Workspace

The Workspace module keeps track of the data files of a project. Using this module will simplify access to data and results using coherent filenames accross experiments and samples.

One can think of a Workspace as a transparent data structure for ClearMap.

Note

Additional standard filenames can be added in the ftype_to_filename dict.

class Workspace(wtype=None, prefix=None, file_type_to_name=None, directory=None, debug=None, **kwargs)

Bases: object

Class to organize files.

create(ftype, dtype=None, shape=None, order=None, file_type_to_name=None, directory=None, expression=None, values=None, prefix=None, extension=None, debug=None, **kwargs)

create_debug(ftype, slicing, debug=None, **kwargs)

expression(*args, **kwargs)

extension(ftype, file_type_to_name=None, directory=None, expression=None, values=None, prefix=None, extension=None, debug=None, **kwargs)

file_list(ftype, file_type_to_name=None, directory=None, expression=None, values=None, prefix=None, extension=None, debug=None, **kwargs)

filename(ftype, file_type_to_name=None, directory=None, expression=None, values=None, prefix=None, extension=None, debug=None, **kwargs)

info(tile_axes=None, check_extensions=True)

load(filename)

Loads the configuration from disk

plot(ftype, **kwargs)

read(*args, **kwargs)

save(filename)

Saves the configuration to disk

source(*args, **kwargs)

update(*args, **kwargs)

property debug

property directory

property file_type_to_name

property prefix

property wtype

filename(ftype, file_type_to_name=None, directory=None, expression=None, values=None, prefix=None, postfix=None, extension=None, debug=None)

Returns the standard file name to use for a result file.

Arguments

ftypestr

The type of the file for which the file name is requested.

directorystr

The working directory of the project.

expressionstr or None

The tag expression to use if ftype is ‘expression’.

file_type_to_namedict

The file types to name mappings. If None, the default is used.

valuesdict or None

The values to use in case a tag expression is given.

prefixstr or None

Optional prefix to the file if not None.

postfixstr or list of str or None

Optional postfix to the file if not None.

extensionstr or None

Optional extension to replace existing one.

debugstr, bool or None

Optional string for debug files in wihch the string is added as postfix. If True, ‘debug’ is added.

Returns

filenamestr

The standard file name of the requested file type.