Inheritance diagram for nipype.caching.memory:
Using nipype with persistence and lazy recomputation but without explicit name-steps pipeline: getting back scope in command-line based programming.
Change directory to provide relative paths for doctests >>> import os >>> filepath = os.path.dirname( os.path.realpath( __file__ ) ) >>> datadir = os.path.realpath(os.path.join(filepath, ‘../testing/data’)) >>> os.chdir(datadir)
Bases: object
Memory context to provide caching for interfaces
Parameters: | base_dir: string :
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Methods
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: a PipeFunc callable object : An object that can be used as a function to apply the interface to arguments. |
clear_previous_runs([warn]) | Remove all the cache that where not used in the latest run of the memory object: i.e. |
clear_previous_runs([warn]) | Remove all the cache that where not used in the latest run of the memory object: i.e. |
Returns a callable that caches the output of an interface
Parameters: | interface: nipype interface :
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Returns: | pipe_func: a PipeFunc callable object :
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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')
We can retrieve the resulting file from the outputs: >>> results.outputs.merged_file # doctest: +SKIP ‘...’
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 :
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Remove all the cache that where not used since the given date
Parameters: | day, month, year: integers, optional :
warn: boolean, optional :
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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')
Methods
__call__(**kwargs) |
Parameters: | interface: a nipype interface class :
base_dir: a string :
callback: a callable :
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Remove all the sub-directories of base_dir, but those listed
Parameters: | base_dir: string :
dirs_to_keep: set :
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