chemparseplot.parse.chemgp_hdf5

HDF5 Layout

• grids/<name>: 2D arrays with attrs x_range, y_range, x_length, y_length

• table/<name>: group of same-length 1D arrays

• paths/<name>: point sequences (x, y or rAB, rBC)

• points/<name>: point sets (x, y or pc1, pc2)

• Root attrs: metadata scalars

.. versionadded:: 1.7.0 Extracted from chemgp.plt_gp to standalone module.

HDF5 file I/O utilities for ChemGP data.

This module provides functions for reading structured data from ChemGP HDF5 output files. The HDF5 layout mirrors the Julia common_plot.jl helpers.

Module Contents

Functions

read_h5_table	Read a group of same-length vectors as a DataFrame.
read_h5_grid	Read a 2D grid with optional axis ranges.
read_h5_path	Read a path (ordered point sequence).
read_h5_points	Read a point set.
read_h5_metadata	Read root-level metadata attributes.
validate_hdf5_structure	Validate HDF5 file has expected structure.

API

chemparseplot.parse.chemgp_hdf5.read_h5_table(f: Any, name: str = 'table') → Any

Read a group of same-length vectors as a DataFrame.

Parameters

f Open HDF5 file object name Name of the table group (default: “table”)

Returns

DataFrame DataFrame with columns from the HDF5 group

chemparseplot.parse.chemgp_hdf5.read_h5_grid(f: Any, name: str) → tuple[numpy.ndarray, numpy.ndarray | None, numpy.ndarray | None]

Read a 2D grid with optional axis ranges.

Parameters

f Open HDF5 file object name Name of the grid dataset

Returns

tuple (data, x_coords, y_coords) where x_coords and y_coords may be None if axis range attributes are not present

chemparseplot.parse.chemgp_hdf5.read_h5_path(f: Any, name: str) → dict[str, numpy.ndarray]

Read a path (ordered point sequence).

Parameters

f Open HDF5 file object name Name of the path dataset

Returns

dict Dictionary mapping coordinate names to arrays

chemparseplot.parse.chemgp_hdf5.read_h5_points(f: Any, name: str) → dict[str, numpy.ndarray]

Read a point set.

Parameters

f Open HDF5 file object name Name of the points dataset

Returns

dict Dictionary mapping coordinate names to arrays

chemparseplot.parse.chemgp_hdf5.read_h5_metadata(f: Any) → dict[str, Any]

Read root-level metadata attributes.

Parameters

f Open HDF5 file object

Returns

dict Dictionary of metadata attributes

chemparseplot.parse.chemgp_hdf5.validate_hdf5_structure(f: Any, required_groups: list[str] | None = None) → list[str]

Validate HDF5 file has expected structure.

Parameters

f Open HDF5 file object required_groups List of required group names (default: [“grids”, “table”])

Returns

list[str] List of missing groups (empty if all present)

Raises

ValueError If required groups are missing