Merge pull request #10 from dbic/adds_populate_intended_for

Two quick and dirty patches while I have tried to use that branch

Author: pvelasco

heudiconv/bids.py

@@ -4,6 +4,7 @@
 import os
 import os.path as op
 import logging
+import numpy as np
 import re
 from collections import OrderedDict
 from datetime import datetime
@@ -612,8 +613,10 @@ def get_key_info_for_fmap_assignment(json_file, matching_parameter='ImagingVolum
     elif matching_parameter == 'ImagingVolume':
         from nibabel import load as nb_load
         nifti_file = glob(remove_suffix(json_file, '.json') + '.nii*')
+        assert len(nifti_file) == 1
+        nifti_file = nifti_file[0] 
         nifti_header = nb_load(nifti_file).header
-        key_info = [nifti_header.affine, nifti_header.dim[1:3]]
+        key_info = [nifti_header.get_best_affine(), nifti_header.get_data_shape()[:3]]
     elif matching_parameter == 'AcquisitionLabel':
         # Check the acq label for the fmap and the modality for others:
         modality = op.basename(op.dirname(json_file))
@@ -677,10 +680,13 @@ def find_compatible_fmaps_for_run(json_file, fmap_groups, matching_parameters=['
         compatible = False
         for param in matching_parameters:
             fm_info = get_key_info_for_fmap_assignment(fm_group[0], param)
-            if json_info[param] == fm_info:
-                compatible = True
+            # for the case in which key_info is a list of strings:
+            if type(json_info[param][0]):
+                compatible = json_info[param] == fm_info
             else:
-                compatible = False
+                # allow for tiny differences between the affines etc
+                compatible = all(np.allclose(x, y) for x, y in zip(json_info[param], fm_info))
+            if not compatible:
                 continue     # don't bother checking more params
         if compatible:
             compatible_fmap_groups[fm_key] = fm_group

heudiconv/main.py

@@ -109,11 +109,15 @@ def process_extra_commands(outdir, command, files, dicom_dir_template,
         from .utils import get_heuristic_description
         print(get_heuristic_description(heuristic, full=True))
     elif command == 'populate-intended-for':
+        kwargs = {}
+        if heuristic:
+            heuristic = load_heuristic(heuristic)
+            kwargs = getattr(heuristic, 'POPULATE_INTENDED_FOR_OPTS', {})
         for subj in subjs:
             session_path = op.join(outdir, 'sub-' + subj)
             if session:
                 session_path = op.join(session_path, 'ses-' + session)
-            populate_intended_for(session_path)
+            populate_intended_for(session_path, **kwargs)
     else:
         raise ValueError("Unknown command %s" % command)
     return

heudiconv/tests/data/sample_nifti.nii.gz

@@ -0,0 +1,5 @@
+-1.99887669 0.0670080110 0.00144872535 109.236588
+0.0650372952 1.94962955 -0.441264838 -71.7261658
+0.0161963794 0.440969884 1.95071352 -64.1231308
+ 0 0 0 1
+ 5 5 5 1

heudiconv/tests/data/sample_nifti_params.txt

@@ -10,18 +10,20 @@
 from datetime import (datetime,
                       timedelta,
                       )
-from collections import (namedtuple,
-                         OrderedDict,
+from collections import (OrderedDict,
                          )
 from glob import glob
 
 import nibabel
+from numpy import testing as np_testing
 
 from heudiconv.utils import (
     load_json,
     save_json,
     create_tree,
+    remove_suffix,
 )
+
 from heudiconv.bids import (
     maybe_na,
     treat_age,
@@ -38,6 +40,10 @@
     BIDSFile,
 )
 
+from .utils import (
+    TESTS_DATA_PATH,
+)
+
 import pytest
 
 def test_maybe_na():
@@ -63,7 +69,7 @@ def test_treat_age():
 TODAY = datetime.today()
 
 
-A_SHIM = ['{0:.4f}'.format(random()) for i in range(SHIM_LENGTH)]
+A_SHIM = [random() for i in range(SHIM_LENGTH)]
 def test_get_shim_setting(tmpdir):
     """ Tests for get_shim_setting """
     json_dir = op.join(str(tmpdir), 'foo')
@@ -80,38 +86,24 @@ def test_get_shim_setting(tmpdir):
     assert get_shim_setting(json_name) == A_SHIM
 
 
-def test_get_key_info_for_fmap_assignment(tmpdir, monkeypatch):
+def test_get_key_info_for_fmap_assignment(tmpdir):
     """
     Test get_key_info_for_fmap_assignment
     """
 
