pyest is broken with core radius offset

src/pymapmanager/annotations/baseAnnotationsCore.py

@@ -677,7 +677,7 @@ def getMedianZ(self, segmentID : int):
         return (x, y, z)
 
     def getSummaryDf(self) -> pd.DataFrame:
-        """DataFrame with per segment info (one segment per ro)
+        """DataFrame with per segment info (one segment per row)
         """
         return self._summaryDf
 
@@ -688,7 +688,7 @@ def _buildSummaryDf(self) -> pd.DataFrame:
 
         segmentDf = self.singleTimepoint.segments[:]
 
-        _columns = ['Segment', 'Points', 'Length', 'Radius', 'Pivot Distance']
+        _columns = ['Segment', 'Points', 'Length', 'Radius', 'Pivot Distance', 'Color']
         summaryDf = pd.DataFrame(columns=_columns)
 
         try:
@@ -697,6 +697,7 @@ def _buildSummaryDf(self) -> pd.DataFrame:
             summaryDf.index = segmentDf.index
             summaryDf['Radius'] = segmentDf['radius']
             summaryDf['Pivot Distance'] = segmentDf['pivotDistance']
+            summaryDf['Color'] = segmentDf['color']
 
         except (AttributeError) as e:
             # when no segments
@@ -792,13 +793,18 @@ def getNumSegments(self) -> int:
         else:
             return len(self._singleTimePoint.segments[:])
 
-    def setValue(self, segmentID, value):
+    # abb this needs to be specifically for 'radius'
+    def setValue(self, colName, segmentID, value):
         """
         """
         from mapmanagercore.schemas.segment import Segment
 
         #  updateSegment(self, segmentId: Keys, value: Segment, replaceLog=False, skipLog=False):
-        _segment = Segment(radius=value)
+        if colName == 'radius':
+            _segment = Segment(radius=value)
+        elif colName == 'color':
+            _segment = Segment(color=value)
+
         self.singleTimepoint.updateSegment(segmentId = segmentID, value=_segment)
 
         self._buildTimepoint()
@@ -816,8 +822,8 @@ def getPivotPoint(self):
             returnPointX: List of Y values of pivot points
             
         """
-        logger.info('self._summaryDf:')
-        print(self._summaryDf)
+        # logger.info('self._summaryDf:')
+        # print(self._summaryDf)
 
         returnPointX = []
         returnPointY = []
@@ -837,32 +843,59 @@ def getPivotPoint(self):
 
         return returnPointX, returnPointY, returnPointZ
 
-    def getLeftRadiusPlot(self, sliceNumber, zPlusMinus):
-        # segmentLines = self._df 
-        # logger.info(f"self._fullMap segments columns {self._fullMap.segments}")
+    import geopandas as gp
+    def getRadiusPlot(self, leftRight : str, sliceNumber, zPlusMinus) -> gp.GeoSeries:
+        """
+        Parameters
+        ==========
+        leftRight : str
+            One of ('leftRadius', 'rightRadius')
+
+        Returns
+        =======
+        df with segmentID labels columns (x, y, z, rowIndex, color)
+        """
+
         zSlice = sliceNumber
         if self.getNumSegments() == 0:
             return None
 
+        # all segments (we are clipping to sliceNumber)
+        # this has color
         segmentDf = self.singleTimepoint.segments[:]
 
-        # logger.info(f"segmentDf['leftRadius'] {segmentDf['leftRadius']}")
+        # logger.info('segmenDf is:')
+        # print(segmentDf.columns)
+
         _startSlice = zSlice - zPlusMinus
         _stopSlice = zSlice + zPlusMinus
-        xyLeft = clipLines(segmentDf['leftRadius'], zRange = (_startSlice, _stopSlice))
-        xyLeft = xyLeft.get_coordinates(include_z=True)
-        xyLeft['rowIndex'] = list(np.arange(len(xyLeft)))
+
+        # one row per segment -> gp.GeoSeries
+        xyLeft = clipLines(segmentDf[leftRight], zRange = (_startSlice, _stopSlice))
+
+        # logger.info('xyLeft is')
+        # print(xyLeft)
+
+        xyLeft = xyLeft.get_coordinates(include_z=True)  # z is empty
+        xyLeft['rowIndex'] = list(np.arange(len(xyLeft)))  # used to determine if points in plot are contiguous
+
+        summaryDf = self.getSummaryDf()  # gives us 'Color' per segment ID
+        xyLeft['color'] = summaryDf.loc[xyLeft.index, 'Color']
+
+        # logger.info('after xyLeft is:')
+        # print(xyLeft)
+
         return xyLeft
 
