Add support for GEOS data to vtk reader (#20141)

* Update config-site for my system. * Add support for GEOS flavor .pvd root files and .vtm timestate files. Each .vtm file is considered as one mesh. Blocks with 'Region' in the name that are Parent to 'Dataset' Blocks are considered groups. Variables defined in the underlying .vtu files are tracked for which blocks they belong to, since they may not be defined in every group. GetMesh and GetVar calls check the validity of the mesh/variable for a given block and return nullptr when not considered valid. * Fix bad logic, add a `return false` case. * Set HasVarsDefinedOnSubMeshes for GEOS flavor. * When checking if block is valid for mesh/var, use all registered variables. * Change domains to blocks. fix ParticleRegion name. * Add support for opening GEOS flavored single .vtm, or grouped .vtm files. * Fix error creating subset plot of 'groups' * Add tests and baselines for geos data. * Update release notes. * Flesh out FreeUpResources in GEOS reader. * Fix per Review comment. Co-authored-by: Mark C. Miller <[email protected]> --------- Co-authored-by: Mark C. Miller <[email protected]>
visit-dav · Jan 9, 2025 · 9b3fbd1 · 9b3fbd1
1 parent 4da381a
commit 9b3fbd1
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diff --git a/data/geos_test_data.tar.xz b/data/geos_test_data.tar.xz
diff --git a/src/config-site/WIN-5525018.cmake b/src/config-site/WIN-5525018.cmake
@@ -1,7 +1,6 @@
 # a windows 11 system
 set(CMAKE_CONFIGURATION_TYPES Release Debug)
 
-include(config-site/windows.cmake)
 
 # disable some warnings
 # 4244 conversion double to float etc
@@ -44,15 +43,10 @@ if(USE_REDUCED_BUILD) # this is just a var I create when I need it
   VISIT_OPTION_DEFAULT(VISIT_WINDOWS_APPLICATION OFF TYPE BOOL)
 
   VISIT_OPTION_DEFAULT(VISIT_SELECTED_DATABASE_PLUGINS "VTK;Silo" TYPE STRING)
-  VISIT_OPTION_DEFAULT(VISIT_SELECTED_PLOT_PLUGINS "Pseudocolor;Curve" TYPE STRING)
+  VISIT_OPTION_DEFAULT(VISIT_SELECTED_PLOT_PLUGINS "Pseudocolor;Curve;Mesh;Subset" TYPE STRING)
   VISIT_OPTION_DEFAULT(VISIT_SELECTED_OPERATOR_PLUGINS "Slice;Lineout" TYPE STRING)
 
 endif()
 
-if(USE_DEBUG_VTK) # this is a var I create when I need it
-  if(MSVC_TOOLSET_VERSION LESS "143")
-    VISIT_OPTION_DEFAULT(VISIT_VTK_DIR C:/A_VisIt/TPForDebugging/vtk-debug/8.1.0)
-  else()
-    VISIT_OPTION_DEFAULT(VISIT_VTK_DIR C:/A_VisIt/TPForDebugging/vtk-debug/9.2.6)
-  endif()
-endif()
+include(config-site/windows.cmake)
+
diff --git a/src/databases/VTK/CMakeLists.txt b/src/databases/VTK/CMakeLists.txt
@@ -15,6 +15,7 @@ VTKPluginInfo.C
 SET(LIBM_SOURCES
 VTKMDServerPluginInfo.C
 ${COMMON_SOURCES}
+avtGEOSFileReader.C
 avtPVDFileReader.C
 avtVTKFileFormat.C
 avtVTKFileReader.C
@@ -27,6 +28,7 @@ VTMParser.C
 SET(LIBE_SOURCES
 VTKEnginePluginInfo.C
 ${COMMON_SOURCES}
+avtGEOSFileReader.C
 avtPVDFileReader.C
 avtVTKFileFormat.C
 avtVTKFileReader.C

diff --git a/src/databases/VTK/VTK.code b/src/databases/VTK/VTK.code
@@ -23,16 +23,134 @@ Definition:
 //    I changed the code so it switches the interface based on how many domains
 //    are present in the 1st file.
 //
+//    Kathleen Biagas, Fri August 13, 2021
+//    Add MTMD for .pvd file types.
+//
+//    Kathleen Biagas, Thu Dec 12, 2024 
+//    Added tests to see if .pvd is GEOS flavor.
+//
 // ****************************************************************************
 
