Repository: nipy/heudiconv

Issue:
Support for complex multi-echo fMRI
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### Summary
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- log of conversion
- heuristic
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Functional phase data (from magnitude+phase reconstruction of fMRI data) is not currently supported as a multi-echo data type. I know that there are plans for a more robust form of support for multi-volume sequences in #346, but in the meantime I think that `_phase` needs to be added to the [list of supported multi-echo data types](https://github.com/nipy/heudiconv/blob/5cfb6f2835f76b8c9d6f19c45e8be0759535900f/heudiconv/convert.py#L583).

### Platform details:

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- [X] Local environment: OSX Mojave, Python 3.6.2
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- [ ] Container
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- Heudiconv version: latest, as of 5cfb6f2
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Comments:

Patch:
diff --git a/heudiconv/bids.py b/heudiconv/bids.py
index 1bbfcf6..9569278 100644
--- a/heudiconv/bids.py
+++ b/heudiconv/bids.py
@@ -240,6 +240,27 @@ def add_participant_record(studydir, subject, age, sex):
             known_subjects = {l.split('\t')[0] for l in f.readlines()}
         if participant_id in known_subjects:
             return
+    else:
+        # Populate particpants.json (an optional file to describe column names in
+        # participant.tsv). This auto generation will make BIDS-validator happy.
+        participants_json = op.join(studydir, 'participants.json')
+        if not op.lexists(participants_json):
+            save_json(participants_json,
+                OrderedDict([
+                    ("participant_id", OrderedDict([
+                        ("Description", "Participant identifier")])),
+                    ("age", OrderedDict([
+                        ("Description", "Age in years (TODO - verify) as in the initial"
+                            " session, might not be correct for other sessions")])),
+                    ("sex", OrderedDict([
+                        ("Description", "self-rated by participant, M for male/F for "
+                            "female (TODO: verify)")])),
+                    ("group", OrderedDict([
+                        ("Description", "(TODO: adjust - by default everyone is in "
+                            "control group)")])),
+                ]),
+                sort_keys=False,
+                indent=2)
     # Add a new participant
     with open(participants_tsv, 'a') as f:
         f.write(
@@ -311,7 +332,8 @@ def save_scans_key(item, bids_files):
 
 def add_rows_to_scans_keys_file(fn, newrows):
     """
-    Add new rows to file fn for scans key filename
+    Add new rows to file fn for scans key filename and generate accompanying json
+    descriptor to make BIDS validator happy.
 
     Parameters
     ----------
@@ -334,6 +356,25 @@ def add_rows_to_scans_keys_file(fn, newrows):
         os.unlink(fn)
     else:
         fnames2info = newrows
+        # Populate _scans.json (an optional file to describe column names in
+        # _scans.tsv). This auto generation will make BIDS-validator happy.
+        scans_json = '.'.join(fn.split('.')[:-1] + ['json'])
+        if not op.lexists(scans_json):
+            save_json(scans_json,
+                OrderedDict([
+                    ("filename", OrderedDict([
+                        ("Description", "Name of the nifti file")])),
+                    ("acq_time", OrderedDict([
+                        ("LongName", "Acquisition time"),
+                        ("Description", "Acquisition time of the particular scan")])),
+                    ("operator", OrderedDict([
+                        ("Description", "Name of the operator")])),
+                    ("randstr", OrderedDict([
+                        ("LongName", "Random string"),
+                        ("Description", "md5 hash of UIDs")])),
+                ]),
+                sort_keys=False,
+                indent=2)
 
     header = ['filename', 'acq_time', 'operator', 'randstr']
     # prepare all the data rows
diff --git a/heudiconv/convert.py b/heudiconv/convert.py
index 5a5db05..1c16bb0 100644
--- a/heudiconv/convert.py
+++ b/heudiconv/convert.py
@@ -580,7 +580,7 @@ def save_converted_files(res, item_dicoms, bids_options, outtype, prefix, outnam
                 else:
                     echo_number = echo_times.index(fileinfo['EchoTime']) + 1
 
-                supported_multiecho = ['_bold', '_epi', '_sbref', '_T1w', '_PDT2']
+                supported_multiecho = ['_bold', '_phase', '_epi', '_sbref', '_T1w', '_PDT2']
                 # Now, decide where to insert it.
                 # Insert it **before** the following string(s), whichever appears first.
                 for imgtype in supported_multiecho:
diff --git a/heudiconv/info.py b/heudiconv/info.py
index b970b3b..feeae46 100644
--- a/heudiconv/info.py
+++ b/heudiconv/info.py
@@ -8,6 +8,19 @@ __longdesc__ = """Convert DICOM dirs based on heuristic info - HeuDiConv
 uses the dcmstack package and dcm2niix tool to convert DICOM directories or
 tarballs into collections of NIfTI files following pre-defined heuristic(s)."""
 
