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 across 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(ws_type=None, directory=None, prefix=None, postfix=None, debug=None, file_type_to_name=None, file_type_synonyms=None, file_type_to_directory_type=None, directory_type_to_name=None, **kwargs)[source]#

Bases: object

Class to organize files.

all_tiles_exist(f_type, file_type_to_name=None, directory=None, expression=None, values=None, prefix=None, extension=None, debug=None, **kwargs)[source]#

create(f_type=None, dtype=None, shape=None, order=None, **kwargs)[source]#

create_debug(f_type, slicing, debug=None, **kwargs)[source]#

directory_name(f_type=None, dirtype=None, ws_type=None, directory=None, default_directory=None, file_type_to_directory_type=None, directory_type_to_name=None, file_type_synonyms=None, return_f_type=False, return_dirtype=False)[source]#

directory_type(f_type=None, ws_type=None, file_type_to_directory_type=None, file_type_synonyms=None, return_f_type=False)[source]#

exists(f_type, file_type_to_name=None, directory=None, expression=None, values=None, prefix=None, extension=None, debug=None, **kwargs)[source]#

expression(*args, **kwargs)[source]#

extension(*args, **kwargs)[source]#

file_list(*args, **kwargs)[source]#

file_name(f_type=None, dirtype=None, ws_type=None, directory=None, expression=None, values=None, prefix=None, postfix=None, extension=None, debug=None, file_type_to_name=None, file_type_synonyms=None, file_type_to_directory_type=None, directory_type_to_name=None, **kwargs)[source]#

filename(*args, **kwargs)[source]#

get_positions(f_type)[source]#

info(tile_axes=None, check_extensions=True, check_directory=True)[source]#

load(file_path)[source]#: Loads the workspace configuration from disk

mosaic_shape(f_type)[source]#

plot(f_type, **kwargs)[source]#

read(*args, **kwargs)[source]#

save(file_path)[source]#: Saves the workspace configuration to disk

source(*args, **kwargs)[source]#

update(*args, **kwargs)[source]#

write(*args, **kwargs)[source]#

property debug#

property directory#

property directory_type_to_name#

property file_type_synonyms#

property file_type_to_directory_type#

property wstype#

directory_name(f_type=None, dirtype=None, ws_type=None, directory=None, default_directory=None, file_type_to_directory_type=None, directory_type_to_name=None, file_type_synonyms=None, return_f_type=False, return_dirtype=False)[source]#

Returns the directory name to use for a file in the work space.

Arguments

f_typestr or None: The type of the file for which the file name is requested. If None, use the
dirtypestr or None: The directory type, overwrites the directory type inferred from the file type if not None.
ws_typestr or None: The type of workspace to use. If None, use the default workspace.
directorystr or None: A specific directory to use.
default_directorystr or None: A default directory to fall back to if not None.
file_type_to_directory_typedict or None: The file type to determine the directory type for. If None, the default is used.
directory_type_to_namedict or None: The mapping between th directory type and the actual directory.
file_type_synonymsdict or None: Additional file type synonyms or abbreviation to use for the file types.
return_f_typebool: If True return also the file type
return_dirtypebool: If True return also the directory type.

Returns

directorystr: The standard directory name of the requested file type.

directory_type(f_type=None, ws_type=None, file_type_to_directory_type=None, file_type_synonyms=None, return_f_type=False)[source]#

file_name(f_type, dirtype=None, ws_type=None, directory=None, default_directory=None, expression=None, values=None, prefix=None, postfix=None, extension=None, debug=None, file_type_to_name=None, file_type_synonyms=None, file_type_to_directory_type=None, directory_type_to_name=None, **kwargs)[source]#

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

Arguments

f_typestr or None: The type of the file for which the file name is requested.
dirtypestr or None: The directory type to use for the requested file name.
ws_typestr or None: The type of workspace to use. If None, use the default workspace.
directorystr or None: A specific directory for the file.
default_directorystr or None: A default directory to fall back to if not None.
expressionstr or None: A tag expression to use if f_type is ‘expression’.
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 testing in which the string is added as postfix. If True, ‘debug’ is added.
file_type_to_namedict or None: The file types to name mappings. If None, the default is used.
file_type_synonymsdict or None: Additional file type synonyms or abbreviation to use for the file types.
file_type_to_directory_typedict or None: The file type to determine the directory type for. If None, the default is used.
directory_type_to_namedict or None: The mapping between th directory type and the actual directory.

Returns

filenamestr: The file name of the requested file specifications.

file_type(f_type=None, ws_type=None, file_type_synonyms=None)[source]#