navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata

class navigate.model.metadata_sources.bdv_metadata.BigDataViewerMetadata

Bases: XMLMetadata

Metadata for BigDataViewer files.

Note

XML spec in section 2.3 of https://arxiv.org/abs/1412.0488.

__init__() → None

Initialize the BigDataViewer metadata object.

Parameters:: configuration (Optional[Dict[str, Any]]) – Configuration dictionary.

Methods

`__init__`()	Initialize the BigDataViewer metadata object.
`affine_matrix_to_stage_positions`(mat)	Convert affine matrix back into stage positions.
`bdv_rotate_transform`()	Calculate the BDV rotation transform matrix.
`bdv_shear_transform`()	Calculate the shear transform matrix.
`bdv_xml_dict`(file_name, views, **kw)	Create a BigDataViewer XML dictionary from a list of views.
`get_affine_parameters`(configuration)	Get the affine transform parameters from the configuration file.
`parse_xml`(root)	Parse a BigDataViewer XML file into our metadata format.
`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
`stage_positions_to_affine_matrix`(x, y, z, theta)	Convert stage positions to an affine matrix.
`to_xml`(file_type[, root])	Convert stored metadata to XML
`write_xml`(file_name, views)	Write BigDataViewer XML metadata.

Attributes

`configuration`	Return configuration dictionary
`per_stack`	Return per stack
`shape`	Return shape as XYCZT.
`voxel_size`	Return voxel size
`shear_data`	Shear the data.
`shear_dimension`	Dimension to shear the data.
`shear_angle`	Angle in degrees to shear the data.
`shear_transform`	Shear transform matrix.
`rotate_data`	Rotate the data.
`rotate_angle_x`	Angle in degrees to rotate the data in X.
`rotate_angle_y`	Angle in degrees to rotate the data in Y.
`rotate_angle_z`	Angle in degrees to rotate the data in Z.
`rotate_transform`	Rotation transform matrix.

affine_matrix_to_stage_positions(mat: Union[_SupportsArray[dtype], _NestedSequence[_SupportsArray[dtype]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]) → tuple

Convert affine matrix back into stage positions.

Ignore theta, focus for now.

Parameters:: mat (npt.ArrayLike) – An affine matrix.
Returns:: A tuple of stage positions.
Return type:: tuple

bdv_rotate_transform()

Calculate the BDV rotation transform matrix.

BDV-specific. Matrix provided is not (4,4), but (3,4).

bdv_shear_transform()

Calculate the shear transform matrix.

BDV-specific. Matrix provided is not (4,4), but (3,4).

bdv_xml_dict(file_name: Optional[Union[str, list]], views: list, **kw) → dict

Create a BigDataViewer XML dictionary from a list of views.

Parameters:

file_name (str) – The file name of the file to be written.
views (list) – A list of dictionaries containing metadata for each view.
**kw – Additional keyword arguments.

Returns:

A dictionary containing the XML metadata.

Return type:

dict

get_affine_parameters(configuration)

Get the affine transform parameters from the configuration file.

Parameters:: configuration (dict) – Configuration dictionary.

parse_xml(root: Union[str, Element]) → tuple

Parse a BigDataViewer XML file into our metadata format.

Parameters:: root (Union[str, ET.Element]) – The root of the XML tree.
Returns:: A tuple containing the file path, setups, and transforms.
Return type:: tuple

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

stage_positions_to_affine_matrix(x: float, y: float, z: float, theta: float, f: Optional[float] = None) → Union[_SupportsArray[dtype], _NestedSequence[_SupportsArray[dtype]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]

Convert stage positions to an affine matrix.

Ignore theta, focus for now.

Parameters:

x (float) – The x position of the stage.
y (float) – The y position of the stage.
z (float) – The z position of the stage.
theta (float) – The theta position of the stage.
f (Optional[float]) – The focus position of the stage, by default None

Returns:

An affine matrix.

Return type:

npt.ArrayLike

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, views: list) → None

Write BigDataViewer XML metadata.

Parameters:

file_name (str) – The file name of the file to be written.
views (list) – A list of dictionaries containing metadata for each view.

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

rotate_angle_x

Angle in degrees to rotate the data in X.

Type:: float

rotate_angle_y

Angle in degrees to rotate the data in Y.

Type:: float

rotate_angle_z

Angle in degrees to rotate the data in Z.

Type:: float

rotate_data

Rotate the data.

Type:: bool

rotate_transform

Rotation transform matrix.

Type:: npt.NDArray

property shape: tuple

Return shape as XYCZT.

Returns:: Shape as XYCZT
Return type:: tuple

shape_c