Merge branch 'enh_filetree' into 'master'

Added filetree to fslpy

See merge request fsl/fslpy!69

tests/test_filetree/extract_vars.tree

+parent
+    opt_layer_test
+        {p1}_{p2}.nii.gz (fn)
+

tests/test_filetree/format.tree

+{var:.0f} (int)
+{var:.1f} (f1)
+{var:.2f} (f2)

tests/test_filetree/parent.tree

+dir1
+    ->eddy basename=1 (sub1)
+    dir2
+        ->eddy basename=2 (sub2)
+    ->eddy basename=1b (sub1b)
+->eddy basename=0 (sub0)
+->eddy basename=subvar_{subvar} (subvar)

tests/test_filetree/test_read.py

+# Sample Test passing with nose and pytest
+from fsl.utils import filetree
+from pathlib import PurePath
+import os.path as op
+import pytest
+from glob import glob
+
+
+def same_path(p1, p2):
+    assert PurePath(p1) == PurePath(p2)
+
+
+def test_simple_tree():
+    tree = filetree.FileTree.read('eddy')
+    assert tree.variables['basename'] == 'eddy_output'
+    same_path(tree.get('basename'), './eddy_output')
+    same_path(tree.get('image'), './eddy_output.nii.gz')
+
+    tree = filetree.FileTree.read('eddy.tree', basename='out')
+    same_path(tree.get('basename'), './out')
+    same_path(tree.update(basename='test').get('basename'), './test')
+    same_path(tree.get('basename'), './out')
+
+    with pytest.raises(ValueError):
+        filetree.FileTree.read('non_existing')
+
+
+def test_complicated_tree():
+    tree = filetree.FileTree.read('HCP_directory').update(subject='100307')
+
+    same_path(tree.get('T1w_acpc_dc'), '100307/T1w/T1w_acpc_dc.nii.gz')
+
+    L_white = '100307/T1w/fsaverage_LR32k/100307.L.white.32k_fs_LR.surf.gii'
+    same_path(tree.update(hemi='L').get('T1w_32k/white'), L_white)
+    same_path(tree.sub_trees['T1w_32k'].update(hemi='L').get('white'), L_white)
+
+    assert tree.exists(('T1w_32k/white', ))
+    assert tree.exists('T1w_32k/white')
+    assert not tree.exists(('T1w_32k/white_misspelled', ))
+    assert not tree.exists(('T1w_32k/white', 'T1w_32k/white_misspelled', ))
+    assert not tree.exists(('T1w_32k_err/white', ))
+    assert not tree.exists(('../test'))
+    with pytest.raises(ValueError):
+        assert not tree.exists(('../test'), error=True)
+    with pytest.raises(ValueError):
+        tree.exists(('T1w_32k_err/white', ), error=True)
+    assert tree.exists(('T1w_32k/white', ), error=True)
+
+
+def test_parent_tree():
+    directory = op.split(__file__)[0]
+    tree = filetree.FileTree.read(op.join(directory, 'parent.tree'))
+    same_path(tree.get('sub0/basename'), '0')
+    same_path(tree.get('sub1/basename'), 'dir1/1')
+    same_path(tree.get('sub1b/basename'), 'dir1/1b')
+    same_path(tree.get('sub2/basename'), 'dir1/dir2/2')
+    same_path(tree.update(subvar='grot').get('subvar/basename'), 'subvar_grot')
+    with pytest.raises(KeyError):
+        tree.get('sub_var/basename')
+
+
+def test_custom_tree():
+    directory = op.split(__file__)[0]
+    tree = filetree.FileTree.read(op.join(directory, 'custom.tree'), directory=directory)
+    same_path(tree.get('sub_file'), op.join(directory, 'parent/sub_file.nii.gz'))
+    same_path(tree.update(opt='test').get('sub_file'), op.join(directory, 'parent/opt_layer_test/sub_file.nii.gz'))
+
+    with pytest.raises(KeyError):
+        tree.get('opt_file')
+    same_path(tree.update(opt='test').get('opt_file'), op.join(directory, 'parent/opt_layer_test/opt_file_test.nii.gz'))
+
+    assert len(tree.update(opt='test').get_all('sub_file')) == 1
+    assert len(tree.update(opt='test').get_all_vars('sub_file')) == 1
+    assert len(tree.update(opt='test2').get_all('sub_file')) == 0
+    assert len(tree.update(opt='test2').get_all_vars('sub_file')) == 0
+    assert len(tree.get_all('sub_file', glob_vars=['opt'])) == 2