-    # Stuff needed to mock reading of a NIfTI file header:
-
-    # affines (qforms/sforms) are 4x4 matrices
-    MY_AFFINE = [[random() for i in range(4)] for j in range(4)]
-    # dims are arrays with 8 elements with the first one indicating the number
-    # of dims in the image; remaining elements are 1:
-    MY_DIM = [4] + [round(256 * random()) for i in range(4)] + [1] * 3
-    # We use namedtuples so that we can use the .dot notation, to mock
-    # nibabel headers:
-    MyHeader = namedtuple('MyHeader', 'affine dim')
-    MY_HEADER = MyHeader(MY_AFFINE, MY_DIM)
-    MyMockNifti = namedtuple('MyMockNifti', 'header')
-
-    def mock_nibabel_load(file):
-        """
-        Pretend we run nibabel.load, but return only a header with just a few fields
-        """
-        return MyMockNifti(MY_HEADER)
-    monkeypatch.setattr(nibabel, "load", mock_nibabel_load)
-
-    json_name = op.join(str(tmpdir), 'foo.json')
+    nifti_file = op.join(TESTS_DATA_PATH, 'sample_nifti.nii.gz')
+    # Get the expected parameters from the NIfTI header:
+    MY_HEADER = nibabel.ni1.np.loadtxt(
+        op.join(TESTS_DATA_PATH, remove_suffix(nifti_file, '.nii.gz') + '_params.txt')
+    )
+    json_name = op.join(TESTS_DATA_PATH, remove_suffix(nifti_file, '.nii.gz') + '.json')
 
     # 1) Call for a non-existing file should give an error:
     with pytest.raises(FileNotFoundError):
         assert get_key_info_for_fmap_assignment('foo.json')
 
     # 2) matching_parameters = 'Shims'
+    json_name = op.join(TESTS_DATA_PATH, remove_suffix(nifti_file, '.nii.gz') + '.json')
     save_json(json_name, {SHIM_KEY: A_SHIM})      # otherwise get_key_info_for_fmap_assignment will give an error
     key_info = get_key_info_for_fmap_assignment(
         json_name, matching_parameter='Shims'
@@ -122,7 +114,8 @@ def mock_nibabel_load(file):
     key_info = get_key_info_for_fmap_assignment(
         json_name, matching_parameter='ImagingVolume'
     )
-    assert key_info == [MY_AFFINE, MY_DIM[1:3]]
+    np_testing.assert_almost_equal(key_info[0], MY_HEADER[:4], decimal=6)
+    np_testing.assert_almost_equal(key_info[1], MY_HEADER[4][:3], decimal=6)
 
     # 4) matching_parameters = 'Force'
     key_info = get_key_info_for_fmap_assignment(
@@ -222,10 +215,10 @@ def create_dummy_pepolar_bids_session(session_path):
     # 1) Simulate the file structure for a session:
 
     # Generate some random ShimSettings:
-    anat_shims = ['{0:.4f}'.format(random()) for i in range(SHIM_LENGTH)]
-    dwi_shims = ['{0:.4f}'.format(random()) for i in range(SHIM_LENGTH)]
-    func_shims_A = ['{0:.4f}'.format(random()) for i in range(SHIM_LENGTH)]
-    func_shims_B = ['{0:.4f}'.format(random()) for i in range(SHIM_LENGTH)]
+    anat_shims = [random() for i in range(SHIM_LENGTH)]
+    dwi_shims = [random() for i in range(SHIM_LENGTH)]
+    func_shims_A = [random() for i in range(SHIM_LENGTH)]
+    func_shims_B = [random() for i in range(SHIM_LENGTH)]
 
     # Dict with the file structure for the session:
     # -anat:
@@ -249,7 +242,7 @@ def create_dummy_pepolar_bids_session(session_path):
         '{p}_acq-A_bold.json'.format(p=prefix): {'ShimSetting': func_shims_A},
         '{p}_acq-B_bold.json'.format(p=prefix): {'ShimSetting': func_shims_B},
         '{p}_acq-unmatched_bold.json'.format(p=prefix): {
-            'ShimSetting': ['{0:.4f}'.format(random()) for i in range(SHIM_LENGTH)]
+            'ShimSetting': [random() for i in range(SHIM_LENGTH)]
         },
     })
     # -fmap:
@@ -541,9 +534,9 @@ def create_dummy_magnitude_phase_bids_session(session_path):
     # 1) Simulate the file structure for a session:
 
     # Generate some random ShimSettings:
-    dwi_shims = ['{0:.4f}'.format(random()) for i in range(SHIM_LENGTH)]
-    func_shims_A = ['{0:.4f}'.format(random()) for i in range(SHIM_LENGTH)]
-    func_shims_B = ['{0:.4f}'.format(random()) for i in range(SHIM_LENGTH)]
+    dwi_shims = [random() for i in range(SHIM_LENGTH)]
+    func_shims_A = [random() for i in range(SHIM_LENGTH)]
+    func_shims_B = [random() for i in range(SHIM_LENGTH)]
 
     # Dict with the file structure for the session:
     # -dwi:
@@ -561,7 +554,7 @@ def create_dummy_magnitude_phase_bids_session(session_path):
         '{p}_acq-A_bold.json'.format(p=prefix): {'ShimSetting': func_shims_A},
         '{p}_acq-B_bold.json'.format(p=prefix): {'ShimSetting': func_shims_B},
         '{p}_acq-unmatched_bold.json'.format(p=prefix): {
-            'ShimSetting': ['{0:.4f}'.format(random()) for i in range(SHIM_LENGTH)]
+            'ShimSetting': [random() for i in range(SHIM_LENGTH)]
         },
     })
     # -fmap: