dataStruct.py

import sys
import os

from typing import Literal

import shutil
import re
import traceback
import time
import datetime
import tempfile
import h5py
import uuid
import difflib
import pathlib
import numpy as np
import pandas as pd
from collections import Counter
from tqdm import tqdm
from natsort import natsorted
from pprint import pprint
from functools import wraps, partial
from itertools import permutations

from qtpy.QtWidgets import (
    QApplication, QMainWindow, QFileDialog,
    QVBoxLayout, QPushButton, QLabel, QStyleFactory,
    QWidget, QMessageBox, QPlainTextEdit, QHBoxLayout
)
from qtpy.QtCore import (
    Qt, QObject, Signal, QThread, QMutex, QWaitCondition,
    QEventLoop
)
from qtpy import QtGui

# Here we use from cellacdc because this script is laucnhed in
# a separate process that doesn't have a parent package
from . import issues_url
from . import exception_handler
from . import apps, myutils, widgets, html_utils, printl
from . import load, settings_csv_path
from . import _palettes
from . import recentPaths_path, cellacdc_path, settings_folderpath
from . import urls
from . import acdc_fiji_path
from . import fiji_macros
from . import acdc_regex
from . import io

if os.name == 'nt':
    try:
        # Set taskbar icon in windows
        import ctypes
        myappid = 'schmollerlab.cellacdc.pyqt.v1' # arbitrary string
        ctypes.windll.shell32.SetCurrentProcessExplicitAppUserModelID(myappid)
    except:
        pass

def worker_exception_handler(func):
    @wraps(func)
    def run(self):
        try:
            result = func(self)
        except Exception as error:
            result = None
            self.critical.emit(error)
        return result
    return run

class bioFormatsWorker(QObject):
    finished = Signal()
    progress = Signal(str)
    progressPbar = Signal(int)
    initPbar = Signal(int)
    criticalError = Signal(str, str, str)
    confirmMetadata = Signal(
        str, float, int, int, int, int,
        float, str, float, float, float,
        str, list, list, str, str, object
    )
    critical = Signal(object)
    sigFinishedReadingSampleImageData = Signal(object)

    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,
            overwrite=False, add_files=False, create_new=False,
            start_pos_n=1
        ):
        QObject.__init__(self)
        self.raw_src_path = raw_src_path
        self.exp_dst_path = exp_dst_path
        self.rawFilenames = rawFilenames
        self.mutex = mutex
        self.waitCond = waitCond
        self.askReplacePosFiles = True
        self.overWriteMetadata = False
        self.trustMetadataReader = False
        self.rawDataStruct = rawDataStruct
        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
    
    def _readSampleDataPythonBioformats(
            self, bioformats, rawFilePath, sampleImgData, SizeC, SizeT, SizeZ,
            sampleSizeT, sampleSizeZ
        ):
        dimsIdx = {}
        allChannelsData = None
        with bioformats.ImageReader(rawFilePath) as reader:
            permut_pbar = tqdm(total=6, ncols=100)
            for dimsOrd in permutations('zct', 3):
                if allChannelsData is not None and self.bioformats_backend == 'bioio':
                    sampleImgData[''.join(dimsOrd)] = allChannelsData
                    permut_pbar.update(1)
                    continue
                
                allChannelsData = []
                idxs = self.buildIndexes(SizeC, SizeT, SizeZ, dimsOrd)
                numIter = SizeC*sampleSizeT*sampleSizeZ
                pbar = tqdm(total=numIter, ncols=100, leave=False)
                skipPermutation = False
                for c in range(SizeC):
                    dimsIdx['c'] = c
                    imgData_tz = []
                    for t in range(sampleSizeT):   
                        dimsIdx['t'] = t
                        imgData_z = []
                        for z in range(sampleSizeZ):
                            dimsIdx['z'] = z
                            try:
                                idx = self.getIndex(idxs, dimsIdx, dimsOrd)
                                imgData = reader.read(
                                    c=c, z=z, t=t, rescale=False, index=idx
                                )
                            except Exception as e:
                                skipPermutation = True
                                break
                            imgData_z.append(imgData) 
                            pbar.update()
                        if skipPermutation:
                            break               
                        imgData_z = np.array(imgData_z, dtype=imgData.dtype)
                        imgData_z = np.squeeze(imgData_z)
                        imgData_tz.append(imgData_z)
                    if not skipPermutation:
                        imgData_tz = np.array(imgData_tz, dtype=imgData.dtype)
                        imgData_tz = np.squeeze(imgData_tz)
                        allChannelsData.append(imgData_tz)
                pbar.close()
                permut_pbar.update(1)
                if not skipPermutation:
                    sampleImgData[''.join(dimsOrd)] = allChannelsData
            permut_pbar.close()

        return sampleImgData
    
    def readSampleData(self, rawFilePath, SizeC, SizeT, SizeZ):
        if self.bioformats_backend == 'bioio':
            from cellacdc import acdc_bioio_bioformats as bioformats
        else:
            import javabridge
            from cellacdc import bioformats
             
        sampleImgData = {}
        self.progress.emit('Reading sample image data...')
        
        if self.bioformats_backend == 'bioio':
            # To avoid running Java in the main process, we spawn a new 
            # process that runs a python script to read sample data, save
            # it to disk, and then load it back here.
            import subprocess
            from . import _process, bioio_sample_data_folderpath
            
            read_sample_data_py_filepath = os.path.join(
                os.path.dirname(bioformats.__file__), '_read_sample_data.py'
            )
            uuid4 = uuid.uuid4()
            command = (
                f'{sys.executable}, '
                f'{read_sample_data_py_filepath}, '
                f'-f, {rawFilePath}, '
                f'-c, {SizeC}, '
                f'-t, {SizeT}, '
                f'-z, {SizeZ},'
                f'-uuid, {uuid4}'
            )
            if not self.lazy_load:
                command = f'{command}, -a'
            
            args = [sys.executable, _process.__file__, '-c', command]
            subprocess.run(args)
            
            bioformats._utils.check_raise_exception(uuid4)
            
            allChannelsData = []
            for c in range(SizeC):
                filepath = os.path.join(
                    bioio_sample_data_folderpath, f"sample_channel_{c}.npy"
                )
                channel_data = np.load(filepath)
                allChannelsData.append(channel_data)
                os.remove(filepath)
            
            for dimsOrd in permutations('zct', 3):
                sampleImgData[''.join(dimsOrd)] = allChannelsData
        else:
            if SizeT >= 4:
                sampleSizeT = 4
            else:
                sampleSizeT = SizeT 
            if SizeZ > 20:
                sampleSizeZ = 20
            else:
                sampleSizeZ = SizeZ
            sampleImgData = self._readSampleDataPythonBioformats(
                bioformats, rawFilePath, sampleImgData, SizeC, SizeT, SizeZ,
                sampleSizeT, sampleSizeZ
            )
            
        self.sigFinishedReadingSampleImageData.emit(sampleImgData)
        return sampleImgData

    def getSizeZ(self, rawFilePath):
        if self.bioformats_backend == 'bioio':
            from cellacdc import acdc_bioio_bioformats as bioformats
        else:
            import javabridge
            from cellacdc import bioformats
            
        try:
            if rawFilePath.endswith('.ome.tif'):
                metadata = load.OMEXML(rawFilePath)
                metadataXML = metadata.omexml_string
            else:
                metadata, metadataXML = self._readMetadataBioIO(rawFilePath)
            SizeZ = int(metadata.image().Pixels.SizeZ)
            return SizeZ
        except Exception as e:
            return self.SizeZ

    def _readMetadataBioIO(self, rawFilePath):
        from . import bioio_sample_data_folderpath, _process
        from . import acdc_bioio_bioformats as bioformats
        
        import subprocess
        
        read_metadata_py_filepath = os.path.join(
            os.path.dirname(bioformats.__file__), '_read_metadata.py'
        )
        uuid4 = uuid.uuid4()
        command = (
            f'{sys.executable}, {read_metadata_py_filepath}, '
            f'-f, {rawFilePath}, '
            f'-uuid, {uuid4}'
        )
        
        args = [sys.executable, _process.__file__, '-c', command]
        subprocess.run(args)
        
        bioformats._utils.check_raise_exception(uuid4)

        metadataXML_filepath = os.path.join(
            bioio_sample_data_folderpath, 'metadataXML.txt'
        )
        metadataXML = bioformats.Metadata().init_from_file(metadataXML_filepath)

        metadata_filepath = os.path.join(
            bioio_sample_data_folderpath, 'metadata.txt'
        )
        metadata = bioformats.OMEXML().init_from_file(
            metadata_filepath, rawFilePath
        )
        return metadata, metadataXML
        
    
    def readMetadata(self, raw_src_path, filename):
        if self.bioformats_backend == 'bioio':
            from cellacdc import acdc_bioio_bioformats as bioformats
        else:
            import javabridge
            from cellacdc import bioformat
            
        rawFilePath = os.path.join(raw_src_path, filename)

        self.progress.emit('Reading OME metadata...')

        try:
            if rawFilePath.endswith('.ome.tif'):
                metadata = load.OMEXML(rawFilePath)
                metadataXML = metadata.omexml_string
            else:
                metadata, metadataXML = self._readMetadataBioIO(rawFilePath)
            self.metadata = metadata
            self.metadataXML = metadataXML
        except Exception as e:
            traceback.print_exc()
            self.isCriticalError = True
            self.criticalError.emit(
                'reading image data or metadata',
                traceback.format_exc(), filename
            )
            return True

        try:
            LensNA = float(metadata.instrument().Objective.LensNA)
        except Exception as e:
            self.progress.emit(
                '===================================================')
            self.progress.emit(rawFilePath)
            self.progress.emit('WARNING: LensNA not found in metadata.')
            self.progress.emit(
                '===================================================')
            LensNA = 1.4

        if self.rawDataStruct != 2:
            try:
                SizeS = int(metadata.get_image_count())
            except Exception as e:
                self.progress.emit(
                    '===================================================')
                self.progress.emit(rawFilePath)
                self.progress.emit('WARNING: SizeS not found in metadata.')
                self.progress.emit(
                    '===================================================')
                SizeS = 1
        else:
            SizeS = self.SizeS

        try:
            SizeZ = int(metadata.image().Pixels.SizeZ)
        except Exception as e:
            self.progress.emit(
                '===================================================')
            self.progress.emit(rawFilePath)
            self.progress.emit('WARNING: SizeZ not found in metadata.')
            self.progress.emit(
                '===================================================')
            SizeZ = 1

        try:
            SizeT = int(metadata.image().Pixels.SizeT)
        except Exception as e:
            self.progress.emit(
                '===================================================')
            self.progress.emit(rawFilePath)
            self.progress.emit('WARNING: SizeT not found in metadata.')
            self.progress.emit(
                '===================================================')
            SizeT = 1

        try:
            Pixels = metadata.image().Pixels
            TimeIncrement = float(Pixels.node.get('TimeIncrement'))
        except Exception as e:
            self.progress.emit(
                '===================================================')
            self.progress.emit(rawFilePath)
            self.progress.emit('WARNING: TimeIncrement not found in metadata.')
            self.progress.emit(
                '===================================================')
            TimeIncrement = 1.0

        try:
            Pixels = metadata.image().Pixels
            TimeIncrementUnit = Pixels.node.get('TimeIncrementUnit')
            if TimeIncrementUnit is None:
                raise
        except Exception as e:
            self.progress.emit(
                '===================================================')
            self.progress.emit(rawFilePath)
            self.progress.emit('WARNING: TimeIncrementUnit not found in metadata.')
            self.progress.emit(
                '===================================================')
            TimeIncrementUnit = 's'

        try:
            SizeC = int(metadata.image().Pixels.SizeC)
        except Exception as e:
            self.progress.emit(
                '===================================================')
            self.progress.emit(rawFilePath)
            self.progress.emit('WARNING: SizeC not found in metadata.')
            self.progress.emit(
                '===================================================')
            SizeC = 1

        try:
            PhysicalSizeX = float(metadata.image().Pixels.PhysicalSizeX)
        except Exception as e:
            self.progress.emit(
                '===================================================')
            self.progress.emit(rawFilePath)
            self.progress.emit('WARNING: PhysicalSizeX not found in metadata.')
            self.progress.emit(
                '===================================================')
            PhysicalSizeX = 1.0

        try:
            PhysicalSizeY = float(metadata.image().Pixels.PhysicalSizeY)
        except Exception as e:
            self.progress.emit(
                '===================================================')
            self.progress.emit(rawFilePath)
            self.progress.emit('WARNING: PhysicalSizeY not found in metadata.')
            self.progress.emit(
                '===================================================')
            PhysicalSizeY = 1.0

        try:
            PhysicalSizeZ = float(metadata.image().Pixels.PhysicalSizeZ)
        except Exception as e:
            self.progress.emit(
                '===================================================')
            self.progress.emit(rawFilePath)
            self.progress.emit('WARNING: PhysicalSizeZ not found in metadata.')
            self.progress.emit(
                '===================================================')
            PhysicalSizeZ = 1.0

        try:
            Pixels = metadata.image().Pixels
            PhysicalSizeUnit = Pixels.node.get('PhysicalSizeXUnit')
            if PhysicalSizeUnit is None:
                raise
        except Exception as e:
            self.progress.emit(
                '===================================================')
            self.progress.emit(rawFilePath)
            self.progress.emit('WARNING: PhysicalSizeUnit not found in metadata.')
            self.progress.emit(
                '===================================================')
            PhysicalSizeUnit = 'μm'

        try:
            ImageName = metadata.image().Name
            if ImageName is None:
                raise
        except Exception as e:
            self.progress.emit(
                '===================================================')
            self.progress.emit(rawFilePath)
            self.progress.emit('WARNING: Image Name not found in metadata.')
            self.progress.emit(
                '===================================================')
            ImageName = ''


        if self.rawDataStruct != 2:
            try:
                chNames = ['']*SizeC
                for c in range(SizeC):
                    try:
                        chNames[c] = metadata.image().Pixels.Channel(c).Name
                    except Exception as e:
                        pass
            except Exception as e:
                self.progress.emit(
                    '===================================================')
                self.progress.emit(rawFilePath)
                self.progress.emit('WARNING: chNames not found in metadata.')
                self.progress.emit(
                    '===================================================')
                chNames = ['']*SizeC
        else:
            chNames = self.chNames
            SizeC = len(self.chNames)

        if self.rawDataStruct != 2:
            try:
                emWavelens = [500.0]*SizeC
                for c in range(SizeC):
                    try:
                        Channel = metadata.image().Pixels.Channel(c)
                        emWavelen = Channel.node.get("EmissionWavelength")
                        emWavelens[c] = float(emWavelen)
                    except Exception as e:
                        emWavelens[c] = 0.0
            except Exception as e:
                traceback.print_exc()
                self.progress.emit(
                    '===================================================')
                self.progress.emit(rawFilePath)
                self.progress.emit('WARNING: EmissionWavelength not found in metadata.')
                self.progress.emit(
                    '===================================================')
                emWavelens = [500.0]*SizeC
        else:
            emWavelens = [500.0]*SizeC

        if self.trustMetadataReader:
            self.LensNA = LensNA
            self.SizeT = SizeT
            self.SizeZ = SizeZ
            self.SizeC = SizeC
            self.SizeS = SizeS
            self.TimeIncrement = TimeIncrement
            self.PhysicalSizeX = PhysicalSizeX
            self.PhysicalSizeY = PhysicalSizeY
            self.PhysicalSizeZ = PhysicalSizeZ
            # self.chNames = chNames
            self.emWavelens = emWavelens
            return False

        sampleImgData = None
        while True:
            self.mutex.lock()
            if self.rawDataStruct != 2:
                sampleImgData = self.readSampleData(
                    rawFilePath, SizeC, SizeT, SizeZ
                )
            self.confirmMetadata.emit(
                filename, LensNA, SizeT, SizeZ, SizeC, SizeS,
                TimeIncrement, TimeIncrementUnit, PhysicalSizeX, PhysicalSizeY,
                PhysicalSizeZ, PhysicalSizeUnit, chNames, emWavelens, ImageName,
                rawFilePath, sampleImgData
            )
            self.waitCond.wait(self.mutex)
            self.mutex.unlock()

            if self.metadataWin.cancel:
                return True

            if not self.metadataWin.requestedReadingSampleImageDataAgain:
                break
            LensNA = self.metadataWin.LensNA
            SizeT = self.metadataWin.SizeT
            SizeZ = self.metadataWin.SizeZ
            SizeC = self.metadataWin.SizeC
            SizeS = self.metadataWin.SizeS
            TimeIncrement = self.metadataWin.TimeIncrement
            PhysicalSizeX = self.metadataWin.PhysicalSizeX
            PhysicalSizeY = self.metadataWin.PhysicalSizeY
            PhysicalSizeZ = self.metadataWin.PhysicalSizeZ
            chNames = self.metadataWin.chNames
            emWavelens = self.metadataWin.emWavelens

        if self.metadataWin.cancel:
            return True
        elif self.metadataWin.overWrite:
            self.overWriteMetadata = True
        elif self.metadataWin.trust:
            self.trustMetadataReader = True

        self.to_h5 = self.metadataWin.to_h5
        self.LensNA = self.metadataWin.LensNA
        self.SizeT = self.metadataWin.SizeT
        self.SizeZ = self.metadataWin.SizeZ
        self.SizeC = self.metadataWin.SizeC
        self.SizeS = self.metadataWin.SizeS
        self.TimeIncrement = self.metadataWin.TimeIncrement
        self.PhysicalSizeX = self.metadataWin.PhysicalSizeX
        self.PhysicalSizeY = self.metadataWin.PhysicalSizeY
        self.PhysicalSizeZ = self.metadataWin.PhysicalSizeZ
        self.selectedPos = self.metadataWin.selectedPos
        self.chNames = self.metadataWin.chNames
        self.timeRangeToSave = self.metadataWin.timeRangeToSave
        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, 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)

        in_file_pos_name = f'Position_{p+1}'
        savePos = (
            '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_{pos_n}')
        images_path = os.path.join(pos_path, 'Images')