+#include <FileFunctions.h>
+#include <vtkNew.h>
+#include <vtkXMLDataElement.h>
+#include <vtkXMLDataParser.h>
+using std::string;
+
+bool
+FindGEOSNestedElement(vtkXMLDataElement *el)
+{
+    if (el->GetNumberOfNestedElements() == 0)
+        return false;
+
+    // check for Blocks with certain name attributes used by GEOS
+    if(el->FindNestedElementWithNameAndAttribute("Block", "name","CellElementRegion") ||
+       el->FindNestedElementWithNameAndAttribute("Block", "name","SurfaceElementRegion") ||
+       el->FindNestedElementWithNameAndAttribute("Block", "name","ParticleRegion") ||
+       el->FindNestedElementWithNameAndAttribute("Block", "name","WellElementRegion") )
+    {
+        return true;
+    }
+    for(int i = 0; i < el->GetNumberOfNestedElements(); ++i)
+        return FindGEOSNestedElement(el->GetNestedElement(i));
+
+    return false;
+}
+
+
+bool
+CheckIfGEOSVTM(const string &vtmFile)
+{
+    vtkNew<vtkXMLDataParser> vtmParser;
+    vtmParser->SetFileName(vtmFile.c_str());
+    if(!vtmParser->Parse())
+        return false;
+
+    vtkXMLDataElement *vtmRoot = vtmParser->GetRootElement();
+    return FindGEOSNestedElement(vtmRoot);
+}
+
+
+bool
+CheckIfGEOSPVD(const string &rootFile)
+{
+    vtkNew<vtkXMLDataParser> pvdParser;
+    pvdParser->SetFileName(rootFile.c_str());
+    if(pvdParser->Parse())
+    {
+        vtkXMLDataElement *root = pvdParser->GetRootElement();
+        if(root)
+        {
+            vtkXMLDataElement *datasetNode = root->LookupElementWithName("DataSet");
+            if(datasetNode) 
+            {
+                string fileName = datasetNode->GetAttribute("file");
+                size_t pos1 = fileName.find_last_of('.');
+                string ext1 = fileName.substr(pos1 + 1);
+                if(ext1 == "vtm")
+                {
+                    // extract dir from rootFile and prepend to fileName:
+                    string dir = FileFunctions::Dirname(rootFile);
+                    string file = dir + VISIT_SLASH_STRING + fileName;
+                    return CheckIfGEOSVTM(file);    
+                }
+            }
+        }
+    }
+    return false;
+}
+
+
 #include <avtSTSDFileFormatInterface.h>
+#include <avtMTMDFileFormatInterface.h>
 
 avtDatabase *
 VTKCommonPluginInfo::SetupDatabase(const char *const *list,
                                    int nList, int nBlock)
 {
     avtDatabase *db = NULL;
 
+    string fn(list[0]);
+    size_t pos = fn.find_last_of('.');
+    string ext = fn.substr(pos+1);
+    if (ext == "pvd")
+    {
+        dbType = DB_TYPE_MTMD;
+
+        // Only using 1 timestepgroup
+        avtMTMDFileFormat **ffl = new avtMTMDFileFormat*[1];
+        if(CheckIfGEOS(fn))
+            ffl[0] = new avtGEOSFileFormat(fn.c_str(), readOptions);
+        else
+            ffl[0] = new avtPVD_MTMDFileFormat(fn.c_str(), readOptions);
+        avtMTMDFileFormatInterface *inter = new avtMTMDFileFormatInterface(ffl, 1);
+        db = new avtGenericDatabase(inter);
+
+        return db;
+    }
+    else if (ext == "vtm")
+    {
+        if(CheckIfGEOSVTM(fn))
+        {
+            dbType = DB_TYPE_STMD;
+            avtSTMDFileFormat **ffl = new avtSTMDFileFormat*[nList];
+            avtGEOSFileReader *reader = new avtGEOSFileReader(list[0], readOptions);
+            for (int i = 0; i < nList; i++)
+            {
+                if(i == 0)
+                    ffl[i] = new avtGEOS_STMDFileFormat(list[i], readOptions, reader);
+                else
+                    ffl[i] = new avtGEOS_STMDFileFormat(list[i], readOptions);
+            }
+            avtSTMDFileFormatInterface *inter
+               = new avtSTMDFileFormatInterface(ffl, nList);
+            db = new avtGenericDatabase(inter);
+
+            return db;
+        }
+    }
+
+
     // Figure out how many domains there are in the 1st file.
     avtVTKFileReader *reader = new avtVTKFileReader(list[0], readOptions);
     int nDomains = 1;

diff --git a/src/databases/VTK/VTKCommonPluginInfo.C b/src/databases/VTK/VTKCommonPluginInfo.C
@@ -3,16 +3,10 @@
 // details.  No copyright assignment is required to contribute to VisIt.
 
