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# The SelectFiles Interfaces

Nipype 0.9 introduces a new interface for intelligently finding files on the disk and feeding them into your workflows: SelectFiles. SelectFiles is intended as a simpler alternative to the DataGrabber interface that was discussed previously in DataGrabber and DataSink explained.

SelectFiles is built on Python format strings, which are similar to the Python string interpolation feature you are likely already familiar with, but advantageous in several respects. Format strings allow you to replace named sections of template strings set off by curly braces ({}), possibly filtered through a set of functions that control how the values are rendered into the string. As a very basic example, we could write

    msg = "This workflow uses {package}"

and then format it with keyword arguments:

    print msg.format(package="FSL")

SelectFiles only requires that you provide templates that can be used to find your data; the actual formatting happens behind the scenes.

Consider a basic example in which you want to select a T1 image and multple functional images for a number of subjects. Invoking SelectFiles in this case is quite straightforward:

    from nipype import SelectFiles
    templates = dict(T1="data/{subject_id}/struct/T1.nii",
                     epi="data/{subject_id}/func/epi_run*.nii")
    sf = SelectFiles(templates)

SelectFiles will take the templates dictionary and parse it to determine its own inputs and oututs. Specifically, each name used in the format spec (here just subject_id) will become an interface input, and each key in the dictionary (here T1 and epi) will become interface outputs. The templates dictionary thus succinctly links the node inputs to the appropriate outputs. You’ll also note that, as was the case with DataGrabber, you can use basic glob syntax to match multiple files for a given output field. Additionally, any of the conversions outlined in the Python documentation for format strings can be used in the templates.

There are a few other options that help make SelectFiles flexible enough to deal with any situation where you need to collect data. Like DataGrabber, SelectFiles has a base_directory parameter that allows you to specify a path that is common to all of the values in the templates dictionary. Additionally, as glob does not return a sorted list, there is also a sort_filelist option, taking a boolean, to control whether sorting should be applied (it is True by default).

The final input is force_lists, which controls how SelectFiles behaves in cases where only a single file matches the template. The default behavior is that when a template matches multiple files they are returned as a list, while a single file is returned as a string. There may be situations where you want to force the outputs to always be returned as a list (for example, you are writing a workflow that expects to operate on several runs of data, but some of your subjects only have a single run). In this case, force_lists can be used to tune the outputs of the interface. You can either use a boolean value, which will be applied to every output the interface has, or you can provide a list of the output fields that should be coerced to a list. Returning to our basic example, you may want to ensure that the epi files are returned as a list, but you only ever will have a single T1 file. In this case, you would do

    sf = SelectFiles(templates, force_lists=["epi"])