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import pathlib |
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import shutil |
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import pytest |
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from hansel.tests.conftest import make_tree_from_crumb |
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from hansel.utils import ParameterGrid |
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9
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10
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@pytest.fixture(scope='session') |
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def readme_base_dir(): |
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base_dir = pathlib.Path('/tmp/hansel/data') |
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if base_dir.exists(): |
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shutil.rmtree(str(base_dir), ignore_errors=True) |
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base_dir.mkdir() |
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yield str(base_dir) |
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shutil.rmtree(str(base_dir), ignore_errors=True) |
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def readme_brain_data_crumb_args(): |
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crumb_path = "{base_dir}/raw/{subject_id}/{session_id}/{image_type}/{image}" |
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values_dict = { |
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'session_id': ['session_1'], |
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'subject_id': ['004000{}'.format(i) for i in range(10)], |
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'image_type': ['anat_1', 'rest_1'], |
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'image': ['mprage.nii.gz'], |
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} |
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return crumb_path, values_dict |
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def readme_proj1_data_crumb_args(): |
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crumb_path = "{base_dir}/proj1/{subject_id}/{session_id}/{image_type}/{image}" |
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values_dict = { |
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'session_id': ['session_1'], |
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'subject_id': ['004000{}'.format(i) for i in range(10)], |
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'image_type': ['anat_1', 'rest_1'], |
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'image': ['mprage.nii.gz', 'rest.nii.gz'], |
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} |
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return crumb_path, values_dict |
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def readme_proj2_data_crumb_args(): |
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crumb_path = "{base_dir}/proj2/{subject_id}/{session_id}/{image_type}/{image}" |
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values_dict = { |
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'session_id': ['session_1'], |
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'subject_id': ['00400{:02}'.format(i + 6) for i in range(10)], |
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'image_type': ['anat_1', 'rest_1'], |
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'image': ['mprage.nii.gz', 'rest.nii.gz'], |
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} |
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return crumb_path, values_dict |
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def readme_proj3_data_crumb_args(): |
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crumb_path = "{base_dir}/proj3/{subject_id}/{session_id}/{image_type}/{image}" |
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values_dict = { |
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'session_id': ['session_1'], |
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'subject_id': ['00400{:02}'.format(i) for i in range(10)], |
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'image_type': ['anat_1'], |
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'image': ['mprage.nii.gz'], |
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} |
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return crumb_path, values_dict |
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def readme_proj4_data_crumb_args(): |
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crumb_path = "{base_dir}/proj4/{subject_id}/{session_id}/{image_type}/{image}" |
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values_dict = { |
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'session_id': ['session_1'], |
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'subject_id': ['00400{:02}'.format(i + 1) for i in range(9)], |
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'image_type': ['anat_1'], |
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'image': ['mprage.nii.gz'], |
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} |
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subject1 = dict( |
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image='anatomical.nii.gz', |
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image_type='anat_1', |
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session_id='session_1', |
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subject_id='00400000' |
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) |
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80
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values_map = [subject1] |
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values_map.extend(list(ParameterGrid(values_dict))) |
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return crumb_path, values_map |
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84
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85
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@pytest.fixture(scope='session') |
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def readme_tree_crumbs(): |
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return [ |
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readme_brain_data_crumb_args, |
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readme_proj1_data_crumb_args, |
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readme_proj2_data_crumb_args, |
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readme_proj3_data_crumb_args, |
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readme_proj4_data_crumb_args, |
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] |
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95
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96
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@pytest.fixture(scope='session') |
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97
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def built_readme_tree_crumbs(readme_base_dir, readme_tree_crumbs): |
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crumbs = [] |
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for crumb_func in readme_tree_crumbs: |
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crumb_path, values_dict = crumb_func() |
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make_tree_from_crumb(readme_base_dir, crumb_path, values_dict) |
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yield crumbs |
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103
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shutil.rmtree(readme_base_dir) |
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104
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105
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106
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@pytest.fixture(autouse=True) |
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107
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def add_base_crumbs(doctest_namespace, built_readme_tree_crumbs): |
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108
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pass |
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109
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alexsavio /
hansel
