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>

viewer/JFJochImageReadingWorker.cpp

@@ -108,7 +108,8 @@ JFJochImageReadingWorker::JFJochImageReadingWorker(const SpotFindingSettings &se
 
     indexing = std::make_unique<IndexerThreadPool>(indexing_settings, IndexerConstruction::OnFirstUse);
     http_reader.Experiment(experiment);
-    file_reader.Experiment(experiment);
+    hdf5_reader.Experiment(experiment);
+    cbf_reader.Experiment(experiment);
     thumb_color_scale_.Select(ColorScaleEnum::Indigo);
 
     autoload_timer = new QTimer(this);
@@ -209,6 +210,7 @@ void JFJochImageReadingWorker::LoadFile_i(const QString &filename, qint64 image_
 
         if (filename.startsWith("http://") || filename.startsWith("https://")) {
             http_mode = true;
+            cbf_mode = false;
             http_reader.ReadURL(filename.toStdString());
             total_images = http_reader.GetNumberOfImages();
             dataset = http_reader.GetDataset();
@@ -265,9 +267,19 @@ void JFJochImageReadingWorker::LoadFile_i(const QString &filename, qint64 image_
                 file_open_retry_attempts++;
             }
 
-            file_reader.ReadFile(filename.toStdString());
-            total_images = file_reader.GetNumberOfImages();
-            dataset = file_reader.GetDataset();
+            // Naming one miniCBF frame opens the sweep it belongs to; anything else is HDF5.
+            // Release the previously open file first, so switching format leaves nothing behind.
+            file_reader->Close();
+            cbf_mode = JFJochCBFReader::CanRead(filename.toStdString());
+            if (cbf_mode) {
+                file_reader = &cbf_reader;
+                cbf_reader.ReadFiles(filename.toStdString());
+            } else {
+                file_reader = &hdf5_reader;
+                hdf5_reader.ReadFile(filename.toStdString());
+            }
+            total_images = file_reader->GetNumberOfImages();
+            dataset = file_reader->GetDataset();
             setAutoLoadMode_i(AutoloadMode::None);
 
             if (retry && file_open_retry_active) {
@@ -334,7 +346,7 @@ void JFJochImageReadingWorker::CloseFile() {
     if (http_mode)
         http_reader.Close();
     else
-        file_reader.Close();
+        file_reader->Close();
 
     status_timer->stop();
     setAutoLoadMode_i(AutoloadMode::None);
@@ -398,7 +410,7 @@ void JFJochImageReadingWorker::LoadImage_i(int64_t image_number, int64_t summati
         } else {
             if (image_number < 0 || image_number + summation > total_images)
                 return;
-            current_image_ptr = file_reader.LoadImage(image_number, summation);
+            current_image_ptr = file_reader->LoadImage(image_number, summation);
         }
 
         if (!current_image_ptr) {
@@ -469,8 +481,8 @@ void JFJochImageReadingWorker::UpdateDataset_i(const std::optional<DiffractionEx
         dataset = http_reader.GetDataset();
     } else {
         if (experiment)
-            file_reader.UpdateGeomMetadata(experiment.value());
-        dataset = file_reader.GetDataset();
+            file_reader->UpdateGeomMetadata(experiment.value());
+        dataset = file_reader->GetDataset();
     }
     if (!dataset) {
         logger.Error("UpdateDataset_i: dataset is null (http_mode={}) - skipping update to avoid crash", http_mode);
@@ -533,7 +545,7 @@ void JFJochImageReadingWorker::Analyze() {
     EmitImageLoaded_i(current_image_ptr);
 }
 
-void JFJochImageReadingWorker::FindCenter(QVector<float> ring_q, bool guess) {
+void JFJochImageReadingWorker::FindCenter(QVector<float> ring_q, bool guess, bool refine_tilt) {
     QMutexLocker locker(&m);
     if (!current_image_ptr)
         return;
@@ -543,9 +555,9 @@ void JFJochImageReadingWorker::FindCenter(QVector<float> ring_q, bool guess) {
     const std::vector<float> ring_Q(ring_q.begin(), ring_q.end());
     try {
         if (guess)
-            GuessGeometry(geom, current_image_ptr->ImageData().spots, ring_Q);
+            GuessGeometry(geom, current_image_ptr->ImageData().spots, ring_Q, refine_tilt);
         else
-            OptimizeGeometry(geom, current_image_ptr->ImageData().spots, ring_Q);
+            OptimizeGeometry(geom, current_image_ptr->ImageData().spots, ring_Q, refine_tilt);
     } catch (const JFJochException &e) {
         logger.ErrorException(e);
         return;
@@ -799,8 +811,8 @@ void JFJochImageReadingWorker::UpdateUserMask_i(const std::vector<uint32_t> &mas
         http_reader.UpdateUserMask(mask);
         dataset = http_reader.GetDataset();
     } else {
-        file_reader.UpdateUserMask(mask);
-        dataset = file_reader.GetDataset();
+        file_reader->UpdateUserMask(mask);
+        dataset = file_reader->GetDataset();
     }
 
     if (!dataset) {
@@ -886,7 +898,7 @@ void JFJochImageReadingWorker::LoadCalibration(QString dataset) {
         auto tmp = std::make_shared<SimpleImage>();
 
