psi-io 1.0.0__tar.gz

psi_io-1.0.0/LICENSE.txt

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psi_io-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: psi-io
+Version: 1.0.0
+Summary: Readers and writers for data formats used by Predictive Science Inc.
+Author: Ronald M. Caplan, Ryder Davidson, Cooper Downs
+Author-email: "Predictive Science Inc." <webmaster@predsci.com>
+License-Expression: Apache-2.0
+Project-URL: Homepage, https://pypi.org/project/psi-io
+Project-URL: Repository, https://github.com/predsci/psi-io
+Keywords: solar physics,space physics,heliophysics,solar,sun,science,magnetohydrodynamic,mas,predsci,psi
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Classifier: Topic :: Scientific/Engineering :: Astronomy
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE.txt
+Requires-Dist: h5py
+Provides-Extra: hdf4
+Requires-Dist: pyhdf; extra == "hdf4"
+Provides-Extra: interp
+Requires-Dist: scipy; extra == "interp"
+Provides-Extra: all
+Requires-Dist: psi-io[hdf4,interp]; extra == "all"
+Dynamic: license-file
+
+# psi-io
+
+---
+
+Python utilities for interacting with scientific data formats used by 
+Predictive Science Inc. (PSI).
+
+Primarily this includes the HDF file format used by several of PSI's
+scientific codes for simulating the solar surface, solar corona, and inner 
+heliosphere, including:
+
+- [MAS](https://www.predsci.com/mas/)
+- [POT3D](https://github.com/predsci/POT3D)
+- [HipFT](https://github.com/predsci/hipft)
+
+
+## Installation
+
+---
+
+```bash
+pip install psi-io
+```
+
+
+## Usage
+
+---
+
+### Basic Reading
+Read the entire dataset from a 3D Br HDF file output by a POT3D solution (spherical r,t,p):
+```python
+import psi_io
+r, t, p, br = psi_io.rdhdf_3d('br.h5')
+```
+Here `r`, `t`, and `p` are the 1D coordinate arrays. `br` is the 3D data array.
+
+There are equivalent routines `rdhdf_1d`, and `rdhdf_2d` for 1D and 2D HDF files.
+
+### Optimized Reading and Interpolation
+One can also read a specific subset of the datasets from disk.
+
+Extract a wedge of data that just spans a range of interest:
+
+```python
+r_range = [1.0, 1.2]
+t_range = [0.5, 1.0]
+p_range = [2.0, 3.0]
+brx, rx, tx, px = psi_io.read_hdf_by_value(r_range, t_range, p_range, ifile='br.h5')
+```
+
+Get 2D t,p slice of data interpolated to a specific radius (e.g. 2.0 Rs).
+```python
+br_slice, t, p = psi_io.np_interpolate_slice_from_hdf(2.5, None, None, ifile='br.h5')
+```
+
+Interpolate the data to specific r, t, p positions (supplied as 1D, 2D, or 3D arrays).
+```python
+import numpy as np
+r_vals = np.array([1.0, 1.1])
+t_vals = np.array([0.7, 0.7])
+t_vals = np.array([1.5, 1.5])
+br_vals = psi_io.interpolate_positions_from_hdf(r_vals, t_vals, t_vals, ifile='br.h5')
+```
+
+### Writing
+Write a new 3D file:
+```python
+psi_io.wrhdf_3d('br_mod.h5', r, t, p, br_mod)
+```
+As before `r`, `t`, and `p` are the 1D coordinate arrays. `br_mod` is the 3D data array.
+
+There are equivalent routines `wrhdf_1d`, and `wrhdf_2d` for 1D and 2D HDF files.
+
+## Requirements
+
+---
+
+This package requires the python HDF5 interface, `h5py`, to work with `.h5` files. 
+
+If you are working with HDF4 `.hdf` files then you must also have the optional
+`pyhdf` HDF4 python interface installed.
+
+Because these packages require the underlying C HDF libraries to be installed, 
+we generally recommend using conda to install these dependencies. This often
+makes life much easier than installing from source:
+
+for HDF5
+```bash
+conda install h5py
+```
+for HDF4
+```bash
+conda install pyhdf
+```
+
+To isolate these to a specific environment, see `environment.yml`
+
+## Disclaimer
+
+---
+
+This package is currently in a pre-release state as we transition from having
+copies of these routines everywhere to centralizing them in a pip-installable
+Python package. Although the basic readers are unlikely to change for historical
+compatibility reasons, some of the newer things like optimized i/o and object 
+oriented hdf reader interface may be more likely to evolve quickly. 
+
+Automated tests and basic documentation are coming soon!

psi_io-1.0.0/README.md

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+# psi-io
+
+---
+
+Python utilities for interacting with scientific data formats used by 
+Predictive Science Inc. (PSI).
+
+Primarily this includes the HDF file format used by several of PSI's
+scientific codes for simulating the solar surface, solar corona, and inner 
+heliosphere, including:
+
+- [MAS](https://www.predsci.com/mas/)
+- [POT3D](https://github.com/predsci/POT3D)
+- [HipFT](https://github.com/predsci/hipft)
+
+
+## Installation
+
+---
+
+```bash
+pip install psi-io
+```
+
+
+## Usage
+
+---
+
+### Basic Reading
+Read the entire dataset from a 3D Br HDF file output by a POT3D solution (spherical r,t,p):
+```python
+import psi_io
+r, t, p, br = psi_io.rdhdf_3d('br.h5')
+```
+Here `r`, `t`, and `p` are the 1D coordinate arrays. `br` is the 3D data array.
+
+There are equivalent routines `rdhdf_1d`, and `rdhdf_2d` for 1D and 2D HDF files.
+
+### Optimized Reading and Interpolation
+One can also read a specific subset of the datasets from disk.
+
+Extract a wedge of data that just spans a range of interest:
+
+```python
+r_range = [1.0, 1.2]
+t_range = [0.5, 1.0]
+p_range = [2.0, 3.0]
+brx, rx, tx, px = psi_io.read_hdf_by_value(r_range, t_range, p_range, ifile='br.h5')
+```
+
+Get 2D t,p slice of data interpolated to a specific radius (e.g. 2.0 Rs).
+```python
+br_slice, t, p = psi_io.np_interpolate_slice_from_hdf(2.5, None, None, ifile='br.h5')
+```
+
+Interpolate the data to specific r, t, p positions (supplied as 1D, 2D, or 3D arrays).
+```python
+import numpy as np
+r_vals = np.array([1.0, 1.1])
+t_vals = np.array([0.7, 0.7])
+t_vals = np.array([1.5, 1.5])
+br_vals = psi_io.interpolate_positions_from_hdf(r_vals, t_vals, t_vals, ifile='br.h5')
+```
+
+### Writing
+Write a new 3D file:
+```python
+psi_io.wrhdf_3d('br_mod.h5', r, t, p, br_mod)
+```
+As before `r`, `t`, and `p` are the 1D coordinate arrays. `br_mod` is the 3D data array.
+
+There are equivalent routines `wrhdf_1d`, and `wrhdf_2d` for 1D and 2D HDF files.
+
+## Requirements
+
+---
+
+This package requires the python HDF5 interface, `h5py`, to work with `.h5` files. 
+
+If you are working with HDF4 `.hdf` files then you must also have the optional
+`pyhdf` HDF4 python interface installed.
+
+Because these packages require the underlying C HDF libraries to be installed, 
+we generally recommend using conda to install these dependencies. This often
+makes life much easier than installing from source:
+
+for HDF5
+```bash
+conda install h5py
+```
+for HDF4
+```bash
+conda install pyhdf
+```
+
+To isolate these to a specific environment, see `environment.yml`
+
+## Disclaimer
+
+---
+
+This package is currently in a pre-release state as we transition from having
+copies of these routines everywhere to centralizing them in a pip-installable
+Python package. Although the basic readers are unlikely to change for historical
+compatibility reasons, some of the newer things like optimized i/o and object 
+oriented hdf reader interface may be more likely to evolve quickly. 
+
+Automated tests and basic documentation are coming soon!

psi_io-1.0.0/psi_io/__init__.py

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+from .psi_io import *