FileSequence¶
- class tifffile.FileSequence(imread, files, *, container=None, sort=None, parse=None, **kwargs)¶
Sequence of files containing compatible array data.
- Parameters:
imread (Callable[..., NDArray[Any]]) – Function to read image array from single file.
files (str | os.PathLike[Any] | Sequence[str | os.PathLike[Any]] | None) – Glob filename pattern or sequence of file names. If None, use ‘*’. All files must contain array data of same shape and dtype. Binary streams are not supported.
container (str | os.PathLike[Any] | None) – Name or open instance of ZIP file in which files are stored.
sort (Callable[..., Any] | bool | None) – Function to sort file names if files is a pattern. The default is
natural_sorted()
. If False, disable sorting.parse (Callable[..., Any] | None) – Function to parse sequence of sorted file names to dims, shape, chunk indices, and filtered file names. The default is
parse_filenames()
if kwargs contains ‘pattern’.**kwargs (Any) – Additional arguments passed to parse function.
Examples
>>> filenames = ['temp_C001T002.tif', 'temp_C001T001.tif'] >>> ims = TiffSequence(filenames, pattern=r'_(C)(\d+)(T)(\d+)') >>> ims[0] 'temp_C001T002.tif' >>> ims.shape (1, 2) >>> ims.axes 'CT'
- imread: Callable[..., NDArray[Any]]¶
Function to read image array from single file.
- axes: str¶
Character codes for dimensions in shape.
- dims: tuple[str, ...]¶
Names of dimensions in shape.
- shape: tuple[int, ...]¶
Shape of file series. Excludes shape of chunks in files.
- indices: tuple[tuple[int, ...]]¶
Indices of files in shape.
- asarray(*, imreadargs=None, chunkshape=None, chunkdtype=None, dtype=None, axestiled=None, out_inplace=None, ioworkers=1, out=None, **kwargs)¶
Return images from files as NumPy array.
- Parameters:
imreadargs (dict[str, Any] | None) – Arguments passed to
FileSequence.imread
.chunkshape (tuple[int, ...] | None) – Shape of chunk in each file. Must match
FileSequence.imread(file, **imreadargs).shape
. By default, this is determined by reading the first file.chunkdtype (DTypeLike | None) – Data type of chunk in each file. Must match
FileSequence.imread(file, **imreadargs).dtype
. By default, this is determined by reading the first file.axestiled (dict[int, int] | Sequence[tuple[int, int]] | None) – Axes to be tiled. Map stacked sequence axis to chunk axis.
ioworkers (int | None) – Maximum number of threads to execute
FileSequence.imread
asynchronously. If 0, use up to_TIFF.MAXIOWORKERS
threads. Using threads can significantly improve runtime when reading many small files from a network share.out_inplace (bool | None) –
FileSequence.imread
decodes directly to the output instead of returning an array, which is copied to the output. Not all imread functions support this, especially in non-contiguous cases.out (OutputType) – Specifies how image array is returned. By default, create a new array. If a numpy.ndarray, a writable array to which the images are copied. If ‘memmap’, create a memory-mapped array in a temporary file. If a string or open file, the file used to create a memory-mapped array.
**kwargs (Any) – Arguments passed to
FileSequence.imread
in addition to imreadargs.dtype (DTypeLike | None)
- Raises:
IndexError, ValueError – Array shapes do not match.
- Return type:
NDArray[Any]
- aszarr(**kwargs)¶
Return images from files as Zarr store.
- Parameters:
**kwargs (Any) – Arguments passed to
ZarrFileSequenceStore
.- Return type:
- close()¶
Close open files.
- Return type:
None
- commonpath()¶
Return longest common sub-path of each file in sequence.
- Return type:
str
- property files_missing: int¶
Number of empty chunks.