-    def getRightRadiusPlot(self, sliceNumber, zPlusMinus):
-        zSlice = sliceNumber
-        if self.getNumSegments() == 0:
-            return None
-
-        segmentDf = self.singleTimepoint.segments[:]
-        _startSlice = zSlice - zPlusMinus
-        _stopSlice = zSlice + zPlusMinus
-        xyRight= clipLines(segmentDf['rightRadius'], zRange = (_startSlice, _stopSlice))
-        xyRight = xyRight.get_coordinates(include_z=True)
-        xyRight['rowIndex'] = list(np.arange(len(xyRight)))
-        return xyRight
+    # def getRightRadiusPlot(self, sliceNumber, zPlusMinus):
+    #     zSlice = sliceNumber
+    #     if self.getNumSegments() == 0:
+    #         return None
+
+    #     segmentDf = self.singleTimepoint.segments[:]
+    #     _startSlice = zSlice - zPlusMinus
+    #     _stopSlice = zSlice + zPlusMinus
+    #     xyRight= clipLines(segmentDf['rightRadius'], zRange = (_startSlice, _stopSlice))
+    #     xyRight = xyRight.get_coordinates(include_z=True)
+    #     xyRight['rowIndex'] = list(np.arange(len(xyRight)))
+    #     return xyRight

src/pymapmanager/interface2/core/search_widget.py

@@ -171,17 +171,26 @@ def data(self, index, role) -> str:
         """
 
         # abb adding segment color
-        if role == Qt.BackgroundRole:
+        # if role == Qt.BackgroundRole:
+        if role == Qt.BackgroundColorRole:
             row = index.row()
             col = index.column()
-            # Get the corresponding row within the actual dataframe
-            # They could be different values due to deleting
-            rowLabel = self._data.index.tolist()[row]
-            # logger.warning(f'row:{row} rowLabel:{rowLabel}')
-            if col==0 and rowLabel == 3:
-                _color = QtGui.QColor('#38ff2a')
+            colName = self._data.columns[col]
+            if colName == 'Color':
+                # Get the corresponding row within the actual dataframe
+                # They could be different values due to deleting
+                rowLabel = self._data.index.tolist()[row]
+                # logger.warning(f'row:{row} rowLabel:{rowLabel} {type(rowLabel)}')
+                _colorHex = self._data.loc[rowLabel, 'Color']
+                # logger.info(f'row:{row} col:{col} colName:{colName} _colorHex:{_colorHex}')
+                _color = QtGui.QColor(_colorHex)
                 return QtGui.QBrush(_color) 
-
+            else:
+                if(index.row() % 2 == 0):
+                    return QtGui.QBrush(QtGui.QColor(0,0,0))
+                else:
+                    return QtGui.QBrush(QtGui.QColor(40,40,40))
+
         # print("data", self.rowCount(None))
         # print("role: ", type(role))
         if role == Qt.DisplayRole:
@@ -331,7 +340,7 @@ def __init__(self, df : pd.DataFrame = None, name : str = None):
         # Selecting only Rows - https://doc.qt.io/qt-6/qabstractitemview.html#SelectionBehavior-enum
         self.setSelectionBehavior(QTableView.SelectRows)
 
-        self.setAlternatingRowColors(True)
+        # self.setAlternatingRowColors(True)
 
         self.setSortingEnabled(True)
 
