def test_make_fetcher():
symmetric362 = SPHERE_FILES['symmetric362']
with TemporaryDirectory() as tmpdir:
stored_md5 = fetcher._get_file_md5(symmetric362)
# create local HTTP Server
testfile_url = op.split(symmetric362)[0] + os.sep
test_server_url = "http://127.0.0.1:8000/"
print(testfile_url)
print(symmetric362)
current_dir = os.getcwd()
# change pwd to directory containing testfile.
os.chdir(testfile_url)
server = HTTPServer(('localhost', 8000), SimpleHTTPRequestHandler)
server_thread = Thread(target=server.serve_forever)
server_thread.deamon = True
server_thread.start()
# test make_fetcher
sphere_fetcher = fetcher._make_fetcher("sphere_fetcher",
tmpdir, test_server_url,
[op.split(symmetric362)[-1]],
["sphere_name"],
md5_list=[stored_md5])
sphere_fetcher()
assert op.isfile(op.join(tmpdir, "sphere_name"))
npt.assert_equal(fetcher._get_file_md5(op.join(tmpdir, "sphere_name")),
stored_md5)
# stop local HTTP Server
server.shutdown()
# change to original working directory
os.chdir(current_dir)
def test_make_fetcher():
symmetric362 = SPHERE_FILES['symmetric362']
with TemporaryDirectory() as tmpdir:
stored_md5 = fetcher._get_file_md5(symmetric362)
# create local HTTP Server
testfile_url = op.split(symmetric362)[0] + os.sep
test_server_url = "http://127.0.0.1:8000/"
print(testfile_url)
print(symmetric362)
current_dir = os.getcwd()
# change pwd to directory containing testfile.
os.chdir(testfile_url)
server = HTTPServer(('localhost', 8000), SimpleHTTPRequestHandler)
server_thread = Thread(target=server.serve_forever)
server_thread.deamon = True
server_thread.start()
# test make_fetcher
sphere_fetcher = fetcher._make_fetcher("sphere_fetcher",
tmpdir,
test_server_url,
[op.split(symmetric362)[-1]],
["sphere_name"],
md5_list=[stored_md5])
sphere_fetcher()
assert op.isfile(op.join(tmpdir, "sphere_name"))
npt.assert_equal(fetcher._get_file_md5(op.join(tmpdir, "sphere_name")),
stored_md5)
# stop local HTTP Server
server.shutdown()
# change to original working directory
os.chdir(current_dir)
def test_make_fetcher():
symmetric362 = SPHERE_FILES['symmetric362']
with TemporaryDirectory() as tmpdir:
stored_md5 = fetcher._get_file_md5(symmetric362)
testfile_url = pathname2url(op.split(symmetric362)[0] + op.sep)
testfile_url = urljoin("file:", testfile_url)
print(testfile_url)
print(symmetric362)
sphere_fetcher = fetcher._make_fetcher("sphere_fetcher",
tmpdir, testfile_url,
[op.split(symmetric362)[-1]],
["sphere_name"],
md5_list=[stored_md5])
sphere_fetcher()
assert op.isfile(op.join(tmpdir, "sphere_name"))
npt.assert_equal(fetcher._get_file_md5(op.join(tmpdir, "sphere_name")),
stored_md5)
def test_make_fetcher():
symmetric362 = SPHERE_FILES['symmetric362']
with TemporaryDirectory() as tmpdir:
stored_md5 = fetcher._get_file_md5(symmetric362)
testfile_url = pathname2url(op.split(symmetric362)[0] + op.sep)
testfile_url = urljoin("file:", testfile_url)
print(testfile_url)
print(symmetric362)
sphere_fetcher = fetcher._make_fetcher("sphere_fetcher",
tmpdir,
testfile_url,
[op.split(symmetric362)[-1]],
["sphere_name"],
md5_list=[stored_md5])
sphere_fetcher()
assert op.isfile(op.join(tmpdir, "sphere_name"))
npt.assert_equal(fetcher._get_file_md5(op.join(tmpdir, "sphere_name")),
stored_md5)
callosum_md5_hashes = [
"709fa90baadeacd64f1d62b5049a4125", "987c6169de807c4e93dc2cbd7a25d506",
"0da114123d0b0097b96fe450a459550b", "6d845bd10504f67f1dc17f9000076d7e",
"e16c7873ef4b08d26b77ef746dab8237", "47193fd4df1ea17367817466de798b90",
"7e78bf9671e6945f4b2f5e7c30595a3c", "8adbb947377ff7b484c88d8c0ffc2125",
"0fd981a4d0847e0642ff96e84fe44e47", "87c4855efa406d8fb004cffb8259180e",
"c7969bcf5f2343fd9ce9c49b336cf14c", "bb4372b88991932150205ffb22aa6cb7",
"d198d4e7db18ddc7236cf143ecb8342e", "d0f6edef64b0c710c92e634496085dda",
"85eaee44665f244db5adae2e259833f6", "25f24eb22879a05d12bda007c81ea55a",
"2664e0b8c2d9c59f13649a89bfcce399"
]
fetch_callosum_templates = _make_fetcher("fetch_callosum_templates",
op.join(afq_home,
'callosum_templates'),
baseurl,
callosum_remote_fnames,
callosum_fnames,
md5_list=callosum_md5_hashes,
doc="Download AFQ callosum templates")
def read_callosum_templates(resample_to=False):
"""Load AFQ callosum templates from file
Returns
-------
dict with: keys: names of template ROIs and values: nibabel Nifti1Image
objects from each of the ROI nifti files.
