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# -*- coding: utf-8 -*-
import os
import logging
import tempfile
import sys
try:
import dipy
dipy_available = True
except ImportError:
dipy_available = False
from trx.utils import split_name_with_gz
def get_trx_tmp_dir():
if os.getenv('TRX_TMPDIR') is not None:
if os.getenv('TRX_TMPDIR') == 'use_working_dir':
trx_tmp_dir = os.getcwd()
else:
trx_tmp_dir = os.getenv('TRX_TMPDIR')
else:
trx_tmp_dir = tempfile.gettempdir()
if sys.version_info[1] >= 10:
return tempfile.TemporaryDirectory(dir=trx_tmp_dir, prefix='trx_',
ignore_cleanup_errors=True)
else:
return tempfile.TemporaryDirectory(dir=trx_tmp_dir, prefix='trx_')
def load_sft_with_reference(filepath, reference=None,
bbox_check=True):
if not dipy_available:
logging.error('Dipy library is missing, cannot use functions related '
'to the StatefulTractogram.')
return None
from dipy.io.streamline import load_tractogram
# Force the usage of --reference for all file formats without an header
_, ext = os.path.splitext(filepath)
if ext == '.trk':
if reference is not None and reference != 'same':
logging.warning('Reference is discarded for this file format '
'{}.'.format(filepath))
sft = load_tractogram(filepath, 'same',
bbox_valid_check=bbox_check)
elif ext in ['.tck', '.fib', '.vtk', '.dpy']:
if reference is None or reference == 'same':
raise IOError('--reference is required for this file format '
'{}.'.format(filepath))
else:
sft = load_tractogram(filepath, reference,
bbox_valid_check=bbox_check)
else:
raise IOError('{} is an unsupported file format'.format(filepath))
return sft
def load(tractogram_filename, reference):
import trx.trx_file_memmap as tmm
in_ext = split_name_with_gz(tractogram_filename)[1]
if in_ext != '.trx' and not os.path.isdir(tractogram_filename):
tractogram_obj = load_sft_with_reference(tractogram_filename,
reference,
bbox_check=False)
else:
tractogram_obj = tmm.load(tractogram_filename)
return tractogram_obj
def save(tractogram_obj, tractogram_filename, bbox_valid_check=False):
if not dipy_available:
logging.error('Dipy library is missing, cannot use functions related '
'to the StatefulTractogram.')
return None
from dipy.io.stateful_tractogram import StatefulTractogram
from dipy.io.streamline import save_tractogram
import trx.trx_file_memmap as tmm
out_ext = split_name_with_gz(tractogram_filename)[1]
if out_ext != '.trx':
if not isinstance(tractogram_obj, StatefulTractogram):
tractogram_obj = tractogram_obj.to_sft()
save_tractogram(tractogram_obj, tractogram_filename,
bbox_valid_check=bbox_valid_check)
else:
if not isinstance(tractogram_obj, tmm.TrxFile):
tractogram_obj = tmm.TrxFile.from_sft(tractogram_obj)
tmm.save(tractogram_obj, tractogram_filename)
tractogram_obj.close()
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