+CLASSIFIERS = [
+    'Environment :: Console',
+    'Intended Audience :: Science/Research',
+    'License :: OSI Approved :: Apache Software License',
+    'Programming Language :: Python :: 2.7',
+    'Programming Language :: Python :: 3.5',
+    'Programming Language :: Python :: 3.6',
+    'Programming Language :: Python :: 3.7',
+    'Topic :: Scientific/Engineering'
+]
+
+PYTHON_REQUIRES = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*"
+
 REQUIRES = [
     'nibabel',
     'pydicom',
diff --git a/heudiconv/utils.py b/heudiconv/utils.py
index abea820..2453e9d 100644
--- a/heudiconv/utils.py
+++ b/heudiconv/utils.py
@@ -19,6 +19,11 @@ from nipype.utils.filemanip import which
 import logging
 lgr = logging.getLogger(__name__)
 
+if sys.version_info[0] > 2:
+    from json.decoder import JSONDecodeError
+else:
+    JSONDecodeError = ValueError
+
 
 seqinfo_fields = [
     'total_files_till_now',  # 0
@@ -172,10 +177,15 @@ def load_json(filename):
     -------
     data : dict
     """
-    with open(filename, 'r') as fp:
-        data = json.load(fp)
-    return data
+    try:
+        with open(filename, 'r') as fp:
+            data = json.load(fp)
+    except JSONDecodeError:
+        lgr.error("{fname} is not a valid json file".format(fname=filename))
+        raise
 
+    return data
+    
 
 def assure_no_file_exists(path):
     """Check if file or symlink (git-annex?) exists, and if so -- remove"""
diff --git a/setup.py b/setup.py
index 6017447..c3a804a 100755
--- a/setup.py
+++ b/setup.py
@@ -47,11 +47,13 @@ def main():
         description=ldict['__description__'],
         long_description=ldict['__longdesc__'],
         license=ldict['__license__'],
+        classifiers=ldict['CLASSIFIERS'],
         packages=heudiconv_pkgs,
         entry_points={'console_scripts': [
             'heudiconv=heudiconv.cli.run:main',
             'heudiconv_monitor=heudiconv.cli.monitor:main',
         ]},
+        python_requires=ldict['PYTHON_REQUIRES'],
         install_requires=ldict['REQUIRES'],
         extras_require=ldict['EXTRA_REQUIRES'],
         package_data={


Test patch:
diff --git a/heudiconv/tests/test_heuristics.py b/heudiconv/tests/test_heuristics.py
index c9485c6..f36bbb4 100644
--- a/heudiconv/tests/test_heuristics.py
+++ b/heudiconv/tests/test_heuristics.py
@@ -165,7 +165,13 @@ def test_notop(tmpdir, bidsoptions):
     runner(args)
 
     assert op.exists(pjoin(tmppath, 'Halchenko/Yarik/950_bids_test4'))
-    for fname in ['CHANGES', 'dataset_description.json', 'participants.tsv', 'README']:
+    for fname in [
+        'CHANGES',
+        'dataset_description.json',
+        'participants.tsv',
+        'README',
+        'participants.json'
+    ]:
         if 'notop' in bidsoptions:
             assert not op.exists(pjoin(tmppath, 'Halchenko/Yarik/950_bids_test4', fname))
         else:
diff --git a/heudiconv/tests/test_main.py b/heudiconv/tests/test_main.py
index 7dcd32e..f4b7700 100644
--- a/heudiconv/tests/test_main.py
+++ b/heudiconv/tests/test_main.py
@@ -22,6 +22,7 @@ from mock import patch
 from os.path import join as opj
 from six.moves import StringIO
 import stat
+import os.path as op
 
 
 @patch('sys.stdout', new_callable=StringIO)
@@ -205,6 +206,7 @@ def test_add_rows_to_scans_keys_file(tmpdir):
         assert dates == sorted(dates)
 
     _check_rows(fn, rows)
+    assert op.exists(opj(tmpdir.strpath, 'file.json'))
     # add a new one
     extra_rows = {
         'a_new_file.nii.gz': ['2016adsfasd23', '', 'fasadfasdf'],
diff --git a/heudiconv/tests/test_utils.py b/heudiconv/tests/test_utils.py
index 47faec4..ad84673 100644
--- a/heudiconv/tests/test_utils.py
+++ b/heudiconv/tests/test_utils.py
@@ -1,10 +1,16 @@
+import json
 import os
 import os.path as op
+
 from heudiconv.utils import (
     get_known_heuristics_with_descriptions,
     get_heuristic_description,
     load_heuristic,
-    json_dumps_pretty)
+    json_dumps_pretty,
+    load_json,
+    create_tree,
+    save_json,
+    JSONDecodeError)
 
 import pytest
 from .utils import HEURISTICS_PATH
@@ -58,4 +64,24 @@ def test_json_dumps_pretty():
           'Mar  3 2017 10:46:13 by eja'
     # just the date which reveals the issue
     # tstr = 'Mar  3 2017 10:46:13 by eja'
-    assert pretty({'WipMemBlock': tstr}) == '{\n  "WipMemBlock": "%s"\n}' % tstr
\ No newline at end of file
+    assert pretty({'WipMemBlock': tstr}) == '{\n  "WipMemBlock": "%s"\n}' % tstr
+
+
+def test_load_json(tmp_path, caplog):
+    # test invalid json
+    ifname = 'invalid.json'
+    invalid_json_file = str(tmp_path / ifname)
+    create_tree(str(tmp_path), {ifname: u"I'm Jason Bourne"})
+
+    with pytest.raises(JSONDecodeError):
+        load_json(str(invalid_json_file))
+
+    assert ifname in caplog.text
+
+    # test valid json
+    vcontent = {"secret": "spy"}
+    vfname = "valid.json"
+    valid_json_file = str(tmp_path / vfname)
+    save_json(valid_json_file, vcontent)
+    
+    assert load_json(valid_json_file) == vcontent