Interface Specifications¶

Before you start¶

Nipype is maintained by an enthusiastic group of developers, and we’re excited to have you join us! In case of trouble, we encourage you to post on NeuroStars with the nipype tag. NeuroStars.org is a platform similar to StackOverflow but dedicated to neuroinformatics. You can also post on the nipype developers mailing list: http://mail.python.org/mailman/listinfo/neuroimaging. As we are sharing a mailing list with the nipy community, please add [nipype] to the message title. Alternatively, you’re welcome to chat with us in the Nipype Gitter channel or in the BrainHack Slack channel. (Click here to join the Slack workspace.)

Overview¶

We’re using the Traits (formerly known as Enthought Traits) package for all of our inputs and outputs. Traits allows us to validate user inputs and provides a mechanism to handle all the special cases in a simple and concise way though metadata. With the metadata, each input/output can have an optional set of metadata attributes (described in more detail below). The machinery for handling the metadata is located in the base classes, so all subclasses use the same code to handle these cases. This is in contrast to our previous code where every class defined it’s own _parse_inputs, run and aggregate_outputs methods to handle these cases. Which of course leads to a dozen different ways to solve the same problem.

Traits is a big package with a lot to learn in order to take full advantage of. But don’t be intimidated! To write a Nipype Trait Specification, you only need to learn a few of the basics of Traits. Here are a few starting points in the documentation:

• What are Traits? The Introduction in the User Manual gives a brief description of the functionality traits provides.

• Traits and metadata. The second section of the User Manual gives more details on traits and how to use them. Plus there a section describing metadata, including the metadata all traits have.

• If your interested in more of a big picture overview, Gael wrote a good tutorial that shows how to write a scientific application using traits for the benefit of the generated UI components. (For now, Nipype is not taking advantage of the generated UI feature of traits.)

Traits version¶

We’re using Traits version 4.x which can be installed from pypi

More documentation¶

Not everything is documented in the User Manual, in those cases the the API docs is your next place to look.

Nipype Interface Specifications¶

Each interface class defines two specifications: 1) an InputSpec and 2) an OutputSpec. Each of these are prefixed with the class name of the interfaces. For example, Bet has these specs:

• BETInputSpec

• BETOutputSpec

Each of these Specs are classes, derived from a base TraitedSpec class (more on these below). The InputSpec consists of attributes which correspond to different parameters for the tool they wrap/interface. In the case of a command-line tool like Bet, the InputSpec attributes correspond to the different command-line parameters that can be passed to Bet. When an interfaces class is instantiated, the InputSpec is bound to the inputs attribute of that object. Below is an example of how the inputs appear to a user for Bet:

>>> from nipype.interfaces import fsl
>>> bet = fsl.BET()
>>> type(bet.inputs)
<class 'nipype.interfaces.fsl.preprocess.BETInputSpec'>
>>> bet.inputs.<TAB>
bet.inputs.__class__           bet.inputs.center
bet.inputs.__delattr__         bet.inputs.environ
bet.inputs.__doc__             bet.inputs.frac
bet.inputs.__getattribute__    bet.inputs.functional
bet.inputs.__hash__            bet.inputs.hashval
bet.inputs.__init__            bet.inputs.infile
bet.inputs.__new__             bet.inputs.items
bet.inputs.__reduce_ex__       bet.inputs.mesh
bet.inputs.__repr__            bet.inputs.nooutput
bet.inputs.__setattr__         bet.inputs.outfile
bet.inputs.__str__             bet.inputs.outline
bet.inputs._generate_handlers  bet.inputs.outputtype
bet.inputs._hash_infile        bet.inputs.reduce_bias
bet.inputs._xor_inputs         bet.inputs.skull
bet.inputs._xor_warn           bet.inputs.threshold


Each Spec inherits from a parent Spec. The parent Specs provide attribute(s) that are common to all child classes. For example, FSL InputSpecs inherit from interfaces.fsl.base.FSLTraitedSpec. FSLTraitedSpec defines an outputtype attribute, which stores the file type (NIFTI, NIFTI_PAIR, etc…) for all generated output files.

InputSpec class hierarchy¶

Below is the current class hierarchy for InputSpec classes (from base class down to subclasses).:

TraitedSpec: Nipype’s primary base class for all Specs. Provides initialization, some nipype-specific methods and any trait handlers we define. Inherits from traits.HasTraits.

BaseInterfaceInputSpec: Defines inputs common to all Interfaces (ignore_exception). If in doubt inherit from this.

