# -*- coding: utf-8 -*-
"""Participant class"""
import logging
from os.path import join as opj
from dcm2bids.utils.utils import DEFAULT
from dcm2bids.version import __version__
class Acquisition(object):
""" Class representing an acquisition
Args:
participant (Participant): A participant object
datatype (str): A functional group of MRI data (ex: func, anat ...)
suffix (str): The modality of the acquisition
(ex: T1w, T2w, bold ...)
custom_entities (str): Optional entities (ex: task-rest)
src_sidecar (Sidecar): Optional sidecar object
"""
def __init__(
self,
participant,
datatype,
suffix,
custom_entities="",
id=None,
src_sidecar=None,
sidecar_changes=None,
**kwargs
):
self.logger = logging.getLogger(__name__)
self._suffix = ""
self._custom_entities = ""
self._id = ""
self.participant = participant
self.datatype = datatype
self.suffix = suffix
self.custom_entities = custom_entities
self.src_sidecar = src_sidecar
if sidecar_changes is None:
self.sidecar_changes = {}
else:
self.sidecar_changes = sidecar_changes
if id is None:
self.id = None
else:
self.id = id
self.dstFile = ''
self.extraDstFile = ''
def __eq__(self, other):
return (
self.datatype == other.datatype
and self.participant.prefix == other.participant.prefix
and self.build_suffix == other.build_suffix
)
@property
def suffix(self):
"""
Returns:
A string '_<suffix>'
"""
return self._suffix
@suffix.setter
def suffix(self, suffix):
""" Prepend '_' if necessary"""
self._suffix = self.prepend(suffix)
@property
def id(self):
"""
Returns:
A string '_<id>'
"""
return self._id
@id.setter
def id(self, value):
self._id = value
@property
def custom_entities(self):
"""
Returns:
A string '_<custom_entities>'
"""
return self._custom_entities
@custom_entities.setter
def custom_entities(self, custom_entities):
""" Prepend '_' if necessary"""
if isinstance(custom_entities, list):
self._custom_entities = self.prepend('_'.join(custom_entities))
else:
self._custom_entities = self.prepend(custom_entities)
@property
def build_suffix(self):
""" The suffix to build filenames
Returns:
A string '_<suffix>' or '_<custom_entities>_<suffix>'
"""
if self.custom_entities.strip() == "":
return self.suffix
else:
return self.custom_entities + self.suffix
@property
def srcRoot(self):
"""
Return:
The sidecar source root to move
"""
if self.src_sidecar:
return self.src_sidecar.root
else:
return None
@property
def dstRoot(self):
"""
Return:
The destination root inside the BIDS structure
"""
return opj(
self.participant.directory,
self.datatype,
self.dstFile,
)
@property
def dstId(self):
"""
Return:
The destination root inside the BIDS structure for description
"""
return opj(
self.participant.session,
self.datatype,
self.dstFile,
)
def setExtraDstFile(self, new_entities):
"""
Return:
The destination filename formatted following
the v1.8.0 BIDS entity key table
https://bids-specification.readthedocs.io/en/v1.8.0/99-appendices/04-entity-table.html
"""
if self.custom_entities.strip() == "":
suffix = new_entities + self.suffix
elif isinstance(new_entities, list):
suffix = '_'.join(new_entities) + self.custom_entities + self.suffix
elif isinstance(new_entities, str):
suffix = new_entities + self.custom_entities + self.suffix
current_name = '_'.join([self.participant.prefix, suffix])
new_name = ''
current_dict = dict(x.split("-") for x in current_name.split("_") if len(x.split('-')) == 2)
suffix_list = [x for x in current_name.split("_") if len(x.split('-')) == 1]
for current_key in DEFAULT.entityTableKeys:
if current_key in current_dict and new_name != '':
new_name += f"_{current_key}-{current_dict[current_key]}"
elif current_key in current_dict:
new_name = f"{current_key}-{current_dict[current_key]}"
current_dict.pop(current_key, None)
for current_key in current_dict:
new_name += f"_{current_key}-{current_dict[current_key]}"
if current_dict:
self.logger.warning(f'Entity \"{list(current_dict.keys())}\"'
' is not a valid BIDS entity.')
# Allow multiple single keys (without value)
new_name += f"_{'_'.join(suffix_list)}"
if len(suffix_list) != 1:
self.logger.warning("There was more than one suffix found "
f"({suffix_list}). This is not BIDS "
"compliant. Make sure you know what "
"you are doing.")
if current_name != new_name:
self.logger.warning(
f"""✅ Filename was reordered according to BIDS entity table order:
from: {current_name}
to: {new_name}""")
self.extraDstFile = opj(self.participant.directory,
self.datatype,
new_name)
def setDstFile(self):
"""
Return:
The destination filename formatted following
the v1.8.0 BIDS entity key table
https://bids-specification.readthedocs.io/en/v1.8.0/99-appendices/04-entity-table.html
"""
current_name = self.participant.prefix + self.build_suffix
new_name = ''
current_dict = dict(x.split("-") for x in current_name.split("_") if len(x.split('-')) == 2)
suffix_list = [x for x in current_name.split("_") if len(x.split('-')) == 1]
for current_key in DEFAULT.entityTableKeys:
if current_key in current_dict and new_name != '':
new_name += f"_{current_key}-{current_dict[current_key]}"
elif current_key in current_dict:
new_name = f"{current_key}-{current_dict[current_key]}"
current_dict.pop(current_key, None)
for current_key in current_dict:
new_name += f"_{current_key}-{current_dict[current_key]}"
if current_dict:
self.logger.warning(f'Entity \"{list(current_dict.keys())}\"'
' is not a valid BIDS entity.')
# Allow multiple single keys (without value)
new_name += f"_{'_'.join(suffix_list)}"
if len(suffix_list) != 1:
self.logger.warning("There was more than one suffix found "
f"({suffix_list}). This is not BIDS "
"compliant. Make sure you know what "
"you are doing.")
if current_name != new_name:
self.logger.warning(
f"""✅ Filename was reordered according to BIDS entity table order:
from: {current_name}
to: {new_name}""")
self.dstFile = new_name
def dstSidecarData(self, idList):
"""
"""
data = self.src_sidecar.origData
data["Dcm2bidsVersion"] = __version__
# TaskName
if 'TaskName' in self.src_sidecar.data:
data["TaskName"] = self.src_sidecar.data["TaskName"]
# sidecar_changes
for key, value in self.sidecar_changes.items():
values = []
if not isinstance(value, list):
value = [value]
for val in value:
if isinstance(val, (bool, str, int, float)):
if val not in idList and key in DEFAULT.keyWithPathsidecar_changes:
logging.warning(f"No id found for '{key}' value '{val}'.")
logging.warning(f"No sidecar changes for field '{key}' "
f"will be made "
f"for json file '{self.dstFile}.json' "
"with this id.")
else:
values.append(idList.get(val, val))
if values[-1] != val:
if isinstance(values[-1], list):
values[-1] = ["bids::" + img_dest for img_dest in values[-1]]
else:
values[-1] = "bids::" + values[-1]
# handle if nested list vs str
flat_value_list = []
for item in values:
if isinstance(item, list):
flat_value_list += item
else:
flat_value_list.append(item)
if len(flat_value_list) == 1:
data[key] = flat_value_list[0]
else:
data[key] = flat_value_list
return data
@staticmethod
def prepend(value, char="_"):
""" Prepend `char` to `value` if necessary
Args:
value (str)
char (str)
"""
if value.strip() == "":
return ""
elif value.startswith(char):
return value
else:
return char + value
class Acquisition(object):
""" Class representing an acquisition
Args:
participant (Participant): A participant object
datatype (str): A functional group of MRI data (ex: func, anat ...)
suffix (str): The modality of the acquisition
(ex: T1w, T2w, bold ...)
custom_entities (str): Optional entities (ex: task-rest)
src_sidecar (Sidecar): Optional sidecar object
"""
def __init__(
self,
participant,
datatype,
suffix,
custom_entities="",
id=None,
src_sidecar=None,
sidecar_changes=None,
**kwargs
):
self.logger = logging.getLogger(__name__)
self._suffix = ""
self._custom_entities = ""
self._id = ""
self.participant = participant
self.datatype = datatype
self.suffix = suffix
self.custom_entities = custom_entities
self.src_sidecar = src_sidecar
if sidecar_changes is None:
self.sidecar_changes = {}
else:
self.sidecar_changes = sidecar_changes
if id is None:
self.id = None
else:
self.id = id
self.dstFile = ''
self.extraDstFile = ''
def __eq__(self, other):
return (
self.datatype == other.datatype
and self.participant.prefix == other.participant.prefix
and self.build_suffix == other.build_suffix
)
@property
def suffix(self):
"""
Returns:
A string '_<suffix>'
"""
return self._suffix
@suffix.setter
def suffix(self, suffix):
""" Prepend '_' if necessary"""
self._suffix = self.prepend(suffix)
@property
def id(self):
"""
Returns:
A string '_<id>'
"""
return self._id
@id.setter
def id(self, value):
self._id = value
@property
def custom_entities(self):
"""
Returns:
A string '_<custom_entities>'
"""
return self._custom_entities
@custom_entities.setter
def custom_entities(self, custom_entities):
""" Prepend '_' if necessary"""
if isinstance(custom_entities, list):
self._custom_entities = self.prepend('_'.join(custom_entities))
else:
self._custom_entities = self.prepend(custom_entities)
@property
def build_suffix(self):
""" The suffix to build filenames
Returns:
A string '_<suffix>' or '_<custom_entities>_<suffix>'
"""
if self.custom_entities.strip() == "":
return self.suffix
else:
return self.custom_entities + self.suffix
@property
def srcRoot(self):
"""
Return:
The sidecar source root to move
"""
if self.src_sidecar:
return self.src_sidecar.root
else:
return None
@property
def dstRoot(self):
"""
Return:
The destination root inside the BIDS structure
"""
return opj(
self.participant.directory,
self.datatype,
self.dstFile,
)
@property
def dstId(self):
"""
Return:
The destination root inside the BIDS structure for description
"""
return opj(
self.participant.session,
self.datatype,
self.dstFile,
)
def setExtraDstFile(self, new_entities):
"""
Return:
The destination filename formatted following
the v1.8.0 BIDS entity key table
https://bids-specification.readthedocs.io/en/v1.8.0/99-appendices/04-entity-table.html
"""
if self.custom_entities.strip() == "":
suffix = new_entities + self.suffix
elif isinstance(new_entities, list):
suffix = '_'.join(new_entities) + self.custom_entities + self.suffix
elif isinstance(new_entities, str):
suffix = new_entities + self.custom_entities + self.suffix
current_name = '_'.join([self.participant.prefix, suffix])
new_name = ''
current_dict = dict(x.split("-") for x in current_name.split("_") if len(x.split('-')) == 2)
suffix_list = [x for x in current_name.split("_") if len(x.split('-')) == 1]
for current_key in DEFAULT.entityTableKeys:
if current_key in current_dict and new_name != '':
new_name += f"_{current_key}-{current_dict[current_key]}"
elif current_key in current_dict:
new_name = f"{current_key}-{current_dict[current_key]}"
current_dict.pop(current_key, None)
for current_key in current_dict:
new_name += f"_{current_key}-{current_dict[current_key]}"
if current_dict:
self.logger.warning(f'Entity \"{list(current_dict.keys())}\"'
' is not a valid BIDS entity.')
