intake_io.source

Submodules

Package Contents

Classes

AutoSource

Intake source for NRRD files.

BioformatsSource

Intake source using Bioformats as backend.

DicomSource

Intake source for DICOM files.

DicomZipSource

Intake source for zipped DICOM file series.

DirSource

Intake source for flat file system directories.

FilePatternSource

ImageIOSource

Intake source using imageio as backend.

ListSource

Intake source for a list of URIs and intake sources.

NiftiSource

Intake source for NIFTI files.

NrrdSource

Intake source for NRRD files.

TifSource

Intake source for TIF files.
class intake_io.source.AutoSource(uri: str, metadata: Optional[dict] = None)

Bases: intake.source.base.DataSource

Intake source for NRRD files.

Attributes:

uri (str): URI (e.g. URL or file system path)

Arguments:

uri (str): URI (e.g. URL or file system path) metadata (dict, optional): Extra metadata, handed over to intake

container = ndarray
name = auto
version = 0.0.1
partition_access = True
class intake_io.source.BioformatsSource(uri: str, **kwargs)

Bases: intake_io.source.base.ImageSource

Intake source using Bioformats as backend.

Attributes:

uri (str): URI (e.g. file system path or URL)

Arguments:

uri (str): URI (e.g. file system path or URL) metadata (dict, optional): Extra metadata, handed over to intake

container = ndarray
name = bioformats
version = 0.0.1
partition_access = True
read(self) → numpy.ndarray
class intake_io.source.DicomSource(uri: str, metadata: Optional[dict] = None)

Bases: intake.source.base.DataSource

Intake source for DICOM files.

Attributes:

uri (str): URI (file system path)

Arguments:

uri (str): URI (e.g. file system path or URL) metadata (dict, optional): Extra metadata, handed over to intake

container = ndarray
name = dicom
version = 0.0.1
partition_access = False
class intake_io.source.DicomZipSource(uri: str, order_by: str = 'z', metadata: Optional[dict] = None)

Bases: intake.source.base.DataSource

Intake source for zipped DICOM file series.

Attributes:

uri (str): URI (file system path) files (list): Files in archive

Arguments:

uri (str): URI (file system path) order_by (str, detault=’z’): Order files by z (‘z’) or t (‘t’) metadata (dict, optional): Extra metadata, handed over to intake

container = ndarray
name = dicomzip
version = 0.0.1
partition_access = True
read(self) → numpy.ndarray
class intake_io.source.DirSource(uri: str, extension: Optional[str] = None, axis: str = 'z', metadata: Optional[dict] = None)

Bases: intake.source.base.DataSource

Intake source for flat file system directories.

Attributes:

uri (str): URI (file system path) extension (str): file name extension to look for axis (str): axis to concatenate files along

Arguments:

uri (str): URI (file system path) extension (str, optional): file name extension to look for axis (str, default=’z’): axis (‘t’, ‘c’, ‘z’) to concatenate files along metadata (dict, optional): Extra metadata, handed over to intake

container = ndarray
name = dir
version = 0.0.1
partition_access = True
read(self) → numpy.ndarray
class intake_io.source.FilePatternSource(folder, axis_tags, extensions, include_filters=[], exclude_filters=[], ixs=None, source: Optional[intake_io.source.base.ImageSource] = None, **kwargs)

Bases: intake_io.source.base.ImageSource

container = ndarray
name = filepattern
version = 0.0.1
partition_access = True
static get(folder, axis_tags, extensions, include_filters=[], exclude_filters=[], source: Optional[intake_io.source.base.ImageSource] = None, **kwargs)
read(self) → numpy.ndarray
class intake_io.source.ImageIOSource(uri: str, metadata: intake_io.util.Optional[dict] = None)

Bases: intake_io.util.intake.source.base.DataSource

Intake source using imageio as backend.

Attributes:

uri (str): URI (e.g. file system path or URL)

Arguments:

uri (str): URI (e.g. file system path or URL) metadata (dict, optional): Extra metadata, handed over to intake

container = ndarray
name = imageio
version = 0.0.1
partition_access = True
read(self) → intake_io.util.np.ndarray
class intake_io.source.ListSource(items: list, axis: Optional[str] = None, as_float32=False, num_workers=6, **kwargs)

Bases: intake_io.source.base.ImageSource

Intake source for a list of URIs and intake sources.

Attributes:

items (list): items axis (str): axis to concatenate items along

Arguments:

items (list): items axis (str, default=’z’): axis to concatenate items along as_float32 (bool, default=False): convert items to float32 pixel type metadata (dict, optional): Extra metadata, handed over to intake

container = ndarray
name = list
version = 0.0.1
partition_access = True
read_partition(self, i: Union[int, str]) → numpy.ndarray
read(self) → numpy.ndarray
sort_items(self)
class intake_io.source.NiftiSource(uri: str, **kwargs)

Bases: intake_io.source.base.ImageSource

Intake source for NIFTI files.

Attributes:

uri (str): URI (file system path)

Arguments:

uri (str): URI (file system path) metadata (dict, optional): Extra metadata, handed over to intake

container = ndarray
name = nifti
version = 0.0.1
partition_access = False
open(self)
class intake_io.source.NrrdSource(uri: str, **kwargs)

Bases: intake_io.source.base.ImageSource

Intake source for NRRD files.

Attributes:

uri (str): URI (file system path)

Arguments:

uri (str): URI (file system path) metadata (dict, optional): Extra metadata, handed over to intake

container = ndarray
name = nrrd
version = 0.0.1
partition_access = False
class intake_io.source.TifSource(uri: str, **kwargs)

Bases: intake_io.source.base.ImageSource

Intake source for TIF files.

Attributes:

uri (str): URI (e.g. file system path or URL)

Arguments:

uri (str): URI (e.g. file system path or URL) metadata (dict, optional): Extra metadata, handed over to intake

container = ndarray
name = tif
version = 0.0.1
partition_access = True
read(self) → numpy.ndarray