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BIDS Files

Classes for navigating BIDS-compliant datasets, parsing filenames into structured entities, and filtering/querying files across subjects and sessions.

BIDS_Global_info

TPTBox.core.bids_files.BIDS_Global_info

Global index of a BIDS dataset, mapping subjects to their files across multiple dataset roots.

Source code in TPTBox/core/bids_files.py 
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class BIDS_Global_info:
    """Global index of a BIDS dataset, mapping subjects to their files across multiple dataset roots."""

    def __init__(
        self,
        datasets: Sequence[Path | str] | Sequence[Path] | Sequence[str] | str | Path,
        parents: Sequence[str] | str = ["rawdata", "derivatives"],
        additional_key: Sequence[str] = ["sequ", "seg", "ovl"],
        verbose: bool = True,
        file_name_manipulation: typing.Callable[[str], str] | None = None,
        sequence_splitting_keys: list[str] | None = None,
        filter_folder: typing.Callable[[Path, int], bool] | None = None,
        additional_file_list: dict[str | Path, list[Path]] | None = None,
    ):
        """This Objects creates a datastructures reflecting BIDS-folders.

        Args:
            datasets (typing.List[str]): List of dataset paths
            parents (typing.List[str]): List of parents (like ["rawdata","sourcedata","derivatives"])
            additional_key (list, optional): Additional keys that are not in the default BIDS but should not raise a warning. Defaults to ["sequ", "seg", "ovl"].
            filter_folder: Filter function, input is the path of the folder and the level of the folder structure. Return True if we should continue searching
                        Example:
                        filter_folder = lambda p, lvl: True if (lvl != 2 or p.name in ["sub-123","sub-456"]) else False
        """
        self.count_file = 0
        if sequence_splitting_keys is None:
            from TPTBox.core.bids_constants import sequence_splitting_keys

            self.sequence_splitting_keys = sequence_splitting_keys

        self.sequence_splitting_keys = sequence_splitting_keys
        if isinstance(datasets, (Path, str)):
            datasets = [datasets]  # type: ignore
        if isinstance(parents, str):
            parents = [parents]
        assert isinstance(datasets, Sequence), "datasets is not a list"
        assert isinstance(parents, Sequence), "parents is not a list"
        self.__bids_list: dict = {}

        self.file_name_manipulation = file_name_manipulation
        # Validate
        for ds in datasets:
            ds_path = Path(ds) if isinstance(ds, str) else ds
            if not ds_path.name.startswith("dataset-"):
                print(f"[!] Dataset {ds_path.name} does not start with 'dataset-'")
        for ps in parents:
            if not any(ps.startswith(lp) for lp in parents):
                print(f"[!] Parentfolder {ps} is not a legal name")

        self.datasets = datasets
        self.parents = parents
        self.subjects: dict[str, Subject_Container] = {}
        self.verbose = verbose

        for k in additional_key:
            if k not in entities:
                entities[k] = k
            if k not in entities_keys:
                entities_keys[k] = k

        # Search and add files
        for ds in datasets:
            if not Path(ds).exists():
                raise FileNotFoundError(ds)
            for ps in parents:
                path = Path(ds, ps)
                if path.exists():
                    self.search_folder(path, ds, filter_folder)
        if additional_file_list is not None:
            for ds, file_list in additional_file_list.items():
                for f in file_list:
                    # if Path(f).is_file():
                    self.add_file_2_subject(f, ds)

        self.entities_keys = entities_keys

    def search_folder(self, path: Path, ds, filter_folder) -> None:
        """Recursively scan *path* and register every file found with the global info.

        Args:
            path: Directory to scan.
            ds: Dataset root path associated with the scanned folder.
            filter_folder: Callable ``(path, level) -> bool``; folders for
                which this returns ``False`` are skipped.
        """
        for entry in _scan_tree(path, filter_folder=filter_folder):
            if entry.is_file():
                self.add_file_2_subject(Path(entry.path), ds)

    def add_file_2_subject(self, bids: BIDS_FILE | Path, ds: Path | str | None = None) -> None:
        """Parse a file path (or pre-built :class:`BIDS_FILE`) and add it to the correct subject bucket.

        Args:
            bids: Either a raw filesystem path or an already-constructed
                :class:`BIDS_FILE` instance.
            ds: Dataset root path.  Required when *bids* is a plain
                :class:`~pathlib.Path`; inferred automatically when *bids*
                is a :class:`BIDS_FILE`.

        Raises:
            AssertionError: If *bids* is a :class:`~pathlib.Path` and *ds*
                is ``None``.
        """
        if isinstance(bids, Path) and "DS_Store" in bids.name:
            return
        if ds is None:
            if isinstance(bids, BIDS_FILE):
                ds = bids.dataset
            else:
                raise AssertionError("Dataset-path required")

        if isinstance(bids, (Path, str)):
            try:
                bids_key, file_type = str(bids).rsplit("/", maxsplit=1)[-1].split(".", maxsplit=1)
                # print(bids_key)
            except Exception:
                print("[!] skip file with out a type declaration:", bids.name)
                # raise e
                return

            if bids_key in self._global_bids_list:
                self._global_bids_list[bids_key].add_file(bids)
                return
            bids = BIDS_FILE(
                bids,
                ds,
                verbose=self.verbose,
                file_name_manipulation=self.file_name_manipulation,
            )

        subject = bids.info.get("sub", "unsorted")
        if subject not in self.subjects:
            self.subjects[subject] = Subject_Container(subject, self.sequence_splitting_keys)
        self.count_file += 1
        (
            print(
                f"Found: {subject}, total file keys {(self.count_file)},  total subjects = {len(self.subjects)}    ",
                end="\r",
            )
            if self.verbose
            else None
        )
        self.subjects[subject].add(bids)

    def enumerate_subjects(self, sort: bool = False, shuffle: bool = False) -> list[tuple[str, Subject_Container]]:
        """Return all subject identifiers together with their :class:`Subject_Container`.

        Args:
            sort: If ``True``, return subjects sorted alphabetically by
                subject ID.
            shuffle: If ``True``, return subjects in a random order.
                Mutually exclusive with *sort* (sort takes precedence).

        Returns:
            A list of ``(subject_id, Subject_Container)`` pairs.
        """
        # TODO Enumerate should put out numbers...
        if sort:
            return sorted(self.subjects.items())
        if shuffle:
            s = list(self.subjects.items())
            random.shuffle(s)
            return s
        return self.subjects.items()  # type: ignore

    def iter_subjects(self, sort: bool = False) -> list[tuple[str, Subject_Container]]:
        """Iterate over all subjects (alias for :meth:`enumerate_subjects` without shuffle).

        Args:
            sort: If ``True``, return subjects sorted alphabetically by
                subject ID.

        Returns:
            A list of ``(subject_id, Subject_Container)`` pairs.
        """
        if sort:
            return sorted(self.subjects.items())
        return self.subjects.items()  # type: ignore

    def __len__(self):
        return len(self.subjects)

    def __str__(self):
        return "BIDS_Global_info: parents=" + str(self.parents) + f"\nDatasets = {self.datasets}"

    @property
    def _global_bids_list(self) -> dict:
        """Internal mapping from BIDS key stem to :class:`BIDS_FILE` instances."""
        return self.__bids_list

__init__ 

__init__(datasets: Sequence[Path | str] | Sequence[Path] | Sequence[str] | str | Path, parents: Sequence[str] | str = ['rawdata', 'derivatives'], additional_key: Sequence[str] = ['sequ', 'seg', 'ovl'], verbose: bool = True, file_name_manipulation: Callable[[str], str] | None = None, sequence_splitting_keys: list[str] | None = None, filter_folder: Callable[[Path, int], bool] | None = None, additional_file_list: dict[str | Path, list[Path]] | None = None)

This Objects creates a datastructures reflecting BIDS-folders.

Parameters:

Name Type Description Default
datasets List[str]

List of dataset paths

 required
parents List[str]

List of parents (like ["rawdata","sourcedata","derivatives"])

 ['rawdata', 'derivatives']
additional_key list

Additional keys that are not in the default BIDS but should not raise a warning. Defaults to ["sequ", "seg", "ovl"].

 ['sequ', 'seg', 'ovl']
filter_folder Callable[[Path, int], bool] | None

Filter function, input is the path of the folder and the level of the folder structure. Return True if we should continue searching Example: filter_folder = lambda p, lvl: True if (lvl != 2 or p.name in ["sub-123","sub-456"]) else False

 None
Source code in TPTBox/core/bids_files.py 
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def __init__(
    self,
    datasets: Sequence[Path | str] | Sequence[Path] | Sequence[str] | str | Path,
    parents: Sequence[str] | str = ["rawdata", "derivatives"],
    additional_key: Sequence[str] = ["sequ", "seg", "ovl"],
    verbose: bool = True,
    file_name_manipulation: typing.Callable[[str], str] | None = None,
    sequence_splitting_keys: list[str] | None = None,
    filter_folder: typing.Callable[[Path, int], bool] | None = None,
    additional_file_list: dict[str | Path, list[Path]] | None = None,
):
    """This Objects creates a datastructures reflecting BIDS-folders.

    Args:
        datasets (typing.List[str]): List of dataset paths
        parents (typing.List[str]): List of parents (like ["rawdata","sourcedata","derivatives"])
        additional_key (list, optional): Additional keys that are not in the default BIDS but should not raise a warning. Defaults to ["sequ", "seg", "ovl"].
        filter_folder: Filter function, input is the path of the folder and the level of the folder structure. Return True if we should continue searching
                    Example:
                    filter_folder = lambda p, lvl: True if (lvl != 2 or p.name in ["sub-123","sub-456"]) else False
    """
    self.count_file = 0
    if sequence_splitting_keys is None:
        from TPTBox.core.bids_constants import sequence_splitting_keys

        self.sequence_splitting_keys = sequence_splitting_keys

    self.sequence_splitting_keys = sequence_splitting_keys
    if isinstance(datasets, (Path, str)):
        datasets = [datasets]  # type: ignore
    if isinstance(parents, str):
        parents = [parents]
    assert isinstance(datasets, Sequence), "datasets is not a list"
    assert isinstance(parents, Sequence), "parents is not a list"
    self.__bids_list: dict = {}

    self.file_name_manipulation = file_name_manipulation
    # Validate
    for ds in datasets:
        ds_path = Path(ds) if isinstance(ds, str) else ds
        if not ds_path.name.startswith("dataset-"):
            print(f"[!] Dataset {ds_path.name} does not start with 'dataset-'")
    for ps in parents:
        if not any(ps.startswith(lp) for lp in parents):
            print(f"[!] Parentfolder {ps} is not a legal name")

    self.datasets = datasets
    self.parents = parents
    self.subjects: dict[str, Subject_Container] = {}
    self.verbose = verbose

    for k in additional_key:
        if k not in entities:
            entities[k] = k
        if k not in entities_keys:
            entities_keys[k] = k

    # Search and add files
    for ds in datasets:
        if not Path(ds).exists():
            raise FileNotFoundError(ds)
        for ps in parents:
            path = Path(ds, ps)
            if path.exists():
                self.search_folder(path, ds, filter_folder)
    if additional_file_list is not None:
        for ds, file_list in additional_file_list.items():
            for f in file_list:
                # if Path(f).is_file():
                self.add_file_2_subject(f, ds)

    self.entities_keys = entities_keys

search_folder 

search_folder(path: Path, ds, filter_folder) -> None

Recursively scan path and register every file found with the global info.

Parameters:

Name Type Description Default
path Path

Directory to scan.

 required
ds

Dataset root path associated with the scanned folder.

 required
filter_folder

Callable (path, level) -> bool; folders for which this returns False are skipped.

 required
Source code in TPTBox/core/bids_files.py 
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def search_folder(self, path: Path, ds, filter_folder) -> None:
    """Recursively scan *path* and register every file found with the global info.

    Args:
        path: Directory to scan.
        ds: Dataset root path associated with the scanned folder.
        filter_folder: Callable ``(path, level) -> bool``; folders for
            which this returns ``False`` are skipped.
    """
    for entry in _scan_tree(path, filter_folder=filter_folder):
        if entry.is_file():
            self.add_file_2_subject(Path(entry.path), ds)

add_file_2_subject 

add_file_2_subject(bids: BIDS_FILE | Path, ds: Path | str | None = None) -> None

Parse a file path (or pre-built :class:BIDS_FILE) and add it to the correct subject bucket.

Parameters:

Name Type Description Default
bids BIDS_FILE | Path

Either a raw filesystem path or an already-constructed :class:BIDS_FILE instance.

 required
ds Path | str | None

Dataset root path. Required when bids is a plain :class:~pathlib.Path; inferred automatically when bids is a :class:BIDS_FILE.

 None

Raises:

Type Description
AssertionError

If bids is a :class:~pathlib.Path and ds is None.
Source code in TPTBox/core/bids_files.py 
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def add_file_2_subject(self, bids: BIDS_FILE | Path, ds: Path | str | None = None) -> None:
    """Parse a file path (or pre-built :class:`BIDS_FILE`) and add it to the correct subject bucket.

    Args:
        bids: Either a raw filesystem path or an already-constructed
            :class:`BIDS_FILE` instance.
        ds: Dataset root path.  Required when *bids* is a plain
            :class:`~pathlib.Path`; inferred automatically when *bids*
            is a :class:`BIDS_FILE`.

    Raises:
        AssertionError: If *bids* is a :class:`~pathlib.Path` and *ds*
            is ``None``.
    """
    if isinstance(bids, Path) and "DS_Store" in bids.name:
        return
    if ds is None:
        if isinstance(bids, BIDS_FILE):
            ds = bids.dataset
        else:
            raise AssertionError("Dataset-path required")

    if isinstance(bids, (Path, str)):
        try:
            bids_key, file_type = str(bids).rsplit("/", maxsplit=1)[-1].split(".", maxsplit=1)
            # print(bids_key)
        except Exception:
            print("[!] skip file with out a type declaration:", bids.name)
            # raise e
            return

        if bids_key in self._global_bids_list:
            self._global_bids_list[bids_key].add_file(bids)
            return
        bids = BIDS_FILE(
            bids,
            ds,
            verbose=self.verbose,
            file_name_manipulation=self.file_name_manipulation,
        )

    subject = bids.info.get("sub", "unsorted")
    if subject not in self.subjects:
        self.subjects[subject] = Subject_Container(subject, self.sequence_splitting_keys)
    self.count_file += 1
    (
        print(
            f"Found: {subject}, total file keys {(self.count_file)},  total subjects = {len(self.subjects)}    ",
            end="\r",
        )
        if self.verbose
        else None
    )
    self.subjects[subject].add(bids)

enumerate_subjects 

enumerate_subjects(sort: bool = False, shuffle: bool = False) -> list[tuple[str, Subject_Container]]

Return all subject identifiers together with their :class:Subject_Container.

Parameters:

Name Type Description Default
sort bool

If True, return subjects sorted alphabetically by subject ID.

 False
shuffle bool

If True, return subjects in a random order. Mutually exclusive with sort (sort takes precedence).

 False

Returns:

Type Description
list[tuple[str, Subject_Container]]

A list of (subject_id, Subject_Container) pairs.
Source code in TPTBox/core/bids_files.py 
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def enumerate_subjects(self, sort: bool = False, shuffle: bool = False) -> list[tuple[str, Subject_Container]]:
    """Return all subject identifiers together with their :class:`Subject_Container`.

    Args:
        sort: If ``True``, return subjects sorted alphabetically by
            subject ID.
        shuffle: If ``True``, return subjects in a random order.
            Mutually exclusive with *sort* (sort takes precedence).

    Returns:
        A list of ``(subject_id, Subject_Container)`` pairs.
    """
    # TODO Enumerate should put out numbers...
    if sort:
        return sorted(self.subjects.items())
    if shuffle:
        s = list(self.subjects.items())
        random.shuffle(s)
        return s
    return self.subjects.items()  # type: ignore

iter_subjects 

iter_subjects(sort: bool = False) -> list[tuple[str, Subject_Container]]

Iterate over all subjects (alias for :meth:enumerate_subjects without shuffle).

Parameters:

Name Type Description Default
sort bool

If True, return subjects sorted alphabetically by subject ID.

 False

Returns:

Type Description
list[tuple[str, Subject_Container]]

A list of (subject_id, Subject_Container) pairs.
Source code in TPTBox/core/bids_files.py 
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def iter_subjects(self, sort: bool = False) -> list[tuple[str, Subject_Container]]:
    """Iterate over all subjects (alias for :meth:`enumerate_subjects` without shuffle).

    Args:
        sort: If ``True``, return subjects sorted alphabetically by
            subject ID.

    Returns:
        A list of ``(subject_id, Subject_Container)`` pairs.
    """
    if sort:
        return sorted(self.subjects.items())
    return self.subjects.items()  # type: ignore

Subject_Container

TPTBox.core.bids_files.Subject_Container

Container for all BIDS files belonging to a single subject, grouped by sequence.

Source code in TPTBox/core/bids_files.py 
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class Subject_Container:
    """Container for all BIDS files belonging to a single subject, grouped by sequence."""

    def __init__(self, name, sequence_splitting_keys: list[str]) -> None:
        self.name = name
        self.sequences: dict[str, list[BIDS_FILE]] = {}
        self.sequence_splitting_keys = sequence_splitting_keys.copy()

    def get_sequence_name(self, bids: BIDS_FILE) -> str:
        """Derive the sequence-bucket key for a given BIDS file.

        Combines the values of :attr:`sequence_splitting_keys` that are
        present in *bids* into a single underscore-joined string.

        Args:
            bids: The file whose sequence name should be resolved.

        Returns:
            A string key identifying the sequence bucket, e.g.
            ``"ses-01_sequ-303"``.
        """
        key_values = []
        for key in self.sequence_splitting_keys:
            key_values.append(bids.info[key]) if key in bids.info else None
        key = str.join("_", key_values)
        # sequence_names are only unique in the same session
        # ses = bids.info.get("ses", None)
        append_id = ""
        # idx = 1
        # This code fixes that in different sessions/same patient the filename can reuse splitting-keys
        # while True:
        #    if key + append_id in self.sequences:
        #        other_ses = self.sequences[key + append_id][0].info.get("ses", None)
        #        if ses == other_ses:
        #            break
        #        idx += 1
        #        append_id = f"_{idx}"
        #    else:
        #        break
        return key + append_id

    def add(self, bids: BIDS_FILE) -> None:
        """Register a BIDS file with this subject container.

        Places *bids* into the correct sequence bucket (determined by
        :meth:`get_sequence_name`) and sets the back-reference on the file.

        Args:
            bids: The BIDS file to add.
        """
        sequ = self.get_sequence_name(bids)
        self.sequences.setdefault(sequ, [])
        if bids not in self.sequences[sequ]:
            self.sequences[sequ].append(bids)
        bids.set_subject(self)

    def new_query(self, flatten=False) -> Searchquery:
        """Make a new search_query.

        Args:
            flatten (bool, optional): If you look for single file set flatten to True,
            If you want to find related files use flatten False and generate a dictionary with get_sequence_files after filtering. Defaults to False.

        Returns:
            Searchquery
        """
        return Searchquery(self, flatten)

    def get_sequence_files(
        self,
        sequ: str,
        key_transform: typing.Callable[[BIDS_FILE], str | None] | None = None,
        key_addendum: list[str] | None = None,
        alternative_sequ_list: list[BIDS_FILE] | None = None,
    ) -> BIDS_Family:
        """Returns a dictionary of all files the related sequence.

        Args:
                        sequ (str): key of the sequence
                        key_transform: function that maps BIDS_FILE to family key
                        key_addendum: list of keys that are used as sequence_naming_keys
                        alternative_sequ_list: when passed, is used instead of the self.sequences

        Returns:
            BIDS_Family that contains a data dictionary.
            dict: The key is the 'format' word (ct, dixon, snp,...), except special naming keys are passed.
            Default naming keys: ["seg", "label"] (see sequence_naming_keys for the up-to-date list)
            All default naming keys as well as those passed in key_addendum are appended as key-value to the family-key.