# Allow multiple single keys (without value)
new_name += f"_{'_'.join(suffix_list)}"
if len(suffix_list) != 1:
self.logger.warning("There was more than one suffix found "
f"({suffix_list}). This is not BIDS "
"compliant. Make sure you know what "
"you are doing.")
if current_name != new_name:
self.logger.warning(
f"""✅ Filename was reordered according to BIDS entity table order:
from: {current_name}
to: {new_name}""")
self.extraDstFile = opj(self.participant.directory,
self.datatype,
new_name)
def setDstFile(self):
"""
Return:
The destination filename formatted following
the v1.8.0 BIDS entity key table
https://bids-specification.readthedocs.io/en/v1.8.0/99-appendices/04-entity-table.html
"""
current_name = self.participant.prefix + self.build_suffix
new_name = ''
current_dict = dict(x.split("-") for x in current_name.split("_") if len(x.split('-')) == 2)
suffix_list = [x for x in current_name.split("_") if len(x.split('-')) == 1]
for current_key in DEFAULT.entityTableKeys:
if current_key in current_dict and new_name != '':
new_name += f"_{current_key}-{current_dict[current_key]}"
elif current_key in current_dict:
new_name = f"{current_key}-{current_dict[current_key]}"
current_dict.pop(current_key, None)
for current_key in current_dict:
new_name += f"_{current_key}-{current_dict[current_key]}"
if current_dict:
self.logger.warning(f'Entity \"{list(current_dict.keys())}\"'
' is not a valid BIDS entity.')
# Allow multiple single keys (without value)
new_name += f"_{'_'.join(suffix_list)}"
if len(suffix_list) != 1:
self.logger.warning("There was more than one suffix found "
f"({suffix_list}). This is not BIDS "
"compliant. Make sure you know what "
"you are doing.")
if current_name != new_name:
self.logger.warning(
f"""✅ Filename was reordered according to BIDS entity table order:
from: {current_name}
to: {new_name}""")
self.dstFile = new_name
def dstSidecarData(self, idList):
"""
"""
data = self.src_sidecar.origData
data["Dcm2bidsVersion"] = __version__
# TaskName
if 'TaskName' in self.src_sidecar.data:
data["TaskName"] = self.src_sidecar.data["TaskName"]
# sidecar_changes
for key, value in self.sidecar_changes.items():
values = []
if not isinstance(value, list):
value = [value]
for val in value:
if isinstance(val, (bool, str, int, float)):
if val not in idList and key in DEFAULT.keyWithPathsidecar_changes:
logging.warning(f"No id found for '{key}' value '{val}'.")
logging.warning(f"No sidecar changes for field '{key}' "
f"will be made "
f"for json file '{self.dstFile}.json' "
"with this id.")
else:
values.append(idList.get(val, val))
if values[-1] != val:
if isinstance(values[-1], list):
values[-1] = ["bids::" + img_dest for img_dest in values[-1]]
else:
values[-1] = "bids::" + values[-1]
# handle if nested list vs str
flat_value_list = []
for item in values:
if isinstance(item, list):
flat_value_list += item
else:
flat_value_list.append(item)
if len(flat_value_list) == 1:
data[key] = flat_value_list[0]
else:
data[key] = flat_value_list
return data
@staticmethod
def prepend(value, char="_"):
""" Prepend `char` to `value` if necessary
Args:
value (str)
char (str)
"""
if value.strip() == "":
return ""
elif value.startswith(char):
return value
else:
return char + value
def dstSidecarData(self, idList):
"""
"""
data = self.src_sidecar.origData
data["Dcm2bidsVersion"] = __version__
# TaskName
if 'TaskName' in self.src_sidecar.data:
data["TaskName"] = self.src_sidecar.data["TaskName"]
# sidecar_changes
for key, value in self.sidecar_changes.items():
values = []
if not isinstance(value, list):
value = [value]
for val in value:
if isinstance(val, (bool, str, int, float)):
if val not in idList and key in DEFAULT.keyWithPathsidecar_changes:
logging.warning(f"No id found for '{key}' value '{val}'.")
logging.warning(f"No sidecar changes for field '{key}' "
f"will be made "
f"for json file '{self.dstFile}.json' "
"with this id.")
