Source code for spinningdiskanalyzer.frontend.pages.segmentation

from .segmentation_ui import Ui_page
from .page            import Page
from .                import page
from ..               import tasks

from PySide6.QtWidgets import QWidget

from pathlib import Path




class Segmentation(page.ConfirmClose, page.NavNext, Page):
    """Segments the cells."""

    def __init__(self, parent: QWidget = None):

        # Load user interface design created in Qt Designer.
        super().__init__(parent)
        self.ui = Ui_page()
        self.ui.setupUi(self)

        # Make sure hiding buttons does not change layout.
        button = self.ui.next
        size_policy = button.sizePolicy()
        size_policy.setRetainSizeWhenHidden(True)
        button.setSizePolicy(size_policy)

        # Connect signals to slots.
        self.ui.back.clicked.connect(self.go_back.emit)
        self.ui.next.clicked.connect(self.go_next.emit)

        # Initialize instance attributes.
        self.task = None



    def on_enter(self):
        """Called when entering the page."""
        self.mark_busy()
        self.segment_cells()




    def segment_cells(self):
        """Triggers the cell segmentation."""
        self.task = tasks.SegmentCells()
        self.task.status_update.connect(self.status_update)
        self.task.status_clear.connect(self.status_clear)
        self.task.finished.connect(self.mark_cells)
        folder = Path(self.parent().select.ui.folder_display.text())
        source = folder/'analysis'/'thresholded.tif'
        target = folder/'analysis'/'cells.tsv'
        x = self.parent().disk.ui.x.value()
        y = self.parent().disk.ui.y.value()
        r = self.parent().disk.ui.r.value()
        self.task.start(source, target, x, y, r)




    def mark_cells(self):
        """Triggers marking the cells in the image."""
        self.task = tasks.MarkCells()
        self.task.status_update.connect(self.status_update)
        self.task.status_clear.connect(self.status_clear)
        self.task.finished.connect(self.tile_image)
        folder = Path(self.parent().select.ui.folder_display.text())
        source = folder/'analysis'/'disk.tif'
        target = folder/'analysis'/'segmented.tif'
        cells  = folder/'analysis'/'cells.tsv'
        self.task.start(source, target, cells)




    def tile_image(self):
        """Triggers tiling of the display image."""
        self.task = tasks.TileImage()
        self.task.finished.connect(self.tasks_done)
        self.task.status_update.connect(self.status_update)
        self.task.status_clear.connect(self.status_clear)
        folder = Path(self.parent().select.ui.folder_display.text())
        source = folder/'analysis'/'segmented.tif'
        target = folder/'tiles'/'segmented.dzi'
        self.task.start(source, target)




    def tasks_done(self):
        """Finishes up when all background tasks are done."""
        self.task = None
        folder = Path(self.parent().select.ui.folder_display.text())
        tiled  = folder/'tiles'/'segmented.dzi'
        self.ui.viewer.load(tiled)
        self.mark_ready()




    def invalidate(self):
        """Invalidates results from this analysis step."""
        self.ui.viewer.load(None)
        self.flush()
        folder = Path(self.parent().select.ui.folder_display.text())
        tasks.delete( (
            folder/'analysis'/'cells.tsv',
            folder/'analysis'/'segmented.tif',
            folder/'tiles'/'segmented.dzi',
            folder/'tiles'/'segmented_files',
        ) )