        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, pos_n, p_idx=p_idx,
        )
        
        return False

    def _saveDataPythonBioformats(
            self, bioformats, rawFilePath, series, images_path, filenameNOext, 
            s0p, idxs
        ):
        SizeZ = self.getSizeZ(rawFilePath)
        with bioformats.ImageReader(rawFilePath) as reader:
            iter = enumerate(zip(self.chNames, self.saveChannels))
            for c, (chName, saveCh) in iter:
                self.progressPbar.emit(1)
                if not saveCh:
                    continue

                self.progress.emit(
                    f'  Saving channel {c+1}/{len(self.chNames)} ({chName})'
                )
                self.saveImgDataChannel(
                    reader, series, images_path, filenameNOext, s0p,
                    chName, c, idxs, SizeZ
                )
    
    def _saveDataPythonBioformatsSingleChannel(
            self, bioformats, rawFilePath, series, images_path, filenameNOext, 
            s0p, idxs, chName, c_idx
        ):
        SizeZ = self.getSizeZ(rawFilePath)
        with bioformats.ImageReader(rawFilePath) as reader:
            self.progress.emit(
                f'  Saving channel {c_idx+1}/{len(self.chNames)} ({chName})'
            )
            imgData_ch = []
            self.saveImgDataChannel(
                reader, series, images_path, filenameNOext, s0p,
                chName, 0, idxs, SizeZ
            )
    
    def removeInvalidCharacters(self, chName_in):
        # Remove invalid charachters
        chName = "".join(
            c if c.isalnum() or c=='_' or c=='' else '_' for c in chName_in
        )
        trim_ = chName.endswith('_')
        while trim_:
            chName = chName[:-1]
            trim_ = chName.endswith('_')

    def getFilename(
            self, filenameNOext, s0p, appendTxt, series, ext, 
            return_basename=False
        ):
        # Do not allow dots in the filename since it breaks stuff here and there
        filenameNOext = filenameNOext.replace('.', '_')
        if self.addImageName:
            try:
                ImageName = self.metadata.image(index=series).Name
                if not isinstance(ImageName, str):
                    raise
            except Exception as e:
                ImageName = ''
            self.removeInvalidCharacters(ImageName)
            basename = f'{filenameNOext}_{ImageName}_s{s0p}_'
            filename = f'{basename}{appendTxt}{ext}'
        else:
            basename = f'{filenameNOext}_s{s0p}_'
            filename = f'{basename}{appendTxt}{ext}'
        if return_basename:
            return filename, basename
        else:
            return filename
    
    def buildIndexes(self, SizeC, SizeT, SizeZ):
        SizesCTZ = {'c': SizeC, 't': SizeT, 'z': SizeZ}
        idxs = {}
        k_key, i_key, j_key = 'ztc'
        idx = 0

        for k in range(SizesCTZ[k_key]):
            for i in range(SizesCTZ[i_key]):
                for j in range(SizesCTZ[j_key]):
                    idxs[(k,i,j)] = idx
                    idx += 1
        return idxs

    def getIndex(self, idxs, dimsIdx):
        dims = tuple([dimsIdx.get(v, 0) for v in 'ztc'])
        return idxs[dims]
            
    def saveImgDataChannel(
            self, reader, series, images_path, filenameNOext, s0p, chName,
            ch_idx, idxs, SizeZ
        ):
        savedSizeT = self.timeRangeToSave[1] - self.timeRangeToSave[0] + 1
        if self.to_h5:
            filename = self.getFilename(
                filenameNOext, s0p, chName, series, '.h5'
            )
            tempDir = tempfile.mkdtemp()
            tempFilepath = os.path.join(tempDir, filename)
            print('==========================================================')
            print(f'.h5 tempfile: "{tempFilepath}"')
            print('==========================================================')
            h5f = h5py.File(tempFilepath, 'w')
            # Read SizeX and SizeY from the shape of one image
            imgData = reader.read(
                c=ch_idx, z=0, t=0, series=series, rescale=False
            )
            shape = (savedSizeT, SizeZ, *imgData.shape)
            chunks = (1,1,*imgData.shape)
            imgData_ch = h5f.create_dataset(
                'data', shape, dtype=imgData.dtype,
                chunks=chunks, shuffle=False
            )
        else:
            filename = self.getFilename(
                filenameNOext, s0p, chName, series, '.tif'
            )
            imgData_ch = []

        framesRange = range(
            self.timeRangeToSave[0]-1, 
            self.timeRangeToSave[1]
        )
        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 out_t, t in enumerate(framesRange):
            imgData_z = []
            dimsIdx['t'] = t
            for z in range(SizeZ):
                pbar.set_description(
                    f'Reading image (z {z+1}/{SizeZ}, t {out_t+1}/{numFrames})'
                )
                dimsIdx['z'] = z
                if self.rawDataStruct != 2:
                    idx = self.getIndex(idxs, dimsIdx)
                else:
                    idx = None
                imgData = reader.read(
                    c=ch_idx, z=z, t=t, series=series, rescale=False,
                    index=idx
                )
                if self.to_h5:
                    imgData_ch[out_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, 
                SizeT=savedSizeT,
                SizeZ=self.SizeZ,
                TimeIncrement=self.TimeIncrement,
                PhysicalSizeZ=self.PhysicalSizeZ,
                PhysicalSizeY=self.PhysicalSizeY,
                PhysicalSizeX=self.PhysicalSizeX,
            )
        else:
            h5f.close()
            shutil.move(tempFilepath, filePath)
            shutil.rmtree(tempDir)

    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(pos_n).zfill(self.numPosDigits)
        self.progress.emit(
            f'Position {pos_n}/{self.numPos}: saving data to {images_path}...'
        )
        filenameNOext, ext = os.path.splitext(filename)

        metadataXML_path = os.path.join(
            images_path,
            self.getFilename(filenameNOext, s0p, 'metadataXML', series, '.txt')
        )
        with open(metadataXML_path, 'w', encoding="utf-8") as txt:
            txt.write(str(self.metadataXML))

        metadata_filename, basename = self.getFilename(
            filenameNOext, s0p, 'metadata', series, '.csv', 
            return_basename=True
        )
        metadata_csv_path = os.path.join(images_path, metadata_filename)
        savedSizeT = (
            self.timeRangeToSave[1] - self.timeRangeToSave[0] + 1
        )
        df = pd.DataFrame({
            'LensNA': self.LensNA,
            'SizeT': savedSizeT,
            'SizeZ': self.SizeZ,
            'TimeIncrement': self.TimeIncrement,
            'PhysicalSizeZ': self.PhysicalSizeZ,
            'PhysicalSizeY': self.PhysicalSizeY,
            'PhysicalSizeX': self.PhysicalSizeX,
            'basename': basename
        }, index=['values']).T
        df.index.name = 'Description'

        ch_metadata = [
            chName for c, chName in enumerate(self.chNames)
            if self.saveChannels[c]
        ]
        description = [
            f'channel_{c}_name' for c in range(self.SizeC) 
            if self.saveChannels[c]
        ]
        ch_metadata.extend([
            wavelen for c, wavelen in enumerate(self.emWavelens)
            if self.saveChannels[c]
        ])
        description.extend([
            f'channel_{c}_emWavelen' for c in range(self.SizeC)
            if self.saveChannels[c]
        ])

        df_channelNames = pd.DataFrame({
            'Description': description,
            'values': ch_metadata
        }).set_index('Description')

        df = pd.concat([df, df_channelNames])

        if os.path.exists(metadata_csv_path):
            # Keep channel names already existing and not saved now
            existing_df = pd.read_csv(metadata_csv_path).set_index('Description')
            for c, chName in enumerate(self.chNames):
                if self.saveChannels[c]:
                    continue
                chName_idx = f'channel_{c}_name'
                chWavelen_idx = f'channel_{c}_emWavelen'
                try:
                    existing_chName = existing_df.at[chName_idx, 'values']
                    df.at[chName_idx, 'values'] = existing_chName
                except Exception as e:
                    traceback.print_exc()
                    pass
                
                try:
                    existing_chWavelen = existing_df.at[chWavelen_idx, 'values']
                    df.at[chWavelen_idx, 'values'] = existing_chWavelen
                except Exception as e:
                    traceback.print_exc()
                    pass

        df.to_csv(metadata_csv_path)

        idxs = self.buildIndexes(self.SizeC, self.SizeT, self.SizeZ)
        if self.rawDataStruct != 2:     
            if self.bioformats_backend == 'bioio':
                import subprocess
                from . import _process
                
