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vtkHDFWriterImplementation.h
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1// SPDX-FileCopyrightText: Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
2// SPDX-License-Identifier: BSD-3-Clause
9
10#ifndef vtkHDFWriterImplementation_h
11#define vtkHDFWriterImplementation_h
12
13#include "vtkAbstractArray.h"
14#include "vtkCellArray.h"
15#include "vtkHDF5ScopedHandle.h"
16#include "vtkHDFWriter.h"
17#include "vtkType.h"
18#include "vtk_hdf5.h"
19
20#include <array>
21#include <string>
22
23VTK_ABI_NAMESPACE_BEGIN
24
26{
27public:
28 hid_t GetRoot() { return this->Root; }
29 hid_t GetFile() { return this->File; }
30 hid_t GetStepsGroup(hid_t currentGroup);
31
38 bool WriteHeader(hid_t group, const char* hdfType);
39
47 bool CreateFile(bool overwrite, const std::string& filename);
48
53 bool OpenFile();
54
60 void CloseFile();
61
67 bool OpenSubfile(const std::string& filename);
68
70
75 void SetSubFilesReady(bool status) { this->SubFilesReady = status; }
76 bool GetSubFilesReady() { return this->SubFilesReady; }
78
83
90 typedef struct
91 {
92 const char* hdfGroupName;
95
99 std::vector<PolyDataTopos> GetCellArraysForTopos(vtkPolyData* polydata);
100
101 // Creation utility functions
102
107 vtkHDF::ScopedH5DHandle CreateAndWriteHdfDataset(hid_t group, hid_t type, hid_t source_type,
108 const char* name, int rank, std::vector<hsize_t> dimensions, const void* data);
109
115 vtkHDF::ScopedH5SHandle CreateSimpleDataspace(int rank, const hsize_t dimensions[]);
116
121 vtkHDF::ScopedH5AHandle CreateScalarAttribute(hid_t group, const char* name, int value);
122
128 vtkHDF::ScopedH5AHandle CreateVectorAttribute(
129 hid_t group, const char* name, hid_t type, hsize_t size, const void* data);
130
135 vtkHDF::ScopedH5AHandle CreateStringAttribute(
136 hid_t group, const char* name, const std::string& value);
137
142 vtkHDF::ScopedH5GHandle CreateHdfGroup(hid_t group, const char* name);
143
148 vtkHDF::ScopedH5GHandle CreateHdfGroupWithLinkOrder(hid_t group, const char* name);
149
154 bool CreateSoftLink(hid_t group, const char* groupName, const char* targetLink);
155
161 hid_t group, const char* filename, const char* source, const char* targetLink);
162
166 vtkHDF::ScopedH5GHandle OpenExistingGroup(hid_t group, const char* name);
167
171 vtkHDF::ScopedH5DHandle OpenDataset(hid_t group, const char* name);
172
176 std::string GetGroupName(hid_t group);
177
182 vtkHDF::ScopedH5DHandle CreateHdfDataset(
183 hid_t group, const char* name, hid_t type, hid_t dataspace);
184
190 vtkHDF::ScopedH5DHandle CreateHdfDataset(
191 hid_t group, const char* name, hid_t type, int rank, const hsize_t dimensions[]);
192
200 bool CreateVirtualDataset(hid_t group, const char* name, hid_t type, int numComp);
201
203
210 bool WriteSumSteps(hid_t group, const char* name);
211 bool WriteSumStepsPolyData(hid_t group, const char* name);
213
219 vtkHDF::ScopedH5SHandle CreateDataspaceFromArray(
220 vtkAbstractArray* dataArray, const std::vector<hsize_t>& dims = {});
221
227 vtkHDF::ScopedH5DHandle CreateDatasetFromDataArray(hid_t group, const char* name, hid_t type,
228 vtkAbstractArray* dataArray, const std::vector<hsize_t>& dims = {});
229
231
235 vtkHDF::ScopedH5DHandle CreateSingleRowDataset(
236 hid_t group, const char* name, const std::vector<vtkIdType>& values);
238
244 bool InitDynamicDataset(hid_t group, const char* name, hid_t type, hsize_t cols,
245 hsize_t chunkSize[], int compressionLevel = 0);
246
252 bool InitDynamicDataset(hid_t group, const char* name, hid_t type,
253 const std::vector<hsize_t>& dims, hsize_t chunkSize[], int compressionLevel = 0);
254
262 hid_t dataset, const std::vector<vtkIdType>& value, bool offset, bool trim = false);
263
268 bool AddFieldDataSizeValueToDataset(hid_t dataset, vtkIdType* value, vtkIdType size, bool offset);
269
278 bool AddArrayToDataset(hid_t dataset, vtkAbstractArray* dataArray, int trim = 0,
279 const std::vector<hsize_t>& dims = {});
280
287 bool AddOrCreateDataset(hid_t group, const char* name, hid_t type, vtkAbstractArray* dataArray,
288 const std::vector<hsize_t>& dims = {});
289