CommandLineInputSpec: Defines inputs common to all command-line classes (args and environ)

FSLTraitedSpec: Defines inputs common to all FSL classes (outputtype)

SPMCommandInputSpec: Defines inputs common to all SPM classes (matlab_cmd, path, and mfile)

FSTraitedSpec: Defines inputs common to all FreeSurfer classes (sbjects_dir)

MatlabInputSpec: Defines inputs common to all Matlab classes (script, nodesktop, nosplash, logfile, single_comp_thread, mfile, script_file, and paths)

SlicerCommandLineInputSpec: Defines inputs common to all Slicer classes (module)

Most developers will only need to code at the the interface-level (i.e. implementing custom class inheriting from one of the above classes).

Output Specs¶

The OutputSpec defines the outputs that are generated, or possibly generated depending on inputs, by the tool. OutputSpecs inherit from interfaces.base.TraitedSpec directly.

Controlling outputs to terminal¶

It is very likely that the software wrapped within the interface writes to the standard output or the standard error of the terminal. Interfaces provide a means to access and retrieve these outputs, by using the terminal_output attribute:

import nipype.interfaces.fsl as fsl
mybet = fsl.BET(from_file='bet-settings.json')
mybet.terminal_output = 'file_split'


In the example, the terminal_output = 'file_split' will redirect the standard output and the standard error to split files (called stdout.nipype and stderr.nipype respectively). The possible values for terminal_output are:

file

Redirects both standard output and standard error to the same file called output.nipype. Messages from both streams will be overlapped as they arrive to the file.

file_split

Redirects the output streams separately, to stdout.nipype and stderr.nipype respectively, as described in the example.

file_stdout

Only the standard output will be redirected to stdout.nipype and the standard error will be discarded.

file_stderr

Only the standard error will be redirected to stderr.nipype and the standard output will be discarded.

stream

Both output streams are redirected to the current logger printing their messages interleaved and immediately to the terminal.

allatonce

Both output streams will be forwarded to a buffer and stored separately in the runtime object that the run() method returns. No files are written nor streams printed out to terminal.

none

In all cases, except for the 'none' setting of terminal_output, the run() method will return a “runtime” object that will contain the streams in the corresponding properties (runtime.stdout for the standard output, runtime.stderr for the standard error, and runtime.merged for both when streams are mixed, eg. when using the file option).

import nipype.interfaces.fsl as fsl
mybet = fsl.BET(from_file='bet-settings.json')
mybet.terminal_output = 'file_split'
...
result = mybet.run()
result.runtime.stdout
' ... captured standard output ...'


Traited Attributes¶

Each specification attribute is an instance of a Trait class. These classes encapsulate many standard Python types like Float and Int, but with additional behavior like type checking. (See the documentation on traits for more information on these trait types.) To handle unique behaviors of our attributes we us traits metadata. These are keyword arguments supplied in the initialization of the attributes. The base classes BaseInterface and CommandLine (defined in nipype.interfaces.base) check for the existence/or value of these metadata and handle the inputs/outputs accordingly. For example, all mandatory parameters will have the mandatory = True metadata:

class BetInputSpec(FSLTraitedSpec):
infile = File(exists=True,
desc = 'input file to skull strip',
argstr='%s', position=0, mandatory=True)


Common¶

exists

For files, use nipype.interfaces.base.File as the trait type. If the file must exist for the tool to execute, specify exists = True in the initialization of File (as shown in BetInputSpec above). This will trigger the underlying traits code to confirm the file assigned to that input actually exists. If it does not exist, the user will be presented with an error message:

>>> bet.inputs.infile = 'does_not_exist.nii'
------------------------------------------------------------
Traceback (most recent call last):
File "<ipython console>", line 1, in <module>
File "/Users/cburns/local/lib/python2.5/site-packages/nipype/interfaces/base.py", line 76, in validate
self.error( object, name, value )
File "/Users/cburns/local/lib/python2.5/site-packages/enthought/traits/trait_handlers.py", line 175, in error
value )
TraitError: The 'infile' trait of a BetInputSpec instance must be a file
name, but a value of 'does_not_exist.nii' <type 'str'> was specified.

hash_files

To be used with inputs that are defining output filenames. When this flag is set to false any Nipype will not try to hash any files described by this input. This is useful to avoid rerunning when the specified output file already exists and has changed.

desc

All trait objects have a set of default metadata attributes. desc is one of those and is used as a simple, one-line docstring. The desc is printed when users use the help() methods.

