Scan viewers#

Three PyQt6 windows for looking at the files MyNXWriter leaves in a data directory: a scan browser, a fluorescence-spectrum viewer, and an image-stack viewer. They were developed at the beamline as standalone scripts and are now part of the package, so they install and update with everything else.

Only the browser has a console script; it opens the other two itself.

scan-viewer [directory]

With no argument it starts in the current directory.

The scan browser#

scan-viewer lists every *_master.hdf in the directory that carries Bluesky scan metadata — one row per scan with its number, plan, motor, range, points and count time, filled in as the listing is read rather than on selection. Detector image files, whether beside the masters or in a per-detector subdirectory, are not listed as scans; instead an Img tick marks the scans whose images were found on disk.

Select one scan, or ctrl/shift-click several, and they are overlaid:

  • Stream box — picks which of entry/instrument/bluesky/streams to show. Most scans only record primary; a dichro scan also writes the XAS and XMCD it computed to dichro_monitor and opens on that.

  • Field table — X / Y / Norm ticks drive the plot. X and Norm take one field each, Y any number. They start on whatever the scan’s own hints nominate, so a scan plots itself the way it was meant to be read. Norm starts clear, because normalizing rescales every number on the plot and in the statistics table.

  • log(mon/det) — plots the absorption rather than a plain ratio, which is what makes a transmission XAS scan readable straight off primary.

  • Statistics, Integrate, Fit — max, min, half-max centre and FWHM per curve; trapezoidal and background-subtracted areas; and peak fitting (Gauss, Lorentzian, Lorentzian², pseudo-Voigt) over a sloping line, with centre, FWHM, height, area and R² reported per curve. Multi fits several peaks at once over one shared line.

  • Show dY/dX — overlays each curve’s derivative and moves the fit onto it, which is how a knife edge or an absorption edge becomes measurable.

  • Log X / Log Y — beside the plot toolbar, put either axis on a log scale (the right-hand Y axes too). Points at or below zero are left out.

  • XMCD panels — reduces the selected scans to XAS, XMCD, XMuCD and XNCD against energy, grouping each energy’s points into the four (polarization, field) quadrants.

  • Remove spikes — drops points taken while the beam was gone, judged by the monitor against its own scan’s median. Only lone points go; a stretch of dead points is a beam-down run and is left visible.

  • Two-motor grid scans are drawn as colour maps instead, one per ticked Y field, with Clip map scale for the odd wild cell and Center on 0 for signed channels in a diverging colormap. Selected grid scans over the same two motors — a map finished by a second scan started where the first stopped — go on one map, and a cell measured by more than one of them is their average.

  • Auto refresh adds scans to the listing as they land, so the browser can be left open during a run. A scan whose file is still being written gets a row with blank cells rather than being dropped.

Note

Read the module docstrings for the full behaviour — they are long and they explain why each default is what it is, usually with the scan numbers that motivated it. They are reproduced in the API reference.

The spectrum viewer — Spc#

The multi-element silicon-drift (Vortex) detector does not write its MCA spectra into the master file. They go into a file of their own, named in entry/instrument/bluesky/metadata/detectors_file_relative_path:

vortex: vortex/scan_000055.h5

holding entry/data/data shaped (frames, elements, bins). The browser’s Spc button opens that file for the selected scan. It can also be opened directly:

python -m polartools.spectrum_viewer path/to/scan_000055_master.hdf

Both the master file and the spectrum file itself are accepted — the master is resolved to its companion.

Neither the element count nor the dead-time bookkeeping is constant between run cycles, so both are read from the file. Dead-time correction (corrected = raw * DTFactor, or ICR / OCR on older files) is on by default, against this package’s general habit of showing what was recorded: on one test scan element 3 runs 8–33% dead while element 6 runs 0.2%, so seven raw curves in a window meant for comparing elements state a wrong conclusion about the hardware rather confidently. The checkbox turns it off.

The Combine box handles scans that took more than one frame per point, and vortex_total_el1 / vortex_total_el7 are offered as monitors.

The image viewer — Img#

Area-detector frames are likewise written outside the master file, by one of two writers — the pvapy streaming consumer (a sibling file named in pva_streaming) or an areaDetector plugin (a per-detector subdirectory, named in detectors_file_relative_path). The viewer resolves either, and falls back to deriving pva_<stem>.h5 when the master records neither.

python -m polartools.image_viewer path/to/pva_tise2_2_00006.h5 [more.h5 ...]

Built on pyqtgraph: pan/zoom, level and colormap control, rectangular ROIs with live sums, and per-frame metadata (entry/data/metadata/ca/<pv> from pvapy, entry/instrument/NDAttributes/<name> from areaDetector) plotted against frame number. Several files can be opened side by side with ROIs shared between the panels.

Compressed frames (LZ4, bitshuffle) need hdf5plugin, which is a dependency of the package and imported for its codec registration.

Troubleshooting#

The window never appears, and the terminal says Could not load the Qt platform plugin "xcb". Missing X11 system libraries — see Qt system libraries on Linux.

A scan is missing from the listing. Only files carrying Bluesky scan metadata are listed. A detector file, or a master written by something other than MyNXWriter, is skipped on purpose.

Spc or Img is greyed out or finds nothing. The companion file is resolved relative to the master’s own directory, because the paths recorded inside name the filesystem the scan was taken on — which a copy of the data is not. Keep the subdirectory layout intact when copying data off the beamline.

See also#