Merge pull request #234 from smoia/int/bids

Move bids-related functions to dedicated file

.travis.yml

@@ -35,7 +35,7 @@ before_install:
       pip install flake8;
     fi
   - if [ "${CHECK_TYPE}" == "test" ]; then
-      pip install "pytest>=3.6" pytest-cov coverage coveralls codecov;
+      pip install "pytest>=4.6" pytest-cov coverage coveralls codecov;
     fi
   - if [ "${CHECK_TYPE}" == "docdoctest" ]; then
       pip install "sphinx>2.0" sphinx_rtd_theme pandas sphinx-argparse;

phys2bids/bids_units.py → phys2bids/bids.py

@@ -1,5 +1,10 @@
+import os
 import logging
 
+from pathlib import Path
+
+from phys2bids import utils
+
 LGR = logging.getLogger(__name__)
 
 UNIT_ALIASES = {
@@ -87,3 +92,81 @@ def bidsify_units(orig_unit):
     LGR.warning(f'The given unit {orig_unit} does not have aliases, '
                 f'passing it as is')
     return orig_unit
+
+
+def use_heuristic(heur_file, sub, ses, filename, outdir, record_label=''):
+    """
+    Import and use the heuristic specified by the user to rename the file.
+
+    Parameters
+    ----------
+    heur_file: path
+        Fullpath to heuristic file.
+    sub: str or int
+        Name of subject.
+    ses: str or int or None
+        Name of session.
+    filename: path
+        Name of the input of phys2bids.
+    outdir: str or path
+        Path to the directory that will become the "site" folder
+        ("root" folder of BIDS database).
+    record_label: str
+        Optional label for the "record" entry of BIDS.
+
+    Returns
+    -------
+    heurpath: str or path
+        Returned fullpath to tsv.gz new file (post BIDS formatting).
+
+    Raises
+    ------
+    KeyError
+        if `bids_keys['task']` is empty
+    """
+    utils.check_file_exists(heur_file)
+
+    # Initialise a dictionary of bids_keys that has already "recording"
+    bids_keys = {'sub': '', 'ses': '', 'task': '', 'acq': '', 'ce': '',
+                 'dir': '', 'rec': '', 'run': '', 'recording': record_label}
+
+    # Start filling bids_keys dictionary and path with subject and session
+    if sub.startswith('sub-'):
+        bids_keys['sub'] = sub[4:]
+        fldr = os.path.join(outdir, sub)
+    else:
+        bids_keys['sub'] = sub
+        fldr = os.path.join(outdir, f'sub-{sub}')
+
+    if ses:
+        if ses.startswith('ses-'):
+            bids_keys['ses'] = ses[4:]
+            fldr = os.path.join(fldr, ses)
+        else:
+            bids_keys['ses'] = ses
+            fldr = os.path.join(fldr, f'ses-{ses}')
+
+    # Load heuristic and use it to fill dictionary
+    heur = utils.load_heuristic(heur_file)
+    bids_keys.update(heur.heur(Path(filename).stem))
+
+    # If bids_keys['task'] is still empty, stop the program
+    if not bids_keys['task']:
+        LGR.warning(f'The heuristic {heur_file} could not deal with'
+                    f'{Path(filename).stem}')
+        raise KeyError('No "task" attribute found')
+
+    # Compose name by looping in the bids_keys dictionary
+    # and adding nonempty keys
+    name = ''
+    for key in bids_keys:
+        if bids_keys[key] != '':
+            name = f'{name}{key}-{bids_keys[key]}_'
+
+    # Finish path, create it, add filename, export
+    fldr = os.path.join(fldr, 'func')
+    utils.path_exists_or_make_it(fldr)
+
+    heurpath = os.path.join(fldr, f'{name}physio')
+
+    return heurpath

phys2bids/phys2bids.py

@@ -30,14 +30,13 @@
 import datetime
 import logging
 from copy import deepcopy
-from pathlib import Path
 
 from numpy import savetxt
 
 from phys2bids import utils, viz, _version
+from phys2bids.bids import bidsify_units, use_heuristic
 from phys2bids.cli.run import _get_parser
 from phys2bids.physio_obj import BlueprintOutput
-from phys2bids.bids_units import bidsify_units
 
