master.py

#!/usr/bin/env python3

import os
import sys
import logging
import importlib
import multiprocessing as mp
from functools import partial
from PyQt5.QtCore import Qt, QSize, QTimer, QUrl
from PyQt5.QtGui import QPixmap, QIcon, QFontMetrics, QKeySequence
from PyQt5.QtWidgets import QApplication, QLabel, QPushButton, QVBoxLayout, QHBoxLayout, QWidget, QLineEdit, QTreeWidget, QAbstractItemView, QSplitter, QStackedWidget, QTreeWidgetItem, QTreeWidgetItemIterator, QShortcut

from modules.registration_module import registration
from modules.zprojection_module import zprojection
from modules.ground_truth_generator_module import ground_truth_generator
from modules.segmentation_module import segmentation
from modules.cell_tracking_module import cell_tracking
from modules.graph_filtering_module import graph_filtering
from modules.events_selection_module import events_selection
from modules.viewer_module import viewer
from modules.file_organization_module import file_organization
from modules.file_conversion_module import file_conversion
from modules.image_cropping_module import image_cropping
from modules.pipeline_module import pipeline
from general import general_functions as gf

from platform import python_version, platform
from cellpose import version as cellpose_version
from napari import __version__ as napari_version
from numpy import __version__ as numpy_version
from torch import __version__ as torch_version
from version import __version__ as vlabapp_version
from cv2 import __version__ as opencv_version
from igraph import __version__ as igraph_version
from packaging.version import Version
from pystackreg import __version__ as pystackreg_version
from skimage import __version__ as skimage_version
from scipy import __version__ as scipy_version
from roifile import __version__ as roifile_version
from ome_types import __version__ as ometypes_version
from bioio import __version__ as bioio_version
from imageio import __version__ as imageio_version
from imageio_ffmpeg import __version__ as imageioffmpeg_version
from tifffile import __version__ as tifffile_version
from matplotlib import __version__ as matplotlib_version
from nd2 import __version__ as nd2_version
from pandas import __version__ as pandas_version
from PyQt5.QtCore import PYQT_VERSION_STR as pyqt_version
try:
    from micro_sam import __version__ as microsam_version
    microsam_available = True
except ImportError:
    microsam_available = False

class AboutVLabApp(QWidget):
    def __init__(self, pipeline_layout=False):
        super().__init__()
        layout = QVBoxLayout()
        logo = QLabel()
        logo.setPixmap(QPixmap(os.path.join(os.path.dirname(__file__),'support_files/logo.png')))
        logo.setAlignment(Qt.AlignCenter)
        layout.addWidget(logo)
        label = QLabel()
        label.setTextFormat(Qt.RichText)
        label.setWordWrap(True)
        label.setOpenExternalLinks(True)
        label.setText('<h2>VLabApp</h2>' +
                      'Home page:<br><a href="https://github.com/vjesticalab/VLabApp">https://github.com/vjesticalab/VLabApp</a><br><br>' +
                      'Documentation:<br><a href="' + QUrl.fromUserInput(os.path.join(os.path.dirname(__file__), 'doc', 'site', 'index.html')).toString() + '">' + os.path.normpath(os.path.join(os.path.dirname(__file__), 'doc', 'site', 'index.html')) + '</a>' +
                      '<h3>Citation</h3>' +
                      'If you use VLabApp in your research, please cite the VLabApp paper:' +
                      '<blockquote>J. Dorier, A. Ravera and A. Vjestica. In preparation</blockquote>' +
                      'If you use the registration module with <a href="https://bigwww.epfl.ch/thevenaz/stackreg/">stackreg</a>, please cite the following <a href="https://doi.org/10.1109/83.650848">publication</a>:' +
                      '<blockquote>P. Thevenaz, U. E. Ruttimann and M. Unser (1998). A pyramid approach to subpixel registration based on intensity. IEEE Transactions on Image Processing, 7(1), 27–41.</blockquote>' +
                      'If you use the segmentation module with <a href="https://www.cellpose.org/">Cellpose</a>, please cite the Cellpose 1.0 <a href="https://doi.org/10.1038/s41592-020-01018-x">publication</a>:' +
                      '<blockquote>C. Stringer, T. Wang, M. Michaelos and M. Pachitariu (2021). Cellpose: a generalist algorithm for cellular segmentation. Nature Methods 18, 100–106.</blockquote>' +
                      'If you fine-tune a Cellpose model, please cite the Cellpose 2.0 <a href="https://doi.org/10.1038/s41592-022-01663-4">publication</a>:' +
                      '<blockquote>M. Pachitariu and C. Stringer (2022). Cellpose 2.0: how to train your own model. Nature Methods 19, 1634–1641.</blockquote>' +
                      'If you use the segmentation module with the `cyto3` Cellpose model, please cite the Cellpose 3.0 <a href="https://doi.org/10.1038/s41592-025-02595-5">publication</a>:' +
                      '<blockquote>C. Stringer and M. Pachitariu (2025). Cellpose3: one-click image restoration for improved cellular segmentation. Nature Methods 22, 592-599.</blockquote>' +
                      ('If you use the segmentation module with  <a href="https://github.com/computational-cell-analytics/micro-sam">Segment Anything for Microscopy</a>, please cite the Segment Anything for Microscopy <a href="https://doi.org/10.1038/s41592-024-02580-4">publication</a>:' if microsam_available else '' ) +
                      ('<blockquote>A. Archit, L. Freckmann, S. Nair et al. (2025). Segment Anything for Microscopy. Nature Methods 22, 579-591.</blockquote>' if microsam_available else '' ) +
                      ('as well as the original <a href="https://segment-anything.com/">Segment Anything</a> <a href="https://doi.org/10.48550/arXiv.2304.02643">publication</a>:' if microsam_available else '' ) +
                      ('<blockquote>A. Kirillov, E. Mintun, N. Ravi et al. (2023). Segment Anything. http://arxiv.org/abs/2304.02643</blockquote>' if microsam_available else '' ) +
                      '<h3>System information</h3>' +
                      '<b>VLabApp:</b> ' + vlabapp_version + '<br>' +
                      '<b>platform:</b> ' + platform() + '<br>' +
                      '<b>python:</b> ' + python_version() + '<br>' +
                      '<b>bioio:</b> ' + bioio_version + '<br>' +
                      '<b>cellpose:</b> ' + cellpose_version + '<br>' +
                      '<b>igraph:</b> ' + igraph_version + '<br>' +
                      '<b>imageio:</b> ' + imageio_version + '<br>' +
                      '<b>imageio-ffmpeg:</b> ' + imageioffmpeg_version + '<br>' +
                      '<b>matplotlib:</b> ' + matplotlib_version + '<br>' +
                      ('<b>micro_sam:</b> ' + microsam_version + '<br>'  if microsam_available else '' ) +
                      '<b>napari:</b> ' + napari_version + '<br>' +
                      '<b>nd2:</b> ' + nd2_version + '<br>' +
                      '<b>numpy:</b> ' + numpy_version + '<br>' +
                      '<b>ome-types:</b> ' + ometypes_version + '<br>' +
                      '<b>opencv:</b> ' + opencv_version + '<br>' +
                      '<b>pandas:</b> ' + pandas_version + '<br>' +
                      '<b>pyqt:</b> ' + pyqt_version + '<br>' +
                      '<b>pystackreg:</b> ' + pystackreg_version + '<br>' +
                      '<b>pytorch:</b> ' + torch_version + '<br>' +
                      '<b>roifile:</b> ' + roifile_version + '<br>' +
                      '<b>scikit-image:</b> ' + skimage_version + '<br>' +
                      '<b>scipy:</b> ' + scipy_version + '<br>' +
                      '<b>tifffile:</b> ' + tifffile_version +
                      '<h3>Credits</h3>' +
                      'Julien Dorier - Bioinformatics Competence Center, <a href="https://www.unil.ch">University of Lausanne</a>.<br>' +
                      'Arianna Ravera - Scientific Computing and Research Support Unit, <a href="https://www.unil.ch">University of Lausanne</a>.<br>' +
                      'Aleksandar Vjestica - Center for Integrative Genomics, <a href="https://www.unil.ch">University of Lausanne</a>.<br>')
        layout.addWidget(label)
        self.setLayout(layout)


class MainWindow(QWidget):
    def __init__(self):
        super().__init__()
        window = QVBoxLayout(self)

        title = "VLabApp"
        self.setWindowTitle(title)

        self.status_line = QLineEdit()
        self.status_line.setEnabled(False)
        self.status_line.setFrame(False)
        font = self.status_line.font()
        font.setItalic(True)
        self.status_line.setFont(font)

        self.module_list = QTreeWidget()
        self.module_list.setColumnCount(1)
        self.module_list.setSortingEnabled(False)
        self.module_list.setSelectionMode(QAbstractItemView.SingleSelection)
        self.module_list.setVerticalScrollMode(QAbstractItemView.ScrollPerPixel)
        self.module_list.setEditTriggers(QAbstractItemView.NoEditTriggers)
        self.module_list.setHeaderHidden(True)

        self.right_panel = QStackedWidget()

        splitter = QSplitter()
        self.left_panel = QWidget()
        self.left_panel.setLayout(QVBoxLayout())
        self.left_panel.layout().setContentsMargins(0, 0, 0, 0)
        self.left_panel.layout().addWidget(self.module_list)
        splitter.addWidget(self.left_panel)
        splitter.addWidget(self.right_panel)
        splitter.setCollapsible(1, False)
        splitter.setStretchFactor(0, 1)
        splitter.setStretchFactor(1, 5)
        window.addWidget(splitter)

        item = QTreeWidgetItem(self.module_list, ["About VLabApp"])
        item.setData(0, Qt.UserRole, self.right_panel.count())
        self.right_panel.addWidget(gf.Page(widget=AboutVLabApp()))

        item = QTreeWidgetItem(self.module_list, ["Registration"])
        item.setData(0, Qt.UserRole, self.right_panel.count())
        item.setFlags(item.flags() & ~Qt.ItemIsSelectable)
        item.setExpanded(True)
        self.right_panel.addWidget(gf.Page(widget=QWidget()))

        subitem = QTreeWidgetItem(item, ["Registration"])
        subitem.setData(0, Qt.UserRole, self.right_panel.count())
        self.right_panel.addWidget(gf.Page(widget=registration.Perform()))

        subitem = QTreeWidgetItem(item, ["Alignment"])
        subitem.setData(0, Qt.UserRole, self.right_panel.count())
        self.right_panel.addWidget(gf.Page(widget=registration.Align()))

        subitem = QTreeWidgetItem(item, ["Editing (manual)"])
        subitem.setData(0, Qt.UserRole, self.right_panel.count())
        self.right_panel.addWidget(gf.Page(widget=registration.ManualEdit()))

        item = QTreeWidgetItem(self.module_list, ["Z-Projection"])
        item.setData(0, Qt.UserRole, self.right_panel.count())
        self.right_panel.addWidget(gf.Page(widget=zprojection.zProjection()))

        item = QTreeWidgetItem(self.module_list, ["Segmentation"])
        item.setData(0, Qt.UserRole, self.right_panel.count())
        self.right_panel.addWidget(gf.Page(widget=segmentation.Segmentation()))

        item = QTreeWidgetItem(self.module_list, ["Cell tracking"])
        item.setData(0, Qt.UserRole, self.right_panel.count())
        self.right_panel.addWidget(gf.Page(widget=cell_tracking.CellTracking()))

        item = QTreeWidgetItem(self.module_list, ["Graph filtering"])
        item.setData(0, Qt.UserRole, self.right_panel.count())
        self.right_panel.addWidget(gf.Page(widget=graph_filtering.GraphFiltering()))

        item = QTreeWidgetItem(self.module_list, ["Events selection"])
        item.setData(0, Qt.UserRole, self.right_panel.count())
        self.right_panel.addWidget(gf.Page(widget=events_selection.EventsSelection()))

        item = QTreeWidgetItem(self.module_list, ["Pipeline"])
        item.setData(0, Qt.UserRole, self.right_panel.count())
        self.right_panel.addWidget(gf.Page(widget=pipeline.Pipeline()))

        item = QTreeWidgetItem(self.module_list, ["Tools"])
        item.setData(0, Qt.UserRole, self.right_panel.count())
        item.setFlags(item.flags() & ~Qt.ItemIsSelectable)
        item.setExpanded(True)
        self.right_panel.addWidget(gf.Page(widget=QWidget()))

        subitem = QTreeWidgetItem(item, ["View image, mask and graph"])
        subitem.setData(0, Qt.UserRole, self.right_panel.count())
        self.right_panel.addWidget(gf.Page(widget=viewer.ImageMaskGraphViewer()))

        subitem = QTreeWidgetItem(item, ["View registration matrix"])
        subitem.setData(0, Qt.UserRole, self.right_panel.count())
        self.right_panel.addWidget(gf.Page(widget=viewer.RegistrationViewer()))

        subitem = QTreeWidgetItem(item, ["View metadata"])
        subitem.setData(0, Qt.UserRole, self.right_panel.count())
        self.right_panel.addWidget(gf.Page(widget=viewer.MetadataViewer(), add_stretch=False))

        subitem = QTreeWidgetItem(item, ["File organization"])
        subitem.setData(0, Qt.UserRole, self.right_panel.count())
        self.right_panel.addWidget(gf.Page(widget=file_organization.FileOrganization()))

        subitem = QTreeWidgetItem(item, ["File conversion (masks and graphs)"])
        subitem.setData(0, Qt.UserRole, self.right_panel.count())
        self.right_panel.addWidget(gf.Page(widget=file_conversion.MaskGraphConversion()))

        subitem = QTreeWidgetItem(item, ["File conversion (lossy preview)"])
        subitem.setData(0, Qt.UserRole, self.right_panel.count())
        self.right_panel.addWidget(gf.Page(widget=file_conversion.ImageMaskConversion()))

        subitem = QTreeWidgetItem(item, ["Image cropping"])
        subitem.setData(0, Qt.UserRole, self.right_panel.count())
        self.right_panel.addWidget(gf.Page(widget=image_cropping.ImageCropping()))

        subitem = QTreeWidgetItem(item, ["Ground truth generator"])
        subitem.setData(0, Qt.UserRole, self.right_panel.count())
        self.right_panel.addWidget(gf.Page(widget=ground_truth_generator.GroundTruthGenerator()))

        ## add plugins
        plugins_path = os.path.join(os.path.dirname(__file__), 'plugins')
        plugins_list = []
        for p in os.listdir(plugins_path):
            if os.path.isfile(os.path.join(plugins_path, p, '__init__.py')):
                module = importlib.import_module('plugins.' + p)
                try:
                    name = module.NAME
                except AttributeError:
                    name = module.__name__.replace('plugins.', '')
                plugins_list.append((name, module))
        if plugins_list:
            item = QTreeWidgetItem(self.module_list, ["Plugins"])
            item.setData(0, Qt.UserRole, self.right_panel.count())
            item.setFlags(item.flags() & ~Qt.ItemIsSelectable)
            item.setExpanded(True)
            self.right_panel.addWidget(gf.Page(widget=QWidget()))
            # add plugins (alphabetical order)
            for name, plugin in sorted(plugins_list, key=lambda x: (x[0].lower())):
                subitem = QTreeWidgetItem(item, [name])
                subitem.setData(0, Qt.UserRole, self.right_panel.count())
                self.right_panel.addWidget(gf.Page(widget=plugin.Widget()))

        w = self.module_list.sizeHintForColumn(0)
        h = round(1.5*self.module_list.sizeHintForRow(0))
        font_metric = QFontMetrics(self.module_list.font())
        iterator = QTreeWidgetItemIterator(self.module_list)
        while iterator.value():
            item = iterator.value()
            item.setSizeHint(0, QSize(w, h))
            iterator += 1
        self.module_list.setMinimumWidth(font_metric.width('a')*25)

        self.module_list.currentItemChanged.connect(self.module_list_current_item_changed)
        self.module_list.setCurrentItem(self.module_list.topLevelItem(0))

        layout = QHBoxLayout()
        layout.addWidget(self.status_line)

        shortcut_quit = QShortcut(QKeySequence.Quit, self)
        shortcut_quit.setContext(Qt.ShortcutContext.WidgetWithChildrenShortcut)
        shortcut_quit.activated.connect(QApplication.quit)

        self.quit_button = QPushButton("Quit", self)
        self.quit_button.clicked.connect(QApplication.quit)
        self.quit_button.setStyleSheet("background: darkred;")
        layout.addWidget(self.quit_button, alignment=Qt.AlignRight)
        window.addLayout(layout)

        # Setup logging
        logging.basicConfig(level=logging.INFO, format="%(asctime)s (%(name)s) [%(levelname)s] %(message)s", handlers=[logging.StreamHandler(sys.stdout)], force=True)

        # Add a handler to output messages to self.status_line
        self.qlabel_handler = gf.QLineEditHandler(self.status_line)
        self.qlabel_handler.setFormatter(logging.Formatter('%(message)s'))
        logging.getLogger().addHandler(self.qlabel_handler)

        # Add a handler to output errors to QMessageBox
        self.qmessagebox_handler = gf.QMessageBoxErrorHandler(self)
        self.qmessagebox_handler.setFormatter(logging.Formatter('%(message)s'))
        self.qmessagebox_handler.setLevel(logging.ERROR)
        self.qmessagebox_handler.name = 'messagebox_error_handler'
        logging.getLogger().addHandler(self.qmessagebox_handler)

        # Temporary workaround to ensure QGroupBox titles are not cropped
        self.setStyleSheet("QLineEdit:disabled {background: transparent} " +
                           "QGroupBox::title {padding-right: 1px}")

    def module_list_current_item_changed(self, current, previous):
        self.right_panel.setCurrentIndex(current.data(0, Qt.UserRole))
        self.setWindowTitle('VLabApp - '+current.text(0))
        self.status_line.setText('')
        if current.childCount():
            current.setExpanded(True)
            self.module_list.setCurrentItem(current.child(0))
            QTimer.singleShot(0, partial(self.module_list.setCurrentItem, current.child(0)))

    def __del__(self):
        # Remove handler to avoid problems after self and self.status_line are destroyed
        logging.getLogger().removeHandler(self.qlabel_handler)
        logging.getLogger().removeHandler(self.qmessagebox_handler)


if __name__ == "__main__":
    # set up some environmental variables
    os.environ['OMP_NUM_THREADS'] = '1'
    os.environ['MKL_NUM_THREADS'] = '1'
    try:
        mp.set_start_method('spawn', force=True)
    except RuntimeError:
        sys.exit(1)
    app = QApplication(sys.argv)
    app.setWindowIcon(QIcon(os.path.join(os.path.dirname(__file__),'support_files/logo.png')))
    w = MainWindow()
    w.show()
    w.resize(1000, 800)
    sys.exit(app.exec_())