.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "gallery/02_writing_files/p01_writing_simple_datasets.py" .. LINE NUMBERS ARE GIVEN BELOW. .. only:: html .. note:: :class: sphx-glr-download-link-note :ref:`Go to the end ` to download the full example code. .. rst-class:: sphx-glr-example-title .. _sphx_glr_gallery_02_writing_files_p01_writing_simple_datasets.py: Writing Simple Datasets ======================= Write 1D, 2D, and 3D arrays to PSI-style HDF5 or HDF4 files. This example demonstrates the basics of writing PSI-style HDF files using :func:`~psi_io.psi_io.write_hdf_data` for generic n-dimensional datasets, and :func:`~psi_io.psi_io.wrhdf_1d`, :func:`~psi_io.psi_io.wrhdf_2d`, :func:`~psi_io.psi_io.wrhdf_3d` for dimensionality-specific writing. .. GENERATED FROM PYTHON SOURCE LINES 12-18 .. code-block:: Python import tempfile from pathlib import Path import numpy as np from psi_io import write_hdf_data, wrhdf_1d, wrhdf_2d, wrhdf_3d, read_hdf_data .. GENERATED FROM PYTHON SOURCE LINES 19-23 Construct a simple 3D dataset representing a hypothetical scalar field on a rectilinear (r, θ, φ) grid. Following PSI's Fortran ordering convention, the data array is C-ordered as (nφ, nθ, nr) while the scales are supplied in physical dimension order (r, θ, φ): .. GENERATED FROM PYTHON SOURCE LINES 23-30 .. code-block:: Python nr, nt, np_ = 10, 20, 30 r = np.linspace(1.0, 5.0, nr, dtype=np.float32) t = np.linspace(0.0, np.pi, nt, dtype=np.float32) p = np.linspace(0.0, 2*np.pi, np_, dtype=np.float32) f3d = np.random.default_rng(0).random((np_, nt, nr)).astype(np.float32) .. GENERATED FROM PYTHON SOURCE LINES 31-33 Write the dataset to an HDF5 file with :func:`~psi_io.psi_io.write_hdf_data`. Scales are passed as positional arguments in physical dimension order (r, θ, φ): .. GENERATED FROM PYTHON SOURCE LINES 33-45 .. code-block:: Python with tempfile.TemporaryDirectory() as tmpdir: out_h5 = Path(tmpdir) / "output.h5" write_hdf_data(out_h5, f3d, r, t, p) f_back, r_back, t_back, p_back = read_hdf_data(out_h5) print(f"Data shape (read back) : {f_back.shape}") print(f"r scale : shape={r_back.shape}, range=[{r_back[0]:.2f}, {r_back[-1]:.2f}]") print(f"t scale : shape={t_back.shape}, range=[{t_back[0]:.4f}, {t_back[-1]:.4f}]") print(f"p scale : shape={p_back.shape}, range=[{p_back[0]:.4f}, {p_back[-1]:.4f}]") print(f"Round-trip exact match : {np.array_equal(f3d, f_back)}") .. rst-class:: sphx-glr-script-out .. code-block:: none Data shape (read back) : (30, 20, 10) r scale : shape=(10,), range=[1.00, 5.00] t scale : shape=(20,), range=[0.0000, 3.1416] p scale : shape=(30,), range=[0.0000, 6.2832] Round-trip exact match : True .. GENERATED FROM PYTHON SOURCE LINES 46-48 Writing to an HDF4 file uses the identical call – only the file extension changes. Dispatch to the correct backend is handled automatically based on the extension: .. GENERATED FROM PYTHON SOURCE LINES 48-57 .. code-block:: Python with tempfile.TemporaryDirectory() as tmpdir: out_hdf = Path(tmpdir) / "output.hdf" write_hdf_data(out_hdf, f3d, r, t, p) f_back_h4 = read_hdf_data(out_hdf, return_scales=False) print(f"HDF4 data shape (read back) : {f_back_h4.shape}") print(f"Round-trip exact match : {np.array_equal(f3d, f_back_h4)}") .. rst-class:: sphx-glr-script-out .. code-block:: none HDF4 data shape (read back) : (30, 20, 10) Round-trip exact match : True .. GENERATED FROM PYTHON SOURCE LINES 58-60 For 1D and 2D datasets the same conventions apply – the scale(s) precede the data in the positional argument list: .. GENERATED FROM PYTHON SOURCE LINES 60-76 .. code-block:: Python x = np.linspace(0.0, 2*np.pi, 64, dtype=np.float32) f1d = np.sin(x) y = np.linspace(0.0, np.pi, 32, dtype=np.float32) f2d = np.outer(np.sin(x), np.cos(y)).astype(np.float32) with tempfile.TemporaryDirectory() as tmpdir: write_hdf_data(Path(tmpdir) / "out1d.h5", f1d, x) write_hdf_data(Path(tmpdir) / "out2d.h5", f2d, x, y) r1d = read_hdf_data(Path(tmpdir) / "out1d.h5") r2d = read_hdf_data(Path(tmpdir) / "out2d.h5") print(f"1D : data={r1d[0].shape}, scale={r1d[1].shape}") print(f"2D : data={r2d[0].shape}, x={r2d[1].shape}, y={r2d[2].shape}") .. rst-class:: sphx-glr-script-out .. code-block:: none 1D : data=(64,), scale=(64,) 2D : data=(64, 32), x=(64,), y=(32,) .. GENERATED FROM PYTHON SOURCE LINES 77-87 The legacy dimension-specific writers (:func:`~psi_io.psi_io.wrhdf_1d`, :func:`~psi_io.psi_io.wrhdf_2d`, :func:`~psi_io.psi_io.wrhdf_3d`) provide a backward-compatible interface for existing PSI codes. .. attention:: The argument order of these writers differs from :func:`~psi_io.psi_io.write_hdf_data`: scales are interleaved between the filename and the data array (*filename*, *x*, [*y*, [*z*,]] *f*). They also default to ``sync_dtype=True``, which silently casts scale arrays to match the data dtype, and always write to PSI's standard dataset identifiers (``'Data-Set-2'`` for HDF4, ``'Data'`` for HDF5). .. GENERATED FROM PYTHON SOURCE LINES 87-96 .. code-block:: Python with tempfile.TemporaryDirectory() as tmpdir: wrhdf_1d(Path(tmpdir) / "legacy1d.h5", x, f1d) wrhdf_2d(Path(tmpdir) / "legacy2d.h5", x, y, f2d) wrhdf_3d(Path(tmpdir) / "legacy3d.h5", r, t, p, f3d) rl3d = read_hdf_data(Path(tmpdir) / "legacy3d.h5") print(f"Legacy 3D : data={rl3d[0].shape}, r={rl3d[1].shape}, t={rl3d[2].shape}, p={rl3d[3].shape}") print(f"Round-trip exact match : {np.array_equal(f3d, rl3d[0])}") .. rst-class:: sphx-glr-script-out .. code-block:: none Legacy 3D : data=(30, 20, 10), r=(10,), t=(20,), p=(30,) Round-trip exact match : True .. rst-class:: sphx-glr-timing **Total running time of the script:** (0 minutes 0.017 seconds) .. _sphx_glr_download_gallery_02_writing_files_p01_writing_simple_datasets.py: .. only:: html .. container:: sphx-glr-footer sphx-glr-footer-example .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: p01_writing_simple_datasets.ipynb ` .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: p01_writing_simple_datasets.py ` .. container:: sphx-glr-download sphx-glr-download-zip :download:`Download zipped: p01_writing_simple_datasets.zip ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_