feat: allow selecting measurements to save to concat df table, see #364

cellacdc/__init__.py

@@ -1,4 +1,4 @@
-print('Initalising...')
+print('Initialising...')
 import os
 import sys
 import shutil

cellacdc/__main__.py

@@ -876,7 +876,9 @@ def launchApplyTrackingFromTableUtil(self):
             )
         )
         self.applyTrackWin.show()
-        func = partial(self._runApplyTrackingFromTableUtil, posPath, self.applyTrackWin)
+        func = partial(
+            self._runApplyTrackingFromTableUtil, posPath, self.applyTrackWin
+        )
         QTimer.singleShot(200, func)
 
     def _runApplyTrackingFromTableUtil(self, posPath, win):
@@ -1334,11 +1336,11 @@ def launchAlignUtil(self, checked=False):
         title = 'Align frames'
         infoText = 'Aligning frames in X and Y with phase cross-correlation...'
         progressDialogueTitle = 'Align frames'
-        self.concatWindow = utilsAlign.alignWin(
+        self.alignWindow = utilsAlign.alignWin(
             selectedExpPaths, self.app, title, infoText, progressDialogueTitle,
             parent=self
         )
-        self.concatWindow.show()
+        self.alignWindow.show()
 
     def launchConcatUtil(self, checked=False):
         self.logger.info(f'Launching utility "{self.sender().text()}"')

cellacdc/apps.py

@@ -1752,7 +1752,7 @@ def __init__(
             self, loadedChNames, notLoadedChNames, isZstack, isSegm3D,
             favourite_funcs=None, parent=None, allPos_acdc_df_cols=None,
             acdc_df_path=None, posData=None, addCombineMetricCallback=None,
-            allPosData=None
+            allPosData=None, is_concat=False
         ):
         super().__init__(parent=parent)
 
@@ -1762,6 +1762,7 @@ def __init__(
 
         self.delExistingCols = False
         self.okClicked = False
+        self.is_concat = is_concat
         self.allPos_acdc_df_cols = allPos_acdc_df_cols
         self.acdc_df_path = acdc_df_path
         self.allPosData = allPosData
@@ -1781,7 +1782,7 @@ def __init__(
         for col, chName in enumerate(loadedChNames):
             channelGBox = widgets.channelMetricsQGBox(
                 isZstack, chName, isSegm3D, favourite_funcs=favourite_funcs,
-                posData=posData
+                posData=posData, is_concat=is_concat
             )
             channelGBox.chName = chName
             groupsLayout.addWidget(channelGBox, 0, col, 3, 1)
@@ -1795,7 +1796,7 @@ def __init__(
         for col, chName in enumerate(notLoadedChNames):
             channelGBox = widgets.channelMetricsQGBox(
                 isZstack, chName, isSegm3D, favourite_funcs=favourite_funcs,
-                posData=posData
+                posData=posData, is_concat=is_concat
             )
             channelGBox.setChecked(False)
             channelGBox.chName = chName
@@ -1862,14 +1863,15 @@ def __init__(
                 self.mixedChannelsCombineMetricsQGBox, 2, current_col
             )
             groupsLayout.setRowStretch(1, 1)
-            self.setDisabledMetricsRequestedForCombined()
-            self.mixedChannelsCombineMetricsQGBox.toggled.connect(
-                self.setDisabledMetricsRequestedForCombined
-            )
-            for combCheckbox in self.mixedChannelsCombineMetricsQGBox.checkBoxes:
-                combCheckbox.toggled.connect(
+            if not self.is_concat:
+                self.setDisabledMetricsRequestedForCombined()
+                self.mixedChannelsCombineMetricsQGBox.toggled.connect(
                     self.setDisabledMetricsRequestedForCombined
                 )
+                for combCheckbox in self.mixedChannelsCombineMetricsQGBox.checkBoxes:
+                    combCheckbox.toggled.connect(
+                        self.setDisabledMetricsRequestedForCombined
+                    )
 
         self.numberCols = current_col
 
@@ -1916,6 +1918,11 @@ def channelCheckboxToggled(self, checkbox):
         if checkbox.text().find('concentration_') == -1:
             return
 