        Example:
            ses-123_msk.nii.gz will get key msk
            seg-subreg_msk.nii.gz will get the key msk_seg-subreg
            ses-123_T1c.nii.gz will get key T1c
        """
        out_dict: dict[str, list[BIDS_FILE]] = {}
        sequ_list: list[BIDS_FILE] = self.sequences[sequ]
        if alternative_sequ_list is not None:
            sequ_list = alternative_sequ_list
        for s in sequ_list:
            key = s.format

            seq_naming_keys = sequence_naming_keys.copy()
            if key_addendum is not None:
                seq_naming_keys += [k for k in key_addendum if k not in sequence_naming_keys]

            for k in seq_naming_keys:
                if k in s.info:
                    key = key + "_" + k + "-" + s.info[k]

            if key_transform is not None:
                out = key_transform(s)
                if isinstance(out, str):
                    key = out

            if key in out_dict:
                s1 = out_dict[key]
                s1.append(s)
            else:
                out_dict[key] = [s]
        return BIDS_Family(out_dict, self.sequence_splitting_keys)

get_sequence_name 

get_sequence_name(bids: BIDS_FILE) -> str

Derive the sequence-bucket key for a given BIDS file.

Combines the values of :attr:sequence_splitting_keys that are present in bids into a single underscore-joined string.

Parameters:

Name Type Description Default
bids BIDS_FILE

The file whose sequence name should be resolved.

 required

Returns:

Type Description
str

A string key identifying the sequence bucket, e.g.
str

"ses-01_sequ-303".
Source code in TPTBox/core/bids_files.py 
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def get_sequence_name(self, bids: BIDS_FILE) -> str:
    """Derive the sequence-bucket key for a given BIDS file.

    Combines the values of :attr:`sequence_splitting_keys` that are
    present in *bids* into a single underscore-joined string.

    Args:
        bids: The file whose sequence name should be resolved.

    Returns:
        A string key identifying the sequence bucket, e.g.
        ``"ses-01_sequ-303"``.
    """
    key_values = []
    for key in self.sequence_splitting_keys:
        key_values.append(bids.info[key]) if key in bids.info else None
    key = str.join("_", key_values)
    # sequence_names are only unique in the same session
    # ses = bids.info.get("ses", None)
    append_id = ""
    # idx = 1
    # This code fixes that in different sessions/same patient the filename can reuse splitting-keys
    # while True:
    #    if key + append_id in self.sequences:
    #        other_ses = self.sequences[key + append_id][0].info.get("ses", None)
    #        if ses == other_ses:
    #            break
    #        idx += 1
    #        append_id = f"_{idx}"
    #    else:
    #        break
    return key + append_id

add 

add(bids: BIDS_FILE) -> None

Register a BIDS file with this subject container.

Places bids into the correct sequence bucket (determined by :meth:get_sequence_name) and sets the back-reference on the file.

Parameters:

Name Type Description Default
bids BIDS_FILE

The BIDS file to add.

 required
Source code in TPTBox/core/bids_files.py 
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def add(self, bids: BIDS_FILE) -> None:
    """Register a BIDS file with this subject container.

    Places *bids* into the correct sequence bucket (determined by
    :meth:`get_sequence_name`) and sets the back-reference on the file.

    Args:
        bids: The BIDS file to add.
    """
    sequ = self.get_sequence_name(bids)
    self.sequences.setdefault(sequ, [])
    if bids not in self.sequences[sequ]:
        self.sequences[sequ].append(bids)
    bids.set_subject(self)

new_query 

new_query(flatten=False) -> Searchquery

Make a new search_query.

Parameters:

Name Type Description Default
flatten bool

If you look for single file set flatten to True,

 False

Returns:

Type Description
Searchquery

Searchquery
Source code in TPTBox/core/bids_files.py 
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def new_query(self, flatten=False) -> Searchquery:
    """Make a new search_query.

    Args:
        flatten (bool, optional): If you look for single file set flatten to True,
        If you want to find related files use flatten False and generate a dictionary with get_sequence_files after filtering. Defaults to False.

    Returns:
        Searchquery
    """
    return Searchquery(self, flatten)

get_sequence_files 

get_sequence_files(sequ: str, key_transform: Callable[[BIDS_FILE], str | None] | None = None, key_addendum: list[str] | None = None, alternative_sequ_list: list[BIDS_FILE] | None = None) -> BIDS_Family

Returns a dictionary of all files the related sequence.

Parameters:

Name Type Description Default
sequ str

key of the sequence

 required
key_transform Callable[[BIDS_FILE], str | None] | None

function that maps BIDS_FILE to family key

 None
key_addendum list[str] | None

list of keys that are used as sequence_naming_keys

 None
alternative_sequ_list list[BIDS_FILE] | None

when passed, is used instead of the self.sequences

 None

Returns:

Name Type Description
BIDS_Family

BIDS_Family that contains a data dictionary.
dict BIDS_Family

The key is the 'format' word (ct, dixon, snp,...), except special naming keys are passed.
BIDS_Family

Default naming keys: ["seg", "label"] (see sequence_naming_keys for the up-to-date list)
BIDS_Family

All default naming keys as well as those passed in key_addendum are appended as key-value to the family-key.
Example

ses-123_msk.nii.gz will get key msk seg-subreg_msk.nii.gz will get the key msk_seg-subreg ses-123_T1c.nii.gz will get key T1c

Source code in TPTBox/core/bids_files.py 
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def get_sequence_files(
    self,
    sequ: str,
    key_transform: typing.Callable[[BIDS_FILE], str | None] | None = None,
    key_addendum: list[str] | None = None,
    alternative_sequ_list: list[BIDS_FILE] | None = None,
) -> BIDS_Family:
    """Returns a dictionary of all files the related sequence.

    Args:
                    sequ (str): key of the sequence
                    key_transform: function that maps BIDS_FILE to family key
                    key_addendum: list of keys that are used as sequence_naming_keys
                    alternative_sequ_list: when passed, is used instead of the self.sequences

    Returns:
        BIDS_Family that contains a data dictionary.
        dict: The key is the 'format' word (ct, dixon, snp,...), except special naming keys are passed.
        Default naming keys: ["seg", "label"] (see sequence_naming_keys for the up-to-date list)
        All default naming keys as well as those passed in key_addendum are appended as key-value to the family-key.

    Example:
        ses-123_msk.nii.gz will get key msk
        seg-subreg_msk.nii.gz will get the key msk_seg-subreg
        ses-123_T1c.nii.gz will get key T1c
    """
    out_dict: dict[str, list[BIDS_FILE]] = {}
    sequ_list: list[BIDS_FILE] = self.sequences[sequ]
    if alternative_sequ_list is not None:
        sequ_list = alternative_sequ_list
    for s in sequ_list:
        key = s.format

        seq_naming_keys = sequence_naming_keys.copy()
        if key_addendum is not None:
            seq_naming_keys += [k for k in key_addendum if k not in sequence_naming_keys]

        for k in seq_naming_keys:
            if k in s.info:
                key = key + "_" + k + "-" + s.info[k]

        if key_transform is not None:
            out = key_transform(s)
            if isinstance(out, str):
                key = out

        if key in out_dict:
            s1 = out_dict[key]
            s1.append(s)
        else:
            out_dict[key] = [s]
    return BIDS_Family(out_dict, self.sequence_splitting_keys)

BIDS_FILE

TPTBox.core.bids_files.BIDS_FILE

Representation of a single BIDS-compliant file with parsed entities and dataset context.

Source code in TPTBox/core/bids_files.py 
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class BIDS_FILE:
    """Representation of a single BIDS-compliant file with parsed entities and dataset context."""

    def __init__(
        self,
        file: Path | str,
        dataset: Path | str,
        verbose=True,
        bids_ds: BIDS_Global_info | None = None,
        file_name_manipulation: typing.Callable[[str], str] | None = None,
    ):
        """Multi-file BIDS record sharing the same identifier (all extensions of one file stem).

        Holds references to `.nii.gz`, `.json`, etc. simultaneously.

        The following fields are imported and can be accessed.
        self.format (str): The last value determining its use/modalities like T1w, msk, dixon
        self.info (dict[str,str]): key,values of the bids file. Can be changed, but will be only reflected in get_changed_path/find_changed_path if the from_info is set True.
                                    Oder of insert matter (requires python >3.7). get/set/loop are for this dict
        self.BIDS_key(str): Hashing key.
        self.file (dict[str,Path]): keys are file extensions and values are paths to those files with given extension
                                    The first file is added by this init, second by add_file-function. This is usually done by the tree generation of BIDS_Global_info
                                    Self generated BIDS_FILE will not automatically have the json/nii.gz pair, except when their are in the same folder.
        self.dataset (Path): root-dataset name. All should paths will start from here.

        Args:
            file (Path): Path to the file in BIDS format.
            dataset (Path): Top Folder of the dataset
            verbose (bool, optional): You will be informed of non-conform Bids names/keys. Defaults to True.
        """
        file = Path(file) if not isinstance(file, Path) else file
        self.dataset = Path(dataset) if not isinstance(dataset, Path) else dataset
        self.verbose = verbose
        if file_name_manipulation is not None:
            if "WS_" in str(file):
                file.rename(file.parent / Path(file_name_manipulation(file.name)))
            name = file_name_manipulation(file.name)
        else:
            name = file.name
        self.format, self.info, self.BIDS_key, file_type = get_values_from_name(name, verbose)

        if bids_ds is not None:
            bids_ds.add_file_2_subject(bids=self, ds=self.dataset)
        self.file = {file_type: file}
        bids_key, _ = file.name.split(".", maxsplit=1)
        for file_type in ["nii.gz", "json", "png"]:
            if file_type in self.file:
                continue
            if os.path.exists(os.path.join(file.parent, bids_key + "." + file_type)):
                self.file[file_type] = Path(file.parent, bids_key + "." + file_type)
        self.file = dict(sorted(self.file.items()))

    def get_file(self, ending: str = "json", default: Path | None = None) -> Path | None:
        """Return the path for a given file extension, or *default* if absent.

        Args:
            ending: File extension to look up, e.g. ``"json"`` or
                ``"nii.gz"``.
            default: Value returned when the extension is not present.

        Returns:
            The :class:`~pathlib.Path` for the requested extension, or
            *default*.
        """
        return self.file.get(ending, default)

    def __str__(self) -> str:
        s = f"{self.BIDS_key}.{list(self.file.keys())}\t parent = {self.get_parent()}"
        return s

    def __repr__(self):
        return str(self)

    def __hash__(self) -> int:
        return self.BIDS_key.__hash__()

    def exists(self) -> bool:
        """Return ``True`` when the primary file (preferring ``nii.gz``) exists on disk.

        Returns:
            ``True`` if the file exists, ``False`` otherwise.
        """
        if "nii.gz" in self.file:
            return self.file["nii.gz"].exists()
        else:
            return self.file[next(iter(self.file.keys()))].exists()

    def unlink(self, missing_ok: bool = True) -> None:
        """Delete all files associated with this BIDS entry from disk.

        Args:
            missing_ok: If ``True``, suppress errors when a file does not
                exist.  Passed directly to :meth:`pathlib.Path.unlink`.
        """
        for f in self.file.values():
            f.unlink(missing_ok=missing_ok)

    def __lt__(self, other):
        return self.BIDS_key < other.BIDS_key

    def __len__(self):
        return 1

    def __getitem__(self, key):
        assert key == 0, key
        return self

    def __iter__(self):
        return iter((self,))

    def __eq__(self, key):
        if hasattr(key, "BIDS_key"):
            return self.BIDS_key == key.BIDS_key
        else:
            return False

    def set_subject(self, sub: Subject_Container) -> None:
        """Attach a back-reference to the owning :class:`Subject_Container`.

        Args:
            sub: The subject container that owns this file.
        """
        self.subject = sub

    def set(self, key: str, value: str) -> None:
        """Set a BIDS entity key-value pair on this file, validating the entity.

        Args:
            key: BIDS entity key (e.g. ``"seg"``).
            value: Value to assign to the key.
        """
        validate_entities(key, value, f"..._{key}-{value}_...", self.verbose)
        self.info[key] = value

    def get(self, key: str, default: str | None = None) -> str | None:
        """Return the value for a BIDS entity key, or *default* if not present.

        Args:
            key: BIDS entity key to look up (e.g. ``"sub"``, ``"ses"``).
            default: Fallback value when *key* is absent.

        Returns:
            The entity value string, or *default*.
        """
        if key in self.info:
            return self.info[key]
        return default

    def loop_keys(self) -> typing.ItemsView[str, str]:
        """Return all BIDS entity key-value pairs for this file.

        Returns:
            A view of ``(key, value)`` pairs from the :attr:`info` dictionary.
        """
        return self.info.items()

    def remove(self, key: str) -> str:
        """Remove and return a BIDS entity key from :attr:`info`.

        Args:
            key: Entity key to remove.  Must not be ``"sub"``.

        Returns:
            The value that was associated with *key*.

        Raises:
            AssertionError: If *key* is ``"sub"`` (subject ID cannot be
                removed).
            KeyError: If *key* is not present in :attr:`info`.
        """
        assert key != "sub", "not allowed to remove subject name"
        return self.info.pop(key)

    def add_file(
        self,
        path: Path,
        bids_ds: BIDS_Global_info | None = None,
    ) -> None:
        """Associate an additional file extension with this BIDS entry.

        Used to register companion files (e.g. a ``.json`` sidecar alongside
        a ``nii.gz``) that share the same BIDS key stem.

        Args:
            path: Path to the companion file.  Its stem must match
                :attr:`BIDS_key`.
            bids_ds: If provided, the global registry is updated so that the
                merged file dictionary is reflected there as well.

        Raises:
            AssertionError: If the stem of *path* does not match
                :attr:`BIDS_key`.
        """
        bids_key, file_type = Path(path).name.split(".", maxsplit=1)

        assert bids_key == self.BIDS_key, f"only aligned data aka same name different file type: {bids_key} != {self.BIDS_key}"
        bids_dic_file = self.file
        if file_type not in self.file:
            bids_dic_file[file_type] = path
            if bids_ds is not None:
                bids_ds._global_bids_list[bids_key].file = dict(sorted(bids_dic_file.items()))
        self.file = dict(sorted(bids_dic_file.items()))

    def rename_files(self, path: Path | str, ending: str = ".nii.gz") -> None:
        """Rename all associated files on disk to a new base path.

        The *ending* suffix is stripped from *path* to obtain the base stem,
        then each extension in :attr:`file` is appended.

        Args:
            path: Target path including the primary extension (e.g.
                ``/out/sub-001_T1w.nii.gz``).
            ending: Extension that terminates *path* and that will be
                stripped before adding per-extension suffixes.

        Raises:
            AssertionError: If *path* does not end with *ending*.
        """
        path = str(path)
        assert path.endswith(ending), f"set 'ending' to the part after the '.'\n {path} does not end with {ending}"
        path = path.replace(ending, "")
        for key, value in self.file.items():
            p = Path(path + "." + key)
            value.rename(p)

    def symlink_files(self, path: Path | str, ending: str = ".nii.gz", exist_ok: bool = False) -> None:
        """Create symbolic links for all associated files at a new base path.

        Equivalent to :meth:`rename_files` but creates symlinks rather than
        moving files.  Existing correct symlinks are silently skipped.

        Args:
            path: Target path including the primary extension (e.g.
                ``/out/sub-001_T1w.nii.gz``).
            ending: Extension used to compute the base stem; a leading dot is
                added automatically if absent.

        Raises:
            AssertionError: If *path* does not end with *ending*, or if an
                existing symlink at the target points elsewhere.
        """
        ending = ending if ending[0] == "." else "." + ending
        path = str(path)
        assert path.endswith(ending), f"set 'ending' to the part after the '.'\n {path} does not end with {ending}"
        path = path.replace(ending, "")
        for key, value in self.file.items():
            p = Path(path + "." + key)

            if os.path.islink(p):
                assert Path(os.readlink(p)) == value, f"{p} exists"
                continue
            if exist_ok and p.exists():
                continue

            os.symlink(value, p)

    def get_path_decomposed(self, file_type: str | None = None) -> tuple[Path, str, str, str]:
        """Decompose the file path relative to the dataset root.

        Args:
            file_type: Extension key to use when selecting which path to
                decompose (e.g. ``"nii.gz"``).  Defaults to the first
                extension in :attr:`file`.

        Returns:
            A 4-tuple ``(dataset_path, parent, sub_path, filename)`` where

            * ``dataset_path`` is the dataset root :class:`~pathlib.Path`,
            * ``parent`` is the top-level folder (e.g. ``"rawdata"``),
            * ``sub_path`` is the intermediate path (e.g.
              ``"sub-001/ses-01"``),
            * ``filename`` is the bare filename including extension.
        """
        if file_type is None:
            file_type = next(iter(self.file.keys()))
        folder_list = str(self.file[file_type].relative_to(self.dataset)).replace("\\\\", "/").replace("\\", "/").split("/")
        parent = folder_list[0]
        subpath = folder_list[1:-1]
        filename = folder_list[-1]
        # print(parent, subpath, filename)
        return self.dataset, parent, str.join("/", subpath), filename

    @property
    def parent(self) -> str:
        """Top-level parent folder name (e.g. ``"rawdata"`` or ``"derivatives"``)."""
        return self.get_parent()

    @property
    def bids_format(self) -> str:
        """Alias for :attr:`format`; the BIDS modality/format label (e.g. ``"T1w"``)."""
        return self.format

    @property
    def mod(self) -> str | None:
        """Modality label, resolving ``"msk"`` to the underlying ``mod`` entity value.

        Returns:
            The ``mod`` entity value for mask files, or :attr:`bids_format`
            for all other formats.
        """
        mod = self.bids_format
        if mod == "msk":
            return self.get("mod")
        return mod

    def get_parent(self, file_type: str | None = None) -> str:
        """Return the top-level parent folder name for this file.

        Args:
            file_type: Extension key used to select which path to inspect.
                Defaults to the first extension in :attr:`file`.

        Returns:
            The parent folder name, e.g. ``"rawdata"`` or ``"derivatives"``.
        """
        return self.get_path_decomposed(file_type)[1]

    def get_changed_bids(
        self,
        file_type: str | None = "nii.gz",
        bids_format: str | None = None,
        parent: str = "derivatives",
        path: str | None = None,
        info: dict | None = None,
        from_info: bool = False,
        auto_add_run_id: bool = False,
        additional_folder: str | None = None,
        dataset_path: str | None = None,
        make_parent: bool = False,
        non_strict_mode: bool = False,
    ) -> BIDS_FILE:
        """Construct a new :class:`BIDS_FILE` pointing to a derived output path.

        Delegates path construction to :meth:`get_changed_path` and wraps the
        result in a :class:`BIDS_FILE` instance.

        Args:
            file_type: Target file extension (e.g. ``"nii.gz"``).
            bids_format: Override the format/modality label.
            parent: Target parent folder (e.g. ``"derivatives"``).
            path: Override the intermediate sub-path; supports ``{key}``
                template substitution.
            info: Additional or overriding entity key-value pairs.
            from_info: If ``True``, use the in-memory :attr:`info` dict
                instead of the original filename entities.
            auto_add_run_id: Append an auto-incremented ``run`` tag when the
                target path already exists.
            additional_folder: Extra folder appended between *path* and the
                filename.
            dataset_path: Override the dataset root.
            make_parent: Create parent directories if they do not exist.
            non_strict_mode: Relax BIDS entity validation.

        Returns:
            A new :class:`BIDS_FILE` pointing to the derived output.
        """
        ds = dataset_path if dataset_path is not None else self.get_path_decomposed()[0]
        return BIDS_FILE(
            self.get_changed_path(
                file_type=file_type,
                bids_format=bids_format,
                parent=parent,
                path=path,
                info=info,
                from_info=from_info,
                auto_add_run_id=auto_add_run_id,
                additional_folder=additional_folder,
                dataset_path=dataset_path,
                make_parent=make_parent,
                non_strict_mode=non_strict_mode,
            ),
            ds,
        )

    def get_changed_path(  # noqa: C901
        self,
        file_type: str | None = "nii.gz",
        bids_format: str | None = None,
        parent: str = "derivatives",
        path: str | None = None,
        info: dict | None = None,
        from_info=False,
        auto_add_run_id=False,
        additional_folder: str | None = None,
        dataset_path: str | Path | None = None,
        make_parent=False,
        no_sorting_mode: bool = False,
        non_strict_mode: bool = False,
    ) -> Path:
        """Changes part of the path to generate new flies. The new parent will be derivatives as a default.

