Merge

Merge indexed reflection data from one or more indexing runs into a single set of structure-factor amplitudes using CrystFEL’s partialator. The output is a merged crystfel.hkl file ready for export to downstream crystallography software.

Inputs

• One or more .stream files from indexing runs (indexingintegration_* or ici_* run folders)

• A unit cell (inferred automatically from the stream header or the matching indexing run folder)

Using the GUI

Open the Merge window from the toolbar or menu. The window has three tabs:

Tab	Contents
Select Run	Choose an indexing run, view its stream files, and combine them.
Settings	Configure Partialator parameters, start the merge, and inspect live and post-merge results.
Compare	Side-by-side comparison of all completed merge runs.

Select Run tab

The left panel shows a dropdown listing all discovered indexing runs (indexingintegration_* and ici_*). Select a run to see its stream files.

Button	Effect
Refresh	Re-scan for indexing runs.
Combine →	Concatenate all streams from the selected run into a new <stem>_merge_<timestamp>/ folder; the combined stream is added to the Settings tab.
Latest All →	Combine the most recent mergeable stream from each INI in the workspace into one combined stream.
Use Selected	Load a previously combined stream from the right panel and switch to the Settings tab.

The right panel (Combined Streams) lists all existing <stem>_merge_* folders and their stream files.

Settings tab

The top of the tab shows the active stream (dropdown), the inferred cell parameters parsed from the stream header or matched indexing run, and — when a workspace-refined unit cell is available — a Cell for merge analysis selector to choose between the indexing cell and the workspace refined cell.

Parameters are on the right panel:

Parameter	Default	Description
Point Group	—	Symmetry point group for merging (-y).
Unique Axis	—	Unique axis suffix for point groups where CrystFEL accepts one.
Threads	cpu_count	Parallel threads (-j).
Min Resolution	5.0 Å	Per-crystal resolution sanity filter; tick ∞ to include all crystals.
Iterations	25	Number of scaling/merging cycles.
Model	offset	Partiality model (offset, xsphere, unity, ggpm).
Min Measurements	5	Minimum observations per reflection.
Max ADU	∞	Saturation cutoff; untick ∞ to set a numeric limit.
Push Resolution	0	Extend merging beyond the observed resolution.
Use B-scaling	off	When unchecked, passes --no-Bscale to Partialator.
Save Partialator Diagnostic Logs	off	Write per-crystal diagnostic files to pr-logs/. Not needed for normal merging or export.

Polarisation is fixed to none for electron diffraction and is not user-configurable. COSEDA always asks Partialator to write intermediate HKL files after each cycle.

Buttons:

• Save Settings — persists settings to the .ini and a JSON file next to the combined stream.

• Merge — creates a merge-run<N>/ subfolder in the combined stream’s folder and starts Partialator. If the stream has been merged before, COSEDA clones it into a fresh timestamped folder first so previous results are preserved.

• Abort — terminates the running Partialator process.

The inner panel shows three sub-tabs that update live as the merge runs:

Merging sub-tab — scaling table updated after each Partialator cycle:

Column	Description
Overall CChalf (%)	Per-cycle overall CC½.
Reflections	Number of reflections used.
deltaCChalf	Change in CC½ from the previous cycle.
deltaCChalf Error (%)	Uncertainty on ΔCC½.
Bad Crystals	Crystals rejected this cycle.
OK Crystals	Crystals accepted this cycle.
Negative delta CC½	Count with negative ΔCC½.

Click any column header to select it for plotting (up to two columns, dual y-axis).

Statistics sub-tab — resolution shell statistics from check_hkl, populated automatically after the merge finishes:

Center 1/nm · # refs · Possible · Compl (%) · Meas · Red · SNR · Mean I · d(Å) · Min 1/nm · Max 1/nm

Click selectable metric headers to plot vs. resolution.

Split Half sub-tab — split-half statistics from compare_hkl (requires crystfel.hkl1/crystfel.hkl2 output):

d(Å) · CC1/2 · CC* · Rsplit (%) · # refs · Center 1/nm · Min 1/nm · Max 1/nm

A Console Output panel at the bottom streams live Partialator output. Use Clear to reset or Save Log… to write it to disk.

Compare tab

Shows all completed merge runs in a summary table:

Run · Point Group · Input Crystals · Used Crystals · CC1/2 Final (%) · Compl ~2Å (%) · Red ~2Å · SNR ~2Å · CC1/2 Split ~2Å · CC* ~2Å · Rsplit ~2Å · Min Res · Push Res · Min Meas · Model · Iterations · Max ADU · B-scale · Partialator Logs · Output

Select one or more rows and choose a metric to compare their resolution-shell curves in the plot below. Use Refresh to re-scan for completed runs.

Outputs

Each merge run creates a merge-run<N>/ subfolder inside the combined stream’s folder:

• crystfel.hkl — merged reflection intensities in CrystFEL format.

• crystfel.hkl1, crystfel.hkl2 — final split-half HKL files written by Partialator.

• harvest.json — detailed per-cycle Partialator statistics.

• stdout.log — full Partialator console output.

• shells.dat — resolution shell statistics from check_hkl.

• compare_hkl_CC.dat, compare_hkl_CCstar.dat, compare_hkl_Rsplit.dat — split-half shell files from compare_hkl.

• merging_table.csv, merging_plot.png — exported Merging sub-tab data.

• statistics_table.csv, statistics_plot.png — exported Statistics sub-tab data.

• split_half_table.csv, split_half_plot.png — exported Split Half sub-tab data.

• pr-logs/ — Partialator per-crystal diagnostic files (only when Save Partialator Diagnostic Logs is enabled).

• Settings JSON (<stem>_merge_settings.json) — full parameter snapshot next to the combined stream.

• NXprocess metadata — written to the source HDF5 files.

Tips

• Point group first. Set the correct symmetry before merging. An incorrect point group will produce misleading statistics.

• Trigonal notation. CrystFEL does not accept bare trigonal symbols such as 32; use explicit forms such as 321_H, 312_H, or 32_R.

• Convergence. Watch Overall CChalf stabilize across cycles in the Merging sub-tab. If it keeps changing, increase the iteration count.

• Re-running. Clicking Merge on a stream that already has results clones it to a fresh timestamped folder, so all previous results are preserved.

• Multiple datasets. Use Latest All → to combine the best stream from each loaded dataset into a single merge for improved completeness.

• Workspace refined cell. If a unit cell fit has been run, the Cell source selector appears in the Settings tab, letting you use the refined cell for check_hkl and compare_hkl statistics without re-merging.