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#! /usr/bin/env python3
# -*- coding: utf-8 -*-
from deepdiff import DeepDiff
import os
import tempfile
import pytest
import numpy as np
from numpy.testing import assert_equal, assert_array_equal, assert_allclose
try:
from dipy.io.streamline import load_tractogram
dipy_available = True
except ImportError:
dipy_available = False
from trx.fetcher import (get_testing_files_dict,
fetch_data, get_home)
import trx.trx_file_memmap as tmm
from trx.workflows import (convert_dsi_studio,
convert_tractogram,
manipulate_trx_datatype,
generate_trx_from_scratch,
validate_tractogram,)
# If they already exist, this only takes 5 seconds (check md5sum)
fetch_data(get_testing_files_dict(), keys=['DSI.zip', 'trx_from_scratch.zip'])
def test_help_option_convert_dsi(script_runner):
ret = script_runner.run('tff_convert_dsi_studio.py', '--help')
assert ret.success
def test_help_option_convert(script_runner):
ret = script_runner.run('tff_convert_tractogram.py', '--help')
assert ret.success
def test_help_option_generate_trx_from_scratch(script_runner):
ret = script_runner.run('tff_generate_trx_from_scratch.py', '--help')
assert ret.success
@pytest.mark.skipif(not dipy_available,
reason='Dipy is not installed.')
def test_execution_convert_dsi():
with tempfile.TemporaryDirectory() as tmp_dir:
in_trk = os.path.join(get_home(), 'DSI',
'CC.trk.gz')
in_nii = os.path.join(get_home(), 'DSI',
'CC.nii.gz')
exp_data = os.path.join(get_home(), 'DSI',
'CC_fix_data.npy')
exp_offsets = os.path.join(get_home(), 'DSI',
'CC_fix_offsets.npy')
out_fix_path = os.path.join(tmp_dir, 'fixed.trk')
convert_dsi_studio(in_trk, in_nii, out_fix_path,
remove_invalid=False,
keep_invalid=True)
data_fix = np.load(exp_data)
offsets_fix = np.load(exp_offsets)
sft = load_tractogram(out_fix_path, 'same')
assert_equal(sft.streamlines._data, data_fix)
assert_equal(sft.streamlines._offsets, offsets_fix)
@pytest.mark.skipif(not dipy_available,
reason='Dipy is not installed.')
def test_execution_convert_to_trx():
with tempfile.TemporaryDirectory() as tmp_dir:
in_trk = os.path.join(get_home(), 'DSI',
'CC_fix.trk')
exp_data = os.path.join(get_home(), 'DSI',
'CC_fix_data.npy')
exp_offsets = os.path.join(get_home(), 'DSI',
'CC_fix_offsets.npy')
out_trx_path = os.path.join(tmp_dir, 'CC_fix.trx')
convert_tractogram(in_trk, out_trx_path, None)
data_fix = np.load(exp_data)
offsets_fix = np.load(exp_offsets)
trx = tmm.load(out_trx_path)
assert_equal(trx.streamlines._data.dtype, np.float32)
assert_equal(trx.streamlines._offsets.dtype, np.uint32)
assert_array_equal(trx.streamlines._data, data_fix)
assert_array_equal(trx.streamlines._offsets, offsets_fix)
trx.close()
@pytest.mark.skipif(not dipy_available,
reason='Dipy is not installed.')
def test_execution_convert_from_trx():
with tempfile.TemporaryDirectory() as tmp_dir:
in_trk = os.path.join(get_home(), 'DSI',
'CC_fix.trk')
in_nii = os.path.join(get_home(), 'DSI',
'CC.nii.gz')
exp_data = os.path.join(get_home(), 'DSI',
'CC_fix_data.npy')
exp_offsets = os.path.join(get_home(), 'DSI',
'CC_fix_offsets.npy')
# Sequential conversions
out_trx_path = os.path.join(tmp_dir, 'CC_fix.trx')
out_trk_path = os.path.join(tmp_dir, 'CC_fix.trk')
out_tck_path = os.path.join(tmp_dir, 'CC_fix.tck')
convert_tractogram(in_trk, out_trx_path, None)
convert_tractogram(out_trx_path, out_tck_path, None)
convert_tractogram(out_trx_path, out_trk_path, None)
data_fix = np.load(exp_data)
offsets_fix = np.load(exp_offsets)
sft = load_tractogram(out_trk_path, 'same')
assert_equal(sft.streamlines._data, data_fix)
assert_equal(sft.streamlines._offsets, offsets_fix)
sft = load_tractogram(out_tck_path, in_nii)
assert_equal(sft.streamlines._data, data_fix)
assert_equal(sft.streamlines._offsets, offsets_fix)
@pytest.mark.skipif(not dipy_available,
reason='Dipy is not installed.')