        Examples:
        subreg_path = ct_bids.get_changed_path(file_type="nii.gz",parent = "derivatives",info={"seg": "subreg"}, format="cdt")

        Args:
            file_type (str | None, optional): Override the file type, like nii.gz to json Defaults to "nii.gz".

            format (str | None, optional): Changes the "format key" like ct, msk, T1w. Defaults to None.

            parent (str, optional): derivatives or rawdata or any parent folder. Defaults to "derivatives".

            path (str | None, optional): If set: replaces the path from parent to file. Use {key} to get dynamic paths like {/sub-{sub}/ses-{ses}}. Defaults to None.

            info (dict | None, optional): Provide additional key,value pairs like {'seg':'subreg'}. Defaults to None.

            from_info (bool, optional): False: The key,value pair from the original file name are used. True: The key,value of the python object are used. Defaults to False.

            auto_add_run_id (bool, optional): Adds a run-{new id} tag, that is not occupied. Defaults to False.

            additional_folder (str | None, optional): add an additional folder towards path. Defaults to None.

            dataset_path (str | None, optional): Override the dataset_path. Defaults to None.

            no_sorting_mode (bool): If true, will keep the order of the origin nii. Defaults to False

        Returns:
            _type_: _description_
        """
        if info is None:
            info = {}
        if non_strict_mode and not self.BIDS_key.startswith("sub"):
            info["sub"] = self.BIDS_key.replace("_", "-").replace(".", "-")
        else:
            # replace _ with - in all info
            self.info = {k: v.replace("_", "-") for k, v in self.info.items()}
        if isinstance(file_type, str) and file_type.startswith("."):
            file_type = file_type[1:]
        path = self.insert_info_into_path(path)
        additional_folder = self.insert_info_into_path(additional_folder) if additional_folder is not None else None
        ds_path, same_parent, same_path, old_filename = self.get_path_decomposed()
        if from_info:
            same_info = self.info
            same_format = self.format
            same_filetype = None
        else:
            same_format, same_info, _, same_filetype = get_values_from_name(
                old_filename, self.verbose
            )  # Oder of keys is deterministic for python >3.7
        while True:
            file_name = ""
            ## Info
            final_info = {}
            for key, value in same_info.items():
                if key in info:
                    value = info[key]  # noqa: PLW2901
                if value is not None:
                    # file_name += f"{key}-{value}_"
                    if non_strict_mode:
                        validate_entities(key, value, f"..._{key}-{value}_...", verbose=True)
                    else:
                        assert validate_entities(key, value, f"..._{key}-{value}_...", verbose=True)
                    final_info[key] = value.replace("_", "-")
            for key, value in info.items():
                # New Keys are getting checked!
                if non_strict_mode:
                    (
                        print(
                            f"[!] {key} is not in list of legal keys. This name '{key}' is invalid. Legal keys are: {list(entities_keys.keys())}. \nFor use see https://bids-specification.readthedocs.io/en/stable/99-appendices/09-entities.html"
                        )
                        if key not in entities_keys
                        else None
                    )
                else:
                    assert key in entities_keys, (
                        f"[!] {key} is not in list of legal keys. This name '{key}' is invalid. Legal keys are: {list(entities_keys.keys())}. \nFor use see https://bids-specification.readthedocs.io/en/stable/99-appendices/09-entities.html"
                    )
                # validate_entities(key, value, f"..._{key}-{value}_...", self.verbose)
                if key in same_info:
                    continue
                if value is not None:
                    if not non_strict_mode:
                        assert validate_entities(key, value, f"..._{key}-{value}_...", True), f"..._{key}-{value}_..."
                    final_info[key] = value
                # file_name += f"{key}-{value}_"
            # sort by order
            keys_order = final_info.keys()
            if not no_sorting_mode:
                entity_keys = list(entities_keys.keys())
                keys_order = sorted(
                    final_info.keys(),
                    key=lambda x: entity_keys.index(x) if x in entity_keys else list(final_info.keys()).index(x) + len(entity_keys),
                )
            for key in keys_order:
                file_name += f"{key}-{final_info[key]}_"
            # End Info
            bids_format = bids_format if bids_format is not None else same_format
            file_type = file_type if file_type is not None else same_filetype
            assert file_type in file_types, (
                f"[!] {file_type} is not in list of file types. Legal file types are: {list(file_types)}. \nFor use see https://bids-specification.readthedocs.io/en/stable/99-appendices/09-entities.html"
            )
            if bids_format not in formats and not non_strict_mode:
                raise ValueError(
                    f"[!] {bids_format} is not in list of formats. Legal formats are: {list(formats)}. \nFor use see https://bids-specification.readthedocs.io/en/stable/99-appendices/09-entities.html"
                )
            file_name += f"{bids_format}.{file_type}"

            out_path = Path(
                dataset_path if dataset_path is not None else ds_path,
                parent if parent is not None else same_parent,
                path if path is not None else same_path,
                additional_folder if additional_folder is not None else "",
                file_name,
            )
            if make_parent:
                out_path.parent.mkdir(exist_ok=True, parents=True)
            if not auto_add_run_id:
                return out_path
            if not out_path.exists():
                return out_path
            if "run" in info:
                info["run"] += 1
            else:
                info["run"] = 2

    def save_changed_path(
        self,
        bids_format: str | None = None,
        parent: str = "derivatives",
        path: str | None = None,
        info: dict | None = None,
        from_info: bool = False,
        auto_add_run_id: bool = False,
        additional_folder: str | None = None,
        dataset_path: str | None = None,
        non_strict_mode: bool = False,
    ) -> None:
        """Copy all associated files to their derived output paths.

        Calls :meth:`get_changed_path` for every extension in :attr:`file`
        and copies each source file to the resulting destination using
        :func:`shutil.copy2`.

        Args:
            bids_format: Override the format/modality label.
            parent: Target parent folder (e.g. ``"derivatives"``).
            path: Override the intermediate sub-path; supports ``{key}``
                template substitution.
            info: Additional or overriding entity key-value pairs.
            from_info: If ``True``, use the in-memory :attr:`info` dict
                instead of the original filename entities.
            auto_add_run_id: Append an auto-incremented ``run`` tag when the
                target path already exists.
            additional_folder: Extra folder appended between *path* and the
                filename.
            dataset_path: Override the dataset root.
            non_strict_mode: Relax BIDS entity validation.
        """
        import shutil

        for key, value in self.file.items():
            out = self.get_changed_path(
                key,
                bids_format=bids_format,
                parent=parent,
                path=path,
                from_info=from_info,
                info=info,
                auto_add_run_id=auto_add_run_id,
                additional_folder=additional_folder,
                dataset_path=dataset_path,
                make_parent=True,
                non_strict_mode=non_strict_mode,
            )
            shutil.copy2(value, out)

    def find_changed_path(
        self,
        bids_ds: BIDS_Global_info,
        bids_format: str | None = None,
        info: dict | None = None,
        from_info: bool = False,
    ) -> BIDS_FILE | None:
        """Look up an already-registered derived file in the global BIDS index.

        Constructs the expected BIDS key for the derived file (applying the
        same entity overrides as :meth:`get_changed_path`) and returns the
        matching :class:`BIDS_FILE` from *bids_ds* if it exists.

        Args:
            bids_ds: The global BIDS dataset to search.
            bids_format: Override the format/modality label.
            info: Additional or overriding entity key-value pairs.
            from_info: If ``True``, use the in-memory :attr:`info` dict
                instead of the original filename entities.

        Returns:
            The matching :class:`BIDS_FILE` if found, otherwise ``None``.
        """
        if info is None:
            info = {}

        if from_info:
            same_info = self.info
            same_format = self.format
        else:
            _, _, _, old_filename = self.get_path_decomposed()
            same_format, same_info, _, _ = get_values_from_name(old_filename, self.verbose)  # Oder of keys is deterministic for python >3.7
        file_name = ""
        for key, value in same_info.items():
            if key in info:
                value = info[key]  # noqa: PLW2901
            file_name += f"{key}-{value}_"
        for key, value in info.items():
            validate_entities(key, value, f"..._{key}-{value}_...", self.verbose)
            if key in same_info:
                continue
            file_name += f"{key}-{value}_"

        file_name += f"{bids_format if bids_format is not None else same_format}"
        return bids_ds._global_bids_list.get(file_name)

    def insert_info_into_path(self, path: str | None) -> str | None:
        """Replace ``{key}`` placeholders in *path* with entity values from :attr:`info`.

        Example::

            # With self.info = {"sub": "patient001", "ses": "01"}
            bids.insert_info_into_path("sub-{sub}/ses-{ses}")
            # -> "sub-patient001/ses-01"

        Args:
            path: Template string containing ``{key}`` placeholders, or
                ``None``.

        Returns:
            The expanded string, or ``None`` when *path* is ``None``.
        """
        if path is None:
            return None
        path = str(path)
        while "{" in path:
            left, right = path.split("{", maxsplit=1)
            middle, right = right.split("}", maxsplit=1)
            a = self.info.get(middle, None)
            if a is None:
                warn(f"{middle} not found in {self}", stacklevel=3)
                a = middle
            path = left + a + right
        return path

    def get_sequence_files(
        self,
        key_transform: typing.Callable[[BIDS_FILE], str | None] | None = None,
        key_addendum: list[str] | None = None,
    ) -> BIDS_Family:
        """Return the :class:`BIDS_Family` that this file belongs to.

        Delegates to :meth:`Subject_Container.get_sequence_files` using the
        sequence name resolved from this file's entities.  The file must be
        part of a subject sequence (i.e. registered via
        :class:`BIDS_Global_info`).

        Args:
            key_transform: Optional callable mapping a :class:`BIDS_FILE` to
                a custom family key string; return ``None`` to use the default
                key.
            key_addendum: Extra entity keys appended to the family key beyond
                the default :attr:`sequence_naming_keys`.

        Returns:
            The :class:`BIDS_Family` containing all related files for this
            sequence.

        Raises:
            AssertionError: If this file has no owning
                :class:`Subject_Container`.
        """
        assert hasattr(self, "subject"), (
            "The BIDS_file must be part of a Sequence-family. Usually automatically generated by tree generation of BIDS_Global_info"
        )
        sequ = self.subject.get_sequence_name(self)
        return self.subject.get_sequence_files(sequ, key_transform=key_transform, key_addendum=key_addendum)

    def open_nii_reorient(self, axcodes_to: tuple[str, ...] = ("P", "I", "R"), verbose: bool = False) -> TPTBox.NII:
        """Open the NIfTI file and reorient it in-place to the target axis codes.

        Args:
            axcodes_to: Desired orientation as a tuple of axis code strings,
                e.g. ``("P", "I", "R")``.
            verbose: If ``True``, print reorientation details.

        Returns:
            The reoriented :class:`~TPTBox.NII` volume.
        """
        return self.open_nii().reorient_(axcodes_to, verbose=verbose)

    def has_json(self) -> bool:
        """Return ``True`` when a JSON sidecar is registered for this file."""
        return "json" in self.file

    def open_json(self) -> dict:
        """Load and return the JSON sidecar as a dictionary.

        Returns:
            Parsed JSON contents.

        Raises:
            KeyError: If no JSON file is registered in :attr:`file`.
        """
        with open(self.file["json"]) as f:
            return json.load(f)

    def open_poi(self, nii: TPTBox.Image_Reference | None = None) -> TPTBox.POI:
        """Load the associated JSON file as a :class:`~TPTBox.POI` (point-of-interest) object.

        If the POI lacks spatial metadata (zoom, shape, etc.) a reference
        NIfTI image is required to fill in those fields.

        Args:
            nii: Optional image reference used to supply missing spatial
                metadata.  Required when the JSON does not embed grid info.

        Returns:
            The loaded :class:`~TPTBox.POI` object with complete spatial
            metadata.

        Raises:
            ValueError: If no JSON file is present or the POI lacks spatial
                metadata and *nii* is ``None``.
        """
        from TPTBox import POI

        try:
            ctd = POI.load(self.file["json"], allow_global=True)
            if ctd.zoom is None or ctd.shape is None or ctd.rotation is None or ctd.origin is None or ctd.orientation is None:
                if nii is None and "ctd.json" in str(self.file["json"]):
                    p = Path(str(self.file["json"]).replace("ctd.json", "msk.nii.gz"))
                    nii = p if p.exists() else nii
                assert nii is not None, (
                    "This file has no zoom info. Use open_ctd(self, nii) with a image reference (BIDS_FILE/PATH) with the same nii"
                )
                nii = TPTBox.to_nii(nii)
                assert isinstance(nii, TPTBox.NII)
                ctd.zoom = nii.zoom
                ctd.shape = nii.shape
                ctd.rotation = nii.rotation
                ctd.origin = nii.origin
                ctd.orientation = nii.orientation
        except KeyError as e:
            raise ValueError(f"json not present. Found only {self.file.keys()}\t{self.file}\n\n{self}") from e
        return ctd

    def open_ctd(self, nii: TPTBox.Image_Reference | None = None) -> TPTBox.POI:
        """Alias for :meth:`open_poi`; load the centroid JSON as a :class:`~TPTBox.POI`.

        Args:
            nii: Optional image reference for missing spatial metadata.

        Returns:
            The loaded :class:`~TPTBox.POI` object.
        """
        return self.open_poi(nii)

    def has_nii(self) -> bool:
        """Return ``True`` when at least one supported NIfTI extension is registered."""
        return any(a in self.file for a in _supported_nii_files)

    def open_nii(self) -> TPTBox.NII:
        """Load the NIfTI file into a :class:`~TPTBox.NII` object.

        Returns:
            The loaded :class:`~TPTBox.NII` volume.

        Raises:
            ValueError: If no NIfTI file (``nii.gz`` / ``nii``) is present.
        """
        try:
            from TPTBox import NII

            return NII.load_bids(self)
        except KeyError as e:
            raise ValueError(f"nii.gz not present. Found only {self.file.keys()}\t{self.file}\n\n{self}") from e

    def get_grid_info(self, add_grid_info_to_json: bool = True) -> Grid | None:
        """Return the spatial grid metadata for this file.

        Looks up the grid info in the associated JSON sidecar.  If the JSON
        does not contain grid information the NIfTI is loaded, the grid is
        computed, and the result is written back to the JSON when
        *add_grid_info_to_json* is ``True``.

        Args:
            add_grid_info_to_json: If ``True``, persist newly computed grid
                info to the JSON sidecar.

        Returns:
            A :class:`~TPTBox.core.nii_poi_abstract.Grid` instance, or
            ``None`` if no NIfTI file is present.
        """
        from TPTBox.core.dicom.dicom_extract import _add_grid_info_to_json
        from TPTBox.core.nii_poi_abstract import Grid

        nii_file = self.get_nii_file()
        if nii_file is None:
            return None
        if not self.has_json():
            self.file["json"] = Path(str(nii_file).split(".")[0] + ".json")
        return Grid(**_add_grid_info_to_json(nii_file, self.file["json"], add=add_grid_info_to_json)["grid"])

    def get_nii_file(self) -> Path | None:
        """Return the path to the first available NIfTI file.

        Checks the supported NIfTI extensions (``nii.gz``, ``nii``, ``mkd``)
        in order and returns the first one present.

        Returns:
            The :class:`~pathlib.Path` to the NIfTI file, or ``None`` if
            none of the supported extensions are registered.
        """
        for key in _supported_nii_files:
            if key in self.file:
                return self.file[key]
        return None

    def has_npz(self) -> bool:
        """Return ``True`` when an NPZ array file is registered for this entry."""
        return "npz" in self.file

    def open_npz(self) -> dict[str, np.ndarray]:
        """Load the associated NPZ file and return its contents as a dictionary.

        Returns:
            A dictionary mapping array names to :class:`numpy.ndarray` objects.

        Raises:
            KeyError: If no NPZ file is registered in :attr:`file`.
        """
        return dict(np.load(self.file["npz"], allow_pickle=False))  # type: ignore

    def open(self, filetype: str, _internal: bool = False) -> Path | TPTBox.NII | dict | None:
        """Open a file by extension, returning the appropriate Python object.

        .. deprecated::
            Use :meth:`open_nii`, :meth:`open_json`, or :attr:`file` directly.

        Args:
            filetype: Extension to open (e.g. ``"nii.gz"``, ``"json"``).
            _internal: Suppress the deprecation warning when called internally.

        Returns:
            * A :class:`~TPTBox.NII` for NIfTI extensions.
            * A :class:`dict` for JSON files.
            * A :class:`~pathlib.Path` for all other file types.
            * ``None`` if *filetype* is not registered in :attr:`file`.
        """
        if not _internal:
            warn("open is deprecated.", DeprecationWarning, stacklevel=2)
        if filetype not in self.file:
            return None
        if filetype == "json":
            return self.open_json()
        if filetype in _supported_nii_files:
            return self.open_nii()
        return self.file[filetype]

    def do_filter(
        self,
        key: str,
        constrain: list[str] | str | typing.Callable[[str | object], bool],
        required: bool = False,
    ) -> bool:
        """Check whether this file satisfies a key/constraint filter.

        If the *key* is not present in this file, the inverse of *required*
        is returned (i.e. absent keys pass when ``required=False`` and fail
        when ``required=True``).

        Args:
            key: The entity to inspect.  Special values: ``"format"`` checks
                :attr:`format`; ``"filetype"`` checks registered extensions;
                ``"parent"`` checks the parent folder; ``"self"`` passes the
                whole :class:`BIDS_FILE`.  Any other value is looked up in
                :attr:`info`, then in :attr:`file` (opening the file when a
                callable is given).
            constrain: Matching criterion — a string for exact match, a list
                of strings for membership, or a callable predicate.
            required: If ``True``, files for which *key* is absent are
                rejected.  Defaults to ``False``.

        Returns:
            ``True`` when the constraint is satisfied, ``False`` otherwise.
        """
        key = key.lower()
        if key == "":
            return False
        if key == "format":
            value = self.format
        elif key == "filetype":
            value = list(self.file.keys())
            if isinstance(constrain, str) and constrain.startswith("."):
                constrain = constrain[1:]
        elif key == "parent":
            value = self.get_parent()
        elif key == "self":
            value = self
        elif key in self.info:
            value = self.info[key]
        elif key in self.file:
            value = self.open(key, _internal=True)
        else:
            return not required

        if not isinstance(value, list):
            value = [value]
        for v in value:
            if isinstance(constrain, list):
                if v in constrain:
                    return True
            elif isinstance(constrain, str):
                if v == constrain:
                    return True
            elif constrain(v):
                return True
        return False

    def get_interpolation_order(self) -> int:
        """Return the interpolation order for this file (0 for masks/segmentations, 3 for images).

        Returns:
            int: interpolation_order
        """
        return 0 if self.format == "msk" or "label" in self.info else 3

    def get_frame_of_reference_uid(self, default: str | None = None) -> str | None:
        """Return a short hash identifying the world-space frame of reference.

        Reads ``FrameOfReferenceUID`` from the JSON sidecar and converts it
        to an 8-character base-36 string.  Falls back to the ``res`` or
        ``ses`` entity, and finally to *default*, when no JSON is available.

        Args:
            default: Value returned when the frame of reference cannot be
                determined.

        Returns:
            An 8-character base-36 hash string, a BIDS entity value, or
            *default*.
        """
        import hashlib

        length = 8
        try:
            uid = self.open_json()["FrameOfReferenceUID"]
        except Exception:
            return self.get("res", self.get("ses", default))
        # Hash the UID
        hash_bytes = hashlib.sha1(uid.encode("utf-8")).digest()
        # Convert to integer, then to base36
        num = int.from_bytes(hash_bytes, "big")
        base36 = ""
        chars = "0123456789abcdefghijklmnopqrstuvwxyz"
        while num:
            num, i = divmod(num, 36)
            base36 = chars[i] + base36
        return base36[:length]

    def get_identifier(self, sequence_splitting_keys: list[str]) -> str:
        """Generates an identifier for the BIDS_FILE based on subject and splitting keys.

        Args:
            sequence_splitting_keys (list[str]): list of keys to use for splitting
        """
        if "sub" not in self.info:
            print(f"family_id, no sub-key, got {self.info}")
            identifier = "sub-404"
        else:
            identifier = "sub-" + self.info["sub"]
        for s in self.info.keys():
            if s in sequence_splitting_keys:
                identifier += "_" + s + "-" + self.info[s]
        return identifier

parent property 

parent: str

Top-level parent folder name (e.g. "rawdata" or "derivatives").

bids_format property 

bids_format: str

Alias for :attr:format; the BIDS modality/format label (e.g. "T1w").

mod property 

mod: str | None

Modality label, resolving "msk" to the underlying mod entity value.

Returns:

Type Description
str | None

The mod entity value for mask files, or :attr:bids_format
str | None

for all other formats.

__init__ 

__init__(file: Path | str, dataset: Path | str, verbose=True, bids_ds: BIDS_Global_info | None = None, file_name_manipulation: Callable[[str], str] | None = None)

Multi-file BIDS record sharing the same identifier (all extensions of one file stem).

Holds references to .nii.gz, .json, etc. simultaneously.

