phoenix 2/2

Author: cudmore

src/pymapmanager/annotations/baseAnnotationsCore.py

@@ -135,7 +135,7 @@ def getSegmentPlot(self,
         return df
 
     def getRow(self, rowIdx : int):
-        """Get columns and values for one row index.
+        """Get columns and values for one row label index.
         """
         df = self.getDataFrame() 
         row = df.loc[rowIdx]
@@ -463,15 +463,15 @@ def editSpine(self, editSpineProperty : List[dict]):
 
     def spineID_Exists(self, spineID : int) -> bool:
         if not isinstance(spineID, int):
-            logger.error(f'got bad spineID:{spineID}, expecting int')
+            logger.error(f'got bad spineID:{spineID} {type(spineID)}, expecting int')
             return False
         if spineID not in self.singleTimepoint.points.index:
             logger.error(f'spineID:{spineID} does not exists')
             # print(self.singleTimepoint.points.index)
             return False
 
-        logger.info(f'spineID:{spineID}')
-        print(self.singleTimepoint.points.index)
+        # logger.info(f'spineID:{spineID}')
+        # print(self.singleTimepoint.points.index)
         return True
 
     def moveSpine(self, spineID :int, x, y, z):

src/pymapmanager/interface2/runInterfaceBob.py

@@ -27,6 +27,8 @@ def run():
     # path = '/Users/cudmore/Desktop/multi_timepoint_map_seg_spine_connected.mmap'
     # path = mapmanagercore.data.getMultiTimepointMap()
 
+    path = '/Users/cudmore/Desktop/olsen_example.mmap'
+
     app = PyMapManagerApp(sys.argv)
     # mw will be map widget if path has multiple timepoints, otherwise mw is a stackwidget2
     mw = app.loadStackWidget(path)

src/pymapmanager/interface2/stackWidgets/spineInfoWidget.py

@@ -36,7 +36,13 @@ def __init__(self, stackWidget : stackWidget2):
 
         # The columns values that are displayed
         # self.infoList = ["index", "segmentID", "note", 'accept', 'userType', 'spineLength']
-        self._displayList = ["index", "segmentID", 'spineLength', 'roiType']
+        self._displayList = ["index",
+                             "segmentID",
+                             'spineLength',
+                             'spineAngle',
+                             'spineSide',
+                             'roiType']
+        # this list can be edited by user
         self.infoList = self._displayList + ["note", 'accept', 'userType']
 
         # Maintain different widgets that display information
@@ -84,9 +90,9 @@ def _selectionInfoUI(self):
             vLayout.addWidget(aLabel, row, col, rowSpan, colSpan)
             col += 1
 
-            # if itemName == 'index':
+            # if itemName in ['index', 'roiType', 'segmentID', 'spineLength']:
             #     aWidget = QtWidgets.QLabel()
-            if itemName in ['index', 'roiType', 'segmentID', 'spineLength']:
+            if itemName in self._displayList:
                 aWidget = QtWidgets.QLabel()
             elif itemName == 'note':
                 aWidget = QtWidgets.QLineEdit('')
@@ -192,13 +198,15 @@ def _updateUI(self, rowIdx : List[int]):
         self._enableAllWidgets(True)
 
         # just the first row selection
-        rowIdx = rowIdx[0]
+        firstRowIndex = rowIdx[0]
+        self._pointRowSelection = firstRowIndex
 
-        self._pointRowSelection = rowIdx
+        logger.info(f'firstRowIndex:{firstRowIndex}')
 
         # keys are all possible columns, we only show columns in infoList
         # values are, well, the values
-        rowDict = self.pa.getRow(rowIdx)
+        rowDict = self.pa.getRow(firstRowIndex)
+        logger.info(f'rowDict:{rowDict}')
 
         for index, itemName in enumerate(self.infoList):
             if itemName not in self.widgetDict.keys():
@@ -208,6 +216,7 @@ def _updateUI(self, rowIdx : List[int]):
 
             if itemName not in rowDict.keys():
                 # our itemName we want to display is not in the backend
+                logger.warning(f'item name "{itemName}" is not in backend keys')
                 continue
 
             backendValue = rowDict[itemName]
@@ -217,9 +226,16 @@ def _updateUI(self, rowIdx : List[int]):
             # self.blockSignals(True)
             self.blockSlotsOn()
 
+            # abb do not hard code items, use the self._displayList
             # ["index", "segmentID", "note", 'accept', 'userType']
-            if itemName in ['index', 'segmentID', 'note', 'spineLength']:
+            # if itemName in ['index', 'segmentID', 'note', 'spineLength']:
+            #     itemWidget.setText(str(backendValue))
+            if itemName in self._displayList:
+                # labels
                 itemWidget.setText(str(backendValue))
+            elif itemName == 'note':
+                logger.warning(f'setting note {firstRowIndex} to "{backendValue}"')
+                itemWidget.setText(backendValue)  # QLineEdit
             elif itemName == 'accept':
                 # logger.info(f'backendValue: {backendValue} {type(backendValue)}')
                 itemWidget.setChecked(bool(backendValue))

src/pymapmanager/timeseriesCore.py

@@ -149,7 +149,7 @@ def __init__(self, path : str):
         # if path.endswith('.mmap') or path.endswith('.mmap/') or path.endswith('.mmap.zip'):
         if _ext in LOAD_SAVE_EXTENSIONS:
             self._load_zarr()
-        elif path.endswith('.tif'):
+        elif path.endswith('.tif') or path.endswith('.nd2'):
             self._import_tiff()
         # elif path.endswith('.ome.zarr'):
         # elif path.endswith('.zarr') or path.endswith('.zarr/'):
@@ -331,22 +331,10 @@ def _import_tiff(self):
         loader = MultiImageLoader()
         loader.read(path, channel=0)
 
-        # TEMPORARY, fake second channel, to debug single channel stack
-        # loader.read(path, channel=1)
-
-        # map = MapAnnotations(loader.build(),
         map = MapAnnotations(loader,
                             lineSegments=pd.DataFrame(),
                             points=pd.DataFrame())
 
-        # abb trying to figure out tree
-        from pprint import pprint
-        logger.info('dataTree???')
-        pprint(loader.dataTree())
-
-        # map.points[:]
-        # map.segments[:]
-
         self._fullMap : MapAnnotations = map
 
     def _import_ome_zarr(self):