def test_execution_convert_dtype_p16_o64():
with tempfile.TemporaryDirectory() as tmp_dir:
in_trk = os.path.join(get_home(), 'DSI',
'CC_fix.trk')
out_convert_path = os.path.join(tmp_dir, 'CC_fix_p16_o64.trx')
convert_tractogram(in_trk, out_convert_path, None,
pos_dtype='float16', offsets_dtype='uint64')
trx = tmm.load(out_convert_path)
assert_equal(trx.streamlines._data.dtype, np.float16)
assert_equal(trx.streamlines._offsets.dtype, np.uint64)
trx.close()
@pytest.mark.skipif(not dipy_available,
reason='Dipy is not installed.')
def test_execution_convert_dtype_p64_o32():
with tempfile.TemporaryDirectory() as tmp_dir:
in_trk = os.path.join(get_home(), 'DSI',
'CC_fix.trk')
out_convert_path = os.path.join(tmp_dir, 'CC_fix_p16_o64.trx')
convert_tractogram(in_trk, out_convert_path, None,
pos_dtype='float64', offsets_dtype='uint32')
trx = tmm.load(out_convert_path)
assert_equal(trx.streamlines._data.dtype, np.float64)
assert_equal(trx.streamlines._offsets.dtype, np.uint32)
trx.close()
def test_execution_generate_trx_from_scratch():
with tempfile.TemporaryDirectory() as tmp_dir:
reference_fa = os.path.join(get_home(), 'trx_from_scratch',
'fa.nii.gz')
raw_arr_dir = os.path.join(get_home(), 'trx_from_scratch',
'test_npy')
expected_trx = os.path.join(get_home(), 'trx_from_scratch',
'expected.trx')
dpv = [(os.path.join(raw_arr_dir, 'dpv_cx.npy'), 'uint8'),
(os.path.join(raw_arr_dir, 'dpv_cy.npy'), 'uint8'),
(os.path.join(raw_arr_dir, 'dpv_cz.npy'), 'uint8')]
dps = [(os.path.join(raw_arr_dir, 'dps_algo.npy'), 'uint8'),
(os.path.join(raw_arr_dir, 'dps_cw.npy'), 'float64')]
dpg = [('g_AF_L', os.path.join(raw_arr_dir, 'dpg_AF_L_mean_fa.npy'), 'float32'),
('g_AF_R', os.path.join(raw_arr_dir, 'dpg_AF_R_mean_fa.npy'), 'float32'),
('g_AF_L', os.path.join(raw_arr_dir, 'dpg_AF_L_volume.npy'), 'float32')]
groups = [(os.path.join(raw_arr_dir, 'g_AF_L.npy'), 'int32'),
(os.path.join(raw_arr_dir, 'g_AF_R.npy'), 'int32'),
(os.path.join(raw_arr_dir, 'g_CST_L.npy'), 'int32')]
out_gen_path = os.path.join(tmp_dir, 'generated.trx')
generate_trx_from_scratch(reference_fa, out_gen_path,
positions=os.path.join(raw_arr_dir,
'positions.npy'),
offsets=os.path.join(raw_arr_dir,
'offsets.npy'),
positions_dtype='float16',
offsets_dtype='uint64',
space_str='rasmm', origin_str='nifti',
verify_invalid=False, dpv=dpv, dps=dps,
groups=groups, dpg=dpg)
exp_trx = tmm.load(expected_trx)
gen_trx = tmm.load(out_gen_path)
assert DeepDiff(exp_trx.get_dtype_dict(),
gen_trx.get_dtype_dict()) == {}
assert_allclose(exp_trx.streamlines._data, gen_trx.streamlines._data,
atol=0.1, rtol=0.1)
assert_equal(exp_trx.streamlines._offsets,
gen_trx.streamlines._offsets)
for key in exp_trx.data_per_vertex.keys():
assert_equal(exp_trx.data_per_vertex[key]._data,
gen_trx.data_per_vertex[key]._data)
assert_equal(exp_trx.data_per_vertex[key]._offsets,
gen_trx.data_per_vertex[key]._offsets)
for key in exp_trx.data_per_streamline.keys():
assert_equal(exp_trx.data_per_streamline[key],
gen_trx.data_per_streamline[key])
for key in exp_trx.groups.keys():
assert_equal(exp_trx.groups[key], gen_trx.groups[key])
for group in exp_trx.groups.keys():
if group in exp_trx.data_per_group:
for key in exp_trx.data_per_group[group].keys():
assert_equal(exp_trx.data_per_group[group][key],
gen_trx.data_per_group[group][key])
exp_trx.close()
gen_trx.close()
@pytest.mark.skipif(not dipy_available,
reason='Dipy is not installed.')
