june 13 before merge with s-dev

Author: cudmore

examples/example.ipynb

@@ -12,5 +12,5 @@
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.post94'
+__version__ = version = '0.0.post103'
 __version_tuple__ = version_tuple = (0, 0)

mapmanagercore/_version.py

@@ -1,4 +1,4 @@
-from typing import Tuple, Union
+from typing import Tuple, Union, Optional
 from mapmanagercore.lazy_geo_pandas.schema import MISSING_VALUE
 from ..schemas import Spine, Segment
 from ..config import SegmentId, SpineId
@@ -16,16 +16,20 @@ class AnnotationsBaseMut(AnnotationsBase):
     def deleteSpine(self, spineId: Keys, skipLog=False) -> None:
         self._drop("Spine", spineId, skipLog=skipLog)
 
-    def deleteSegment(self, segmentId: Keys, skipLog=False) -> None:
+    def deleteSegment(self, segmentId: Keys, skipLog=False) -> bool:
         try:
             if not self.points[["segmentID"]].reset_index().set_index(["segmentID", "t"]).loc[segmentId].empty:
-                raise ValueError(
-                    f"Cannot delete segment(s) {segmentId} as it has an attached spine(s)")
+                # abb
+                logger.info(f'Cannot delete segment(s) {segmentId} as it has an attached spine(s)')
+                return False
+                # raise ValueError(
+                #     f"Cannot delete segment(s) {segmentId} as it has an attached spine(s)")
         except KeyError:
             pass
 
         self._drop("Segment", segmentId, skipLog=skipLog)
-
+        return True
+    
     def updateSpine(self, spineId: Keys, value: Spine, replaceLog=False, skipLog=False):
         """
         Set the spine with the given ID to the specified value.

mapmanagercore/annotations/mutation.py

@@ -150,7 +150,14 @@ def __init__(self, annotations: Annotations, t: int) -> None:
 
     def __str__(self):
         logger.info('')
-        numTimepoints = len(self._images._imagesSrcs.keys())
+        
+        # get the number of time points
+        numTimepoints = 'abb ???'
+        try:
+            numTimepoints = len(self._images._imagesSrcs.keys())
+        except (AttributeError) as e:
+            logger.error(e)
+
         numPnts = len(self._annotations._points._rootDf)
         numSegments = len(self._annotations._segments._rootDf)
         return f't:{numTimepoints}, points:{numPnts} segments:{numSegments}'

mapmanagercore/annotations/single_time_point/base.py

@@ -130,10 +130,11 @@ def addSpine(self, segmentId: SpineId, x: int, y: int, z: int) -> Union[SpineId,
         """
         point = Point(x, y, z)
 
+        logger.error(f'1 FutureWarning: The `drop` keyword ...')
         anchor = self.nearestAnchor(segmentId, point, findBrightest=True)
 
         spineId = self.newUnassignedSpineId()
-        
+
         self.updateSpine(spineId, Spine.withDefaults(
             segmentID=segmentId,
             point=Point(point.x, point.y),
@@ -144,6 +145,7 @@ def addSpine(self, segmentId: SpineId, x: int, y: int, z: int) -> Union[SpineId,
             yBackgroundOffset=0.0,
         ))
 
+        logger.error(f'4 FutureWarning: The `drop` keyword ...')
         self.snapBackgroundOffset(spineId)
 
         return spineId

mapmanagercore/annotations/single_time_point/interactions.py

@@ -6,6 +6,7 @@
 import geopandas as gp
 from shapely.geometry import Polygon, Point
 
+from mapmanagercore.logger import logger
 
 class PolygonLayer(Layer):
     def box(minx, miny, maxx, maxy):

mapmanagercore/layers/polygon.py

@@ -392,8 +392,17 @@ def __getitem__(self, items):
 
     @timer
     def _getFiltered(self, key):
-        return self._df[key]
-
+        try:
+            return self._df[key]
+        except(KeyError) as e:
+            # abb
+            logger.error('KeyError requesting key:')
+            print(key)
+            logger.error('available keys are self._df.columns:')
+            print(self._df.columns)
+            logger.error('returning full _df')
+            return self._df
+        
     def undo(self) -> None:
         self._store.undo()
 

mapmanagercore/lazy_geo_pandas/lazy.py

@@ -6,6 +6,7 @@
 from shapely.geometry.base import BaseGeometry
 from .attributes import ColumnAttributes, _ColumnAttributes
 
+from mapmanagercore.logger import logger
 
 class MISSING_VALUE:
     def __repr__(self):
@@ -120,6 +121,7 @@ def setColumnTypes(cls, df: pd.DataFrame) -> gp.GeoDataFrame:
 
         if df.index.nlevels != len(cls._index):
             if len(cls._index) != 0:
+                logger.info('drop=True')
                 df.set_index(cls._index, inplace=True, drop=True)
                 if df.index.nlevels > 1:
                     df.sort_index(level=0, inplace=True)

mapmanagercore/lazy_geo_pandas/schema.py

@@ -181,7 +181,6 @@ def spineSide(frame: LazyGeoFrame):
         segmentFrame = frame.getFrame("Segment")
         df = frame[["segmentID", "point"]].join(
             segmentFrame[["segment", "radius"]], on=["segmentID", "t"])
-        # print(df)
         _ret = df.apply(lambda d: getSpineSide(d["segment"], d["point"]), axis=1)
 
         return _ret
@@ -199,7 +198,6 @@ def angle(frame: LazyGeoFrame):
         segmentFrame = frame.getFrame("Segment")
         df = frame[["segmentID", "point", "anchorLine"]].join(
             segmentFrame[["segment"]], on=["segmentID", "t"])
-        print("spineAngle df:", df)
 
         # # Create a dataframe of 
         _ret = df.apply(lambda d: getSpineAngle(d["segment"], d["anchorLine"]), axis=1)

mapmanagercore/schemas/spine.py

@@ -15,12 +15,15 @@
     'numpy',
     'pandas',
     'shapely',
-    'geopandas==1.0.0a1',
+    # 'geopandas==1.0.0a1',  # removed 20240608
+    'geopandas',
     'scikit-image',
     'zarr',
     'platformdirs',  # to get platform specific App paths
     'plotly',
     'brightest-path-lib',
+    #'bioimage',
+    #
 ]
 
 testRequirements = [