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Jan Caron authoredAdded environment.yml and requirement.txt. GitLab should now produce html coverage artifacts. io_vectordata: now warns if grid spacing is not equal in all directions.
Jan Caron authoredAdded environment.yml and requirement.txt. GitLab should now produce html coverage artifacts. io_vectordata: now warns if grid spacing is not equal in all directions.
io_vectordata.py 11.47 KiB
# -*- coding: utf-8 -*-
# Copyright 2016 by Forschungszentrum Juelich GmbH
# Author: J. Caron
#
"""IO functionality for VectorData objects."""
import logging
import os
import numpy as np
from ..fielddata import VectorData
__all__ = ['load_vectordata']
_log = logging.getLogger(__name__)
def load_vectordata(filename, a=None, **kwargs):
"""Load supported file into a :class:`~pyramid.fielddata.VectorData` instance.
The function loads the file according to the extension:
- hdf5 for HDF5.
- EMD Electron Microscopy Dataset format (also HDF5).
- llg format.
- ovf format.
- npy or npz for numpy formats.
Any extra keyword is passed to the corresponsing reader. For
available options see their individual documentation.
Parameters
----------
filename: str
The filename to be loaded.
a: float or None, optional
If the grid spacing is not None, it will override a possibly loaded value from the files.
Returns
-------
vectordata : :class:`~.VectorData`
A :class:`~.VectorData` object containing the loaded data.
"""
_log.debug('Calling load_vectordata')
extension = os.path.splitext(filename)[1]
# Load from llg-files:
if extension in ['.llg', '.txt']:
return _load_from_llg(filename, a)
# Load from ovf-files:
if extension in ['.ovf', '.omf', '.ohf', 'obf']:
return _load_from_ovf(filename, a)
# Load from npy-files:
elif extension in ['.npy', '.npz']:
return _load_from_npy(filename, a, **kwargs)
# Load with HyperSpy:
else:
if extension == '':
filename = '{}.hdf5'.format(filename) # Default!
return _load_from_hs(filename, a, **kwargs)
def _load_from_llg(filename, a):
_log.debug('Calling load_from_llg')
SCALE = 1.0E-9 / 1.0E-2 # From cm to nm
data = np.genfromtxt(filename, skip_header=2)
dim = tuple(np.genfromtxt(filename, dtype=int, skip_header=1, skip_footer=len(data[:, 0])))
if a is None:
a = (data[1, 0] - data[0, 0]) / SCALE
field = data[:, 3:6].T.reshape((3,) + dim)
return VectorData(a, field)
def _load_from_ovf(filename, a):
_log.debug('Calling load_from_ovf')
with open(filename, 'rb') as mag_file:
# TODO: Also handle OOMF 1.0? See later TODOs...
line = mag_file.readline()
assert line.startswith(b'# OOMMF') # File has OVF format!
read_header, read_data = False, False
header = {'version': line.split()[-1].decode('utf-8')}
x_mag, y_mag, z_mag = [], [], []
data_mode = None
while True:
# Read in additional info:
if not read_header and not read_data:
line = mag_file.readline()
if line == b'':
break # End of file is reached!
if line.startswith(b'# Segment count'):
header['segment_count'] = int(line.split()[-1])
# TODO: currently new segments overwrite last ones. read more than one? return
# TODO: navigation axis (segment count > 1) if implemented in HyperSpy reader!
elif line.startswith(b'# Begin: Header'):
read_header = True
elif line.startswith(b'# Begin: Data'):
read_data = True
data_mode = ' '.join(line.decode('utf-8').split()[3:])
assert data_mode in ['text', 'Text', 'Binary 4', 'Binary 8'], \
'Data mode {} is currently not supported by this reader!'.format(data_mode)
assert header.get('meshtype') == 'rectangular', \
'Only rectangular grids can be currently read!'
