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fixes ERROR: Inconsistent literal block quoting. PEP8 fixes
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nipype/interfaces/fsl/possum.py

Lines changed: 22 additions & 22 deletions
Original file line numberDiff line numberDiff line change
@@ -10,7 +10,6 @@
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.. Note:: This was written to work with FSL version 5.0.6.
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.. testsetup::
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# Change directory to provide relative paths for doctests
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import os
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filepath = os.path.dirname( os.path.realpath( __file__ ) )
@@ -30,32 +29,33 @@ class B0CalcInputSpec(FSLCommandInputSpec):
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name_template='%s_b0field', output_name='out_file',
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desc='filename of B0 output volume')
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x_grad = traits.Float(0.0, argstr='--gx=%0.4f',
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desc='Value for zeroth-order x-gradient field (per mm)')
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y_grad = traits.Float(0.0, argstr='--gy=%0.4f',
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desc='Value for zeroth-order y-gradient field (per mm)')
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z_grad = traits.Float(0.0, argstr='--gz=%0.4f',
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desc='Value for zeroth-order z-gradient field (per mm)')
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x_grad = traits.Float(0.0, argstr='--gx=%0.4f', desc=('Value for zeroth-order x-gradient field '
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'(per mm)'))
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y_grad = traits.Float(0.0, argstr='--gy=%0.4f', desc=('Value for zeroth-order y-gradient field '
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'(per mm)'))
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z_grad = traits.Float(0.0, argstr='--gz=%0.4f', desc=('Value for zeroth-order z-gradient field '
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'(per mm)'))
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x_b0 = traits.Float(0.0, argstr='--b0x=%0.2f', desc=('Value for zeroth-order b0 field '
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'(x-component), in Tesla'), xor=['xyz_b0'])
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y_b0 = traits.Float(0.0, argstr='--b0y=%0.2f', desc=('Value for zeroth-order b0 field '
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'(y-component), in Tesla'), xor=['xyz_b0'])
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z_b0 = traits.Float(1.0, argstr='--b0=%0.2f', desc=('Value for zeroth-order b0 field '
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'(z-component), in Tesla'), xor=['xyz_b0'])
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x_b0 = traits.Float(0.0, argstr='--b0x=%0.2f', xor=['xyz_b0'],
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desc='Value for zeroth-order b0 field (x-component), in Tesla')
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y_b0 = traits.Float(0.0, argstr='--b0y=%0.2f', xor=['xyz_b0'],
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desc='Value for zeroth-order b0 field (y-component), in Tesla')
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z_b0 = traits.Float(1.0, argstr='--b0=%0.2f', xor=['xyz_b0'],
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desc='Value for zeroth-order b0 field (z-component), in Tesla')
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xyz_b0 = traits.Tuple(
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traits.Float, traits.Float, traits.Float,
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argstr='--b0x=%0.2f --b0y=%0.2f --b0=%0.2f', xor=['x_b0','y_b0','z_b0'],
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argstr='--b0x=%0.2f --b0y=%0.2f --b0=%0.2f', xor=['x_b0', 'y_b0', 'z_b0'],
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desc='Zeroth-order B0 field in Tesla')
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delta = traits.Float(-9.45e-6, argstr='-d %e', desc='Delta value (chi_tissue - chi_air)')
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chi_air = traits.Float(4.0e-7, argstr='--chi0=%e', desc='susceptibility of air')
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delta = traits.Float(-9.45e-6, argstr='-d %e',
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desc='Delta value (chi_tissue - chi_air)')
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chi_air = traits.Float(
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4.0e-7, argstr='--chi0=%e', desc='susceptibility of air')
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compute_xyz = traits.Bool(False, argstr='--xyz',
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desc='calculate and save all 3 field components (i.e. x,y,z)')
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extendboundary = traits.Float(1.0, argstr='--extendboundary=%0.2f', desc=('Relative proportion to '
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'extend voxels at boundary'))
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extendboundary = traits.Float(1.0, argstr='--extendboundary=%0.2f',
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desc='Relative proportion to extend voxels at boundary')
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directconv = traits.Bool(False, argstr='--directconv',
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desc='use direct (image space) convolution, not FFT')
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@@ -65,13 +65,15 @@ class B0CalcOutputSpec(TraitedSpec):
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class B0Calc(FSLCommand):
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"""
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B0 inhomogeneities occur at interfaces of materials with different magnetic susceptibilities,
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such as tissue-air interfaces. These differences lead to distortion in the local magnetic field,
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as Maxwell’s equations need to be satisfied. An example of B0 inhomogneity is the first volume
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of the 4D volume ```$FSLDIR/data/possum/b0_ppm.nii.gz```.
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74-
Examples ::
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Examples
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--------
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>>> from nipype.interfaces.fsl import B0Calc
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>>> b0calc = B0Calc()
@@ -85,5 +87,3 @@ class B0Calc(FSLCommand):
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_cmd = 'b0calc'
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input_spec = B0CalcInputSpec
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output_spec = B0CalcOutputSpec
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