merge j-dev 20241206

Author: cudmore

pymapmanager/annotations/baseAnnotationsCore.py

@@ -22,6 +22,9 @@
 
 from pymapmanager._logger import logger
 
+def getUserTypeMarkers_mpl():
+    return ['o', 'v', '^', '<', '>', 'D', 'd', '*', 'p' ,'h']
+
 class AnnotationsCore:
     def __init__(self,
                  timeSeriesCore : TimeSeriesCore,  # multi timepoint
@@ -262,7 +265,7 @@ def getDirty(self):
         return self._isDirty 
 
 class SpineAnnotationsCore(AnnotationsCore):
-        
+    
     def _buildDataFrame(self):
         """Dataframe representing backend spines, one row per spine.
         
@@ -289,7 +292,26 @@ def _buildDataFrame(self):
                 print(allSpinesDf)
 
         allSpinesDf['roiType'] = 'spineROI'
-        allSpinesDf.insert(0,'index', allSpinesDf.index)  # index is first column
+        allSpinesDf.insert(0,'index', allSpinesDf.index)  # index is first column (use this as row label)
+
+        # if len(allSpinesDf) > 0:
+            # TODO make this work
+            # marker color
+            # allSpinesDf['markerColor'] = 'm'
+            # try:
+            #     _notAcceptRowLabels = allSpinesDf[ not allSpinesDf['accept'] ]
+            #     allSpinesDf.loc[_notAcceptRowLabels, 'markerColor'] = 'w'
+            # except (KeyError) as e:
+            #     logger.error(f'{e}')
+            #     logger.error(f'available columns are: {allSpinesDf.columns}')
+
+            # TODO make this work
+            # _userTypeMarkers = getUserTypeMarkers_mpl()
+            # allSpinesDf['mplMarker'] = 'o'
+            # for userType in range(10):
+            #     # 10 user types
+            #     _userTypeRowLabels = allSpinesDf[ allSpinesDf['userType'] == userType]
+            #     allSpinesDf.loc[_userTypeRowLabels, 'mplMarker'] = _userTypeMarkers[userType]
 
         self._df = allSpinesDf
 
@@ -740,6 +762,8 @@ def getPivotPoint(self):
 
         # find pivotDistance within point distance, that is what we plot
         pivotDistances = self._summaryDf["Pivot Distance"]
+        """List[float], one item per segment id"""
+        
         pointDistance = self._summaryDf["Point Distances"]
 
         returnPointX = []

pymapmanager/interface2/core/scatter_plot_widget.py

@@ -503,7 +503,7 @@ def on_scatter_toolbar_table_click(self):
         statName = self.myTableWidget.item(row,0).text()
         self.signalUpdateStat.emit(self._id, statName)
 
-class ScatterPlotWidget(QtWidgets.QWidget):
+class ScatterPlotWidget_(QtWidgets.QWidget):
     """Plot x/y statistics as a scatter.
 
     Get stat names and variables from sanpy.bAnalysisUtil.getStatList()
@@ -721,8 +721,7 @@ def getfilteredDFWithIndexList(self, filterStr, filterColumn) -> pd.DataFrame:
         return df, indexList
 
     def getFilteredIndexList(self, filterDF):
-        """
-            Calculate the new list of indexes after hue filtering DF
+        """Calculate the new list of indexes after hue filtering DF.
         """
         hueColumn = self.dict["hueColumn"]
         currentHueID = float(self.dict["currentHueID"]) 
@@ -756,7 +755,7 @@ def setScatterPlot(self, xStat, yStat, xyStatIndex):
                     myColorMap.append("white")
                 else:
                     if hueColumn != "None":
-                        logger.info(f"hueColumn {hueColumn} id:{id}")
+                        logger.info(f'hueColumn: "{hueColumn}" id:{id}')
                         hueId = self._df[hueColumn].iloc[id]
                         myColorMap.append(self.color[hueId])
 
@@ -1222,39 +1221,28 @@ def _switchScatter(self):
         self.myHighlighter.resetHighlighter(self.axScatter, np.array([]), np.array([]), np.array([]))
 
     # IMPORTANT SIGNAL-SLOT CONNECTION (outside wrapper -> inside)
-    def selectHighlighterPoints(self, rowIndexes):    
+    def selectHighlighterPoints(self, rowIndexes : List[int]):    
         """ Select Data in Highlighter Class
 
