Fixing Auto Connect Spine Functionality

pymapmanager/annotations/baseAnnotationsCore.py

@@ -196,6 +196,20 @@ def manualConnectSpine(self, spineID : int, x, y, z):
         # rebuild df from mutated full map
         self._buildDataFrame()
 
+    #abj
+    def autoResetBrightestIndex(self, spineID, segmentID, point, findBrightest : bool = True):
+
+        if not isinstance(spineID, int):
+            logger.error(f'got bad spineID:{spineID}, expecting int')
+            return
+
+        # Update brightest path
+        brightestIdx = self._fullMap.autoConnectBrightestIndex(spineID, segmentID, point, findBrightest)
+        logger.info(f"brightestIdx {brightestIdx}")
+
+        # refreshDataFrame
+        self._buildDataFrame()
+
     def setValue(self, colName : str, row : int, value):
         """Set a single value in a row and column.
         
@@ -541,7 +555,7 @@ def getLeftRadiusPlot(self, segmentID,
         _stopSlice = zSlice + zPlusMinus
 
         # logger.info(f"self._fullMap.segments['segment']:{self._fullMap.segments['segment']}")
-        logger.info(f"self._fullMap.segments:{self._fullMap.segments[:]}")
+        # logger.info(f"self._fullMap.segments:{self._fullMap.segments[:]}")
 
         segmentLines = clipLines(self._fullMap.segments['segment'], zRange = (_startSlice, _stopSlice))
         xyLeft = shapely.offset_curve(segmentLines, radiusOffset * -1)

pymapmanager/interface2/runInterfaceJohnson.py

@@ -53,5 +53,5 @@ def run2():
     sys.exit(app.exec_())
 
 if __name__ == '__main__':
-    # run()
-    run2()
+    run()
+    # run2()

pymapmanager/interface2/stackWidgets/annotationPlotWidget2.py

@@ -864,6 +864,19 @@ def manualConnectSpineEvent(self, event : pmmEvent):
 
         self._refreshSlice()
 
+    def autoConnectSpineEvent(self, event : pmmEvent):
+        """Update plots on auto connect spine event.
+        """
+        for spine in event:
+            # update label
+            spineID = spine['spineID']
+            self._pointLabels.updateLabel(spineID)
+
+        # remake all spine lines
+        self._bMakeSpineLines()
+
+        self._refreshSlice()
+
     def undoEvent(self, event : UndoSpineEvent):
         """
         """

pymapmanager/interface2/stackWidgets/event/spineEvent.py

@@ -377,4 +377,20 @@ def _getItem(self, item : SpineEdit):
                   col=item['col'],
                   value=item['value'])
         return item
-
+
+#abj
+class AutoConnectSpineEvent(_EditSpine):
+    """Used Auto Connect Spine to its brightest point on a line segment
+    """
+    def __init__(self,
+                 mmWidget : mmWidget2,
+                 spineID : int = None):
+        super().__init__(pmmEventType.autoConnectSpine, mmWidget)
+        if spineID is not None:
+            self.addEdit(spineID=spineID)
+
+    def _getItem(self, item : SpineEdit):
+        """Get the meaningful keys for this edit type.
+        """
+        item = SpineEdit(spineID=item['spineID'])
+        return item

pymapmanager/interface2/stackWidgets/imagePlotWidget2.py

@@ -10,7 +10,9 @@
                 EditSpinePropertyEvent,
                 AddSpineEvent,
                 MoveSpineEvent,
-                ManualConnectSpineEvent)
+                ManualConnectSpineEvent,
+                AutoConnectSpineEvent #abj
+                )
 
 from pymapmanager.interface2.stackWidgets.event.segmentEvent import (
     AddSegmentPoint
@@ -240,12 +242,20 @@ def contextMenuEvent(self, event : QtGui.QContextMenuEvent):
 