+        if self.is_concat:
+            # When this dialogue is used in concatenate pos utility we do not 
+            # need to check that certain metrics are present
+            return
+
         pattern = r'.+_from_vol_([a-z]+)(_3D)?(_?[A-Za-z0-9]*)'
         repl = r'cell_vol_\1\2'
         cell_vol_metric_name = re.sub(pattern, repl, checkbox.text())
@@ -1957,6 +1964,10 @@ def sizeMetricToggled(self, checked):
         checked : bool
             State of the checkbox toggled
         """
+        if self.is_concat:
+            # When this dialogue is used in concatenate pos utility we do not 
+            # need to check that certain metrics are present
+            return
 
         checkbox = self.sender()
         if not hasattr(checkbox, 'isRequired'):
@@ -2137,6 +2148,11 @@ def loadLastSelection(self):
         self.doNotWarn = False
 
     def setDisabledMetricsRequestedForCombined(self, checked=True):
+        if self.is_concat:
+            # When this dialogue is used in concatenate pos utility we do not 
+            # need to check that certain metrics are present
+            return
+
         # Set checked and disable those metrics that are requested for 
         # combined measurements
         allCheckboxes = []
@@ -2178,11 +2194,61 @@ def keyPressEvent(self, a0: QKeyEvent) -> None:
     def closeEvent(self, event):
         if self.cancel:
             self.sigCancel.emit()
+        super().closeEvent(event)
 
     def restart(self):
         self.cancel = False
         self.close()
         self.sigRestart.emit()
+
+    def setDisabledNotExistingMeasurements(self, existing_colnames):
+        for chNameGroupbox in self.chNameGroupboxes:
+            for checkBox in chNameGroupbox.checkBoxes:
+                colname = checkBox.text()
+                if colname in existing_colnames:
+                    checkBox.setChecked(True)
+                    continue
+
+                checkBox.setChecked(False)
+                checkBox.setDisabled(True)
+                self.setNotExistingMeasurementTooltip(checkBox)
+
+        for checkBox in self.sizeMetricsQGBox.checkBoxes:
+            colname = checkBox.text()
+            if colname in existing_colnames:
+                checkBox.setChecked(True)
+                continue
+            checkBox.setChecked(False)
+            checkBox.setDisabled(True)
+            self.setNotExistingMeasurementTooltip(checkBox)
+
+        for checkBox in self.regionPropsQGBox.checkBoxes:
+            colname = checkBox.text()
+            if any([col == colname for col in existing_colnames]):
+                checkBox.setChecked(True)
+                continue
+            checkBox.setChecked(False)
+            checkBox.setDisabled(True)
+            self.setNotExistingMeasurementTooltip(checkBox)
+
+        if self.mixedChannelsCombineMetricsQGBox is None:
+            return
+
+        for combCheckbox in self.mixedChannelsCombineMetricsQGBox.checkBoxes:
+            colname = combCheckbox.text()
+            if colname in existing_colnames:
+                combCheckbox.setChecked(True)
+                continue
+            combCheckbox.setChecked(False)
+            combCheckbox.setDisabled(True)
+            self.setNotExistingMeasurementTooltip(combCheckbox)
+
+    def setNotExistingMeasurementTooltip(self, checkBox):
+        checkBox.setToolTip(
+            'Measurement is disabled because it is not present in selected '
+            'acdc_output tables, hence it cannot be addded to concatenated '
+            'table. '
+        )
 
     def ok_cb(self):
         if self.allPos_acdc_df_cols is None:

cellacdc/gui.py

@@ -11925,7 +11925,6 @@ def postProcessSegmValueChanged(self, lab, delObjs: dict):
 
