v1.0.0-rc.166 (#76)

* `rugnux --mode calibration` writes `<prefix>.json` beside the `.poni`, whose `dataset_settings` member is a `jfjoch_broker` `dataset_settings` body as it stands.
* `rugnux` and `jfjoch_viewer` read PILATUS miniCBF sweeps natively, without conversion.
* Masters written by other facilities open, including Eiger 1.x and third-party NXmx variants.
* `rugnux` measures the beam centre on every run, and indexes with it when the file's value indexes nothing.
* A detector swung out on a 2theta arm is placed where the file says it stands, and the calibration can hold the tilt fixed.
* `rugnux` writes the unmerged MTZ by default, and a P1 merge beside it, so a wrong space group can be re-merged without reprocessing.
* Significant improvements to symmetry handling in `rugnux`: the lattice, the point group, the setting and the systematic absences.
* The `rugnux` report gives the resolution the CC1/2 fit reached, beside the range the reflections were written to.
* The `rugnux` report gives the twinning statistics measured before the space group was decided, beside the ones measured after.
* The `rugnux` report gives the strong-direction diffraction limit, and warns when CC1/2 is not monotone with resolution.
* `rugnux` ranks screw axes on the evidence their absences carry, rather than on how many control reflections a candidate happens to have.
* Twinning is no longer reported when the L-test contradicts it.
* The `rugnux` report gives the detector tilt, the measured tilt and the direct beam beside the beam centre, and a post-refined beam centre is judged against the run's own measurement rather than the file's.
* `--no-refine-tilt` holds the detector tilt at the value in the file, instead of zeroing it, when the calibration starts from the spots.
* The `jfjoch_viewer` grid scan view draws the cells in the proportion of the scan steps, so the map has the shape of the scanned area.

Reviewed-on: #76
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>

reader/HDF5ImageSource.cpp

@@ -71,7 +71,7 @@ HDF5ImageLocator::Location HDF5ImageSource::Resolve(int64_t global) const {
 
 StoredPixelFormat HDF5ImageSource::GetStoredPixelFormat() const {
     auto loc = locator_.Resolve(0);
-    HDF5DataSet dataset(*loc.file, "/entry/data/data");
+    HDF5DataSet dataset(*loc.file, loc.dataset);
     HDF5DataType datatype(dataset);
     return {static_cast<int64_t>(datatype.GetElemSize()) * 8, datatype.IsSigned()};
 }
@@ -85,12 +85,13 @@ std::vector<HDF5DataSourceMessage> HDF5ImageSource::GetSourceMapping(uint64_t fi
 
 const HDF5ImageSource::OpenDataset &
 HDF5ImageSource::GetDataset(const HDF5ImageLocator::Location &loc) const {
-    if (auto it = dataset_cache_.find(loc.file.get()); it != dataset_cache_.end())
+    auto key = std::make_pair(loc.file.get(), loc.dataset);
+    if (auto it = dataset_cache_.find(key); it != dataset_cache_.end())
         return it->second;
 
     OpenDataset entry;
     entry.file = loc.file;
-    entry.dataset = std::make_unique<HDF5DataSet>(*loc.file, "/entry/data/data");
+    entry.dataset = std::make_unique<HDF5DataSet>(*loc.file, loc.dataset);
 
     HDF5DataSpace dataspace(*entry.dataset);
     HDF5DataType datatype(*entry.dataset);
@@ -98,7 +99,7 @@ HDF5ImageSource::GetDataset(const HDF5ImageLocator::Location &loc) const {
 
     if (dataspace.GetNumOfDimensions() != 3)
         throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
-                              "/entry/data/data dataset must be 3D");
+                              loc.dataset + " dataset must be 3D");
 
     if (datatype.IsFloat())
         throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
@@ -115,20 +116,37 @@ HDF5ImageSource::GetDataset(const HDF5ImageLocator::Location &loc) const {
     if (entry.direct_chunk)
         entry.algorithm = dcpl.GetCompression();
 
-    if (entry.direct_chunk && !loc.path.empty()) {
-        entry.raw = std::make_shared<RawFile>(loc.path);
-        if (!entry.raw->IsOpen())
-            entry.raw.reset();
-        hid_t fcpl = H5Fget_create_plist(loc.file->GetID());
-        if (fcpl >= 0) {
-            hsize_t user_block = 0;
-            if (H5Pget_userblock(fcpl, &user_block) >= 0)
-                entry.user_block = user_block;
-            H5Pclose(fcpl);
+    if (entry.direct_chunk) {
+        // A positional read needs the file the PIXELS are in, and that is not always the file that
+        // was opened: a dataset reached through an external link lives elsewhere, and a chunk
+        // address is an offset into ITS file - as is the user block the address counts from. Ask
+        // HDF5 which file the dataset ended up in rather than assuming it is the one we asked.
+        std::string path = loc.path;
+        const hid_t owner = H5Iget_file_id(entry.dataset->GetID());
+        if (owner >= 0) {
+            const ssize_t name_size = H5Fget_name(owner, nullptr, 0);
+            if (name_size > 0) {
+                std::string name(static_cast<size_t>(name_size), '\0');
+                if (H5Fget_name(owner, name.data(), name.size() + 1) >= 0)
+                    path = name;
+            }
+            const hid_t fcpl = H5Fget_create_plist(owner);
+            if (fcpl >= 0) {
+                hsize_t user_block = 0;
+                if (H5Pget_userblock(fcpl, &user_block) >= 0)
+                    entry.user_block = user_block;
+                H5Pclose(fcpl);
+            }
+            H5Fclose(owner);
+        }
+        if (!path.empty()) {
+            entry.raw = std::make_shared<RawFile>(path);
+            if (!entry.raw->IsOpen())
+                entry.raw.reset();
         }
     }
 
-    return dataset_cache_.emplace(loc.file.get(), std::move(entry)).first->second;
+    return dataset_cache_.emplace(std::move(key), std::move(entry)).first->second;
 }
 
 std::optional<HDF5ImageSource::DirectChunk>