Merge branch 'cudmore-dev' into johnson-dev

.github/workflows/test.yml

@@ -10,10 +10,12 @@ permissions:
 
 jobs:
   test:
-    runs-on: ubuntu-latest
+    # runs-on: ubuntu-latest
+    runs-on: ${{ matrix.platform }}
     strategy:
       matrix:
-        platform: [ubuntu-latest, windows-latest, macos-latest]
+        # platform: [ubuntu-latest, windows-latest, macos-latest]
+        platform: [windows-latest, macos-latest]
         python-version: ["3.11"]
     steps:
     - uses: actions/checkout@v3
@@ -25,8 +27,11 @@ jobs:
         cache-dependency-path: setup.py
     - name: Install dependencies
       run: |
+        # pip install .
         pip install '.[tests]'
-
+        # so we don't need to depend on pip install MapManagerCore
+        git clone -b cudmore-dev https://github.com/mapmanager/MapManagerCore.git
+        pip install MapManagerCore/.
     - name: Run flake8
       run: |
         flake8 ./pymapmanager --count --select=E9,F63,F7,F82 --show-source --statistics
@@ -35,7 +40,10 @@ jobs:
       run: |
         # exlude anything that requires large data (it is not included in PyPi)
         # pytest --cov=./tests --cov-report=xml --ignore=tests/test_gen_example_notebook.py
-        pytest --cov=./tests --cov-report=xml
+        # need to specify tests/ folder because now we have a
+        # MapManagerCore folder which has its own tests/
+        pytest -s --cov=./tests --cov-report=xml tests/
+        # pytest tests/interface/test_app_tmp.py
 
     - name: Upload coverage reports to Codecov
       uses: codecov/[email protected]

pymapmanager/analysisParams.py

@@ -415,7 +415,7 @@ def _getDocs(self) -> str:
 # Save button will send the signals to backend for whatever changed
 
 if __name__ == '__main__':
-    dp = AnalysisParams()
+    dp = _old_AnalysisParams()
     print(dp._getDocs())
 
     # dp.buildAnalysisParamUI()

pymapmanager/annotations/baseAnnotationsCore.py

@@ -9,12 +9,13 @@
 from mapmanagercore import MapAnnotations
 from mapmanagercore.layers.line import clipLines
 
+from pymapmanager.interface2.stackWidgets.event.spineEvent import EditSpinePropertyEvent
+
 from pymapmanager._logger import logger
 
 class AnnotationsCore:
     def __init__(self,
-                 mapAnnotations : "???",  # TODO: update on merge 20240513
-                #  analysisParams : "AnalysisParams",
+                 mapAnnotations : MapAnnotations,
                  sessionID = 0,
                  ):
         """
@@ -26,7 +27,7 @@ def __init__(self,
         self._sessionID = sessionID
 
         # full map, multiple session ids (timepoint, t)
-        self._fullMap : "AnnotationsLayers" = mapAnnotations
+        self._fullMap : MapAnnotations = mapAnnotations
         # mapmanagercore.annotations.single_time_point.layers.AnnotationsLayers
 
         #filtered down to just sessionID
@@ -112,7 +113,7 @@ def getValue(self, colName : str, rowIdx : int):
     def getValues(self,
                     colName : List[str],
                     rowIdx : Union[int, List[int], None] = None,
-                    ) -> Union[np.ndarray, None]:
+                    ) -> Optional[np.ndarray]:
         """Get value(s) from a column or list of columns.
 
         Parameters
@@ -130,17 +131,17 @@ def getValues(self,
         # logger.info(f'{rowIdx} {type(rowIdx)}')
 
         df = self.getDataFrame()  # geopandas.geodataframe.GeoDataFrame
-
-        # TODO: 042024 implement a list of columns
-        # if not isinstance(colName, list):
-        #     colName = [colName]
 
-        #if not self.columns.columnIsValid(colName):
+        # print('df:')
+        # print(df.index)
+
         if colName not in list(df.columns):
             logger.error(f'did not find column name "{colName}"')
             return
 
         if rowIdx is None:
+            # TODO: this won't work, need to get actual row labels
+            # some may be missing after delet
             rowIdx = range(self.numAnnotations)  # get all rows
         elif not isinstance(rowIdx, list):
             rowIdx = [rowIdx]
@@ -150,7 +151,7 @@ def getValues(self,
             return ret
 
         except (KeyError):
-            logger.error(f'bad rowIdx(s) {rowIdx}, colName:{colName} range is 0...{len(self)-1}')
+            logger.error(f'bad rowIdx(s) {rowIdx}, colName:{colName} values are in row labels')
             return None
 
     def moveSpine(self, spineID :int, x, y, z):
@@ -347,7 +348,7 @@ def deleteAnnotation(self, rowIdx : Union[int, List[int]]) -> None:
 
         self._buildDataFrame()
 