+    assert len(tree.get_all('sub_file', glob_vars='all')) == 2
+    assert len(tree.get_all('sub_file')) == 1
+    assert len(tree.update(opt=None).get_all('sub_file')) == 1
+    assert len(tree.update(opt=None).get_all('sub_file', glob_vars=['opt'])) == 1
+    assert len(tree.update(opt=None).get_all('sub_file', glob_vars='all')) == 1
+
+    for fn, settings in zip(tree.get_all('sub_file', glob_vars='all'),
+                            tree.get_all_vars('sub_file', glob_vars='all')):
+        same_path(fn, tree.update(**settings).get('sub_file'))
+
+    assert len(tree.update(opt='test2').get_all('opt_file')) == 0
+    assert len(tree.update(opt='test').get_all('opt_file')) == 1
+    with pytest.raises(KeyError):
+        tree.get_all('opt_file')
+    assert len(tree.get_all('opt_file', glob_vars=['opt'])) == 1
+
+    for vars in ({'opt': None}, {'opt': 'test'}):
+        filename = tree.update(**vars).get('sub_file')
+        assert vars == tree.extract_variables('sub_file', filename)
+    assert {'opt': None} == tree.extract_variables('sub_file', tree.get('sub_file'))
+
+    assert tree.exists(('sub_file', 'opt_file'), error=True, on_disk=True, glob_vars=['opt'])
+    assert tree.exists(('sub_file', 'opt_file'), on_disk=True, glob_vars=['opt'])
+    assert not tree.exists(('sub_file', 'opt_file'), error=False, on_disk=True)
+    with pytest.raises(KeyError):
+        assert tree.exists(('sub_file', 'opt_file'), error=True, on_disk=True)
+    assert not tree.update(opt='test2').exists(('sub_file', 'opt_file'), on_disk=True)
+    with pytest.raises(IOError):
+        tree.update(opt='test2').exists(('sub_file', 'opt_file'), on_disk=True, error=True)
+
+    assert tree.template_variables() == {'opt'}
+    assert tree.template_variables(optional=False) == {'opt'}
+    assert tree.template_variables(required=False) == set()
+    assert tree.template_variables(required=False, optional=False) == set()
+
+    assert tree.template_variables('sub_file') == {'opt'}
+    assert tree.template_variables('sub_file', required=False) == {'opt'}
+    assert tree.template_variables('sub_file', optional=False) == set()
+    assert tree.template_variables('sub_file', optional=False, required=False) == set()
+
+    assert tree.template_variables('opt_file') == {'opt'}
+    assert tree.template_variables('opt_file', required=False) == set()
+    assert tree.template_variables('opt_file', optional=False) == {'opt'}
+    assert tree.template_variables('opt_file', optional=False, required=False) == set()
+
+
+def test_format():
+    directory = op.split(__file__)[0]
+    tree = filetree.FileTree.read(op.join(directory, 'format.tree'), var=1.23)
+    same_path(tree.get('int'), '1')
+    same_path(tree.get('f1'), '1.2')
+    same_path(tree.get('f2'), '1.23')
+
+
+def test_read_all():
+    for directory in filetree.tree_directories:
+        if directory != '.':
+            for filename in glob(op.join(directory, '*.tree')):
+                filetree.FileTree.read(filename)
+
+
+def test_extract_vars_but():
+    """
+    Reproduces a bug where the already provided variables are ignored
+    """
+    directory = op.split(__file__)[0]
+    tree = filetree.FileTree.read(op.join(directory, 'extract_vars.tree'))
+    fn = 'parent/opt_layer_test/opt_file_test.nii.gz'
+    assert {'p1': 'opt_file', 'p2': 'test'} == tree.extract_variables('fn', fn)
+    assert {'p1': 'opt_file', 'p2': 'test'} == tree.update(p1='opt_file').extract_variables('fn', fn)
+    assert {'p1': 'opt', 'p2': 'file_test'} == tree.update(p1='opt').extract_variables('fn', fn)
+    assert {'p1': 'opt_{p3}', 'p2': 'test', 'p3': 'file'} == tree.update(p1='opt_{p3}').extract_variables('fn', fn)

