Field3D
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Provides reading of .f3d (internally, hdf5) files.Refer to using_files for examples of how to use this in your code. More...
#include <Field3DFile.h>
Public Member Functions | |
bool | open (const std::string &filename) |
Opens the given file. | |
bool | readGroupMembership (GroupMembershipMap &gpMembershipMap) |
Read the group membership for the partitions. | |
Constructors & destructor | |
Field3DInputFile () | |
virtual | ~Field3DInputFile () |
Reading layers from disk | |
template<class Data_T > | |
Field< Data_T >::Vec | readScalarLayers (const std::string &layerName=std::string("")) const |
Retrieves all the layers of scalar type and maintains their on-disk data types. | |
template<class Data_T > | |
Field< Data_T >::Vec | readScalarLayers (const std::string &partitionName, const std::string &layerName) const |
This one allows the allows the partitionName to be passed in. | |
template<class Data_T > | |
Field< FIELD3D_VEC3_T< Data_T > >::Vec | readVectorLayers (const std::string &layerName=std::string("")) const |
Retrieves all the layers of vector type and maintains their on-disk data types. | |
template<class Data_T > | |
Field< FIELD3D_VEC3_T< Data_T > >::Vec | readVectorLayers (const std::string &partitionName, const std::string &layerName) const |
This version allows you to pass in the partition name. | |
template<template< typename T > class Field_T, class Data_T > | |
Field_T< Data_T >::Vec | readScalarLayersAs (const std::string &layerName=std::string("")) const |
Retrieves all layers for all partitions. Converts it to the given template type if needed. | |
template<template< typename T > class Field_T, class Data_T > | |
Field_T< Data_T >::Vec | readScalarLayersAs (const std::string &partitionName, const std::string &layerName) const |
Retrieves a layers given their and its parent partition's name. Converts it to the given template type if needed. | |
template<template< typename T > class Field_T, class Data_T > | |
Field_T< Data_T >::Vec | readVectorLayersAs (const std::string &layerName=std::string("")) const |
Retrieves a layers for all partitions. Converts it to the given template type if needed. | |
template<template< typename T > class Field_T, class Data_T > | |
Field_T< Data_T >::Vec | readVectorLayersAs (const std::string &partitionName, const std::string &layerName) const |
Retrieves a layers given their and its parent partition's name. Converts it to the given template type if needed. | |
Reading proxy data from disk | |
template<class Data_T > | |
EmptyField< Data_T >::Vec | readProxyLayer (const std::string &partitionName, const std::string &layerName, bool isVectorLayer) const |
Retrieves a proxy version (EmptyField) of each layer . | |
template<class Data_T > | |
EmptyField< Data_T >::Vec | readProxyScalarLayers (const std::string &name=std::string("")) const |
Retrieves a proxy version (EmptyField) of each scalar layer. | |
template<class Data_T > | |
EmptyField< Data_T >::Vec | readProxyVectorLayers (const std::string &name=std::string("")) const |
Retrieves a proxy version (EmptyField) of each vector layer. | |
Internal utility methods | |
herr_t | parsePartition (hid_t loc_id, const std::string partitionName) |
Gets called from parsePartitions. Not intended for any other use. | |
herr_t | parseLayer (hid_t loc_id, const std::string &partitionName, const std::string &layerName) |
Gets called from parsePartitions. Not intended for any other use. | |
Private Member Functions | |
template<class Data_T > | |
Field< Data_T >::Ptr | readLayer (const std::string &intPartitionName, const std::string &layerName, bool isVectorLayer) const |
This call does the actual reading of a layer. Notice that it expects a unique -internal- partition name. | |
bool | readMetadata (hid_t metadata_id, FieldBase::Ptr field) const |
Read metadata for this layer. | |
bool | readMetadata (hid_t metadata_id) |
Read global metadata for this file. | |
bool | readPartitionAndLayerInfo () |
Sets up all the partitions and layers, but does not load any data. | |
template<class Data_T > | |
Field< Data_T >::Ptr | readScalarLayer (const std::string &intPartitionName, const std::string &layerName) const |
Retrieves a single layer given its and its parent partition's name. Maintains the on-disk data types. | |
template<class Data_T > | |
Field< FIELD3D_VEC3_T< Data_T > >::Ptr | readVectorLayer (const std::string &intPartitionName, const std::string &layerName) const |
Retrieves a single layer given its and its parent partition's name. Maintains the on-disk data types. | |
Private Attributes | |
std::string | m_filename |
Filename, only to be set by open(). |
Provides reading of .f3d (internally, hdf5) files.
