Field3DInputFile Class Reference
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>
Inheritance diagram for Field3DInputFile:
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(). | |
Detailed Description
Provides reading of .f3d (internally, hdf5) files.
Refer to using_files for examples of how to use this in your code.
- Note:
- We distinguish between scalar and vector layers even though both are templated. A scalarField<float> layer is interchangeable with a scalarField<double> (conceptually) but not with a scalar<V3f>, and thus not with vectorField<float>.
Definition at line 431 of file Field3DFile.h.
Constructor & Destructor Documentation
| Field3DInputFile::Field3DInputFile | ( | ) |
Definition at line 561 of file Field3DFile.cpp.
{
// Empty
}
| Field3DInputFile::~Field3DInputFile | ( | ) | [virtual] |
Member Function Documentation
template<class Data_T >
| 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.
- Parameters:
-
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;
}
template<class Data_T >
| 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;
}
template<class Data_T >
| 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.
- Parameters:
-
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;
}
template<class Data_T >
| 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;
}
template<template< typename T > class Field_T, class Data_T >
| 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;
}
template<template< typename T > class Field_T, class Data_T >
| 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;
}
template<template< typename T > class Field_T, class Data_T >
| 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;
}
template<template< typename T > class Field_T, class Data_T >
| 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;
}
template<class Data_T >
| 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 .
- Note:
- Although the call is templated, all fields are read, regardless of bit depth.
- Parameters:
-
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;
}
template<class Data_T >
| EmptyField< Data_T >::Vec Field3DInputFile::readProxyScalarLayers | ( | const std::string & | name = std::string("") | ) | const |
Retrieves a proxy version (EmptyField) of each scalar layer.
- Note:
- Although the call is templated, all fields are read, regardless of bit depth.
- Parameters:
-
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;
}
template<class Data_T >
| EmptyField< Data_T >::Vec Field3DInputFile::readProxyVectorLayers | ( | const std::string & | name = std::string("") | ) | const |
Retrieves a proxy version (EmptyField) of each vector layer.
- Note:
- Although the call is templated, all fields are read, regardless of bit depth.
- Parameters:
-
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.
- Returns:
- Whether successful
| 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.
- Note:
- Don't throw exceptions into the hdf5 lib.
- Todo:
- Set some sort of flag if we fail during this call. We can't throw exceptions inside hdf5.
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;
}
template<class Data_T >
| 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);
}
template<class Data_T >
| 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);
}
template<class Data_T >
| 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.
- Todo:
- Replace char* with std::string
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.
- Todo:
- Replace char* with std::string
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;
}
Member Data Documentation
std::string Field3DInputFile::m_filename [private] |
Filename, only to be set by open().
Definition at line 603 of file Field3DFile.h.
Referenced by readLayer().
The documentation for this class was generated from the following files:
- export/Field3DFile.h
- src/Field3DFile.cpp
