Merge remote-tracking branch 'abi/main' into biunit_bladder

src/scaffoldmaker/utils/exportvtk.py

@@ -1,6 +1,6 @@
-'''
+"""
 Class for exporting a Scaffold from Zinc to legacy vtk text format.
-'''
+"""
 
 import io
 import os
@@ -14,17 +14,17 @@
 
 
 class ExportVtk:
-    '''
+    """
     Class for exporting a Scaffold from Zinc to legacy vtk text format.
     Limited to writing only 3-D hexahedral elements. Assumes all nodes have field defined.
-    '''
+    """
 
-    def __init__(self, region, description, annotationGroups = None):
-        '''
+    def __init__(self, region, description, annotationGroups=None):
+        """
         :param region: Region containing finite element model to export.
         :param description: Single line text description up to 256 characters.
         :param annotationGroups: Optional list of AnnotationGroup for model.
-        '''
+        """
         self._region = region
         self._fieldmodule = self._region.getFieldmodule()
         for dimension in range(3, 1, -1):
@@ -43,7 +43,7 @@ def __init__(self, region, description, annotationGroups = None):
 
     def _write(self, outstream):
         if version_info.major > 2:
-          assert isinstance(outstream, io.TextIOBase), 'ExportVtk.write:  Invalid outstream argument'
+            assert isinstance(outstream, io.TextIOBase), 'ExportVtk.write:  Invalid outstream argument'
         outstream.write('# vtk DataFile Version 2.0\n')
         outstream.write(self._description + '\n')
         outstream.write('ASCII\n')
@@ -67,7 +67,7 @@ def _write(self, outstream):
                 result, x = self._coordinates.evaluateReal(cache, coordinatesCount)
                 if result != RESULT_OK:
                     print("Coordinates not found for node", node.getIdentifier())
-                    x = [ 0.0 ]*coordinatesCount
+                    x = [0.0] * coordinatesCount
                 if coordinatesCount < 3:
                     for c in range(coordinatesCount - 1, 3):
                         x.append(0.0)
@@ -78,15 +78,15 @@ def _write(self, outstream):
         # following assumes all hex (3-D) or all quad (2-D) elements
         if self._mesh.getDimension() == 2:
             localNodeCount = 4
-            vtkIndexing = [ 0, 1, 3, 2 ]
+            vtkIndexing = [0, 1, 3, 2]
             cellTypeString = '9'
         else:
             localNodeCount = 8
-            vtkIndexing = [ 0, 1, 3, 2, 4, 5, 7, 6 ]
+            vtkIndexing = [0, 1, 3, 2, 4, 5, 7, 6]
             cellTypeString = '12'
         localNodeCountStr = str(localNodeCount)
         cellCount = self._mesh.getSize()
-        cellListSize = (1 + localNodeCount)*cellCount
+        cellListSize = (1 + localNodeCount) * cellCount
         outstream.write('CELLS ' + str(cellCount) + ' ' + str(cellListSize) + '\n')
         elementIter = self._mesh.createElementiterator()
         element = elementIter.next()
@@ -119,7 +119,7 @@ def _write(self, outstream):
             for annotationGroup in cellAnnotationGroups:
                 safeName = annotationGroup.getName().replace(' ', '_')
                 outstream.write('SCALARS ' + safeName + ' int 1\n')
-                outstream.write('LOOKUP_TABLE default\n') 
+                outstream.write('LOOKUP_TABLE default\n')
                 meshGroup = annotationGroup.getMeshGroup(self._mesh)
                 elementIter = self._mesh.createElementiterator()
                 element = elementIter.next()
@@ -133,7 +133,7 @@ def _write(self, outstream):
             for annotationGroup in pointAnnotationGroups:
                 safeName = annotationGroup.getName().replace(' ', '_')
                 outstream.write('SCALARS ' + safeName + ' int 1\n')
-                outstream.write('LOOKUP_TABLE default\n') 
+                outstream.write('LOOKUP_TABLE default\n')
                 nodesetGroup = annotationGroup.getNodesetGroup(self._nodes)
                 nodeIter = self._nodes.createNodeiterator()
                 node = nodeIter.next()
@@ -143,7 +143,6 @@ def _write(self, outstream):
                     node = nodeIter.next()
                 outstream.write('\n')
 
-
     def _writeMarkers(self, outstream):
         coordinatesCount = self._coordinates.getNumberOfComponents()
         cache = self._fieldmodule.createFieldcache()
@@ -163,11 +162,10 @@ def _writeMarkers(self, outstream):
                     node = nodeIter.next()
                 del markerCoordinates
 
-
     def writeFile(self, filename):
-        '''
+        """
         Export to legacy vtk file.
-        '''
+        """
         try:
             with open(filename, 'w') as outstream:
                 self._write(outstream)