Watershed workflow

.gitignore

@@ -1,4 +1,5 @@
 .project
+docs/_build
 .pydevproject
 #KDevelop project files
 *.kdev4

lazyflow/operator.py

@@ -131,7 +131,7 @@ class Operator(object):
 
     Operators consist of a class inheriting from this class
     and need to specify their inputs and outputs via
-    thei inputSlot and outputSlot class properties.
+    their inputSlot and outputSlot class properties.
 
     Each instance of an operator obtains individual
     copies of the inputSlots and outputSlots, which are
@@ -562,4 +562,4 @@ def debug_text(self):
 
 #    @debug_text.setter
 #    def debug_text(self, text):
-#        self._debug_text = text
+#        self._debug_text = text

lazyflow/operatorWrapper.py

@@ -269,7 +269,6 @@ def _removeInnerOperator(self, index, length):
 
         op = self.innerOperators.pop(index)
         for slot in op.inputs.values():
-            slot.backpropagate_values = False
             slot.unregisterDisconnect(self.handleEarlyDisconnect)
 
         for oslot in self.outputs.values():
@@ -279,6 +278,9 @@ def _removeInnerOperator(self, index, length):
             if outerSlot.name in self.promotedSlotNames:
                 outerSlot.removeSlot(index, length)
 
+        for slot in op.inputs.values():
+            slot.backpropagate_values = False
+
         op.cleanUp()
 
     def _setupOutputs(self):

lazyflow/operators/opCompressedCache.py

@@ -523,11 +523,7 @@ def _setInSlotInput(self, slot, subindex, roi, value, store_zero_blocks=True):
 
                     # If we can, remove this block entirely.
                     if not store_zero_blocks and new_block_sum == 0 and (dataset[:] == 0).all():
-                        with self._lock:
-                            with self._blockLocks[block_start]:
-                               self._cacheFiles[block_start].close()
-                               del self._cacheFiles[block_start]
-                            del self._blockLocks[block_start]
+                        self._deleteBlock(block_start)
 
             # Here, we assume that if this function is used to update ANY PART of a 
             #  block, he is responsible for updating the ENTIRE block.
@@ -538,6 +534,13 @@ def _setInSlotInput(self, slot, subindex, roi, value, store_zero_blocks=True):
     #            self.OutputHdf5._sig_value_changed()
     #            self.CleanBlocks._sig_value_changed()
 
+    def _deleteBlock(self, block_start):
+        with self._lock:
+            with self._blockLocks[block_start]:
+               self._cacheFiles[block_start].close()
+               del self._cacheFiles[block_start]
+            del self._blockLocks[block_start]
+
     def _setInSlotInputHdf5(self, slot, subindex, roi, value):
         logger.debug("Setting block {} from hdf5".format( roi ))
         if self.Output.meta.has_mask:

lazyflow/operators/opCompressedUserLabelArray.py

@@ -83,6 +83,15 @@ def clearLabel(self, label_value):
         """
         self._purge_label( label_value, False )
 
+    def clearAllLabels(self):
+        """
+        Nearly the same as _purge_label but deleting all the >0 entries. 
+        """
+        for block_start in list(self._blockLocks.keys()):
+            self._deleteBlock(block_start)
+        self._dirtyBlocks = set()
+        self.Output.setDirty()
+
     def mergeLabels(self, from_label, into_label):
         self._purge_label(from_label, True, into_label)
 
@@ -173,7 +182,6 @@ def _purge_label(self, label_to_purge, decrement_remaining, replacement_value=0)
                 changed_block_rois.append( block_roi )
 
         for block_roi in changed_block_rois:
-            # FIXME: Shouldn't this dirty notification be handled in OpUnmanagedCompressedCache?
             self.Output.setDirty( *block_roi )
 
     def execute(self, slot, subindex, roi, destination):

lazyflow/operators/opReorderAxes.py

@@ -162,6 +162,11 @@ def propagateDirty(self, inputSlot, subindex, in_roi):
         else:
             assert False, "Unknown input slot: {}".format( inputSlot.name )
 
+
+    def setInSlot(self, slot, subindex, roi, value):
+        #TODO #FIXME added here, otherwise always a NotImplementedError
+        pass
+
 # Helper function: Like list.index(), but return -1 for missing elements instead of raising a ValueError
 def _index(tup, element):
     try: