working on connect() spine

Author: cudmore

examples/example.ipynb

@@ -29,8 +29,12 @@ def __init__(self, loader: Loader):
         self._zarrPath : str = loader.getZarrPath()
 
     def getZarrPath(self):
-        return self._zarrPath
-    
+        try:
+            return self._zarrPath
+        except (AttributeError) as e:
+            logger.warning(f'{e}')
+
+    # abb
     def __str__(self):
         """Print info about the map.
         
@@ -40,8 +44,18 @@ def __str__(self):
         numTimepoints = len(self._images._imagesSrcs.keys())
         numPnts = len(self.points._rootDf)
         numSegments = len(self.segments._rootDf)
-        return f't:{numTimepoints}, points:{numPnts} segments:{numSegments} zarr:{zarrPath}'
 
+        # images
+        # numTimepoints = self.numTimepoints()
+
+        return f't:{numTimepoints}, points:{numPnts} segments:{numSegments} zarr:{zarrPath}'
+    
+    #abb
+    # def numTimepoints(self) -> int:
+    #     """Get the number of timepoints.
+    #     """
+    #     return self._images.shape(t=0)[0]
+    
     @property
     def segments(self) -> LazyGeoFrame:
         return self._segments

mapmanagercore/annotations/base.py

@@ -38,6 +38,8 @@ def updateSpine(self, spineId: Keys, value: Spine, replaceLog=False, skipLog=Fal
             value (Union[dict, gp.Series, pd.Series]): The value to set for the spine.
         """
 
+        # abb, remove this?
+        # When we connect, we want to mutate the multiindex (spineID, t)
         if value.t != MISSING_VALUE:
             raise ValueError(
                 f"Invalid type for column 't' must be set on the spine key")
@@ -76,17 +78,28 @@ def newUnassignedSegmentId(self) -> SegmentId:
         return self.segments.index.get_level_values(0).max() + 1
 
     def connect(self, spineKey: Tuple[SpineId, int], toSpineKey: Tuple[SpineId, int]):
-        if self.points[toSpineKey, "segmentID"] != self.points[spineKey, "segmentID"]:
+        
+        # ValueError: Can only compare identically-labeled Series objects
+        # if self.points[toSpineKey, "segmentID"] != self.points[spineKey, "segmentID"]:
+        _segmentID = self.points[spineKey, "segmentID"].values[0]
+        _toSegmentID = self.points[toSpineKey, "segmentID"].values[0]
+        if _toSegmentID != _segmentID:
             raise ValueError("Cannot connect spines from different segments.")
-
+        
         # check if the key already exists in the time point
-        existingKey = (toSpineKey[0], spineKey[0])
+        # existingKey = (toSpineKey[0], spineKey[0])
+        # abb
+        existingKey = (spineKey[0], toSpineKey[1])
         if existingKey in self.points.index:
             self.disconnect(existingKey)
 
         # Propagate the spine ID to all future time points
-        self.updateSpine(range(spineKey, spineKey[0]), Spine(
-            spineID=toSpineKey[0],
+        # self.updateSpine(range(spineKey, spineKey[0]), Spine(
+        #     spineID=toSpineKey[0],
+        # ))
+        # abb
+        self.updateSpine(toSpineKey[0], Spine(
+            spineID=spineKey[0],
         ))
 
     def disconnect(self, spineKey: Tuple[SpineId, int]):

mapmanagercore/annotations/mutation.py

@@ -57,7 +57,7 @@ def __getitem__(self, items: Any) -> Any:
 
     # abb
     def __len__(self):
-        return len(self._root._rootDf)
+        return len(self._root._df)
 
     @property
     def index(self):

mapmanagercore/annotations/single_time_point/base.py

@@ -29,9 +29,10 @@ def getSpineDistance(self, segmentID: SegmentId,
         minProjection = segment.project(point)
         return minProjection
 
+    # abb added findBrightest=False, do not find brightest by default
     def nearestAnchor(self, segmentID: SegmentId,
                       point: Point,
-                      findBrightest = False):
+                      findBrightest : bool = False):
         """Finds the nearest anchor point on a given line segment to a given point.
 
         Args:
@@ -48,12 +49,12 @@ def nearestAnchor(self, segmentID: SegmentId,
         minProjection = segment.project(point)
 
         if np.isnan(minProjection):
-            logger.info(f'minProjection:{minProjection}')
-            logger.info(f'segment:{segment}')
-            logger.info(f'point:{point}')
+            logger.warning(f'minProjection:{minProjection}')
+            logger.warning(f'segment:{segment}')
+            logger.warning(f'point:{point}')
 
         if not findBrightest:
-            # Default to the closest path
+            # Default to the closest point (not brightest)
             anchor = segment.interpolate(minProjection)
             anchor = roundPoint(anchor, 1)
             return anchor
@@ -140,8 +141,6 @@ def addSpine(self, segmentId: SpineId, x: int, y: int, z: int) -> Union[SpineId,
             anchorZ=int(anchor.z),
             xBackgroundOffset=0.0,
             yBackgroundOffset=0.0,
-            # abb
-            # spineDistance = spineDistance
         ))
 
         self.snapBackgroundOffset(spineId)
@@ -196,19 +195,13 @@ def moveAnchor(self, spineId: SpineId,
         """
         segmentId = self.points[spineId, "segmentID"]
 
+        # abb
         # when moving, do not find brightest
         anchor = self.nearestAnchor(segmentId, Point(x, y, z))
 
-        logger.info(f'segmentId:{segmentId} anchor:{anchor}')
-
-        # abb, now handled dynamically with laze
-        # _point = self.points[spineId, "point"]
-        # spineDistance = self.getSpineDistance(segmentId, _point)
-
         self.updateSpine(spineId, Spine(
             anchorZ=int(anchor.z),
             anchor=Point(anchor.x, anchor.y),
-            # spineDistance=spineDistance,
         ), state != DragState.START and state != DragState.MANUAL)
 
         return True

mapmanagercore/annotations/single_time_point/interactions.py

@@ -324,6 +324,10 @@ def _parseKeyRow(self, items):
 
         return row, key
 
+    # abb
+    def __len__(self):
+      return len(self._df)
+      
     def __getitem__(self, items):
         row, key = self._parseKeyRow(items)
 

mapmanagercore/lazy_geo_pandas/lazy.py

@@ -96,8 +96,8 @@ def imread(path: str) -> ImageLoader:
         return _MultiImageLoader(imread(path))
 
     # abb
-    def getNumTimepoints(self):
-       return len(self._images.keys())
+    # def getNumTimepoints(self):
+    #    return len(self._images.keys())
 
     def read(self, path : Union[str, np.ndarray], time: int = 0, channel: int = 0):
         """

mapmanagercore/loader/imageio.py

@@ -115,10 +115,6 @@ class Spine:
     point: Point
     anchor: Point
 
-    # abb
-    # spinePosition: float
-    # spineSide: str  # calculate on addSpine and moveSpine
-
     xBackgroundOffset: float
     yBackgroundOffset: float
     z: int