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Merge pull request #1251 from FCP-INDI/develop
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Develop
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@sgiavasis
sgiavasis authored Apr 17, 2020
2 parents 931af2c + 93b8de6 commit eb267de
Showing 1 changed file with 53 additions and 43 deletions.
96 changes: 53 additions & 43 deletions CPAC/utils/bids_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,30 +16,30 @@ def bids_decode_fname(file_path, dbg=False):
"a nifti or json file")

if dbg:
print "parsing %s" % file_path
print("parsing %s" % file_path)

# first figure out if there is a site directory level, this isn't
# specified in BIDS currently, but hopefully will be in the future
file_path_vals = os.path.dirname(file_path).split('/')
sub = [s for s in file_path_vals if 'sub-' in s]
if dbg:
print "found subject %s in %s" % (sub, str(file_path_vals))
print("found subject %s in %s" % (sub, str(file_path_vals)))

if len(sub) > 1:
print ("Odd that there is more than one subject directory" +
print("Odd that there is more than one subject directory" +
"in (%s), does the filename conform to" % file_path +
" BIDS format?")
if sub:
sub_ndx = file_path_vals.index(sub[0])
if sub_ndx > 0 and file_path_vals[sub_ndx - 1]:
if dbg:
print "setting site to %s" % (file_path_vals[sub_ndx - 1])
print("setting site to %s" % (file_path_vals[sub_ndx - 1]))
f_dict["site"] = file_path_vals[sub_ndx - 1]
else:
f_dict["site"] = "none"
elif file_path_vals[-1]:
if dbg:
print ("looking for subject id didn't pan out settling for last"+
print("looking for subject id didn't pan out settling for last"+
"subdir %s" % (str(file_path_vals[-1])))
f_dict["site"] = file_path_vals[-1]
else:
Expand Down Expand Up @@ -104,15 +104,15 @@ def bids_retrieve_params(bids_config_dict, f_dict, dbg=False):
key = "-".join([level, "none"])

if dbg:
print key
print(key)
# if the key doesn't exist in the config dictionary, check to see if
# the generic key exists and return that
if key in t_dict:
t_dict = t_dict[key]
else:
if dbg:
print "Couldn't find %s, so going with %s" % (key,
"-".join([level, "none"]))
print("Couldn't find %s, so going with %s" % (key,
"-".join([level, "none"])))
key = "-".join([level, "none"])
if key in t_dict:
t_dict = t_dict[key]
Expand All @@ -123,15 +123,15 @@ def bids_retrieve_params(bids_config_dict, f_dict, dbg=False):
# sidecare files

if dbg:
print t_dict
print(t_dict)

for key in t_dict.keys():
if u'RepetitionTime' in key:
if 'RepetitionTime' in key:
params = t_dict
break

for k, v in params.items():
if isinstance(v, unicode):
if isinstance(v, str):
params[k] = v.encode('ascii', errors='ignore')

return params
Expand Down Expand Up @@ -166,23 +166,26 @@ def bids_parse_sidecar(config_dict, dbg=False):
t_dict = t_dict[key]

if dbg:
print bids_config_dict
print(bids_config_dict)

# get the paths to the json yaml files in config_dict, the paths contain
# the information needed to map the parameters from the jsons (the vals
# of the config_dict) to corresponding nifti files. We sort the list
# by the number of path components, so that we can iterate from the outer
# most path to inner-most, which will help us address the BIDS inheritance
# principle
config_paths = sorted(config_dict.keys(), key=lambda p: len(p.split('/')))
config_paths = sorted(
list(config_dict.keys()),
key=lambda p: len(p.split('/'))
)

if dbg:
print config_paths
print(config_paths)

for cp in config_paths:

if dbg:
print "processing %s" % (cp)
print("processing %s" % (cp))

# decode the filepath into its various components as defined by BIDS
f_dict = bids_decode_fname(cp)
Expand Down Expand Up @@ -248,15 +251,15 @@ def gen_bids_outputs_sublist(base_path, paths_list, key_list, creds_path):
top_keys = list(set(key_list) - set(func_keys))
bot_keys = list(set(key_list).intersection(func_keys))

print top_keys
print bot_keys
print(top_keys)
print(bot_keys)

subjdict = {}

if not base_path.endswith('/'):
base_path = base_path + '/'