@@ -391,8 +400,8 @@ def showColumns(self, showColList : List[str]):
                 index = self.df.columns.get_loc(colName)
                 self.showColumn(index)
             except (KeyError) as e:
-                logger.error(f'did not find column name {colName}')
-                logger.error(e)
+                logger.error(f'did not find column name "{colName}"')
+                logger.error(f'available columns are: {self.df.columns}')
 
     def updateCurrentCol(self, newColName):
         """Called whenever signal is received to update column name
@@ -530,10 +539,23 @@ def getSelectedRows(self):
         # logger.info(f"selectedRows {selectedRows}")
         return selectedRows
 
-    # def keyPressEvent(self, event : QtGui.QKeyEvent):
-    #     super().keyPressEvent(event)
-    #     # abb on_selectionChanged is not using its params
-    #     # self.on_selectionChanged(None)
+    def _getSelectedRowLabels(self):
+        """Get selected row labels (points or segment) using row index of table
+        """
+        selectedRows = self.getSelectedRows()
+
+        rowLabelList = []
+        for row in selectedRows:
+            try:
+                rowLabel = self.model._data.index[row]  # abb new
+                rowLabel = int(rowLabel)
+                rowLabelList.append(rowLabel)
+            except (KeyError) as e:
+                logger.error(f'myQTableView did not find row label: {row}')
+                logger.error('df is:')
+                print(self.model._data)
+
+        return rowLabelList
 
     def on_selectionChanged(self, item):
         """Respond to user selection.

src/pymapmanager/interface2/pyMapManagerApp2.py

@@ -197,7 +197,8 @@ def loadPlugins(pluginType : str, verbose = False) -> dict:
             if _widgetName == 'Stack Widget':
                 continue
 
-            logger.info(f'   adding {pluginType} moduleName:{moduleName} _widgetName:{_widgetName}')
+            if verbose:
+                logger.info(f'   adding {pluginType} moduleName:{moduleName} _widgetName:{_widgetName}')
             # _showInMenu = obj.showInMenu  # showInMenu is a static bool
             onePluginDict = {
                 "pluginClass": moduleName,

src/pymapmanager/interface2/runInterfaceBob.py

@@ -9,42 +9,40 @@
 from pymapmanager._logger import logger
 
 def run():
-    app = PyMapManagerApp(sys.argv)
-
-    # open a single timepoint map with segments and spines
-    # path = mapmanagercore.data.getSingleTimepointMap()
-
-    # a single timepoint tif file (import)
-    # path = mapmanagercore.data.getTiffChannel_1()
-
-    # .ome.zar (local)
-    # path = '/Users/cudmore/Sites/MapManagerCore-Data/data/single_timepoint_v3.ome.zarr'
-    # path = '/Users/cudmore/Sites/MapManagerCore-Data/data/single_timepoint.ome.zarr'
-
-    # .ome.zar (remote)
-    # path = 'https://github.com/mapmanager/MapManagerCore-Data/raw/main/data/single_timepoint.ome.zarr'
 
     # random ome zarr file (remote)
     # path = 'https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr'
     # random ome zarr file (local)
     # path = '/Users/cudmore/Dropbox/data/ome-zarr/6001240.ome.zarr'
 
+    # open a single timepoint map with segments and spines
+    # path = mapmanagercore.data.getSingleTimepointMap()
+
+    # a single timepoint tif file (import)
+    path = mapmanagercore.data.getTiffChannel_1()
+
     # path = mapmanagercore.data.getSingleTimepointMap()
 
     # a mmap with multiple timepoints, connects segments and spines
     # path = '/Users/cudmore/Desktop/multi_timepoint_map_seg_spine_connected.mmap'
-    path = mapmanagercore.data.getMultiTimepointMap()
-
-    # path = '/Users/cudmore/Desktop/yyy4.mmap'
-    # path = '/Users/cudmore/Desktop/single_timepoint.mmap'
-
-    # path = 'https://github.com/mapmanager/MapManagerCore-Data/raw/main/data/single_timepoint.zip.mmap'
-
-    logger.info(path)
+    # path = mapmanagercore.data.getMultiTimepointMap()
 
