From bb9b74ab91a651455573bee0e8ed1c1d00266e79 Mon Sep 17 00:00:00 2001
From: William F Godoy <williamfgc@yahoo.com>
Date: Mon, 23 Mar 2020 16:23:54 -0400
Subject: [PATCH] Added Mantid::NeXus::HDF5Descriptor class
Populates Metadata entries in constructor
Internal reference accessible in public function
Added unit test
Address CI issue with POSIX strdup function
---
Framework/Nexus/CMakeLists.txt | 13 +-
.../inc/MantidNexus/NexusHDF5Descriptor.h | 75 ++++++
Framework/Nexus/src/NexusHDF5Descriptor.cpp | 220 ++++++++++++++++++
.../Nexus/test/NexusHDF5DescriptorTest.h | 58 +++++
4 files changed, 362 insertions(+), 4 deletions(-)
create mode 100644 Framework/Nexus/inc/MantidNexus/NexusHDF5Descriptor.h
create mode 100644 Framework/Nexus/src/NexusHDF5Descriptor.cpp
create mode 100644 Framework/Nexus/test/NexusHDF5DescriptorTest.h
diff --git a/Framework/Nexus/CMakeLists.txt b/Framework/Nexus/CMakeLists.txt
index 0a00f9f80e7..e481148ce38 100644
--- a/Framework/Nexus/CMakeLists.txt
+++ b/Framework/Nexus/CMakeLists.txt
@@ -1,12 +1,13 @@
-set(SRC_FILES src/MuonNexusReader.cpp src/NexusClasses.cpp src/NexusFileIO.cpp)
+set(SRC_FILES src/MuonNexusReader.cpp src/NexusClasses.cpp src/NexusFileIO.cpp src/NexusHDF5Descriptor.cpp)
set(INC_FILES
inc/MantidNexus/MuonNexusReader.h
inc/MantidNexus/NexusClasses.h
inc/MantidNexus/NexusFileIO.h
- inc/MantidNexus/NexusIOHelper.h)
+ inc/MantidNexus/NexusIOHelper.h
+ inc/MantidNexus/NexusHDF5Descriptor.h)
-set(TEST_FILES NexusIOHelperTest.h)
+set(TEST_FILES NexusIOHelperTest.h NexusHDF5DescriptorTest.h)
if(COVERALLS)
foreach(loop_var ${SRC_FILES} ${INC_FILES})
@@ -38,12 +39,16 @@ set_property(TARGET Nexus PROPERTY FOLDER "MantidFramework")
include_directories(inc)
+target_include_directories(Nexus
+ PRIVATE ${HDF5_INCLUDE_DIRS})
+
target_link_libraries(Nexus
LINK_PRIVATE
${TCMALLOC_LIBRARIES_LINKTIME}
${MANTIDLIBS}
${NEXUS_C_LIBRARIES}
- ${NEXUS_LIBRARIES})
+ ${NEXUS_LIBRARIES}
+ ${HDF5_LIBRARIES})
# Add the unit tests directory
add_subdirectory(test)
diff --git a/Framework/Nexus/inc/MantidNexus/NexusHDF5Descriptor.h b/Framework/Nexus/inc/MantidNexus/NexusHDF5Descriptor.h
new file mode 100644
index 00000000000..d41db1717c8
--- /dev/null
+++ b/Framework/Nexus/inc/MantidNexus/NexusHDF5Descriptor.h
@@ -0,0 +1,75 @@
+// 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 +
+#pragma once
+
+#include "MantidKernel/System.h"
+
+#include <map>
+#include <set>
+#include <string>
+
+namespace Mantid {
+namespace NeXus {
+
+class DLLExport NexusHDF5Descriptor {
+
+public:
+ /**
+ * Unique constructor
+ * @param filename input HDF5 Nexus file name
+ */
+ NexusHDF5Descriptor(const std::string &filename);
+
+ NexusHDF5Descriptor() = delete;
+
+ /**
+ * Using RAII components, no need to deallocate explicitly
+ */
+ ~NexusHDF5Descriptor() = default;
+
+ /**
+ * Returns a copy of the current file name
+ * @return
+ */
+ std::string getFilename() const noexcept;
+
+ /**
+ * Returns a const reference of the internal map holding all entries in the
+ * NeXus HDF5 file
+ * @return map holding all entries by group class
+ * <pre>
+ * key: group_class (e.g. NXentry, NXlog)
+ * value: set with absolute entry names for the group_class key
+ * (e.g. /entry/log)
+ * </pre>
+ */
+ const std::map<std::string, std::set<std::string>> &getAllEntries() const
+ noexcept;
+
+private:
+ /**
+ * Sets m_allEntries, called in HDF5 constructor.
