Module: `micpy.bin`¶

The micpy.bin module provides methods to read and write binary files.

`Chunk` `dataclass` ¶

A chunk of uncompressed binary data.

`iterate(file, chunk_size, compressed=True, offset=0, decompressobj=None)` `staticmethod` ¶

Yield chunks of uncompressed binary data.

`Field` ¶

Bases: ndarray

A field.

`dimensions(shape)` `staticmethod` ¶

Get the number of dimensions of a shape.

`from_bytes(data, shape=None, spacing=None)` `staticmethod` ¶

Create a new time step from bytes.

`read(position, shape=None, spacing=None)` `staticmethod` ¶

Read a field from a binary file.

`to_bytes()` ¶

Convert the field to bytes.

`to_file(file, geometry=True)` ¶

Write the field to a binary file.

Parameters:

Name	Type	Description	Default
`file`	`IO[bytes]`	Binary file.	required
`geometry`	`bool`	`True` if geometry should be written, `False` otherwise. Defaults to `True`.	`True`

`write(filename, compressed=True, geometry=True)` ¶

Write the field to a binary file.

Parameters:

Name	Type	Description	Default
`filename`	`str`	Filename of the binary file.	required
`compressed`	`bool`	`True` if file should be compressed, `False` otherwise. Defaults to `True`.	`True`
`geometry`	`bool`	`True` if geometry should be written, `False` otherwise. Defaults to `True`.	`True`

`File` ¶

A binary file.

`init(filename, chunk_size=Chunk.DEFAULT_SIZE, verbose=True)` ¶

Initialize a binary file.

Parameters:

Name	Type	Description	Default
`filename`	`str`	File name.	required
`chunk_size`	`int`	Chunk size in bytes. Defaults to `8388608` (8 MiB).	`DEFAULT_SIZE`
`verbose`	`bool`	Verbose output. Defaults to `True`.	`True`

Raises:

Type	Description
`FileNotFoundError`	If file is not found.

`close()` ¶

Close the file.

`create_index()` ¶

Create an index of the file.

`find_geometry(compressed=None)` ¶

Find geometry file and read it.

Parameters:

Name	Type	Description	Default
`compressed`	`bool`	True if file is compressed, False otherwise. Defaults to `None` (auto).	`None`

Raises:

Type	Description
`GeometryFileNotFoundError`	If no geometry file is found.
`MultipleGeometryFilesError`	If multiple geometry files are found.

`index()` ¶

Get the index of the file.

`iterate()` ¶

Iterate over fields in the file.

Returns:

Type	Description
`Generator[Field, None, None]`	A generator of fields.

`open()` ¶

Open the file.

`print_geometry()` ¶

Get a string representation of the geometry.

`read(key=None)` ¶

Read a series of fields from the file.

Parameters:

Name	Type	Description	Default
`key`	`Union[int, slice, list, Callable[[Field], bool]]`	Key to list of	`None`

Returns:

Type	Description
`Series`	Series of fields.

`read_field(field_id)` ¶

Read a field from the file.

Parameters:

Name	Type	Description	Default
`field_id`	`int`	Field ID.	required

Returns:

Type	Description
`Field`	Field.

`read_geometry(filename, compressed=None)` ¶

Read geometry from a file.

Parameters:

Name	Type	Description	Default
`filename`	`str`	Filename of a geometry file.	required
`compressed`	`bool`	`True` if file is compressed, `False` otherwise. Defaults to `None` (auto).	`None`

`set_geometry(shape, spacing)` ¶

Set the geometry.

Parameters:

Name	Type	Description	Default
`shape`	`Tuple[int, int, int]`	Shape of the geometry (z, y, x).	required
`spacing`	`Tuple[float, float, float]`	Spacing of the geometry (dz, dy, dx) in μm.	required

`times()` ¶

Get the times of the fields in the file.

Returns:

Type	Description
`List[float]`	List of times.