Refer to using_files for examples of how to use this in your code.
Definition at line 431 of file Field3DFile.h.
Field3DInputFile::Field3DInputFile | ( | ) |
Definition at line 561 of file Field3DFile.cpp.
{
// Empty
}
Field3DInputFile::~Field3DInputFile | ( | ) | [virtual] |
Field< Data_T >::Vec Field3DInputFile::readScalarLayers | ( | const std::string & | layerName = std::string("") | ) | const |
Retrieves all the layers of scalar type and maintains their on-disk data types.
layerName | If a string is passed in, only layers of that name will be read from disk. |
Definition at line 769 of file Field3DFile.h.
References Field3DFileBase::getIntPartitionNames(), and Field3DFileBase::getIntScalarLayerNames().
{ using namespace std; typedef typename Field<Data_T>::Ptr FieldPtr; typedef typename Field<Data_T>::Vec FieldList; FieldList ret; std::vector<std::string> parts; getIntPartitionNames(parts); for (vector<string>::iterator p = parts.begin(); p != parts.end(); ++p) { std::vector<std::string> layers; getIntScalarLayerNames(layers, *p); for (vector<string>::iterator l = layers.begin(); l != layers.end(); ++l) { // Only read if it matches the name if ((name.length() == 0) || (*l == name)) { FieldPtr mf = readScalarLayer<Data_T>(*p, *l); if (mf) { ret.push_back(mf); } } } } return ret; }
Field< Data_T >::Vec Field3DInputFile::readScalarLayers | ( | const std::string & | partitionName, |
const std::string & | layerName | ||
) | const |
This one allows the allows the partitionName to be passed in.
Definition at line 801 of file Field3DFile.h.
References Field3DFileBase::getIntPartitionNames(), Field3DFileBase::getIntScalarLayerNames(), and Field3DFileBase::removeUniqueId().
{ using namespace std; typedef typename Field<Data_T>::Ptr FieldPtr; typedef typename Field<Data_T>::Vec FieldList; FieldList ret; if ((layerName.length() == 0) || (partitionName.length() == 0)) return ret; std::vector<std::string> parts; getIntPartitionNames(parts); for (vector<string>::iterator p = parts.begin(); p != parts.end(); ++p) { std::vector<std::string> layers; getIntScalarLayerNames(layers, *p); if (removeUniqueId(*p) == partitionName) { for (vector<string>::iterator l = layers.begin(); l != layers.end(); ++l) { // Only read if it matches the name if (*l == layerName) { FieldPtr mf = readScalarLayer<Data_T>(*p, *l); if (mf) ret.push_back(mf); } } } } return ret; }
Field< FIELD3D_VEC3_T< Data_T > >::Vec Field3DInputFile::readVectorLayers | ( | const std::string & | layerName = std::string("") | ) | const |
Retrieves all the layers of vector type and maintains their on-disk data types.
layerName | If a string is passed in, only layers of that name will be read from disk. |
Definition at line 840 of file Field3DFile.h.
References Field3DFileBase::getIntPartitionNames(), and Field3DFileBase::getIntVectorLayerNames().
{ using namespace std; typedef typename Field<FIELD3D_VEC3_T<Data_T> >::Ptr FieldPtr; typedef typename Field<FIELD3D_VEC3_T<Data_T> >::Vec FieldList; FieldList ret; std::vector<std::string> parts; getIntPartitionNames(parts); for (vector<string>::iterator p = parts.begin(); p != parts.end(); ++p) { std::vector<std::string> layers; getIntVectorLayerNames(layers, *p); for (vector<string>::iterator l = layers.begin(); l != layers.end(); ++l) { // Only read if it matches the name if ((name.length() == 0) || (*l == name)) { FieldPtr mf = readVectorLayer<Data_T>(*p, *l); if (mf) ret.push_back(mf); } } } return ret; }
Field< FIELD3D_VEC3_T< Data_T > >::Vec Field3DInputFile::readVectorLayers | ( | const std::string & | partitionName, |
const std::string & | layerName | ||
) | const |
This version allows you to pass in the partition name.
Definition at line 872 of file Field3DFile.h.
References Field3DFileBase::getIntPartitionNames(), Field3DFileBase::getIntVectorLayerNames(), and Field3DFileBase::removeUniqueId().
{ using namespace std; typedef typename Field<FIELD3D_VEC3_T<Data_T> >::Ptr FieldPtr; typedef typename Field<FIELD3D_VEC3_T<Data_T> >::Vec FieldList; FieldList ret; if ((layerName.length() == 0) || (partitionName.length() == 0)) return ret; std::vector<std::string> parts; getIntPartitionNames(parts); for (vector<string>::iterator p = parts.begin(); p != parts.end(); ++p) { std::vector<std::string> layers; getIntVectorLayerNames(layers, *p); if (removeUniqueId(*p) == partitionName) { for (vector<string>::iterator l = layers.begin(); l != layers.end(); ++l) { // Only read if it matches the name if (*l == layerName) { FieldPtr mf = readVectorLayer<Data_T>(*p, *l); if (mf) ret.push_back(mf); } } } } return ret; }
Field_T< Data_T >::Vec Field3DInputFile::readScalarLayersAs | ( | const std::string & | layerName = std::string("") | ) | const |
Retrieves all layers for all partitions. Converts it to the given template type if needed.
Definition at line 990 of file Field3DFile.h.
References field_dynamic_cast().
{ typedef typename Field<Data_T>::Vec FieldList; typedef typename Field_T<Data_T>::Vec TypedFieldList; // First, read the layers as-is FieldList originals; originals = readScalarLayers<Data_T>(layerName); // Loop over fields, converting if needed TypedFieldList output; typename FieldList::iterator i = originals.begin(); for (; i != originals.end(); ++i) { typename Field_T<Data_T>::Ptr targetField; targetField = field_dynamic_cast<Field_T<Data_T> >(*i); if (targetField) { output.push_back(targetField); } else { typename Field_T<Data_T>::Ptr newTarget(new Field_T<Data_T>); newTarget->name = (*i)->name; newTarget->attribute = (*i)->attribute; newTarget->copyMetadata(*i); newTarget->copyFrom(*i); output.push_back(newTarget); } } return output; }
Field_T< Data_T >::Vec Field3DInputFile::readScalarLayersAs | ( | const std::string & | partitionName, |
const std::string & | layerName | ||
) | const |
Retrieves a layers given their and its parent partition's name. Converts it to the given template type if needed.
Definition at line 1024 of file Field3DFile.h.
References field_dynamic_cast().
{ typedef typename Field<Data_T>::Vec FieldList; typedef typename Field_T<Data_T>::Vec TypedFieldList; // First, read the layers as-is FieldList originals; originals = readScalarLayers<Data_T>(partitionName, layerName); // Loop over fields, converting if needed TypedFieldList output; typename FieldList::iterator i = originals.begin(); for (; i != originals.end(); ++i) { typename Field_T<Data_T>::Ptr targetField; targetField = field_dynamic_cast<Field_T<Data_T> >(*i); if (targetField) { output.push_back(targetField); } else { typename Field_T<Data_T>::Ptr newTarget(new Field_T<Data_T>); newTarget->name = (*i)->name; newTarget->attribute = (*i)->attribute; newTarget->copyMetadata(**i); newTarget->copyFrom(*i); output.push_back(newTarget); } } return output; }
Field_T< Data_T >::Vec Field3DInputFile::readVectorLayersAs | ( | const std::string & | layerName = std::string("") | ) | const |
Retrieves a layers for all partitions. Converts it to the given template type if needed.
Definition at line 1059 of file Field3DFile.h.
References field_dynamic_cast().
{ typedef typename Field<Data_T>::Vec FieldList; typedef typename Field_T<Data_T>::Vec TypedFieldList; // First, read the layers as-is FieldList originals; originals = readVectorLayers<Data_T>(layerName); // Loop over fields, converting if needed TypedFieldList output; typename FieldList::iterator i = originals.begin(); for (; i != originals.end(); ++i) { typename Field_T<Data_T>::Ptr targetField; targetField = field_dynamic_cast<Field_T<Data_T> >(*i); if (targetField) { output.push_back(targetField); } else { typename Field_T<Data_T>::Ptr newTarget(new Field_T<Data_T>); newTarget->name = (*i)->name; newTarget->attribute = (*i)->attribute; newTarget->copyMetadata(*i); newTarget->copyFrom(*i); output.push_back(newTarget); } } return output; }
Field_T< Data_T >::Vec Field3DInputFile::readVectorLayersAs | ( | const std::string & | partitionName, |
const std::string & | layerName | ||
) | const |
Retrieves a layers given their and its parent partition's name. Converts it to the given template type if needed.
Definition at line 1093 of file Field3DFile.h.
References field_dynamic_cast().