def test_execution_concatenate_validate_trx():
with tempfile.TemporaryDirectory() as tmp_dir:
trx1 = tmm.load(os.path.join(get_home(), 'gold_standard',
'gs.trx'))
trx2 = tmm.load(os.path.join(get_home(), 'gold_standard',
'gs.trx'))
# trx2.streamlines._data += 0.001
trx = tmm.concatenate([trx1, trx2], preallocation=False)
# Right size
assert_equal(len(trx.streamlines), 2*len(trx1.streamlines))
# Right data
end_idx = trx1.header['NB_VERTICES']
assert_allclose(
trx.streamlines._data[:end_idx], trx1.streamlines._data)
assert_allclose(
trx.streamlines._data[end_idx:], trx2.streamlines._data)
# Right data_per_*
for key in trx.data_per_vertex.keys():
assert_equal(trx.data_per_vertex[key]._data[:end_idx],
trx1.data_per_vertex[key]._data)
assert_equal(trx.data_per_vertex[key]._data[end_idx:],
trx2.data_per_vertex[key]._data)
end_idx = trx1.header['NB_STREAMLINES']
for key in trx.data_per_streamline.keys():
assert_equal(trx.data_per_streamline[key][:end_idx],
trx1.data_per_streamline[key])
assert_equal(trx.data_per_streamline[key][end_idx:],
trx2.data_per_streamline[key])
# Validate
out_concat_path = os.path.join(tmp_dir, 'concat.trx')
out_valid_path = os.path.join(tmp_dir, 'valid.trx')
tmm.save(trx, out_concat_path)
validate_tractogram(out_concat_path, None, out_valid_path,
remove_identical_streamlines=True,
precision=0)
trx_val = tmm.load(out_valid_path)
# # Right dtype and size
assert DeepDiff(trx.get_dtype_dict(), trx_val.get_dtype_dict()) == {}
assert_equal(len(trx1.streamlines), len(trx_val.streamlines))
trx.close()
trx1.close()
trx2.close()
trx_val.close()
@pytest.mark.skipif(not dipy_available,
reason='Dipy is not installed.')
def test_execution_manipulate_trx_datatype():
with tempfile.TemporaryDirectory() as tmp_dir:
expected_trx = os.path.join(get_home(), 'trx_from_scratch',
'expected.trx')
trx = tmm.load(expected_trx)
expected_dtype = {'positions': np.dtype('float16'),
'offsets': np.dtype('uint64'),
'dpv': {'dpv_cx': np.dtype('uint8'),
'dpv_cy': np.dtype('uint8'),
'dpv_cz': np.dtype('uint8')},
'dps': {'dps_algo': np.dtype('uint8'),
'dps_cw': np.dtype('float64')},
'dpg': {'g_AF_L':
{'dpg_AF_L_mean_fa': np.dtype('float32'),
'dpg_AF_L_volume': np.dtype('float32')},
'g_AF_R':
{'dpg_AF_R_mean_fa': np.dtype('float32')}},
'groups': {'g_AF_L': np.dtype('int32'),
'g_AF_R': np.dtype('int32')}}
assert DeepDiff(trx.get_dtype_dict(), expected_dtype) == {}
trx.close()
generated_dtype = {'positions': np.dtype('float32'),
'offsets': np.dtype('uint32'),
'dpv': {'dpv_cx': np.dtype('uint16'),
'dpv_cy': np.dtype('uint16'),
'dpv_cz': np.dtype('uint16')},
'dps': {'dps_algo': np.dtype('uint8'),
'dps_cw': np.dtype('float32')},
'dpg': {'g_AF_L':
{'dpg_AF_L_mean_fa': np.dtype('float64'),
'dpg_AF_L_volume': np.dtype('float32')},
'g_AF_R':
{'dpg_AF_R_mean_fa': np.dtype('float64')}},
'groups': {'g_AF_L': np.dtype('uint16'),
'g_AF_R': np.dtype('uint16')}}
out_gen_path = os.path.join(tmp_dir, 'generated.trx')
manipulate_trx_datatype(expected_trx, out_gen_path, generated_dtype)
trx = tmm.load(out_gen_path)
assert DeepDiff(trx.get_dtype_dict(), generated_dtype) == {}
trx.close()
|
