nipype.caching.memory module

Using nipype with persistence and lazy recomputation but without explicit name-steps pipeline: getting back scope in command-line based programming.

class nipype.caching.memory.Memory(base_dir)

Bases: object

Memory context to provide caching for interfaces

Parameters:base_dir (string) – The directory name of the location for the caching

cache()

Creates a cacheable function from an nipype Interface class

clear_previous_runs()

Removes from the disk all the runs that where not used after the creation time of the specific Memory instance

clear_previous_runs()

Removes from the disk all the runs that where not used after the given time

cache(interface)

Returns a callable that caches the output of an interface

Parameters:interface (nipype interface) – The nipype interface class to be wrapped and cached Returns:pipe_func – An object that can be used as a function to apply the interface to arguments. Inputs of the interface are given as keyword arguments, bearing the same name as the name in the inputs specs of the interface. Return type:a PipeFunc callable object

Examples

>>> from tempfile import mkdtemp
>>> mem = Memory(mkdtemp())
>>> from nipype.interfaces import fsl

Here we create a callable that can be used to apply an fsl.Merge interface to files

>>> fsl_merge = mem.cache(fsl.Merge)

Now we apply it to a list of files. We need to specify the list of input files and the dimension along which the files should be merged.

>>> results = fsl_merge(in_files=['a.nii', 'b.nii'],
...                     dimension='t') # doctest: +SKIP

We can retrieve the resulting file from the outputs: >>> results.outputs.merged_file # doctest: +SKIP ‘…’

clear_previous_runs(warn=True)

Remove all the cache that where not used in the latest run of the memory object: i.e. since the corresponding Python object was created.

Parameters:warn (boolean, optional) – If true, echoes warning messages for all directory removed

clear_runs_since(day=None, month=None, year=None, warn=True)

Remove all the cache that where not used since the given date

Parameters:

• month, year (day,) – The integers specifying the latest day (in localtime) that a node should have been accessed to be kept. If not given, the current date is used.
• warn (boolean, optional) – If true, echoes warning messages for all directory removed

class nipype.caching.memory.PipeFunc(interface, base_dir, callback=None)

Bases: object

Callable interface to nipype.interface objects

Use this to wrap nipype.interface object and call them specifying their input with keyword arguments:

fsl_merge = PipeFunc(fsl.Merge, base_dir='.')
out = fsl_merge(in_files=files, dimension='t')

nipype.caching.memory.read_log(filename, run_dict=None)

nipype.caching.memory.rm_all_but(base_dir, dirs_to_keep, warn=False)

Remove all the sub-directories of base_dir, but those listed

Parameters:

• base_dir (string) – The base directory
• dirs_to_keep (set) – The names of the directories to keep