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963 | # -*- coding: utf-8 -*-
"""sidecars classes"""
import itertools
import logging
import os
import re
from collections import defaultdict, OrderedDict
from fnmatch import fnmatch
from dcm2bids.acquisition import Acquisition
from dcm2bids.utils.io import load_json
from dcm2bids.utils.utils import (DEFAULT, convert_dir, combine_dict_extractors,
splitext_)
compare_float_keys = ["lt", "gt", "le", "ge", "btw", "btwe"]
class Sidecar(object):
""" A sidecar object
Args:
filename (str): Path of a JSON sidecar
keyComp (list): A list of keys from the JSON sidecar to compare sidecars
default=["SeriesNumber","AcquisitionTime","SideCarFilename"]
"""
def __init__(self, filename, compKeys=DEFAULT.compKeys):
self._origData = {}
self._data = {}
self.filename = filename
self.root, _ = splitext_(filename)
self.data = filename
self.compKeys = compKeys
def __lt__(self, other):
lts = []
for key in self.compKeys:
try:
if all(key in d for d in (self.data, other.data)):
if self.data.get(key) == other.data.get(key):
lts.append(None)
else:
lts.append(self.data.get(key) < other.data.get(key))
else:
lts.append(None)
except Exception:
lts.append(None)
for lt in lts:
if lt is not None:
return lt
def __eq__(self, other):
return self.data == other.data
def __hash__(self):
return hash(self.filename)
@property
def origData(self):
return self._origData
@property
def data(self):
return self._data
@data.setter
def data(self, filename):
"""
Args:
filename (path): path of a JSON file
Return:
A dictionary of the JSON content plus the SidecarFilename
"""
try:
data = load_json(filename)
except Exception:
data = {}
self._origData = data.copy()
data["SidecarFilename"] = os.path.basename(filename)
self._data = data
class SidecarPairing(object):
"""
Args:
sidecars (list): List of Sidecar objects
descriptions (list): List of dictionaries describing acquisitions
"""
def __init__(self,
sidecars,
descriptions,
extractors=DEFAULT.extractors,
auto_extractor=DEFAULT.auto_extract_entities,
do_not_reorder_entities=DEFAULT.do_not_reorder_entities,
search_method=DEFAULT.search_method,
case_sensitive=DEFAULT.case_sensitive,
dup_method=DEFAULT.dup_method,
post_op=DEFAULT.post_op,
bids_uri=DEFAULT.bids_uri):
self.logger = logging.getLogger(__name__)
self._search_method = ""
self._dup_method = ""
self._post_op = ""
self._bids_uri = ""
self.graph = OrderedDict()
self.acquisitions = []
self.extractors = extractors
self.auto_extract_entities = auto_extractor
self.do_not_reorder_entities = do_not_reorder_entities
self.sidecars = sidecars
self.descriptions = descriptions
self.search_method = search_method
self.case_sensitive = case_sensitive
self.dup_method = dup_method
self.post_op = post_op
self.bids_uri = bids_uri
@property
def search_method(self):
return self._search_method
@search_method.setter
def search_method(self, value):
"""
Checks if the search method is implemented
Warns the user if not and fall back to default
"""
if value in DEFAULT.search_methodChoices:
self._search_method = value
else:
self._search_method = DEFAULT.search_method
self.logger.warning(f"'{value}' is not a search method implemented")
self.logger.warning(f"Falling back to default: {DEFAULT.search_method}")
self.logger.warning(
f"Search methods implemented: {DEFAULT.search_methodChoices}"
)
@property
def dup_method(self):
return self._dup_method
@dup_method.setter
def dup_method(self, value):
"""
Checks if the duplicate method is implemented
Warns the user if not and fall back to default
"""
if value in DEFAULT.dup_method_choices:
self._dup_method = value
else:
self._dup_method = DEFAULT.dup_method
self.logger.warning(
"Duplicate methods implemented: %s", DEFAULT.dup_method_choices)
self.logger.warning(f"{value} is not a duplicate method implemented.")
self.logger.warning(f"Falling back to default: {DEFAULT.dup_method}.")
@property
def post_op(self):
return self._post_op
@post_op.setter
def post_op(self, value):
"""
Checks if post_op commands don't overlap
"""
post_op = []
if isinstance(value, dict):
value = [value]
elif not isinstance(value, list):
raise ValueError("post_op should be a list of dict."