# output directories are a bit different than standard BIDS, so
# output directories are a bit different than standard BIDS, so
# we handle things differently

for p in paths_list:
Expand Down Expand Up @@ -285,33 +288,33 @@ def gen_bids_outputs_sublist(base_path, paths_list, key_list, creds_path):
if run_info not in subjdict[subj_info]["funcs"]:
subjdict[subj_info]["funcs"][run_info] = {'run_info': run_info}
if resource in subjdict[subj_info]["funcs"][run_info]:
print ("warning resource %s already exists in subjdict ??" %
(resource))
print("warning resource %s already exists in subjdict ??" %
(resource))
subjdict[subj_info]["funcs"][run_info][resource] = p
else:
subjdict[subj_info][resource] = p

sublist = []
for subj_info, subj_res in subjdict.iteritems():
for subj_info, subj_res in subjdict.items():
missing = 0
for tkey in top_keys:
if tkey not in subj_res:
print "%s not found for %s" % (tkey, subj_info)
print("%s not found for %s" % (tkey, subj_info))
missing += 1
break

if missing == 0:
for func_key, func_res in subj_res["funcs"].iteritems():
for func_key, func_res in subj_res["funcs"].items():
for bkey in bot_keys:
if bkey not in func_res:
print "%s not found for %s" % (bkey,
func_key)
print("%s not found for %s" % (bkey,
func_key))
missing += 1
break
if missing == 0:
print "adding: %s, %s, %d" % (subj_info,
print("adding: %s, %s, %d" % (subj_info,
func_key,
len(sublist))
len(sublist)))
tdict = copy.deepcopy(subj_res)
del tdict["funcs"]
tdict.update(func_res)
Expand Down Expand Up @@ -343,11 +346,13 @@ def bids_gen_cpac_sublist(bids_dir, paths_list, config_dict, creds_path, dbg=Fal
"""

if dbg:
print( "gen_bids_sublist called with:")
print( " bids_dir: {0}".format(bids_dir))
print( " # paths: {0}".format(str(len(paths_list))))
print( " config_dict: {0}".format( "missing" if not config_dict else "found"))
print( " creds_path: {0}".format(creds_path))
print("gen_bids_sublist called with:")
print(" bids_dir: {0}".format(bids_dir))
print(" # paths: {0}".format(str(len(paths_list))))
print(" config_dict: {0}".format(
"missing" if not config_dict else "found")
)
print(" creds_path: {0}".format(creds_path))

# if configuration information is not desired, config_dict will be empty,
# otherwise parse the information in the sidecar json files into a dict
Expand All @@ -369,7 +374,7 @@ def bids_gen_cpac_sublist(bids_dir, paths_list, config_dict, creds_path, dbg=Fal
t_params = bids_retrieve_params(bids_config_dict,
f_dict)
if not t_params:
print f_dict
print(f_dict)
print("Did not receive any parameters for %s," % (p) +
" is this a problem?")

Expand Down Expand Up @@ -452,13 +457,17 @@ def bids_gen_cpac_sublist(bids_dir, paths_list, config_dict, creds_path, dbg=Fal
if "fMRI" in f_dict["acq"]:
if "fmap" not in subdict[f_dict["sub"]][f_dict["ses"]]:
subdict[f_dict["sub"]][f_dict["ses"]]["fmap"] = {}
if "epi_{0}".format(pe_dir) not in subdict[f_dict["sub"]][f_dict["ses"]]["fmap"].keys():
subdict[f_dict["sub"]][f_dict["ses"]]["fmap"]["epi_{0}".format(pe_dir)] = task_info
if "epi_{0}".format(
pe_dir
) not in subdict[f_dict["sub"]][f_dict["ses"]]["fmap"]:
subdict[f_dict["sub"]][
f_dict["ses"]
]["fmap"]["epi_{0}".format(pe_dir)] = task_info



sublist = []
for ksub, sub in subdict.iteritems():
for kses, ses in sub.iteritems():
for ksub, sub in subdict.items():
for kses, ses in sub.items():
if "anat" in ses and "func" in ses:
sublist.append(ses)
else:
Expand Down Expand Up @@ -488,7 +497,8 @@ def collect_bids_files_configs(bids_dir, aws_input_creds=''):
file_paths = []
config_dict = {}

suffixes = ['T1w', 'bold', 'acq-fMRI_epi', 'phasediff', 'magnitude']
suffixes = ['T1w', 'bold', 'acq-fMRI_epi', 'phasediff', 'magnitude',
'magnitude1', 'magnitude2']

if bids_dir.lower().startswith("s3://"):
# s3 paths begin with s3://bucket/
Expand All @@ -504,7 +514,7 @@ def collect_bids_files_configs(bids_dir, aws_input_creds=''):
from indi_aws import fetch_creds
bucket = fetch_creds.return_bucket(aws_input_creds, bucket_name)

print "gathering files from S3 bucket (%s) for %s" % (bucket, prefix)
print("gathering files from S3 bucket (%s) for %s" % (bucket, prefix))

for s3_obj in bucket.objects.filter(Prefix=prefix):
for suf in suffixes:
Expand All @@ -514,9 +524,9 @@ def collect_bids_files_configs(bids_dir, aws_input_creds=''):
config_dict[s3_obj.key.replace(prefix, "").lstrip('/')] \
= json.loads(s3_obj.get()["Body"].read())
except Exception as e:
print ("Error retrieving %s (%s)" %
(s3_obj.key.replace(prefix, ""),
e.message))
print("Error retrieving %s (%s)" %
(s3_obj.key.replace(prefix, ""),
e.message))
raise
elif 'nii' in str(s3_obj.key):
file_paths.append(str(s3_obj.key)
Expand Down

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