fix: uses custom FloatLineEdit for metadata dialogue

cellacdc/_debug.py

@@ -1,9 +1,35 @@
 import inspect
 
+import numpy as np
 import pandas as pd
 
 from . import printl
 
+def split_segm_masks_mother_bud_line(lab, obj, obj_bud, interc_perp, slope_perp):
+    import matplotlib.pyplot as plt
+
+    lab = np.zeros_like(lab)
+    lab[obj.slice][obj.image] = obj.label
+    lab[obj_bud.slice][obj_bud.image] = obj_bud.label
+
+    y0 = 0
+    x0 = (y0 - interc_perp)/slope_perp
+
+    x1 = lab.shape[1]
+    y1 = slope_perp*x1 + interc_perp
+
+    x2 = 0
+    y2 = interc_perp
+
+    y3 = lab.shape[0]
+    x3 = (y3 - interc_perp)/slope_perp
+
+    plt.imshow(lab) 
+    plt.plot([x0, x1, x2, x3], [y0, y1, y2, y3], 'r')  
+    plt.show()
+
+    import pdb; pdb.set_trace()
+
 def print_all_callers():
     currentframe = inspect.currentframe()
     outerframes = inspect.getouterframes(currentframe, 2)

cellacdc/apps.py

@@ -5025,11 +5025,8 @@ def __init__(
         gridLayout.addWidget(
             self.TimeIncrementLabel, row, 0, alignment=Qt.AlignRight
         )
-        self.TimeIncrementSpinBox = QDoubleSpinBox()
-        self.TimeIncrementSpinBox.setDecimals(7)
-        self.TimeIncrementSpinBox.setMaximum(2147483647.0)
+        self.TimeIncrementSpinBox = widgets.FloatLineEdit()
         self.TimeIncrementSpinBox.setValue(TimeIncrement)
-        self.TimeIncrementSpinBox.setAlignment(Qt.AlignCenter)
         gridLayout.addWidget(self.TimeIncrementSpinBox, row, 1)
 
         if SizeT == 1 or not ask_TimeIncrement:
@@ -5041,11 +5038,8 @@ def __init__(
         gridLayout.addWidget(
             self.PhysicalSizeZLabel, row, 0, alignment=Qt.AlignRight
         )
-        self.PhysicalSizeZSpinBox = QDoubleSpinBox()
-        self.PhysicalSizeZSpinBox.setDecimals(7)
-        self.PhysicalSizeZSpinBox.setMaximum(2147483647.0)
+        self.PhysicalSizeZSpinBox = widgets.FloatLineEdit()
         self.PhysicalSizeZSpinBox.setValue(PhysicalSizeZ)
-        self.PhysicalSizeZSpinBox.setAlignment(Qt.AlignCenter)
         gridLayout.addWidget(self.PhysicalSizeZSpinBox, row, 1)
 
         if SizeZ==1 or not ask_PhysicalSizes:
@@ -5057,11 +5051,8 @@ def __init__(
         gridLayout.addWidget(
             self.PhysicalSizeYLabel, row, 0, alignment=Qt.AlignRight
         )
-        self.PhysicalSizeYSpinBox = QDoubleSpinBox()
-        self.PhysicalSizeYSpinBox.setDecimals(7)
-        self.PhysicalSizeYSpinBox.setMaximum(2147483647.0)
+        self.PhysicalSizeYSpinBox = widgets.FloatLineEdit()
         self.PhysicalSizeYSpinBox.setValue(PhysicalSizeY)
-        self.PhysicalSizeYSpinBox.setAlignment(Qt.AlignCenter)
         gridLayout.addWidget(self.PhysicalSizeYSpinBox, row, 1)
 
         if not ask_PhysicalSizes:
@@ -5073,11 +5064,8 @@ def __init__(
         gridLayout.addWidget(
             self.PhysicalSizeXLabel, row, 0, alignment=Qt.AlignRight
         )
-        self.PhysicalSizeXSpinBox = QDoubleSpinBox()
-        self.PhysicalSizeXSpinBox.setDecimals(7)
-        self.PhysicalSizeXSpinBox.setMaximum(2147483647.0)
+        self.PhysicalSizeXSpinBox = widgets.FloatLineEdit()
         self.PhysicalSizeXSpinBox.setValue(PhysicalSizeX)
-        self.PhysicalSizeXSpinBox.setAlignment(Qt.AlignCenter)
         gridLayout.addWidget(self.PhysicalSizeXSpinBox, row, 1)
 
         if not ask_PhysicalSizes:
@@ -9937,14 +9925,15 @@ class SelectSegmFileDialog(QDialog):
     def __init__(
             self, images_ls, parent_path, parent=None, 
             addNewFileButton=False, basename='', infoText=None, 
-            fileType='segmentation'
+            fileType='segmentation', allowMultipleSelection=False
         ):
         self.cancel = True
         self.selectedItemText = ''
         self.selectedItemIdx = None
         self.removeOthers = False
         self.okAllPos = False
         self.newSegmEndName = None
+        self.allowMultipleSelection = allowMultipleSelection
         self.basename = basename
         images_ls = sorted(images_ls, key=len)
 