Required: This metadata is required by all nipype interface

classes.

usedefault

Set this metadata to True when the default value for the trait type of this attribute is an acceptable value. All trait objects have a default value, traits.Int has a default of 0, traits.Float has a default of 0.0, etc… You can also define a default value when you define the class. For example, in the code below all objects of Foo will have a default value of 12 for x:

>>> import enthought.traits.api as traits
>>> class Foo(traits.HasTraits):
...     x = traits.Int(12)
...     y = traits.Int
...
>>> foo = Foo()
>>> foo.x
12
>>> foo.y
0


Nipype only passes inputs on to the underlying package if they have been defined (more on this later). So if you specify usedefault = True, you are telling the parser to pass the default value on to the underlying package. Let’s look at the InputSpec for SPM Realign:

class RealignInputSpec(BaseInterfaceInputSpec):
jobtype = traits.Enum('estwrite', 'estimate', 'write',
desc='one of: estimate, write, estwrite',
usedefault=True)


Here we’ve defined jobtype to be an enumerated trait type, Enum, which can be set to one of the following: estwrite, estimate, or write. In a container, the default is always the first element. So in this case, the default will be estwrite:

>>> from nipype.interfaces import spm
>>> rlgn = spm.Realign()
>>> rlgn.inputs.infile
<undefined>
>>> rlgn.inputs.jobtype
'estwrite'

xor and requires

Both of these accept a list of trait names. The xor metadata reflects mutually exclusive traits, while the requires metadata reflects traits that have to be set together. When a xor-ed trait is set, all other traits belonging to the list are set to Undefined. The function check_mandatory_inputs ensures that all requirements (both mandatory and via the requires metadata are satisfied). These are also reflected in the help function.

copyfile

This is metadata for a File or Directory trait that is relevant only in the context of wrapping an interface in a Node and MapNode. copyfile can be set to either True or False. False indicates that contents should be symlinked, while True indicates that the contents should be copied over.

min_ver and max_ver

These metadata determine if a particular trait will be available when a given version of the underlying interface runs. Note that this check is performed at runtime.:

class RealignInputSpec(BaseInterfaceInputSpec):
jobtype = traits.Enum('estwrite', 'estimate', 'write', min_ver='5',
usedefault=True)

deprecated and new_name

This is metadata for removing or renaming an input field from a spec.:

class RealignInputSpec(BaseInterfaceInputSpec):
jobtype = traits.Enum('estwrite', 'estimate', 'write',
deprecated='0.8',
desc='one of: estimate, write, estwrite',
usedefault=True)


In the above example this means that the jobtype input is deprecated and will be removed in version 0.8. Deprecation should be set to two versions from current release. Raises TraitError after package version crosses the deprecation version.

For inputs that are being renamed, one can specify the new name of the field.:

class RealignInputSpec(BaseInterfaceInputSpec):
jobtype = traits.Enum('estwrite', 'estimate', 'write',
deprecated='0.8', new_name='job_type',
desc='one of: estimate, write, estwrite',
usedefault=True)
job_type = traits.Enum('estwrite', 'estimate', 'write',
desc='one of: estimate, write, estwrite',
usedefault=True)


In the above example, the jobtype field is being renamed to job_type. When new_name is provided it must exist as a trait, otherwise an exception will be raised.

Note

The version information for min_ver, max_ver and deprecated has to be provided as a string. For example, min_ver=’0.1’.

CommandLine¶

argstr

The metadata keyword for specifying the format strings for the parameters. This was the value string in the opt_map dictionaries of Nipype 0.2 code. If we look at the FlirtInputSpec, the argstr for the reference file corresponds to the argument string I would need to provide with the command-line version of flirt:

class FlirtInputSpec(FSLTraitedSpec):
reference = File(exists = True, argstr = '-ref %s', mandatory = True,
position = 1, desc = 'reference file')


Required: This metadata is required by all command-line interface classes.

position

This metadata is used to specify the position of arguments. Both positive and negative values are accepted. position = 0 will position this argument as the first parameter after the command name. position = -1 will position this argument as the last parameter, after all other parameters.

genfile

If True, the genfile metadata specifies that a filename should be generated for this parameter if-and-only-if the user did not provide one. The nipype convention is to automatically generate output filenames when not specified by the user both as a convenience for the user and so the pipeline can easily gather the outputs. Requires _gen_filename() method to be implemented. This way should be used if the desired file name is dependent on some runtime variables (such as file name of one of the inputs, or current working directory). In case when it should be fixed it’s recommended to just use usedefault.

sep

For List traits the string with which elements of the list will be joined.

name_source

Indicates the list of input fields from which the value of the current File output variable will be drawn. This input field must be the name of a File. Chaining is allowed, meaning that an input field can point to another as name_source, which also points as name_source to a third field. In this situation, the templates for substitutions are also accumulated.

name_template

By default a %s_generated template is used to create the output filename. This metadata keyword allows overriding the generated name.

keep_extension

Use this and set it True if you want the extension from the input to be kept.

