First completed attempt to capture errors from VTK

Author: jafranc

geos-mesh/src/geos/mesh/processing/MergeBlockEnhanced.py

@@ -7,6 +7,7 @@
 from typing_extensions import Self
 
 from geos.utils.Logger import Logger, getLogger
+from geos.utils.Errors import VTKError
 from geos.mesh.utils.multiblockModifiers import mergeBlocks
 
 from vtkmodules.vtkCommonDataModel import (
@@ -32,6 +33,8 @@
 .. code-block:: python
 
     from geos.mesh.processing.MergeBlockEnhanced import MergeBlockEnhanced
+    import logging
+    from geos.utils.Errors import VTKError
 
     # Define filter inputs
     multiblockdataset: vtkMultiblockDataSet
@@ -45,7 +48,10 @@
     filter.setLoggerHandler( yourHandler )
 
     # Do calculations
-    filter.applyFilter()
+    try:
+        filter.applyFilter()
+    except VTKError:
+        logging.error("Something went wrong in VTK")
 
     # Get the merged mesh
     filter.getOutput()
@@ -110,7 +116,7 @@ def applyFilter( self: Self ) -> None:
         outputMesh: vtkUnstructuredGrid
         try:
             outputMesh = mergeBlocks( self.inputMesh, keepPartialAttributes=True, logger=self.logger )
-        except ( TypeError, ValueError ):
+        except ( VTKError ):
             self.logger.info( f"The filter {self.logger.name} failed." )
             raise
         else:

geos-mesh/src/geos/mesh/utils/multiblockModifiers.py

@@ -2,9 +2,11 @@
 # SPDX-FileCopyrightText: Copyright 2023-2024 TotalEnergies.
 # SPDX-FileContributor: Martin Lemay, Paloma Martinez
 from typing import Union
+
 from vtkmodules.vtkCommonDataModel import ( vtkCompositeDataSet, vtkDataObjectTreeIterator, vtkMultiBlockDataSet,
                                             vtkUnstructuredGrid, vtkDataSet )
 from packaging.version import Version
+from vtkmodules.vtkCommonCore import vtkLogger
 
 # TODO: remove this condition when all codes are adapted for VTK newest version.
 import vtk
@@ -14,11 +16,10 @@
     from vtkmodules.vtkFiltersCore import vtkAppendDataSets
 
 from geos.mesh.utils.arrayModifiers import fillAllPartialAttributes
-from geos.utils.Logger import ( getLogger, Logger )
+from geos.utils.Logger import ( getLogger, Logger, VTKCaptureLog, RegexExceptionFilter )
 
 __doc__ = """Contains a method to merge blocks of a VTK multiblock dataset."""
 
-
 def mergeBlocks(
     inputMesh: Union[ vtkMultiBlockDataSet, vtkCompositeDataSet ],
     keepPartialAttributes: bool = False,
@@ -36,7 +37,7 @@ def mergeBlocks(
         vtkUnstructuredGrid: Merged dataset or input mesh if it's already a single block
 
     Raises:
-        ValueError:
+        geos.utilsVTKError ():
 
     .. Note::
         Default filling values:
@@ -50,6 +51,9 @@ def mergeBlocks(
     if logger is None:
         logger: Logger = getLogger( "mergeBlocks", True )
 
+    vtkLogger.SetStderrVerbosity(vtkLogger.VERBOSITY_TRACE)
+    logger.addFilter(RegexExceptionFilter())
+
     # Fill the partial attributes with default values to keep them during the merge.
     if keepPartialAttributes and not fillAllPartialAttributes( inputMesh, logger ):
         logger.warning( "Failed to fill partial attributes. Merging without keeping partial attributes." )
@@ -66,18 +70,24 @@ def mergeBlocks(
             logger.warning( "Input mesh is already a single block." )
             outputMesh = inputMesh
         else:
-            af: vtkAppendDataSets = vtkAppendDataSets()
-            af.MergePointsOn()
-            iterator: vtkDataObjectTreeIterator = vtkDataObjectTreeIterator()
-            iterator.SetDataSet( inputMesh )
-            iterator.VisitOnlyLeavesOn()
-            iterator.GoToFirstItem()
-            while iterator.GetCurrentDataObject() is not None:
-                block: vtkDataSet = vtkDataSet.SafeDownCast( iterator.GetCurrentDataObject() )
-                af.AddInputData( block )
-                iterator.GoToNextItem()
-            af.Update()
-
+            with VTKCaptureLog() as captured_log:
+
+                af: vtkAppendDataSets = vtkAppendDataSets()
+                af.MergePointsOn()
+                iterator: vtkDataObjectTreeIterator = vtkDataObjectTreeIterator()
+                iterator.SetDataSet( inputMesh )
+                iterator.VisitOnlyLeavesOn()
+                iterator.GoToFirstItem()
+                while iterator.GetCurrentDataObject() is not None:
+                    block: vtkDataSet = vtkDataSet.SafeDownCast( iterator.GetCurrentDataObject() )
+                    af.AddInputData( block )
+                    iterator.GoToNextItem()
+                
+                af.Update()
+                captured_log.seek(0) #be kind let's just rewind
+                captured = captured_log.read().decode()
+
+            logger.error(captured.strip())
             outputMesh: vtkUnstructuredGrid = af.GetOutputDataObject( 0 )
 
     return outputMesh

geos-mesh/tests/test_MergeBlocksEnhanced.py

@@ -8,6 +8,7 @@
 from vtkmodules.vtkCommonDataModel import vtkMultiBlockDataSet
 from geos.mesh.processing.MergeBlockEnhanced import MergeBlockEnhanced
 from unittest import TestCase
+from geos.utils.Errors import VTKError
 