"""
files, folder = fetch_callosum_templates()
template_dict = {}
callosum_md5_hashes = [
"709fa90baadeacd64f1d62b5049a4125", "987c6169de807c4e93dc2cbd7a25d506",
"0da114123d0b0097b96fe450a459550b", "6d845bd10504f67f1dc17f9000076d7e",
"e16c7873ef4b08d26b77ef746dab8237", "47193fd4df1ea17367817466de798b90",
"7e78bf9671e6945f4b2f5e7c30595a3c", "8adbb947377ff7b484c88d8c0ffc2125",
"0fd981a4d0847e0642ff96e84fe44e47", "87c4855efa406d8fb004cffb8259180e",
"c7969bcf5f2343fd9ce9c49b336cf14c", "bb4372b88991932150205ffb22aa6cb7",
"d198d4e7db18ddc7236cf143ecb8342e", "d0f6edef64b0c710c92e634496085dda",
"85eaee44665f244db5adae2e259833f6", "25f24eb22879a05d12bda007c81ea55a",
"2664e0b8c2d9c59f13649a89bfcce399"
]
fetch_callosum_templates = _make_fetcher("fetch_callosum_templates",
op.join(afq_home,
'callosum_templates'),
baseurl,
callosum_remote_fnames,
callosum_fnames,
md5_list=callosum_md5_hashes,
doc="Download AFQ callosum templates")
def read_callosum_templates():
"""Load AFQ callosum templates from file
Returns
-------
dict with: keys: names of template ROIs and values: nibabel Nifti1Image
objects from each of the ROI nifti files.
"""
files, folder = fetch_callosum_templates()
template_dict = {}
"7e78bf9671e6945f4b2f5e7c30595a3c",
"8adbb947377ff7b484c88d8c0ffc2125",
"0fd981a4d0847e0642ff96e84fe44e47",
"87c4855efa406d8fb004cffb8259180e",
"c7969bcf5f2343fd9ce9c49b336cf14c",
"bb4372b88991932150205ffb22aa6cb7",
"d198d4e7db18ddc7236cf143ecb8342e",
"d0f6edef64b0c710c92e634496085dda",
"85eaee44665f244db5adae2e259833f6",
"25f24eb22879a05d12bda007c81ea55a",
"2664e0b8c2d9c59f13649a89bfcce399"]
fetch_callosum_templates = _make_fetcher("fetch_callosum_templates",
op.join(afq_home,
'callosum_templates'),
baseurl, callosum_remote_fnames,
callosum_fnames,
md5_list=callosum_md5_hashes,
doc="Download AFQ callosum templates")
def read_callosum_templates():
"""Load AFQ callosum templates from file
Returns
-------
dict with: keys: names of template ROIs and values: nibabel Nifti1Image
objects from each of the ROI nifti files.
