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|
# -*- coding: utf-8 -*-
import os
from nibabel.streamlines.tests.test_tractogram import make_dummy_streamline
from nibabel.streamlines import LazyTractogram
import numpy as np
import pytest
try:
import dipy
dipy_available = True
except ImportError:
dipy_available = False
from trx.io import get_trx_tmp_dir
import trx.trx_file_memmap as tmm
from trx.fetcher import (get_testing_files_dict,
fetch_data, get_home)
fetch_data(get_testing_files_dict(), keys=['memmap_test_data.zip'])
tmp_dir = get_trx_tmp_dir()
@pytest.mark.parametrize(
"arr,expected,value_error",
[
(np.ones((5, 5, 5), dtype=np.int16), None, True),
(np.ones((5, 4), dtype=np.int16), "mean_fa.4.int16", False),
(np.ones((5, 4), dtype=np.float64), "mean_fa.4.float64", False),
(np.ones((5, 1), dtype=np.float64), "mean_fa.float64", False),
(np.ones((1), dtype=np.float64), "mean_fa.float64", False),
],
)
def test__generate_filename_from_data(
arr, expected, value_error, filename="mean_fa.bit"
):
if value_error:
with pytest.raises(ValueError):
new_fn = tmm._generate_filename_from_data(arr=arr,
filename=filename)
assert new_fn is None
else:
new_fn = tmm._generate_filename_from_data(arr=arr, filename=filename)
assert new_fn == expected
@pytest.mark.parametrize(
"filename,expected,value_error",
[
("mean_fa.float64", ("mean_fa", 1, ".float64"), False),
("mean_fa.5.int32", ("mean_fa", 5, ".int32"), False),
("mean_fa", None, True),
("mean_fa.5.4.int32", None, True),
pytest.param(
"mean_fa.fa", None, True, marks=pytest.mark.xfail,
id="invalid extension"
),
],
)
def test__split_ext_with_dimensionality(filename, expected, value_error):
if value_error:
with pytest.raises(ValueError):
assert tmm._split_ext_with_dimensionality(filename) == expected
else:
assert tmm._split_ext_with_dimensionality(filename) == expected
@pytest.mark.parametrize(
"offsets,nb_vertices,expected",
[
(np.array(range(5), dtype=np.int16), 4, np.array([1, 1, 1, 1, 0])),
(np.array([0, 1, 1, 3, 4], dtype=np.int32),
4, np.array([1, 0, 2, 1, 0])),
(np.array(range(4), dtype=np.uint64), 4, np.array([1, 1, 1, 1])),
pytest.param(np.array([0, 1, 0, 3, 4], dtype=np.int16), 4,
np.array([1, 3, 0, 1, 0]), marks=pytest.mark.xfail,
id="offsets not sorted"),
],
)
def test__compute_lengths(offsets, nb_vertices, expected):
offsets = tmm._append_last_offsets(offsets, nb_vertices)
lengths = tmm._compute_lengths(offsets=offsets)
assert np.array_equal(lengths, expected)
@pytest.mark.parametrize(
"ext,expected",
[
(".bit", True),
(".int16", True),
(".float32", True),
(".ushort", True),
(".txt", False),
],
)
def test__is_dtype_valid(ext, expected):
assert tmm._is_dtype_valid(ext) == expected
@pytest.mark.parametrize(
"arr,l_bound,r_bound,expected",
[
(np.array(range(5), dtype=np.int16), None, None, 4),
(np.array([0, 1, 0, 3, 4], dtype=np.int16), None, None, 1),
(np.array([0, 1, 2, 0, 4], dtype=np.int16), None, None, 2),
(np.array(range(5), dtype=np.int16), 1, 2, 2),
(np.array(range(5), dtype=np.int16), 3, 3, 3),
(np.zeros((5), dtype=np.int16), 3, 3, -1),
],
)
def test__dichotomic_search(arr, l_bound, r_bound, expected):
end_idx = tmm._dichotomic_search(arr, l_bound=l_bound, r_bound=r_bound)
assert end_idx == expected
@pytest.mark.parametrize(
"basename, create, expected",
[
("offsets.int16", True, np.array(range(12), dtype=np.int16).reshape((
3, 4))),
("offsets.float32", False, None),
],
)
def test__create_memmap(basename, create, expected):
if create:
# Need to create array before evaluating
with get_trx_tmp_dir() as dirname:
filename = os.path.join(dirname, basename)
fp = np.memmap(filename, dtype=np.int16, mode="w+", shape=(3, 4))
fp[:] = expected[:]
mmarr = tmm._create_memmap(filename=filename, shape=(3, 4),
dtype=np.int16)
assert np.array_equal(mmarr, expected)
else:
with get_trx_tmp_dir() as dirname:
filename = os.path.join(dirname, basename)
mmarr = tmm._create_memmap(filename=filename, shape=(0,),
dtype=np.int16)
assert os.path.isfile(filename)
assert np.array_equal(mmarr, np.zeros(
shape=(0,), dtype=np.float32))
# need dpg test with missing keys
@pytest.mark.parametrize(
"path,check_dpg,value_error",
[
("small_compressed.trx", False, False),
("small.trx", True, False),
("small_fldr.trx", False, False),
("dontexist.trx", False, True),
],
)
def test_load(path, check_dpg, value_error):
path = os.path.join(get_home(), 'memmap_test_data', path)
# Need to perhaps improve test
if value_error:
with pytest.raises(ValueError):
assert not isinstance(
tmm.load(input_obj=path, check_dpg=check_dpg), tmm.TrxFile
