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v1.0.0-rc.134 (#43)
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Browse Source 
This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132.

* jfjoch_broker: Add better locking for detector object - should help, when detector initialization takes too long
* jfjoch_writer: Enable writing single, integrated HDF5 file with both data and metadata
* XDS plugin: Add generation of Jungfraujoch plugin for XDS
* CI: Add tests with XDS and DIALS (`xia2.ssx`)

Reviewed-on: #43
This commit was merged in pull request #43.
This commit is contained in:
leonarski_f
2026-04-09 13:30:47 +02:00
parent 81bd9a06a1
commit 4a852b4d6b
174 changed files with 1981 additions and 325 deletions
Download Patch File Download Diff File Expand all files Collapse all files
writer/HDF5Objects.cpp
+108 -49
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@@ -315,76 +315,119 @@ void HDF5Fapl::SetVersionTo1p10orNewer() {
H5Pset_libver_bounds(id, H5F_LIBVER_V110, H5F_LIBVER_LATEST);
}
template <typename T>
static HDF5Object& WriteOrCreateScalarAttr(HDF5Object& object, const std::string& name, const T& val) {
HDF5DataSpace dataspace;
HDF5DataType datatype(val);
hid_t attr_id = -1;
if (H5Aexists(object.GetID(), name.c_str()) > 0) {
attr_id = H5Aopen(object.GetID(), name.c_str(), H5P_DEFAULT);
if (attr_id < 0)
throw JFJochException(JFJochExceptionCategory::HDF5, "Cannot open attribute " + name);
hid_t existing_type = H5Aget_type(attr_id);
if (existing_type < 0) {
H5Aclose(attr_id);
throw JFJochException(JFJochExceptionCategory::HDF5, "Cannot get attribute type " + name);
}
const bool recreate =
(H5Tget_class(existing_type) != H5Tget_class(datatype.GetID())) ||
(H5Tget_size(existing_type) != H5Tget_size(datatype.GetID()));
H5Tclose(existing_type);
H5Aclose(attr_id);
if (recreate) {
if (H5Adelete(object.GetID(), name.c_str()) < 0)
throw JFJochException(JFJochExceptionCategory::HDF5, "Cannot delete attribute " + name);
attr_id = H5Acreate2(object.GetID(), name.c_str(), datatype.GetID(), dataspace.GetID(), H5P_DEFAULT, H5P_DEFAULT);
} else {
attr_id = H5Aopen(object.GetID(), name.c_str(), H5P_DEFAULT);
}
} else {
attr_id = H5Acreate2(object.GetID(), name.c_str(), datatype.GetID(), dataspace.GetID(), H5P_DEFAULT, H5P_DEFAULT);
}
if (attr_id < 0)
throw JFJochException(JFJochExceptionCategory::HDF5, "Cannot create/open attribute " + name);
herr_t ret = H5Awrite(attr_id, datatype.GetID(), &val);
H5Aclose(attr_id);
if (ret < 0)
throw JFJochException(JFJochExceptionCategory::HDF5, "Attribute write unsuccessful");
return object;
}
HDF5Object & HDF5Object::Attr(const std::string &name, const std::string &val) {
HDF5DataSpace dataspace;
HDF5DataType datatype(val);
hid_t attr_id = H5Acreate2(id, name.c_str(), datatype.GetID(), dataspace.GetID(), H5P_DEFAULT, H5P_DEFAULT);
hid_t attr_id = -1;
if (H5Aexists(id, name.c_str()) > 0) {
attr_id = H5Aopen(id, name.c_str(), H5P_DEFAULT);
if (attr_id < 0)
throw JFJochException(JFJochExceptionCategory::HDF5, "Cannot open attribute " + name);
hid_t existing_type = H5Aget_type(attr_id);
if (existing_type < 0) {
H5Aclose(attr_id);
throw JFJochException(JFJochExceptionCategory::HDF5, "Cannot get attribute type " + name);
}
const bool recreate =
(H5Tget_class(existing_type) != H5T_STRING) ||
(H5Tget_size(existing_type) < val.length() + 1);
H5Tclose(existing_type);
H5Aclose(attr_id);
if (recreate) {
if (H5Adelete(id, name.c_str()) < 0)
throw JFJochException(JFJochExceptionCategory::HDF5, "Cannot delete attribute " + name);
attr_id = H5Acreate2(id, name.c_str(), datatype.GetID(), dataspace.GetID(), H5P_DEFAULT, H5P_DEFAULT);
} else {
attr_id = H5Aopen(id, name.c_str(), H5P_DEFAULT);
}
} else {
attr_id = H5Acreate2(id, name.c_str(), datatype.GetID(), dataspace.GetID(), H5P_DEFAULT, H5P_DEFAULT);
}
if (attr_id < 0)
throw JFJochException(JFJochExceptionCategory::HDF5, "Cannot create/open attribute " + name);
herr_t ret = H5Awrite(attr_id, datatype.GetID(), val.c_str());