The following fields are imported and can be accessed. self.format (str): The last value determining its use/modalities like T1w, msk, dixon self.info (dict[str,str]): key,values of the bids file. Can be changed, but will be only reflected in get_changed_path/find_changed_path if the from_info is set True. Oder of insert matter (requires python >3.7). get/set/loop are for this dict self.BIDS_key(str): Hashing key. self.file (dict[str,Path]): keys are file extensions and values are paths to those files with given extension The first file is added by this init, second by add_file-function. This is usually done by the tree generation of BIDS_Global_info Self generated BIDS_FILE will not automatically have the json/nii.gz pair, except when their are in the same folder. self.dataset (Path): root-dataset name. All should paths will start from here.

Parameters:

Name Type Description Default
file Path

Path to the file in BIDS format.

 required
dataset Path

Top Folder of the dataset

 required
verbose bool

You will be informed of non-conform Bids names/keys. Defaults to True.

 True
Source code in TPTBox/core/bids_files.py 
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def __init__(
    self,
    file: Path | str,
    dataset: Path | str,
    verbose=True,
    bids_ds: BIDS_Global_info | None = None,
    file_name_manipulation: typing.Callable[[str], str] | None = None,
):
    """Multi-file BIDS record sharing the same identifier (all extensions of one file stem).

    Holds references to `.nii.gz`, `.json`, etc. simultaneously.

    The following fields are imported and can be accessed.
    self.format (str): The last value determining its use/modalities like T1w, msk, dixon
    self.info (dict[str,str]): key,values of the bids file. Can be changed, but will be only reflected in get_changed_path/find_changed_path if the from_info is set True.
                                Oder of insert matter (requires python >3.7). get/set/loop are for this dict
    self.BIDS_key(str): Hashing key.
    self.file (dict[str,Path]): keys are file extensions and values are paths to those files with given extension
                                The first file is added by this init, second by add_file-function. This is usually done by the tree generation of BIDS_Global_info
                                Self generated BIDS_FILE will not automatically have the json/nii.gz pair, except when their are in the same folder.
    self.dataset (Path): root-dataset name. All should paths will start from here.

    Args:
        file (Path): Path to the file in BIDS format.
        dataset (Path): Top Folder of the dataset
        verbose (bool, optional): You will be informed of non-conform Bids names/keys. Defaults to True.
    """
    file = Path(file) if not isinstance(file, Path) else file
    self.dataset = Path(dataset) if not isinstance(dataset, Path) else dataset
    self.verbose = verbose
    if file_name_manipulation is not None:
        if "WS_" in str(file):
            file.rename(file.parent / Path(file_name_manipulation(file.name)))
        name = file_name_manipulation(file.name)
    else:
        name = file.name
    self.format, self.info, self.BIDS_key, file_type = get_values_from_name(name, verbose)

    if bids_ds is not None:
        bids_ds.add_file_2_subject(bids=self, ds=self.dataset)
    self.file = {file_type: file}
    bids_key, _ = file.name.split(".", maxsplit=1)
    for file_type in ["nii.gz", "json", "png"]:
        if file_type in self.file:
            continue
        if os.path.exists(os.path.join(file.parent, bids_key + "." + file_type)):
            self.file[file_type] = Path(file.parent, bids_key + "." + file_type)
    self.file = dict(sorted(self.file.items()))

get_file 

get_file(ending: str = 'json', default: Path | None = None) -> Path | None

Return the path for a given file extension, or default if absent.

Parameters:

Name Type Description Default
ending str

File extension to look up, e.g. "json" or "nii.gz".

 'json'
default Path | None

Value returned when the extension is not present.

 None

Returns:

Name Type Description
The Path | None

class:~pathlib.Path for the requested extension, or
Path | None

default.
Source code in TPTBox/core/bids_files.py 
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def get_file(self, ending: str = "json", default: Path | None = None) -> Path | None:
    """Return the path for a given file extension, or *default* if absent.

    Args:
        ending: File extension to look up, e.g. ``"json"`` or
            ``"nii.gz"``.
        default: Value returned when the extension is not present.

    Returns:
        The :class:`~pathlib.Path` for the requested extension, or
        *default*.
    """
    return self.file.get(ending, default)

exists 

exists() -> bool

Return True when the primary file (preferring nii.gz) exists on disk.

Returns:

Type Description
bool

True if the file exists, False otherwise.
Source code in TPTBox/core/bids_files.py 
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def exists(self) -> bool:
    """Return ``True`` when the primary file (preferring ``nii.gz``) exists on disk.

    Returns:
        ``True`` if the file exists, ``False`` otherwise.
    """
    if "nii.gz" in self.file:
        return self.file["nii.gz"].exists()
    else:
        return self.file[next(iter(self.file.keys()))].exists()

unlink(missing_ok: bool = True) -> None

Delete all files associated with this BIDS entry from disk.

Parameters:

Name Type Description Default
missing_ok bool

If True, suppress errors when a file does not exist. Passed directly to :meth:pathlib.Path.unlink.

 True
Source code in TPTBox/core/bids_files.py 
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def unlink(self, missing_ok: bool = True) -> None:
    """Delete all files associated with this BIDS entry from disk.

    Args:
        missing_ok: If ``True``, suppress errors when a file does not
            exist.  Passed directly to :meth:`pathlib.Path.unlink`.
    """
    for f in self.file.values():
        f.unlink(missing_ok=missing_ok)

set_subject 

set_subject(sub: Subject_Container) -> None

Attach a back-reference to the owning :class:Subject_Container.

Parameters:

Name Type Description Default
sub Subject_Container

The subject container that owns this file.

 required
Source code in TPTBox/core/bids_files.py 
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def set_subject(self, sub: Subject_Container) -> None:
    """Attach a back-reference to the owning :class:`Subject_Container`.

    Args:
        sub: The subject container that owns this file.
    """
    self.subject = sub

set 

set(key: str, value: str) -> None

Set a BIDS entity key-value pair on this file, validating the entity.

Parameters:

Name Type Description Default
key str

BIDS entity key (e.g. "seg").

 required
value str

Value to assign to the key.

 required
Source code in TPTBox/core/bids_files.py 
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def set(self, key: str, value: str) -> None:
    """Set a BIDS entity key-value pair on this file, validating the entity.

    Args:
        key: BIDS entity key (e.g. ``"seg"``).
        value: Value to assign to the key.
    """
    validate_entities(key, value, f"..._{key}-{value}_...", self.verbose)
    self.info[key] = value

get 

get(key: str, default: str | None = None) -> str | None

Return the value for a BIDS entity key, or default if not present.

Parameters:

Name Type Description Default
key str

BIDS entity key to look up (e.g. "sub", "ses").

 required
default str | None

Fallback value when key is absent.

 None

Returns:

Type Description
str | None

The entity value string, or default.
Source code in TPTBox/core/bids_files.py 
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def get(self, key: str, default: str | None = None) -> str | None:
    """Return the value for a BIDS entity key, or *default* if not present.

    Args:
        key: BIDS entity key to look up (e.g. ``"sub"``, ``"ses"``).
        default: Fallback value when *key* is absent.

    Returns:
        The entity value string, or *default*.
    """
    if key in self.info:
        return self.info[key]
    return default

loop_keys 

loop_keys() -> typing.ItemsView[str, str]

Return all BIDS entity key-value pairs for this file.

Returns:

Type Description
ItemsView[str, str]

A view of (key, value) pairs from the :attr:info dictionary.
Source code in TPTBox/core/bids_files.py 
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def loop_keys(self) -> typing.ItemsView[str, str]:
    """Return all BIDS entity key-value pairs for this file.

    Returns:
        A view of ``(key, value)`` pairs from the :attr:`info` dictionary.
    """
    return self.info.items()

remove 

remove(key: str) -> str

Remove and return a BIDS entity key from :attr:info.

Parameters:

Name Type Description Default
key str

Entity key to remove. Must not be "sub".

 required

Returns:

Type Description
str

The value that was associated with key.

Raises:

Type Description
AssertionError

If key is "sub" (subject ID cannot be removed).
KeyError

If key is not present in :attr:info.
Source code in TPTBox/core/bids_files.py 
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def remove(self, key: str) -> str:
    """Remove and return a BIDS entity key from :attr:`info`.

    Args:
        key: Entity key to remove.  Must not be ``"sub"``.

    Returns:
        The value that was associated with *key*.

    Raises:
        AssertionError: If *key* is ``"sub"`` (subject ID cannot be
            removed).
        KeyError: If *key* is not present in :attr:`info`.
    """
    assert key != "sub", "not allowed to remove subject name"
    return self.info.pop(key)

add_file 

add_file(path: Path, bids_ds: BIDS_Global_info | None = None) -> None

Associate an additional file extension with this BIDS entry.

Used to register companion files (e.g. a .json sidecar alongside a nii.gz) that share the same BIDS key stem.

Parameters:

Name Type Description Default
path Path

Path to the companion file. Its stem must match :attr:BIDS_key.

 required
bids_ds BIDS_Global_info | None

If provided, the global registry is updated so that the merged file dictionary is reflected there as well.

 None

Raises:

Type Description
AssertionError

If the stem of path does not match :attr:BIDS_key.
Source code in TPTBox/core/bids_files.py 
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def add_file(
    self,
    path: Path,
    bids_ds: BIDS_Global_info | None = None,
) -> None:
    """Associate an additional file extension with this BIDS entry.

    Used to register companion files (e.g. a ``.json`` sidecar alongside
    a ``nii.gz``) that share the same BIDS key stem.

    Args:
        path: Path to the companion file.  Its stem must match
            :attr:`BIDS_key`.
        bids_ds: If provided, the global registry is updated so that the
            merged file dictionary is reflected there as well.

    Raises:
        AssertionError: If the stem of *path* does not match
            :attr:`BIDS_key`.
    """
    bids_key, file_type = Path(path).name.split(".", maxsplit=1)

    assert bids_key == self.BIDS_key, f"only aligned data aka same name different file type: {bids_key} != {self.BIDS_key}"
    bids_dic_file = self.file
    if file_type not in self.file:
        bids_dic_file[file_type] = path
        if bids_ds is not None:
            bids_ds._global_bids_list[bids_key].file = dict(sorted(bids_dic_file.items()))
    self.file = dict(sorted(bids_dic_file.items()))

rename_files 

rename_files(path: Path | str, ending: str = '.nii.gz') -> None

Rename all associated files on disk to a new base path.

The ending suffix is stripped from path to obtain the base stem, then each extension in :attr:file is appended.

Parameters:

Name Type Description Default
path Path | str

Target path including the primary extension (e.g. /out/sub-001_T1w.nii.gz).

 required
ending str

Extension that terminates path and that will be stripped before adding per-extension suffixes.

 '.nii.gz'

Raises:

Type Description
AssertionError

If path does not end with ending.
Source code in TPTBox/core/bids_files.py 
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def rename_files(self, path: Path | str, ending: str = ".nii.gz") -> None:
    """Rename all associated files on disk to a new base path.

    The *ending* suffix is stripped from *path* to obtain the base stem,
    then each extension in :attr:`file` is appended.

    Args:
        path: Target path including the primary extension (e.g.
            ``/out/sub-001_T1w.nii.gz``).
        ending: Extension that terminates *path* and that will be
            stripped before adding per-extension suffixes.

    Raises:
        AssertionError: If *path* does not end with *ending*.
    """
    path = str(path)
    assert path.endswith(ending), f"set 'ending' to the part after the '.'\n {path} does not end with {ending}"
    path = path.replace(ending, "")
    for key, value in self.file.items():
        p = Path(path + "." + key)
        value.rename(p)

symlink_files(path: Path | str, ending: str = '.nii.gz', exist_ok: bool = False) -> None

Create symbolic links for all associated files at a new base path.

Equivalent to :meth:rename_files but creates symlinks rather than moving files. Existing correct symlinks are silently skipped.

Parameters:

Name Type Description Default
path Path | str

Target path including the primary extension (e.g. /out/sub-001_T1w.nii.gz).

 required
ending str

Extension used to compute the base stem; a leading dot is added automatically if absent.

 '.nii.gz'

Raises:

Type Description
AssertionError

If path does not end with ending, or if an existing symlink at the target points elsewhere.
Source code in TPTBox/core/bids_files.py 
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def symlink_files(self, path: Path | str, ending: str = ".nii.gz", exist_ok: bool = False) -> None:
    """Create symbolic links for all associated files at a new base path.

    Equivalent to :meth:`rename_files` but creates symlinks rather than
    moving files.  Existing correct symlinks are silently skipped.

    Args:
        path: Target path including the primary extension (e.g.
            ``/out/sub-001_T1w.nii.gz``).
        ending: Extension used to compute the base stem; a leading dot is
            added automatically if absent.

    Raises:
        AssertionError: If *path* does not end with *ending*, or if an
            existing symlink at the target points elsewhere.
    """
    ending = ending if ending[0] == "." else "." + ending
    path = str(path)
    assert path.endswith(ending), f"set 'ending' to the part after the '.'\n {path} does not end with {ending}"
    path = path.replace(ending, "")
    for key, value in self.file.items():
        p = Path(path + "." + key)

        if os.path.islink(p):
            assert Path(os.readlink(p)) == value, f"{p} exists"
            continue
        if exist_ok and p.exists():
            continue

        os.symlink(value, p)

get_path_decomposed 

get_path_decomposed(file_type: str | None = None) -> tuple[Path, str, str, str]

Decompose the file path relative to the dataset root.

Parameters:

Name Type Description Default
file_type str | None

Extension key to use when selecting which path to decompose (e.g. "nii.gz"). Defaults to the first extension in :attr:file.

 None

Returns:

Type Description
Path

A 4-tuple (dataset_path, parent, sub_path, filename) where
str
  • dataset_path is the dataset root :class:~pathlib.Path,
str
  • parent is the top-level folder (e.g. "rawdata"),
str
  • sub_path is the intermediate path (e.g. "sub-001/ses-01"),
tuple[Path, str, str, str]
  • filename is the bare filename including extension.
Source code in TPTBox/core/bids_files.py 
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def get_path_decomposed(self, file_type: str | None = None) -> tuple[Path, str, str, str]:
    """Decompose the file path relative to the dataset root.

    Args:
        file_type: Extension key to use when selecting which path to
            decompose (e.g. ``"nii.gz"``).  Defaults to the first
            extension in :attr:`file`.

    Returns:
        A 4-tuple ``(dataset_path, parent, sub_path, filename)`` where

        * ``dataset_path`` is the dataset root :class:`~pathlib.Path`,
        * ``parent`` is the top-level folder (e.g. ``"rawdata"``),
        * ``sub_path`` is the intermediate path (e.g.
          ``"sub-001/ses-01"``),
        * ``filename`` is the bare filename including extension.
    """
    if file_type is None:
        file_type = next(iter(self.file.keys()))
    folder_list = str(self.file[file_type].relative_to(self.dataset)).replace("\\\\", "/").replace("\\", "/").split("/")
    parent = folder_list[0]
    subpath = folder_list[1:-1]
    filename = folder_list[-1]
    # print(parent, subpath, filename)
    return self.dataset, parent, str.join("/", subpath), filename

get_parent 

get_parent(file_type: str | None = None) -> str

Return the top-level parent folder name for this file.

Parameters:

Name Type Description Default
file_type str | None

Extension key used to select which path to inspect. Defaults to the first extension in :attr:file.

 None

Returns:

Type Description
str

The parent folder name, e.g. "rawdata" or "derivatives".
Source code in TPTBox/core/bids_files.py 
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def get_parent(self, file_type: str | None = None) -> str:
    """Return the top-level parent folder name for this file.

    Args:
        file_type: Extension key used to select which path to inspect.
            Defaults to the first extension in :attr:`file`.

    Returns:
        The parent folder name, e.g. ``"rawdata"`` or ``"derivatives"``.
    """
    return self.get_path_decomposed(file_type)[1]

get_changed_bids 

get_changed_bids(file_type: str | None = 'nii.gz', bids_format: str | None = None, parent: str = 'derivatives', path: str | None = None, info: dict | None = None, from_info: bool = False, auto_add_run_id: bool = False, additional_folder: str | None = None, dataset_path: str | None = None, make_parent: bool = False, non_strict_mode: bool = False) -> BIDS_FILE

Construct a new :class:BIDS_FILE pointing to a derived output path.

Delegates path construction to :meth:get_changed_path and wraps the result in a :class:BIDS_FILE instance.

Parameters:

Name Type Description Default
file_type str | None

Target file extension (e.g. "nii.gz").

 'nii.gz'
bids_format str | None

Override the format/modality label.

 None
parent str

Target parent folder (e.g. "derivatives").

 'derivatives'
path str | None

Override the intermediate sub-path; supports {key} template substitution.

 None
info dict | None

Additional or overriding entity key-value pairs.

 None
from_info bool

If True, use the in-memory :attr:info dict instead of the original filename entities.

 False
auto_add_run_id bool

Append an auto-incremented run tag when the target path already exists.

 False
additional_folder str | None

Extra folder appended between path and the filename.

 None
dataset_path str | None

Override the dataset root.

 None
make_parent bool

Create parent directories if they do not exist.

 False
non_strict_mode bool

Relax BIDS entity validation.

 False

Returns:

Type Description
BIDS_FILE

A new :class:BIDS_FILE pointing to the derived output.
Source code in TPTBox/core/bids_files.py 
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def get_changed_bids(
    self,
    file_type: str | None = "nii.gz",
    bids_format: str | None = None,
    parent: str = "derivatives",
    path: str | None = None,
    info: dict | None = None,
    from_info: bool = False,
    auto_add_run_id: bool = False,
    additional_folder: str | None = None,
    dataset_path: str | None = None,
    make_parent: bool = False,
    non_strict_mode: bool = False,
) -> BIDS_FILE:
    """Construct a new :class:`BIDS_FILE` pointing to a derived output path.

    Delegates path construction to :meth:`get_changed_path` and wraps the
    result in a :class:`BIDS_FILE` instance.

    Args:
        file_type: Target file extension (e.g. ``"nii.gz"``).
        bids_format: Override the format/modality label.
        parent: Target parent folder (e.g. ``"derivatives"``).
        path: Override the intermediate sub-path; supports ``{key}``
            template substitution.
        info: Additional or overriding entity key-value pairs.
        from_info: If ``True``, use the in-memory :attr:`info` dict
            instead of the original filename entities.
        auto_add_run_id: Append an auto-incremented ``run`` tag when the
            target path already exists.
        additional_folder: Extra folder appended between *path* and the
            filename.
        dataset_path: Override the dataset root.
        make_parent: Create parent directories if they do not exist.
        non_strict_mode: Relax BIDS entity validation.

    Returns:
        A new :class:`BIDS_FILE` pointing to the derived output.
    """
    ds = dataset_path if dataset_path is not None else self.get_path_decomposed()[0]
    return BIDS_FILE(
        self.get_changed_path(
            file_type=file_type,
            bids_format=bids_format,
            parent=parent,
            path=path,
            info=info,
            from_info=from_info,
            auto_add_run_id=auto_add_run_id,
            additional_folder=additional_folder,
            dataset_path=dataset_path,
            make_parent=make_parent,
            non_strict_mode=non_strict_mode,
        ),
        ds,
    )

get_changed_path 

get_changed_path(file_type: str | None = 'nii.gz', bids_format: str | None = None, parent: str = 'derivatives', path: str | None = None, info: dict | None = None, from_info=False, auto_add_run_id=False, additional_folder: str | None = None, dataset_path: str | Path | None = None, make_parent=False, no_sorting_mode: bool = False, non_strict_mode: bool = False) -> Path

Changes part of the path to generate new flies. The new parent will be derivatives as a default.

Examples: subreg_path = ct_bids.get_changed_path(file_type="nii.gz",parent = "derivatives",info={"seg": "subreg"}, format="cdt")

Parameters:

Name Type Description Default
file_type str | None

Override the file type, like nii.gz to json Defaults to "nii.gz".

 'nii.gz'
format str | None

Changes the "format key" like ct, msk, T1w. Defaults to None.

 required
parent str

derivatives or rawdata or any parent folder. Defaults to "derivatives".

 'derivatives'
path str | None

If set: replaces the path from parent to file. Use {key} to get dynamic paths like {/sub-{sub}/ses-{ses}}. Defaults to None.

 None
info dict | None

Provide additional key,value pairs like {'seg':'subreg'}. Defaults to None.

 None
from_info bool

False: The key,value pair from the original file name are used. True: The key,value of the python object are used. Defaults to False.

 False
auto_add_run_id bool

Adds a run-{new id} tag, that is not occupied. Defaults to False.

 False
additional_folder str | None

add an additional folder towards path. Defaults to None.

 None
dataset_path str | None

Override the dataset_path. Defaults to None.

 None
no_sorting_mode bool

If true, will keep the order of the origin nii. Defaults to False

 False

Returns:

Name Type Description
_type_ Path

description
Source code in TPTBox/core/bids_files.py 
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def get_changed_path(  # noqa: C901
    self,
    file_type: str | None = "nii.gz",
    bids_format: str | None = None,
    parent: str = "derivatives",
    path: str | None = None,
    info: dict | None = None,
    from_info=False,
    auto_add_run_id=False,
    additional_folder: str | None = None,
    dataset_path: str | Path | None = None,
    make_parent=False,
    no_sorting_mode: bool = False,
    non_strict_mode: bool = False,
) -> Path:
    """Changes part of the path to generate new flies. The new parent will be derivatives as a default.

    Examples:
    subreg_path = ct_bids.get_changed_path(file_type="nii.gz",parent = "derivatives",info={"seg": "subreg"}, format="cdt")

    Args:
        file_type (str | None, optional): Override the file type, like nii.gz to json Defaults to "nii.gz".

        format (str | None, optional): Changes the "format key" like ct, msk, T1w. Defaults to None.

        parent (str, optional): derivatives or rawdata or any parent folder. Defaults to "derivatives".

        path (str | None, optional): If set: replaces the path from parent to file. Use {key} to get dynamic paths like {/sub-{sub}/ses-{ses}}. Defaults to None.

        info (dict | None, optional): Provide additional key,value pairs like {'seg':'subreg'}. Defaults to None.

        from_info (bool, optional): False: The key,value pair from the original file name are used. True: The key,value of the python object are used. Defaults to False.

        auto_add_run_id (bool, optional): Adds a run-{new id} tag, that is not occupied. Defaults to False.

        additional_folder (str | None, optional): add an additional folder towards path. Defaults to None.

        dataset_path (str | None, optional): Override the dataset_path. Defaults to None.

        no_sorting_mode (bool): If true, will keep the order of the origin nii. Defaults to False

    Returns:
        _type_: _description_
    """
    if info is None:
        info = {}
    if non_strict_mode and not self.BIDS_key.startswith("sub"):
        info["sub"] = self.BIDS_key.replace("_", "-").replace(".", "-")
    else:
        # replace _ with - in all info
        self.info = {k: v.replace("_", "-") for k, v in self.info.items()}
    if isinstance(file_type, str) and file_type.startswith("."):
        file_type = file_type[1:]
    path = self.insert_info_into_path(path)
    additional_folder = self.insert_info_into_path(additional_folder) if additional_folder is not None else None
    ds_path, same_parent, same_path, old_filename = self.get_path_decomposed()
    if from_info:
        same_info = self.info
        same_format = self.format
        same_filetype = None
    else:
        same_format, same_info, _, same_filetype = get_values_from_name(
            old_filename, self.verbose
        )  # Oder of keys is deterministic for python >3.7
    while True:
        file_name = ""
        ## Info
        final_info = {}
        for key, value in same_info.items():
            if key in info:
                value = info[key]  # noqa: PLW2901
            if value is not None:
                # file_name += f"{key}-{value}_"
                if non_strict_mode:
                    validate_entities(key, value, f"..._{key}-{value}_...", verbose=True)
                else:
                    assert validate_entities(key, value, f"..._{key}-{value}_...", verbose=True)
                final_info[key] = value.replace("_", "-")
        for key, value in info.items():
            # New Keys are getting checked!
            if non_strict_mode:
                (
                    print(
                        f"[!] {key} is not in list of legal keys. This name '{key}' is invalid. Legal keys are: {list(entities_keys.keys())}. \nFor use see https://bids-specification.readthedocs.io/en/stable/99-appendices/09-entities.html"
                    )
                    if key not in entities_keys
                    else None
                )
            else:
                assert key in entities_keys, (
                    f"[!] {key} is not in list of legal keys. This name '{key}' is invalid. Legal keys are: {list(entities_keys.keys())}. \nFor use see https://bids-specification.readthedocs.io/en/stable/99-appendices/09-entities.html"
                )
            # validate_entities(key, value, f"..._{key}-{value}_...", self.verbose)
            if key in same_info:
                continue
            if value is not None:
                if not non_strict_mode:
                    assert validate_entities(key, value, f"..._{key}-{value}_...", True), f"..._{key}-{value}_..."
                final_info[key] = value
            # file_name += f"{key}-{value}_"
        # sort by order
        keys_order = final_info.keys()
        if not no_sorting_mode:
            entity_keys = list(entities_keys.keys())
            keys_order = sorted(
                final_info.keys(),
                key=lambda x: entity_keys.index(x) if x in entity_keys else list(final_info.keys()).index(x) + len(entity_keys),
            )
        for key in keys_order:
            file_name += f"{key}-{final_info[key]}_"
        # End Info
        bids_format = bids_format if bids_format is not None else same_format
        file_type = file_type if file_type is not None else same_filetype
        assert file_type in file_types, (
            f"[!] {file_type} is not in list of file types. Legal file types are: {list(file_types)}. \nFor use see https://bids-specification.readthedocs.io/en/stable/99-appendices/09-entities.html"
        )
        if bids_format not in formats and not non_strict_mode:
            raise ValueError(
                f"[!] {bids_format} is not in list of formats. Legal formats are: {list(formats)}. \nFor use see https://bids-specification.readthedocs.io/en/stable/99-appendices/09-entities.html"
            )
        file_name += f"{bids_format}.{file_type}"

        out_path = Path(
            dataset_path if dataset_path is not None else ds_path,
            parent if parent is not None else same_parent,
            path if path is not None else same_path,
            additional_folder if additional_folder is not None else "",
            file_name,
        )
        if make_parent:
            out_path.parent.mkdir(exist_ok=True, parents=True)
        if not auto_add_run_id:
            return out_path
        if not out_path.exists():
            return out_path
        if "run" in info:
            info["run"] += 1
        else:
            info["run"] = 2

save_changed_path 

save_changed_path(bids_format: str | None = None, parent: str = 'derivatives', path: str | None = None, info: dict | None = None, from_info: bool = False, auto_add_run_id: bool = False, additional_folder: str | None = None, dataset_path: str | None = None, non_strict_mode: bool = False) -> None

Copy all associated files to their derived output paths.

Calls :meth:get_changed_path for every extension in :attr:file and copies each source file to the resulting destination using :func:shutil.copy2.

Parameters:

Name Type Description Default
bids_format str | None

Override the format/modality label.

 None
parent str

Target parent folder (e.g. "derivatives").

 'derivatives'
path str | None

Override the intermediate sub-path; supports {key} template substitution.

 None
info dict | None

Additional or overriding entity key-value pairs.

 None
from_info bool

If True, use the in-memory :attr:info dict instead of the original filename entities.

 False
auto_add_run_id bool

Append an auto-incremented run tag when the target path already exists.

 False
additional_folder str | None

Extra folder appended between path and the filename.

 None
dataset_path str | None

Override the dataset root.

 None
non_strict_mode bool

Relax BIDS entity validation.

 False
Source code in TPTBox/core/bids_files.py 
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def save_changed_path(
    self,
    bids_format: str | None = None,
    parent: str = "derivatives",
    path: str | None = None,
    info: dict | None = None,
    from_info: bool = False,
    auto_add_run_id: bool = False,
    additional_folder: str | None = None,
    dataset_path: str | None = None,
    non_strict_mode: bool = False,
) -> None:
    """Copy all associated files to their derived output paths.

    Calls :meth:`get_changed_path` for every extension in :attr:`file`
    and copies each source file to the resulting destination using
    :func:`shutil.copy2`.

    Args:
        bids_format: Override the format/modality label.
        parent: Target parent folder (e.g. ``"derivatives"``).
        path: Override the intermediate sub-path; supports ``{key}``
            template substitution.
        info: Additional or overriding entity key-value pairs.
        from_info: If ``True``, use the in-memory :attr:`info` dict
            instead of the original filename entities.
        auto_add_run_id: Append an auto-incremented ``run`` tag when the
            target path already exists.
        additional_folder: Extra folder appended between *path* and the
            filename.
        dataset_path: Override the dataset root.
        non_strict_mode: Relax BIDS entity validation.
    """
    import shutil

    for key, value in self.file.items():
        out = self.get_changed_path(
            key,
            bids_format=bids_format,
            parent=parent,
            path=path,
            from_info=from_info,
            info=info,
            auto_add_run_id=auto_add_run_id,
            additional_folder=additional_folder,
            dataset_path=dataset_path,
            make_parent=True,
            non_strict_mode=non_strict_mode,
        )
        shutil.copy2(value, out)

find_changed_path 

find_changed_path(bids_ds: BIDS_Global_info, bids_format: str | None = None, info: dict | None = None, from_info: bool = False) -> BIDS_FILE | None

Look up an already-registered derived file in the global BIDS index.

Constructs the expected BIDS key for the derived file (applying the same entity overrides as :meth:get_changed_path) and returns the matching :class:BIDS_FILE from bids_ds if it exists.

Parameters:

Name Type Description Default
bids_ds BIDS_Global_info

The global BIDS dataset to search.

 required
bids_format str | None

Override the format/modality label.

 None
info dict | None

Additional or overriding entity key-value pairs.

 None
from_info bool

If True, use the in-memory :attr:info dict instead of the original filename entities.

 False

Returns:

Type Description
BIDS_FILE | None

The matching :class:BIDS_FILE if found, otherwise None.
Source code in TPTBox/core/bids_files.py 
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def find_changed_path(
    self,
    bids_ds: BIDS_Global_info,
    bids_format: str | None = None,
    info: dict | None = None,
    from_info: bool = False,
) -> BIDS_FILE | None:
    """Look up an already-registered derived file in the global BIDS index.

    Constructs the expected BIDS key for the derived file (applying the
    same entity overrides as :meth:`get_changed_path`) and returns the
    matching :class:`BIDS_FILE` from *bids_ds* if it exists.

    Args:
        bids_ds: The global BIDS dataset to search.
        bids_format: Override the format/modality label.
        info: Additional or overriding entity key-value pairs.
        from_info: If ``True``, use the in-memory :attr:`info` dict
            instead of the original filename entities.

    Returns:
        The matching :class:`BIDS_FILE` if found, otherwise ``None``.
    """
    if info is None:
        info = {}

    if from_info:
        same_info = self.info
        same_format = self.format
    else:
        _, _, _, old_filename = self.get_path_decomposed()
        same_format, same_info, _, _ = get_values_from_name(old_filename, self.verbose)  # Oder of keys is deterministic for python >3.7
    file_name = ""
    for key, value in same_info.items():
        if key in info:
            value = info[key]  # noqa: PLW2901
        file_name += f"{key}-{value}_"
    for key, value in info.items():
        validate_entities(key, value, f"..._{key}-{value}_...", self.verbose)
        if key in same_info:
            continue
        file_name += f"{key}-{value}_"

    file_name += f"{bids_format if bids_format is not None else same_format}"
    return bids_ds._global_bids_list.get(file_name)

insert_info_into_path 

insert_info_into_path(path: str | None) -> str | None

Replace {key} placeholders in path with entity values from :attr:info.

Example::

# With self.info = {"sub": "patient001", "ses": "01"}
bids.insert_info_into_path("sub-{sub}/ses-{ses}")
# -> "sub-patient001/ses-01"

Parameters:

Name Type Description Default
path str | None

Template string containing {key} placeholders, or None.

 required

Returns:

Type Description
str | None

The expanded string, or None when path is None.
Source code in TPTBox/core/bids_files.py 
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def insert_info_into_path(self, path: str | None) -> str | None:
    """Replace ``{key}`` placeholders in *path* with entity values from :attr:`info`.

    Example::

        # With self.info = {"sub": "patient001", "ses": "01"}
        bids.insert_info_into_path("sub-{sub}/ses-{ses}")
        # -> "sub-patient001/ses-01"

    Args:
        path: Template string containing ``{key}`` placeholders, or
            ``None``.

    Returns:
        The expanded string, or ``None`` when *path* is ``None``.
    """
    if path is None:
        return None
    path = str(path)
    while "{" in path:
        left, right = path.split("{", maxsplit=1)
        middle, right = right.split("}", maxsplit=1)
        a = self.info.get(middle, None)
        if a is None:
            warn(f"{middle} not found in {self}", stacklevel=3)
            a = middle
        path = left + a + right
    return path

get_sequence_files 

get_sequence_files(key_transform: Callable[[BIDS_FILE], str | None] | None = None, key_addendum: list[str] | None = None) -> BIDS_Family

Return the :class:BIDS_Family that this file belongs to.

Delegates to :meth:Subject_Container.get_sequence_files using the sequence name resolved from this file's entities. The file must be part of a subject sequence (i.e. registered via :class:BIDS_Global_info).

Parameters:

Name Type Description Default
key_transform Callable[[BIDS_FILE], str | None] | None

Optional callable mapping a :class:BIDS_FILE to a custom family key string; return None to use the default key.

 None
key_addendum list[str] | None

Extra entity keys appended to the family key beyond the default :attr:sequence_naming_keys.

 None

Returns:

Name Type Description
The BIDS_Family

class:BIDS_Family containing all related files for this
BIDS_Family

sequence.

Raises:

Type Description
AssertionError

If this file has no owning :class:Subject_Container.
Source code in TPTBox/core/bids_files.py 
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def get_sequence_files(
    self,
    key_transform: typing.Callable[[BIDS_FILE], str | None] | None = None,
    key_addendum: list[str] | None = None,
) -> BIDS_Family:
    """Return the :class:`BIDS_Family` that this file belongs to.

    Delegates to :meth:`Subject_Container.get_sequence_files` using the
    sequence name resolved from this file's entities.  The file must be
    part of a subject sequence (i.e. registered via
    :class:`BIDS_Global_info`).

    Args:
        key_transform: Optional callable mapping a :class:`BIDS_FILE` to
            a custom family key string; return ``None`` to use the default
            key.
        key_addendum: Extra entity keys appended to the family key beyond
            the default :attr:`sequence_naming_keys`.

    Returns:
        The :class:`BIDS_Family` containing all related files for this
        sequence.

    Raises:
        AssertionError: If this file has no owning
            :class:`Subject_Container`.
    """
    assert hasattr(self, "subject"), (
        "The BIDS_file must be part of a Sequence-family. Usually automatically generated by tree generation of BIDS_Global_info"
    )
    sequ = self.subject.get_sequence_name(self)
    return self.subject.get_sequence_files(sequ, key_transform=key_transform, key_addendum=key_addendum)

open_nii_reorient 

open_nii_reorient(axcodes_to: tuple[str, ...] = ('P', 'I', 'R'), verbose: bool = False) -> TPTBox.NII

Open the NIfTI file and reorient it in-place to the target axis codes.

Parameters:

Name Type Description Default
axcodes_to tuple[str, ...]

Desired orientation as a tuple of axis code strings, e.g. ("P", "I", "R").

 ('P', 'I', 'R')
verbose bool

If True, print reorientation details.

 False

Returns:

Type Description
NII

The reoriented :class:~TPTBox.NII volume.
Source code in TPTBox/core/bids_files.py 
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def open_nii_reorient(self, axcodes_to: tuple[str, ...] = ("P", "I", "R"), verbose: bool = False) -> TPTBox.NII:
    """Open the NIfTI file and reorient it in-place to the target axis codes.

    Args:
        axcodes_to: Desired orientation as a tuple of axis code strings,
            e.g. ``("P", "I", "R")``.
        verbose: If ``True``, print reorientation details.

    Returns:
        The reoriented :class:`~TPTBox.NII` volume.
    """
    return self.open_nii().reorient_(axcodes_to, verbose=verbose)

has_json 

has_json() -> bool

Return True when a JSON sidecar is registered for this file.

Source code in TPTBox/core/bids_files.py 
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def has_json(self) -> bool:
    """Return ``True`` when a JSON sidecar is registered for this file."""
    return "json" in self.file

open_json 

open_json() -> dict

Load and return the JSON sidecar as a dictionary.

Returns:

Type Description
dict

Parsed JSON contents.

Raises:

Type Description
KeyError

If no JSON file is registered in :attr:file.
Source code in TPTBox/core/bids_files.py 
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def open_json(self) -> dict:
    """Load and return the JSON sidecar as a dictionary.

    Returns:
        Parsed JSON contents.

    Raises:
        KeyError: If no JSON file is registered in :attr:`file`.
    """
    with open(self.file["json"]) as f:
        return json.load(f)

open_poi 

open_poi(nii: Image_Reference | None = None) -> TPTBox.POI

Load the associated JSON file as a :class:~TPTBox.POI (point-of-interest) object.

If the POI lacks spatial metadata (zoom, shape, etc.) a reference NIfTI image is required to fill in those fields.

Parameters:

Name Type Description Default
nii Image_Reference | None

Optional image reference used to supply missing spatial metadata. Required when the JSON does not embed grid info.

 None

Returns:

Type Description
POI

The loaded :class:~TPTBox.POI object with complete spatial
POI

metadata.

Raises:

Type Description
ValueError

If no JSON file is present or the POI lacks spatial metadata and nii is None.
Source code in TPTBox/core/bids_files.py 
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def open_poi(self, nii: TPTBox.Image_Reference | None = None) -> TPTBox.POI:
    """Load the associated JSON file as a :class:`~TPTBox.POI` (point-of-interest) object.

    If the POI lacks spatial metadata (zoom, shape, etc.) a reference
    NIfTI image is required to fill in those fields.

    Args:
        nii: Optional image reference used to supply missing spatial
            metadata.  Required when the JSON does not embed grid info.

    Returns:
        The loaded :class:`~TPTBox.POI` object with complete spatial
        metadata.

    Raises:
        ValueError: If no JSON file is present or the POI lacks spatial
            metadata and *nii* is ``None``.
    """
    from TPTBox import POI

    try:
        ctd = POI.load(self.file["json"], allow_global=True)
        if ctd.zoom is None or ctd.shape is None or ctd.rotation is None or ctd.origin is None or ctd.orientation is None:
            if nii is None and "ctd.json" in str(self.file["json"]):
                p = Path(str(self.file["json"]).replace("ctd.json", "msk.nii.gz"))
                nii = p if p.exists() else nii
            assert nii is not None, (
                "This file has no zoom info. Use open_ctd(self, nii) with a image reference (BIDS_FILE/PATH) with the same nii"
            )
            nii = TPTBox.to_nii(nii)
            assert isinstance(nii, TPTBox.NII)
            ctd.zoom = nii.zoom
            ctd.shape = nii.shape
            ctd.rotation = nii.rotation
            ctd.origin = nii.origin
            ctd.orientation = nii.orientation
    except KeyError as e:
        raise ValueError(f"json not present. Found only {self.file.keys()}\t{self.file}\n\n{self}") from e
    return ctd

open_ctd 

open_ctd(nii: Image_Reference | None = None) -> TPTBox.POI

Alias for :meth:open_poi; load the centroid JSON as a :class:~TPTBox.POI.

Parameters:

Name Type Description Default
nii Image_Reference | None

Optional image reference for missing spatial metadata.

 None

Returns:

Type Description
POI

The loaded :class:~TPTBox.POI object.
Source code in TPTBox/core/bids_files.py 
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def open_ctd(self, nii: TPTBox.Image_Reference | None = None) -> TPTBox.POI:
    """Alias for :meth:`open_poi`; load the centroid JSON as a :class:`~TPTBox.POI`.

    Args:
        nii: Optional image reference for missing spatial metadata.

    Returns:
        The loaded :class:`~TPTBox.POI` object.
    """
    return self.open_poi(nii)

has_nii 

has_nii() -> bool

Return True when at least one supported NIfTI extension is registered.

Source code in TPTBox/core/bids_files.py 
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def has_nii(self) -> bool:
    """Return ``True`` when at least one supported NIfTI extension is registered."""
    return any(a in self.file for a in _supported_nii_files)

open_nii 

open_nii() -> TPTBox.NII

Load the NIfTI file into a :class:~TPTBox.NII object.

Returns:

Type Description
NII

The loaded :class:~TPTBox.NII volume.

Raises:

Type Description
ValueError

If no NIfTI file (nii.gz / nii) is present.
Source code in TPTBox/core/bids_files.py 
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def open_nii(self) -> TPTBox.NII:
    """Load the NIfTI file into a :class:`~TPTBox.NII` object.

    Returns:
        The loaded :class:`~TPTBox.NII` volume.