297 bool AddOrCreateSingleRowDataset(hid_t group, const char* name,
298 const std::vector<vtkIdType>& value, bool offset = false, bool trim = false);
299
308 hid_t group, const char* name, vtkIdType* value, vtkIdType size, bool offset = false);
309
313 vtkHDF::ScopedH5GHandle GetSubfileNonNullPart(const std::string& blockPath, int& type);
314
321
322 Implementation(vtkHDFWriter* writer);
324
325private:
326 vtkHDFWriter* Writer;
327 vtkHDF::ScopedH5FHandle File;
328 vtkHDF::ScopedH5GHandle Root;
329 vtkHDF::ScopedH5GHandle StepsGroup;
330 std::vector<vtkHDF::ScopedH5FHandle> Subfiles;
331 std::vector<std::string> SubfileNames;
332 bool SubFilesReady = false;
333
334 const std::array<std::string, 4> PrimitiveNames = { { "Vertices", "Lines", "Polygons",
335 "Strips" } };
336
341 hsize_t GetNumberOfCellsSubfile(const std::string& basePath, std::size_t subfileId, hsize_t part,
342 bool isPolyData, const std::string& groupName);
343
349 char GetPrimitive(hid_t group);
350
358 hsize_t GetSubfileNumberOf(const std::string& base, const std::string& qualifier,
359 std::size_t subfileId, hsize_t part, char primitive = 0xff);
360
361 std::string GetBasePath(const std::string& fullPath);
362
366 bool DatasetAndGroupExist(const std::string& dataset, hid_t group);
367
373 bool GetSubFilesDatasetSize(
374 const std::string& datasetPath, const std::string& groupName, hsize_t& totalSize);
375
376 // Possible indexing mode of VTKHDF datasets. See `GetDatasetIndexationMode`
377 enum class IndexingMode
378 {
379 Points,
380 Cells,
381 Connectivity,
382 TreeDepths,
383 Trees,
384 Descriptor,
385 HTGCoords,
386 MetaData,
387 Undefined
388 };
389
397 IndexingMode GetDatasetIndexationMode(const std::string& path);
398};
399
400VTK_ABI_NAMESPACE_END
401#endif
402// VTK-HeaderTest-Exclude: vtkHDFWriterImplementation.h
Abstract superclass for all arrays.
object to represent cell connectivity
general representation of visualization data
bool GetSubFilesReady()
Inform the implementation that all the data has been written in subfiles, and that the virtual datase...
vtkHDF::ScopedH5AHandle CreateScalarAttribute(hid_t group, const char *name, int value)
Create a scalar integer attribute in the given group.
bool AddOrCreateDataset(hid_t group, const char *name, hid_t type, vtkAbstractArray *dataArray, const std::vector< hsize_t > &dims={})
Append the given array to the dataset with the given name, creating it if it does not exist yet.
vtkHDF::ScopedH5GHandle CreateHdfGroup(hid_t group, const char *name)
Retrieve group if it exists, create it if needed.
vtkHDF::ScopedH5DHandle CreateAndWriteHdfDataset(hid_t group, hid_t type, hid_t source_type, const char *name, int rank, std::vector< hsize_t > dimensions, const void *data)
Create a dataset in the given group with the given parameters and write data to it Returned scoped ha...
hid_t GetStepsGroup(hid_t currentGroup)
bool AddOrCreateFieldDataSizeValueDataset(hid_t group, const char *name, vtkIdType *value, vtkIdType size, bool offset=false)
Append a 2D integer value to the dataset with name FieldDataSize.
bool WriteSumSteps(hid_t group, const char *name)
For temporal multi-piece meta-files, write the dataset name in group group, which must be the "steps"...
bool CreateFile(bool overwrite, const std::string &filename)
Create the file from the filename and create the root VTKHDF group.
vtkHDF::ScopedH5GHandle CreateHdfGroupWithLinkOrder(hid_t group, const char *name)
Retrieve or create a group that keeps track of link creation order Returned scoped handle may be inva...
vtkHDF::ScopedH5DHandle CreateDatasetFromDataArray(hid_t group, const char *name, hid_t type, vtkAbstractArray *dataArray, const std::vector< hsize_t > &dims={})
Creates a dataset in the given group from a dataArray and write data to it dims provides the dimensio...
vtkHDF::ScopedH5DHandle OpenDataset(hid_t group, const char *name)
Open and return an existing dataset using its group id and dataset name.
vtkHDF::ScopedH5GHandle OpenExistingGroup(hid_t group, const char *name)
Open and return an existing group thanks to id and a relative or absolute path to this group.
bool OpenFile()
Open existing VTKHDF file and set Root and File members.