     def readSavedCustomAnnot(self):
         tempAnnot = {}
-        printl(custom_annot_path)
         if os.path.exists(custom_annot_path):
             self.logger.info('Loading saved custom annotations...')
             tempAnnot = load.read_json(
@@ -20630,7 +20629,7 @@ def showSetMeasurements(self, checked=False):
             allPos_acdc_df_cols=list(allPos_acdc_df_cols),
             acdc_df_path=posData.images_path, posData=posData,
             addCombineMetricCallback=self.addCombineMetric,
-            allPosData=self.data
+            allPosData=self.data, parent=self
         )
         self.measurementsWin.sigClosed.connect(self.setMeasurements)
         self.measurementsWin.show()

cellacdc/load.py

@@ -194,6 +194,13 @@ def load_segm_file(images_path, end_name_segm_file='segm', return_path=False):
         else:
             return 
 
+def load_metadata_df(images_path):
+    for file in myutils.listdir(images_path):
+        if not file.endswith('metadata.csv'):
+            continue
+        filepath = os.path.join(images_path, file)
+        return pd.read_csv(filepath).set_index('Description')
+
 def _add_will_divide_column(acdc_df):
     if 'cell_cycle_stage' not in acdc_df.columns:
         return acdc_df

cellacdc/measurements.py

@@ -110,6 +110,8 @@ def get_custom_metrics_func():
     scripts = os.listdir(acdc_metrics_path)
     custom_func_dict = {}
     for file in scripts:
+        if file == '__init__.py':
+            continue
         module_name, ext = os.path.splitext(file)
         if ext != '.py':
             # print(f'The file {file} is not a python file. Ignoring it.')

cellacdc/myutils.py

@@ -1664,6 +1664,7 @@ def check_install_cellpose():
         if major < 2:
             _install_pip_package('cellpose')
     except Exception as e:
+        printl(traceback.format_exc())
         _inform_install_package_failed('cellpose')
 
 def check_install_segment_anything():
@@ -1697,6 +1698,7 @@ def check_install_package(
             else:
                 _install_pip_package(pkg_name)
         except Exception as e:
+            printl(traceback.format_exc())
             _inform_install_package_failed(
                 pkg_name, parent=parent, do_exit=raise_on_cancel
             )
@@ -1724,6 +1726,7 @@ def check_matplotlib_version(qparent=None):
                 [sys.executable, '-m', 'pip', 'install', '-U', 'matplotlib']
             )
         except Exception as e:
+            printl(traceback.format_exc())
             _inform_install_package_failed(
                 'matplotlib', parent=qparent, do_exit=False
             )
@@ -1747,8 +1750,6 @@ def _inform_install_package_failed(pkg_name, parent=None, do_exit=True):
         f'`pip install --upgrade {pkg_name}`'
     )
     print('^'*50)
-    if do_exit:
-        exit()
 
 def _install_package_msg(
         pkg_name, note='', parent=None, upgrade=False, caller_name='Cell-ACDC'

cellacdc/utils/concat.py

@@ -1,6 +1,7 @@
 from qtpy.QtWidgets import QFileDialog
 
 from .. import apps, myutils, workers, widgets, html_utils
+from .. import printl
 
 from .base import NewThreadMultipleExpBaseUtil
 
@@ -20,11 +21,96 @@ def runWorker(self):
         self.worker = workers.ConcatAcdcDfsWorker(self)
         self.worker.sigAskFolder.connect(self.askFolderWhereToSaveAllExp)
         self.worker.sigAborted.connect(self.workerAborted)
+        self.worker.sigAskAppendName.connect(self.askAppendName)
+        self.worker.sigSetMeasurements.connect(self.askSetMeasurements)
         super().runWorker(self.worker)
 