         This function needs to be connected within wrapper class. 
         Outside selection emits signal to this function to update highlighter plot
         Args:
             rowIndexes: indexes of rows that need to be selected within highlighter plot
         """
-
-        # If nothing is selected empty highlighter plot
-        if rowIndexes == None:
+        if rowIndexes is None or rowIndexes == []:
             self.myHighlighter._setData([], [])
         else: 
-            # Otherwise get the appropriate values and plot
             columnNameX = self.xPlotWidget.getCurrentStat()
             columnNameY = self.yPlotWidget.getCurrentStat()
-
-            # Get column values into respective lists
-            xFilteredVals =  self._df[columnNameX].tolist()
-            yFilteredVals = self._df[columnNameY].tolist()
-            # logger.info(f"rowIndexes {rowIndexes}")
-            # logger.info(f"xFilteredVals {xFilteredVals}")
-            # logger.info(f"yFilteredVals {yFilteredVals}")
 
-            # Acquire only selected rowIndexes from the lists
-            xDFStat = [xFilteredVals[i] for i in rowIndexes]
-            yDFStat = [yFilteredVals[i] for i in rowIndexes]
-            self.myHighlighter._setData(xDFStat, yDFStat)
+            # pull x/y values from selected row(s)
+            xSelectValues =  self._df.loc[rowIndexes, columnNameX].tolist()
+            ySelectValues = self._df.loc[rowIndexes, columnNameY].tolist()
+
+            self.myHighlighter._setData(xSelectValues, ySelectValues)
 
             # Store selected rows for later use
             self.storedRowIdx = rowIndexes
-            logger.info(f"self.storedRowIdx {self.storedRowIdx}")
-            logger.info("select Highlighter Points called")
 
     def getHighlightedIndexes(self):
         return self.storedRowIdx

pymapmanager/interface2/mapWidgets/mapWidget.py

@@ -188,11 +188,9 @@ def openStackRun(self,
             # toggle interface
             # dict_keys(['top toolbar', 'Point List', 'Line List', 'image plot', 'Histogram'])
             if _multipleTp:
-                bsw._toggleWidget("top toolbar", False)
+                bsw._toggleWidget("Top Toolbar", False)
                 bsw._toggleWidget("Point List", False)
-                bsw._toggleWidget("Line List", False)
-                # bsw._toggleWidget("tracing widget qqq", False)
-                bsw._toggleWidget("Histogram", False)
+                bsw._toggleWidget("Segment List", False)
                 # bsw._toggleWidget("Status Bar", False)
 
             # select a point and zoom

pymapmanager/interface2/runInterfaceBob.py

@@ -11,13 +11,31 @@
 def run():
     app = PyMapManagerApp(sys.argv)
 
-    #
     # open a single timepoint map with segments and spines
-    # path = mapmanagercore.data.getSingleTimepointMap()
+    path = mapmanagercore.data.getSingleTimepointMap()
+
+    # path = '/Users/cudmore/Sites/data/rr30a_s0u_20241205.mmap'
+
+    # path = '/Users/cudmore/Dropbox/data/ome-zarr/single_timepoint_v2.ome.zarr'
+
+    # .mmap (zarr folder, local)
+    # path = '/Users/cudmore/Sites/MapManagerCore-Data/data/multi_timepoint_map.mmap'
+
+    # .mmap (zip file, local)
+    # path = '/Users/cudmore/Sites/MapManagerCore-Data/data/multi_timepoint_map_zip.mmap'
+
+    # .ome.zar (local)
+    # 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'
 
     # a single timepoint tif file
-    # error in images
-    # IndexError: index -2 is out of bounds for axis 0 with size 1
     # path = mapmanagercore.data.getTiffChannel_1()
 
     # map with segments and spines (no segments connected)
@@ -35,7 +53,7 @@ def run():
 
     # 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 = mapmanagercore.data.getMultiTimepointMap()
 
     # mw will be map widget if path has multiple timepoints, otherwise mw is a stackwidget2
     mw = app.loadStackWidget(path)

pymapmanager/interface2/stackWidgets/imagePlotWidget2.py

@@ -648,8 +648,11 @@ def _setSlice(self, sliceNumber : int, doEmit = True):
 
             # print('2) ch1_image:', ch1_image.shape, ch1_image.dtype)
 
+            _xShape = ch0_image.shape[0]
+            _yShape = ch0_image.shape[1]
+            sliceImage = np.ndarray((_xShape,_yShape,3))
+            
             # magenta is blue + red
-            sliceImage = np.ndarray((1024,1024,3))
             sliceImage[:,:,0] = ch1_image  # red
             sliceImage[:,:,1] = ch0_image  # green
             sliceImage[:,:,2] = ch1_image  # blue