navigate.model.metadata_sources.metadata.XMLMetadata

class navigate.model.metadata_sources.metadata.XMLMetadata

Bases: Metadata

XML Metadata

This is a base class for dealing with metadata that is stored as an XML, e.g. in OME-TIFF or BigDataViewer. There are multiple methods for storing XML. In OME-TIFF, the XML is stored in the header of the first OME-TIFF file in a directory. In BigDataViewer, it is stored in a separate XML. Both have proprietary XML formats. To address this, we store their metadata in a nested dictionary, defined by {file_type}_xml_dict() (e.g. ome_tiff_xml_dict()) (see to_xml()). We then parse this nested dictionary into an XML file. Similarly, we can parse from an XML file to a nested dictionary and map these values back to our internal representation of metadata values (TODO: Not implemented. Will use xml_tools.parse_xml() for the first bit.)

__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
`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 stored metadata to XML
`write_xml`(file_name, file_type[, root])	Write to XML file.

Attributes

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

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, root: Optional[str] = None, **kw) → str

Convert stored metadata to XML

Parameters:

file_type (str) – File type
root (Optional[str]) – Root, by default None
**kw – Keyword arguments

Returns:

XML string

Return type:

str

write_xml(file_name: str, file_type: str, root: Optional[str] = None, **kw) → None

Write to XML file. Assumes we do not include the XML header in our nested metadata dictionary.

Parameters:

file_name (str) – File name
file_type (str) – File type
root (Optional[str]) – Root, 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

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