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Merge branch 'main' of github.com:PennLINC/CuBIDS
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@scovitz
scovitz committed Jun 5, 2023
2 parents 0c2f3c8 + 1379f66 commit 71a7026
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Showing 2 changed files with 85 additions and 58 deletions.
2 changes: 1 addition & 1 deletion .circleci/config.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -75,7 +75,7 @@ jobs:
conda config --set always_yes yes
conda update conda
conda info -a
conda create -n cubids python=3.7
conda create -n cubids python=3.8
source activate cubids
conda install -c conda-forge -y datalad
conda install pip
Expand Down
141 changes: 84 additions & 57 deletions cubids/cubids.py
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Original file line number Diff line number Diff line change
Expand Up @@ -56,9 +56,9 @@ def __init__(self, data_root, use_datalad=False, acq_group_level='subject',
@property
def layout(self):
if self._layout is None:
print("SETTING LAYOUT OBJECT")
# print("SETTING LAYOUT OBJECT")
self.reset_bids_layout()
print("LAYOUT OBJECT SET")
# print("LAYOUT OBJECT SET")
return self._layout

def reset_bids_layout(self, validate=False):
Expand Down Expand Up @@ -499,6 +499,9 @@ def change_filename(self, filepath, entities):
# json_file = self.layout.get_file(str(path))
# data = json_file.get_dict()
data = get_sidecar_metadata(str(path))
if data == "Erroneous sidecar":
print('Error parsing sidecar: ', str(path))
continue

if 'IntendedFor' in data.keys():
# check if IntendedFor field is a str or list
Expand Down Expand Up @@ -630,9 +633,11 @@ def _purge_associations(self, scans):
# json_file = self.layout.get_file(str(path))
# data = json_file.get_dict()
data = get_sidecar_metadata(str(path))
if data == "Erroneous sidecar":
print('Error parsing sidecar: ', str(path))
continue

# remove scan references in the IntendedFor

if 'IntendedFor' in data.keys():
# check if IntendedFor field value is a list or a string
if isinstance(data['IntendedFor'], str):
Expand Down Expand Up @@ -757,7 +762,11 @@ def _cache_fieldmaps(self):
for fmap_file in tqdm(fmap_files):
# intentions = listify(fmap_file.get_metadata().get("IntendedFor"))
fmap_json = img_to_new_ext(fmap_file.path, '.json')
if_list = get_sidecar_metadata(fmap_json).get("IntendedFor")
metadata = get_sidecar_metadata(fmap_json)
if metadata == "Erroneous sidecar":
print('Error parsing sidecar: ', str(fmap_json))
continue
if_list = metadata.get("IntendedFor")
intentions = listify(if_list)
subject_prefix = "sub-%s" % fmap_file.entities['subject']

Expand Down Expand Up @@ -824,6 +833,9 @@ def get_param_groups_from_key_group(self, key_group):
to_include, self.layout, self.fieldmap_lookup, key_group,
self.grouping_config, modality, self.keys_files)

if ret == "erroneous sidecar found":
return "erroneous sidecar found"

# add modality to the retun tuple
l_ret = list(ret)
l_ret.append(modality)
Expand Down Expand Up @@ -946,8 +958,11 @@ def get_param_groups_dataframes(self):
labeled_files = []
param_group_summaries = []
for key_group in key_groups:
labeled_file_params, param_summary, modality = \
self.get_param_groups_from_key_group(key_group)
try:
labeled_file_params, param_summary, modality = \
self.get_param_groups_from_key_group(key_group)
except Exception:
continue
if labeled_file_params is None:
continue
param_group_summaries.append(param_summary)
Expand Down Expand Up @@ -1148,7 +1163,7 @@ def get_TSVs(self, path_prefix):
group_by_acquisition_sets(path_prefix + "_files.tsv", path_prefix,
self.acq_group_level)

print("Detected " + str(len(summary)) + " Parameter Groups.")
print("CuBIDS detected " + str(len(summary)) + " Parameter Groups.")

def get_key_groups(self):
'''Identifies the key groups for the bids dataset'''
Expand Down Expand Up @@ -1338,58 +1353,62 @@ def _get_param_groups(files, layout, fieldmap_lookup, key_group_name,

dfs = []
# path needs to be relative to the root with no leading prefix

for path in files:
# metadata = layout.get_metadata(path)
metadata = get_sidecar_metadata(img_to_new_ext(path, '.json'))
intentions = metadata.get("IntendedFor", [])
slice_times = metadata.get("SliceTiming", [])

wanted_keys = metadata.keys() & imaging_params
example_data = {key: metadata[key] for key in wanted_keys}
example_data["KeyGroup"] = key_group_name