vtkHDF::ScopedH5DHandle CreateHdfDataset(hid_t group, const char *name, hid_t type, int rank, const hsize_t dimensions[])
Create a dataset in the given group It internally creates a dataspace from a rank and dimensions Retu...
vtkHDF::ScopedH5SHandle CreateDataspaceFromArray(vtkAbstractArray *dataArray, const std::vector< hsize_t > &dims={})
Creates a dataspace to the exact array dimensions dims provides the dimensions of the structured data...
bool AddFieldDataSizeValueToDataset(hid_t dataset, vtkIdType *value, vtkIdType size, bool offset)
Add a 2D value of integer type to an existing dataspace which represents the FieldDataSize.
vtkHDF::ScopedH5DHandle CreateSingleRowDataset(hid_t group, const char *name, const std::vector< vtkIdType > &values)
Creates a dataset and write a row of values to it.
Implementation(vtkHDFWriter *writer)
bool InitDynamicDataset(hid_t group, const char *name, hid_t type, hsize_t cols, hsize_t chunkSize[], int compressionLevel=0)
Create a chunked dataset with an empty extendable dataspace using chunking and set the desired level ...
bool CreateExternalLink(hid_t group, const char *filename, const char *source, const char *targetLink)
Create an external link to the real group containing the block dataset.
bool CreateSoftLink(hid_t group, const char *groupName, const char *targetLink)
Create a soft link to the real group containing the block dataset.
bool AddArrayToDataset(hid_t dataset, vtkAbstractArray *dataArray, int trim=0, const std::vector< hsize_t > &dims={})
Append a full data array at the end of an existing infinite dataspace.
void CreateArraysFromNonNullPart(hid_t group, vtkDataObject *data)
Initialize empty data object array structures from a base group.
bool AddOrCreateSingleRowDataset(hid_t group, const char *name, const std::vector< vtkIdType > &value, bool offset=false, bool trim=false)
Append a single row of integer values to the dataset with name name in group group.
void CloseFile()
Close currently handled file, open using CreateFile or OpenFile.
vtkHDF::ScopedH5GHandle GetSubfileNonNullPart(const std::string &blockPath, int &type)
Find the first non null part for the given path in all subfiles.
vtkHDF::ScopedH5AHandle CreateVectorAttribute(hid_t group, const char *name, hid_t type, hsize_t size, const void *data)
Create a vector attribute (1D array) with arbitrary type and size in the given group.
vtkHDF::ScopedH5AHandle CreateStringAttribute(hid_t group, const char *name, const std::string &value)
Create a string attribute in the given group.
std::vector< PolyDataTopos > GetCellArraysForTopos(vtkPolyData *polydata)
Get the cell array for the POLY_DATA_TOPOS.
bool CreateStepsGroup(hid_t group)
Create the steps group in the given group.
bool InitDynamicDataset(hid_t group, const char *name, hid_t type, const std::vector< hsize_t > &dims, hsize_t chunkSize[], int compressionLevel=0)
Create a chunked dataset with an empty extendable dataspace using chunking and set the desired level ...
bool WriteHeader(hid_t group, const char *hdfType)
Write version and type attributes to the root group A root must be open for the operation to succeed ...
std::string GetGroupName(hid_t group)
Return the name of a group given its id.
void SetSubFilesReady(bool status)
Inform the implementation that all the data has been written in subfiles, and that the virtual datase...
vtkHDF::ScopedH5SHandle CreateSimpleDataspace(int rank, const hsize_t dimensions[])
Create a HDF dataspace It is simple (not scalar or null) which means that it is an array of elements ...
vtkHDF::ScopedH5DHandle CreateHdfDataset(hid_t group, const char *name, hid_t type, hid_t dataspace)
Create a dataset in the given group from a dataspace Returned scoped handle may be invalid.
bool CreateVirtualDataset(hid_t group, const char *name, hid_t type, int numComp)
Create a virtual dataset from all the subfiles that have been added.
bool OpenSubfile(const std::string &filename)
Open subfile where data has already been written, and needs to be referenced by the main file using v...
bool AddSingleRowToDataset(hid_t dataset, const std::vector< vtkIdType > &value, bool offset, bool trim=false)
Add a single row of integer type to an existing dataspace.
bool WriteSumStepsPolyData(hid_t group, const char *name)
For temporal multi-piece meta-files, write the dataset name in group group, which must be the "steps"...
concrete dataset represents vertices, lines, polygons, and triangle strips
Stores a group name and the corresponding cell array.
boost::graph_traits< vtkGraph * >::vertex_descriptor source(boost::graph_traits< vtkGraph * >::edge_descriptor e, vtkGraph *)
@ Cells
A cell specified by degrees of freedom held in arrays.
int64_t hid_t
int vtkIdType
Definition vtkType.h:363