`update_index()` ¶

Update the index of the file.

`Footer` ¶

A field footer.

`to_bytes()` ¶

Convert the footer to bytes.

`Header` ¶

A field header.

`from_bytes(data)` `staticmethod` ¶

Create a new header from bytes.

`read(filename, compressed=True)` `staticmethod` ¶

Read the header of a binary file.

`to_bytes()` ¶

Convert the header to bytes.

`Index` ¶

Bases: List[Position]

An index of fields in a binary file.

`from_file(file, verbose=True, chunk_size=Chunk.DEFAULT_SIZE, compressed=True, position=None)` `staticmethod` ¶

Build an index from a binary file.

`from_filename(filename, verbose=True, chunk_size=Chunk.DEFAULT_SIZE, compressed=True)` `staticmethod` ¶

Build an index from a binary file.

`PlotArgs` `dataclass` ¶

Arguments for plotting a field.

Parameters:

Name	Type	Description	Default
`title`	`str`	Title of the plot. Defaults to `None`.	`None`
`xlabel`	`str`	Label of the x-axis. Defaults to `None`.	`None`
`ylabel`	`str`	Label of the y-axis. Defaults to `None`.	`None`
`figsize`	`Tuple[float, float]`	Figure size. Defaults to `None`.	`None`
`dpi`	`int`	Figure DPI. Defaults to `None`.	`None`
`aspect`	`str`	Aspect ratio. Defaults to `equal`.	`'equal'`
`ax`	`Axes`	Axes of the plot. Defaults to `None`.	`None`
`cax`	`Axes`	Axes of the color bar. Defaults to `None`.	`None`
`vmin`	`float`	Minimum value of the color bar. Defaults to `None`.	`None`
`vmax`	`float`	Maximum value of the color bar. Defaults to `None`.	`None`
`cmap`	`str`	Colormap. Defaults to `micpy`.	`'micpy'`
`alpha`	`float`	Transparency of the plot. Defaults to `1.0`.	`1.0`
`interpolation`	`str`	Interpolation method. Defaults to `none`.	`'none'`
`extent`	`Tuple[float, float, float, float]`	Extent of the plot.	`None`

`Position` `dataclass` ¶

A field position in a binary file.

`iterate(file=None, compressed=True, chunk_size=Chunk.DEFAULT_SIZE, position=None)` `staticmethod` ¶

Yield positions of fields in a binary file.

`Series` ¶

Bases: ndarray

`get_field(index)` ¶

Get a field from the series.

Parameters:

Name	Type	Description	Default
`index`	`int`	Index of the field.	required

Returns:

Type	Description
`Field`	Field.

`get_series(key)` ¶

Get a series of fields.

Parameters:

Name	Type	Description	Default
`key`	`Union[int, slice, list]`	Key to list of field IDs, a slice object, or a list of field IDs.	required

Returns:

Type	Description
`Series`	Series of fields.

`iter_field()` ¶

Iterate over fields in the series.

Yields:

Type	Description
	Field.

`write(filename, compressed=True, geometry=True)` ¶

Write the series to a binary file.

Parameters:

Name	Type	Description	Default
`filename`	`str`	Filename of the binary file.	required
`compressed`	`bool`	`True` if file should be compressed, `False` otherwise. Defaults to `True`.	`True`
`geometry`	`bool`	`True` if geometry should be written, `False` otherwise. Defaults to `True`.	`True`

`plot(field, axis='y', index=0, args=None)` ¶

Plot a slice of the field.

Parameters:

Name	Type	Description	Default
`field`	`Field`	Field to plot.	required
`axis`	`str`	Axis to plot. Possible values are `x`, `y`, and `z`. Defaults to `y`.	`'y'`
`index`	`int`	Index of the slice. Defaults to `0`.	`0`
`args`	`PlotArgs`	Arguments for plotting. Defaults to `None`.	`None`

Returns:

Type	Description
`Tuple[Figure, Axes]`	Matplotlib figure, axes, and color bar.

Module: micpy.bin¶

Chunk dataclass ¶

iterate(file, chunk_size, compressed=True, offset=0, decompressobj=None) staticmethod ¶

Field ¶

dimensions(shape) staticmethod ¶

from_bytes(data, shape=None, spacing=None) staticmethod ¶

read(position, shape=None, spacing=None) staticmethod ¶

to_bytes() ¶

to_file(file, geometry=True) ¶

write(filename, compressed=True, geometry=True) ¶

File ¶

__init__(filename, chunk_size=Chunk.DEFAULT_SIZE, verbose=True) ¶

close() ¶

create_index() ¶

find_geometry(compressed=None) ¶

index() ¶

iterate() ¶

open() ¶

print_geometry() ¶

read(key=None) ¶

read_field(field_id) ¶

read_geometry(filename, compressed=None) ¶

set_geometry(shape, spacing) ¶

times() ¶

update_index() ¶

Footer ¶

to_bytes() ¶

Header ¶

from_bytes(data) staticmethod ¶

read(filename, compressed=True) staticmethod ¶

to_bytes() ¶

Index ¶

from_file(file, verbose=True, chunk_size=Chunk.DEFAULT_SIZE, compressed=True, position=None) staticmethod ¶

from_filename(filename, verbose=True, chunk_size=Chunk.DEFAULT_SIZE, compressed=True) staticmethod ¶

PlotArgs dataclass ¶

Position dataclass ¶

iterate(file=None, compressed=True, chunk_size=Chunk.DEFAULT_SIZE, position=None) staticmethod ¶

Series ¶

get_field(index) ¶

get_series(key) ¶

iter_field() ¶

write(filename, compressed=True, geometry=True) ¶

plot(field, axis='y', index=0, args=None) ¶

Module: `micpy.bin`¶

`Chunk` `dataclass` ¶

`iterate(file, chunk_size, compressed=True, offset=0, decompressobj=None)` `staticmethod` ¶

`Field` ¶

`dimensions(shape)` `staticmethod` ¶

`from_bytes(data, shape=None, spacing=None)` `staticmethod` ¶

`read(position, shape=None, spacing=None)` `staticmethod` ¶

`to_bytes()` ¶

`to_file(file, geometry=True)` ¶

`write(filename, compressed=True, geometry=True)` ¶

`File` ¶

`init(filename, chunk_size=Chunk.DEFAULT_SIZE, verbose=True)` ¶

`close()` ¶

`create_index()` ¶

`find_geometry(compressed=None)` ¶

`index()` ¶

`iterate()` ¶

`open()` ¶

`print_geometry()` ¶

`read(key=None)` ¶

`read_field(field_id)` ¶

`read_geometry(filename, compressed=None)` ¶

`set_geometry(shape, spacing)` ¶

`times()` ¶

`update_index()` ¶

`Footer` ¶

`to_bytes()` ¶

`Header` ¶

`from_bytes(data)` `staticmethod` ¶

`read(filename, compressed=True)` `staticmethod` ¶

`to_bytes()` ¶

`Index` ¶

`from_file(file, verbose=True, chunk_size=Chunk.DEFAULT_SIZE, compressed=True, position=None)` `staticmethod` ¶

`from_filename(filename, verbose=True, chunk_size=Chunk.DEFAULT_SIZE, compressed=True)` `staticmethod` ¶

`PlotArgs` `dataclass` ¶

`Position` `dataclass` ¶

`iterate(file=None, compressed=True, chunk_size=Chunk.DEFAULT_SIZE, position=None)` `staticmethod` ¶

`Series` ¶

`get_field(index)` ¶

`get_series(key)` ¶

`iter_field()` ¶

`write(filename, compressed=True, geometry=True)` ¶

`plot(field, axis='y', index=0, args=None)` ¶