# Read header line by line:
elif read_header:
line = mag_file.readline()
if line.startswith(b'# End: Header'): # Header is done:
read_header = False
continue
line = line.decode('utf-8') # Decode to use strings here!
line_list = line.split()
if '##' in line_list: # Strip trailing comments:
del line_list[line_list.index('##'):]
if len(line_list) <= 1: # Just '#' or empty line:
continue
key, value = line_list[1].strip(':'), ' '.join(line_list[2:])
if key not in header: # Add new key, value pair if not existant:
header[key] = value
elif key == 'Desc': # Can go over several lines:
header['Desc'] = ' '.join([header['Desc'], value])
# Read in data:
# TODO: Make it work for both text and binary! Put into HyperSpy?
# TODO: http://math.nist.gov/oommf/doc/userguide11b2/userguide/vectorfieldformat.html
# TODO: http://math.nist.gov/oommf/doc/userguide12a5/userguide/OVF_2.0_format.html
# TODO: 1.0 and 2.0 DIFFER (little and big endian in binary data -.-)
elif read_data: # Currently in a data block:
if data_mode in ['text', 'Text']: # Read data as text, line by line:
line = mag_file.readline()
if line.startswith(b'# End: Data'): # Header is done:
read_data = False
else:
x, y, z = [float(i) for i in line.split()]
x_mag.append(x)
y_mag.append(y)
z_mag.append(z)
elif 'Binary' in data_mode: # Read data as binary, all bytes at the same time:
count = int(data_mode.split()[-1])
if header['version'] == '1.0': # Big endian:
dtype = '>f{}'.format(count)
elif header['version'] == '2.0': # Little endian:
dtype = '<f{}'.format(count)
dim = (int(header['znodes']), int(header['ynodes']), int(header['xnodes']))
test = np.fromfile(mag_file, dtype=dtype, count=1)
if count == 4: # Binary 4:
assert test == 1234567.0, 'Wrong test bytes!'
elif count == 8: # Binary 8:
assert test == 123456789012345.0, 'Wrong test bytes!'
data = np.fromfile(mag_file, dtype=dtype, count=3*np.prod(dim))
x_mag, y_mag, z_mag = data[0::3], data[1::3], data[2::3]
read_data = False # Stop reading data and search for new Segments (if any).
# Format after reading:
dim = (int(header['znodes']), int(header['ynodes']), int(header['xnodes']))
x_mag = np.asarray(x_mag).reshape(dim)
y_mag = np.asarray(y_mag).reshape(dim)
z_mag = np.asarray(z_mag).reshape(dim)
field = np.asarray((x_mag, y_mag, z_mag)) * float(header.get('valuemultiplier', 1))
if a is None:
# TODO: If transferred to HyperSpy, this has to stay in Pyramid reader!
if not header.get('xstepsize') == header.get('ystepsize') == header.get('zstepsize'):
_log.warning('Grid spacing is not equal in x, y and z (x will be used)!')
a = float(header.get('xstepsize', 1.))
meshunit = header.get('meshunit', 'nm')
a *= {'m': 1e9, 'mm': 1e6, 'µm': 1e3, 'nm': 1}[meshunit] # Conversion to nm
return VectorData(a, field)
def _load_from_npy(filename, a, **kwargs):
_log.debug('Calling load_from_npy')
if a is None:
a = 1. # Use default!
return VectorData(a, np.load(filename, **kwargs))
def _load_from_hs(filename, a, **kwargs):
_log.debug('Calling load_from_hs')
try:
import hyperspy.api as hs
except ImportError:
_log.error('This method recquires the hyperspy package!')