         elif action == autoConnectAction:
             logger.warning('Auto Connecting Spine')
-            # Dont need to acquire any new data,
-            #everything should be known because of the current selection
-            eventType = pmmEventType.autoConnectSpine
-            event = pmmEvent(eventType, self)
-            event.setSliceNumber(self._currentSlice)
-            self.emitEvent(event, blockSlots=True)
+
+            # pass in ID
+            # possible x,y,z to simplify stackwidget function
+            acs = AutoConnectSpineEvent(self, firstPointSelection)
+            self.emitEvent(acs)
+
+            # eventType = pmmEventType.autoConnectSpine
+            # event = pmmEvent(eventType, self)
+            # event.setSliceNumber(self._currentSlice)
+            # self.emitEvent(event)
+
+            # event = pmmEvent(pmmEventType.stateChange, self)
+            # # event.setStateChange(pmmStates.autoConnectSpine)
+            # self.emitEvent(event, blockSlots=True)
 
         elif action == deleteAction:
             logger.warning('deleting the selected annotation')

pymapmanager/interface2/stackWidgets/mmWidget2.py

@@ -94,7 +94,7 @@ def getState(self):
     def setState(self, state : pmmStates):
         self._dict['state'] = state
 
-    # ABJ
+    #abj
     def getCurrentPointSlice(self):
         pointSelections = self.getPointSelection()
 
@@ -183,6 +183,9 @@ def hasPointSelection(self) -> bool:
         return len(self.getPointSelection()) > 0
 
     def firstPointSelection(self) -> Optional[int]:
+        """
+            returns index of first point selection
+        """
         _points = self.getPointSelection()
         if len(_points) > 0:
             return _points[0]

pymapmanager/interface2/stackWidgets/stackWidget2.py

@@ -5,6 +5,8 @@
 import os
 from typing import TYPE_CHECKING
 
+from shapely import Point
+
 import pymapmanager.interface2
 import pymapmanager.interface2.stackWidgets
 import pymapmanager.interface2.stackWidgets.histogramWidget2
@@ -693,6 +695,7 @@ def _afterEdit2(self, event):
 
         # reselect spine
         spines = event.getSpines()  # [int]
+        # logger.info(f"afterEdit2 spines: {spines}")
         self.zoomToPointAnnotation(spines)
 
         self.slot_setStatus('Ready')
@@ -782,29 +785,26 @@ def autoConnectSpineEvent(self, event):
         logger.warning('=== ===   STACK WIDGET PERFORMING AUTO CONNECT   === ===')
         logger.error('TODO (Cudmore) need to implement auto connect')
 
-        # set backend
+        segmentID = _stackSelection.firstSegmentSelection()
+
+        _pointAnnotations = self.getStack().getPointAnnotations()
+        x = _pointAnnotations.getValue('x', spineIndex)
+        y = _pointAnnotations.getValue('y', spineIndex)
+        z = _pointAnnotations.getValue('z', spineIndex)
+        # point = _pointAnnotations.getValue("point", spineIndex)
 
-        # Getting channel and img from stack
-        # channel = self.getStack().getImageChannel()
+        point = Point(x, y, z)
+        # logger.info(f"point {point}")
 
-        # TODO: Need to get color channel from stack
-        channel = 2
-        # channel = event.getColorChannel()
-        logger.info(f"channel {channel}")
         z = _stackSelection.getCurrentPointSlice() # this might need to be checked, currently getting slice point selected
-        img = self.getStack().getImageSlice(z, channel=channel)
         _pointAnnotations = self.getStack().getPointAnnotations()
-        _lineAnnotations = self.getStack().getLineAnnotations()
-        autoBrightestIndex = _pointAnnotations.calculateSingleBrightestIndex(channel, spineIndex, _lineAnnotations, img)
-        _pointAnnotations.setValue('brightestIndex', spineIndex, autoBrightestIndex)
-        _pointAnnotations.updateSpineInt2(spineIndex, self.getStack())
+        _pointAnnotations.autoResetBrightestIndex(spineIndex, segmentID, point, True)
+
+        #abj TODO: Check if spine intensity is being updated
+        # _pointAnnotations.updateSpineInt2(spineIndex, self.getStack())
 
-        newEvent = pmmEvent(pmmEventType.selection, self)
-        newEvent.getStackSelection().setPointSelection(items)
-        sliceNum = event.getSliceNumber()
-        logger.info(f"autoConnect sliceNum {sliceNum}")
-        newEvent.setSliceNumber(sliceNum)
-        self._afterEdit(newEvent)
+        self.getUndoRedo().addUndo(event)
+        self._afterEdit2(event)
 
     def setSliceEvent(self, event):
         # logger.info(event)