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.. python_interface_devel:
===========================
How to wrap a Python script
===========================
This is a minimal pure python interface. As you can see all you need to do is to
do is to define inputs, outputs, _run_interface() (not run()), and _list_outputs.
.. testcode::
from nipype.interfaces.base import BaseInterface, \
BaseInterfaceInputSpec, traits, File, TraitedSpec
from nipype.utils.filemanip import split_filename
import nibabel as nb
import numpy as np
import os
class SimpleThresholdInputSpec(BaseInterfaceInputSpec):
volume = File(exists=True, desc='volume to be thresholded', mandatory=True)
threshold = traits.Float(desc='everything below this value will be set to zero',
mandatory=True)
class SimpleThresholdOutputSpec(TraitedSpec):
thresholded_volume = File(exists=True, desc="thresholded volume")
class SimpleThreshold(BaseInterface):
input_spec = SimpleThresholdInputSpec
output_spec = SimpleThresholdOutputSpec
def _run_interface(self, runtime):
fname = self.inputs.volume
img = nb.load(fname)
data = np.array(img.get_data())
active_map = data > self.inputs.threshold
thresholded_map = np.zeros(data.shape)
thresholded_map[active_map] = data[active_map]
new_img = nb.Nifti1Image(thresholded_map, img.affine, img.header)
_, base, _ = split_filename(fname)
nb.save(new_img, base + '_thresholded.nii')
return runtime
def _list_outputs(self):
outputs = self._outputs().get()
fname = self.inputs.volume
_, base, _ = split_filename(fname)
outputs["thresholded_volume"] = os.path.abspath(base + '_thresholded.nii')
return outputs
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