Module: micpy.geo¶
The micpy.geo modules provides methods to read and write geometry files.
GeometryFileError ¶
Bases: Exception
Base exception for geometry file errors.
GeometryFileNotFoundError ¶
Bases: GeometryFileError
Raised when a geometry file is not found.
MultipleGeometryFilesError ¶
Bases: GeometryFileError
Raised when multiple potential geometry files are found.
Type ¶
Bases: Enum
Data type of geometry file.
build(filename, shape, spacing) ¶
Create a basic geometry.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
filename | str | Filename of a binary file. | required |
shape | tuple | Shape of the geometry (z, y, x). | required |
spacing | tuple | Spacing of the geometry (dz, dy, dx) in μm. | required |
find(filename) ¶
Find the geometry file for a given binary file.
This method assumes that (a) both files share a common basename and (b) the file extension of the geometry file starts with either .geoF or _geoF.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
filename | str | Filename of a binary file. | required |
Returns:
| Type | Description |
|---|---|
Path | Path to the geometry file. |
read(filename, type=Type.EXTENDED, compressed=True) ¶
Read a geometry file.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
filename | str | Filename of a geometry file. | required |
type | Type | Data type to be read. Defaults to | EXTENDED |
compressed | bool | True if file is compressed, False otherwise. Defaults to | True |
Returns:
| Type | Description |
|---|---|
dict | Dictionary representation of the geometry file. |
read_ndarray(filename, type=Type.EXTENDED, compressed=True) ¶
Read a geometry file.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
filename | str | Filename of a geometry file. | required |
type | Type | Data type to be read. Defaults to | EXTENDED |
compressed | bool |
| True |
Returns:
| Type | Description |
|---|---|
ndarray | NumPy array representation of the geometry file. |
write(filename, data, type=Type.EXTENDED, compressed=True) ¶
Write a geometry file.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
filename | str | Filename of a geometry file. | required |
data | dict | Dictionary representation of a geometry file. | required |
type | Type | Data type to be written. Defaults to | EXTENDED |
compressed | bool |
| True |
write_ndarray(filename, data, compressed=True) ¶
Write a geometry file.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
filename | str | Filename of a geometry file. | required |
data | ndarray | NumPy array representation of a geometry file. | required |
compressed | bool |
| True |