# Get the fieldmaps out and add their types
if 'FieldmapKey' in relational_params:
fieldmap_types = sorted([_file_to_key_group(fmap.path) for
fmap in fieldmap_lookup[path]])

# check if config says columns or bool
if relational_params['FieldmapKey']['display_mode'] == \
'bool':
if len(fieldmap_types) > 0:
example_data['HasFieldmap'] = True
if metadata == "Erroneous sidecar":
print('Error parsing sidecar: ', img_to_new_ext(path, '.json'))
else:
intentions = metadata.get("IntendedFor", [])
slice_times = metadata.get("SliceTiming", [])

wanted_keys = metadata.keys() & imaging_params
example_data = {key: metadata[key] for key in wanted_keys}
example_data["KeyGroup"] = key_group_name

# Get the fieldmaps out and add their types
if 'FieldmapKey' in relational_params:
fieldmap_types = sorted([_file_to_key_group(fmap.path) for
fmap in fieldmap_lookup[path]])

# check if config says columns or bool
if relational_params['FieldmapKey']['display_mode'] == \
'bool':
if len(fieldmap_types) > 0:
example_data['HasFieldmap'] = True
else:
example_data['HasFieldmap'] = False
else:
example_data['HasFieldmap'] = False
else:
for fmap_num, fmap_type in enumerate(fieldmap_types):
example_data['FieldmapKey%02d' % fmap_num] = fmap_type
for fmap_num, fmap_type in enumerate(fieldmap_types):
example_data['FieldmapKey%02d' % fmap_num] = fmap_type

# Add the number of slice times specified
if "NSliceTimes" in derived_params:
example_data["NSliceTimes"] = len(slice_times)
# Add the number of slice times specified
if "NSliceTimes" in derived_params:
example_data["NSliceTimes"] = len(slice_times)

example_data["FilePath"] = path
example_data["FilePath"] = path

# If it's a fieldmap, see what key group it's intended to correct
if "IntendedForKey" in relational_params:
intended_key_groups = sorted([_file_to_key_group(intention) for
intention in intentions])
# If it's a fieldmap, see what key group it's intended to correct
if "IntendedForKey" in relational_params:
intended_key_groups = sorted([_file_to_key_group(intention) for
intention in intentions])

# check if config says columns or bool
if relational_params['IntendedForKey']['display_mode'] == \
'bool':
if len(intended_key_groups) > 0:
example_data["UsedAsFieldmap"] = True
# check if config says columns or bool
if relational_params['IntendedForKey']['display_mode'] == \
'bool':
if len(intended_key_groups) > 0:
example_data["UsedAsFieldmap"] = True
else:
example_data["UsedAsFieldmap"] = False
else:
example_data["UsedAsFieldmap"] = False
else:
for intention_num, intention_key_group in \
enumerate(intended_key_groups):
example_data[
"IntendedForKey%02d" % intention_num] = \
intention_key_group
for intention_num, intention_key_group in \
enumerate(intended_key_groups):
example_data[
"IntendedForKey%02d" % intention_num] = \
intention_key_group

dfs.append(example_data)
dfs.append(example_data)

# Assign each file to a ParamGroup

Expand All @@ -1406,10 +1425,13 @@ def _get_param_groups(files, layout, fieldmap_lookup, key_group_name,
if "Cluster_" + col not in list(df.columns) and col != 'FilePath':
check_cols.append(col)

# Find the unique ParamGroups and assign ID numbers in "ParamGroup"
deduped = df.drop('FilePath', axis=1).drop_duplicates(subset=check_cols,
ignore_index=True)
# Find the unique ParamGroups and assign ID numbers in "ParamGroup"\
try:
deduped = df.drop('FilePath', axis=1)
except Exception:
return "erroneous sidecar found"

deduped = deduped.drop_duplicates(subset=check_cols, ignore_index=True)
deduped["ParamGroup"] = np.arange(deduped.shape[0]) + 1

# add the modality as a column
Expand Down Expand Up @@ -1464,18 +1486,23 @@ def round_params(param_group_df, config, modality):
if column_name not in param_group_df:
continue
if 'precision' in column_fmt:
param_group_df[column_name] = \
param_group_df[column_name].round(column_fmt['precision'])
if isinstance(param_group_df[column_name], float):
param_group_df[column_name] = \
param_group_df[column_name].round(column_fmt['precision'])

return param_group_df


def get_sidecar_metadata(json_file):
# get all metadata values in a file's sidecar
# transform json dictionary to python dictionary
with open(json_file) as json_file:
data = json.load(json_file)
return data
try:
with open(json_file) as json_file:
data = json.load(json_file)
return data
except Exception:
# print("Error loading sidecar: ", json_filename)
return "Erroneous sidecar"


def format_params(param_group_df, config, modality):
Expand Down

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