         try {
-            tmp->image = file_reader.ReadCalibration(tmp->buffer, dataset.toStdString());
+            tmp->image = hdf5_reader.ReadCalibration(tmp->buffer, dataset.toStdString());
 
             std::shared_ptr<const SimpleImage> ctmp = tmp;
             emit simpleImageLoaded(ctmp);
@@ -1043,7 +1055,7 @@ void JFJochImageReadingWorker::LoadSpots(int64_t start_image, int64_t end_image,
     if (http_mode)
         result = http_reader.ReadAllSpots(start_image, end_image, stride);
     else
-        result = file_reader.ReadAllSpots(start_image, end_image, stride);
+        result = file_reader->ReadAllSpots(start_image, end_image, stride);
     emit spotsLoaded(result);
 }
 
@@ -1065,8 +1077,8 @@ ReprocessingInputs JFJochImageReadingWorker::GetReprocessingInputs() const {
 
 void JFJochImageReadingWorker::ActivateSnapshot_i(const QString &name) {
     // Assumes m locked! Switch the reader's active metadata snapshot and refresh the view.
-    file_reader.SetActiveSnapshot(name.toStdString());
-    auto dataset = file_reader.GetDataset();
+    hdf5_reader.SetActiveSnapshot(name.toStdString());
+    auto dataset = hdf5_reader.GetDataset();
     if (!dataset)
         return;
 
@@ -1077,9 +1089,9 @@ void JFJochImageReadingWorker::ActivateSnapshot_i(const QString &name) {
     EmitDatasetLoaded_i(dataset);
 
     QStringList names;
-    for (const auto &n: file_reader.SnapshotNames())
+    for (const auto &n: hdf5_reader.SnapshotNames())
         names << QString::fromStdString(n);
-    emit snapshotsChanged(names, QString::fromStdString(file_reader.ActiveSnapshot()));
+    emit snapshotsChanged(names, QString::fromStdString(hdf5_reader.ActiveSnapshot()));
     EmitRuns_i();
 
     if (current_image.has_value()) {
@@ -1096,13 +1108,13 @@ void JFJochImageReadingWorker::EmitRuns_i() {
     // Assumes m locked! Build the run list (every snapshot dataset + its display label).
     QVector<RunData> runs;
     if (!http_mode) {
-        for (const auto &[id, dataset]: file_reader.AllSnapshotDatasets()) {
+        for (const auto &[id, dataset]: hdf5_reader.AllSnapshotDatasets()) {
             const auto it = run_labels_.find(id);
             const QString label = (it != run_labels_.end()) ? it->second : QString::fromStdString(id);
             runs.push_back(RunData{QString::fromStdString(id), label, dataset});
         }
     }
-    emit runsChanged(runs, http_mode ? QString() : QString::fromStdString(file_reader.ActiveSnapshot()));
+    emit runsChanged(runs, http_mode ? QString() : QString::fromStdString(hdf5_reader.ActiveSnapshot()));
 }
 
 void JFJochImageReadingWorker::RenameRun(QString id, QString label) {
@@ -1115,20 +1127,22 @@ void JFJochImageReadingWorker::RemoveRun(QString id) {
     QMutexLocker ul(&m);
     if (http_mode || id == "Original")
         return;
-    file_reader.RemoveSnapshot(id.toStdString());
+    hdf5_reader.RemoveSnapshot(id.toStdString());
     run_labels_.erase(id.toStdString());
     // Refresh the (possibly now-Original) active view; ActivateSnapshot_i also re-emits runsChanged.
-    ActivateSnapshot_i(QString::fromStdString(file_reader.ActiveSnapshot()));
+    ActivateSnapshot_i(QString::fromStdString(hdf5_reader.ActiveSnapshot()));
 }
 
 void JFJochImageReadingWorker::RegisterProcessingSnapshot(QString id, QString label, QString master_path) {
     QMutexLocker ul(&m);
-    if (http_mode) {
-        logger.Error("Processing snapshots are only available for files");
+    if (http_mode || cbf_mode) {
+        // A snapshot is metadata read back over the SAME images the reader is serving, which only the
+        // HDF5 reader can do; a CBF sweep's job output is a stand-alone file, opened like any other.
+        logger.Error("Processing snapshots are only available for HDF5 files");
         return;
     }
     try {
-        file_reader.RegisterSnapshot(id.toStdString(), master_path.toStdString());
+        hdf5_reader.RegisterSnapshot(id.toStdString(), master_path.toStdString());
         run_labels_[id.toStdString()] = label;
         ActivateSnapshot_i(id);   // activates + emits datasetLoaded / snapshotsChanged / runsChanged
     } catch (const std::exception &e) {
@@ -1184,7 +1198,7 @@ QImage JFJochImageReadingWorker::RenderThumbnail_i(int64_t image_number, bool sh
             QMutexLocker locker(&m);
             if (http_mode || image_number < 0 || image_number >= total_images)
                 return {};
-            img = file_reader.LoadImage(image_number, 1);
+            img = file_reader->LoadImage(image_number, 1);
         }
         if (!img)
             return {};