-    def editSpine(self, editSpineProperty : "EditSpineProperty"):
+    def editSpine(self, editSpineProperty : EditSpinePropertyEvent):
         # spineID:117 col:isBad value:True
         # logger.info(editSpineProperty)
         logger.info(f"stack widget editSpineProperty {editSpineProperty}")
@@ -362,6 +363,16 @@ def editSpine(self, editSpineProperty : "EditSpineProperty"):
 
 class LineAnnotationsCore(AnnotationsCore):
 
+    @property
+    def numSegments(self):
+        return len(self._fullMap.segments[:])
+
+    def newSegment(self):
+        return self._fullMap.newSegment()
+
+    def appendSegmentPoint(self, segmentID : int, x : int, y: int, z : int):
+        self._fullMap.appendSegmentPoint(segmentID, x, y, z)
+
     def getSummaryDf(self):
         """DataFrame with per segment info (one segment per ro)
         """
@@ -373,6 +384,11 @@ def _buildSummaryDf(self) -> pd.DataFrame:
         self._summaryDf = pd.DataFrame()
         self._summaryDf['segmentID'] = self._df['segmentID'].unique()
 
+        lengthList = []
+        for row in range(len(self._summaryDf)):
+            lengthList.append(self._fullMap.segments['segment'].loc[row].length)
+        self._summaryDf['length'] = lengthList
+
     def _buildDataFrame(self):  
 
         _startSec = time.time()
@@ -414,7 +430,7 @@ def _buildDataFrame(self):
 
         #
         # left/right 
-        logger.warning('left/right is slow, can we get this pre-built and saved into zarr')
+        # logger.warning('left/right is slow, can we get this pre-built and saved into zarr')
 
         # TODO: 6/19 fix xyLeft and xyRight
         # TODO: put ths back in, the backend changed. We no longer have "segmentLeft" or "segmentRight"
@@ -499,36 +515,3 @@ def getMedianZ(self, segmentID : int):
         yMedian = np.median(df['y'])
         zMedian = np.median(df['z'])
         return (int(xMedian), int(yMedian), int(zMedian) )
-
-if __name__ == '__main__':
-    from pymapmanager._logger import setLogLevel
-    setLogLevel()
-
-    # _testEditSpineProperty()
-
-    sys.exit(1)
-
-    zarrPath = '../MapManagerCore/data/rr30a_s0us.mmap'
-    map = MapAnnotations(MMapLoader(zarrPath).cached())
-
-    sac = SpineAnnotationsCore(map)
-
-    print(sac.getDataFrame().columns)
-
-    segmentID = None
-    roiTypes = None
-    zSlice = 20
-    zPlusMinus = 5
-
-    value = sac.getValue('x', 2)
-    print(f'x:{value}')
-    value = sac.getValues('y', [2, 3, 4])
-    print(f'y:{value}')
-    print(type(value))
-
-    row = sac.getRow(2)
-    print('row')
-    print(row)
-
-    # spineDf = sac.getSegmentPlot(segmentID, roiTypes, zSlice, zPlusMinus)
-    # print(spineDf)

pymapmanager/interface2/__init__.py

@@ -1,9 +1,8 @@
 from .pyMapManagerApp2 import PyMapManagerApp
 
 from .mainMenus import PyMapManagerMenus
-
 from .mainWindow import MainWindow
 
 from .preferences import Preferences
 
-from .appDisplayOptions import AppDisplayOptions
+from .appDisplayOptions import AppDisplayOptions

pymapmanager/interface2/appDisplayOptions.py

@@ -1,3 +1,5 @@
+from pymapmanager._logger import logger
+
 class AppDisplayOptions():
     """Class to encapsulate all display options.
     
@@ -43,6 +45,7 @@ def _getDefaultDisplayOptions(self):
         theDict['windowState']['height'] = 500  # position on screen
 
         # TODO: pass into imageplotwidget
+        theDict['windowState']['doSlidingZ'] = False  # added 20240706
         theDict['windowState']['zPlusMinus'] = 3
 
         # interface.pointPlotWidget
@@ -91,5 +94,4 @@ def _getDefaultDisplayOptions(self):
         # abj: 6/20
         theDict['lineDisplay']['radius'] = 3
 
-
         return theDict

pymapmanager/interface2/core/scatter_plot_widget.py

@@ -524,7 +524,9 @@ def __init__(self,
         """
 
         super().__init__(parent=parent)
-        self._blockSlots : bool = False
+
+        # abb not used
+        # self._blockSlots : bool = False
 
         self.dict = {"X Stat" : "", 
                      "Y Stat" : "",