+    app = PyMapManagerApp(sys.argv)
     # mw will be map widget if path has multiple timepoints, otherwise mw is a stackwidget2
     mw = app.loadStackWidget(path)
 
+    # run a stack plugin
+    # mw.runPlugin('Stack Contrast')
+
+    # works
+    from pprint import pprint
+    # logger.info('getTimeSeriesCore')
+    # pprint(mw.getTimeSeriesCore().getMapImages().metadata(0).experimentMetadata.getValue('Species'))
+    # pprint(mw.getTimeSeriesCore().getMapImages().metadata(0).experimentMetadata.asDict())
+
+    # print('segments:')
+    # pprint(mw.getTimeSeriesCore().getSegments()['color'])
+
     # zoom to point (single timepoint)
     # sw2.zoomToPointAnnotation(120, isAlt=True)
 

src/pymapmanager/interface2/stackWidgets/annotationListWidget2.py

@@ -42,6 +42,44 @@ def __init__(self,
         self._buildGui(name=name)
         self._setModel()
 
+        # rewire context menu
+        self._myTableView.contextMenuEvent = self._contextMenuEvent
+
+    def _contextMenuEvent(self, event):
+        self.menu = QtWidgets.QMenu(self)
+        colorAction = QtWidgets.QAction('Set Color', self)
+        colorAction.triggered.connect(lambda: self._colorPickerSlot(event))
+        self.menu.addAction(colorAction)
+
+        # action = _menu.exec_(self.mapToGlobal(event.pos()))
+        self.menu.popup(QtGui.QCursor.pos())
+
+    def _colorPickerSlot(self, event):
+        """Show color dialog and set segment color.
+        """
+        selectedRowLabels = self._myTableView._getSelectedRowLabels()
+        # logger.warning(f'getSelectedRows:{selectedRowLabels}')
+        if len(selectedRowLabels) > 0:
+            selectedRowLabel = selectedRowLabels[0]
+            _hexColor = self._myTableView.model._data.loc[selectedRowLabel, 'Color']
+            # logger.info(f'_hexColor:{_hexColor}')
+
+            colorDialog = QtWidgets.QColorDialog(self)
+            _initColor = QtGui.QColor(_hexColor)
+            # logger.info(f'_initColor.name():{_initColor.name()}')
+
+            # abb TODO this is not setting the color in the dialog?
+            colorDialog.setCurrentColor(_initColor)
+
+            # logger.info('getting color')
+            newColor = colorDialog.getColor()  # QColor
+            if newColor.isValid():
+                logger.info(f'selected color:{newColor.name()}')  # name defaults to hex
+                # TODO emit color change event
+                from pymapmanager.interface2.stackWidgets.event.segmentEvent import SetSegmentColorEvent
+                setSegmentColorEvent = SetSegmentColorEvent(self, selectedRowLabel, newColor.name())
+                self.emitEvent(setSegmentColorEvent)
+
     def undoEvent(self, event):
         # TODO: make distinction between undo spine and segment edits
         # possibly make distinction between undo (add, delet, edit)
@@ -311,13 +349,13 @@ def on_table_selection(self, itemList : List[int], isAlt : bool = False):
     def _deleteSelected(self):
         """Delete currently selected annotations.
         """
-        items = self._myTableView.getSelectedRows()
-        logger.info(f'items:{items}')
+        # items = self._myTableView.getSelectedRows()
+        # logger.info(f'items:{items}')
 
         spineLabelList = self._getSelectedRowLabels()
         logger.info(f'  delete spine label list:{spineLabelList}')
 
-        if len(items) > 0:
+        if len(spineLabelList) > 0:
             deleteSpineEvent = DeleteSpineEvent(self, spineLabelList)
             self.emitEvent(deleteSpineEvent)
 
@@ -491,6 +529,10 @@ def setRadiusEvent(self, event):
         # reselect current segment
         self._myTableView._selectRow([segmentID])
 
+    def setSegmentColorEvent(self, event):
+        logger.info('')
+        self._setModel()
+
     def updateSegmentRadius(self, newRadius):
         """ Update segment radius stored in backend
             - each segment has its own unique radius stored