@@ -9994,6 +9983,10 @@ def __init__(
         listWidget.addItems(images_ls)
         listWidget.setCurrentRow(0)
         listWidget.itemDoubleClicked.connect(self.listDoubleClicked)
+        if allowMultipleSelection:
+            listWidget.setSelectionMode(
+                QAbstractItemView.SelectionMode.ExtendedSelection
+            )
         self.items = list(images_ls)
         self.listWidget = listWidget
 
@@ -10063,6 +10056,10 @@ def ok_cb(self, event=None):
         self.cancel = False
         self.selectedItemText = self.listWidget.selectedItems()[0].text()
         self.selectedItemIdx = self.items.index(self.selectedItemText)
+        self.selectedItemTexts = [
+            selectedItem.text() 
+            for selectedItem in self.listWidget.selectedItems()
+        ]
         self.close()
 
     def exec_(self):

cellacdc/core.py

@@ -2599,4 +2599,93 @@ def fucci_pipeline_executor_map(input, **filter_kwargs):
     processed_img = preprocess.fucci_filter(sum_img, **filter_kwargs)
 
     return frame_i, processed_img
-
+
+def split_segm_masks_mother_bud_line(
+        cells_segm_data, segm_data_to_split, acdc_df, 
+        debug=False
+    ):
+    acdc_df = acdc_df.set_index(['frame_i', 'Cell_ID'])
+    split_segm_away = np.zeros_like(segm_data_to_split)
+    split_segm_close = np.zeros_like(segm_data_to_split)
+
+    pbar = tqdm(total=len(cells_segm_data), ncols=100, position=1, leave=False)
+    for frame_i, lab in enumerate(cells_segm_data):
+        rp = skimage.measure.regionprops(lab)
+        rp_mapper = {obj.label:obj for obj in rp}
+        for obj in rp:
+            try:
+                ccs = acdc_df.at[(frame_i, obj.label), 'cell_cycle_stage']
+            except Exception as err:
+                pbar.update()
+                continue
+
+            if ccs != 'S':
+                pbar.update()
+                continue
+
+            try:
+                relationship = acdc_df.at[(frame_i, obj.label), 'relationship']
+            except Exception as err:
+                pbar.update()
+                continue
+
+            if relationship == 'bud':
+                pbar.update()
+                continue
+
+            bud_ID = int(acdc_df.at[(frame_i, obj.label), 'relative_ID'])
+            obj_bud = rp_mapper[bud_ID]
+
+            moth_ID = obj.label
+            yc_m, xc_m = obj.centroid
+            yc_b, xc_b = obj_bud.centroid
+
+            slope_mb = (yc_b - yc_m)/(xc_b - yc_b)
+            if slope_mb != 0:
+                slope_perp = -1/slope_mb
+                interc_perp = yc_m - xc_m*slope_perp
+
+            if debug:
+                from cellacdc import _debug
+                _debug.split_segm_masks_mother_bud_line(
+                    lab, obj, obj_bud, interc_perp, slope_perp
+                )
+
+
+
+
+
+        pbar.update()
+    pbar.close()        
+
+def get_split_line_ref_points_img(img, slope_perp, interc_perp):
+    if slope_perp == np.inf:
+        ...
+    else:
+        Y, X = lab.shape
+        y0 = 0
+        x0 = y0 - interc_perp/slope_perp
+
+        x1 = X
+        y1 = slope_perp*x1 + interc_perp
+
+        x2 = 0
+        y2 = interc_perp
+
+        y3 = Y
+        x3 = y3 - interc_perp/slope_perp
+
+        if x0 < X:
+            x_ref_0 = x0
+            y_ref_0 = y0
+        else:
+            x_ref_0 = x1
+            y_ref_0 = y1
+
+        if x1 > 0:
+            x_ref1 = x1
+            y_ref1 = y1
+        else:
+            x_ref1 = x2
+            y_ref1 = 0
+

cellacdc/load.py

@@ -695,6 +695,35 @@ def get_segm_files(images_path):
     ]
     return segm_files            
 