 LGR = logging.getLogger(__name__)
 
@@ -111,84 +110,6 @@ def print_json(outfile, samp_freq, time_offset, ch_name):
     utils.writejson(outfile, summary, indent=4, sort_keys=False)
 
 
-def use_heuristic(heur_file, sub, ses, filename, outdir, record_label=''):
-    """
-    Import and use the heuristic specified by the user to rename the file.
-
-    Parameters
-    ----------
-    heur_file: path
-        Fullpath to heuristic file.
-    sub: str or int
-        Name of subject.
-    ses: str or int or None
-        Name of session.
-    filename: path
-        Name of the input of phys2bids.
-    outdir: str or path
-        Path to the directory that will become the "site" folder
-        ("root" folder of BIDS database).
-    record_label: str
-        Optional label for the "record" entry of BIDS.
-
-    Returns
-    -------
-    heurpath: str or path
-        Returned fullpath to tsv.gz new file (post BIDS formatting).
-
-    Raises
-    ------
-    KeyError
-        if `bids_keys['task']` is empty
-    """
-    utils.check_file_exists(heur_file)
-
-    # Initialise a dictionary of bids_keys that has already "recording"
-    bids_keys = {'sub': '', 'ses': '', 'task': '', 'acq': '', 'ce': '',
-                 'dir': '', 'rec': '', 'run': '', 'recording': record_label}
-
-    # Start filling bids_keys dictionary and path with subject and session
-    if sub.startswith('sub-'):
-        bids_keys['sub'] = sub[4:]
-        fldr = os.path.join(outdir, sub)
-    else:
-        bids_keys['sub'] = sub
-        fldr = os.path.join(outdir, f'sub-{sub}')
-
-    if ses:
-        if ses.startswith('ses-'):
-            bids_keys['ses'] = ses[4:]
-            fldr = os.path.join(fldr, ses)
-        else:
-            bids_keys['ses'] = ses
-            fldr = os.path.join(fldr, f'ses-{ses}')
-
-    # Load heuristic and use it to fill dictionary
-    heur = utils.load_heuristic(heur_file)
-    bids_keys.update(heur.heur(Path(filename).stem))
-
-    # If bids_keys['task'] is still empty, stop the program
-    if not bids_keys['task']:
-        LGR.warning(f'The heuristic {heur_file} could not deal with'
-                    f'{Path(filename).stem}')
-        raise KeyError('No "task" attribute found')
-
-    # Compose name by looping in the bids_keys dictionary
-    # and adding nonempty keys
-    name = ''
-    for key in bids_keys:
-        if bids_keys[key] != '':
-            name = f'{name}{key}-{bids_keys[key]}_'
-
-    # Finish path, create it, add filename, export
-    fldr = os.path.join(fldr, 'func')
-    utils.path_exists_or_make_it(fldr)
-
-    heurpath = os.path.join(fldr, f'{name}physio')
-
-    return heurpath
-
-
 def phys2bids(filename, info=False, indir='.', outdir='.', heur_file=None,
               sub=None, ses=None, chtrig=0, chsel=None, num_timepoints_expected=0,
               tr=1, thr=None, ch_name=[], chplot='', debug=False, quiet=False):

