feat: Adding optionable converter MD->SG (#253)

* PR gen from script by copilot
* scrap vtk full import
* using writing and reading logic
* adding some tests
* adding component splitter
* fix test w/ cc
* yapf
* copilot review

Author: jafranc

mesh-doctor/src/geos/mesh_doctor/actions/convertMD2SG.py

@@ -19,6 +19,7 @@
 ORPHAN_2D = "orphan2d"
 CHECK_INTERNAL_TAGS = "checkInternalTags"
 EULER = "euler"
+CONVERT_MD2SG = "convertMD2SG"
 
 
 @dataclass( frozen=True )

mesh-doctor/src/geos/mesh_doctor/parsing/__init__.py

@@ -0,0 +1,76 @@
+# SPDX-License-Identifier: Apache-2.0
+# SPDX-FileCopyrightText: Copyright 2023-2024 TotalEnergies.
+# SPDX-FileContributor: GitHub Copilot, Jacques Franc
+from __future__ import annotations
+from argparse import _SubParsersAction
+from typing import Any
+
+from geos.mesh_doctor.actions.convertMD2SG import Options, Result
+from geos.mesh_doctor.parsing import CONVERT_MD2SG
+from geos.mesh_doctor.parsing._sharedChecksParsingLogic import getOptionsUsedMessage
+from geos.mesh_doctor.parsing.cliParsing import setupLogger, addVtuInputFileArgument
+from geos.mesh.io.vtkIO import VtkOutput
+
+__ATTRS = "attrs"
+__OUTPUT_FILE = "outputFile"
+__SKIP_CLEAN = "skipCleanCollocated"
+__SKIP_FILTER = "skipFilterVolumeCells"
+
+
+def convert( parsedOptions: dict[ str, Any ] ) -> Options:
+    """Convert parsed command-line options to Options object.
+
+    Args:
+        parsedOptions: Dictionary of parsed command-line options.
+
+    Returns:
+        Options: Converted options object.
+    """
+    return Options( attrs=tuple( parsedOptions.get( __ATTRS, [] ) ),
+                    skipCleanCollocated=parsedOptions.get( __SKIP_CLEAN, False ),
+                    skipFilterVolumeCells=parsedOptions.get( __SKIP_FILTER, False ),
+                    meshVtkOutput=VtkOutput( output=parsedOptions.get( __OUTPUT_FILE ), isDataModeBinary=True ) )
+
+
+def fillSubparser( subparsers: _SubParsersAction[ Any ] ) -> None:
+    """Fill the argument parser for the convertMD2SG action.
+
+    Args:
+        subparsers: Subparsers from the main argument parser.
+    """
+    p = subparsers.add_parser( CONVERT_MD2SG,
+                               help="Convert a mesh-doctor dataset to a SurfaceGen-compatible VTU file." )
+    addVtuInputFileArgument( p )
+    p.add_argument( '-z',
+                    '--' + __ATTRS,
+                    type=int,
+                    nargs='+',
+                    default=[],
+                    help="[int ...]: Attributes to include when filtering surface cells." )
+    p.add_argument( '--' + __OUTPUT_FILE,
+                    type=str,
+                    default="converted.vtu",
+                    help="[string]: Optional output VTU file path." )
+    p.add_argument( '--' + __SKIP_CLEAN, action='store_true', help="Skip the collocated node cleanup step." )
+    p.add_argument( '--' + __SKIP_FILTER,
+                    action='store_true',
+                    help="Skip the surface/volume extraction step when input is a single VTU file." )
+
+
+def displayResults( options: Options, result: Result ) -> None:
+    """Display the results of the convertMD2SG action.
+
+    Args:
+        options: The options used for the conversion.
+        result: The results of the conversion.
+    """
+    setupLogger.results( getOptionsUsedMessage( options ) )
+    setupLogger.results( "Converted mesh saved to: {0}".format( options.meshVtkOutput.output ) )
+    setupLogger.results( f"  Points: {result.numPoints:,}" )
+    setupLogger.results( f"  Cells: {result.numCells:,}" )
+    setupLogger.results( f"  Bounds: {result.bounds}" )
+    setupLogger.results(
+        f"  Skip clean collocated(npoints cleaned): {result.skipCleanCollocated} ({result.nCleanCollocated})" )
+    setupLogger.results(
+        f"  Skip filter volume cells(ncells removed): {result.skipFilterVolumeCells} ({result.nFilterVolumeCells})" )
+    setupLogger.results( f"  Number of connected components for faultNodes: {result.nColors}" )

