80GC reproduction

narps_open/core/interfaces/afni.py

@@ -0,0 +1,226 @@
+#!/usr/bin/python
+# coding: utf-8
+
+""" AFNI interfaces for Nipype """
+
+from os.path import abspath
+
+from nipype.interfaces.base import traits, File, Str, InputMultiPath, isdefined
+from nipype.interfaces.afni.base import (
+    AFNICommand,
+    AFNICommandInputSpec,
+    AFNICommandOutputSpec
+)
+
+class TtestppInputSpec(AFNICommandInputSpec):
+    """ The input specification of the 3dttest++ interface """
+
+    set_a_label = Str(
+        desc='label for setA',
+        argstr='-labelA %s ',
+        mandatory=True
+        )
+    set_a = InputMultiPath(
+        traits.Tuple(
+            File(desc='3D dataset', exists=True),
+            traits.Int(desc='Index of the data in the dataset'),
+        ),
+        desc='specifies a set of input datasets for setA + their label.',
+        argstr='-setA %s ', # Data tuples will be formatted in the _format_arg method
+        requires=['set_a_label'],
+        mandatory=True
+    )
+    set_b_label = Str(
+        desc='label for setB',
+        argstr='-labelB %s ',
+        )
+    set_b = InputMultiPath(
+        traits.Tuple(
+            File(desc='3D dataset', exists=True),
+            traits.Int(desc='Index of the data in the dataset'),
+        ),
+        desc='specifies a set of input datasets for setB + their label.',
+        argstr='-setB %s ', # Data tuples will be formatted in the _format_arg method
+        requires=['set_b_label'],
+    )
+    set_a_weight = File(
+        desc='Name of a file with the weights for the -setA datasets.',
+        argstr='-setweightA %s ',
+        requires=['set_a'],
+        exists=True,
+        )
+    set_b_weight = File(
+        desc='Name of a file with the weights for the -setB datasets.',
+        argstr='-setweightB %s ',
+        requires=['set_b'],
+        exists=True,
+        )
+    covariates = File(
+        desc='name of a text file with a table for the covariate(s).'
+        ' Each column in the file is treated as a separate covariate, and each'
+        ' row contains the values of these covariates for one sample (dataset).',
+        argstr='-covariates %s ',
+        exists=True,
+        )
+    center = traits.Enum('NONE', 'DIFF', 'SAME',
+        desc='how the mean across subjects of a covariate will be processed.',
+        argstr='-center %s ',
+        requires=['covariates'],
+        )
+    paired = traits.Bool(
+        desc='specifies the use of a paired-sample t-test to compare setA and setB.',
+        argstr='-paired ',
+        requires=['set_a', 'set_b'],
+    )
+    unpooled = traits.Bool(
+        desc='specifies that the variance estimates for setA and setB be computed '
+        'separately (not pooled together).',
+        argstr='-paired ',
+        requires=['set_a', 'set_b'],
+        xor=['paired', 'covariates']
+    )
+    toz = traits.Bool(
+        desc='convert output t-statistics to z-scores.',
+        argstr='-toz ',
+    )
+    rankize = traits.Bool(
+        desc='convert the data (and covariates, if any) into ranks before '
+        'doing the 2-sample analyses.',
+        argstr='-rankize ',
+    )
+    no1sam = traits.Bool(
+        desc='do not calculate 1-sample test results when '
+        'doing 2-sample analyses.',
+        argstr='-no1sam ',
+    )
+    nomeans = traits.Bool(
+        desc='turn off output of the `mean` sub-bricks.',
+        argstr='-nomeans ',
+    )
+    notests = traits.Bool(
+        desc='turn off output of the `test` sub-bricks.',
+        argstr='-notests ',
+    )
+    mask = File(
+        desc='Only compute results for voxels in the specified mask.',
+        argstr='-mask %s ',
+        exists=True,
+    )
+    exblur = traits.Float(
+        desc='Before doing the t-test, apply some extra blurring to the input datasets; '
+        "parameter 'b' is the Gaussian FWHM of the smoothing kernel (in mm).",
+        argstr='-exblur %d ',
+    )
+    brickwise = traits.Bool(