phys2bids/tests/test_bids.py

@@ -0,0 +1,60 @@
+import os
+
+from pkg_resources import resource_filename
+
+import pytest
+
+from phys2bids.bids import bidsify_units, use_heuristic
+from phys2bids.bids import UNIT_ALIASES
+
+
+def test_bidsify_units():
+    # Add a dictionary of test possibilities
+    unit_tests = {
+                  # test unit with standard prefix
+                  'centik': 'cK', 'CENTIk': 'cK',
+                  # test unit with not standard prefix
+                  'matV': 'matV', 'BigV': 'BigV',
+                  # test unit that are not bids standard
+                  'mmHg': 'mmHg', 'mmlie': 'mmlie', 'MMLIE': 'MMLIE',
+                 }
+    # Actually test
+    for unit_key in unit_tests.keys():
+        assert bidsify_units(unit_key) == unit_tests[unit_key]
+    # test there is not problem with every unit in the dict
+    for unit_key in UNIT_ALIASES.keys():
+        assert bidsify_units(unit_key) == UNIT_ALIASES[unit_key]
+
+
+@pytest.mark.parametrize('test_sub', ['SBJ01', 'sub-006', '006'])
+@pytest.mark.parametrize('test_ses', ['', 'S05', 'ses-42', '42'])
+def test_use_heuristic(tmpdir, test_sub, test_ses):
+    test_heur_path = resource_filename('phys2bids', 'heuristics')
+    test_heur_file = 'heur_test_acq.py'
+    test_full_heur_path = os.path.join(test_heur_path, test_heur_file)
+    test_input_path = resource_filename('phys2bids', 'tests/data')
+    test_input_file = 'Test_belt_pulse_samefreq.acq'
+    test_full_input_path = os.path.join(test_input_path, test_input_file)
+    test_outdir = tmpdir
+    test_record_label = 'test'
+
+    heur_path = use_heuristic(test_full_heur_path, test_sub, test_ses,
+                              test_full_input_path, test_outdir, test_record_label)
+
+    if test_sub[:4] == 'sub-':
+        test_sub = test_sub[4:]
+
+    test_result_path = (f'{tmpdir}/sub-{test_sub}')
+    test_result_name = (f'sub-{test_sub}')
+
+    if test_ses[:4] == 'ses-':
+        test_ses = test_ses[4:]
+
+    if test_ses:
+        test_result_path = (f'{test_result_path}/ses-{test_ses}')
+        test_result_name = (f'{test_result_name}_ses-{test_ses}')
+
+    test_result = (f'{test_result_path}/func/{test_result_name}'
+                   f'_task-test_rec-biopac_run-01_recording-test_physio')
+
+    assert os.path.normpath(test_result) == os.path.normpath(str(heur_path))

phys2bids/tests/test_phys2bids.py

@@ -4,9 +4,6 @@
 
 import json
 import os
-from pkg_resources import resource_filename
-
-import pytest
 
 from phys2bids import phys2bids
 
@@ -44,37 +41,3 @@ def test_print_json(tmpdir):
         loaded_data = json.load(src)
 
     assert test_json_data == loaded_data
-
-
-@pytest.mark.parametrize('test_sub', ['SBJ01', 'sub-006', '006'])
-@pytest.mark.parametrize('test_ses', ['', 'S05', 'ses-42', '42'])
-def test_use_heuristic(tmpdir, test_sub, test_ses):
-    test_heur_path = resource_filename('phys2bids', 'heuristics')
-    test_heur_file = 'heur_test_acq.py'
-    test_full_heur_path = os.path.join(test_heur_path, test_heur_file)
-    test_input_path = resource_filename('phys2bids', 'tests/data')
-    test_input_file = 'Test_belt_pulse_samefreq.acq'
-    test_full_input_path = os.path.join(test_input_path, test_input_file)
-    test_outdir = tmpdir
-    test_record_label = 'test'
-
-    heur_path = phys2bids.use_heuristic(test_full_heur_path, test_sub, test_ses,
-                                        test_full_input_path, test_outdir, test_record_label)
-
-    if test_sub[:4] == 'sub-':
-        test_sub = test_sub[4:]
-
-    test_result_path = (f'{tmpdir}/sub-{test_sub}')
-    test_result_name = (f'sub-{test_sub}')
-
-    if test_ses[:4] == 'ses-':
-        test_ses = test_ses[4:]
-
-    if test_ses:
-        test_result_path = (f'{test_result_path}/ses-{test_ses}')
-        test_result_name = (f'{test_result_name}_ses-{test_ses}')
-
-    test_result = (f'{test_result_path}/func/{test_result_name}'
-                   f'_task-test_rec-biopac_run-01_recording-test_physio')
-
-    assert os.path.normpath(test_result) == os.path.normpath(str(heur_path))