{ typedef typename Field<Data_T>::Vec FieldList; typedef typename Field_T<Data_T>::Vec TypedFieldList; // First, read the layers as-is FieldList originals; originals = readVectorLayers<Data_T>(partitionName, layerName); // Loop over fields, converting if needed TypedFieldList output; typename FieldList::iterator i = originals.begin(); for (; i != originals.end(); ++i) { typename Field_T<Data_T>::Ptr targetField; targetField = field_dynamic_cast<Field_T<Data_T> >(*i); if (targetField) { output.push_back(targetField); } else { typename Field_T<Data_T>::Ptr newTarget(new Field_T<Data_T>); newTarget->name = (*i)->name; newTarget->attribute = (*i)->attribute; newTarget->copyMetadata(*i); newTarget->copyFrom(*i); output.push_back(newTarget); } } return output; }
EmptyField< Data_T >::Vec Field3DInputFile::readProxyLayer | ( | const std::string & | partitionName, |
const std::string & | layerName, | ||
bool | isVectorLayer | ||
) | const |
Retrieves a proxy version (EmptyField) of each layer .
name | If a string is passed in, only layers of that name will be read from disk. |
Definition at line 1128 of file Field3DFile.h.
References FieldBase::attribute, Field3DFileBase::getIntPartitionNames(), Field3DFileBase::getIntScalarLayerNames(), Field3DFileBase::getIntVectorLayerNames(), Field3DFileBase::m_file, FieldBase::name, File::Layer::name, File::Layer::parent, Field3DFileBase::partition(), Msg::print(), Hdf5Util::readAttribute(), readMetadata(), Field3DFileBase::removeUniqueId(), FieldRes::setMapping(), ResizableField< Data_T >::setSize(), and Msg::SevWarning.
{ using namespace boost; using namespace std; using namespace Hdf5Util; // Instantiate a null pointer for easier code reading typename EmptyField<Data_T>::Vec emptyList, output; if ((layerName.length() == 0) || (partitionName.length() == 0)) return emptyList; std::vector<std::string> parts, layers; getIntPartitionNames(parts); bool foundPartition = false; for (vector<string>::iterator p = parts.begin(); p != parts.end(); ++p) { if (removeUniqueId(*p) == partitionName) { foundPartition = true; if (isVectorLayer) { getIntVectorLayerNames(layers, *p); } else { getIntScalarLayerNames(layers, *p); } for (vector<string>::iterator l = layers.begin(); l != layers.end(); ++l) { if (*l == layerName) { // Find the partition File::Partition::Ptr part = partition(*p); if (!part) { Msg::print(Msg::SevWarning, "Couldn't find partition: " + *p); return emptyList; } // Find the layer const File::Layer *layer; if (isVectorLayer) layer = part->vectorLayer(layerName); else layer = part->scalarLayer(layerName); if (!layer) { Msg::print(Msg::SevWarning, "Couldn't find layer: " + layerName); return emptyList; } // Open the layer group string layerPath = layer->parent + "/" + layer->name; H5ScopedGopen layerGroup(m_file, layerPath.c_str()); if (layerGroup.id() < 0) { Msg::print(Msg::SevWarning, "Couldn't find layer group " + layerName + " in .f3d file "); return emptyList; } // Read the extents and data window Box3i extents, dataW; if (!readAttribute(layerGroup, "extents", 6, extents.min.x)) { return emptyList; } if (!readAttribute(layerGroup, "data_window", 6, dataW.min.x)) { return emptyList; } // Construct the field and load the data typename EmptyField<Data_T>::Ptr field(new EmptyField<Data_T>); field->setSize(extents, dataW); // read the metadata string metadataPath = layerPath + "/metadata"; H5ScopedGopen metadataGroup(m_file, metadataPath.c_str()); if (metadataGroup.id() > 0) { readMetadata(metadataGroup.id(), field); } // ... Set the name of the field so it's possible to // ... re-create the file field->name = partitionName; field->attribute = layerName; field->setMapping(part->mapping); // Add field to output output.push_back(field); } } } } if (!foundPartition) { Msg::print(Msg::SevWarning, "Couldn't find partition: " + partitionName); return emptyList; } return output; }
EmptyField< Data_T >::Vec Field3DInputFile::readProxyScalarLayers | ( | const std::string & | name = std::string("") | ) | const |
Retrieves a proxy version (EmptyField) of each scalar layer.
name | If a string is passed in, only layers of that name will be read from disk. |
Definition at line 1225 of file Field3DFile.h.
References Field3DFileBase::getPartitionNames(), and Field3DFileBase::getScalarLayerNames().