                save_data_py_filepath = os.path.join(
                    os.path.dirname(bioformats.__file__), '_save_data.py'
                )
                zyx_physical_sizes = (
                    self.PhysicalSizeZ, self.PhysicalSizeY, self.PhysicalSizeX
                )
                zyx_physical_sizes = " ".join(
                    [str(val) for val in zyx_physical_sizes]
                )
                uuid4 = uuid.uuid4()
                command = (
                    f'{sys.executable}, {save_data_py_filepath}, '
                    f'-f, {rawFilePath}, '
                    f'-d, {" ".join([str(val) for val in self.saveChannels])}, '
                    f'-c, {" ".join(self.chNames)}, '
                    f'-s, {series}, '
                    f'-i, {images_path}, '
                    f'-p, {filenameNOext}, '
                    f'-pos, {s0p}, '
                    f'-t, {self.SizeT}, '
                    f'-z, {self.getSizeZ(rawFilePath)}, '
                    f'-time_increment, {self.TimeIncrement}, '
                    f'-zyx, {zyx_physical_sizes}, '
                    f'-r, {" ".join([str(val) for val in self.timeRangeToSave])}, '
                    f'-uuid, {uuid4}'
                )
                if self.to_h5:
                    command = f'{command}, -to_h5'
                
                if not self.lazy_load:
                    command = f'{command}, -a'
                    
                args = [sys.executable, _process.__file__, '-c', command]
                subprocess.run(args)
                
                bioformats._utils.check_raise_exception(uuid4)
                
                self.progressPbar.emit(len(self.chNames))
            else:  
                self._saveDataPythonBioformats(
                    bioformats, rawFilePath, series, images_path, 
                    filenameNOext, s0p, idxs
                )

        elif self.rawDataStruct == 2:
            iter = enumerate(zip(self.chNames, self.saveChannels))
            pos_rawFilenames = []
            basename = filename
            for c, (chName, saveCh) in iter:
                self.progressPbar.emit(1)
                if not saveCh:
                    continue

                rawFilename = f'{basename}{pos_n}_{chName}'
                pos_rawFilenames.append(rawFilename)
                raw_src_path = os.path.dirname(rawFilePath)
                rawFilePath = [
                    os.path.join(raw_src_path, f)
                    for f in myutils.listdir(raw_src_path)
                    if f.find(rawFilename)!=-1
                ][0]

                if self.bioformats_backend == 'bioio':
                    import subprocess
                    from . import _process
                    
                    save_data_py_filepath = os.path.join(
                        os.path.dirname(bioformats.__file__), 
                        '_save_data_single_channel.py'
                    )
                    zyx_physical_sizes = (
                        self.PhysicalSizeZ, 
                        self.PhysicalSizeY, 
                        self.PhysicalSizeX
                    )
                    zyx_physical_sizes = " ".join(
                        [str(val) for val in zyx_physical_sizes]
                    )
                    uuid4 = uuid.uuid4()
                    command = (
                        f'{sys.executable}, {save_data_py_filepath}, '
                        f'-f, {rawFilePath}, '
                        f'-d, {" ".join([str(val) for val in self.saveChannels])}, '
                        f'-c, {chName}, '
                        f'-ch_idx, {c}, '
                        f'-s, {series}, '
                        f'-i, {images_path}, '
                        f'-p, {filenameNOext}, '
                        f'-pos, {s0p}, '
                        f'-t, {self.SizeT}, '
                        f'-z, {self.getSizeZ(rawFilePath)}, '
                        f'-time_increment, {self.TimeIncrement}, '
                        f'-zyx, {zyx_physical_sizes}, '
                        f'-r, {" ".join([str(val) for val in self.timeRangeToSave])}, '
                        f'-uuid, {uuid4}'
                    )
                    if self.to_h5:
                        command = f'{command}, -to_h5'
                    
                    args = [sys.executable, _process.__file__, '-c', command]
                    subprocess.run(args)
                    
                    bioformats._utils.check_raise_exception(uuid4)
                    
                    self.progressPbar.emit(1)
                else:  
                    self._saveDataPythonBioformatsSingleChannel(
                        bioformats, rawFilePath, series, images_path, 
                        filenameNOext, s0p, idxs, chName, c
                    )

            if self.moveOtherFiles or self.copyOtherFiles:
                # Move the other files present in the folder if they
                # contain "otherFilename" in the name
                otherFilename = f'{basename}{pos_n}'
                rawFilePath = set()
                for f in myutils.listdir(raw_src_path):
                    notRawFile = all(
                        [f.find(rawName)==-1 for rawName in pos_rawFilenames]
                    )
                    isPosFile = f.find(otherFilename)!=-1
                    if isPosFile and notRawFile:
                        rawFilePath.add(os.path.join(raw_src_path, f))

                for file in rawFilePath:
                    # Determine basename, posNum and chName to build
                    # filename as "basename_s01_chName.ext"
                    _filename = os.path.basename(file)
                    m = re.findall(fr'{basename}(\d+)_(.+)', _filename)
                    if not m or len(m[0])!=2:
                        dst = os.path.join(images_path, _filename)
                    else:
                        _chNameWithExt = m[0][1]
                        _filename = f'{filenameNOext}_s{s0p}_{_chNameWithExt}'
                        dst = os.path.join(images_path, _filename)
                    if self.moveOtherFiles:
                        try:
                            shutil.move(file, dst)
                        except Exception as e:
                            self.progress.emit(e)
                    elif self.copyOtherFiles:
                        try:
                            shutil.copy(file, dst)
                        except Exception as e:
                            self.progress.emit(e)

    @worker_exception_handler
    def run(self):
        raw_src_path = self.raw_src_path
        exp_dst_path = self.exp_dst_path
        
        if self.bioformats_backend == 'python-bioformats':
            import javabridge
            from cellacdc import bioformats
            javabridge.start_vm(class_path=bioformats.JARS, run_headless=True)
            self.progress.emit('Java VM running.')
            
        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:
                    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 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 cancel:
                        self.cancelled = True
                        break

            elif self.rawDataStruct == 1:
                if not self.overWriteMetadata:
                    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)
                cancel = self.saveToPosFolder(
                    p, raw_src_path, exp_dst_path, filename, 0, pos_n
                )
                if cancel:
                    self.cancelled = True
                    break

            else:
                break

            # Move files to raw_microscopy_files folder
            self.move_to_raw_microscopy_files_folder(
                self.raw_src_path, filename    
            )

        if self.rawDataStruct == 2:
            filename = self.rawFilenames[0]
            if not self.overWriteMetadata:
                abort = self.readMetadata(raw_src_path, filename)
                if abort:
                    self.cancelled = True
                    if self.bioformats_backend == 'python-bioformats':
                        javabridge.kill_vm()
                    self.finished.emit()
                    return
      
            self.numPos = len(self.posNums)
            self.numPosDigits = len(str(self.numPos))
            self.initPbar.emit(self.numPos*self.SizeC)
            for p_idx, pos in enumerate(self.posNums):
                p = pos-1
                abort = self.saveToPosFolder(
                    p, raw_src_path, exp_dst_path, self.basename, 0,
                    pos, p_idx=p_idx
                )
                if abort:
                    self.cancelled = True
                    break

            for filename in self.rawFilenames:
                self.move_to_raw_microscopy_files_folder(
                    self.raw_src_path, filename    
                )

        if self.bioformats_backend == 'python-bioformats':
            javabridge.kill_vm()
        self.finished.emit()
    
    def move_to_raw_microscopy_files_folder(self, raw_src_path, filename):
        # Move files to raw_microscopy_files folder
        foldername = os.path.basename(raw_src_path)
        
        if self.cancelled:
            return
        
        if foldername == 'raw_microscopy_files':
            return
        
        if not self.move_raw_microscopy_files:
            return
        
        rawFilePath = os.path.join(self.raw_src_path, filename)
        raw_path = os.path.join(raw_src_path, 'raw_microscopy_files')
        if not os.path.exists(raw_path):
            os.mkdir(raw_path)
        dst = os.path.join(raw_path, filename)
        try:
            shutil.move(rawFilePath, dst)
        except PermissionError as e:
            self.progress.emit(e)

class createDataStructWin(QMainWindow):
    def __init__(
            self, parent=None, allowExit=False, buttonToRestore=None, 
            mainWin=None, start_JVM=True, version=None
        ):
        super().__init__(parent)

        self._version = version

        logger, logs_path, log_path, log_filename = myutils.setupLogger(
            module='dataStruct'
        )
        self.logger = logger
        self.log_path = log_path
        self.log_filename = log_filename
        self.logs_path = logs_path

        if self._version is not None:
            logger.info(f'Initializing Data structure module v{self._version}...')
        else:
            logger.info(f'Initializing Data structure module...')

