pyextal.jaxGeo.io¶

Finding and loading a dataset: the .h5, the .dat it was built against.

Functions¶

`to_wsl_path`(path)	Accepts a Windows path as well as a WSL one.
`resolve_h5`(path)	The dataset file, given the file itself or the folder holding it.
`_out_count`(dat)	Number of output reflections in a `.dat`'s `out` block, or None.
`resolve_dat`(h5, n_beams)	Finds the `.dat` a dataset file was built against.
`check_pre_refinement`(h5)	Raises if the file lacks the `/pre_refinement` group this needs.
`load_dataset`(h5[, subsample])	The refinement inputs from a dataset file, spatially subsampled.

Module Contents¶

pyextal.jaxGeo.io.to_wsl_path(path)¶

Accepts a Windows path as well as a WSL one.

C:\Users\<user>\Box\... maps to /mnt/box/... (where Box is mounted under WSL) and any other X:\... to /mnt/x/.... POSIX paths pass through unchanged.

Parameters:: path (str | Path) – The path as typed.
Returns:: A path usable from WSL.
Return type:: Path

pyextal.jaxGeo.io.resolve_h5(path)¶

The dataset file, given the file itself or the folder holding it.

Parameters:: path (Path) – A .h5 file, or a folder containing exactly one.
Returns:: The .h5 file.
Return type:: Path
Raises:: SetupError – If path does not exist, or a folder holds no .h5 or several.

pyextal.jaxGeo.io._out_count(dat)¶: Number of output reflections in a .dat’s out block, or None.

pyextal.jaxGeo.io.resolve_dat(h5, n_beams)¶

Finds the .dat a dataset file was built against.

In order: the dat recorded in the file’s /paths group (relative to the file’s folder, or to the recorded base); otherwise the one .dat beside the file whose out block lists exactly n_beams reflections – the experimental beam axis must match it one to one.

Parameters:

h5 (Path) – The dataset file.
n_beams (int) – Reflections on its experimental beam axis.

Returns:

(Path, str) – the .dat and how it was chosen.

Return type:

tuple

Raises:

SetupError – If no single .dat qualifies.

pyextal.jaxGeo.io.check_pre_refinement(h5)¶

Raises if the file lacks the /pre_refinement group this needs.

Parameters:: h5 (Path) – The dataset file.
Raises:: SetupError – With a message naming what the file holds instead.

pyextal.jaxGeo.io.load_dataset(h5, subsample=1)¶

The refinement inputs from a dataset file, spatially subsampled.

Parameters:

h5 (Path) – The dataset file.
subsample (int) – Take every Nth scan point in each direction.

Returns:

(data, g_include). data holds tilts (rows, cols, 3), experimental_data and variance (rows, cols, n_beams) and the pre-refined geometry dict; g_include (n_beams, 3) labels the experimental beam axis.

Return type:

tuple