"Please check the documentation.")
try:
pairs = []
for curr_post_op in value:
post_op.append(curr_post_op)
datatype = curr_post_op['datatype']
suffix = curr_post_op['suffix']
if 'custom_entities' in curr_post_op:
post_op[-1]['custom_entities'] = curr_post_op['custom_entities']
if isinstance(curr_post_op['cmd'], str):
cmd_split = curr_post_op['cmd'].split()
else:
raise ValueError("post_op cmd should be a string."
"Please check the documentation.")
if 'src_file' not in cmd_split or 'dst_file' not in cmd_split:
raise ValueError("post_op cmd is not defined correctly. "
"<src_file> and/or <dst_file> is missing. "
"Please check the documentation.")
if isinstance(datatype, str):
post_op[-1]['datatype'] = [datatype]
datatype = [datatype]
if isinstance(suffix, str):
# It will be compare with acq.suffix which has a `_` character
post_op[-1]['suffix'] = ['_' + suffix]
suffix = [suffix]
elif isinstance(suffix, list):
post_op[-1]['suffix'] = ['_' + curr_suffix for curr_suffix in suffix]
pairs = pairs + list(itertools.product(datatype, suffix))
res = list(set([ele for ele in pairs if pairs.count(ele) > 1]))
if res:
raise ValueError("Some post operations apply on "
"the same combination of datatype/suffix. "
"Please fix post_op key in your config file."
f"{pairs}")
self._post_op = post_op
except Exception:
raise ValueError("post_op is not defined correctly. "
"Please check the documentation.")
@property
def bids_uri(self):
return self._bids_uri
@bids_uri.setter
def bids_uri(self, value):
"""
Checks if the method bids_uri is using is implemented
Warns the user if not and fall back to default
"""
if value in DEFAULT.bids_uri_choices:
self._bids_uri = value
else:
self.bids_uri = DEFAULT.bids_uri
self.logger.warning(
"BIDS URI methods implemented: %s", DEFAULT.bids_uri_choices)
self.logger.warning(f"{value} is not a bids URI method implemented.")
self.logger.warning(f"Falling back to default: {DEFAULT.bids_uri}.")
@property
def case_sensitive(self):
return self._case_sensitive
@case_sensitive.setter
def case_sensitive(self, value):
if isinstance(value, bool):
self._case_sensitive = value
else:
self._case_sensitive = DEFAULT.case_sensitive
self.logger.warning(f"'{value}' is not a boolean")
self.logger.warning(f"Falling back to default: {DEFAULT.case_sensitive}")
self.logger.warning(f"Search methods implemented: {DEFAULT.case_sensitive}")
def build_graph(self):
"""
Test all the possible links between the list of sidecars and the
description dictionaries and build a graph from it
The graph is in a OrderedDict object. The keys are the Sidecars and
the values are a list of possible descriptions
Returns:
A graph (OrderedDict)
"""
graph = OrderedDict((_, []) for _ in self.sidecars)
possibleLinks = itertools.product(self.sidecars, self.descriptions)
for sidecar, description in possibleLinks:
criteria = description.get("criteria", None)
if criteria and self.isLink(sidecar.data, criteria):
graph[sidecar].append(description)
self.graph = graph
return graph
def isLink(self, data, criteria):
"""
Args:
data (dict): Dictionary data of a sidecar
criteria (dict): Dictionary criteria
Returns:
boolean
"""
def compare(name, pattern):
name = str(name)
if self.search_method == "re":
return bool(re.match(pattern, name))
else:
pattern = str(pattern)
if not self.case_sensitive:
name = name.lower()
pattern = pattern.lower()
return fnmatch(name, pattern)
def compare_list(name, pattern):
try:
subResult = [
len(name) == len(pattern),
isinstance(pattern, list),
]
for subName, subPattern in zip(name, pattern):
subResult.append(compare(subName, subPattern))
except Exception:
subResult = [False]
return all(subResult)
def compare_complex(name, pattern):
sub_result = []
compare_type = None
try:
for compare_type, patterns in pattern.items():
for sub_pattern in patterns:
if isinstance(name, list):
sub_result.append(compare_list(name, sub_pattern))
else:
sub_result.append(compare(name, sub_pattern))
except Exception:
sub_result = [False]
if compare_type == "any":
return any(sub_result)
else:
return False
def compare_float(name, pattern):
try:
comparison = list(pattern.keys())[0]
name_float = float(name)
sub_pattern = pattern[list(pattern.keys())[0]]
if comparison in ["btwe", "btw"]:
if not isinstance(sub_pattern, list):
raise ValueError("You should be using a list "
"for float comparison "
f"with key {comparison}. "
f"Error val: {sub_pattern}")
if len(sub_pattern) != 2:
raise ValueError(f"List for key {comparison} "
"should have two values. "
f"Error val: {sub_pattern}")
elif comparison == "btwe":
return name_float >= float(sub_pattern[0]) and name_float <= float(sub_pattern[1])
elif comparison == "btw":
return name_float > float(sub_pattern[0]) and name_float < float(sub_pattern[1])
if isinstance(sub_pattern, list):
if len(sub_pattern) != 1:
raise ValueError(f"List for key {comparison} "
"should have only one value. "
"Error val: {sub_pattern}")
sub_pattern = float(sub_pattern[0])
else:
sub_pattern = float(sub_pattern)
if comparison == 'gt':
return sub_pattern < name_float
elif comparison == 'lt':
return sub_pattern > name_float
elif comparison == 'ge':
return sub_pattern <= name_float
elif comparison == 'le':
return sub_pattern >= name_float
except Exception:
return False
result = []
for tag, pattern in criteria.items():
name = data.get(tag, '')
if isinstance(pattern, dict):
if len(pattern.keys()) == 1:
if "any" in pattern.keys():
result.append(compare_complex(name, pattern))
elif list(pattern.keys())[0] in compare_float_keys:
result.append(compare_float(name, pattern))
else:
self.logger.warning(f"This key {list(pattern.keys())[0]} "
"is not allowed.")
else:
raise ValueError("Dictionary used as criteria should be "
"using only one key.")
elif isinstance(name, list):
result.append(compare_list(name, pattern))
else:
result.append(compare(name, pattern))
return all(result)
def build_acquisitions(self, participant):
"""
Args:
participant (Participant): Participant object to create acquisitions
Returns:
A list of acquisition objects
"""
acquisitions_id = []
acquisitions = []
self.logger.info("Sidecar pairing".upper())
for sidecar, valid_descriptions in self.graph.items():
sidecarName = os.path.basename(sidecar.root)
# only one description for the sidecar
if len(valid_descriptions) == 1:
desc = valid_descriptions[0]
desc, sidecar = self.searchDcmTagEntity(sidecar, desc)
acq = Acquisition(participant,
src_sidecar=sidecar,
bids_uri=self.bids_uri,
do_not_reorder_entities=self.do_not_reorder_entities,
**desc)
acq.setDstFile()
if acq.id:
acquisitions_id.append(acq)
else:
acquisitions.append(acq)
self.logger.info(
f"{acq.dstFile.replace(f'{acq.participant.prefix}-', '')}"
f" <- {sidecarName}")
elif len(valid_descriptions) == 0:
self.logger.info(f"No Pairing <- {sidecarName}")
else:
self.logger.warning(f"Several Pairing <- {sidecarName}")
for desc in valid_descriptions:
acq = Acquisition(participant,
bids_uri=self.bids_uri,
do_not_reorder_entities=self.do_not_reorder_entities,
**desc)
self.logger.warning(f" -> {acq.suffix}")
self.acquisitions = acquisitions_id + acquisitions
return self.acquisitions
def searchDcmTagEntity(self, sidecar, desc):
"""
Add DCM Tag to custom_entities
"""
descWithTask = desc.copy()
concatenated_matches = {}
keys_custom_entities = []
entities = []
if "custom_entities" in desc.keys() or self.auto_extract_entities:
if 'custom_entities' in desc.keys():
if isinstance(descWithTask["custom_entities"], str):
descWithTask["custom_entities"] = [descWithTask["custom_entities"]]
else:
descWithTask["custom_entities"] = []
keys_custom_entities = [curr_entity.split('-')[0] for curr_entity in descWithTask["custom_entities"]]
if self.auto_extract_entities:
self.extractors = combine_dict_extractors(self.extractors, DEFAULT.auto_extractors)
# Loop to check if we find self.extractor
for dcmTag in self.extractors:
if dcmTag in sidecar.data.keys():
dcmInfo = sidecar.data.get(dcmTag)
for regex in self.extractors[dcmTag]:
compile_regex = re.compile(regex)
if not isinstance(dcmInfo, list):
if compile_regex.search(str(dcmInfo)) is not None:
concatenated_matches.update(
compile_regex.search(str(dcmInfo)).groupdict())
else:
for curr_dcmInfo in dcmInfo:
if compile_regex.search(curr_dcmInfo) is not None:
concatenated_matches.update(
compile_regex.search(curr_dcmInfo).groupdict())
break
# Keep entities asked in custom_entities
# If dir found in custom_entities and concatenated_matches.keys we keep it
if "custom_entities" in desc.keys() and not self.auto_extract_entities:
entities = desc["custom_entities"]
elif "custom_entities" in desc.keys():
entities = set(concatenated_matches.keys()).intersection(set(descWithTask["custom_entities"]))
# custom_entities not a key for extractor or auto_extract_entities
complete_entities = [ent for ent in descWithTask["custom_entities"] if '-' in ent]
entities = entities.union(set(complete_entities))
if self.auto_extract_entities:
auto_acq = '_'.join([descWithTask['datatype'], descWithTask["suffix"]])
if auto_acq in DEFAULT.auto_entities:
# Check if these auto entities have been found before merging
auto_entities = set(concatenated_matches.keys()).intersection(set(DEFAULT.auto_entities[auto_acq]))
left_auto_entities = auto_entities.symmetric_difference(set(DEFAULT.auto_entities[auto_acq]))
left_auto_entities = left_auto_entities.difference(keys_custom_entities)
if left_auto_entities:
self.logger.warning(f"Entities {left_auto_entities} have not been found "
f"for datatype '{descWithTask['datatype']}' "
f"and suffix '{descWithTask['suffix']}'.")
entities = list(entities) + list(auto_entities)
entities = list(set(entities))
descWithTask["custom_entities"] = entities
for curr_entity in entities:
if curr_entity in concatenated_matches.keys():
if curr_entity == 'dir':
descWithTask["custom_entities"] = list(map(lambda x: x.replace(curr_entity, '-'.join([curr_entity, convert_dir(concatenated_matches[curr_entity])])), descWithTask["custom_entities"]))
elif curr_entity == 'task':
sidecar.data['TaskName'] = concatenated_matches[curr_entity]
descWithTask["custom_entities"] = list(map(lambda x: x.replace(curr_entity, '-'.join([curr_entity, concatenated_matches[curr_entity]])), descWithTask["custom_entities"]))
else:
descWithTask["custom_entities"] = list(map(lambda x: x.replace(curr_entity, '-'.join([curr_entity, concatenated_matches[curr_entity]])), descWithTask["custom_entities"]))
# Remove entities without -
for curr_entity in descWithTask["custom_entities"]:
if '-' not in curr_entity:
self.logger.info(f"Removing entity '{curr_entity}' since it "
"does not fit the basic BIDS specification "
"(Entity-Value)")
descWithTask["custom_entities"].remove(curr_entity)
return descWithTask, sidecar
def find_runs(self):
"""
Check if there is duplicate destination roots in the acquisitions
and add '_run-' to the custom_entities of the acquisition
"""
def duplicates(seq):
""" Find duplicate items in a list
Args:
seq (list)
Yield:
A tuple of 2 items (item, list of index)
ref: http://stackoverflow.com/a/5419576
"""
tally = defaultdict(list)
for i, item in enumerate(seq):
tally[item].append(i)
for key, locs in tally.items():
if len(locs) > 1:
yield key, locs
dstRoots = [_.dstRoot for _ in self.acquisitions]
templateDup = DEFAULT.runTpl
if self.dup_method == 'dup':
templateDup = DEFAULT.dupTpl
for dstRoot, dup in duplicates(dstRoots):
self.logger.info(f"{dstRoot} has {len(dup)} runs")
self.logger.info(f"Adding {self.dup_method} information to the acquisition")
if self.dup_method == 'dup':
dup = dup[0:-1]
for runNum, acqInd in enumerate(dup):
runStr = templateDup.format(runNum+1)
self.acquisitions[acqInd].custom_entities += runStr
self.acquisitions[acqInd].setDstFile()
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