return
vectordata = VectorData.from_signal(hs.load(filename, **kwargs))
if a is not None:
vectordata.a = a
return vectordata
def save_vectordata(vectordata, filename, **kwargs):
"""%s"""
_log.debug('Calling save_vectordata')
extension = os.path.splitext(filename)[1]
if extension == '.llg': # Save to llg-files:
_save_to_llg(vectordata, filename)
elif extension == '.ovf': # Save to ovf-files:
_save_to_ovf(vectordata, filename, **kwargs)
elif extension in ['.npy', '.npz']: # Save to npy-files:
_save_to_npy(vectordata, filename, **kwargs)
else: # Try HyperSpy:
_save_to_hs(vectordata, filename, **kwargs)
save_vectordata.__doc__ %= VectorData.save.__doc__
def _save_to_llg(vectordata, filename):
_log.debug('Calling save_to_llg')
dim = vectordata.dim
SCALE = 1.0E-9 / 1.0E-2 # from nm to cm
# Create 3D meshgrid and reshape it and the field into a list where x varies first:
zz, yy, xx = vectordata.a * SCALE * (np.indices(dim) + 0.5).reshape(3, -1)
x_vec, y_vec, z_vec = vectordata.field.reshape(3, -1)
data = np.array([xx, yy, zz, x_vec, y_vec, z_vec]).T
# Save data to file:
with open(filename, 'w') as mag_file:
mag_file.write('LLGFileCreator: {:s}\n'.format(filename))
mag_file.write(' {:d} {:d} {:d}\n'.format(*dim))
mag_file.writelines('\n'.join(' '.join('{:7.6e}'.format(cell)
for cell in row) for row in data))
def _save_to_ovf(vectordata, filename):
_log.debug('Calling save_to_ovf')
with open(filename, 'w') as mag_file:
mag_file.write('# OOMMF OVF 2.0\n')
mag_file.write('# Segment count: 1\n')
mag_file.write('# Begin: Segment\n')
# Write Header:
mag_file.write('# Begin: Header\n')
name = os.path.split(os.path.split(filename)[1])
mag_file.write('# Title: PYRAMID-VECTORDATA {}\n'.format(name))
mag_file.write('# meshtype: rectangular\n')
mag_file.write('# meshunit: nm\n')
mag_file.write('# valueunit: A/m\n')
mag_file.write('# valuemultiplier: 1.\n')
mag_file.write('# xmin: 0.\n')
mag_file.write('# ymin: 0.\n')
mag_file.write('# zmin: 0.\n')
mag_file.write('# xmax: {}\n'.format(vectordata.a * vectordata.dim[2]))
mag_file.write('# ymax: {}\n'.format(vectordata.a * vectordata.dim[1]))
mag_file.write('# zmax: {}\n'.format(vectordata.a * vectordata.dim[0]))
mag_file.write('# xbase: 0.\n')
mag_file.write('# ybase: 0.\n')
mag_file.write('# zbase: 0.\n')
mag_file.write('# xstepsize: {}\n'.format(vectordata.a))
mag_file.write('# ystepsize: {}\n'.format(vectordata.a))
mag_file.write('# zstepsize: {}\n'.format(vectordata.a))
mag_file.write('# xnodes: {}\n'.format(vectordata.dim[2]))
mag_file.write('# ynodes: {}\n'.format(vectordata.dim[1]))
mag_file.write('# znodes: {}\n'.format(vectordata.dim[0]))
mag_file.write('# End: Header\n')
# Write data:
mag_file.write('# Begin: Data Text\n')
x_mag, y_mag, z_mag = vectordata.field
x_mag = x_mag.ravel()
y_mag = y_mag.ravel()
z_mag = z_mag.ravel()
for i in range(np.prod(vectordata.dim)):
mag_file.write('{:g} {:g} {:g}\n'.format(x_mag[i], y_mag[i], z_mag[i]))
mag_file.write('# End: Data Text\n')
mag_file.write('# End: Segment\n')
def _save_to_npy(vectordata, filename, **kwargs):
_log.debug('Calling save_to_npy')
np.save(filename, vectordata.field, **kwargs)
def _save_to_hs(vectordata, filename, **kwargs):
_log.debug('Calling save_to_hyperspy')
vectordata.to_signal().save(filename, **kwargs)