{ using namespace std; typedef typename EmptyField<Data_T>::Ptr FieldPtr; typedef std::vector<FieldPtr> FieldList; FieldList ret; std::vector<std::string> parts; getPartitionNames(parts); for (vector<string>::iterator p = parts.begin(); p != parts.end(); ++p) { std::vector<std::string> layers; getScalarLayerNames(layers, *p); for (vector<string>::iterator l = layers.begin(); l != layers.end(); ++l) { // Only read if it matches the name if ((name.length() == 0) || (*l == name)) { FieldList f = readProxyLayer<Data_T>(*p, *l, false); for (typename FieldList::iterator i = f.begin(); i != f.end(); ++i) { if (*i) { ret.push_back(*i); } } } } } return ret; }
EmptyField< Data_T >::Vec Field3DInputFile::readProxyVectorLayers | ( | const std::string & | name = std::string("") | ) | const |
Retrieves a proxy version (EmptyField) of each vector layer.
name | If a string is passed in, only layers of that name will be read from disk. |
Definition at line 1260 of file Field3DFile.h.
References Field3DFileBase::getPartitionNames(), and Field3DFileBase::getVectorLayerNames().
{ using namespace std; typedef typename EmptyField<Data_T>::Ptr FieldPtr; typedef std::vector<FieldPtr> FieldList; FieldList ret; std::vector<std::string> parts; getPartitionNames(parts); for (vector<string>::iterator p = parts.begin(); p != parts.end(); ++p) { std::vector<std::string> layers; getVectorLayerNames(layers, *p); for (vector<string>::iterator l = layers.begin(); l != layers.end(); ++l) { // Only read if it matches the name if ((name.length() == 0) || (*l == name)) { FieldList f = readProxyLayer<Data_T>(*p, *l, true); for (typename FieldList::iterator i = f.begin(); i != f.end(); ++i) { if (*i) { ret.push_back(*i); } } } } } return ret; }
bool Field3DInputFile::open | ( | const std::string & | filename | ) |
Opens the given file.
herr_t Field3DInputFile::parsePartition | ( | hid_t | loc_id, |
const std::string | partitionName | ||
) |
Gets called from parsePartitions. Not intended for any other use.
Definition at line 784 of file Field3DFile.cpp.
References Field3DFileBase::m_partitionNames.
Referenced by InputFile::parsePartitions().
{ // Add the partition --- m_partitionNames.push_back(string(itemName)); return 0; }
herr_t Field3DInputFile::parseLayer | ( | hid_t | layerGroup, |
const std::string & | partitionName, | ||
const std::string & | layerName | ||
) |
Gets called from parsePartitions. Not intended for any other use.
Definition at line 798 of file Field3DFile.cpp.
References Field3DFileBase::m_layerInfo, Msg::print(), Hdf5Util::readAttribute(), and Msg::SevWarning.
Referenced by InputFile::parseLayers().
{ int components; if (!readAttribute(layerGroup, string("components"), 1, components)) { Msg::print(Msg::SevWarning, "Couldn't read components attribute for layer " + partitionName + "/" + layerName); return 0; } LayerInfo linfo(partitionName,layerName,components); m_layerInfo.push_back(linfo); return 0; }
bool Field3DInputFile::readGroupMembership | ( | GroupMembershipMap & | gpMembershipMap | ) |
Read the group membership for the partitions.
Definition at line 1039 of file Field3DFile.cpp.
References Hdf5Util::H5Base::id(), Field3DFileBase::m_file, Field3DFileBase::m_groupMembership, Msg::print(), Hdf5Util::readAttribute(), Field3DFileBase::removeUniqueId(), and Msg::SevWarning.
{ if (!H5Lexists(m_file, "field3d_group_membership", H5P_DEFAULT)) { return false; } H5ScopedGopen memberGroup(m_file, "field3d_group_membership"); if (memberGroup < 0) { return false; } typedef boost::tokenizer<boost::char_separator<char> > Tok; hsize_t num_attrs = H5Aget_num_attrs(memberGroup); if (num_attrs > 0) { for (hsize_t idx=0; idx < num_attrs ; ++idx) { H5ScopedAopenIdx attrIdx(memberGroup, idx); size_t len = H5Aget_name(attrIdx.id(), 0, NULL); if (len>0) { char *name = new char[len+1]; if (H5Aget_name(attrIdx.id(), len+1, name) > 0) { if (string(name) == "is_field3d_group_membership") continue; H5ScopedAopen attr(memberGroup, name, H5P_DEFAULT); H5ScopedAget_space attrSpace(attr); H5ScopedAget_type attrType(attr); H5T_class_t typeClass = H5Tget_class(attrType); if (typeClass == H5T_STRING) { string value; if (!readAttribute(memberGroup, name, value)) { Msg::print(Msg::SevWarning, "Failed to read group membership data " + string(name)); continue; } { boost::char_separator<char> sep(" :"); Tok tok(value, sep); string new_value; for(Tok::iterator beg=tok.begin(); beg!=tok.end();){ string fieldgroup = *beg; ++beg; fieldgroup = removeUniqueId(fieldgroup) + ":" + *beg; ++beg; new_value += fieldgroup + " "; } m_groupMembership[name] = value; gpMembershipMap[name] = new_value; } } } } } } return true; }
Field< Data_T >::Ptr Field3DInputFile::readScalarLayer | ( | const std::string & | intPartitionName, |
const std::string & | layerName | ||
) | const [private] |
Retrieves a single layer given its and its parent partition's name. Maintains the on-disk data types.