+    def askSetMeasurements(self, kwargs):
+        loadedChNames = kwargs['loadedChNames']
+        notLoadedChNames = kwargs['notLoadedChNames']
+        isZstack = kwargs['isZstack']
+        isSegm3D = kwargs['isSegm3D']
+        self.setMeasurementsWin = apps.setMeasurementsDialog(
+            loadedChNames, notLoadedChNames, isZstack, isSegm3D,
+            is_concat=True, parent=self
+        )
+        existing_colnames = kwargs['existing_colnames']
+        self.setMeasurementsWin.setDisabledNotExistingMeasurements(
+            existing_colnames
+        )
+        self.setMeasurementsWin.sigClosed.connect(self.setMeasurements)
+        self.setMeasurementsWin.sigCancel.connect(self.setMeasurementsCancelled)
+        self.setMeasurementsWin.show()
+
+    def setMeasurements(self):
+        selectedColumns = []
+        for chNameGroupbox in self.setMeasurementsWin.chNameGroupboxes:
+            chName = chNameGroupbox.chName
+            if not chNameGroupbox.isChecked():
+                # Skip entire channel
+                continue
+
+            for checkBox in chNameGroupbox.checkBoxes:
+                if not checkBox.isChecked():
+                    continue
+                colname = checkBox.text()
+                selectedColumns.append(colname)
+
+        if self.setMeasurementsWin.sizeMetricsQGBox.isChecked():
+            for checkBox in self.setMeasurementsWin.sizeMetricsQGBox.checkBoxes:
+                if not checkBox.isChecked():
+                    continue
+                colname = checkBox.text()
+                selectedColumns.append(colname)
+
+        if self.setMeasurementsWin.regionPropsQGBox.isChecked():
+            for checkBox in self.setMeasurementsWin.regionPropsQGBox.checkBoxes:
+                if not checkBox.isChecked():
+                    continue
+                colname = checkBox.text()
+                selectedColumns.append(colname)
+
+        checkMixedChannel = (
+            self.setMeasurementsWin.mixedChannelsCombineMetricsQGBox is not None
+            and self.setMeasurementsWin.mixedChannelsCombineMetricsQGBox.isChecked()
+        )
+        if checkMixedChannel:
+            win = self.setMeasurementsWin
+            checkBoxes = win.mixedChannelsCombineMetricsQGBox.checkBoxes
+            for checkBox in checkBoxes:
+                if not checkBox.isChecked():
+                    continue
+                colname = checkBox.text()
+                selectedColumns.append(colname)
+
+        self.worker.selectedColumns = selectedColumns
+        self.worker.abort = False
+        self.worker.waitCond.wakeAll()
+
+    def setMeasurementsCancelled(self):
+        self.worker.abort = True
+        self.worker.waitCond.wakeAll()
+
     def showEvent(self, event):
         self.runWorker()
 
+    def askAppendName(self, basename, existingEndnames):
+        win = apps.filenameDialog(
+            basename=basename,
+            hintText='Insert a name for the <b>concatenated table</b> file:',
+            existingNames=existingEndnames, 
+            allowEmpty=True,
+            ext='.csv'
+        )
+        win.exec_()
+        if win.cancel:
+            self.worker.abort = True
+            self.worker.waitCond.wakeAll()
+            return
+
+        self.worker.concat_df_filename = win.filename
+        self.worker.waitCond.wakeAll()
+
     def askFolderWhereToSaveAllExp(self, allExp_filename):
         txt = html_utils.paragraph(f"""
             After clicking "Ok" you will be asked to <b>select a folder where you
@@ -53,7 +139,8 @@ def askFolderWhereToSaveAllExp(self, allExp_filename):
         self.worker.waitCond.wakeAll()
 
     def workerAborted(self):
-        self.workerFinished(None, aborted=True)
+        self.worker.signals.finished.emit(self)
+        self.workerFinished(self.worker, aborted=True)
 
     def workerFinished(self, worker, aborted=False):
         if aborted: