "series") separated, one for each file'
+            'Positions (aka "series") separated, one for each file',
+            'Positions (aka "series") and channels separated, one for each file'
         ])
         gridLayout.addWidget(self.filesStructureCombobox, row, 1)
+        self.filesStructureCombobox.currentTextChanged.connect(
+            self.fileStructureChanged
+        )
         infoButton = widgets.infoPushButton()
         gridLayout.addWidget(infoButton, row, 2)
         infoButton.clicked.connect(self.showInfoFileStructure)
@@ -17412,6 +17416,16 @@ def __init__(self, parent=None):
         browseButton.sigPathSelected.connect(
             partial(self.updateFolderPath, lineEdit=self.folderPathLineEdit)
         )
+        self.folderPathLineEdit.textChanged.connect(self.srcFolderPathChanged)
+
+        row += 1
+        label = QLabel('Destination folder: ')
+        gridLayout.addWidget(label, row, 0)
+        self.dstfolderPathLineEdit = widgets.ElidingLineEdit()
+        gridLayout.addWidget(self.dstfolderPathLineEdit, row, 1)
+        browseButton = widgets.browseFileButton(openFolder=True)
+        gridLayout.addWidget(browseButton, row, 2)
+        browseButton.sigPathSelected.connect(self.dstfolderPathLineEdit.setText)
 
         row += 1
         label = QLabel('Channel(s) name: ')
@@ -17420,11 +17434,15 @@ def __init__(self, parent=None):
             additionalChars=' ,'
         )
         gridLayout.addWidget(self.channelNamesLineEdit, row, 1)
+        checkButton = widgets.TestPushButton('Check')
+        gridLayout.addWidget(checkButton, row, 3)
+        checkButton.clicked.connect(self.checkChannelNames)
+        checkButton.setDisabled(True)
+        self.checkButton = checkButton
         infoButton = widgets.infoPushButton()
         gridLayout.addWidget(infoButton, row, 2)
         infoButton.clicked.connect(self.showInfoChannelName)
 
-
         buttonsLayout = widgets.CancelOkButtonsLayout()
 
         buttonsLayout.okButton.clicked.connect(self.ok_cb)
@@ -17433,13 +17451,50 @@ def __init__(self, parent=None):
         gridLayout.setColumnStretch(0, 0)
         gridLayout.setColumnStretch(1, 1)
         gridLayout.setColumnStretch(2, 0)
-
+        gridLayout.setColumnStretch(3, 0)
+
         mainLayout.addLayout(gridLayout)
         mainLayout.addSpacing(20)
         mainLayout.addLayout(buttonsLayout)
 
         self.setLayout(mainLayout)
 
+    def fileStructureChanged(self, text):
+        self.checkButton.setDisabled(not 'channels separated' in text)
+
+    def checkChannelNames(self, checked=False):
+        proceed = self.validate()
+        if not proceed:
+            return
+
+        src_folderpath = self.folderPath()
+        channel_names = self.channelNames()
+        extension = os.listdir(src_folderpath)[0].split('.')[-1]
+        basenames = io.move_separate_channels_tiffs_to_pos_folders(
+            src_folderpath, channel_names, get_only_basenames=True,
+            extension=extension
+        )
+        pos_folders_texts = []
+        for p, basename in enumerate(basenames):
+            pos_folders_texts.append(f'Position_{p+1}: <code>{basename}</code>')
+
+        pos_folders_html_list = html_utils.to_list(
+            pos_folders_texts, ordered=True
+        )
+        text = html_utils.paragraph(
+            'The following Position folders will be created based on the provided channel names:<br>'
+            f'{pos_folders_html_list}'
+        )
+        msg = widgets.myMessageBox(wrapText=False)
+        msg.information(self, 'Position folders', text)
+
+    def srcFolderPathChanged(self, text):
+        if self.dstfolderPathLineEdit.text():
+            return
+
+        folderPath = self.folderPathLineEdit.text()
+        self.dstfolderPathLineEdit.setText(folderPath)
+
     def showInfoFileStructure(self):
         txt = html_utils.paragraph("""
             Select whether the microscopy files contains multiple "series".<br><br>
@@ -17456,9 +17511,14 @@ def showInfoChannelName(self):
             Enter the channels name. Separate multiple channels with a comma.<br><br>
             The channel names will be used to name the individual TIFF files 
             (one for each channel).<br><br>
-            Make sure that you write the <b>channels in the right order</b>. 
-            If you are unsure, open the file in Fiji first<br> 
-            and check the order of channels.
+            If multiple channels are embedded in the microscopy file, make sure that you write the <b>channels in the right order</b>.<br> 
+            If you are unsure, open the file in Fiji first
+            and check the order of channels.<br><br>
+            If the channels are already separated, make sure to write the 
+            full channel name as it appears in the file, including capitalization and spaces.<br>
+            For example, if the files are named "pos1_ch1.tif", "pos1_ch2.tif", etc., the channels names should be "ch1, ch2".<br><br>
+            After providing the channel names, you can check that they are correct by clicking on the "Check" button next to the channel names field.<br>
+            The number of Positions that will be created will be displayed alongside the basename.
         """)
         msg = widgets.myMessageBox(wrapText=False)
         msg.information(self, 'Files structure info', txt)
@@ -17484,10 +17544,10 @@ def updateFolderPath(self, path, lineEdit=''):
                 return
 
         lineEdit.setText(path)
-    
-    def warnPathEmpty(self):
-        txt = html_utils.paragraph("""
-            Folder path <b>cannot be empty</b>.
+
+    def warnPathEmpty(self, path_name):
+        txt = html_utils.paragraph(f"""
+            {path_name} <b>cannot be empty</b>.
         """)
         msg = widgets.myMessageBox(wrapText=False)
         msg.warning(self, 'Empty folder path', txt)
@@ -17531,19 +17591,25 @@ def warnChannelNamesEmpty(self):
 
     def validate(self):
         path = self.folderPath()
-        if not path:
-            self.warnPathEmpty()
-            return False
-
-        if not os.path.exists(path):
-            self.warnSelectedPathDoesNotExist(path)
-            return False
-
-        if not os.path.isdir(path):
-            self.warnSelectedPathNotAFolder(path)
-            return False
+        dst_path = self.dstfolderPathLineEdit.text()
+        paths = {
+            'Source folder': path,
+            'Destination folder': dst_path,
+        }
+        for _path_name, _path in paths.items():
+            if not _path:
+                self.warnPathEmpty(_path_name)
+                return False
+
+            if not os.path.exists(_path):
+                self.warnSelectedPathDoesNotExist(_path)
+                return False
+
+            if not os.path.isdir(_path):
+                self.warnSelectedPathNotAFolder(_path)
+                return False
 
-        files = os.listdir(path)
+        files = myutils.listdir(path)
         extensions = set([os.path.splitext(file)[1] for file in files])
         if len(extensions) > 1:
             self.warnMultipleExtensionsPresent(path, extensions)
@@ -17558,6 +17624,11 @@ def validate(self):
     def folderPath(self):
         return self.folderPathLineEdit.text()
 
+    def channelNames(self):
+        channel_names = self.channelNamesLineEdit.text().split(',')
+        channel_names = [ch.strip() for ch in channel_names]
+        return channel_names
+
     def ok_cb(self):
         proceed = self.validate()
         if not proceed:
@@ -17566,10 +17637,14 @@ def ok_cb(self):
         self.selectedFolderPath = self.folderPath()
         self.filesStructure = self.filesStructureCombobox.currentText()
         is_multiple_files = self.filesStructure.find('separated') != -1
+        is_separate_channels = 'channels separated' in self.filesStructure
+        dst_folderpath = self.dstfolderPathLineEdit.text()
         self.init_macro_args = (
-            self.folderPath(), is_multiple_files, 
-            self.channelNamesLineEdit.text().split(',')
-
+            self.folderPath(), 
+            is_multiple_files, 
+            is_separate_channels,
+            dst_folderpath,
+            self.channelNames(),
         )
         self.cancel = False
         self.close()

cellacdc/dataStruct.py

@@ -2210,11 +2210,11 @@ def __init__(self, acdcLauncher):
 
     def askSelectInstalledFiji(self):
         if os.path.exists(myutils.get_fiji_exec_folderpath()):
-            return
+            return False, False
 
         txt = html_utils.paragraph(f"""    
             Do you already have Fiji (ImageJ)?<br><br>
-            If yes, click on the <code>Select Fiji location</code> button below<br>
+            If yes, click on the <code>Select Fiji location</code> button below 
             and select where you have the Fiji app.<br><br>
             Alternatively, you can ignore this and let Cell-ACDC automatically 
             download Fiji for you.
@@ -2226,6 +2226,7 @@ def askSelectInstalledFiji(self):
             widgets.DownloadPushButton('Download Fiji.app')
         )
         msg = widgets.myMessageBox(wrapText=False)
+        msg.did_user_selected_fiji = False
         msg.question(
             self.acdcLauncher, 'Select Fiji location', txt, 
             buttonsTexts=(
@@ -2239,7 +2240,7 @@ def askSelectInstalledFiji(self):
         )
         msg.exec_()
 
-        return msg.cancel
+        return msg.cancel, msg.did_user_selected_fiji
 
     def selectFijiLocation(self, checked=True, messagebox=None):
         import qtpy.compat
@@ -2253,15 +2254,14 @@ def selectFijiLocation(self, checked=True, messagebox=None):
 
         from cellacdc import fiji_location_filepath
         with open(fiji_location_filepath, 'w') as txt:
-            txt.write(
-                os.path.join(filepath, 'Contents', 'MacOS', 'ImageJ-macosx')
-            )
+            txt.write(os.path.join(filepath))
 
+        messagebox.did_user_selected_fiji = True
         messagebox.cancel = False
         messagebox.close()
 
     def run(self):
-        cancel = self.askSelectInstalledFiji()
+        cancel, did_user_selected_fiji = self.askSelectInstalledFiji()
         if cancel:
             self.cancel()
             return
@@ -2278,18 +2278,23 @@ def run(self):
         fiji_success = myutils.test_fiji_base_command(self.logger.info)
         commands = None
         if not fiji_success:
-            try:
-                shutil.rmtree(acdc_fiji_path)
-            except Exception as err:
-                pass
+            if not did_user_selected_fiji:
+                try:
+                    shutil.rmtree(acdc_fiji_path)
+                except Exception as err:
+                    pass
+
             href = html_utils.href_tag('here', urls.fiji_downloads)
             note_download_txt = (f"""
                 Before continuing, Fiji will be <b>automatically downloaded
                 now</b>.<br><br>
                 If the download fails, please download the zip file from {href} 
                 and unzip it in the following location:
             """)
-            txt = f'{txt}<br><br>{note_download_txt}'
+            admon = html_utils.to_admonition(
+                note_download_txt, admonition_type='note'
+            )
+            txt = f'{txt}<br>{admon}'
             commands = (acdc_fiji_path,)
 
         txt = html_utils.paragraph(txt)
@@ -2311,28 +2316,55 @@ def run(self):
             self.cancel()
             return
 
-        macro_filepath = fiji_macros.init_macro(*win.init_macro_args)
+        init_macro_args = win.init_macro_args
+        is_separate_channels = init_macro_args[2]
+        macro_filepath = fiji_macros.init_macro(*init_macro_args)
         macro_command = fiji_macros.command_run_macro(macro_filepath)
 