+        desc='carry out t-tests sub-brick by sub-brick',
+        argstr='-brickwise ',
+        position=0
+    )
+    out_file = Str(
+        desc='the name of the output dataset file.',
+        argstr='-prefix %s ',
+        position=-1
+        )
+    out_residuals = Str(
+        desc='output the residuals into a dataset with given prefix.',
+        argstr='-resid %s ',
+        position=-2
+        )
+    clustsim = traits.Bool(
+        desc='run the cluster-size threshold simulation program 3dClustSim.',
+        argstr='-Clustsim ',
+        position=-4
+    )
+    seed = traits.Tuple(
+        traits.Int, traits.Int,
+        desc='This option is used to set the random number seed for'
+        '`-randomsign` to the first positive integer. If a second integer'
+        'follows, then that value is used for the random number seed for `-permute`.',
+        argstr='-seed %d %d ',
+        requires=['clustsim'],
+        position=-3
+    )
+
+class Ttestpp(AFNICommand):
+    """ Gosset (Student) t-test of sets of 3D datasets.
+
+    For complete details, see the `3dttest++ Documentation.
+    <https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dttest++.html>`_
+    """
+
+    _cmd = '3dttest++'
+    input_spec = TtestppInputSpec
+    output_spec = AFNICommandOutputSpec
+
+    def _format_arg(self, name, trait_spec, value):
+        """ Format arguments before actually building the command line """
+        out_value = value
+
+        # For arguments -setA and -setB, we want a list such as :
+        #      dataset1'[index]' dataset2'[index]' dataset3'[index]' ...
+        if name in ['set_a', 'set_b']:
+            out_value = ''
+            for set_tuple in value:
+                out_value += f'{set_tuple[0]}\'[{set_tuple[1]}]\' '
+            out_value = [out_value] # Return a list as the input value
+
+        return super()._format_arg(name, trait_spec, out_value)
+
+    def _list_outputs(self):
+        outputs = self.output_spec().get()
+
+        for key in outputs.keys():
+            if isdefined(self.inputs.get()[key]):
+                outputs[key] = abspath(self.inputs.get()[key])
+
+        return outputs
+
+class SelectSBInputSpec(AFNICommandInputSpec):
+    """ The input specification for SelectSubBrick """
+    in_file = File(
+        desc = 'File name to select a subbrick from.',
+        argstr = '%s',
+        position = -2,
+        mandatory = True,
+        copyfile = False,
+        exists = True
+    )
+    index = traits.Int(
+        desc = 'Index of the subbrick inside in_file.',
+        mandatory = True
+    )
+    out_file = File(desc = 'Output image file name.', argstr = '-prefix %s', genfile = True)
+
+class SelectSubBrick(AFNICommand):
+    """ Sub-brick selection from AFNI files.
+
+    For complete details, see the `3dTcat Documentation.
+    <https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dTcat.html>
+    """
+
+    _cmd = '3dTcat'
+    input_spec = SelectSBInputSpec
+    output_spec = AFNICommandOutputSpec
+
+    #def _gen_filename(self, name):
+    #    if name == 'out_file':
+    #        return self._gen_fname(self.inputs.in_file, suffix = '_tcat')
+
+    def _list_outputs(self):
+        outputs = self.output_spec().get()
+
+        for key in outputs.keys():
+            if isdefined(self.inputs.get()[key]):
+                outputs[key] = abspath(self.inputs.get()[key])
+
+        return outputs
+
+    def _format_arg(self, name, trait_spec, value):
+        """ Format arguments before actually building the command line """
+        out_value = value
+
+        # For argument in_file, append index, such as : in_file'[index]'
+        if name == 'in_file':
+            out_value = f'{value}\'[{self.inputs.index}]\''
+
+        return super()._format_arg(name, trait_spec, out_value)

narps_open/pipelines/__init__.py

@@ -33,7 +33,7 @@
     '5G9K': None,
     '6FH5': None,
     '6VV2': None,
-    '80GC': None,
+    '80GC': 'PipelineTeam80GC',
     '94GU': None,
     '98BT': 'PipelineTeam98BT',
     '9Q6R': None,