Newer
Older
// Mantid Repository : https://github.com/mantidproject/mantid
//
// Copyright © 2007 ISIS Rutherford Appleton Laboratory UKRI,
// NScD Oak Ridge National Laboratory, European Spallation Source,
// Institut Laue - Langevin & CSNS, Institute of High Energy Physics, CAS
// SPDX - License - Identifier: GPL - 3.0 +
#include "MantidKernel/NexusHDF5Descriptor.h"
#include <hdf5.h>
#include <cstdlib> // malloc, calloc
#include <cstring> // strcpy
#include <stdexcept> // std::invalid_argument
/// hdf5 specific functions, stay in anonymous namespace to make hdf5 linking
/// PRIVATE
namespace {
/**
* populate a string attribute from HDF5 attribute handler
* @param attr input HDF5 atttribute handler
* @param data
* @return
*/
herr_t readStringAttribute(hid_t attr, char **data) {
herr_t iRet = 0;
hsize_t thedims[H5S_MAX_RANK];
hid_t atype = H5Aget_type(attr);
hsize_t sdim = H5Tget_size(atype);
hid_t space = H5Aget_space(attr);
int ndims = H5Sget_simple_extent_dims(space, thedims, NULL);
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
if (ndims == 0) {
if (H5Tis_variable_str(atype)) {
hid_t btype = H5Tget_native_type(atype, H5T_DIR_ASCEND);
iRet = H5Aread(attr, btype, data);
H5Tclose(btype);
} else {
*data = (char *)malloc(sdim + 1);
iRet = H5Aread(attr, atype, *data);
(*data)[sdim] = '\0';
}
} else if (ndims == 1) {
unsigned int i;
char **strings;
strings = (char **)malloc(thedims[0] * sizeof(char *));
if (!H5Tis_variable_str(atype)) {
strings[0] = (char *)malloc(thedims[0] * sdim * sizeof(char));
for (i = 1; i < thedims[0]; i++) {
strings[i] = strings[0] + i * sdim;
}
}
iRet = H5Aread(attr, atype, strings[0]);
*data = (char *)calloc((sdim + 2) * thedims[0], sizeof(char));
for (i = 0; i < thedims[0]; i++) {
if (i == 0) {
strncpy(*data, strings[i], sdim);
} else {
strcat(*data, ", ");
strncat(*data, strings[i], sdim);
}
}
if (H5Tis_variable_str(atype)) {
H5Dvlen_reclaim(atype, space, H5P_DEFAULT, strings);
} else {
free(strings[0]);
}
free(strings);
} else {
*data = (char *)malloc(33);
strcpy(*data, " higher dimensional string array");
*data[32] = '\0';
}
H5Tclose(atype);
H5Sclose(space);
if (iRet < 0)
return -1;
return 0;
}
/**
* Reads a string attribute of N-dimensions
* @param attr input HDF5 attribute handler
* @param data output attribute data
* @param maxlen
* @return
*/
herr_t readStringAttributeN(hid_t attr, char *data, int maxlen) {
herr_t iRet;
char *vdat = NULL;
iRet = readStringAttribute(attr, &vdat);
if (iRet >= 0) {
strncpy(data, vdat, maxlen);
free(vdat);
}
data[maxlen - 1] = '\0';
return iRet;
}
void getGroup(hid_t groupID,
std::map<std::string, std::set<std::string>> &allEntries) {
/**
* Return the NX_class attribute associate with objectName group entry
*/
auto lf_getNxClassAttribute = [&](hid_t groupID,
const char *objectName) -> std::string {
std::string attribute = "";
hid_t attributeID = H5Aopen_by_name(groupID, objectName, "NX_class",
H5P_DEFAULT, H5P_DEFAULT);
if (attributeID < 0) {
H5Aclose(attributeID);
return attribute;
}
hid_t type = H5T_C_S1;
hid_t atype = H5Tcopy(type);
char data[128];
H5Tset_size(atype, sizeof(data));
readStringAttributeN(attributeID, data, sizeof(data));
// already null terminated in readStringAttributeN
attribute = std::string(data);
H5Tclose(atype);
H5Aclose(attributeID);
return attribute;
};
// using HDF5 C API
constexpr std::size_t maxLength = 1024;
char groupName[maxLength];
char memberName[maxLength];
std::size_t groupNameLength =
static_cast<std::size_t>(H5Iget_name(groupID, groupName, maxLength));
hsize_t nObjects = 0;
H5Gget_num_objs(groupID, &nObjects);
const std::string groupNameStr(groupName, groupNameLength);
const std::string nxClass =
(groupNameStr == "/")
? ""
: lf_getNxClassAttribute(groupID, groupNameStr.c_str());
if (!nxClass.empty()) {
allEntries[nxClass].insert(groupNameStr);
}
for (unsigned int i = 0; i < nObjects; ++i) {
const int type = H5Gget_objtype_by_idx(groupID, static_cast<size_t>(i));
const std::size_t memberNameLength =
static_cast<std::size_t>(H5Gget_objname_by_idx(
groupID, static_cast<hsize_t>(i), memberName, maxLength));
if (type == H5O_TYPE_GROUP) {
hid_t subGroupID = H5Gopen2(groupID, memberName, H5P_DEFAULT);
getGroup(subGroupID, allEntries);
H5Gclose(subGroupID);
} else if (type == H5O_TYPE_DATASET) {
const std::string memberNameStr(memberName, memberNameLength);
const std::string absoluteEntryName = groupNameStr + "/" + memberNameStr;
allEntries["SDS"].insert(absoluteEntryName);
}
}
}
} // namespace
bool NexusHDF5Descriptor::isReadable(const std::string &filename) {
// use existing function to do the work
return NexusDescriptor::isReadable(filename,
NexusDescriptor::Version::Version5);
NexusHDF5Descriptor::NexusHDF5Descriptor(const std::string &filename)
: m_filename(filename), m_allEntries(initAllEntries()) {}
// PUBLIC
std::string NexusHDF5Descriptor::getFilename() const noexcept {
return m_filename;
}
const std::map<std::string, std::set<std::string>> &
NexusHDF5Descriptor::getAllEntries() const noexcept {
return m_allEntries;
}
// PRIVATE
std::map<std::string, std::set<std::string>>
NexusHDF5Descriptor::initAllEntries() {
hid_t fileID = H5Fopen(m_filename.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
if (fileID < 0) {
throw std::invalid_argument(
"ERROR: Kernel::NexusHDF5Descriptor couldn't open hdf5 file " +
m_filename + "\n");
}
hid_t groupID = H5Gopen2(fileID, "/", H5P_DEFAULT);
std::map<std::string, std::set<std::string>> allEntries;
// scan file recursively starting with root group "/"
getGroup(groupID, allEntries);
H5Gclose(groupID);
H5Fclose(fileID);
// rely on move semantics
return allEntries;
}