    Raises:
        ValueError: If no NIfTI file (``nii.gz`` / ``nii``) is present.
    """
    try:
        from TPTBox import NII

        return NII.load_bids(self)
    except KeyError as e:
        raise ValueError(f"nii.gz not present. Found only {self.file.keys()}\t{self.file}\n\n{self}") from e

get_grid_info 

get_grid_info(add_grid_info_to_json: bool = True) -> Grid | None

Return the spatial grid metadata for this file.

Looks up the grid info in the associated JSON sidecar. If the JSON does not contain grid information the NIfTI is loaded, the grid is computed, and the result is written back to the JSON when add_grid_info_to_json is True.

Parameters:

Name Type Description Default
add_grid_info_to_json bool

If True, persist newly computed grid info to the JSON sidecar.

 True

Returns:

Name Type Description
A Grid | None

class:~TPTBox.core.nii_poi_abstract.Grid instance, or
Grid | None

None if no NIfTI file is present.
Source code in TPTBox/core/bids_files.py 
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def get_grid_info(self, add_grid_info_to_json: bool = True) -> Grid | None:
    """Return the spatial grid metadata for this file.

    Looks up the grid info in the associated JSON sidecar.  If the JSON
    does not contain grid information the NIfTI is loaded, the grid is
    computed, and the result is written back to the JSON when
    *add_grid_info_to_json* is ``True``.

    Args:
        add_grid_info_to_json: If ``True``, persist newly computed grid
            info to the JSON sidecar.

    Returns:
        A :class:`~TPTBox.core.nii_poi_abstract.Grid` instance, or
        ``None`` if no NIfTI file is present.
    """
    from TPTBox.core.dicom.dicom_extract import _add_grid_info_to_json
    from TPTBox.core.nii_poi_abstract import Grid

    nii_file = self.get_nii_file()
    if nii_file is None:
        return None
    if not self.has_json():
        self.file["json"] = Path(str(nii_file).split(".")[0] + ".json")
    return Grid(**_add_grid_info_to_json(nii_file, self.file["json"], add=add_grid_info_to_json)["grid"])

get_nii_file 

get_nii_file() -> Path | None

Return the path to the first available NIfTI file.

Checks the supported NIfTI extensions (nii.gz, nii, mkd) in order and returns the first one present.

Returns:

Name Type Description
The Path | None

class:~pathlib.Path to the NIfTI file, or None if
Path | None

none of the supported extensions are registered.
Source code in TPTBox/core/bids_files.py 
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def get_nii_file(self) -> Path | None:
    """Return the path to the first available NIfTI file.

    Checks the supported NIfTI extensions (``nii.gz``, ``nii``, ``mkd``)
    in order and returns the first one present.

    Returns:
        The :class:`~pathlib.Path` to the NIfTI file, or ``None`` if
        none of the supported extensions are registered.
    """
    for key in _supported_nii_files:
        if key in self.file:
            return self.file[key]
    return None

has_npz 

has_npz() -> bool

Return True when an NPZ array file is registered for this entry.

Source code in TPTBox/core/bids_files.py 
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def has_npz(self) -> bool:
    """Return ``True`` when an NPZ array file is registered for this entry."""
    return "npz" in self.file

open_npz 

open_npz() -> dict[str, np.ndarray]

Load the associated NPZ file and return its contents as a dictionary.

Returns:

Type Description
dict[str, ndarray]

A dictionary mapping array names to :class:numpy.ndarray objects.

Raises:

Type Description
KeyError

If no NPZ file is registered in :attr:file.
Source code in TPTBox/core/bids_files.py 
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def open_npz(self) -> dict[str, np.ndarray]:
    """Load the associated NPZ file and return its contents as a dictionary.

    Returns:
        A dictionary mapping array names to :class:`numpy.ndarray` objects.

    Raises:
        KeyError: If no NPZ file is registered in :attr:`file`.
    """
    return dict(np.load(self.file["npz"], allow_pickle=False))  # type: ignore

open 

open(filetype: str, _internal: bool = False) -> Path | TPTBox.NII | dict | None

Open a file by extension, returning the appropriate Python object.

.. deprecated:: Use :meth:open_nii, :meth:open_json, or :attr:file directly.

Parameters:

Name Type Description Default
filetype str

Extension to open (e.g. "nii.gz", "json").

 required
_internal bool

Suppress the deprecation warning when called internally.

 False

Returns:

Type Description
Path | NII | dict | None
  • A :class:~TPTBox.NII for NIfTI extensions.
Path | NII | dict | None
  • A :class:dict for JSON files.
Path | NII | dict | None
  • A :class:~pathlib.Path for all other file types.
Path | NII | dict | None
  • None if filetype is not registered in :attr:file.
Source code in TPTBox/core/bids_files.py 
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def open(self, filetype: str, _internal: bool = False) -> Path | TPTBox.NII | dict | None:
    """Open a file by extension, returning the appropriate Python object.

    .. deprecated::
        Use :meth:`open_nii`, :meth:`open_json`, or :attr:`file` directly.

    Args:
        filetype: Extension to open (e.g. ``"nii.gz"``, ``"json"``).
        _internal: Suppress the deprecation warning when called internally.

    Returns:
        * A :class:`~TPTBox.NII` for NIfTI extensions.
        * A :class:`dict` for JSON files.
        * A :class:`~pathlib.Path` for all other file types.
        * ``None`` if *filetype* is not registered in :attr:`file`.
    """
    if not _internal:
        warn("open is deprecated.", DeprecationWarning, stacklevel=2)
    if filetype not in self.file:
        return None
    if filetype == "json":
        return self.open_json()
    if filetype in _supported_nii_files:
        return self.open_nii()
    return self.file[filetype]

do_filter 

do_filter(key: str, constrain: list[str] | str | Callable[[str | object], bool], required: bool = False) -> bool

Check whether this file satisfies a key/constraint filter.

If the key is not present in this file, the inverse of required is returned (i.e. absent keys pass when required=False and fail when required=True).

Parameters:

Name Type Description Default
key str

The entity to inspect. Special values: "format" checks :attr:format; "filetype" checks registered extensions; "parent" checks the parent folder; "self" passes the whole :class:BIDS_FILE. Any other value is looked up in :attr:info, then in :attr:file (opening the file when a callable is given).

 required
constrain list[str] | str | Callable[[str | object], bool]

Matching criterion — a string for exact match, a list of strings for membership, or a callable predicate.

 required
required bool

If True, files for which key is absent are rejected. Defaults to False.

 False

Returns:

Type Description
bool

True when the constraint is satisfied, False otherwise.
Source code in TPTBox/core/bids_files.py 
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def do_filter(
    self,
    key: str,
    constrain: list[str] | str | typing.Callable[[str | object], bool],
    required: bool = False,
) -> bool:
    """Check whether this file satisfies a key/constraint filter.

    If the *key* is not present in this file, the inverse of *required*
    is returned (i.e. absent keys pass when ``required=False`` and fail
    when ``required=True``).

    Args:
        key: The entity to inspect.  Special values: ``"format"`` checks
            :attr:`format`; ``"filetype"`` checks registered extensions;
            ``"parent"`` checks the parent folder; ``"self"`` passes the
            whole :class:`BIDS_FILE`.  Any other value is looked up in
            :attr:`info`, then in :attr:`file` (opening the file when a
            callable is given).
        constrain: Matching criterion — a string for exact match, a list
            of strings for membership, or a callable predicate.
        required: If ``True``, files for which *key* is absent are
            rejected.  Defaults to ``False``.

    Returns:
        ``True`` when the constraint is satisfied, ``False`` otherwise.
    """
    key = key.lower()
    if key == "":
        return False
    if key == "format":
        value = self.format
    elif key == "filetype":
        value = list(self.file.keys())
        if isinstance(constrain, str) and constrain.startswith("."):
            constrain = constrain[1:]
    elif key == "parent":
        value = self.get_parent()
    elif key == "self":
        value = self
    elif key in self.info:
        value = self.info[key]
    elif key in self.file:
        value = self.open(key, _internal=True)
    else:
        return not required

    if not isinstance(value, list):
        value = [value]
    for v in value:
        if isinstance(constrain, list):
            if v in constrain:
                return True
        elif isinstance(constrain, str):
            if v == constrain:
                return True
        elif constrain(v):
            return True
    return False

get_interpolation_order 

get_interpolation_order() -> int

Return the interpolation order for this file (0 for masks/segmentations, 3 for images).

Returns:

Name Type Description
int int

interpolation_order
Source code in TPTBox/core/bids_files.py 
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def get_interpolation_order(self) -> int:
    """Return the interpolation order for this file (0 for masks/segmentations, 3 for images).

    Returns:
        int: interpolation_order
    """
    return 0 if self.format == "msk" or "label" in self.info else 3

get_frame_of_reference_uid 

get_frame_of_reference_uid(default: str | None = None) -> str | None

Return a short hash identifying the world-space frame of reference.

Reads FrameOfReferenceUID from the JSON sidecar and converts it to an 8-character base-36 string. Falls back to the res or ses entity, and finally to default, when no JSON is available.

Parameters:

Name Type Description Default
default str | None

Value returned when the frame of reference cannot be determined.

 None

Returns:

Type Description
str | None

An 8-character base-36 hash string, a BIDS entity value, or
str | None

default.
Source code in TPTBox/core/bids_files.py 
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def get_frame_of_reference_uid(self, default: str | None = None) -> str | None:
    """Return a short hash identifying the world-space frame of reference.

    Reads ``FrameOfReferenceUID`` from the JSON sidecar and converts it
    to an 8-character base-36 string.  Falls back to the ``res`` or
    ``ses`` entity, and finally to *default*, when no JSON is available.

    Args:
        default: Value returned when the frame of reference cannot be
            determined.

    Returns:
        An 8-character base-36 hash string, a BIDS entity value, or
        *default*.
    """
    import hashlib

    length = 8
    try:
        uid = self.open_json()["FrameOfReferenceUID"]
    except Exception:
        return self.get("res", self.get("ses", default))
    # Hash the UID
    hash_bytes = hashlib.sha1(uid.encode("utf-8")).digest()
    # Convert to integer, then to base36
    num = int.from_bytes(hash_bytes, "big")
    base36 = ""
    chars = "0123456789abcdefghijklmnopqrstuvwxyz"
    while num:
        num, i = divmod(num, 36)
        base36 = chars[i] + base36
    return base36[:length]

get_identifier 

get_identifier(sequence_splitting_keys: list[str]) -> str

Generates an identifier for the BIDS_FILE based on subject and splitting keys.

Parameters:

Name Type Description Default
sequence_splitting_keys list[str]

list of keys to use for splitting

 required
Source code in TPTBox/core/bids_files.py 
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def get_identifier(self, sequence_splitting_keys: list[str]) -> str:
    """Generates an identifier for the BIDS_FILE based on subject and splitting keys.

    Args:
        sequence_splitting_keys (list[str]): list of keys to use for splitting
    """
    if "sub" not in self.info:
        print(f"family_id, no sub-key, got {self.info}")
        identifier = "sub-404"
    else:
        identifier = "sub-" + self.info["sub"]
    for s in self.info.keys():
        if s in sequence_splitting_keys:
            identifier += "_" + s + "-" + self.info[s]
    return identifier

Searchquery

TPTBox.core.bids_files.Searchquery

Query builder for filtering and retrieving BIDS files from a Subject_Container.

Source code in TPTBox/core/bids_files.py 
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class Searchquery:
    """Query builder for filtering and retrieving BIDS files from a Subject_Container."""

    def __init__(self, subj: Subject_Container, flatten=False) -> None:
        """Filter for specific files.

        Args:
            subj (Subject_Container): The Subject class in with filter and action is applied
            flatten (bool, optional): If true, you are filtering for single files. If False you looking for sequences. Defaults to False.
        """
        self.candidates: list[BIDS_FILE] | dict[str, list[BIDS_FILE]] = []
        if flatten:
            for value_lists in subj.sequences.values():
                for value in value_lists:
                    self.candidates.append(value)
        else:
            self.candidates = subj.sequences.copy()

        self.subject = subj
        self._flatten = flatten

    @classmethod
    def from_BIDS_Family(cls, fam: BIDS_Family) -> Searchquery:
        """Construct a :class:`Searchquery` pre-filtered to a single :class:`BIDS_Family`.

        Args:
            fam: The family whose sequence bucket will be the sole candidate.

        Returns:
            A new :class:`Searchquery` containing only the sequence that
            produced *fam*.
        """
        dic = fam.data_dict
        any_file = dic[next(iter(dic.keys()))][0]
        sub = any_file.subject
        query = Searchquery(subj=sub, flatten=False)
        query._filter_fam_id(fam)
        # query.candidates = dic.copy()
        return query

    def _filter_fam_id(self, fam: BIDS_Family) -> None:
        """Restrict candidates to the single sequence bucket that produced *fam*."""
        self.unflatten()
        dic = fam.data_dict
        any_file = dic[next(iter(dic.keys()))][0]
        subject_id = any_file.subject.get_sequence_name(any_file)
        c = self.candidates
        self.candidates = {}
        self.candidates[subject_id] = c[subject_id]  # type: ignore

    def copy(self) -> Searchquery:
        """Return a shallow copy of this query with the same candidates.

        Returns:
            A new :class:`Searchquery` sharing the same subject and flatten
            mode, with an independent copy of the candidates collection.
        """
        copy = Searchquery(self.subject, self._flatten)
        copy.candidates = self.candidates.copy()
        return copy

    def flatten(self) -> None:
        """Transform from multi-file-mode (sequence buckets) to single-file-mode.

        After calling this method, :attr:`candidates` is a flat
        :class:`list` of :class:`BIDS_FILE` instances and
        :meth:`loop_list` can be used to iterate over them.
        """
        if self._flatten:
            return
        a: list[BIDS_FILE] = []
        assert isinstance(self.candidates, dict)
        for value_lists in self.candidates.values():
            for value in value_lists:
                a.append(value)  # noqa: PERF402
        self.candidates = a
        self._flatten = True

    def unflatten(self) -> None:
        """Transform from single-file-mode back to multi-file-mode (sequence buckets).

        Previously filtered files remain excluded.  After calling this method
        :meth:`loop_dict` can be used to iterate over sequence families.
        """
        if not self._flatten:
            return
        a = {}
        assert isinstance(self.candidates, list)
        for value in self.candidates:
            key = self.subject.get_sequence_name(value)
            a.setdefault(key, [])
            a[key].append(value)
        self.candidates = a
        self._flatten = False

    def filter_self(self, filter_fun: typing.Callable[[BIDS_FILE], bool], required: bool = True) -> None:
        """Filter candidates by applying *filter_fun* directly to each :class:`BIDS_FILE`.

        Args:
            filter_fun: Predicate receiving a :class:`BIDS_FILE`; return
                ``True`` to keep the file.
            required: Passed to :meth:`filter`.
        """
        return self.filter("self", filter_fun, required=required)  # type: ignore

    def filter_json(self, filter_fun: typing.Callable[[dict], bool], required: bool = True) -> None:
        """Filter candidates by applying *filter_fun* to the parsed JSON sidecar.

        Args:
            filter_fun: Predicate receiving the JSON dictionary; return
                ``True`` to keep the file.
            required: If ``True``, files without a JSON sidecar are removed.
        """
        return self.filter("json", filter_fun, required=required)  # type: ignore

    def filter(
        self,
        key: str,
        filter_fun: list[str] | str | typing.Callable[[str | object], bool],
        required: bool = True,
    ) -> None:
        """Remove candidates from the query that do not satisfy the filter.

        In flatten mode (single-file mode), individual files that do not pass
        are removed.  In unflatten mode (sequence mode), a sequence bucket is
        removed when *no* file in the bucket satisfies the filter.

        Args:
            key: The entity to inspect.  Special values: ``"format"``,
                ``"filetype"``, ``"parent"``, ``"self"``; otherwise looked up
                in :attr:`BIDS_FILE.info` or :attr:`BIDS_FILE.file`.
            filter_fun: Matching criterion — a string for exact match, a list
                of accepted strings, or a callable predicate.
            required: If ``True``, candidates where *key* is absent are
                removed.  If ``False``, absent keys are silently kept.
                Defaults to ``True``.
        """
        if self._flatten:
            assert isinstance(self.candidates, list)
            for bids_file in self.candidates.copy():
                if not bids_file.do_filter(key, filter_fun, required=required):
                    self.candidates.remove(bids_file)
        else:
            assert isinstance(self.candidates, dict)
            for sequences, bids_files in self.candidates.copy().items():
                # print(sequences, list(bids_file.do_filter(key, filter_fun, required=required) for bids_file in bids_files))
                if not any(bids_file.do_filter(key, filter_fun, required=required) for bids_file in bids_files):
                    self.candidates.pop(sequences)

    def filter_format(self, filter_fun: list[str] | str | typing.Callable[[str | object], bool]) -> None:
        """Keep only files whose format label satisfies *filter_fun*.

        Args:
            filter_fun: A format string, a list of accepted format strings,
                or a callable predicate applied to the format label.
        """
        if isinstance(filter_fun, list):
            return self.filter_format(lambda x: x in filter_fun)
        return self.filter("format", filter_fun=filter_fun, required=True)

    def filter_filetype(self, filter_fun: list[str] | str | typing.Callable[[str | object], bool], required: bool = True) -> None:
        """Keep only files that have a matching file extension.

        Args:
            filter_fun: An extension string (e.g. ``"nii.gz"``), a list of
                accepted extensions, or a callable predicate.
            required: If ``True``, files without any registered extension
                are removed.
        """
        return self.filter("filetype", filter_fun=filter_fun, required=required)

    def filter_non_existence(
        self,
        key: str,
        filter_fun: str | typing.Callable[[str | object], bool] = lambda x: True,  # noqa: ARG005
        required=True,
    ) -> None:
        """Remove family/file from the Searchquery if the filter condition is met.

            (unflatten-mode) ANY single file exist in the family returns True

            (unflatten-mode) the filter_fun returns True

            If a key is not present the inverse of the "required" value is returned

        Args:
            key (str): The key for which we filter. Can be "format", a filetype, a key from the info-dict
                        In case of filetype + filter_fun is a callable you get a opened Nifti, opened json or Path
            filter_fun (str | typing.Callable[[str  |  object], bool]):
                If a string is given: An exact string match is looked up
                If a callable: The function is called with the value of the key.
            required (bool, optional): If True: A key must exist or the family/file is filtered.
                If False: Only if the key exist the family/file will be considers for filtering. Defaults to True.
        """
        if self._flatten:
            assert isinstance(self.candidates, list)
            for bids_file in self.candidates.copy():
                if bids_file.do_filter(key, filter_fun, required=required):
                    self.candidates.remove(bids_file)
        else:
            assert isinstance(self.candidates, dict)
            for sequences, bids_files in self.candidates.copy().items():
                # print(sequences, list(bids_file.do_filter(key, filter_fun, required=required) for bids_file in bids_files))
                if any(bids_file.do_filter(key, filter_fun, required=required) for bids_file in bids_files):
                    self.candidates.pop(sequences)

    def filter_dixon_only_inphase(self) -> None:
        """Remove Dixon files that are fat, water, out-of-phase, or difference images.

        Retains only in-phase (or unlabelled) Dixon acquisitions by
        inspecting both the JSON ``ImageType`` field and the ``rec``,
        ``acq``, and ``part`` entities.
        """

        def json_filter(x: dict) -> bool:
            """Return True if JSON ImageType does not indicate a fat/water/outphase channel."""
            return "ImageType" not in x or (
                "W" not in x["ImageType"]
                and "F" not in x["ImageType"]
                and "FAT" not in x["ImageType"]
                and "WATER" not in x["ImageType"]
                and "OP" not in x["ImageType"]
            )

        def lam_filter(x: str) -> bool:
            """Return True if the entity value does not indicate a non-inphase Dixon channel."""
            return (
                x.upper() != "W"
                and x.upper() != "F"
                and x.upper() != "FAT"
                and x.upper() != "WATER"
                and x.upper() != "OP"
                and x.upper() != "OPP"
                and x.upper() != "OUTPHASE"
                and x.upper() != "DIFFERENCE"
            )

        self.filter_json(json_filter, required=False)
        self.filter("rec", lam_filter, required=False)  # type: ignore DEPRECATED
        self.filter("acq", lam_filter, required=False)  # type: ignore DEPRECATED
        self.filter("part", "inphase", required=False)  # type: ignore

    def filter_dixon_water(self, _keys: list[str] | None = None) -> None:
        """Keep only Dixon water-channel images (requires flatten mode).

        Args:
            _keys: Image-type labels that identify the water channel.
                Defaults to ``["W", "WATER"]``.
        """
        if _keys is None:
            _keys = ["W", "WATER"]
        assert self._flatten

        def json_filter(x: dict) -> bool:
            """Return True if JSON ImageType contains all required channel keys."""
            return "ImageType" not in x or all(k in x["ImageType"] for k in _keys)

        def lam_filter(x: str) -> bool:
            """Return True if the entity value matches one of the target channel keys."""
            return any(k == x.upper() for k in _keys)

        self.filter_json(json_filter, required=False)
        self.filter("rec", lam_filter, required=False)  # type: ignore
        self.filter("part", lam_filter, required=False)  # type: ignore

    def filter_dixon_fat(self) -> None:
        """Keep only Dixon fat-channel images (requires flatten mode)."""
        self.filter_dixon_water(_keys=["F", "FAT"])

    def filter_dixon_outphase(self) -> None:
        """Keep only Dixon out-of-phase images (requires flatten mode)."""
        self.filter_dixon_water(_keys=["OP", "OPP", "OUTPHASE"])

    def action(
        self,
        action_fun: typing.Callable[[BIDS_FILE], None],
        filter_fun: str | typing.Callable[[str | object], bool] = lambda x: True,  # noqa: ARG005
        key: str = "",
        required: bool = True,
        all_in_sequence: bool = False,
    ) -> None:
        """Apply *action_fun* to every candidate file that passes the filter.

        Args:
            action_fun: Callable invoked with each matching
                :class:`BIDS_FILE` as its sole argument.
            key: The entity to inspect for filtering (same semantics as in
                :meth:`filter`).  An empty string matches everything.
            filter_fun: Matching criterion — a string for exact match or a
                callable predicate.  Defaults to a predicate that always
                returns ``True`` (act on all candidates).
            required: If ``True``, candidates where *key* is absent are
                skipped.  Defaults to ``True``.
            all_in_sequence: In unflatten mode, when ``True`` and at least
                one file in a sequence bucket matches, *action_fun* is called
                on *every* file in that bucket.  Defaults to ``False``.

        Raises:
            AssertionError: If both :attr:`_flatten` and *all_in_sequence*
                are ``True`` (incompatible combination).
        """
        assert not (self._flatten and all_in_sequence)
        if self._flatten:
            assert isinstance(self.candidates, list)
            for bids_file in self.candidates.copy():
                if bids_file.do_filter(key, filter_fun, required=required):
                    action_fun(bids_file)
        else:
            assert isinstance(self.candidates, dict)
            for bids_files in self.candidates.copy().values():
                if all_in_sequence:  # noqa: SIM102
                    if any(bids_file.do_filter(key, filter_fun, required=required) for bids_file in bids_files):
                        for bids_file in bids_files:
                            action_fun(bids_file)

                for bids_file in bids_files:
                    if bids_file.do_filter(key, filter_fun, required=required):
                        action_fun(bids_file)

    def __str__(self) -> str:
        if self._flatten:
            s = f"Filter of {self.subject.name}\n"
            assert isinstance(self.candidates, list)
            for bids_file in self.candidates:
                s += "\t"
                s += str(bids_file)
                s += "\n"
            return s
        else:
            s = f"Filter of {self.subject.name}\n"
            assert isinstance(self.candidates, dict)
            for sequences, bids_files in self.candidates.items():
                s += f"\tsequences {sequences}\n"
                for bids_file in bids_files:
                    s += "\t\t"
                    s += str(bids_file)
                    s += "\n"
            return s

    def loop_list(self, sort=False) -> typing.Iterator[BIDS_FILE]:
        """Returns an iterator. Flatten must be True.

        Args:
            sort (bool, optional): Sort alphabetically. Defaults to False.

        Returns:
            typing.Iterator[BIDS_FILE]: _description_
        """
        assert isinstance(self.candidates, list), "call flatten() before looping as a list"
        if sort:
            return sorted(self.candidates.__iter__())  # type: ignore
        return self.candidates.__iter__()

    def loop_dict(
        self,
        sort=False,
        key_transform: typing.Callable[[BIDS_FILE], str | None] | None = None,
        key_addendum: list[str] | None = None,  # type: ignore
    ) -> typing.Iterator[BIDS_Family]:
        """Returns an iterator. Flatten must be False: it iterates over all families, where the return is the dict from the get_sequence_files function.

        Args:
            sort (bool, optional): Sort alphabetically. Defaults to False.
            key_transform (typing.Callable[[BIDS_FILE], str | None]): provide alternative dict name for certain fils, if default should be used return None
        Returns:
            typing.Iterator[typing.Dict[str, BIDS_FILE | list[BIDS_FILE]]]
        """
        assert not self._flatten, "call unflatten first"
        assert isinstance(self.candidates, dict)
        l: typing.Iterator[BIDS_Family] = (
            self.subject.get_sequence_files(
                sequ,
                key_transform=key_transform,
                key_addendum=key_addendum,
                alternative_sequ_list=values,
            )
            for sequ, values in self.candidates.items()
        )
        if sort:
            l = sorted(l)  # type: ignore
        return l

__init__ 

__init__(subj: Subject_Container, flatten=False) -> None

Filter for specific files.

Parameters:

Name Type Description Default
subj Subject_Container

The Subject class in with filter and action is applied

 required
flatten bool

If true, you are filtering for single files. If False you looking for sequences. Defaults to False.

 False
Source code in TPTBox/core/bids_files.py 
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def __init__(self, subj: Subject_Container, flatten=False) -> None:
    """Filter for specific files.

    Args:
        subj (Subject_Container): The Subject class in with filter and action is applied
        flatten (bool, optional): If true, you are filtering for single files. If False you looking for sequences. Defaults to False.
    """
    self.candidates: list[BIDS_FILE] | dict[str, list[BIDS_FILE]] = []
    if flatten:
        for value_lists in subj.sequences.values():
            for value in value_lists:
                self.candidates.append(value)
    else:
        self.candidates = subj.sequences.copy()

    self.subject = subj
    self._flatten = flatten

from_BIDS_Family classmethod 

from_BIDS_Family(fam: BIDS_Family) -> Searchquery

Construct a :class:Searchquery pre-filtered to a single :class:BIDS_Family.

Parameters:

Name Type Description Default
fam BIDS_Family

The family whose sequence bucket will be the sole candidate.

 required

Returns:

Type Description
Searchquery

A new :class:Searchquery containing only the sequence that
Searchquery

produced fam.
Source code in TPTBox/core/bids_files.py 
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@classmethod
def from_BIDS_Family(cls, fam: BIDS_Family) -> Searchquery:
    """Construct a :class:`Searchquery` pre-filtered to a single :class:`BIDS_Family`.

    Args:
        fam: The family whose sequence bucket will be the sole candidate.

    Returns:
        A new :class:`Searchquery` containing only the sequence that
        produced *fam*.
    """
    dic = fam.data_dict
    any_file = dic[next(iter(dic.keys()))][0]
    sub = any_file.subject
    query = Searchquery(subj=sub, flatten=False)
    query._filter_fam_id(fam)
    # query.candidates = dic.copy()
    return query

copy 

copy() -> Searchquery

Return a shallow copy of this query with the same candidates.

Returns:

Type Description
Searchquery

A new :class:Searchquery sharing the same subject and flatten
Searchquery

mode, with an independent copy of the candidates collection.
Source code in TPTBox/core/bids_files.py 
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def copy(self) -> Searchquery:
    """Return a shallow copy of this query with the same candidates.

    Returns:
        A new :class:`Searchquery` sharing the same subject and flatten
        mode, with an independent copy of the candidates collection.
    """
    copy = Searchquery(self.subject, self._flatten)
    copy.candidates = self.candidates.copy()
    return copy

flatten 

flatten() -> None

Transform from multi-file-mode (sequence buckets) to single-file-mode.

After calling this method, :attr:candidates is a flat :class:list of :class:BIDS_FILE instances and :meth:loop_list can be used to iterate over them.

Source code in TPTBox/core/bids_files.py 
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def flatten(self) -> None:
    """Transform from multi-file-mode (sequence buckets) to single-file-mode.

    After calling this method, :attr:`candidates` is a flat
    :class:`list` of :class:`BIDS_FILE` instances and
    :meth:`loop_list` can be used to iterate over them.
    """
    if self._flatten:
        return
    a: list[BIDS_FILE] = []
    assert isinstance(self.candidates, dict)
    for value_lists in self.candidates.values():
        for value in value_lists:
            a.append(value)  # noqa: PERF402
    self.candidates = a
    self._flatten = True

unflatten 

unflatten() -> None

Transform from single-file-mode back to multi-file-mode (sequence buckets).

Previously filtered files remain excluded. After calling this method :meth:loop_dict can be used to iterate over sequence families.

Source code in TPTBox/core/bids_files.py 
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def unflatten(self) -> None:
    """Transform from single-file-mode back to multi-file-mode (sequence buckets).

    Previously filtered files remain excluded.  After calling this method
    :meth:`loop_dict` can be used to iterate over sequence families.
    """
    if not self._flatten:
        return
    a = {}
    assert isinstance(self.candidates, list)
    for value in self.candidates:
        key = self.subject.get_sequence_name(value)
        a.setdefault(key, [])
        a[key].append(value)
    self.candidates = a
    self._flatten = False

filter_self 

filter_self(filter_fun: Callable[[BIDS_FILE], bool], required: bool = True) -> None

Filter candidates by applying filter_fun directly to each :class:BIDS_FILE.

Parameters:

Name Type Description Default
filter_fun Callable[[BIDS_FILE], bool]

Predicate receiving a :class:BIDS_FILE; return True to keep the file.

 required
required bool

Passed to :meth:filter.

 True
Source code in TPTBox/core/bids_files.py 
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def filter_self(self, filter_fun: typing.Callable[[BIDS_FILE], bool], required: bool = True) -> None:
    """Filter candidates by applying *filter_fun* directly to each :class:`BIDS_FILE`.

    Args:
        filter_fun: Predicate receiving a :class:`BIDS_FILE`; return
            ``True`` to keep the file.
        required: Passed to :meth:`filter`.
    """
    return self.filter("self", filter_fun, required=required)  # type: ignore

filter_json 

filter_json(filter_fun: Callable[[dict], bool], required: bool = True) -> None

Filter candidates by applying filter_fun to the parsed JSON sidecar.

Parameters:

Name Type Description Default
filter_fun Callable[[dict], bool]

Predicate receiving the JSON dictionary; return True to keep the file.

 required
required bool

If True, files without a JSON sidecar are removed.

 True
Source code in TPTBox/core/bids_files.py 
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def filter_json(self, filter_fun: typing.Callable[[dict], bool], required: bool = True) -> None:
    """Filter candidates by applying *filter_fun* to the parsed JSON sidecar.

    Args:
        filter_fun: Predicate receiving the JSON dictionary; return
            ``True`` to keep the file.
        required: If ``True``, files without a JSON sidecar are removed.
    """
    return self.filter("json", filter_fun, required=required)  # type: ignore

filter 

filter(key: str, filter_fun: list[str] | str | Callable[[str | object], bool], required: bool = True) -> None

Remove candidates from the query that do not satisfy the filter.

In flatten mode (single-file mode), individual files that do not pass are removed. In unflatten mode (sequence mode), a sequence bucket is removed when no file in the bucket satisfies the filter.

Parameters:

Name Type Description Default
key str

The entity to inspect. Special values: "format", "filetype", "parent", "self"; otherwise looked up in :attr:BIDS_FILE.info or :attr:BIDS_FILE.file.

 required
filter_fun list[str] | str | Callable[[str | object], bool]

Matching criterion — a string for exact match, a list of accepted strings, or a callable predicate.

 required
required bool

If True, candidates where key is absent are removed. If False, absent keys are silently kept. Defaults to True.

 True
Source code in TPTBox/core/bids_files.py 
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def filter(
    self,
    key: str,
    filter_fun: list[str] | str | typing.Callable[[str | object], bool],
    required: bool = True,
) -> None:
    """Remove candidates from the query that do not satisfy the filter.

    In flatten mode (single-file mode), individual files that do not pass
    are removed.  In unflatten mode (sequence mode), a sequence bucket is
    removed when *no* file in the bucket satisfies the filter.

    Args:
        key: The entity to inspect.  Special values: ``"format"``,
            ``"filetype"``, ``"parent"``, ``"self"``; otherwise looked up
            in :attr:`BIDS_FILE.info` or :attr:`BIDS_FILE.file`.
        filter_fun: Matching criterion — a string for exact match, a list
            of accepted strings, or a callable predicate.
        required: If ``True``, candidates where *key* is absent are
            removed.  If ``False``, absent keys are silently kept.
            Defaults to ``True``.
    """
    if self._flatten:
        assert isinstance(self.candidates, list)
        for bids_file in self.candidates.copy():
            if not bids_file.do_filter(key, filter_fun, required=required):
                self.candidates.remove(bids_file)
    else:
        assert isinstance(self.candidates, dict)
        for sequences, bids_files in self.candidates.copy().items():
            # print(sequences, list(bids_file.do_filter(key, filter_fun, required=required) for bids_file in bids_files))
            if not any(bids_file.do_filter(key, filter_fun, required=required) for bids_file in bids_files):
                self.candidates.pop(sequences)

filter_format 

filter_format(filter_fun: list[str] | str | Callable[[str | object], bool]) -> None

Keep only files whose format label satisfies filter_fun.

Parameters:

Name Type Description Default
filter_fun list[str] | str | Callable[[str | object], bool]

A format string, a list of accepted format strings, or a callable predicate applied to the format label.

 required
Source code in TPTBox/core/bids_files.py 
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def filter_format(self, filter_fun: list[str] | str | typing.Callable[[str | object], bool]) -> None:
    """Keep only files whose format label satisfies *filter_fun*.

    Args:
        filter_fun: A format string, a list of accepted format strings,
            or a callable predicate applied to the format label.
    """
    if isinstance(filter_fun, list):
        return self.filter_format(lambda x: x in filter_fun)
    return self.filter("format", filter_fun=filter_fun, required=True)

filter_filetype 

filter_filetype(filter_fun: list[str] | str | Callable[[str | object], bool], required: bool = True) -> None

Keep only files that have a matching file extension.

Parameters:

Name Type Description Default
filter_fun list[str] | str | Callable[[str | object], bool]

An extension string (e.g. "nii.gz"), a list of accepted extensions, or a callable predicate.

 required
required bool

If True, files without any registered extension are removed.

 True
Source code in TPTBox/core/bids_files.py 
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def filter_filetype(self, filter_fun: list[str] | str | typing.Callable[[str | object], bool], required: bool = True) -> None:
    """Keep only files that have a matching file extension.

    Args:
        filter_fun: An extension string (e.g. ``"nii.gz"``), a list of
            accepted extensions, or a callable predicate.
        required: If ``True``, files without any registered extension
            are removed.
    """
    return self.filter("filetype", filter_fun=filter_fun, required=required)

filter_non_existence 

filter_non_existence(key: str, filter_fun: str | Callable[[str | object], bool] = lambda x: True, required=True) -> None

Remove family/file from the Searchquery if the filter condition is met.

(unflatten-mode) ANY single file exist in the family returns True

(unflatten-mode) the filter_fun returns True

If a key is not present the inverse of the "required" value is returned

Parameters:

Name Type Description Default
key str

The key for which we filter. Can be "format", a filetype, a key from the info-dict In case of filetype + filter_fun is a callable you get a opened Nifti, opened json or Path

 required
filter_fun str | Callable[[str | object], bool]

If a string is given: An exact string match is looked up If a callable: The function is called with the value of the key.

 lambda x: True
required bool

If True: A key must exist or the family/file is filtered. If False: Only if the key exist the family/file will be considers for filtering. Defaults to True.

 True
Source code in TPTBox/core/bids_files.py 
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def filter_non_existence(
    self,
    key: str,
    filter_fun: str | typing.Callable[[str | object], bool] = lambda x: True,  # noqa: ARG005
    required=True,
) -> None:
    """Remove family/file from the Searchquery if the filter condition is met.

        (unflatten-mode) ANY single file exist in the family returns True

        (unflatten-mode) the filter_fun returns True

        If a key is not present the inverse of the "required" value is returned

    Args:
        key (str): The key for which we filter. Can be "format", a filetype, a key from the info-dict
                    In case of filetype + filter_fun is a callable you get a opened Nifti, opened json or Path
        filter_fun (str | typing.Callable[[str  |  object], bool]):
            If a string is given: An exact string match is looked up
            If a callable: The function is called with the value of the key.
        required (bool, optional): If True: A key must exist or the family/file is filtered.
            If False: Only if the key exist the family/file will be considers for filtering. Defaults to True.
    """
    if self._flatten:
        assert isinstance(self.candidates, list)
        for bids_file in self.candidates.copy():
            if bids_file.do_filter(key, filter_fun, required=required):
                self.candidates.remove(bids_file)
    else:
        assert isinstance(self.candidates, dict)
        for sequences, bids_files in self.candidates.copy().items():
            # print(sequences, list(bids_file.do_filter(key, filter_fun, required=required) for bids_file in bids_files))
            if any(bids_file.do_filter(key, filter_fun, required=required) for bids_file in bids_files):
                self.candidates.pop(sequences)

filter_dixon_only_inphase 

filter_dixon_only_inphase() -> None

Remove Dixon files that are fat, water, out-of-phase, or difference images.

Retains only in-phase (or unlabelled) Dixon acquisitions by inspecting both the JSON ImageType field and the rec, acq, and part entities.

Source code in TPTBox/core/bids_files.py 
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def filter_dixon_only_inphase(self) -> None:
    """Remove Dixon files that are fat, water, out-of-phase, or difference images.

    Retains only in-phase (or unlabelled) Dixon acquisitions by
    inspecting both the JSON ``ImageType`` field and the ``rec``,
    ``acq``, and ``part`` entities.
    """

    def json_filter(x: dict) -> bool:
        """Return True if JSON ImageType does not indicate a fat/water/outphase channel."""
        return "ImageType" not in x or (
            "W" not in x["ImageType"]
            and "F" not in x["ImageType"]
            and "FAT" not in x["ImageType"]
            and "WATER" not in x["ImageType"]
            and "OP" not in x["ImageType"]
        )

    def lam_filter(x: str) -> bool:
        """Return True if the entity value does not indicate a non-inphase Dixon channel."""
        return (
            x.upper() != "W"
            and x.upper() != "F"
            and x.upper() != "FAT"
            and x.upper() != "WATER"
            and x.upper() != "OP"
            and x.upper() != "OPP"
            and x.upper() != "OUTPHASE"
            and x.upper() != "DIFFERENCE"
        )

    self.filter_json(json_filter, required=False)
    self.filter("rec", lam_filter, required=False)  # type: ignore DEPRECATED
    self.filter("acq", lam_filter, required=False)  # type: ignore DEPRECATED
    self.filter("part", "inphase", required=False)  # type: ignore

filter_dixon_water 

filter_dixon_water(_keys: list[str] | None = None) -> None

Keep only Dixon water-channel images (requires flatten mode).

Parameters:

Name Type Description Default
_keys list[str] | None

Image-type labels that identify the water channel. Defaults to ["W", "WATER"].

 None
Source code in TPTBox/core/bids_files.py 
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def filter_dixon_water(self, _keys: list[str] | None = None) -> None:
    """Keep only Dixon water-channel images (requires flatten mode).

    Args:
        _keys: Image-type labels that identify the water channel.
            Defaults to ``["W", "WATER"]``.
    """
    if _keys is None:
        _keys = ["W", "WATER"]
    assert self._flatten

    def json_filter(x: dict) -> bool:
        """Return True if JSON ImageType contains all required channel keys."""
        return "ImageType" not in x or all(k in x["ImageType"] for k in _keys)

    def lam_filter(x: str) -> bool:
        """Return True if the entity value matches one of the target channel keys."""
        return any(k == x.upper() for k in _keys)

    self.filter_json(json_filter, required=False)
    self.filter("rec", lam_filter, required=False)  # type: ignore
    self.filter("part", lam_filter, required=False)  # type: ignore

filter_dixon_fat 

filter_dixon_fat() -> None

Keep only Dixon fat-channel images (requires flatten mode).

Source code in TPTBox/core/bids_files.py 
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def filter_dixon_fat(self) -> None:
    """Keep only Dixon fat-channel images (requires flatten mode)."""
    self.filter_dixon_water(_keys=["F", "FAT"])

filter_dixon_outphase 

filter_dixon_outphase() -> None

Keep only Dixon out-of-phase images (requires flatten mode).

Source code in TPTBox/core/bids_files.py 
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def filter_dixon_outphase(self) -> None:
    """Keep only Dixon out-of-phase images (requires flatten mode)."""
    self.filter_dixon_water(_keys=["OP", "OPP", "OUTPHASE"])

action 

action(action_fun: Callable[[BIDS_FILE], None], filter_fun: str | Callable[[str | object], bool] = lambda x: True, key: str = '', required: bool = True, all_in_sequence: bool = False) -> None

Apply action_fun to every candidate file that passes the filter.

Parameters:

Name Type Description Default
action_fun Callable[[BIDS_FILE], None]

Callable invoked with each matching :class:BIDS_FILE as its sole argument.

 required
key str

The entity to inspect for filtering (same semantics as in :meth:filter). An empty string matches everything.

 ''
filter_fun str | Callable[[str | object], bool]

Matching criterion — a string for exact match or a callable predicate. Defaults to a predicate that always returns True (act on all candidates).

 lambda x: True
required bool

If True, candidates where key is absent are skipped. Defaults to True.

 True
all_in_sequence bool

In unflatten mode, when True and at least one file in a sequence bucket matches, action_fun is called on every file in that bucket. Defaults to False.

 False

Raises:

Type Description
AssertionError

If both :attr:_flatten and all_in_sequence are True (incompatible combination).
Source code in TPTBox/core/bids_files.py 
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def action(
    self,
    action_fun: typing.Callable[[BIDS_FILE], None],
    filter_fun: str | typing.Callable[[str | object], bool] = lambda x: True,  # noqa: ARG005
    key: str = "",
    required: bool = True,
    all_in_sequence: bool = False,
) -> None:
    """Apply *action_fun* to every candidate file that passes the filter.

    Args:
        action_fun: Callable invoked with each matching
            :class:`BIDS_FILE` as its sole argument.
        key: The entity to inspect for filtering (same semantics as in
            :meth:`filter`).  An empty string matches everything.
        filter_fun: Matching criterion — a string for exact match or a
            callable predicate.  Defaults to a predicate that always
            returns ``True`` (act on all candidates).
        required: If ``True``, candidates where *key* is absent are
            skipped.  Defaults to ``True``.
        all_in_sequence: In unflatten mode, when ``True`` and at least
            one file in a sequence bucket matches, *action_fun* is called
            on *every* file in that bucket.  Defaults to ``False``.

    Raises:
        AssertionError: If both :attr:`_flatten` and *all_in_sequence*
            are ``True`` (incompatible combination).
    """
    assert not (self._flatten and all_in_sequence)
    if self._flatten:
        assert isinstance(self.candidates, list)
        for bids_file in self.candidates.copy():
            if bids_file.do_filter(key, filter_fun, required=required):
                action_fun(bids_file)
    else:
        assert isinstance(self.candidates, dict)
        for bids_files in self.candidates.copy().values():
            if all_in_sequence:  # noqa: SIM102
                if any(bids_file.do_filter(key, filter_fun, required=required) for bids_file in bids_files):
                    for bids_file in bids_files:
                        action_fun(bids_file)

            for bids_file in bids_files:
                if bids_file.do_filter(key, filter_fun, required=required):
                    action_fun(bids_file)

loop_list 

loop_list(sort=False) -> typing.Iterator[BIDS_FILE]

Returns an iterator. Flatten must be True.

Parameters:

Name Type Description Default
sort bool

Sort alphabetically. Defaults to False.

 False

Returns:

Type Description
Iterator[BIDS_FILE]

typing.Iterator[BIDS_FILE]: description
Source code in TPTBox/core/bids_files.py 
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def loop_list(self, sort=False) -> typing.Iterator[BIDS_FILE]:
    """Returns an iterator. Flatten must be True.

    Args:
        sort (bool, optional): Sort alphabetically. Defaults to False.

    Returns:
        typing.Iterator[BIDS_FILE]: _description_
    """
    assert isinstance(self.candidates, list), "call flatten() before looping as a list"
    if sort:
        return sorted(self.candidates.__iter__())  # type: ignore
    return self.candidates.__iter__()

loop_dict 

loop_dict(sort=False, key_transform: Callable[[BIDS_FILE], str | None] | None = None, key_addendum: list[str] | None = None) -> typing.Iterator[BIDS_Family]

Returns an iterator. Flatten must be False: it iterates over all families, where the return is the dict from the get_sequence_files function.

Parameters:

Name Type Description Default
sort bool

Sort alphabetically. Defaults to False.

 False
key_transform Callable[[BIDS_FILE], str | None]

provide alternative dict name for certain fils, if default should be used return None

 None

Returns: typing.Iterator[typing.Dict[str, BIDS_FILE | list[BIDS_FILE]]]

Source code in TPTBox/core/bids_files.py 
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def loop_dict(
    self,
    sort=False,
    key_transform: typing.Callable[[BIDS_FILE], str | None] | None = None,
    key_addendum: list[str] | None = None,  # type: ignore
) -> typing.Iterator[BIDS_Family]:
    """Returns an iterator. Flatten must be False: it iterates over all families, where the return is the dict from the get_sequence_files function.

    Args:
        sort (bool, optional): Sort alphabetically. Defaults to False.
        key_transform (typing.Callable[[BIDS_FILE], str | None]): provide alternative dict name for certain fils, if default should be used return None
    Returns:
        typing.Iterator[typing.Dict[str, BIDS_FILE | list[BIDS_FILE]]]
    """
    assert not self._flatten, "call unflatten first"
    assert isinstance(self.candidates, dict)
    l: typing.Iterator[BIDS_Family] = (
        self.subject.get_sequence_files(
            sequ,
            key_transform=key_transform,
            key_addendum=key_addendum,
            alternative_sequ_list=values,
        )
        for sequ, values in self.candidates.items()
    )
    if sort:
        l = sorted(l)  # type: ignore
    return l

BIDS_Family

TPTBox.core.bids_files.BIDS_Family

A group of related BIDS files sharing the same sequence-splitting key values.

Source code in TPTBox/core/bids_files.py 
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class BIDS_Family:
    """A group of related BIDS files sharing the same sequence-splitting key values."""

    def __init__(
        self,
        family_data: dict[str, list[BIDS_FILE]],
        sequence_splitting_keys: list[str],
    ):
        k = []
        for x in family_data.values():
            for y in x:
                assert y.BIDS_key not in k, family_data
                k.append(y.BIDS_key)
        self.sequence_splitting_keys = sequence_splitting_keys.copy()
        self.data_dict = family_data.copy()
        self.family_id = self.get_identifier()

    def __getitem__(self, item: str) -> list[BIDS_FILE]:
        try:
            return self.data_dict[item]
        except KeyError as e:
            raise KeyError(f"BIDS_Family does not contain key '{item}', only {list(self.keys())}; {self.family_id=}") from e

    def __setitem__(self, key, value):
        self.data_dict[key] = value

    def __str__(self) -> str:
        s = ""
        for k, v in self:
            s += f"{k:30} : {v}\n"
        return s[:-1]

    def __repr__(self) -> str:
        return str(self)

    def __contains__(self, key: str | list[str]):
        if isinstance(key, list):
            contains = True
            for k in key:
                contains = contains and k in self.data_dict
            return contains
        return key in self.data_dict

    def __len__(self) -> int:
        # number of underlying BIDS files
        return sum([v for k, v in self.get_key_len().items()])

    def __iter__(self):
        return iter(self.data_dict.items())

    def __hash__(self) -> int:
        return str(self).__hash__()

    def __lt__(self, other):
        return str(self) < str(other)

    def get_identifier(self) -> str:
        """Return the subject+sequence identifier string for this family.

        Delegates to :meth:`BIDS_FILE.get_identifier` on the first file in
        the family.

        Returns:
            A string like ``"sub-001_ses-01_sequ-303"`` derived from the
            sequence splitting keys.
        """
        first_e = self.data_dict[next(iter(self.data_dict.keys()))][0]
        return first_e.get_identifier(self.sequence_splitting_keys)

    def items(self) -> typing.ItemsView[str, list[BIDS_FILE]]:
        """Return ``(format_key, [BIDS_FILE, ...])`` pairs from the family dictionary."""
        return self.data_dict.items()

    def keys(self) -> typing.KeysView[str]:
        """Return the format keys present in this family."""
        return self.data_dict.keys()

    def sort(self) -> None:
        """Sort the family dictionary alphabetically by format key in-place."""
        self.data_dict = dict(sorted(self.data_dict.items()))

    def values(self) -> list[list[BIDS_FILE]]:
        """Return all lists of :class:`BIDS_FILE` objects in this family."""
        return list(self.data_dict.values())

    def new_query(self, flatten: bool = False) -> Searchquery:
        """Create a :class:`Searchquery` scoped to this family's sequence.

        Args:
            flatten: If ``True``, the query starts in single-file mode.

        Returns:
            A :class:`Searchquery` pre-filtered to this family's sequence
            bucket.
        """
        q = Searchquery.from_BIDS_Family(self)
        if flatten:
            q.flatten()
        return q

    def get_key_len(self) -> dict[str, int]:
        """Return the number of :class:`BIDS_FILE` instances for each format key.

        Returns:
            A dictionary mapping format key to the count of associated files.
        """
        return {k: len(v) for k, v in self}

    def get_format_len(self) -> dict[str, tuple[int, int]]:
        """Return per-base-format counts aggregated across all sub-keys.

        Groups family keys by their base format (the part before the first
        ``_``) and accumulates ``(key_count, file_count)`` tuples.

        Returns:
            A dictionary mapping base-format label to a
            ``(number_of_keys, total_file_count)`` tuple.
        """
        format_len = {}
        for k, v in self:
            bids_format = k.split("_")[0]
            if bids_format not in format_len:
                format_len[bids_format] = (0, 0)
            format_len[bids_format] = (
                format_len[bids_format][0] + 1,
                format_len[bids_format][1] + len(v),
            )
        return format_len

    def get_files_with_multiples(self) -> dict[str, list[dict]]:
        """Return file-path dictionaries for all format keys that have more than one file.

        Returns:
            A dictionary mapping format key to a list of :attr:`BIDS_FILE.file`
            dicts, restricted to keys that hold more than one file.
        """
        return self.get_files(key=[k for k, v in self.get_key_len().items() if v > 1])

    def get_files(self, key: list[str] | str | None = None) -> dict[str, list[dict]]:
        """Return the raw file-path dictionaries for one or more format keys.

        Args:
            key: A single format key, a list of format keys, or ``None`` to
                include all keys.

        Returns:
            A dictionary mapping each requested format key to a list of
            :attr:`BIDS_FILE.file` dicts (one per associated
            :class:`BIDS_FILE`).
        """
        if key is None:
            key = [k for k, v in self]
        if isinstance(key, str):
            key = [key]
        family_dict_files: dict[str, list[dict]] = {}
        for k in key:
            family_dict_files[k] = [b.file for b in self[k]]
        return family_dict_files

    def get(self, item: str | list[str], default: list[BIDS_FILE] | None = None) -> list[BIDS_FILE] | None:
        """Return the list of :class:`BIDS_FILE` instances for the first matching key.

        When *item* is a list the method tries each element in order and
        returns the first hit.

        Args:
            item: A single format key or an ordered list of candidate keys.
            default: Value returned when none of the keys are found.

        Returns:
            The list of :class:`BIDS_FILE` instances, or *default*.
        """
        if not isinstance(item, list):
            item = [item]
        for i in item:
            if i in self:
                return self[i]
        return default

    def get_bids_files_as_dict(self, keys: list[str]) -> dict[str, BIDS_FILE]:
        """Checks each entry of the list, if everything is there, loads everything, one for each entry in keys.

        Args:
            keys: list of (keys or list of keys)

        Returns:
            If all keys are present, returns dictionary[key, BIDS_File], else, returns first key that is not found (str)
        """
        loaded_files: dict[str, BIDS_FILE] = {}
        for k in keys:
            if k not in self:
                raise KeyError(f"{k} not in {self.get_key_len()}")
            bids_f = self.get(k)[0]  # type: ignore
            loaded_files[k] = bids_f
        return loaded_files

get_identifier 

get_identifier() -> str

Return the subject+sequence identifier string for this family.

Delegates to :meth:BIDS_FILE.get_identifier on the first file in the family.

Returns:

Type Description
str

A string like "sub-001_ses-01_sequ-303" derived from the
str

sequence splitting keys.
Source code in TPTBox/core/bids_files.py 
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def get_identifier(self) -> str:
    """Return the subject+sequence identifier string for this family.

    Delegates to :meth:`BIDS_FILE.get_identifier` on the first file in
    the family.

    Returns:
        A string like ``"sub-001_ses-01_sequ-303"`` derived from the
        sequence splitting keys.
    """
    first_e = self.data_dict[next(iter(self.data_dict.keys()))][0]
    return first_e.get_identifier(self.sequence_splitting_keys)

items 

items() -> typing.ItemsView[str, list[BIDS_FILE]]

Return (format_key, [BIDS_FILE, ...]) pairs from the family dictionary.

Source code in TPTBox/core/bids_files.py 
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def items(self) -> typing.ItemsView[str, list[BIDS_FILE]]:
    """Return ``(format_key, [BIDS_FILE, ...])`` pairs from the family dictionary."""
    return self.data_dict.items()

keys 

keys() -> typing.KeysView[str]

Return the format keys present in this family.

Source code in TPTBox/core/bids_files.py 
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def keys(self) -> typing.KeysView[str]:
    """Return the format keys present in this family."""
    return self.data_dict.keys()

sort 

sort() -> None

Sort the family dictionary alphabetically by format key in-place.

Source code in TPTBox/core/bids_files.py 
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def sort(self) -> None:
    """Sort the family dictionary alphabetically by format key in-place."""
    self.data_dict = dict(sorted(self.data_dict.items()))

values 

values() -> list[list[BIDS_FILE]]

Return all lists of :class:BIDS_FILE objects in this family.

Source code in TPTBox/core/bids_files.py 
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def values(self) -> list[list[BIDS_FILE]]:
    """Return all lists of :class:`BIDS_FILE` objects in this family."""
    return list(self.data_dict.values())

new_query 

new_query(flatten: bool = False) -> Searchquery

Create a :class:Searchquery scoped to this family's sequence.

Parameters:

Name Type Description Default
flatten bool

If True, the query starts in single-file mode.

 False

Returns:

Name Type Description
A Searchquery

class:Searchquery pre-filtered to this family's sequence
Searchquery

bucket.
Source code in TPTBox/core/bids_files.py 
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def new_query(self, flatten: bool = False) -> Searchquery:
    """Create a :class:`Searchquery` scoped to this family's sequence.

    Args:
        flatten: If ``True``, the query starts in single-file mode.

    Returns:
        A :class:`Searchquery` pre-filtered to this family's sequence
        bucket.
    """
    q = Searchquery.from_BIDS_Family(self)
    if flatten:
        q.flatten()
    return q

get_key_len 

get_key_len() -> dict[str, int]

Return the number of :class:BIDS_FILE instances for each format key.

Returns:

Type Description
dict[str, int]

A dictionary mapping format key to the count of associated files.
Source code in TPTBox/core/bids_files.py 
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def get_key_len(self) -> dict[str, int]:
    """Return the number of :class:`BIDS_FILE` instances for each format key.

    Returns:
        A dictionary mapping format key to the count of associated files.
    """
    return {k: len(v) for k, v in self}

get_format_len 

get_format_len() -> dict[str, tuple[int, int]]

Return per-base-format counts aggregated across all sub-keys.

Groups family keys by their base format (the part before the first _) and accumulates (key_count, file_count) tuples.

Returns:

Type Description
dict[str, tuple[int, int]]

A dictionary mapping base-format label to a
dict[str, tuple[int, int]]

(number_of_keys, total_file_count) tuple.
Source code in TPTBox/core/bids_files.py 
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def get_format_len(self) -> dict[str, tuple[int, int]]:
    """Return per-base-format counts aggregated across all sub-keys.

    Groups family keys by their base format (the part before the first
    ``_``) and accumulates ``(key_count, file_count)`` tuples.

    Returns:
        A dictionary mapping base-format label to a
        ``(number_of_keys, total_file_count)`` tuple.
    """
    format_len = {}
    for k, v in self:
        bids_format = k.split("_")[0]
        if bids_format not in format_len:
            format_len[bids_format] = (0, 0)
        format_len[bids_format] = (
            format_len[bids_format][0] + 1,
            format_len[bids_format][1] + len(v),
        )
    return format_len

get_files_with_multiples 

get_files_with_multiples() -> dict[str, list[dict]]

Return file-path dictionaries for all format keys that have more than one file.

Returns:

Type Description
dict[str, list[dict]]

A dictionary mapping format key to a list of :attr:BIDS_FILE.file
dict[str, list[dict]]

dicts, restricted to keys that hold more than one file.
Source code in TPTBox/core/bids_files.py 
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def get_files_with_multiples(self) -> dict[str, list[dict]]:
    """Return file-path dictionaries for all format keys that have more than one file.

    Returns:
        A dictionary mapping format key to a list of :attr:`BIDS_FILE.file`
        dicts, restricted to keys that hold more than one file.
    """
    return self.get_files(key=[k for k, v in self.get_key_len().items() if v > 1])

get_files 

get_files(key: list[str] | str | None = None) -> dict[str, list[dict]]

Return the raw file-path dictionaries for one or more format keys.

Parameters:

Name Type Description Default
key list[str] | str | None

A single format key, a list of format keys, or None to include all keys.

 None

Returns:

Type Description
dict[str, list[dict]]

A dictionary mapping each requested format key to a list of
dict[str, list[dict]]

attr:BIDS_FILE.file dicts (one per associated
dict[str, list[dict]]

class:BIDS_FILE).
Source code in TPTBox/core/bids_files.py 
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def get_files(self, key: list[str] | str | None = None) -> dict[str, list[dict]]:
    """Return the raw file-path dictionaries for one or more format keys.

    Args:
        key: A single format key, a list of format keys, or ``None`` to
            include all keys.

    Returns:
        A dictionary mapping each requested format key to a list of
        :attr:`BIDS_FILE.file` dicts (one per associated
        :class:`BIDS_FILE`).
    """
    if key is None:
        key = [k for k, v in self]
    if isinstance(key, str):
        key = [key]
    family_dict_files: dict[str, list[dict]] = {}
    for k in key:
        family_dict_files[k] = [b.file for b in self[k]]
    return family_dict_files

get 

get(item: str | list[str], default: list[BIDS_FILE] | None = None) -> list[BIDS_FILE] | None

Return the list of :class:BIDS_FILE instances for the first matching key.

When item is a list the method tries each element in order and returns the first hit.

Parameters:

Name Type Description Default
item str | list[str]

A single format key or an ordered list of candidate keys.

 required
default list[BIDS_FILE] | None

Value returned when none of the keys are found.

 None

Returns:

Type Description
list[BIDS_FILE] | None

The list of :class:BIDS_FILE instances, or default.
Source code in TPTBox/core/bids_files.py 
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def get(self, item: str | list[str], default: list[BIDS_FILE] | None = None) -> list[BIDS_FILE] | None:
    """Return the list of :class:`BIDS_FILE` instances for the first matching key.

    When *item* is a list the method tries each element in order and
    returns the first hit.

    Args:
        item: A single format key or an ordered list of candidate keys.
        default: Value returned when none of the keys are found.

    Returns:
        The list of :class:`BIDS_FILE` instances, or *default*.
    """
    if not isinstance(item, list):
        item = [item]
    for i in item:
        if i in self:
            return self[i]
    return default

get_bids_files_as_dict 

get_bids_files_as_dict(keys: list[str]) -> dict[str, BIDS_FILE]

Checks each entry of the list, if everything is there, loads everything, one for each entry in keys.

Parameters:

Name Type Description Default
keys list[str]

list of (keys or list of keys)

 required

Returns:

Type Description
dict[str, BIDS_FILE]

If all keys are present, returns dictionary[key, BIDS_File], else, returns first key that is not found (str)
Source code in TPTBox/core/bids_files.py 
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def get_bids_files_as_dict(self, keys: list[str]) -> dict[str, BIDS_FILE]:
    """Checks each entry of the list, if everything is there, loads everything, one for each entry in keys.

    Args:
        keys: list of (keys or list of keys)

    Returns:
        If all keys are present, returns dictionary[key, BIDS_File], else, returns first key that is not found (str)
    """
    loaded_files: dict[str, BIDS_FILE] = {}
    for k in keys:
        if k not in self:
            raise KeyError(f"{k} not in {self.get_key_len()}")
        bids_f = self.get(k)[0]  # type: ignore
        loaded_files[k] = bids_f
    return loaded_files