v1.0.0-rc.31

writer/HDF5Objects.cpp

@@ -177,6 +177,23 @@ size_t HDF5DataType::GetElemSize() const {
     return H5Tget_size(id);
 }
 
+bool HDF5DataType::IsSigned() const {
+    if (IsFloat())
+        return true;
+    else if (IsInteger())
+        return H5Tget_sign(id) == H5T_SGN_2;
+    else
+        return false;
+}
+
+bool HDF5DataType::IsInteger() const {
+    return H5Tget_class(id) == H5T_INTEGER;
+}
+
+bool HDF5DataType::IsFloat() const {
+    return H5Tget_class(id) == H5T_FLOAT;
+}
+
 HDF5Dcpl::HDF5Dcpl() : HDF5Id() {
     id = H5Pcreate(H5P_DATASET_CREATE);
 }
@@ -205,6 +222,14 @@ void HDF5Dcpl::SetFillValue16(int16_t val) {
     H5Pset_fill_value(id, H5T_NATIVE_INT16, &val);
 }
 
+void HDF5Dcpl::SetFillValueU32(uint32_t val) {
+    H5Pset_fill_value(id, H5T_NATIVE_UINT32, &val);
+}
+
+void HDF5Dcpl::SetFillValueU16(uint16_t val) {
+    H5Pset_fill_value(id, H5T_NATIVE_UINT16, &val);
+}
+
 void HDF5Dcpl::SetVirtual(const std::string &path, const std::string &dataset, const HDF5DataSpace &src_dataspace, const HDF5DataSpace &dest_dataspace) {
     std::string filename = ExtractFilename(path);
     if (H5Pset_virtual(id, dest_dataspace.GetID(), filename.c_str(), dataset.c_str(), src_dataspace.GetID()) < 0)
@@ -357,6 +382,12 @@ HDF5Object & HDF5Object::HardLink(const std::string &source, const std::string &
     return *this;
 }
 
+std::vector<hsize_t> HDF5Object::GetDimension(const std::string &name) {
+    HDF5DataSet dataset(*this, name);
+    HDF5DataSpace dscp(dataset);
+    return dscp.GetDimensions();
+}
+
 std::unique_ptr<HDF5DataSet> HDF5Object::SaveScalar(const std::string &name, const std::string &val) {
     return SaveScalar(name, val.c_str());
 }
@@ -398,8 +429,12 @@ HDF5Group::~HDF5Group() {
     H5Gclose(id);
 }
 
-HDF5File::HDF5File(const std::string& filename) : HDF5Object() {
-    id = H5Fcreate(filename.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+HDF5File::HDF5File(const std::string& filename, bool v1_10) : HDF5Object() {
+    HDF5Fapl fapl;
+
+    if (v1_10)
+        fapl.SetVersionTo1p10orNewer();
+    id = H5Fcreate(filename.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, fapl.GetID());
     if (id < 0)
         throw JFJochException(JFJochExceptionCategory::HDF5, "Cannot open/create data HDF5 file " + filename);
 }
@@ -447,10 +482,10 @@ HDF5DataSet::HDF5DataSet(const HDF5Object &parent, const std::string &name, cons
 HDF5DataSet::HDF5DataSet(const HDF5Object &parent, const std::string &name) : ndim(0) {
     id = H5Dopen2(parent.GetID(), name.c_str(), H5P_DEFAULT);
 
-    ndim = HDF5DataSpace(*this).GetNumOfDimensions();
-
     if (id < 0)
-        throw JFJochException(JFJochExceptionCategory::HDF5, "Cannot open HDF5 dataset");
+        throw JFJochException(JFJochExceptionCategory::HDF5, "Cannot open HDF5 dataset " + name);
+
+    ndim = HDF5DataSpace(*this).GetNumOfDimensions();
 }
 
 void HDF5DataSet::SetExtent(const std::vector<hsize_t> &dims) {
@@ -496,7 +531,7 @@ std::string HDF5DataSet::ReadString() const {
     if (H5Dread(id, file_data_type.GetID(), H5S_ALL, H5S_ALL, H5P_DEFAULT, tmp) < 0)
         throw JFJochException(JFJochExceptionCategory::HDF5, "Dataset read unsuccessful");
 
-    return std::string(tmp);
+    return {tmp};
 }
 
 HDF5DataSet::~HDF5DataSet() {
@@ -556,4 +591,56 @@ std::string ExtractFilename(const std::string& str) {
     std::filesystem::path path(str);
     // if (std::filesystem::is_regular_file(path))
     return path.filename();
+}
+
+float HDF5Object::GetFloat(const std::string &name) const {
+    HDF5DataSet dataset(*this, name);
+    return dataset.ReadScalar<float>();
+}
+
+int64_t HDF5Object::GetInt(const std::string &name) const {
+    HDF5DataSet dataset(*this, name);
+    return dataset.ReadScalar<int64_t>();
+}
+
+std::optional<float> HDF5Object::GetOptFloat(const std::string &name) const {
+    if (Exists(name))
+        return GetFloat(name);
+    return {};
+}
+
+std::optional<int64_t> HDF5Object::GetOptInt(const std::string &name) const {
+    if (Exists(name))
+        return GetInt(name);
+    return {};
+}
+
+std::string HDF5Object::GetString(const std::string &name) const {
+    if (Exists(name)) {
+        HDF5DataSet dataset(*this, name);
+        return dataset.ReadString();
+    }
+    return "";
+}
+
+bool HDF5Object::Exists(const std::string &name) const {
+    return H5Lexists(GetID(), name.c_str(), H5P_DEFAULT) > 0;
+}
+
+herr_t func(hid_t group, const char *name, const H5L_info2_t *info, void *op_data) {
+    auto ret = reinterpret_cast<std::vector<std::string> *>(op_data);
+    ret->emplace_back(name);
+    return 0;
+}
+
+std::vector<std::string> HDF5Object::FindLeafs(const std::string &name) const {
+    hid_t gid = H5Gopen(id, name.c_str(), H5P_DEFAULT);
+    if (gid < 0)
+        throw JFJochException(JFJochExceptionCategory::HDF5, "Cannot open HDF5 group " + name);
+    std::vector<std::string> ret;
+    hsize_t idx = 0;
+    H5Literate(gid, H5_INDEX_NAME, H5_ITER_INC, &idx, func, &ret);
+
+    H5Gclose(gid);
+    return ret;
 }