navigate.model.data_sources.data_source.DataSource

class navigate.model.data_sources.data_source.DataSource(file_name: Optional[str] = None, mode: str = 'w')

Bases: object

__init__(file_name: Optional[str] = None, mode: str = 'w') → None

Base class for data sources, which can be of arbitrary file type.

This implements read and write methods for accessing each data source. We expect to open the file for read or write during initialization.

file_name stores the name of the file to read/write from data stores a pointer to the actual data in the data source and metadata stores a pointer to the metadata.

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

Parameters:

• file_name (str) – Name of the file to read/write from.

• mode (str) – Mode to open the file in. Can be ‘r’ or ‘w’.

Methods

__init__([file_name, mode])	Base class for data sources, which can be of arbitrary file type.
close()	Clean up any leftover file pointers, etc.
get_data([timepoint, position, channel, z, ...])	Get data according to timepoint, position, channel and z-axis id
get_shape_from_metadata()	Get the shape of the data source from the metadata.
read()	Read data from file.
set_metadata(metadata_config)	Sets the metadata
set_metadata_from_configuration_experiment(...)	Sets the metadata from according to the microscope configuration.
setup()	Additional steps for establishing the initial file setup.
write(data, **kw)	Writes 2D image to the data source.

Attributes

data	Return array representation of data stored in data source.
mode	Getter for the mode of the data source.
nbytes	Getter for the size of this data source in bytes.
shape	Getter for the shape as XYCZT.
voxel_size	Getter for the voxel size
logger	Logger for this class.
file_name	Name of the file to read/write from.
metadata	Pointer to the metadata.
bits	Number of bits per pixel.
dx	Pixel size in x dimension (microns).
dy	Pixel size in x dimension (microns).
dz	Pixel size in x dimension (microns).
dt	The time interval between frames (seconds).
dc	Step size between channels (always 1)
shape_x	Size of the data source in x dimension.
shape_y	Size of the data source in y dimension.
shape_z	Size of the data source in z dimension.
shape_t	Size of the data source in t dimension.
shape_c	Size of the data source in c dimension.
positions	Number of positions in the data source.

close() → None

Clean up any leftover file pointers, etc.

get_data(timepoint: int = 0, position: int = 0, channel: int = 0, z: int = -1, resolution: int = 1) → Union[_SupportsArray[dtype], _NestedSequence[_SupportsArray[dtype]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]

Get data according to timepoint, position, channel and z-axis id

Parameters:

• timepoint (int) – The timepoint value

• position (int) – The position id in multi-position table

• channel (int) – The channel id

• z (int) – The index of Z in a Z-stack. Return all z if -1.

• resolution (int) – values from 1, 2, 4, 8

Returns:

data – Image data

Return type:

npt.ArrayLike

Raises:

NotImplementedError – If not implemented in a derived class.

get_shape_from_metadata()

Get the shape of the data source from the metadata.

read() → None

Read data from file.

Raises:

NotImplementedError – If not implemented in a derived class.

set_metadata(metadata_config: dict) → None

Sets the metadata

Parameters:

metadata_config (dict) – shape configuration: “c”, “z”, “t”, “p”, “is_dynamic”, “per_stack”

set_metadata_from_configuration_experiment(configuration: Dict[str, Any], microscope_name: Optional[str] = None) → None

Sets the metadata from according to the microscope configuration.

Parameters:

• configuration (Dict[str, Any]) – Configuration experiment.

• microscope_name (str) – The microscope name

setup()

Additional steps for establishing the initial file setup.

write(data: Union[_SupportsArray[dtype], _NestedSequence[_SupportsArray[dtype]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]], **kw) → None

Writes 2D image to the data source.

Parameters:

• data (npt.ArrayLike) – Data to write to file.

• **kw (dict) – Additional keyword arguments.

Raises:

NotImplementedError – If not implemented in a derived class.

bits

Number of bits per pixel.

Type:

int

property data: Union[_SupportsArray[dtype], _NestedSequence[_SupportsArray[dtype]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]

Return array representation of data stored in data source.

Returns:

Array representation of data stored in data source.

Return type:

npt.ArrayLike

Raises:

NotImplementedError – If not implemented in a derived class.

dc

Step size between channels (always 1)

Type:

float

dt

The time interval between frames (seconds).

Type:

float

dx

Pixel size in x dimension (microns). float: Pixel size in y dimension (microns). float: Pixel size in z dimension (microns).

Type:

float

dy

Pixel size in x dimension (microns). float: Pixel size in y dimension (microns). float: Pixel size in z dimension (microns).

Type:

float

dz

Pixel size in x dimension (microns). float: Pixel size in y dimension (microns). float: Pixel size in z dimension (microns).

Type:

float

file_name

Name of the file to read/write from.

Type:

str

logger

Logger for this class.

Type:

logging.Logger

metadata

Pointer to the metadata.

Type:

npt.ArrayLike

property mode: str

Getter for the mode of the data source.

Returns:

Mode of the data source.

Return type:

str

property nbytes: int

Getter for the size of this data source in bytes.

Does not account for pyramidal data sources. That process is handled by the bdv_data_source class, which is a child of this class.

Returns:

total_bytes – Size of this data source in bytes.

Return type:

int

positions

Number of positions in the data source.

Type:

int

property shape: tuple

Getter for the shape as XYCZT.

Returns:

Shape of the data source in XYCZT format.

Return type:

tuple

shape_c

Size of the data source in c dimension.

Type:

int

shape_t

Size of the data source in t dimension.

Type:

int

shape_x

Size of the data source in x dimension.

Type:

int

shape_y

Size of the data source in y dimension.

Type:

int

shape_z

Size of the data source in z dimension.

Type:

int

property voxel_size: tuple

Getter for the voxel size

Returns:

Voxel size in x, y, z dimensions.

Return type:

tuple