SPM¶

field

name of the structure refered by the SPM job manager

Required: This metadata is required by all SPM-mediated

interface classes.

Defining an interface class¶

Common¶

When you define an interface class, you will define these attributes and methods:

• input_spec: the InputSpec

• output_spec: the OutputSpec

• _list_outputs(): Returns a dictionary containing names of generated files that are expected after package completes execution. This is used by BaseInterface.aggregate_outputs to gather all output files for the pipeline.

CommandLine¶

For command-line interfaces:

• _cmd: the command-line command

If you used genfile:

• _gen_filename(name): Generate filename, used for filenames that nipype generates as a convenience for users. This is for parameters that are required by the wrapped package, but we’re generating from some other parameter. For example, BET.inputs.outfile is required by BET but we can generate the name from BET.inputs.infile. Override this method in subclass to handle.

And optionally:

• _redirect_x: If set to True it will make Nipype start Xvfb before running the interface and redirect X output to it. This is useful for commandlines that spawn a graphical user interface.

• _format_arg(name, spec, value): For extra formatting of the input values before passing them to generic _parse_inputs() method.

For example this is the class definition for Flirt, minus the docstring:

class FLIRTInputSpec(FSLCommandInputSpec):
in_file = File(exists=True, argstr='-in %s', mandatory=True,
position=0, desc='input file')
reference = File(exists=True, argstr='-ref %s', mandatory=True,
position=1, desc='reference file')
out_file = File(argstr='-out %s', desc='registered output file',
name_source=['in_file'], name_template='%s_flirt',
position=2, hash_files=False)
out_matrix_file = File(argstr='-omat %s',
name_source=['in_file'], keep_extension=True,
name_template='%s_flirt.mat',
desc='output affine matrix in 4x4 asciii format',
position=3, hash_files=False)
out_log = File(name_source=['in_file'], keep_extension=True,
requires=['save_log'],
name_template='%s_flirt.log', desc='output log')
...

class FLIRTOutputSpec(TraitedSpec):
out_file = File(exists=True,
desc='path/name of registered file (if generated)')
out_matrix_file = File(exists=True,
desc='path/name of calculated affine transform '
'(if generated)')
out_log = File(desc='path/name of output log (if generated)')

class Flirt(FSLCommand):
_cmd = 'flirt'
input_spec = FlirtInputSpec
output_spec = FlirtOutputSpec


There are two possible output files outfile and outmatrix, both of which can be generated if not specified by the user.

Also notice the use of self._gen_fname() - a FSLCommand helper method for generating filenames (with extensions conforming with FSLOUTPUTTYPE).

SPM¶

For SPM-mediated interfaces:

• _jobtype and _jobname: special names used used by the SPM job manager. You can find them by saving your batch job as an .m file and looking up the code.

And optionally:

• _format_arg(name, spec, value): For extra formatting of the input values before passing them to generic _parse_inputs() method.

Undefined inputs¶

All the inputs and outputs that were not explicitly set (And do not have a usedefault flag - see above) will have Undefined value. To check if something is defined you have to explicitly call isdefiend function (comparing to None will not work).

Example of inputs¶

Below we have an example of using Bet. We can see from the help which inputs are mandatory and which are optional, along with the one-line description provided by the desc metadata:

>>> from nipype.interfaces import fsl
>>> fsl.BET.help()
Inputs
------

Mandatory:
infile: input file to skull strip

Optional:
args: Additional parameters to the command
center: center of gravity in voxels
environ: Environment variables (default={})
frac: fractional intensity threshold
functional: apply to 4D fMRI data
mesh: generate a vtk mesh brain surface
nooutput: Don't generate segmented output
outfile: name of output skull stripped image
outline: create surface outline image
outputtype: None
reduce_bias: bias field and neck cleanup
skull: create skull image
threshold: apply thresholding to segmented brain image and mask

Outputs
-------
meshfile: path/name of vtk mesh file (if generated)
outfile: path/name of skullstripped file
outlinefile: path/name of outline file (if generated)


Here we create a bet object and specify the required input. We then check our inputs to see which are defined and which are not:

>>> bet = fsl.BET(infile = 'f3.nii')
>>> bet.inputs
args = <undefined>
center = <undefined>
environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
frac = <undefined>
functional = <undefined>
infile = f3.nii
mesh = <undefined>
nooutput = <undefined>
outfile = <undefined>
outline = <undefined>
outputtype = NIFTI_GZ

We also checked the command-line that will be generated when we run the command and can see the generated output filename f3_brain.nii.gz.