+def get_segm_endnames_from_exp_path(exp_path, pos_foldernames=None):
+    if pos_foldernames is None:
+        pos_foldernames = myutils.get_pos_foldernames(exp_path)
+
+    existingEndNames = set()
+    for p, pos in enumerate(pos_foldernames):
+        pos_path = os.path.join(exp_path, pos)
+        images_path = os.path.join(pos_path, 'Images')
+        basename, chNames = myutils.getBasenameAndChNames(images_path)
+        # Use first found channel, it doesn't matter for metrics
+        for chName in chNames:
+            filePath = myutils.getChannelFilePath(images_path, chName)
+            if filePath:
+                break
+        else:
+            raise FileNotFoundError(
+                f'None of the channels "{chNames}" were found in the path '
+                f'"{images_path}".'
+            )
+        _posData = loadData(filePath, chName)
+        _posData.getBasenameAndChNames()
+        found_files = get_segm_files(_posData.images_path)
+        _existingEndnames = get_endnames(
+            _posData.basename, found_files
+        )
+        existingEndNames.update(_existingEndnames)
+
+    return existingEndNames
+
 def get_files_with(images_path: os.PathLike, with_text: str, ext: str=None):
     ls = myutils.listdir(images_path)
     found_files = []

cellacdc/scripts/split_segm_mask_yeast.py

@@ -0,0 +1,107 @@
+import os
+
+from tqdm import tqdm
+
+import qtpy.compat
+
+from cellacdc import printl, myutils, apps, load, core
+from cellacdc._run import _setup_app
+from cellacdc.utils.base import NewThreadMultipleExpBaseUtil
+
+DEBUG = True
+
+def ask_select_folder():
+    selected_path = qtpy.compat.getexistingdirectory(
+        caption='Select experiment folder to analyse', 
+        basedir=myutils.getMostRecentPath()
+    )
+    return selected_path
+
+def get_exp_path_pos_foldernames(selected_path):
+    folder_type = myutils.determine_folder_type(selected_path)
+    is_pos_folder, is_images_folder, exp_path = folder_type
+    if is_pos_folder:
+        exp_path = os.path.dirname(selected_path)
+        pos_foldernames = myutils.get_pos_foldernames(exp_path)
+    elif is_images_folder:
+        pos_path = os.path.dirname(selected_path)
+        exp_path = os.path.dirname(pos_path)
+        pos_foldernames = [os.path.basename(pos_path)]
+    else:
+        exp_path = selected_path
+        pos_foldernames = myutils.get_pos_foldernames(exp_path)
+
+    return exp_path, pos_foldernames
+
+def select_segm_masks(exp_path, pos_foldernames):
+    infoText = 'Select which segmentation file <b>OF THE CELLS</b>:'
+    existingEndNames = load.get_segm_endnames_from_exp_path(
+        exp_path, pos_foldernames=pos_foldernames
+    )
+    win = apps.SelectSegmFileDialog(
+        existingEndNames, exp_path, 
+        infoText=infoText, 
+        fileType='segmentation'
+    )
+    win.exec_()
+    if win.cancel:
+        return
+
+    cells_segm_endname = win.selectedItemText
+
+    infoText = 'Select segmentation files <b>to SPLIT</b>:'
+    existingEndNames.discard(cells_segm_endname)
+    win = apps.SelectSegmFileDialog(
+        existingEndNames, exp_path, 
+        infoText=infoText, 
+        fileType='segmentation',
+        allowMultipleSelection=True
+    )
+    win.exec_()
+    if win.cancel:
+        return
+
+    list_segm_endnames_to_split = win.selectedItemTexts
+    return cells_segm_endname, list_segm_endnames_to_split
+
+def run():
+    app, splashScreen = _setup_app(splashscreen=True)  
+    splashScreen.close()
+
+    selected_path = ask_select_folder()
+    if not selected_path:
+        exit('Execution cancelled')
+
+    myutils.addToRecentPaths(selected_path)
+    exp_path, pos_foldernames = get_exp_path_pos_foldernames(selected_path)
+
+    selected_segm_endnames = select_segm_masks(exp_path, pos_foldernames)
+    if selected_segm_endnames is None:
+        exit('Execution cancelled')
+
+    cells_segm_endname, list_segm_endnames_to_split = selected_segm_endnames
+    acdc_df_endname = cells_segm_endname.replace('segm', 'acdc_output')
+    pbar = tqdm(total=len(pos_foldernames), ncols=100)
+    for pos in pos_foldernames:
+        images_path = os.path.join(exp_path, pos, 'Images')
+        cells_segm_data = load.load_segm_file(
+            images_path, end_name_segm_file=cells_segm_endname
+        )
+        acdc_df = load.load_acdc_df_file(
+            images_path, end_name_acdc_df_file=acdc_df_endname
+        )
+        for segm_endname in list_segm_endnames_to_split:
+            segm_data_to_split = load.load_segm_file(
+                images_path, end_name_segm_file=segm_endname
+            )
+            core.split_segm_masks_mother_bud_line(
+                cells_segm_data, segm_data_to_split, acdc_df, 
+                debug=DEBUG
+            )
+        pbar.update()
+
+    pbar.close()
+
+
+if __name__ == '__main__':
+    run()