"""
High-level read/write functions for several formats.
"""
# Author: Oualid Benkarim <oualid.benkarim@mcgill.ca>
# License: BSD 3 clause
import tempfile
import gzip
import os
from vtk import (vtkPLYReader, vtkPLYWriter, vtkXMLPolyDataReader,
vtkXMLPolyDataWriter, vtkPolyDataReader, vtkPolyDataWriter)
from ..vtk_interface.io_support import (vtkFSReader, vtkFSWriter,
vtkGIFTIReader, vtkGIFTIWriter)
from ..vtk_interface.pipeline import serial_connect, get_output
from ..vtk_interface.decorators import wrap_output
# 'fs' type for FreeSurfer geometry data (also read FreeSurfer ascii as .asc)
supported_types = ['ply', 'obj', 'vtp', 'vtk', 'asc', 'fs', 'gii']
supported_formats = ['binary', 'ascii']
@wrap_output
def _select_reader(itype):
if itype == 'ply':
reader = vtkPLYReader()
# elif itype == 'obj':
# reader = vtkOBJReader()
elif itype == 'vtp':
reader = vtkXMLPolyDataReader()
elif itype == 'vtk':
reader = vtkPolyDataReader()
elif itype in ['asc', 'fs']:
reader = vtkFSReader()
if itype == 'asc':
reader.SetFileTypeToASCII()
elif itype == 'gii':
reader = vtkGIFTIReader()
else:
raise TypeError('Unknown input type \'{0}\'.'.format(itype))
return reader
@wrap_output
def _select_writer(otype):
if otype == 'ply':
writer = vtkPLYWriter()
# elif otype == 'obj':
# writer = vtkOBJWriter()
elif otype == 'vtp':
writer = vtkXMLPolyDataWriter()
elif otype == 'vtk':
writer = vtkPolyDataWriter()
elif otype in ['asc', 'fs']:
writer = vtkFSWriter()
elif otype == 'gii':
writer = vtkGIFTIWriter()
else:
raise TypeError('Unknown output type \'{0}\'.'.format(otype))
return writer
def _uncompress(ipth, opth, block_size=65536):
"""Uncompresses files. Currently only supports gzip.
Parameters
----------
ipth : str
Input filename.
opth : str
Output filename.
block_size : int, optional
Size of blocks of the input that are read at a time, by default 65536
"""
if ipth.split('.')[-1] == 'gz':
with gzip.open(ipth, 'rb') as i_file, open(opth, 'wb') as o_file:
while True:
block = i_file.read(block_size)
if not block:
break
else:
o_file.write(block)
else:
ValueError('Unknown file format.')
[docs]def read_surface(ipth, itype=None, return_data=True, update=True):
"""Read surface data.
See `itype` for supported file types.
Parameters
----------
ipth : str
Input filename.
itype : {'ply', 'vtp', 'vtk', 'fs', 'asc', 'gii'}, optional
Input file type. If None, it is deduced from `ipth`. Files compressed
with gzip (.gz) are also supported. Default is None.
return_data : bool, optional
Whether to return data instead of filter. Default is False
update : bool, optional
Whether to update filter When return_data=True, filter is
automatically updated. Default is True.
Returns
-------
output : BSAlgorithm or BSPolyData
Surface as a filter or BSPolyData.
Notes
-----
Function can read FreeSurfer geometry data in binary ('fs') and ascii
('asc') format. Gifti surfaces can also be loaded if nibabel is installed.
See Also
--------
:func:`write_surface`
"""
if itype is None:
itype = ipth.split('.')[-1]
if itype == 'gz':
extension = ipth.split('.')[-2]
tmp = tempfile.NamedTemporaryFile(suffix='.' + extension, delete=False)
tmp_name = tmp.name
# Close and reopen because windows throws permission errors when both
# reading and writing.
tmp.close()
_uncompress(ipth, tmp_name)
result = read_surface(tmp_name, extension, return_data=return_data,
update=update)
os.unlink(tmp_name)
return result
reader = _select_reader(itype)
reader.filename = ipth
return get_output(reader, update=update, as_data=return_data)
[docs]def write_surface(ifilter, opth, oformat=None, otype=None):
"""Write surface data.
See `otype` for supported file types.
Parameters
----------
ifilter : BSAlgorithm or BSDataObject
Input filter or data.
opth : str
Output filename.
oformat : {'ascii', 'binary'}, optional
File format. Defaults to writer's default format.
Only used when writer accepts format. Default is None.
otype : {'ply', 'vtp', 'vtk', 'fs', 'asc', 'gii'}, optional
File type. If None, type is deduced from `opth`. Default is None.
Notes
-----
Function can save data in FreeSurfer binary ('fs') and ascii ('asc')
format. Gifti surfaces can also be saved if nibabel is installed.
See Also
--------
:func:`read_surface`
"""
if otype is None:
otype = opth.split('.')[-1]
writer = _select_writer(otype)
writer.filename = opth
if otype not in ['vtp', 'tri', 'gii', 'obj']:
if oformat == 'ascii' or otype == 'asc':
writer.SetFileTypeToASCII()
else:
writer.SetFileTypeToBinary()
serial_connect(ifilter, writer, update=True, as_data=False, port=None)
def convert_surface(ipth, opth, itype=None, otype=None, oformat=None):
"""Convert between file types.
Parameters
----------
ipth : str
Input filename.
opth : str
Output filename.
itype : str, optional
Input file type. If None, type is deduced from input filename's
extension. Default is None.
otype : str, optional
Output file type. If None, type is deduced from output filename's
extension. Default is None.
oformat : {'ascii', 'binary'}
Output file format. Defaults to writer's default format.
Only used when writer accepts format. Default is None.
"""
reader = read_surface(ipth, itype=itype, return_data=False, update=False)
write_surface(reader, opth, oformat=oformat, otype=otype)