        self.start_JVM = start_JVM
        self.allowExit = allowExit
        self.processFinished = False
        self.buttonToRestore = buttonToRestore
        self.mainWin = mainWin
        self.metadataDialogIsOpen = False
        self.df_settings = pd.read_csv(
            settings_csv_path, index_col='setting'
        )

        version = myutils.read_version()
        self.setWindowTitle(f"Cell-ACDC v{version} - Data structure")
        self.setWindowIcon(QtGui.QIcon(":icon.ico"))

        mainContainer = QWidget()
        self.setCentralWidget(mainContainer)

        mainLayout = QVBoxLayout()

        label = QLabel(
            'Creating data structure from raw microscopy file(s)...'
        )

        label.setStyleSheet("padding:5px 10px 10px 10px;")
        label.setAlignment(Qt.AlignCenter)
        font = QtGui.QFont()
        font.setPixelSize(14)
        font.setBold(True)
        label.setFont(font)
        mainLayout.addWidget(label)

        informativeHtml = (
        """
        <html>
        <head>
        <title></title>
        <style type="text/css">
        blockquote {
         margin: 5;
         padding: 0;
        }
        </style>
        </head>
        <body>
        <blockquote>
        <p style="font-size:14px; line-height:1.2">
            This <b>wizard</b> will guide you through the <b>creation of the required
            data structure</b><br> starting from the raw microscopy file(s)
        </p>
        <p style="font-size:12px; line-height:1.2">
            Follow the instructions in the pop-up windows.<br>
            Note that pop-ups might be minimized or behind other open windows.<br>
            Keep an eye on the terminal/console in case of any error.
        </p>
        <p style="font-size:12px; line-height:1.2">
            Progress will be displayed below.
        </p>
        </blockquote>
        </body>
        </html>
        """
        )

        informativeText = QLabel(self)

        informativeText.setTextFormat(Qt.RichText)
        informativeText.setText(informativeHtml)
        informativeText.setStyleSheet("padding:5px 0px 10px 0px;")
        mainLayout.addWidget(informativeText)

        self.logWin = QPlainTextEdit()
        self.logWin.setReadOnly(True)
        mainLayout.addWidget(self.logWin)

        abortButton = widgets.cancelPushButton(' Stop processs ')
        abortButton.clicked.connect(self.close)
        
        buttonsLayout = QHBoxLayout()
        buttonsLayout.addStretch(1)
        buttonsLayout.addWidget(abortButton)
        
        mainLayout.addLayout(buttonsLayout)

        mainLayout.setContentsMargins(20, 0, 20, 20)
        mainContainer.setLayout(mainLayout)

        self.mainLayout = mainLayout
        
        try:
            import javabridge
            from cellacdc import bioformats
            self.bioformats_backend = 'python-bioformats'
        except Exception as e:
            pass
        
        self.bioformats_backend = 'bioio'
        success = self.checkInstallBioIO(parent)
        if success:
            return
        
        self.bioformats_backend = 'python-bioformats'
        self.checkInstallPythonBioformats(parent)

    def checkInstallBioIO(self, parent):
        myutils.check_install_package(
            'BioIO', 
            import_pkg_name='bioio', 
            pypi_name='bioio', 
            min_version='0.1.0',
            parent=parent,
        )
        
        return True
    
    def checkInstallPythonBioformats(self, parent):
        from . import is_win, is_mac
        
        if not is_win and not is_mac:
            if parent is None:
                self.show()
            self.criticalOSnotSupported()
            self.close()
            raise OSError('This module is supported ONLY on Windows 10/10 and macOS')

        success, jar_dst_path = myutils.download_bioformats_jar(
            qparent=self, logger_info=self.logger.info, 
            logger_exception=self.logger.exception
        )
        self.logger.info('Checking if Java is installed...')
        myutils.check_upgrade_javabridge()
        try:
            import javabridge
        except ModuleNotFoundError as e:
            print('======================================')
            traceback_str = traceback.format_exc()
            self.logger.exception(traceback_str)
            print('======================================')
            cancel = myutils.install_javabridge_help(parent=self)
            if cancel:
                raise ModuleNotFoundError(
                    'User cancelled javabridge installation'
                )

            isGitInstalled = myutils.check_git_installed(parent=self)
            if not isGitInstalled:
                raise ModuleNotFoundError(
                    'Git is not installed. Install from '
                    'https://git-scm.com/book/en/v2/Getting-Started-Installing-Git'
                )

            try:
                jre_path, jdk_path, url = myutils.download_java()
            except Exception as e:
                print('======================================')
                traceback_str = traceback.format_exc()
                self.logger.exception(traceback_str)
                print('======================================')
                java_info = myutils.get_java_url()
                url, file_size, os_foldername, unzipped_foldername = java_info
                acdc_java_path, _ = myutils.get_acdc_java_path()
                java_href = f'<a href="{url}">this</a>'
                s = (
                    f'1. Download {java_href} .zip file and unzip it.<br>'
                    '2. Inside the unzipped folder there should be a folder called '
                    f'"{unzipped_foldername}". Open that folder and copy its '
                    'content to the following path:<br><br>'
                    f'{os.path.join(acdc_java_path, os_foldername)}'
                )
                note = (
                    '<br><br><i>NOTE: if clicking on the link above does not work '
                    'copy the link below and paste it into the browser</i><br><br>'
                    f'{url}'
                )
                msg = widgets.myMessageBox(wrapText=False)
                txt = html_utils.paragraph(f"""
                    This module requires Java to work.<br><br>
                    Follow the instructions below and then try
                    launching this module again.<br><br>
                    {s}{note}
                """)
                msg.warning(self, 'Java not found', txt)
                
                err = s.replace('<br>', ' ')
                err = err.replace('<a href=', '')
                err = err.replace('>this</a>', '')
                raise ModuleNotFoundError(
                    'Installation of module "javabridge" failed. '
                    f'{err}'
                )

            if not is_win:
                cancel = myutils.install_java()
                if cancel:
                    raise ModuleNotFoundError(
                        'User cancelled Java installation'
                    )
                    return

            myutils.install_javabridge()

        except Exception as e:
            print('======================================')
            traceback_str = traceback.format_exc()
            self.logger.exception(traceback_str)
            print('======================================')
            cancel = myutils.install_java()
            if cancel:
                raise ModuleNotFoundError(
                    'User cancelled Java installation'
                )
                return
            myutils.install_javabridge(
                force_compile=True, attempt_uninstall_first=True
            )

        try:
            import javabridge
            from cellacdc import bioformats
        except Exception as e:
            print('===============================================================')
            traceback_str = traceback.format_exc()
            self.logger.exception(traceback_str)
            error_msg = (
                'Error while importing "javabridge" and "bioformats".\n\n'
                f'Please report error here: {issues_url}\n'
            )
            print(error_msg)
            print('===============================================================')

            title = 'Import javabridge/bioformats error'
            txt = error_msg.replace('\n', '<br>')
            txt = txt.replace(
                issues_url, html_utils.href_tag(issues_url, issues_url)
            )
            txt = html_utils.paragraph(txt)
            msg = widgets.myMessageBox(wrapText=False)
            msg.critical(
                self, title, txt, detailsText=traceback_str
            )
            raise ModuleNotFoundError(
                'Error when importing javabridge. See above for details.'
            )

    def criticalOSnotSupported(self):
        from cellacdc import widgets
        if self.parent() is None:
            msg = widgets.myMessageBox(self)
        else:
            msg = widgets.myMessageBox(self.parent())
        msg.setIcon(iconName='SP_MessageBoxCritical')
        msg.setWindowTitle('Not a supported OS')
        msg.addButton('    Ok     ')
        err_msg = (f"""
        <p style="font-size:12px">
        Unfortunately, the module "0. Create data structure from microscopy file(s)"
        is functional <b>only on Windows 10/11 and macOS</b>.<br><br>
        We are working on extending support to other Operating Systems.<br><br>
        Please open an issue on our
        <a href="https://github.com/SchmollerLab/Cell_ACDC/issues">
            GitHub page
        </a> to request this feature.<br>
        Note that <b>all other modules are functional</b> on
        macOS, Linux and Windows.<br><br>
        In the meantine, to create the required data structure,
        you can use an <b>automated Fiji macro</b> that you can download from
        <a href="https://github.com/SchmollerLab/Cell_ACDC/tree/main/FijiMacros">
            here
        </a>.<br><br>
        Check out the <b>instructions</b> on how to use the macros
        in the section  <b>"Create data structure using Fiji Macros"</b> of the
        user manual.<br><br>
        You can download the user manual from
        <a href="https://github.com/SchmollerLab/Cell_ACDC/blob/main/UserManual/Cell-ACDC_User_Manual.pdf">
            here
        </a>.
        </p>
        """)
        msg.addText(err_msg)
        # msg_label = msg.findChild(QLabel, "qt_msgbox_label")
        # msg_label.setOpenExternalLinks(False)
        # msg_label.linkActivated.connect(self.on_linkActivated)
        msg.exec_()


    def on_linkActivated(self, link):
        if link == 'manual':
            systems = {
                'nt': os.startfile,
                'posix': lambda foldername: os.system('xdg-open "%s"' % foldername),
                'os2': lambda foldername: os.system('open "%s"' % foldername)
                 }

            main_path = pathlib.Path(__file__).resolve().parents[1]
            userManual_path = main_path / 'UserManual'
            systems.get(os.name, os.startfile)(userManual_path)
        elif link == 'fiji':
            systems = {
                'nt': os.startfile,
                'posix': lambda foldername: os.system('xdg-open "%s"' % foldername),
                'os2': lambda foldername: os.system('open "%s"' % foldername)
                 }

            main_path = pathlib.Path(__file__).resolve().parents[1]
            fijiMacros_path = main_path / 'FijiMacros'
            systems.get(os.name, os.startfile)(fijiMacros_path)


    def getMostRecentPath(self):
        if os.path.exists(recentPaths_path):
            df = pd.read_csv(recentPaths_path, index_col='index')
            if 'opened_last_on' in df.columns:
                df = df.sort_values('opened_last_on', ascending=False)
            self.MostRecentPath = df.iloc[0]['path']
            if not isinstance(self.MostRecentPath, str):
                self.MostRecentPath = ''
        else:
            self.MostRecentPath = ''

    def addToRecentPaths(self, raw_src_path):
        if not os.path.exists(raw_src_path):
            return
        if os.path.exists(recentPaths_path):
            df = pd.read_csv(recentPaths_path, index_col='index')
            recentPaths = df['path'].to_list()
            if 'opened_last_on' in df.columns:
                openedOn = df['opened_last_on'].to_list()
            else:
                openedOn = [np.nan]*len(recentPaths)
            if raw_src_path in recentPaths:
                pop_idx = recentPaths.index(raw_src_path)
                recentPaths.pop(pop_idx)
                openedOn.pop(pop_idx)
            recentPaths.insert(0, raw_src_path)
            openedOn.insert(0, datetime.datetime.now())
            # Keep max 20 recent paths
            if len(recentPaths) > 20:
                recentPaths.pop(-1)
                openedOn.pop(-1)
        else:
            recentPaths = [raw_src_path]
            openedOn = [datetime.datetime.now()]
        df = pd.DataFrame({'path': recentPaths,
                           'opened_last_on': pd.Series(openedOn,
                                                       dtype='datetime64[ns]')})
        df.index.name = 'index'
        df.to_csv(recentPaths_path)

    @exception_handler
    def main(self):
        self.log('Asking how raw data is structured...')
        rawDataStruct, abort = self.askRawDataStruct()
        if abort:
            self.close()
            return

        self.rawDataStruct = rawDataStruct

        if rawDataStruct == 3:
            self.instructManualStruct()
            self.close()
            return

        self.log('Instructing to move raw data...')
        proceed = self.instructMoveRawFiles()
        if not proceed:
            self.close()
            return

        self.log(
            'Asking to select the folder that contains the microscopy files...'
        )
        self.getMostRecentPath()
        raw_src_path = QFileDialog.getExistingDirectory(
            self, 'Select folder containing the microscopy files', 
            self.MostRecentPath
        )
        self.addToRecentPaths(raw_src_path)

        if raw_src_path == '':
            self.close()
            return
        
        self.log(f'Selected folder: "{raw_src_path}"')
        
        self.log(
            'Checking file format of loaded files...'
        )
        rawFilenames = self.checkFileFormat(raw_src_path)
        if not rawFilenames:
            self.close()
            return
        
        self.log(
            'Checking file names of loaded files...'
        )
        proceed, rawFilenames = self.checkFileNames(rawFilenames, raw_src_path)
        if not proceed:
            self.close()
            return

        if rawDataStruct == 2:
            proceed = self.attemptSeparateMultiChannel(rawFilenames)
            if not proceed:
                self.close()
                return

        self.log(
            'Asking in which folder to save the images files...'
        )
        exp_dst_path = QFileDialog.getExistingDirectory(
            self, 'Select the folder in which to save the images files',
            raw_src_path
        )
        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:
            self.close()
            return
        
        if not loadEntirePosIntoRam:
            self._installLazyLoadModules()
        
        self.loadEntirePosIntoRam = loadEntirePosIntoRam

        self.addToRecentPaths(exp_dst_path)

        self.addPbar()
        
        self.initBioIO(raw_src_path, rawFilenames)
        
        move_raw_microscopy_files = False
        if exp_dst_path == raw_src_path:
            move_raw_microscopy_files, cancel = self.askMoveRawMicroscopyFiles()
            if cancel:
                self.close()
                return

        # Set up separate thread for bioFormatsWorker class
        self.mutex = QMutex()
        self.waitCond = QWaitCondition()
        self.thread = QThread()
        self.worker = bioFormatsWorker(
            raw_src_path, rawFilenames, exp_dst_path,
            self.mutex, self.waitCond, rawDataStruct, 
            self.bioformats_backend, 
            lazy_load=not self.loadEntirePosIntoRam,
            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
            self.worker.SizeS = self.SizeS
            self.worker.posNums = self.posNums
            self.worker.chNames = self.chNames
            self.worker.moveOtherFiles = self.moveOtherFiles
            self.worker.copyOtherFiles = self.copyOtherFiles

        self.worker.moveToThread(self.thread)

        self.worker.finished.connect(self.thread.quit)
        self.worker.finished.connect(self.worker.deleteLater)
        self.worker.finished.connect(self.taskEnded)
        self.thread.finished.connect(self.thread.deleteLater)
        self.worker.initPbar.connect(self.setPbarMax)
        self.worker.progressPbar.connect(self.updatePbar)
        self.worker.progress.connect(self.log)
        self.worker.critical.connect(self.workerCritical)
        self.worker.criticalError.connect(self.criticalBioFormats)
        self.worker.confirmMetadata.connect(self.askConfirmMetadata)
        self.thread.started.connect(self.worker.run)

        self.thread.start()
    
    def askMoveRawMicroscopyFiles(self):
        msg = widgets.myMessageBox(wrapText=False)
        txt = html_utils.paragraph(f"""
            At the end of the conversion process, do you want that Cell-ACDC  
            <b>moves the raw microscopy files</b> <br>
            to a sub-folder called <code>raw_microscopy_files</code>?
        """)
        _, doNotMoveButton, moveButton = msg.warning(
            self, 'Too many objects', txt,
            buttonsTexts=(
                'Cancel', 'No, do not move the files', 'Yes, move the files'        
            )
        )
        return msg.clickedButton == moveButton, msg.cancel
    
    def _installLazyLoadModules(self):
        myutils.check_install_package(
            'zarr',
            installer='pip', 
            is_cli=False,
            parent=self,
        )
    
    @exception_handler
    def workerCritical(self, error):
        raise error

    def instructManualStruct(self):
        manual_url = 'https://github.com/SchmollerLab/Cell_ACDC/blob/main/UserManual/Cell-ACDC_User_Manual.pdf'
        txt = (
        f"""
        <p style="font-size:11px;">
        If you would like to add compatibility with your raw microscopy files,<br>
        you can request a new feature <a href=\"{issues_url}">here</a>.<br><br>
        Please label the issue as "enhancement" and provide as many details as
        possible about how your raw microscopy files are structured.<br><br>
        A second option is to create the required data structure manually.
        Please have a look at the instruction on the
        <a href=\"{manual_url}">User manual</a> at the section called
        "Manually create data structure from microscopy file(s)"
        </p>
        """
        )
        msg = QMessageBox(self)
        msg.setWindowTitle('Data structure not available')
        msg.setIcon(msg.Information)
        msg.setText(txt)
        msg.setTextInteractionFlags(Qt.TextBrowserInteraction)
        msg.setTextFormat(Qt.RichText)
        msg.exec_()

    def initBioIO(self, raw_src_path, raw_filenames):
        if self.bioformats_backend == 'python-bioformats':
            return
        
        from cellacdc import acdc_bioio_bioformats as bioformats
        raw_filepath = os.path.join(raw_src_path, raw_filenames[0])
        
        bioformats.install.install_reader_dependencies(
            raw_filepath, 
            exception=Exception(
                'Failed installing reader dependencies from the GUI, '
                'trying from terminal...'
            ),
            qparent=self
        )
        
        import subprocess
        from . import _process
        
        init_reader_py_filepath = os.path.join(
            os.path.dirname(bioformats.__file__), '_init_reader.py'
        )
        uuid4 = uuid.uuid4()
        command = (
            f'{sys.executable}, {init_reader_py_filepath}, '
            f'-f, {raw_filepath}, '
            f'-uuid, {uuid4}'
        )
        
        args = [sys.executable, _process.__file__, '-c', command]
        subprocess.run(args)
        
        bioformats._utils.check_raise_exception(uuid4)
    
    def addPbar(self):
        self.QPbar = widgets.ProgressBar(self)
        self.QPbar.setValue(0)
        self.mainLayout.insertWidget(3, self.QPbar)

    def updatePbar(self, deltaPbar):
        self.QPbar.setValue(self.QPbar.value()+deltaPbar)

    def setPbarMax(self, max):
        self.QPbar.setMaximum(max)

    def taskEnded(self):
        if self.worker.cancelled and not self.worker.isCriticalError:
            msg = widgets.myMessageBox(wrapText=False)
            txt = html_utils.paragraph(
                'Conversion task cancelled.'
            )
            msg.critical(
               self, 'Conversion task cancelled.', txt
            )
            self.close()
        elif not self.worker.cancelled:
            msg = widgets.myMessageBox(wrapText=False)
            txt = html_utils.paragraph(
                'Conversion task ended.<br><br>'
                'Files saved to'
            )
            abort = msg.information(
               self, 'Conversion task ended.', txt,
               commands=(self.worker.exp_dst_path,),
               path_to_browse=self.worker.exp_dst_path
            )
            self.close()

    def log(self, text):
        self.logWin.appendPlainText(text)
        self.logger.info(text)

    def askRawDataStruct(self):
        infoText =  html_utils.paragraph(
            'Select how you have your <b>raw microscopy files arranged</b>'
        )
        win = apps.QDialogCombobox(
            'Raw data structure',
            [
                'Single microscopy file with multiple positions',
                'One or more microscopy files, one for each position',
                'One or more microscopy files, one for each channel',
                'NONE of the above'
            ],
            infoText, CbLabel='', parent=self
        )
        win.exec_()
        if not win.cancel:
            self.log(f'Selected files arrangement: "{win.selectedItemText}"')
        return win.selectedItemIdx, win.cancel

    def instructMoveRawFiles(self):
        msg = widgets.myMessageBox(showCentered=False, wrapText=False)
        tip_admon = html_utils.to_admonition(
            'If you have a single gray-scale TIFF file, '
            'placing into a folder called <code>Images</code> will be enough.',
            admonition_type='tip',
        )
        txt = html_utils.paragraph(f"""
            Put all of the raw microscopy files from the <b>same experiment</b>
            into an <b>empty folder</b> before closing this dialogue.<br><br>

            Note that there should be <b>no other files</b> in this folder.<br><br>
            
            Microscopy files are those files that are typically generated 
            by the microscope, for example '.czi' (Zeiss), '.nd2' (Nikon), 
            '.lif' (Leica), etc.<br><br>
            {tip_admon}
        """
        )
        msg.information(
            self, 'Microscopy files location', txt, 
            buttonsTexts=('Cancel', widgets.okPushButton('Done'))
        )
        if msg.cancel:
            return False
        else:
            return True

    def askHowToLoadData(self):
        msg = widgets.myMessageBox(wrapText=False)
        txt = html_utils.paragraph(
            """
            Do you want to load the entire position into RAM at once?
            <br><br>
            <b>NOTE:</b> Loading the entire position into RAM is much faster,
            but it requires more memory.<br>
            Keep an eye on the ram usage and, if Cell-ACDC crashes or RAM is 
            full, you can re-start<br>
            the process and select "Load one frame at a time".
            """
        )
        _, loadFrameButton, loadPosButton = msg.warning(
            self, 'Loading data', txt, 
            buttonsTexts=(
                'Cancel', 
                widgets.twoDPushButton('No, load one frame (2D) at a time'), 
                widgets.FutureAllPushButton('Yes, load entire position at once')
            )
        )
        if msg.cancel:
            return None

        return msg.clickedButton == loadPosButton
    
    def warnSelectedPathEmpty(self, raw_src_path):
        msg = widgets.myMessageBox(wrapText=False)
        txt = html_utils.paragraph(
            f"""
            The selected folder (see below) is either <b>empty</b> 
            or does not contain any files.<br><br>
            Please select a folder that contains raw microscopy files.<br><br>
            Thank you for your patience!
            """
        )
        msg.warning(
            self, 'Empty folder', txt, 
            commands=(raw_src_path, ),
            path_to_browse=raw_src_path
        )
    
    def checkFileFormat(self, raw_src_path):
        self.moveOtherFiles = False
        self.copyOtherFiles = False
        ls = natsorted(myutils.listdir(raw_src_path))
        files = [
            filename for filename in ls
            if os.path.isfile(os.path.join(raw_src_path, filename))
        ]
        if not files:
            self.warnSelectedPathEmpty(raw_src_path)
            return []
        all_ext = [
            os.path.splitext(filename)[1] for filename in ls
            if os.path.isfile(os.path.join(raw_src_path, filename))
        ]
        counter = Counter(all_ext)
        unique_ext = list(counter.keys())
        is_ext_unique = len(unique_ext) == 1
        most_common_ext, _ = counter.most_common(1)[0]
        if not is_ext_unique:
            if not most_common_ext:
                most_common_ext_msg = '<empty>'
            else:
                most_common_ext_msg = most_common_ext
            
            msg = widgets.myMessageBox(showCentered=False)
            txt = html_utils.paragraph(f"""
                The following folder

                <br><br><code>{raw_src_path}</code><br><br>

                contains files with different file extensions 
                (extensions detected: {unique_ext})<br><br>
                However, the most common extension is 
                <b>{most_common_ext_msg}</b>,
                do you want to proceed with
                loading only files with extension <b>{most_common_ext_msg}</b>?
                <br>
            """)
            _, yesButton, noButton = msg.warning(
                self, 'Multiple extensions detected', txt, 
                buttonsTexts=(
                    'Cancel', 'Yes, load only most common', 
                    'No, load all files'
                )
            )
            if msg.cancel:
                return []
            if msg.clickedButton == yesButton:
                files = [
                    filename for filename in files
                    if os.path.splitext(filename)[1] == most_common_ext
                ]
                otherExt = [
                    ext for ext in unique_ext if ext != most_common_ext]
                files = self.askActionWithOtherFiles(files, otherExt)
            else:
                return files

        if self.rawDataStruct == 0 and len(files) > 1:
            files = self.warnMultipleFiles(files)

        return files

    def checkFileNames(self, raw_filenames, raw_src_path):
        for file in raw_filenames:
            if not acdc_regex.is_alphanumeric_filename(file):
                msg = widgets.myMessageBox(wrapText=False)
                txt = html_utils.paragraph(
                    f"""
                    The filename <code>{file}</code> contains <b>invalid 
                    characters</b>.<br><br>
                    Valid characters are letters, numbers, spaces, underscores 
                    and dashes.<br><br>
                    Please stop the process, <b>rename the file</b>, 
                    and try again, or choose one of the options below.<br><br>
                    Thank you for your patience!
                    """
                )
                renameWithUnderscoresButton = widgets.editPushButton(
                    'Rename file (replace invalid characters with "_")'
                )
                renameWithDashesButton = widgets.editPushButton(
                    'Rename file (replace invalid characters with "-")'
                )
                msg.warning(
                    self, 'Invalid filename', txt, 
                    path_to_browse=raw_src_path,
                    buttonsTexts=(
                        'Let me rename files myself', 
                        renameWithUnderscoresButton, 
                        renameWithDashesButton
                    )
                )
                if msg.clickedButton == renameWithUnderscoresButton:
                    self.log(
                        'Renaming files to replace invalid characters with "_"...'
                    )
                    renamed_filenames = io.rename_files_replace_invalid_chars(
                        raw_filenames, raw_src_path, replacement_char='_'
                    )
                    return True, renamed_filenames
                elif msg.clickedButton == renameWithDashesButton:
                    self.log(
                        'Renaming files to replace invalid characters with "-"...'
                    )
                    renamed_filenames = io.rename_files_replace_invalid_chars(
                        raw_filenames, raw_src_path, replacement_char='-'
                    )
                    return True, renamed_filenames
                else:
                    return False, []

        return True, raw_filenames
        
    def askActionWithOtherFiles(self, files, otherExt):
        self.moveOtherFiles = False
        msg = QMessageBox(self)
        msg.setWindowTitle('Action with the other files?')
        txt = (f"""
        <p style="font-size:11px">
            What should I do with the other files (ext: {otherExt})
            in the folder?<br><br>
            <i>NOTE: Only the files with the same basename and position number
            as the raw files will be moved or copied.</i>
        </p>

        """)
        msg.setIcon(msg.Question)
        msg.setText(txt)
        leaveButton = QPushButton(
                'Leave them where they are'
        )
        moveButton = QPushButton(
                'Attempt MOVING to their Position folder'
        )
        copyButton = QPushButton(
                'Attempt COPYING to their Position folder'
        )
        cancelButton = QPushButton(
                'Cancel'
        )
        msg.addButton(leaveButton, msg.YesRole)
        msg.addButton(moveButton, msg.NoRole)
        msg.addButton(copyButton, msg.RejectRole)
        msg.addButton(cancelButton, msg.ApplyRole)
        msg.exec_()
        if msg.clickedButton() == leaveButton:
            self.moveOtherFiles = False
            self.copyOtherFiles = False
            return files
        elif msg.clickedButton() == moveButton:
            self.moveOtherFiles = True
            self.copyOtherFiles = False
            return files
        elif msg.clickedButton() == copyButton:
            self.moveOtherFiles = False
            self.copyOtherFiles = True
            return files
        elif msg.clickedButton() == cancelButton:
            return []


    def warnMultipleFiles(self, files):
        win = apps.QDialogCombobox(
            'Multiple microscopy files detected!', files,
             '<p style="font-size:13px">'
             'You selected "Single microscopy file", '
             'but the <b>folder contains multiple files</b>.<br>'
             '</p>',
             CbLabel='Select which file to load: ', parent=self,
             iconPixmap=QtGui.QPixmap(':warning.svg')
        )
        win.exec_()
        if win.cancel:
            return []
        else:
            files = [win.selectedItemText]
            return files

    def attemptSeparateMultiChannel(self, rawFilenames):
        self.chNames = set()
        self.posNums = set()
        stripped_filenames = []
        for file in rawFilenames:
            filename, ext = os.path.splitext(file)
            m_iter = myutils.findalliter(fr'(\d+)_(.+)', filename)
            if len(m_iter) <= 1:
                self.criticalNoFilenamePattern()
                return False
            else:
                m = m_iter[-2]

            try:
                posNum, chName = int(m[0][0]), m[0][1]
                self.chNames.add(chName)
                self.posNums.add(posNum)
                ch_idx = filename.find(f'{posNum}_{chName}')
                stripped_filenames.append(filename[:ch_idx])
            except Exception as e:
                traceback_str = traceback.format_exc()
                self.logger.exception(traceback_str)
                self.criticalNoFilenamePattern(error=traceback.format_exc())
                return False

        basename = myutils.getBasename(stripped_filenames)
        if not basename:
            self.criticalNoFilenamePattern()
            return False

        self.basename = basename

        self.posNums = sorted(list(self.posNums))
        self.chNames = list(self.chNames)
        self.SizeS = len(self.posNums)
        return True


    def criticalNoFilenamePattern(self, error=''):
        txt = (
        """
        <b>Files are named with a non-compatible pattern.</b><br><br>
        In order to automatically generate the required data structure
        from "Multiple files, one for each channel" the filenames must
        be named with a specific pattern:<br><br>
        - basenameN_channelName1, e.g., [ASY015_1_GFP, ASY015_1_mNeon]<br><br>
        where "ASY015" is the basename common to ALL files, "1" is the Position number
        and ["GFP", "mNeon"] are the channel names.<br><br>
        <i>Note that the channel MUST be separated
        from the rest of the name by an underscore "_"</i>
        """
        )
        msg = QMessageBox(self)
        msg.setWindowTitle('Non-compatible pattern')
        msg.setIcon(msg.Critical)
        msg.setText(txt)
        if error:
            msg.setDetailedText(error)
        msg.exec_()

    def criticalBioFormats(self, actionTxt, tracebackFormat, filename):
        msg = widgets.myMessageBox(self, wrapText=True)

        url = 'https://docs.openmicroscopy.org/bio-formats/6.7.0/supported-formats.html'
        seeHere = f'<a href=\"{url}">here</a>'

        _, ext = os.path.splitext(filename)
        txt = html_utils.paragraph(
            f"""
            Error while {actionTxt} with Bio-Formats.<br><br>

            This is most likely because the <b>file format {ext} is not fully supported</b>
            by the Bio-Formats library.<br><br>

            See {seeHere} for details about supported formats.<br><br>

            Try loading file in Fiji and create the data structure manually.<br><br>
            Alternatively, if you are trying to load a video file, you can try
            to open the main GUI and then go to "File --> Open image/video file..."<br><br>
            You were trying to read file: {filename}
            """
        )
        
        msg.critical(
            self, 'Error with Bio-Formats', txt, detailsText=tracebackFormat
        )

        self.close()

    def askConfirmMetadata(
            self, filename, LensNA, SizeT, SizeZ, SizeC, SizeS,
            TimeIncrement, TimeIncrementUnit, PhysicalSizeX, PhysicalSizeY,
            PhysicalSizeZ, PhysicalSizeUnit, chNames, emWavelens, ImageName,
            rawFilePath, sampleImgData
        ):
        if self.rawDataStruct == 2:
            filename = self.basename
        self.metadataDialogIsOpen = True
        self.metadataWin = apps.QDialogMetadataXML(
            title=f'Metadata for {filename}', rawFilename=filename,
            LensNA=LensNA, SizeT=SizeT, SizeZ=SizeZ, SizeC=SizeC, SizeS=SizeS,
            TimeIncrement=TimeIncrement, TimeIncrementUnit=TimeIncrementUnit,
            PhysicalSizeX=PhysicalSizeX, PhysicalSizeY=PhysicalSizeY,
            PhysicalSizeZ=PhysicalSizeZ, PhysicalSizeUnit=PhysicalSizeUnit,
            ImageName=ImageName, chNames=chNames, emWavelens=emWavelens,
            parent=self, rawDataStruct=self.rawDataStruct,
            sampleImgData=sampleImgData, rawFilePath=rawFilePath
        )
        self.metadataWin.exec_()
        self.metadataDialogIsOpen = False
        self.worker.metadataWin = self.metadataWin
        self.waitCond.wakeAll()

    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(
            '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?'
        )
        _, 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:
            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...')
        handlers = self.logger.handlers[:]
        for handler in handlers:
            handler.close()
            self.logger.removeHandler(handler)

        if self.buttonToRestore is not None:
            button, color = self.buttonToRestore
            button.setText('0. Attempt "Create data structure" again')
            button.setStyleSheet(
                f'QPushButton {{background-color: {color};}}')
            self.mainWin.setWindowState(Qt.WindowNoState)
            self.mainWin.setWindowState(Qt.WindowActive)
            self.mainWin.raise_()

class InitFijiMacro:
    def __init__(self, acdcLauncher):
        self.acdcLauncher = acdcLauncher
        self.logger = self.acdcLauncher.logger
    
    def askSelectInstalledFiji(self):
        if os.path.exists(myutils.get_fiji_exec_folderpath()):
            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 
            and select where you have the Fiji app.<br><br>
            Alternatively, you can ignore this and let Cell-ACDC automatically 
            download Fiji for you.
        """)
        selectFijiButton = (
            widgets.OpenFilePushButton('Select Fiji.app location')
        )
        downloadFijiButton = (
            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=(
                'Cancel', selectFijiButton, downloadFijiButton
            ), 
            showDialog=False
        )
        selectFijiButton.clicked.disconnect()
        selectFijiButton.clicked.connect(
            partial(self.selectFijiLocation, messagebox=msg)
        )
        msg.exec_()
        
        return msg.cancel, msg.did_user_selected_fiji
    
    def selectFijiLocation(self, checked=True, messagebox=None):
        import qtpy.compat
        filepath = qtpy.compat.getopenfilename(
            parent=messagebox, 
            caption='Select Fiji.app location', 
            filters='Application (*.app);;All Files (*)'
        )[0]
        if not filepath:
            return
        
        from cellacdc import fiji_location_filepath
        with open(fiji_location_filepath, 'w') as txt:
            txt.write(os.path.join(filepath))
        
        messagebox.did_user_selected_fiji = True
        messagebox.cancel = False
        messagebox.close()
    
    def run(self):
        cancel, did_user_selected_fiji = self.askSelectInstalledFiji()
        if cancel:
            self.cancel()
            return
        
        txt = (f"""    
            In order to run Bio-Formats on your system, Cell-ACDC will use 
            <b>Fiji (ImageJ) from the command line</b>.<br><br>
            The process entails the creation of a macro (.ijm) file and 
            its execution from the command line.<br><br>
            If you prefer to run the macro yourself, you can go through 
            its creation process and cancel its execution later.
        """)
        self.logger.info('Testing Fiji command...')
        fiji_success = myutils.test_fiji_base_command(self.logger.info)
        commands = None
        if not fiji_success:
            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:
            """)
            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)
        msg = widgets.myMessageBox(wrapText=False)
        msg.information(
            self.acdcLauncher, 'Running Fiji in the command line', txt, 
            buttonsTexts=('Cancel', 'Ok'),
            commands=commands
        )
        if msg.cancel:
            self.cancel()
            return
        
        myutils.download_fiji(logger_func=self.logger.info)
        
        win = apps.InitFijiMacroDialog(parent=self.acdcLauncher)
        win.exec_()
        if win.cancel:
            self.cancel()
            return
        
        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 = ("""
            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>
        """)
        
        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)
        _, _, okButton = msg.information(
            self.acdcLauncher, 'Fiji macro command', txt, 
            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 = 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. 
                Path to the macro file:
            """)
            msg_func = 'information'
        else:
            href = html_utils.href_tag('GitHub page', urls.issues_url)
            txt = html_utils.paragraph(f"""
                Macro execution completed with errors. More details in the 
                terminal.<br><br> 
                If you cannot solve this, please report the issue on our 
                {href}<br><br>
                Path to the macro file:
            """)
            msg_func = 'information'
        
        msg = widgets.myMessageBox(wrapText=False)
        getattr(msg, msg_func)(
            self.acdcLauncher, 'Macro execution completed', txt, 
            commands=(macro_filepath,)
        )
    
    def cancel(self):
        self.logger.info('Running Bio-Formats from Fiji process cancelled.')