mesh-doctor/src/geos/mesh_doctor/parsing/convertMD2SGParsing.py

@@ -59,7 +59,7 @@ def registerParsingActions(
                         parsing.FIX_ELEMENTS_ORDERINGS, parsing.GENERATE_CUBE, parsing.GENERATE_FRACTURES,
                         parsing.GENERATE_GLOBAL_IDS, parsing.MAIN_CHECKS, parsing.NON_CONFORMAL,
                         parsing.SELF_INTERSECTING_ELEMENTS, parsing.SUPPORTED_ELEMENTS, parsing.ORPHAN_2D,
-                        parsing.CHECK_INTERNAL_TAGS, parsing.EULER ):
+                        parsing.CHECK_INTERNAL_TAGS, parsing.EULER, parsing.CONVERT_MD2SG ):
         __HELPERS[ actionName ] = actionName
         __ACTIONS[ actionName ] = actionName
 

mesh-doctor/src/geos/mesh_doctor/register.py

@@ -0,0 +1,7 @@
+<?xml version="1.0"?>
+<VTKFile type="vtkMultiBlockDataSet" version="1.0" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
+  <vtkMultiBlockDataSet>
+    <DataSet index="0" name="main" file="base_tetra_shift/domain_ids.vtu"/>
+    <DataSet index="1" name="fault" file="base_tetra_shift/domain_fracture_2_ids.vtu"/>
+  </vtkMultiBlockDataSet>
+</VTKFile>

mesh-doctor/tests/data/base_hexa_shift_2.vtu

@@ -0,0 +1,55 @@
+<?xml version="1.0"?>
+<VTKFile type="UnstructuredGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
+  <UnstructuredGrid>
+    <Piece NumberOfPoints="295" NumberOfCells="390">
+      <PointData GlobalIds="GLOBAL_IDS_POINTS">
+        <DataArray type="Int64" IdType="1" Name="collocated_nodes" NumberOfComponents="2" format="binary" RangeMin="1113.0004492362077" RangeMax="2930.1435118437457">
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+          <InformationKey name="L2_NORM_RANGE" location="vtkDataArray" length="2">
+            <Value index="0">
+              1113.0004492
+            </Value>
+            <Value index="1">
+              2930.1435118
+            </Value>
+          </InformationKey>
+        </DataArray>
+        <DataArray type="Int64" IdType="1" Name="GLOBAL_IDS_POINTS" format="binary" RangeMin="0" RangeMax="294">
+          AQAAAACAAAA4CQAA/AEAAA==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
+        </DataArray>
+      </PointData>
+      <CellData GlobalIds="GLOBAL_IDS_CELLS">
+        <DataArray type="Int64" Name="attribute" format="binary" RangeMin="2" RangeMax="2">
+          AQAAAACAAAAwDAAAHwAAAA==eJztxaENAAAMArCF/4+ewHFDa5qr2LZt2/b8qo4DDQ==
+        </DataArray>
+        <DataArray type="Int64" IdType="1" Name="GLOBAL_IDS_CELLS" format="binary" RangeMin="0" RangeMax="389">
+          AQAAAACAAAAwDAAAiQIAAA==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+      </CellData>
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+      </Cells>
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+  </UnstructuredGrid>
+</VTKFile>