 def test_MergeBlocksEnhancedFilter( dataSetTest: vtkMultiBlockDataSet, ) -> None:
     """Test MergeBlockEnhanced vtk filter."""
@@ -16,7 +17,8 @@ def test_MergeBlocksEnhancedFilter( dataSetTest: vtkMultiBlockDataSet, ) -> None
     filter.applyFilter()
 
 class RaiseMergeBlocksEnhanced(TestCase):
-    def test_TypeError(self):
+    """Test failure on empty multiBlockDataSet."""
+    def test_TypeError(self) -> None:
         multiBlockDataset = vtkMultiBlockDataSet()
         filter: MergeBlockEnhanced = MergeBlockEnhanced( multiBlockDataset )
-        self.assertRaises((TypeError,ValueError), filter.applyFilter )
+        self.assertRaises(VTKError, filter.applyFilter )

geos-posp/src/PVplugins/PVMohrCirclePlot.py

@@ -38,6 +38,7 @@
     GeosMeshOutputsEnum,
 )
 from geos.utils.Logger import Logger, getLogger
+from geos.utils.Errors import VTKError
 from geos.utils.PhysicalConstants import (
     DEFAULT_FRICTION_ANGLE_DEG,
     DEFAULT_FRICTION_ANGLE_RAD,
@@ -805,7 +806,7 @@ def createMohrCirclesAtTimeStep(
         # get mesh and merge if needed
         try:
             meshMerged: vtkUnstructuredGrid = mergeBlocks( mesh )
-        except (ValueError,TypeError):
+        except (VTKError):
             raise
 
         # assert meshMerged is not None, "Input data is undefined"

geos-posp/src/geos_posp/filters/GeosBlockMerge.py

@@ -11,6 +11,7 @@
     getRockSuffixRenaming,
 )
 from geos.utils.Logger import Logger, getLogger
+from geos.utils.Errors import VTKError
 from typing_extensions import Self
 from vtkmodules.util.vtkAlgorithm import VTKPythonAlgorithmBase
 from vtkmodules.vtkCommonCore import (
@@ -367,7 +368,7 @@ def mergeChildBlocks( self: Self, compositeBlock: vtkMultiBlockDataSet ) -> vtkU
         # merge blocks
         try:
             mergedBlocks = mergeBlocks( compositeBlock )
-        except (ValueError,TypeError):
+        except (VTKError):
             raise
         else:
             return mergedBlocks

geos-utils/src/geos/utils/Errors.py

@@ -0,0 +1,4 @@
+
+class VTKError(Exception):
+    """ Captured and adapted VTKError from log (see Logger.py)"""
+    pass

geos-utils/src/geos/utils/Logger.py

@@ -2,15 +2,99 @@
 # SPDX-FileCopyrightText: Copyright 2023-2024 TotalEnergies.
 # SPDX-FileContributor: Martin Lemay
 import logging
-from typing import Any, Union
+from typing import Any, Union, Generator
 from typing_extensions import Self
 
+import sys
+import os
+import re
+import tempfile
+from contextlib import contextmanager
+
+from geos.utils.Errors import VTKError
+
 __doc__ = """
 Logger module manages logging tools.
 
 Code was modified from <https://stackoverflow.com/questions/384076/how-can-i-color-python-logging-output>
+
+It also include adaptor strategy to make vtkLogger behave as a logging's logger.
+Indeed, C++ adapted class is based on private Callback assignement which is not compatible
+with logging python's logic.
+
+usage:
+    #near logger definition
+    from vtkmodules.vtkCommonCore import vtkLogger
+
+    vtkLogger.SetStderrVerbosity(vtkLogger.VERBOSITY_TRACE)
+    logger.addFilter(RegexExceptionFilter())
+
+    ...
+
+    #near VTK calls
+     with VTKCaptureLog() as captured_log:
+        vtkcalls..
+        captured_log.seek(0) # be kind let's just rewind
+        captured = captured_log.read().decode()
+    
+    logger.error(captured.strip())
+
 """
 
+class RegexExceptionFilter(logging.Filter):
+    """
+        Class to regexp VTK messages rethrown into logger by VTKCaptureLog.
+    """
+
+    pattern : str = r"vtkExecutive.cxx" #pattern captured that will raise a vtkError
+
+    def __init__(self):
+        super().__init__()
+        self.regex = re.compile(self.pattern)
+
+    def filter(self, record : logging.LogRecord):
+        """
+            Filter VTK Error from stdErr
+            
+            Args:
+                record(loggging.LogRecord)
+        """
+        message = record.getMessage()
+        if self.regex.search(message):
+            raise VTKError(f"Log message matched forbidden pattern: {message}")
+        return True  # Allow other messages to pass
+
+
+@contextmanager
+def VTKCaptureLog()->Generator[Any,Any,Any]:
+    """
+        Hard way of adapting C-like vtkLogger to logging class by throwing in
+        stderr and reading back from it.
+
+        Return:
+            Generator buffering os.stderr
+
+    """
+    #equiv to pyvista's        
+    # from pyvista.utilities import VtkErrorCatcher
+    # with VtkErrorCatcher() as err:
+    #     append_filter.Update()
+    #     print(err)
+
+    # Save original stderr file descriptor
+    original_stderr_fd = sys.stderr.fileno()
+    saved_stderr_fd = os.dup(original_stderr_fd)
+
+    # Create a temporary file to capture stderr
+    with tempfile.TemporaryFile(mode='w+b') as tmp:
+        os.dup2(tmp.fileno(), original_stderr_fd)
+        try:
+            yield tmp
+        finally:
+            # Restore original stderr
+            os.dup2(saved_stderr_fd, original_stderr_fd)
+            os.close(saved_stderr_fd)
+
 
 class CountWarningHandler( logging.Handler ):
     """Create an handler to count the warnings logged."""