Definition at line 1295 of file Field3DFile.h.
References Field3DFileBase::intPartitionName().
{ return readLayer<Data_T>(intPartitionName, layerName, false); }
Field< FIELD3D_VEC3_T< Data_T > >::Ptr Field3DInputFile::readVectorLayer | ( | const std::string & | intPartitionName, |
const std::string & | layerName | ||
) | const [private] |
Retrieves a single layer given its and its parent partition's name. Maintains the on-disk data types.
Definition at line 1305 of file Field3DFile.h.
References Field3DFileBase::intPartitionName().
{ return readLayer<FIELD3D_VEC3_T<Data_T> >(intPartitionName, layerName, true); }
Field< Data_T >::Ptr Field3DInputFile::readLayer | ( | const std::string & | intPartitionName, |
const std::string & | layerName, | ||
bool | isVectorLayer | ||
) | const [private] |
This call does the actual reading of a layer. Notice that it expects a unique -internal- partition name.
Definition at line 911 of file Field3DFile.h.
References Field3DFileBase::m_file, m_filename, Field3DFileBase::partition(), Msg::print(), Hdf5Util::readAttribute(), readMetadata(), Field3DFileBase::removeUniqueId(), and Msg::SevWarning.
{ using namespace boost; using namespace std; using namespace Hdf5Util; // Instantiate a null pointer for easier code reading typename Field<Data_T>::Ptr nullPtr; // Find the partition File::Partition::Ptr part = partition(intPartitionName); if (!part) { Msg::print(Msg::SevWarning, "Couldn't find partition: " + intPartitionName); return nullPtr; } // Find the layer in the partition const File::Layer *l; if (isVectorLayer) l = part->vectorLayer(layerName); else l = part->scalarLayer(layerName); if (!l) { Msg::print(Msg::SevWarning, "Couldn't find layer: " + layerName ); return nullPtr; } // Open the layer group string layerPath = l->parent + "/" + l->name; H5ScopedGopen layerGroup(m_file, layerPath.c_str()); if (layerGroup.id() < 0) { Msg::print(Msg::SevWarning, "Couldn't find layer group " + layerName + " in .f3d file "); return nullPtr; } // Get the class name string className; if (!readAttribute(layerGroup.id(), "class_name", className)) { Msg::print(Msg::SevWarning, "Couldn't find class_name attrib in layer " + layerName); return nullPtr; } // Construct the field and load the data typename Field<Data_T>::Ptr field; field = readField<Data_T>(className, layerGroup.id(), m_filename, layerPath); if (!field) { #if 0 // This isn't really an error Msg::print(Msg::SevWarning, "Couldn't read the layer data of layer: " + layerName); #endif return nullPtr; } // read the metadata string metadataPath = layerPath + "/metadata"; H5ScopedGopen metadataGroup(m_file, metadataPath.c_str()); if (metadataGroup.id() > 0) { readMetadata(metadataGroup.id(), field); } // Set the name of the field so it's possible to re-create the file field->name = removeUniqueId(intPartitionName); field->attribute = layerName; field->setMapping(part->mapping); return field; }
bool Field3DInputFile::readPartitionAndLayerInfo | ( | ) | [private] |
Sets up all the partitions and layers, but does not load any data.
Definition at line 692 of file Field3DFile.cpp.
References InputFile::ParseLayersInfo::file, Hdf5Util::H5Base::id(), Field3DFileBase::m_file, Field3DFileBase::m_layerInfo, Field3DFileBase::m_partitionNames, Field3DFileBase::m_partitions, File::Layer::name, File::Layer::parent, InputFile::parseLayers(), InputFile::parsePartitions(), Field3DFileBase::partition(), InputFile::ParseLayersInfo::partitionName, Msg::print(), readFieldMapping(), and Msg::SevWarning.
{ using namespace InputFile; // First, find the partitions --- herr_t status; status = H5Literate(m_file, H5_INDEX_NAME, H5_ITER_NATIVE, NULL, &parsePartitions, this); // Get the partition names to store m_partitions.clear(); for (size_t i=0; i < m_partitionNames.size(); i++) { Partition::Ptr part(new Partition); part->name = m_partitionNames[i]; m_partitions.push_back(part); } // For each partition, find its mapping --- for (PartitionList::iterator i = m_partitions.begin(); i != m_partitions.end(); ++i) { // Open the partition H5ScopedGopen partitionGroup(m_file, (**i).name); string mappingPath = "/" + (**i).name + "/" + k_mappingStr; // Open up the mapping group H5ScopedGopen mappingGroup(m_file, mappingPath); if (mappingGroup.id() < 0) throw MissingGroupException((**i).name + "/" + k_mappingStr); // Try to build a mapping from it FieldMapping::Ptr mapping; mapping = readFieldMapping(mappingGroup.id()); if (!mapping) { Msg::print(Msg::SevWarning, "Got a null pointer when reading mapping"); throw ReadMappingException((**i).name); } // Attach the mapping to the partition (**i).mapping = mapping; } // ... And then find its layers --- for (PartitionList::const_iterator i = m_partitions.begin(); i != m_partitions.end(); ++i) { // Open the partition H5ScopedGopen partitionGroup(m_file, (**i).name); // Set up the info struct for the callback ParseLayersInfo info; info.file = this; info.partitionName = (**i).name; m_layerInfo.clear(); status = H5Literate(partitionGroup.id(), H5_INDEX_NAME, H5_ITER_NATIVE, NULL, &parseLayers, &info); //set the layer information on the partitions here for (std::vector<LayerInfo>::iterator i = m_layerInfo.begin(); i != m_layerInfo.end(); i++) { std::string parent = i->parentName; Partition::Ptr part = partition(parent); Layer layer; layer.name = i->name; layer.parent = i->parentName; if (i->components == 1) { part->addScalarLayer(layer); } else if (i->components == 3) { part->addVectorLayer(layer); } } } return true; }
bool Field3DInputFile::readMetadata | ( | hid_t | metadata_id, |
FieldBase::Ptr | field | ||
) | const [private] |
Read metadata for this layer.
Definition at line 821 of file Field3DFile.cpp.
References Hdf5Util::H5Base::id(), Msg::print(), Hdf5Util::readAttribute(), and Msg::SevWarning.
Referenced by readLayer(), and readProxyLayer().
{ hsize_t num_attrs = H5Aget_num_attrs(metadata_id); if (num_attrs > 0) { for (hsize_t idx=0; idx < num_attrs ; ++idx) { H5ScopedAopenIdx attrIdx(metadata_id, idx); size_t len = H5Aget_name(attrIdx.id(), 0, NULL); if (len > 0) { char *name = new char[len+1]; if (H5Aget_name(attrIdx.id(), len+1, name) > 0) { H5ScopedAopen attr(metadata_id, name, H5P_DEFAULT); H5ScopedAget_space attrSpace(attr); H5ScopedAget_type attrType(attr); H5T_class_t typeClass = H5Tget_class(attrType); if (typeClass == H5T_STRING) { string value; if (!readAttribute(metadata_id, name, value)) { Msg::print(Msg::SevWarning, "Failed to read metadata " + string(name)); if (name) { delete[] name; } continue; } field->metadata().setStrMetadata(name, value); } else { if (H5Sget_simple_extent_ndims(attrSpace) != 1) { Msg::print(Msg::SevWarning, "Bad attribute rank for attribute " + string(name)); if (name) { delete[] name; } continue; } hsize_t dims[1]; H5Sget_simple_extent_dims(attrSpace, dims, NULL); if (typeClass == H5T_INTEGER) { if (dims[0] == 1){ int value; if (!readAttribute(metadata_id, name, dims[0], value)) Msg::print(Msg::SevWarning, "Failed to read metadata " + string(name)); field->metadata().setIntMetadata(name, value); } else if (dims[0] == 3){ V3i value; if (!readAttribute(metadata_id, name, dims[0], value.x)) Msg::print(Msg::SevWarning, "Failed to read metadata " + string(name) ); field->metadata().setVecIntMetadata(name, value); } else { Msg::print(Msg::SevWarning, "Attribute of size " + boost::lexical_cast<std::string>(dims[0]) + " is not valid for metadata"); } } else if (typeClass == H5T_FLOAT) { if (dims[0] == 1){ float value; if (!readAttribute(metadata_id, name, dims[0], value)) Msg::print(Msg::SevWarning, "Failed to read metadata " + string(name) ); field->metadata().setFloatMetadata(name, value); } else if (dims[0] == 3){ V3f value; if (!readAttribute(metadata_id, name, dims[0], value.x)) Msg::print(Msg::SevWarning, "Failed to read metadata "+ string(name) ); field->metadata().setVecFloatMetadata(name, value); } else { Msg::print(Msg::SevWarning, "Attribute of size " + boost::lexical_cast<std::string>(dims[0]) + " is not valid for metadata"); } } else { Msg::print(Msg::SevWarning, "Attribute '" + string(name) + + "' has unsupported data type for metadata"); } } } if (name) { delete[] name; } } } } return true; }
bool Field3DInputFile::readMetadata | ( | hid_t | metadata_id | ) | [private] |
Read global metadata for this file.