H5Aclose(attr_id);
if (ret < 0) throw JFJochException(JFJochExceptionCategory::HDF5, "Attribute write unsuccessful");
if (ret < 0)
throw JFJochException(JFJochExceptionCategory::HDF5, "Attribute write unsuccessful");
return *this;
}
HDF5Object & HDF5Object::Attr(const std::string &name, int32_t val) {
HDF5DataSpace dataspace;
HDF5DataType datatype(val);
hid_t attr_id = H5Acreate2(id, name.c_str(), datatype.GetID(), dataspace.GetID(), H5P_DEFAULT, H5P_DEFAULT);
herr_t ret = H5Awrite(attr_id, datatype.GetID(), &val);
H5Aclose(attr_id);
if (ret < 0) throw JFJochException(JFJochExceptionCategory::HDF5, "Atrribute write unsucessful");
return *this;
return WriteOrCreateScalarAttr(*this, name, val);
}
HDF5Object & HDF5Object::Attr(const std::string &name, uint32_t val) {
HDF5DataSpace dataspace;
HDF5DataType datatype(val);
hid_t attr_id = H5Acreate2(id, name.c_str(), datatype.GetID(), dataspace.GetID(), H5P_DEFAULT, H5P_DEFAULT);
herr_t ret = H5Awrite(attr_id, datatype.GetID(), &val);
H5Aclose(attr_id);
if (ret < 0) throw JFJochException(JFJochExceptionCategory::HDF5, "Atrribute write unsucessful");
return *this;
return WriteOrCreateScalarAttr(*this, name, val);
}
HDF5Object & HDF5Object::Attr(const std::string &name, int64_t val) {
HDF5DataSpace dataspace;
HDF5DataType datatype(val);
hid_t attr_id = H5Acreate2(id, name.c_str(), datatype.GetID(), dataspace.GetID(), H5P_DEFAULT, H5P_DEFAULT);
herr_t ret = H5Awrite(attr_id, datatype.GetID(), &val);
H5Aclose(attr_id);
if (ret < 0) throw JFJochException(JFJochExceptionCategory::HDF5, "Atrribute write unsucessful");
return *this;
return WriteOrCreateScalarAttr(*this, name, val);
}
HDF5Object & HDF5Object::Attr(const std::string &name, uint64_t val) {
HDF5DataSpace dataspace;
HDF5DataType datatype(val);
hid_t attr_id = H5Acreate2(id, name.c_str(), datatype.GetID(), dataspace.GetID(), H5P_DEFAULT, H5P_DEFAULT);
herr_t ret = H5Awrite(attr_id, datatype.GetID(), &val);
H5Aclose(attr_id);
if (ret < 0) throw JFJochException(JFJochExceptionCategory::HDF5, "Atrribute write unsucessful");
return *this;
return WriteOrCreateScalarAttr(*this, name, val);
}
HDF5Object & HDF5Object::Attr(const std::string &name, double val) {
HDF5DataSpace dataspace;
HDF5DataType datatype(val);
hid_t attr_id = H5Acreate2(id, name.c_str(), datatype.GetID(), dataspace.GetID(), H5P_DEFAULT, H5P_DEFAULT);
herr_t ret = H5Awrite(attr_id, datatype.GetID(), &val);
H5Aclose(attr_id);
if (ret < 0) throw JFJochException(JFJochExceptionCategory::HDF5, "Atrribute write unsucessful");
return *this;
return WriteOrCreateScalarAttr(*this, name, val);
}
HDF5Object & HDF5Object::Attr(const std::string &name, const std::vector<double> &val) {
@@ -632,14 +675,19 @@ HDF5Group::HDF5Group(const HDF5Object& parent, const std::string &name) : HDF5Gr
}
HDF5Group::HDF5Group(const HDF5Object& parent, const char *name) : HDF5Object() {
id = H5Gcreate(parent.GetID(), name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (H5Lexists(parent.GetID(), name, H5P_DEFAULT) > 0)
id = H5Gopen(parent.GetID(), name, H5P_DEFAULT);
else
id = H5Gcreate(parent.GetID(), name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (id < 0)
throw JFJochException(JFJochExceptionCategory::HDF5, "Cannot open/create HDF5 group " + std::string(name));
}
HDF5Group::~HDF5Group() {
H5Gclose(id);
}
HDF5File::HDF5File(const std::string& filename, bool v1_10) : HDF5Object() {
HDF5Fapl fapl;
@@ -894,6 +942,17 @@ std::vector<std::string> HDF5Object::FindLeafs(const std::string &name) const {
return ret;
}
bool HDF5Object::IsExternalLink(const std::string& name) const {
H5L_info2_t link_info;
// Get information about the link
if (H5Lget_info(id, name.c_str(), &link_info, H5P_DEFAULT) < 0)
throw JFJochException(JFJochExceptionCategory::HDF5,
"Failed to retrieve information about the link");
return (link_info.type == H5L_TYPE_EXTERNAL);
}
std::string HDF5Object::GetLinkedFileName(const std::string& name) const {
H5L_info2_t link_info;