Shell and process utilities

library.utilities.utilities_process.convert(img, target_type_min, target_type_max, target_type)

Converts an image from one type to another and also resizes

Parameters:

• img – numpy array

• target_type_min – min size

• target_type_max – max size

• target_type – dtype of array

Returns:

library.utilities.utilities_process.convert_size(size_bytes: int) → str

Function takes unformatted bytes, calculates human-readable format [with units] and returns string

Parameters:

size_bytes (int) –

Returns:

str:

library.utilities.utilities_process.create_downsample(file_key)

takes a big tif and scales it down to a manageable size. This method is used in PrepCreator For 16bit images, this is a good number near the high end.

library.utilities.utilities_process.get_cpus()

Helper method to return the number of CPUs to use

library.utilities.utilities_process.get_hostname() → str

Returns hostname of server where code is processed

Returns:

string of the current workstation

library.utilities.utilities_process.get_image_size(filepath: str)

Returns width, height of single image

Parameters:

filepath – path of input file

Returns:

tuple of int width and height of the file

library.utilities.utilities_process.read_image(file_path: str)

Reads an image from the filesystem with exceptions

library.utilities.utilities_process.test_dir(animal: str, directory, section_count, downsample: bool = True, same_size: bool = False) → int

Verify image stack directory for section count and max width, height

Parameters:

• animal – string of animal name.

• directory – directory we are testing.

• section_count – integer how many sections are in the stack

• downsample – boolean on whether to downsample or not

• same_size – boolean on whether all files are same size

Returns:

string of error messages

library.utilities.utilities_process.write_image(file_path, data, message: str = 'Error') → None

Writes an image to the filesystem