feat: Adding optionable converter MD->SG

mesh-doctor/src/geos/mesh_doctor/parsing/__init__.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/convertMD2SGParsing.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( result.outputFile ) )
+    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/register.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/tests/data/base_tetra_shift.vtm

@@ -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_tetra_shift/domain_fracture_2_ids.vtu

@@ -0,0 +1,55 @@
+<?xml version="1.0"?>
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+  <UnstructuredGrid>
+    <Piece NumberOfPoints="295" NumberOfCells="390">
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+            <Value index="1">
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+      </PointData>
+      <CellData GlobalIds="GLOBAL_IDS_CELLS">
+        <DataArray type="Int64" Name="attribute" format="binary" RangeMin="2" RangeMax="2">
+          AQAAAACAAAAwDAAAHwAAAA==eJztxaENAAAMArCF/4+ewHFDa5qr2LZt2/b8qo4DDQ==
+        </DataArray>
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+</VTKFile>