tests/test_filetree/test_registration.py

+from fsl.utils.filetree import register_tree, FileTree
+import os.path as op
+
+
+class SubFileTree(FileTree):
+    pass
+
+
+def test_register_parent():
+    directory = op.split(__file__)[0]
+    filename = op.join(directory, 'parent.tree')
+
+    # call from sub-type
+    tree = SubFileTree.read(filename)
+    assert isinstance(tree, FileTree)
+    assert isinstance(tree, SubFileTree)
+    for child in tree.sub_trees.values():
+        assert isinstance(child, FileTree)
+        assert not isinstance(child, SubFileTree)
+
+    # call from FileTree
+    tree = FileTree.read(filename)
+    assert isinstance(tree, FileTree)
+    assert not isinstance(tree, SubFileTree)
+    for child in tree.sub_trees.values():
+        assert isinstance(child, FileTree)
+        assert not isinstance(child, SubFileTree)
+
+    # register + call from FileTree
+    register_tree('parent', SubFileTree)
+    tree = FileTree.read(filename)
+    assert isinstance(tree, FileTree)
+    assert isinstance(tree, SubFileTree)
+    for child in tree.sub_trees.values():
+        assert isinstance(child, FileTree)
+        assert not isinstance(child, SubFileTree)
+
+    # register + call from SubFileTree
+    register_tree('parent', FileTree)
+    tree = SubFileTree.read(filename)
+    assert isinstance(tree, FileTree)
+    assert not isinstance(tree, SubFileTree)
+    for child in tree.sub_trees.values():
+        assert isinstance(child, FileTree)
+        assert not isinstance(child, SubFileTree)
+
+
+def test_children():
+    directory = op.split(__file__)[0]
+    filename = op.join(directory, 'parent.tree')
+
+    tree = SubFileTree.read(filename)
+    assert isinstance(tree, FileTree)
+    assert not isinstance(tree, SubFileTree)
+    for child in tree.sub_trees.values():
+        assert isinstance(child, FileTree)
+        assert not isinstance(child, SubFileTree)
+
+    register_tree('eddy', SubFileTree)
+    tree = SubFileTree.read(filename)
+    assert isinstance(tree, FileTree)
+    assert not isinstance(tree, SubFileTree)
+    for child in tree.sub_trees.values():
+        assert isinstance(child, FileTree)
+        assert isinstance(child, SubFileTree)
+
+    register_tree('eddy', FileTree)
+    tree = SubFileTree.read(filename)
+    assert isinstance(tree, FileTree)
+    assert not isinstance(tree, SubFileTree)
+    for child in tree.sub_trees.values():
+        assert isinstance(child, FileTree)
+        assert not isinstance(child, SubFileTree)

tests/test_filetree/test_template.py

+from fsl.utils.filetree import utils
+import pytest
+
+
+def test_variables():
+    assert ('var', 'other_var', 'var') == tuple(utils.find_variables('some{var}_{other_var}_{var}'))
+    assert ('var', 'other_var', 'var') == tuple(utils.find_variables('some{var}_[{other_var}_{var}]'))
+    assert {'other_var'} == utils.optional_variables('some{var}_[{other_var}_{var}]')
+
+
+def test_get_variables():
+    assert {'var': 'test'} == utils.extract_variables('{var}', 'test')
+    assert {'var': 'test'} == utils.extract_variables('2{var}', '2test')
+    assert {'var': 'test', 'other_var': None} == utils.extract_variables('{var}[_{other_var}]', 'test')
+    assert {'var': 'test', 'other_var': 'foo'} == utils.extract_variables('{var}[_{other_var}]', 'test_foo')
+    assert {'var': 'test', 'other_var': 'foo'} == utils.extract_variables('{var}[_{other_var}]_{var}', 'test_foo_test')
+    assert {'var': 'test', 'other_var': None} == utils.extract_variables('{var}[_{other_var}]_{var}', 'test_test')
+    with pytest.raises(ValueError):
+        utils.extract_variables('{var}[_{other_var}]_{var}', 'test_foo')
+    with pytest.raises(ValueError):
+        utils.extract_variables('{var}[_{other_var}]_{var}', 'test_foo_bar')
+    with pytest.raises(ValueError):
+        utils.extract_variables('bar{var}[_{other_var}]_{var}', 'test')