Definition at line 930 of file Field3DFile.cpp.
References Hdf5Util::H5Base::id(), Field3DFileBase::metadata(), Msg::print(), Hdf5Util::readAttribute(), FieldMetadata< CallBack_T >::setFloatMetadata(), FieldMetadata< CallBack_T >::setIntMetadata(), FieldMetadata< CallBack_T >::setStrMetadata(), FieldMetadata< CallBack_T >::setVecFloatMetadata(), FieldMetadata< CallBack_T >::setVecIntMetadata(), and Msg::SevWarning.
{ hsize_t num_attrs = H5Aget_num_attrs(metadata_id); if (num_attrs > 0) { for (hsize_t idx=0; idx < num_attrs ; ++idx) { H5ScopedAopenIdx attrIdx(metadata_id, idx); size_t len = H5Aget_name(attrIdx.id(), 0, NULL); if (len > 0) { char *name = new char[len+1]; if (H5Aget_name(attrIdx.id(), len+1, name) > 0) { H5ScopedAopen attr(metadata_id, name, H5P_DEFAULT); H5ScopedAget_space attrSpace(attr); H5ScopedAget_type attrType(attr); H5T_class_t typeClass = H5Tget_class(attrType); if (typeClass == H5T_STRING) { string value; if (!readAttribute(metadata_id, name, value)) { Msg::print(Msg::SevWarning, "Failed to read metadata " + string(name)); if (name) { delete[] name; } continue; } metadata().setStrMetadata(name, value); } else { if (H5Sget_simple_extent_ndims(attrSpace) != 1) { Msg::print(Msg::SevWarning, "Bad attribute rank for attribute " + string(name)); if (name) { delete[] name; } continue; } hsize_t dims[1]; H5Sget_simple_extent_dims(attrSpace, dims, NULL); if (typeClass == H5T_INTEGER) { if (dims[0] == 1){ int value; if (!readAttribute(metadata_id, name, dims[0], value)) Msg::print(Msg::SevWarning, "Failed to read metadata " + string(name)); metadata().setIntMetadata(name, value); } else if (dims[0] == 3){ V3i value; if (!readAttribute(metadata_id, name, dims[0], value.x)) Msg::print(Msg::SevWarning, "Failed to read metadata " + string(name) ); metadata().setVecIntMetadata(name, value); } else { Msg::print(Msg::SevWarning, "Attribute of size " + boost::lexical_cast<std::string>(dims[0]) + " is not valid for metadata"); } } else if (typeClass == H5T_FLOAT) { if (dims[0] == 1){ float value; if (!readAttribute(metadata_id, name, dims[0], value)) Msg::print(Msg::SevWarning, "Failed to read metadata " + string(name) ); metadata().setFloatMetadata(name, value); } else if (dims[0] == 3){ V3f value; if (!readAttribute(metadata_id, name, dims[0], value.x)) Msg::print(Msg::SevWarning, "Failed to read metadata "+ string(name) ); metadata().setVecFloatMetadata(name, value); } else { Msg::print(Msg::SevWarning, "Attribute of size " + boost::lexical_cast<std::string>(dims[0]) + " is not valid for metadata"); } } else { Msg::print(Msg::SevWarning, "Attribute '" + string(name) + + "' has unsupported data type for metadata"); } } } if (name) { delete[] name; } } } } return true; }
std::string Field3DInputFile::m_filename [private] |
Filename, only to be set by open().
Definition at line 603 of file Field3DFile.h.
Referenced by readLayer().