else:
values.append(idList.get(val, val))
if values[-1] != val:
if isinstance(values[-1], list):
values[-1] = ["bids::" + img_dest for img_dest in values[-1]]
else:
values[-1] = "bids::" + values[-1]
# handle if nested list vs str
flat_value_list = []
for item in values:
if isinstance(item, list):
flat_value_list += item
else:
flat_value_list.append(item)
if len(flat_value_list) == 1:
data[key] = flat_value_list[0]
else:
data[key] = flat_value_list
return data
The destination filename formatted following
the v1.8.0 BIDS entity key table
https://bids-specification.readthedocs.io/en/v1.8.0/99-appendices/04-entity-table.html
def setDstFile(self):
"""
Return:
The destination filename formatted following
the v1.8.0 BIDS entity key table
https://bids-specification.readthedocs.io/en/v1.8.0/99-appendices/04-entity-table.html
"""
current_name = self.participant.prefix + self.build_suffix
new_name = ''
current_dict = dict(x.split("-") for x in current_name.split("_") if len(x.split('-')) == 2)
suffix_list = [x for x in current_name.split("_") if len(x.split('-')) == 1]
for current_key in DEFAULT.entityTableKeys:
if current_key in current_dict and new_name != '':
new_name += f"_{current_key}-{current_dict[current_key]}"
elif current_key in current_dict:
new_name = f"{current_key}-{current_dict[current_key]}"
current_dict.pop(current_key, None)
for current_key in current_dict:
new_name += f"_{current_key}-{current_dict[current_key]}"
if current_dict:
self.logger.warning(f'Entity \"{list(current_dict.keys())}\"'
' is not a valid BIDS entity.')
# Allow multiple single keys (without value)
new_name += f"_{'_'.join(suffix_list)}"
if len(suffix_list) != 1:
self.logger.warning("There was more than one suffix found "
f"({suffix_list}). This is not BIDS "
"compliant. Make sure you know what "
"you are doing.")
if current_name != new_name:
self.logger.warning(
f"""✅ Filename was reordered according to BIDS entity table order:
from: {current_name}
to: {new_name}""")
self.dstFile = new_name
The destination filename formatted following
the v1.8.0 BIDS entity key table
https://bids-specification.readthedocs.io/en/v1.8.0/99-appendices/04-entity-table.html
def setExtraDstFile(self, new_entities):
"""
Return:
The destination filename formatted following
the v1.8.0 BIDS entity key table
https://bids-specification.readthedocs.io/en/v1.8.0/99-appendices/04-entity-table.html
"""
if self.custom_entities.strip() == "":
suffix = new_entities + self.suffix
elif isinstance(new_entities, list):
suffix = '_'.join(new_entities) + self.custom_entities + self.suffix
elif isinstance(new_entities, str):
suffix = new_entities + self.custom_entities + self.suffix
current_name = '_'.join([self.participant.prefix, suffix])
new_name = ''
current_dict = dict(x.split("-") for x in current_name.split("_") if len(x.split('-')) == 2)
suffix_list = [x for x in current_name.split("_") if len(x.split('-')) == 1]
for current_key in DEFAULT.entityTableKeys:
if current_key in current_dict and new_name != '':
new_name += f"_{current_key}-{current_dict[current_key]}"
elif current_key in current_dict:
new_name = f"{current_key}-{current_dict[current_key]}"
current_dict.pop(current_key, None)
for current_key in current_dict:
new_name += f"_{current_key}-{current_dict[current_key]}"
if current_dict:
self.logger.warning(f'Entity \"{list(current_dict.keys())}\"'
' is not a valid BIDS entity.')
# Allow multiple single keys (without value)
new_name += f"_{'_'.join(suffix_list)}"
if len(suffix_list) != 1:
self.logger.warning("There was more than one suffix found "
f"({suffix_list}). This is not BIDS "
"compliant. Make sure you know what "
"you are doing.")
if current_name != new_name:
self.logger.warning(
f"""✅ Filename was reordered according to BIDS entity table order:
from: {current_name}
to: {new_name}""")
self.extraDstFile = opj(self.participant.directory,
self.datatype,
new_name)