# -*- coding: utf-8 -*-
################################################################
# The contents of this file are subject to the BSD 3Clause (New) License
# you may not use this file except in
# compliance with the License. You may obtain a copy of the License at
# http://directory.fsf.org/wiki/License:BSD_3Clause
# Software distributed under the License is distributed on an "AS IS"
# basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the
# License for the specific language governing rights and limitations
# under the License.
# The Original Code is part of the PyRadi toolkit.
# The Initial Developer of the Original Code is CJ Willers,
# Portions created by CJ Willers are Copyright (C) 2006-2012
# All Rights Reserved.
# Contributor(s): MS Willers.
################################################################
"""
This module provides functions for file input/output. These are all wrapper
functions, based on existing functions in other Python classes. Functions are
provided to save a two-dimensional array to a text file, load selected columns
of data from a text file, load a column header line, compact strings to include
only legal filename characters, and a function from the Python Cookbook to
recursively match filename patterns.
See the __main__ function for examples of use.
This package was partly developed to provide additional material in support of students
and readers of the book Electro-Optical System Analysis and Design: A Radiometry
Perspective, Cornelius J. Willers, ISBN 9780819495693, SPIE Monograph Volume
PM236, SPIE Press, 2013. http://spie.org/x648.html?product_id=2021423&origin_id=x646
"""
__version__ = '0.1.0'
__author__='pyradi team'
__all__ = [
'open_HDF', 'erase_create_HDF', 'get_HDF_DS',
'print_HDF5_text', 'print_HDF5_dataset_value',
'get_HDF_branches', 'plotHDF5Bitmaps', 'plotHDF5Images', 'plotHDF5Histograms',
]
import os
import numpy as np
import h5py
from skimage.io import imsave
######################################################################################
[docs]
def open_HDF(filename, mode='r'):
"""Open and return an HDF5 file with the given filename.
See https://github.com/NelisW/pyradi/blob/master/pyradi/hdf5-as-data-format.md
for more information on using HDF5 as a data structure.
Default open mode is read, cam be overridden by any of these:
'r', 'r+', 'w', 'w-'/'x', 'a'
https://h5py.readthedocs.io/en/stable/quick.html
https://h5py.readthedocs.io/en/stable/high/file.html#opening-creating-files
Args:
| filename (string): name of the file to be opened
Returns:
| HDF5 file.
Raises:
| No exception is raised.
Author: CJ Willers
"""
f = h5py.File(filename,mode)
return f
######################################################################################
[docs]
def erase_create_HDF(filename):
"""Create and return a new HDS5 file with the given filename, erase the file if existing.
See https://github.com/NelisW/pyradi/blob/master/pyradi/hdf5-as-data-format.md
for more information on using HDF5 as a data structure.
open for writing, truncate if exists
https://h5py.readthedocs.io/en/stable/high/file.html#opening-creating-files
Args:
| filename (string): name of the file to be created
Returns:
| HDF5 file.
Raises:
| No exception is raised.
Author: CJ Willers
"""
if os.path.isfile(filename):
os.remove(filename)
f = h5py.File(filename,'w')
return f
######################################################################################
[docs]
def get_HDF_DS(hdf5File, path):
"""Check to see if a path is present in an HDF5 file and then return the dataset.
Args:
| hdf5File (string): HDF5 file to be read
| path (string): path to the dataset
Returns:
| HDF5 contents along the path, or None.
Raises:
| No exception is raised.
Author: CJ Willers
"""
if path in hdf5File:
rtn = hdf5File[path]
else:
rtn = None
return rtn
######################################################################################
[docs]
def print_HDF5_text(vartext):
"""Prints text in visiting algorithm in HDF5 file.
See https://github.com/NelisW/pyradi/blob/master/pyradi/hdf5-as-data-format.md
for more information on using HDF5 as a data structure.
Args:
| vartext (string): string to be printed
Returns:
| None.
Raises:
| No exception is raised.
Author: CJ Willers
"""
print(vartext)
######################################################################################
[docs]
def print_HDF5_dataset_value(var, obj):
"""Prints a data set in visiting algorithm in HDF5 file.
See https://github.com/NelisW/pyradi/blob/master/pyradi/hdf5-as-data-format.md
for more information on using HDF5 as a data structure.
Args:
| var (string): path to a dataset
| obj (h5py dataset): dataset to be printed
Returns:
| None.
Raises:
| No exception is raised.
Author: CJ Willers
"""
if isinstance(obj.file[var], h5py.Dataset):
print(var, obj.file[var].name)
######################################################################################
[docs]
def get_HDF_branches(hdf5File):
"""Print list of all the branches in the file.
See https://github.com/NelisW/pyradi/blob/master/pyradi/hdf5-as-data-format.md
for more information on using HDF5 as a data structure.
Note: this function passes itself as the h5py visitor callback. h5py then
calls get_HDF_branches(name_string) for each item in the hierarchy. Since
a string has no .visit() method this raises AttributeError for any non-empty
file. The behaviour is preserved unchanged (calling on an empty file returns
None safely).
Args:
| hdf5File (H5py file): the open HDF5 file to inspect
Returns:
| None (h5py visit() always returns None when the callback never
| returns a non-None value).
Raises:
| AttributeError: for any non-empty HDF5 file (see note above).
Author: CJ Willers
"""
return hdf5File.visit(get_HDF_branches)
######################################################################################
[docs]
def plotHDF5Bitmaps(hfd5f, prefix, pformat='png', lstimgs=None, debug=False):
"""Plot arrays in the HFD5 as scaled bitmap images.
See https://github.com/NelisW/pyradi/blob/master/pyradi/hdf5-as-data-format.md
for more information on using HDF5 as a data structure.
Retain zero in the array as black in the image, only scale the max value to 255
Args:
| hfd5f (H5py file): the file to be opened
| prefix (string): prefix to be prepended to filename
| pformat (string): type of file to be created png/jpeg
| lstimgs ([string]): list of paths to image in the HFD5 file
Returns:
| Nothing.
Raises:
| No exception is raised.
Author: CJ Willers
"""
from . import ryplot
for lstimg in lstimgs:
arr = hfd5f[f'{lstimg}'][...]
if debug:
print(f'data set {lstimg} has shape {arr.shape} ')
# if arr.shape is not ():
if arr.shape != ():
if np.max(arr) != 0.:
arr = 255 * arr/np.max(arr)
imsave(f"{prefix}-{lstimg.replace('/', '-')}.{pformat}", arr.astype(np.uint8))
######################################################################################
[docs]
def plotHDF5Images(hfd5f, prefix, colormap=None, cbarshow=True, lstimgs=None, logscale=False, debug=False):
"""Plot images contained in hfd5f with colour map to show magnitude.
See https://github.com/NelisW/pyradi/blob/master/pyradi/hdf5-as-data-format.md
for more information on using HDF5 as a data structure.
https://scipy-cookbook.readthedocs.io/items/Matplotlib_Show_colormaps.html
Args:
| hfd5f (H5py file): the file to be opened
| prefix (string): prefix to be prepended to filename
| colormap (Matplotlib colour map): colour map to be used in plot
| cbarshow (boolean): indicate if colour bar must be shown
| lstimgs ([string]): list of paths to image in the HFD5 file
| logscale (boolean): True if display must be on log scale
Returns:
| Nothing.
Raises:
| No exception is raised.
Author: CJ Willers
"""
from matplotlib import cm as mcm # lazy -- only needed when this function is called
if colormap is None:
colormap = mcm.jet
from . import ryplot
for lstimg in lstimgs:
arr = hfd5f[f'{lstimg}'][...]
if debug:
print(f'data set {lstimg} has shape {arr.shape} ')
# if arr.shape is not ():
if arr.shape != ():
if logscale:
filename = f"{prefix}-plot-{lstimg.replace('/', '-')}-log.png"
with ryplot.savePlot(1,1,1,figsize=(8,8), saveName=[filename]) as p:
p.showImage(1, np.log10(arr), ptitle=lstimg, cmap=colormap, cbarshow=cbarshow);
else:
filename = f"{prefix}-plot-{lstimg.replace('/', '-')}.png"
with ryplot.savePlot(1,1,1,figsize=(8,8), saveName=[filename]) as p:
p.showImage(1, arr, ptitle=lstimg, cmap=colormap, cbarshow=cbarshow);
######################################################################################
[docs]
def plotHDF5Histograms(hfd5f, prefix, format='png', lstimgs=None, bins=50):
"""Plot histograms of images contained in hfd5f
See https://github.com/NelisW/pyradi/blob/master/pyradi/hdf5-as-data-format.md
for more information on using HDF5 as a data structure.
Retain zero in the array as black in the image, only scale the max value to 255
Args:
| hfd5f (H5py file): the file to be opened
| prefix (string): prefix to be prepended to filename
| format (string): type of file to be created png/jpeg
| lstimgs ([string]): list of paths to image in the HFD5 file
| bins ([int]): Number of bins to be used in histogram
Returns:
| Nothing.
Raises:
| No exception is raised.
Author: CJ Willers
"""
from . import ryplot
for lstimg in lstimgs:
arr = hfd5f[f'{lstimg}'][...]
his, bin = np.histogram(arr,bins=bins)
filename = f"{prefix}-hist-plot-{lstimg.replace('/', '-')}.{format}"
with ryplot.savePlot(1,1,1,figsize=(8,4), saveName=[filename]) as p:
p.plot(1, (bin[1:]+bin[:-1])/2, his, f'{lstimg}, {bins} bins', 'Magnitude','Counts / bin',maxNX=5)
################################################################
################################################################
##
##
if __name__ == '__main__':
pass
