navigate.model.metadata_sources.ome_tiff_metadata.OMETIFFMetadata

class navigate.model.metadata_sources.ome_tiff_metadata.OMETIFFMetadata

Bases: XMLMetadata

Metadata for OME-TIFF files.

Note

OME-XML spec at https://docs.openmicroscopy.org/ome-model/6.3.1/ome-xml/index.html.

__init__() → None

Metadata class

Store and convert internal representation of metadata (configuration, experiment, etc.) to alternative file types.

Note

Concept and some of the code borrowed from python-microscopy (https://github.com/python-microscopy/python-microscopy/).

Methods

__init__()	Metadata class
ome_tiff_xml_dict([c, t, file_name, uid, views])	Generates dictionary with same hierarchical structure as OME-XML.
set_from_configuration_experiment()	Set from configuration experiment
set_from_dict(metadata_config)	Set from a dictionary
set_shape_from_configuration_experiment()	Set shape from configuration experiment
set_stack_order_from_configuration_experiment()	Set stack order from configuration experiment
to_xml([file_type, root])	Convert OME-XML to string.
write_xml(file_name[, file_type, root])	Write OME-XML to file.

Attributes

configuration	Return configuration dictionary
per_stack	Return per stack
shape	Return shape as XYCZT.
voxel_size	Return voxel size

ome_tiff_xml_dict(c: int = 0, t: int = 0, file_name: Optional[Union[str, list]] = None, uid: Optional[Union[str, list]] = None, views: Optional[list] = None, **kw)

Generates dictionary with same hierarchical structure as OME-XML. Useful for OME-TIFF and OME-XML.

Parameters:

• c (int, optional) – Channel index, by default 0

• t (int, optional) – Time point index, by default 0

• file_name (Union[str, list, None], optional) – File name or list of file names, by default None

• uid (Union[str, list, None]) – Unique identifier or list of unique identifiers, by default None

• views (Optional[list], optional) – List of views, by default None

• kw (dict, optional) – Additional keyword arguments, by default None

Returns:

OME TIFF metadata dictionary

Return type:

ome_dict

set_from_configuration_experiment() → None

Set from configuration experiment

set_from_dict(metadata_config: dict) → None

Set from a dictionary

Parameters:

metadata_config (dict) – dictionary of metadata: “c”, “z”, “t”, “p”, “is_dynamic”, “per_stack”

set_shape_from_configuration_experiment() → None

Set shape from configuration experiment

set_stack_order_from_configuration_experiment() → None

Set stack order from configuration experiment

to_xml(file_type: str = 'OME-TIFF', root: Optional[str] = 'OME', **kw) → str

Convert OME-XML to string.

Parameters:

• file_type (str, optional) – File type, by default “OME-TIFF”

• root (Optional[str], optional) – Root element, by default “OME”

• kw (dict, optional) – Additional keyword arguments, by default None

Returns:

OME-XML string

Return type:

str

write_xml(file_name: str, file_type: str = 'OME-TIFF', root: Optional[str] = 'OME', **kw) → None

Write OME-XML to file.

Parameters:

• file_name (str) – File name

• file_type (str, optional) – File type, by default “OME-TIFF”

• root (Optional[str], optional) – Root element, by default “OME”

• kw (dict, optional) – Additional keyword arguments, by default None

active_microscope

Active microscope

Type:

str

property configuration: Optional[DictProxy]

Return configuration dictionary

Returns:

configuration – Configuration dictionary

Return type:

Optional[DictProxy]

dc

Step size between channels, should always be 1

Type:

int

dt

Time displacement (s)

Type:

float

dx

Pixel size in x (um) float: Pixel size in y (um) float: Pixel size in z (um)

Type:

float

dy

Pixel size in x (um) float: Pixel size in y (um) float: Pixel size in z (um)

Type:

float

dz

Pixel size in x (um) float: Pixel size in y (um) float: Pixel size in z (um)

Type:

float

misc

misc notes

Type:

str

property per_stack: bool

Return per stack

Returns:

True if per stack, False otherwise

Return type:

bool

positions

Number of positions

Type:

int

property shape: tuple

Return shape as XYCZT.

Returns:

Shape as XYCZT

Return type:

tuple

shape_c

Shape of the data in x int: Shape of the data in y int: Shape of the data in z int: Shape of the data in t int: Shape of the data in c

Type:

int

shape_t

Shape of the data in x int: Shape of the data in y int: Shape of the data in z int: Shape of the data in t int: Shape of the data in c

Type:

int

shape_x

Shape of the data in x int: Shape of the data in y int: Shape of the data in z int: Shape of the data in t int: Shape of the data in c

Type:

int

shape_y

Shape of the data in x int: Shape of the data in y int: Shape of the data in z int: Shape of the data in t int: Shape of the data in c

Type:

int

shape_z

Shape of the data in x int: Shape of the data in y int: Shape of the data in z int: Shape of the data in t int: Shape of the data in c

Type:

int

property voxel_size: tuple

Return voxel size

Returns:

Voxel size

Return type:

tuple