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# -*- coding: utf-8 -*-
from copy import deepcopy
import os
import psutil
from tempfile import TemporaryDirectory
import zipfile
import pytest
import numpy as np
from numpy.testing import assert_allclose
try:
from dipy.io.streamline import save_tractogram, load_tractogram
dipy_available = True
except ImportError:
dipy_available = False
import trx.trx_file_memmap as tmm
from trx.trx_file_memmap import TrxFile
from trx.io import load, save, get_trx_tmp_dir
from trx.fetcher import (get_testing_files_dict,
fetch_data, get_home)
fetch_data(get_testing_files_dict(), keys=['gold_standard.zip'])
@pytest.mark.parametrize("path", [("gs.trk"), ("gs.tck"),
("gs.vtk")])
@pytest.mark.skipif(not dipy_available, reason='Dipy is not installed.')
def test_seq_ops_sft(path):
with TemporaryDirectory() as tmp_dir:
gs_dir = os.path.join(get_home(), 'gold_standard')
path = os.path.join(tmp_dir, path)
obj = load(os.path.join(gs_dir, 'gs.trx'),
os.path.join(gs_dir, 'gs.nii'))
sft_1 = obj.to_sft()
save_tractogram(sft_1, path)
obj.close()
save_tractogram(sft_1, os.path.join(tmp_dir, 'tmp.trk'))
sft_2 = load_tractogram(os.path.join(tmp_dir, 'tmp.trk'), 'same')
def test_seq_ops_trx():
with TemporaryDirectory() as tmp_dir:
gs_dir = os.path.join(get_home(), 'gold_standard')
path = os.path.join(gs_dir, 'gs.trx')
trx_1 = tmm.load(path)
tmm.save(trx_1, os.path.join(tmp_dir, 'tmp.trx'))
trx_1.close()
trx_2 = tmm.load(os.path.join(tmp_dir, 'tmp.trx'))
trx_2.close()
@pytest.mark.parametrize("path", [("gs.trx"), ("gs.trk"), ("gs.tck"),
("gs.vtk")])
@pytest.mark.skipif(not dipy_available, reason='Dipy is not installed.')
def test_load_vox(path):
gs_dir = os.path.join(get_home(), 'gold_standard')
path = os.path.join(gs_dir, path)
coord = np.loadtxt(os.path.join(get_home(), 'gold_standard',
'gs_vox_space.txt'))
obj = load(path, os.path.join(gs_dir, 'gs.nii'))
sft = obj.to_sft() if isinstance(obj, TrxFile) else obj
sft.to_vox()
assert_allclose(sft.streamlines._data, coord, rtol=1e-04, atol=1e-06)
if isinstance(obj, TrxFile):
obj.close()
@pytest.mark.parametrize("path", [("gs.trx"), ("gs.trk"), ("gs.tck"),
("gs.vtk")])
@pytest.mark.skipif(not dipy_available, reason='Dipy is not installed.')
def test_load_voxmm(path):
gs_dir = os.path.join(get_home(), 'gold_standard')
path = os.path.join(gs_dir, path)
coord = np.loadtxt(os.path.join(get_home(), 'gold_standard',
'gs_voxmm_space.txt'))
obj = load(path, os.path.join(gs_dir, 'gs.nii'))
sft = obj.to_sft() if isinstance(obj, TrxFile) else obj
sft.to_voxmm()
assert_allclose(sft.streamlines._data, coord, rtol=1e-04, atol=1e-06)
if isinstance(obj, TrxFile):
obj.close()
@pytest.mark.parametrize("path", [("gs.trk"), ("gs.trx"), ("gs_fldr.trx")])
@pytest.mark.skipif(not dipy_available, reason='Dipy is not installed.')
def test_multi_load_save_rasmm(path):
with TemporaryDirectory() as tmp_gs_dir:
gs_dir = os.path.join(get_home(), 'gold_standard')
basename, ext = os.path.splitext(path)
path = os.path.join(gs_dir, path)
coord = np.loadtxt(os.path.join(get_home(), 'gold_standard',
'gs_rasmm_space.txt'))
obj = load(path, os.path.join(gs_dir, 'gs.nii'))
for i in range(3):
out_path = os.path.join(
tmp_gs_dir, '{}_tmp{}_{}'.format(basename, i, ext))
save(obj, out_path)
if isinstance(obj, TrxFile):
obj.close()
obj = load(out_path, os.path.join(gs_dir, 'gs.nii'))
assert_allclose(obj.streamlines._data, coord, rtol=1e-04, atol=1e-06)
if isinstance(obj, TrxFile):
obj.close()
@pytest.mark.parametrize("path", [("gs.trx"), ("gs_fldr.trx")])
@pytest.mark.skipif(not dipy_available, reason='Dipy is not installed.')
def test_delete_tmp_gs_dir(path):
gs_dir = os.path.join(get_home(), 'gold_standard')
path = os.path.join(gs_dir, path)
trx1 = tmm.load(path)
if os.path.isfile(path):
tmp_gs_dir = deepcopy(trx1._uncompressed_folder_handle.name)
assert os.path.isdir(tmp_gs_dir)
sft = trx1.to_sft()
trx1.close()
coord_rasmm = np.loadtxt(os.path.join(get_home(), 'gold_standard',
'gs_rasmm_space.txt'))
coord_vox = np.loadtxt(os.path.join(get_home(), 'gold_standard',
'gs_vox_space.txt'))
# The folder trx representation does not need tmp files
if os.path.isfile(path):
assert not os.path.isdir(tmp_gs_dir)
assert_allclose(sft.streamlines._data, coord_rasmm, rtol=1e-04, atol=1e-06)
# Reloading the TRX and checking its data, then closing
trx2 = tmm.load(path)
assert_allclose(trx2.streamlines._data,
sft.streamlines._data, rtol=1e-04, atol=1e-06)
trx2.close()
sft.to_vox()
assert_allclose(sft.streamlines._data, coord_vox, rtol=1e-04, atol=1e-06)
trx3 = tmm.load(path)
assert_allclose(trx3.streamlines._data,
coord_rasmm, rtol=1e-04, atol=1e-06)
trx3.close()
@pytest.mark.parametrize("path", [("gs.trx")])
@pytest.mark.skipif(not dipy_available, reason='Dipy is not installed.')
def test_close_tmp_files(path):
gs_dir = os.path.join(get_home(), 'gold_standard')
path = os.path.join(gs_dir, path)
trx = tmm.load(path)
process = psutil.Process(os.getpid())
open_files = process.open_files()
expected_content = ['offsets.uint32', 'positions.3.float32',
'header.json', 'random_coord.3.float32',
'color_y.float32', 'color_x.float32',
'color_z.float32']
count = 0
for open_file in open_files:
basename = os.path.basename(open_file.path)
if basename in expected_content:
count += 1
assert count == 6
trx.close()
open_files = process.open_files()
count = 0
for open_file in open_files:
basename = os.path.basename(open_file.path)
if basename in expected_content:
count += 1
assert not count
@pytest.mark.parametrize("tmp_path", [("~"), ("use_working_dir")])
def test_change_tmp_dir(tmp_path):
gs_dir = os.path.join(get_home(), 'gold_standard')
path = os.path.join(gs_dir, 'gs.trx')
if tmp_path == 'use_working_dir':
os.environ['TRX_TMPDIR'] = 'use_working_dir'
else:
os.environ['TRX_TMPDIR'] = os.path.expanduser(tmp_path)
trx = tmm.load(path)
tmp_gs_dir = deepcopy(trx._uncompressed_folder_handle.name)
if tmp_path == 'use_working_dir':
assert os.path.dirname(tmp_gs_dir) == os.getcwd()
else:
assert os.path.dirname(tmp_gs_dir) == os.path.expanduser(tmp_path)
trx.close()
assert not os.path.isdir(tmp_gs_dir)
@pytest.mark.parametrize("path", [("gs.trx"), ("gs_fldr.trx")])
def test_complete_dir_from_trx(path):
gs_dir = os.path.join(get_home(), 'gold_standard')
path = os.path.join(gs_dir, path)
trx = tmm.load(path)
if trx._uncompressed_folder_handle is None:
dir_to_check = path
else:
dir_to_check = trx._uncompressed_folder_handle.name
file_paths = []
for dirpath, _, filenames in os.walk(dir_to_check):
for filename in filenames:
full_path = os.path.join(dirpath, filename)
cut_path = full_path.split(dir_to_check)[1][1:].replace('\\', '/')
file_paths.append(cut_path)
expected_content = ['offsets.uint32', 'positions.3.float32',
'header.json', 'dps/random_coord.3.float32',
'dpv/color_y.float32', 'dpv/color_x.float32',
'dpv/color_z.float32']
assert set(file_paths) == set(expected_content)
def test_complete_zip_from_trx():
gs_dir = os.path.join(get_home(), 'gold_standard')
path = os.path.join(gs_dir, 'gs.trx')
with zipfile.ZipFile(path, mode="r") as zf:
zip_file_list = zf.namelist()
expected_content = ['offsets.uint32', 'positions.3.float32',
'header.json', 'dps/random_coord.3.float32',
'dpv/color_y.float32', 'dpv/color_x.float32',
'dpv/color_z.float32']
assert set(zip_file_list) == set(expected_content)
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