)
else:
assert isinstance(tmm.load(input_obj=path, check_dpg=check_dpg),
tmm.TrxFile)
@pytest.mark.parametrize("path", [("small.trx")])
def test_load_zip(path):
path = os.path.join(get_home(), 'memmap_test_data', path)
assert isinstance(tmm.load_from_zip(path), tmm.TrxFile)
@pytest.mark.parametrize("path", [("small_fldr.trx")])
def test_load_directory(path):
path = os.path.join(get_home(), 'memmap_test_data', path)
assert isinstance(tmm.load_from_directory(path), tmm.TrxFile)
@pytest.mark.parametrize("path", [("small.trx")])
def test_concatenate(path):
path = os.path.join(get_home(), 'memmap_test_data', path)
trx1 = tmm.load(path)
trx2 = tmm.load(path)
concat = tmm.concatenate([trx1, trx2])
assert len(concat) == 2 * len(trx2)
trx1.close()
trx2.close()
concat.close()
@pytest.mark.parametrize("path", [("small.trx")])
def test_resize(path):
path = os.path.join(get_home(), 'memmap_test_data', path)
trx1 = tmm.load(path)
concat = tmm.TrxFile(nb_vertices=1000000, nb_streamlines=10000,
init_as=trx1)
tmm.concatenate([concat, trx1], preallocation=True, delete_groups=True)
concat.resize()
assert len(concat) == len(trx1)
trx1.close()
concat.close()
@pytest.mark.parametrize(
"path, buffer",
[
("small.trx", 10000),
("small.trx", 0)
]
)
def test_append(path, buffer):
path = os.path.join(get_home(), 'memmap_test_data', path)
trx1 = tmm.load(path)
concat = tmm.TrxFile(nb_vertices=1, nb_streamlines=1,
init_as=trx1)
concat.append(trx1, extra_buffer=buffer)
if buffer > 0:
concat.resize()
assert len(concat) == len(trx1)
trx1.close()
concat.close()
@pytest.mark.parametrize("path, buffer", [("small.trx", 10000)])
@pytest.mark.skipif(not dipy_available, reason="Dipy is not installed")
def test_append_StatefulTractogram(path, buffer):
path = os.path.join(get_home(), 'memmap_test_data', path)
trx = tmm.load(path)
obj = trx.to_sft()
concat = tmm.TrxFile(nb_vertices=1, nb_streamlines=1, init_as=trx)
concat.append(obj, extra_buffer=buffer)
if buffer > 0:
concat.resize()
assert len(concat) == len(obj)
trx.close()
concat.close()
@pytest.mark.parametrize("path, buffer", [("small.trx", 10000)])
def test_append_Tractogram(path, buffer):
path = os.path.join(get_home(), 'memmap_test_data', path)
trx = tmm.load(path)
obj = trx.to_tractogram()
concat = tmm.TrxFile(nb_vertices=1, nb_streamlines=1, init_as=trx)
concat.append(obj, extra_buffer=buffer)
if buffer > 0:
concat.resize()
assert len(concat) == len(obj)
trx.close()
concat.close()
@pytest.mark.parametrize("path, size, buffer", [("small.trx", 50, 10000),
("small.trx", 0, 10000),
("small.trx", 25000, 10000),
("small.trx", 50, 0),
("small.trx", 0, 0),
("small.trx", 25000, 10000)])
def test_from_lazy_tractogram(path, size, buffer):
_ = np.random.RandomState(1776)
streamlines = []
fa = []
commit_weights = []
clusters_QB = []
gen_range = [1, 2, 5, 2, 1] * (size // 5)
for i in gen_range:
data = make_dummy_streamline(i)
streamline, data_per_point, data_for_streamline = data
streamlines.append(streamline)
fa.append(data_per_point['fa'].astype(np.float16))
commit_weights.append(
data_for_streamline['mean_curvature'].astype(np.float32))
clusters_QB.append(
data_for_streamline['mean_torsion'].astype(np.uint16))
def streamlines_func(): return (e for e in streamlines)
data_per_point_func = {'fa': lambda: (e for e in fa)}
data_per_streamline_func = {
'commit_weights': lambda: (e for e in commit_weights),
'clusters_QB': lambda: (e for e in clusters_QB)}
obj = LazyTractogram(streamlines_func,
data_per_streamline_func,
data_per_point_func,
affine_to_rasmm=np.eye(4))
dtype_dict = {'positions': np.float32, 'offsets': np.uint32,
'dpv': {'fa': np.float16},
'dps': {'commit_weights': np.float32,
'clusters_QB': np.uint16}}
path = os.path.join(get_home(), 'memmap_test_data', path)
trx = tmm.TrxFile.from_lazy_tractogram(obj, reference=path,
extra_buffer=buffer,
chunk_size=1000,
dtype_dict=dtype_dict)
assert len(trx) == len(gen_range)
def test_zip_from_folder():
pass
def test_trxfile_init():
pass
def test_trxfile_print():
pass
def test_trxfile_len():
fake = tmm.TrxFile(nb_vertices=100, nb_streamlines=10)
assert len(fake) == 10
def test_trxfile_getitem():
pass
def test_trxfile_deepcopy():
pass
def test_get_real_len():
fake = tmm.TrxFile(nb_vertices=100, nb_streamlines=10)
assert fake._get_real_len() == (0, 0)
def test_copy_fixed_arrays_from():
pass
def test_initialize_empty_trx():
pass
def test_create_trx_from_pointer():
pass
def test_trxfile_getgroup():
pass
def test_trxfile_select():
pass
def test_trxfile_to_memory():
pass
def test_trxfile_close():
pass
|