 #include <VTKPluginInfo.h>
-
 #include <avtVTKFileFormat.h>
-#include <avtVTKOptions.h>
-
-#include <avtSTSDFileFormatInterface.h>
 #include <avtSTMDFileFormatInterface.h>
-#include <avtMTMDFileFormatInterface.h>
 #include <avtGenericDatabase.h>
-
-using std::string;
+#include <avtVTKOptions.h>
 
 VTKCommonPluginInfo::VTKCommonPluginInfo() : CommonDatabasePluginInfo(), VTKGeneralPluginInfo()
 {
@@ -58,11 +52,86 @@ VTKCommonPluginInfo::GetDatabaseType()
 //    I changed the code so it switches the interface based on how many domains
 //    are present in the 1st file.
 //
-//    Kathleen Biagas, Fri Augus 13, 2021
+//    Kathleen Biagas, Fri August 13, 2021
 //    Add MTMD for .pvd file types.
 //
+//    Kathleen Biagas, Thu Dec 12, 2024 
+//    Added tests to see if .pvd is GEOS flavor.
+//
 // ****************************************************************************
 
+#include <FileFunctions.h>
+#include <vtkNew.h>
+#include <vtkXMLDataElement.h>
+#include <vtkXMLDataParser.h>
+using std::string;
+
+bool
+FindGEOSNestedElement(vtkXMLDataElement *el)
+{
+    if(el->GetNumberOfNestedElements() == 0)
+        return false;
+
+    // check for Blocks with certain name attributes used by GEOS
+    if(el->FindNestedElementWithNameAndAttribute("Block", "name","CellElementRegion") ||
+       el->FindNestedElementWithNameAndAttribute("Block", "name","SurfaceElementRegion") ||
+       el->FindNestedElementWithNameAndAttribute("Block", "name","ParticleRegion") ||
+       el->FindNestedElementWithNameAndAttribute("Block", "name","WellElementRegion") )
+    {
+        return true;
+    }
+    for(int i = 0; i < el->GetNumberOfNestedElements(); ++i)
+        return FindGEOSNestedElement(el->GetNestedElement(i));
+
+    return false;
+}
+
+bool
+CheckIfGEOSVTM(const string &vtmFile)
+{
+    vtkNew<vtkXMLDataParser> vtmParser;
+    vtmParser->SetFileName(vtmFile.c_str());
+    if(!vtmParser->Parse())
+        return false;
+
+    vtkXMLDataElement *vtmRoot = vtmParser->GetRootElement();
+    return FindGEOSNestedElement(vtmRoot);
+}
+
+
+bool
+CheckIfGEOSPVD(const string &rootFile)
+{
+    vtkNew<vtkXMLDataParser> pvdParser;
+    pvdParser->SetFileName(rootFile.c_str());
+    if(pvdParser->Parse())
+    {
+        vtkXMLDataElement *root = pvdParser->GetRootElement();
+        if(root)
+        {
+            vtkXMLDataElement *datasetNode = root->LookupElementWithName("DataSet");
+            if(datasetNode) 
+            {
+                string fileName = datasetNode->GetAttribute("file");
+                size_t pos1 = fileName.find_last_of('.');
+                string ext1 = fileName.substr(pos1 + 1);
+                if(ext1 == "vtm")
+                {
+                    // extract dir from rootFile and prepend to fileName:
+                    string dir = FileFunctions::Dirname(rootFile);
+                    string file = dir + VISIT_SLASH_STRING + fileName;
+                    return CheckIfGEOSVTM(file);
+                }
+            }
+        }
+    }
+    return false;
+}
+
+
+#include <avtSTSDFileFormatInterface.h>
+#include <avtMTMDFileFormatInterface.h>
+
 avtDatabase *
 VTKCommonPluginInfo::SetupDatabase(const char *const *list,
                                    int nList, int nBlock)
@@ -78,12 +147,37 @@ VTKCommonPluginInfo::SetupDatabase(const char *const *list,
 
         // Only using 1 timestepgroup
         avtMTMDFileFormat **ffl = new avtMTMDFileFormat*[1];
-        ffl[0] = new avtPVD_MTMDFileFormat(fn.c_str(), readOptions);
+        if(CheckIfGEOSPVD(fn))
+            ffl[0] = new avtGEOSFileFormat(fn.c_str(), readOptions);
+        else
+            ffl[0] = new avtPVD_MTMDFileFormat(fn.c_str(), readOptions);
         avtMTMDFileFormatInterface *inter = new avtMTMDFileFormatInterface(ffl, 1);
         db = new avtGenericDatabase(inter);
 
         return db;
     }
+    else if (ext == "vtm")
+    {
+        if(CheckIfGEOSVTM(fn))
+        {
+            dbType = DB_TYPE_STMD;
+            avtSTMDFileFormat **ffl = new avtSTMDFileFormat*[nList];
+            avtGEOSFileReader *reader = new avtGEOSFileReader(list[0], readOptions);
+            for (int i = 0; i < nList; i++)
+            {
+                if(i == 0)
+                    ffl[i] = new avtGEOS_STMDFileFormat(list[i], readOptions, reader);
+                else
+                    ffl[i] = new avtGEOS_STMDFileFormat(list[i], readOptions);
+            }
+            avtSTMDFileFormatInterface *inter
+               = new avtSTMDFileFormatInterface(ffl, nList);
+            db = new avtGenericDatabase(inter);
+
+            return db;
+        }
+    }
+
 
     // Figure out how many domains there are in the 1st file.
     avtVTKFileReader *reader = new avtVTKFileReader(list[0], readOptions);