feat: new utility to convert segm.npz to a dataframe of objects coord…

…inates

cellacdc/__main__.py

@@ -105,6 +105,7 @@ def eventFilter(self, object, event):
     from cellacdc.utils import compute as utilsCompute
     from cellacdc.utils import repeat as utilsRepeat
     from cellacdc.utils import toImageJroi as utilsToImageJroi
+    from cellacdc.utils import toObjCoords as utilsToObjCoords
     from cellacdc.utils import acdcToSymDiv as utilsSymDiv
     from cellacdc.utils import trackSubCellObjects as utilsTrackSubCell
     from cellacdc.utils import createConnected3Dsegm as utilsConnected3Dsegm
@@ -464,6 +465,7 @@ def createMenuBar(self):
         convertMenu.addAction(self.TiffToNpzAction)
         convertMenu.addAction(self.h5ToNpzAction)
         convertMenu.addAction(self.toImageJroiAction)
+        convertMenu.addAction(self.toObjsCoordsAction)
 
         segmMenu = utilsMenu.addMenu('Segmentation')
         segmMenu.addAction(self.createConnected3Dsegm)
@@ -584,6 +586,9 @@ def createActions(self):
         self.toImageJroiAction = QAction(
             'Convert _segm.npz file(s) to ImageJ ROIs...'
         )
+        self.toObjsCoordsAction = QAction(
+            'Convert _segm.npz file(s) to object coordinates (CSV)...'
+        )
         self.createConnected3Dsegm = QAction(
             'Create connected 3D segmentation mask from z-slices segmentation...'
         )   
@@ -634,6 +639,9 @@ def connectActions(self):
         self.TiffToNpzAction.triggered.connect(self.launchConvertFormatUtil)
         self.h5ToNpzAction.triggered.connect(self.launchConvertFormatUtil)
         self.toImageJroiAction.triggered.connect(self.launchToImageJroiUtil)
+        self.toObjsCoordsAction.triggered.connect(
+            self.launchToObjectsCoordsUtil
+        )
         self.createConnected3Dsegm.triggered.connect(
             self.launchConnected3DsegmActionUtil
         )
@@ -922,6 +930,26 @@ def _launchArboretum(self):
         )
         self.arboretumWindow.show()
 
+    def launchToObjectsCoordsUtil(self):
+        self.logger.info(f'Launching utility "{self.sender().text()}"')
+
+        selectedExpPaths = self.getSelectedExpPaths(
+            'From _segm.npz to objects coordinates (CSV)'
+        )
+        if selectedExpPaths is None:
+            return
+
+        title = 'Convert _segm.npz file(s) to objects coordinates (CSV)'
+        infoText = 'Launching to to objects coordinates process...'
+        progressDialogueTitle = (
+            'Converting _segm.npz file(s) to to objects coordinates (CSV)'
+        )
+        self.toObjCoordsWin = utilsToObjCoords.toObjCoordsUtil(
+            selectedExpPaths, self.app, title, infoText, progressDialogueTitle,
+            parent=self
+        )
+        self.toObjCoordsWin.show()
+
     def launchToImageJroiUtil(self):
         self.logger.info(f'Launching utility "{self.sender().text()}"')
         myutils.check_install_package('roifile', parent=self)

cellacdc/myutils.py

@@ -1325,6 +1325,24 @@ def imagej_tiffwriter(
     with TiffWriter(new_path, bigtiff=True) as new_tif:
         new_tif.save(data)
 
