EpiQ-Map 0.1.0

Reciprocal-space reconstruction and inspection for epitaxial thin films

EpiQ-Map

Reciprocal-space inspection for epitaxial thin films.

Tools for working with bounded reciprocal-space maps (RSMs): an interactive viewer, a processing monitor, and the shared scientific library.

Created by Ben Gregory and Andrej Singer.

Installation

Install a published wheel:

python -m pip install EpiQ-Map

The default install includes the napari viewer and pyqtgraph, alongside the scientific library, reconstruction stack, monitor, and native kernel. Select a concrete Qt binding through an extra:

# Recommended Qt 6 installation
python -m pip install "EpiQ-Map[qt6]"

# Optional Qt 5 target
python -m pip install "EpiQ-Map[qt5]"

# Qt 6, Qt for Python
python -m pip install "EpiQ-Map[pyside6]"

# Qt 5, Qt for Python (PySide2, not PySide5)
python -m pip install "EpiQ-Map[pyside2]"

QtPy selects the installed binding. When several bindings are installed, set QT_API to pyqt5, pyqt6, pyside2, or pyside6 before launching. Current napari supports PyQt5, PyQt6, and PySide6. PySide2 remains usable by the monitor, but current napari no longer supports it.

Install a development checkout:

python -m pip install -e ".[test]"

The PyPI distribution is named EpiQ-Map; its import package is epiq_map because Python package identifiers cannot contain hyphens.

Running

rsm_viewer --file scan.nxs
rsm_monitor --config epiq_monitor.toml

Optional viewer flags (all have sensible defaults): --u-matrix FILE, --q1-range LO HI, --q2-range LO HI, --q3-range LO HI, --shape N1 N2 N3, --memory-limit-mb MB.

The default target installs the comparatively heavy napari and pyqtgraph dependencies. A concrete Qt binding is selected through a separate extra, as shown under Installation.

Copy examples/epiq_monitor.toml into the working directory and edit the beamtime paths. The bundled reconstruction modules are used by default; an external script can still be selected with --autorsm.

Contents

Path	Purpose
src/epiq_map/rsm_viewer.py	EpiQ-Map napari viewer.
src/epiq_map/rsm_monitor.py	Qt processing monitor.
src/epiq_map/rsm_viewer_ctr.py	High-resolution HKL-rod front end.
src/epiq_map/visualize_rsm_lib.py	Shared scientific library.
src/epiq_map/hkl_convert/	autoRSM acquisition stack and native C kernel.
tests/unit/	Dependency-light unit tests.
tests/integration/	Native-kernel and acquisition-stack tests.

Viewer: the U matrix

U is the orientation matrix that aligns the measured data to the crystal frame. The viewer offers four ways to set it:

• Calculate U -- pick a substrate from the dropdown (read from substrate_lattice_constants.txt) and click Calculate U. Peaks are found in the loaded volume and indexed against the substrate cell; the status line reports the inlier count and RMS.
• Substrate normal -- the Normal field (e.g. [0 0 1]) pins the indexed frame so the result is reproducible: the normal becomes the out-of-plane axis and two in-plane axes are chosen orthogonal to it. Leave blank for an unconstrained (run-dependent) orientation.
• Load U matrix / Save U matrix -- read or write a U as a plain text file (numpy.loadtxt/savetxt format).
• Use identity -- skip indexing and view the raw data frame.

Viewer: oriented Q axes and the region

The Oriented Q axes table defines the bounded region to interpolate. Each row is one output axis:

• Q1 (horizontal), Q2 (vertical), Q3 (napari slider).
• Direction -- the crystal direction for that axis in the U-aligned frame (default [1 0 0], [0 1 0], [0 0 1]). The three must be mutually orthogonal. The range below each is cut along that (rotated) direction.
• Q min / Q max / Samples -- the bounds and grid size for that axis.