+ * m_filename must be set
+ */
+ std::map<std::string, std::set<std::string>> initAllEntries();
+
+ /** NeXus HDF5 file name */
+ std::string m_filename;
+
+ /**
+ * All entries metadata
+ * <pre>
+ * key: group_class (e.g. NXentry, NXlog)
+ * value: set with absolute entry names for the group_class key
+ * (e.g. /entry/log)
+ * </pre>
+ */
+ std::map<std::string, std::set<std::string>> m_allEntries;
+};
+
+} // namespace NeXus
+} // namespace Mantid
diff --git a/Framework/Nexus/src/NexusHDF5Descriptor.cpp b/Framework/Nexus/src/NexusHDF5Descriptor.cpp
new file mode 100644
index 00000000000..39e0bbe6b12
--- /dev/null
+++ b/Framework/Nexus/src/NexusHDF5Descriptor.cpp
@@ -0,0 +1,220 @@
+// 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 "MantidNexus/NexusHDF5Descriptor.h"
+
+#include <hdf5.h>
+
+#include <cstdlib> // malloc, calloc
+#include <cstring> // strcpy
+#include <stdexcept> // std::invalid_argument
+
+namespace Mantid {
+namespace NeXus {
+
+/// 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;
+ hid_t atype = -1;
+ hid_t space;
+ int ndims;
+ hsize_t thedims[H5S_MAX_RANK], sdim;
+
+ atype = H5Aget_type(attr);
+ sdim = H5Tget_size(atype);
+ space = H5Aget_space(attr);
+ ndims = H5Sget_simple_extent_dims(space, thedims, NULL);
+
+ 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
+
+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: NeXus::HDF5Descriptor 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;
+}
+
+} // namespace NeXus
+} // namespace Mantid
diff --git a/Framework/Nexus/test/NexusHDF5DescriptorTest.h b/Framework/Nexus/test/NexusHDF5DescriptorTest.h
new file mode 100644
index 00000000000..0ebf44e369a
--- /dev/null
+++ b/Framework/Nexus/test/NexusHDF5DescriptorTest.h
@@ -0,0 +1,58 @@
+// Mantid Repository : https://github.com/mantidproject/mantid
+//
+// Copyright © 2018 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 +
+#pragma once
+
+#include "MantidAPI/FileFinder.h"
+#include "MantidNexus/NexusHDF5Descriptor.h"
+
+#include <cstddef> // std::size_t
+
+#include <cxxtest/TestSuite.h>
+
+class NexusHDF5DescriptorTest : public CxxTest::TestSuite {
+
+public:
+ // test get functions getFilename and getAllEntries
+ void test_nexus_hdf5_descriptor_get() {
+ const std::string filename =
+ Mantid::API::FileFinder::Instance().getFullPath("EQSANS_89157.nxs.h5");
+
+ Mantid::NeXus::NexusHDF5Descriptor nexusHDF5Descriptor(filename);
+
+ TS_ASSERT_EQUALS(filename, nexusHDF5Descriptor.getFilename());
+
+ const std::map<std::string, std::set<std::string>> &allEntries =
+ nexusHDF5Descriptor.getAllEntries();
+
+ TS_ASSERT_EQUALS(allEntries.size(), 12);
+
+ // confirms existence of groupClass key and expectedSize for value set
+ auto lf_TestSet = [&](const std::string &groupClass,
+ const std::size_t expectedSize) -> std::size_t {
+ auto itClass = allEntries.find(groupClass);
+ TS_ASSERT_DIFFERS(itClass, allEntries.end());
+ TS_ASSERT_EQUALS(itClass->second.size(), expectedSize);
+ return expectedSize;
+ };
+
+ std::size_t nEntries = 0;
+ nEntries += lf_TestSet("NXcollection", 39);
+ nEntries += lf_TestSet("NXdetector", 48);
+ nEntries += lf_TestSet("NXdisk_chopper", 4);
+ nEntries += lf_TestSet("NXentry", 1);
+ nEntries += lf_TestSet("NXevent_data", 48);
+ nEntries += lf_TestSet("NXinstrument", 1);
+ nEntries += lf_TestSet("NXlog", 204);
+ nEntries += lf_TestSet("NXmonitor", 3);
+ nEntries += lf_TestSet("NXnote", 1);
+ nEntries += lf_TestSet("NXsample", 1);
+ nEntries += lf_TestSet("NXuser", 6);
+ nEntries += lf_TestSet("SDS", 2567);
+
+ TS_ASSERT_EQUALS(nEntries, 2923);
+ }
+};
--
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