+def from_lab_to_obj_coords(lab):
+    rp = skimage.measure.regionprops(lab)
+    dfs = []
+    keys = []
+    for obj in rp:
+        keys.append(obj.label)
+        obj_coords = obj.coords
+        ndim = obj_coords.shape[1]
+        if ndim == 3:
+            columns = ['z', 'y', 'x']
+        else:
+            columns = ['y', 'x']
+        df_obj = pd.DataFrame(data=obj_coords, columns=columns)
+        dfs.append(df_obj)
+    df = pd.concat(dfs, keys = keys, names=['Cell_ID', 'idx']).droplevel(1)
+    return df
+
+
 def from_lab_to_imagej_rois(lab, ImagejRoi, t=0, SizeT=1, max_ID=None):
     if max_ID is None:
         max_ID = lab.max()

cellacdc/utils/toObjCoords.py

@@ -0,0 +1,29 @@
+from .. import myutils, workers, widgets, html_utils
+
+from .base import NewThreadMultipleExpBaseUtil
+
+class toObjCoordsUtil(NewThreadMultipleExpBaseUtil):
+    def __init__(
+            self, expPaths, app, title: str, infoText: str, 
+            progressDialogueTitle: str, parent=None):
+        module = myutils.get_module_name(__file__)
+        super().__init__(
+            expPaths, app, title, module, infoText, progressDialogueTitle, 
+            parent=parent
+        )
+        self.expPaths = expPaths
+
+    def runWorker(self):
+        self.worker = workers.ToObjCoordsWorker(self)
+        super().runWorker(self.worker)
+
+    def showEvent(self, event):
+        self.runWorker()
+
+    def workerFinished(self, worker):
+        super().workerFinished(worker)
+        txt = 'Converting to object coordinates completed.'
+        self.logger.info(txt)
+        msg = widgets.myMessageBox(wrapText=False, showCentered=False)
+        msg.information(self, 'Process completed', html_utils.paragraph(txt))
+        self.close()

cellacdc/workers.py

@@ -3018,3 +3018,72 @@ def saveAlignedData(
             np.savez_compressed(filePath, data)
         elif ext == '.h5':
             load.save_to_h5(filePath, data)
+
+class ToObjCoordsWorker(BaseWorkerUtil):
+    def __init__(self, mainWin):
+        super().__init__(mainWin)
+
+    @worker_exception_handler
+    def run(self):
+        debugging = False
+        expPaths = self.mainWin.expPaths
+        tot_exp = len(expPaths)
+        self.signals.initProgressBar.emit(0)
+        for i, (exp_path, pos_foldernames) in enumerate(expPaths.items()):
+            self.errors = {}
+            tot_pos = len(pos_foldernames)
+
+            abort = self.emitSelectSegmFiles(exp_path, pos_foldernames)
+            if abort:
+                self.signals.finished.emit(self)
+                return
+
+            for p, pos in enumerate(pos_foldernames):
+                if self.abort:
+                    self.signals.finished.emit(self)
+                    return
+
+                self.logger.log(
+                    f'Processing experiment n. {i+1}/{tot_exp}, '
+                    f'{pos} ({p+1}/{tot_pos})'
+                )
+
+                images_path = os.path.join(exp_path, pos, 'Images')
+                endFilenameSegm = self.mainWin.endFilenameSegm
+                ls = myutils.listdir(images_path)
+                file_path = [
+                    os.path.join(images_path, f) for f in ls 
+                    if f.endswith(f'{endFilenameSegm}.npz')
+                ][0]
+
+                posData = load.loadData(file_path, '')
+
+                self.signals.sigUpdatePbarDesc.emit(f'Processing {posData.pos_path}')
+
+                posData.getBasenameAndChNames()
+                posData.buildPaths()
+
+                posData.loadOtherFiles(
+                    load_segm_data=True,
+                    load_metadata=True,
+                    end_filename_segm=endFilenameSegm
+                )
+
+                if posData.SizeT > 1:
+                    posData.segm_data = posData.segm_data[np.newaxis]
+
+                dfs = []
+                for frame_i, lab in enumerate(posData.segm_data):
+                    df_coords_i = myutils.from_lab_to_obj_coords(
+                        posData.segm_data
+                    )
+                    dfs.append(df_coords_i)
+
+                df_filepath = posData.segm_npz_path.replace('.npz', '.csv')
+                df_filepath = df_filepath.replace('_segm', '_objects_coordinates')
+
+                keys = list(range(len(posData.segm_data)))
+                df = pd.concat(dfs, keys=keys, names=['frame_i'])
+                df.to_csv(df_filepath)
+
+        self.signals.finished.emit(self)