Click Interpolate region to resample the source onto this grid (in a background thread). Other controls:

• Order -- spline interpolation order for the resampling (0 = nearest, 1 = trilinear (default), up to 5).
• Intensity -- display transform: Linear, log1p, or log10(I + 1).
• Use UB matrix (plot in RLU) -- sample at U.B*.x so the axes are in reciprocal lattice units (hkl) instead of A^-1. Requires a substrate cell from Calculate U; the axis labels and units update accordingly.
• Equal axes (cube) -- render the region as a cube regardless of how unequal the Q ranges are. Uncheck for the true physical proportions.

Colormap and 3D rendering mode are set from napari's built-in layer-controls panel on the left (select the RSM intensity layer).

Viewer: navigation and line cuts

In the 2D slice view:

• Box zoom -- left-click-drag a rectangle to zoom to it. Normal scroll/drag pan and zoom still work; Reset view / Center camera restore the full view.
• Hover readout -- the status bar shows the exact Q (or hkl) position under the cursor to three decimals, plus the intensity there.

The Line cuts dock (right) takes axis-aligned or arbitrary-line cuts. Plots accumulate: each cut becomes a named curve (#<file number> <axis>) in the plot, with a checklist to toggle curves on/off for comparison, and Clear all to reset. Save CSV / Copy CSV export the most recent cut.

Viewer: HKL rods (CTR)

The RSM rods dock opens a multi-rod CTR file (the autoRSM_rods output -- one NXdata per rod). Open rod file… lists the rods by (h, k); Show rod in viewer makes the chosen rod the active volume, so the RSM region / image / line-cut docks all operate on that one rod (it is loaded as file.nxs::rod_<h>_<k>). Plot rod profile / Plot all overlay the integrated rod intensity I(L) (sum or mean over the H/K window), accumulating as named curves with Log Y and Save CSV -- the CTR line shapes side by side.

Monitor: CTR rods (high-resolution HKL rods)

For crystal-truncation-rod work the monitor can reconstruct a small, high-resolution sampling of just the HKL rods instead of one big coarse cube. Select a group of phi-scan rows (click the Dataset column) and press CTR rods…:

1. Find UB -- pick a substrate (and surface normal) and re-index every selected scan's volume against it; the per-scan orientations are averaged into one UB. Two non-blocking helper windows open on demand and can be closed (window X) without interrupting setup:
   • Found peaks… -- a table of the found-and-indexed peaks (hkl, |q|, residual, inlier) so you can see what is there; Add selected (h, k) as rods turns reflections into rods.
   • Projection… -- the data summed along the substrate normal, with the two in-plane crystal directions on the axes.
2. HKL rods -- set integer H and K ranges and Populate pairs to list every (h, k), or From indexed peaks; delete rows to make the set sparse. L spans the full range at high resolution (default 2000 points) and each rod is a narrow (H, K) window about its center (default ±0.1, 100 points). The Coordinates directions rotate the rod axes to chosen crystal directions (like the viewer's oriented Q axes).

autoRSM_rods.py then reconstructs every rod in a single pass over the CBF frames (read once; each rod is binned with its own tight, self-clipping grid). The output is one NeXus file under {Output Directory}/rod_objects/ with one NXdata per rod (rod_<h>_<k>, each carrying its own H, K, L, counts, norm) plus the averaged UB, substrate lattice, and scan list.

Tests

python -m pytest tests/unit

tests/unit/test_rsm_viewer.py covers the GUI-independent viewer helpers (cuts, interpolation, U-from-normal, equal-axes scaling, file naming). tests/unit/test_rsm_viewer_ctr.py covers the CTR-rod helpers (pair population, U averaging, rod-config round trip; the rod-grid/kernel tests need the the acquisition stack and native kernel). Integration tests live under tests/integration/.

Build and release

The native hklBen library is built by setuptools as part of the wheel:

python -m pip install --upgrade build twine
python -m build
python -m twine check dist/*

No Makefile or hand-copied shared library is needed. Linux wheels use OpenMP, Windows wheels use MSVC OpenMP, and macOS wheels use a portable serial fallback. Tagging a release as vX.Y.Z runs .github/workflows/release.yml, builds CPython wheels for common Linux, Windows, Intel macOS, and Apple Silicon targets, creates a GitHub release, and publishes to PyPI using trusted publishing. Add a matching ## [X.Y.Z] section to CHANGELOG.md before creating the tag.