-        txt = html_utils.paragraph("""
+        txt = ("""
             Cell-ACDC will now run the macro in the terminal.<br><br>
             During the process, the <b>GUI will be unresponsive</b>, while 
             progress will be displayed in the terminal.<br><br>
             If you prefer, you can stop the process now and run the command 
-            yourself, or even run the macro directly from the Fiji GUI.<br><br>
-            Command to run the macro:
+            yourself, or even run the macro directly from the Fiji GUI.<br>
         """)
+
+        if is_separate_channels:
+            important_admon = html_utils.to_admonition(
+                'There are still steps to run after the macro finishes, so '
+                'if you run it yourself, '
+                'please close this dialogue only after the macro completes.',
+                admonition_type='important'
+            )
+            txt = f'{txt}{important_admon}'
+
+        txt = f'{txt}<br>Command to run the macro:'
+
+        txt = html_utils.paragraph(txt)
         msg = widgets.myMessageBox(wrapText=False)
-        msg.information(
+        _, _, okButton = msg.information(
             self.acdcLauncher, 'Fiji macro command', txt, 
-            buttonsTexts=('Cancel', 'Ok'),
-            commands=(macro_filepath)
+            buttonsTexts=('Cancel', 'I already ran the macro', 'Ok'),
+            commands=(macro_filepath),
+            path_to_browse=os.path.dirname(macro_filepath)
         )
         if msg.cancel:
             self.cancel()
             return
 
-        success = fiji_macros.run_macro(macro_command)
+        success = True
+        if msg.clickedButton == okButton:
+            success = fiji_macros.run_macro(macro_command)            
+
+        files_folderpath = init_macro_args[0]
+        dst_folderpath = init_macro_args[3]
+        channels = init_macro_args[4]
+        if success and is_separate_channels:
+            self.logger.info('Moving files to Position folders...')
+            success = io.move_separate_channels_tiffs_to_pos_folders(
+                dst_folderpath, channels
+            )
+
         if success:
             txt = html_utils.paragraph("""
                 Macro execution completed. 

cellacdc/fiji_macros/__init__.py

@@ -10,15 +10,21 @@
 def init_macro(
         files_folderpath: os.PathLike, 
         is_multiple_files: bool,
+        is_separate_channels: bool,
+        dst_folderpath: os.PathLike, 
         channels: Iterable[str]
     ):
     macros_folderpath = os.path.join(acdc_fiji_path, 'macros')
     os.makedirs(macros_folderpath, exist_ok=True)
 
     macros_template_folderpath = os.path.dirname(os.path.abspath(__file__))
-    macro_template_filename = (
-        'multiple_files.ijm' if is_multiple_files else 'single_file.ijm'
-    )
+    if is_separate_channels:
+        macro_template_filename = 'multiple_files_separate_channels.ijm'
+    elif is_multiple_files:
+        macro_template_filename = 'multiple_files.ijm'
+    else:
+        macro_template_filename = 'single_file.ijm'
+
     macro_template_filepath = os.path.join(
         macros_template_folderpath, macro_template_filename
     )
@@ -31,11 +37,17 @@ def init_macro(
         'channels = newArray(...)', 
         f'channels = newArray({channels_macro})'
     )
+
     files_path = files_folderpath.replace('\\', '/')
     files_path = f'"{files_path}/"'
     macro_txt = macro_txt.replace('id = ...', f'id = {files_path}')
 
-    date_time = datetime.datetime.now().strftime('%Y-%m-%d_%H-%M-%S')
+    dst_folderpath = dst_folderpath.replace('\\', '/')
+    macro_txt = macro_txt.replace(
+        'dst_folderpath = ...', f'dst_folderpath = "{dst_folderpath}"'
+    )
+
+    date_time = datetime.datetime.now().strftime(r'%Y-%m-%d_%H-%M-%S')
     id = uuid4()
     macro_filename = f'{date_time}_{id}_{macro_template_filename}'
     macro_filepath = os.path.join(macros_folderpath, macro_filename)