"""
files, folder = fetch_callosum_templates()
template_dict = {}
import tempfile
from pathlib import Path
import numpy as np
import nibabel as nb
import pytest
from dipy.data.fetcher import _make_fetcher, UW_RW_URL
_dipy_datadir_root = os.getenv('DMRIPREP_TESTS_DATA') or Path.home()
dipy_datadir = Path(_dipy_datadir_root) / '.cache' / 'data'
dipy_datadir.mkdir(parents=True, exist_ok=True)
_make_fetcher(
"fetch_sherbrooke_3shell",
str(dipy_datadir),
UW_RW_URL + "1773/38475/",
['HARDI193.nii.gz', 'HARDI193.bval', 'HARDI193.bvec'],
['HARDI193.nii.gz', 'HARDI193.bval', 'HARDI193.bvec'], [
'0b735e8f16695a37bfbd66aab136eb66', 'e9b9bb56252503ea49d31fb30a0ac637',
'0c83f7e8b917cd677ad58a078658ebb7'
],
doc="Download a 3shell HARDI dataset with 192 gradient direction")()
_sherbrooke_data = {
'dwi_file': dipy_datadir / "HARDI193.nii.gz",
'bvecs': np.loadtxt(dipy_datadir / "HARDI193.bvec").T,
'bvals': np.loadtxt(dipy_datadir / "HARDI193.bval"),
}
@pytest.fixture(autouse=True)
def doctest_autoimport(doctest_namespace):
"""Make available some fundamental modules to doctest modules."""
from os.path import join as pjoin
from dipy.data.fetcher import _make_fetcher, dipy_home
dname = '../data/' # or dipy_home
fetch_sherby = _make_fetcher(
"fetch_sherby",
pjoin(dname, 'sherby'),
'https://dl.dropboxusercontent.com/u/2481924/',
['Sherby.zip'],
['Sherby.zip'],
['2979482087f5e37846e802ea19542d52'],
doc="Download 2 subjects with DWI and T1 datasets",
data_size="200MB",
unzip=True)
fetch_sherby()
# 64 directions
# 50x50x50 voxels
fetch_isbi2013_challenge = _make_fetcher(
"fetch_isbi2013_challenge", os.path.join(dipy_home, 'isbi2013_challenge'),
'http://hardi.epfl.ch/static/events/2013_ISBI/_downloads/', [
'testing-data_DWIS_hardi-scheme_SNR-10.nii.gz',
'testing-data_DWIS_hardi-scheme_SNR-20.nii.gz',
'testing-data_DWIS_hardi-scheme_SNR-30.nii.gz',
'hardi-scheme.bval',
'hardi-scheme.bvec',
'ground-truth-peaks.nii.gz',
], [
'hardi-scheme_SNR-10.nii.gz',
'hardi-scheme_SNR-20.nii.gz',
'hardi-scheme_SNR-30.nii.gz',
'hardi-scheme.bval',
'hardi-scheme.bvec',
'ground-truth-peaks.nii.gz',
], [
'c3d97559f418358bb69467a0b5809630',
'33640b1297c8b498e0328fe268dbd5c1',
'a508716c5eec555a77a34817acafb0ca',
'92811d6e800a6a56d7498b0c4b5ed0c2',
'c8f5025b9d91037edb6cd00af9bd3e41',
'fc3ecd9636d6130b0f0488812b3a341c',
])
def read_isbi2013_challenge(snr=30):
""" Load ISBI 2013's HARDI reconstruction challenge dataset
"7e78bf9671e6945f4b2f5e7c30595a3c",
"8adbb947377ff7b484c88d8c0ffc2125",
"0fd981a4d0847e0642ff96e84fe44e47",
"87c4855efa406d8fb004cffb8259180e",
"c7969bcf5f2343fd9ce9c49b336cf14c",
"bb4372b88991932150205ffb22aa6cb7",
"d198d4e7db18ddc7236cf143ecb8342e",
"d0f6edef64b0c710c92e634496085dda",
"85eaee44665f244db5adae2e259833f6",
"25f24eb22879a05d12bda007c81ea55a",
"2664e0b8c2d9c59f13649a89bfcce399"]
fetch_callosum_templates = _make_fetcher("fetch_callosum_templates",
op.join(afq_home,
'callosum_templates'),
baseurl, callosum_remote_fnames,
callosum_fnames,
md5_list=callosum_md5_hashes,
doc="Download AFQ callosum templates")
def read_callosum_templates():
"""Load AFQ callosum templates from file
Returns
-------
dict with: keys: names of template ROIs and values: nibabel Nifti1Image
objects from each of the ROI nifti files.
"""
files, folder = fetch_callosum_templates()
template_dict = {}