3 d-@sdZddlmZmZmZmZmZddlmZddlm Z m Z ddl Z d Z Gd d d eZ Gd d d eZGddde ZGdddeZGdddeZGddde ZGdddeZGdddeZGddde ZGdddeZGdddeZGd d!d!e ZGd"d#d#eZGd$d%d%eZGd&d'd'e ZGd(d)d)eZGd*d+d+eZGd,d-d-e ZGd.d/d/e eZGd0d1d1e eZ Gd2d3d3e eZ!Gd4d5d5e eZ"Gd6d7d7e eZ#Gd8d9d9e eZ$Gd:d;d;e eZ%dS)>> from nipype.interfaces import dtitk >>> node = dtitk.TVAdjustVoxSp() >>> node.inputs.in_file = 'im1.nii' >>> node.inputs.target_file = 'im2.nii' >>> node.cmdline 'TVAdjustVoxelspace -in im1.nii -out im1_avs.nii -target im2.nii' >>> node.run() # doctest: +SKIP ZTVAdjustVoxelspaceN) rrr__doc__r input_specr" output_spec_cmdr r r r!r#Csr#c@seZdZedddddZedddddd Zed d d d gdZejej ej ej fdddgdZ ejej ej ej fdddgdZ dS)SVAdjustVoxSpInputSpeczscalar volume to modifyTz-in %s)rrrrz output pathz-out %srz%s_avs)rrrrrztarget volume to matchz -target %srr)rrrz%xyz voxel size (superseded by target)z-vsize %g %g %grz!xyz origin (superseded by target)z-origin %g %g %gN) rrrrrrrrrrrrr r r r!r(Xs( r(c@seZdZeddZdS)SVAdjustVoxSpOutputSpecT)rN)rrrrrr r r r!r)tsr)c@seZdZdZeZeZdZdS) SVAdjustVoxSpas Adjusts the voxel space of a scalar volume. Example ------- >>> from nipype.interfaces import dtitk >>> node = dtitk.SVAdjustVoxSp() >>> node.inputs.in_file = 'im1.nii' >>> node.inputs.target_file = 'im2.nii' >>> node.cmdline 'SVAdjustVoxelspace -in im1.nii -out im1_avs.nii -target im2.nii' >>> node.run() # doctest: +SKIP ZSVAdjustVoxelspaceN) rrrr$r(r%r)r&r'r r r r!r*xsr*c@seZdZedddddZedddddd Zed d d d dgdZejdddddZ ejdddddZ ej ej ej ej fddgddZ ej ejejejfddgddZej ejejejfddgddZd S)!TVResampleInputSpecztensor volume to resampleTz-in %s)rrrrz output pathrz %s_resampledz-out %s)rrrrrz!specs read from the target volumez -target %s array_sizerr)rrrcenterz -align %sz*how to align output volume to input volume)rrZLEIZEIz -interp %sz%Log Euclidean Euclidean Interpolationzresampled array sizerz-size %d %d %d)rrrzresampled voxel sizez-vsize %g %g %gz xyz originz-origin %g %g %gN)rrrrrrrrEnumalign interpolationrIntr,rrrr r r r!r+sDr+c@seZdZeddZdS)TVResampleOutputSpecT)rN)rrrrrr r r r!r2sr2c@seZdZdZeZeZdZdS) TVResamplea] Resamples a tensor volume. Example ------- >>> from nipype.interfaces import dtitk >>> node = dtitk.TVResample() >>> node.inputs.in_file = 'im1.nii' >>> node.inputs.target_file = 'im2.nii' >>> node.cmdline 'TVResample -in im1.nii -out im1_resampled.nii -target im2.nii' >>> node.run() # doctest: +SKIP N) rrrr$r+r%r2r&r'r r r r!r3sr3c@seZdZedddddZedddddd Zed d d d dgdZejdddddZ ej ej ej ej fddgddZ ej ej ej ej fddgddZej ej ej ej fddgddZdS)SVResampleInputSpeczimage to resampleTz-in %s)rrrrz output pathrz %s_resampledz-out %s)rrrrrz!specs read from the target volumez -target %sr,rr)rrrr-z -align %sz*how to align output volume to input volume)rrzresampled array sizerz-size %d %d %d)rrrzresampled voxel sizez-vsize %g %g %gz xyz originz-origin %g %g %gN)rrrrrrrrr.r/rr1r,rrrr r r r!r4s@r4c@seZdZeddZdS)SVResampleOutputSpecT)rN)rrrrrr r r r!r5sr5c@seZdZdZeZeZdZdS) SVResamplea] Resamples a scalar volume. Example ------- >>> from nipype.interfaces import dtitk >>> node = dtitk.SVResample() >>> node.inputs.in_file = 'im1.nii' >>> node.inputs.target_file = 'im2.nii' >>> node.cmdline 'SVResample -in im1.nii -out im1_resampled.nii -target im2.nii' >>> node.run() # doctest: +SKIP N) rrrr$r4r%r5r&r'r r r r!r6sr6c @sBeZdZedddddZejddddd d d d d ZedddZdS)TVtoolInputSpeczscalar volume to resampleTz-in %s)rrrrfatradrdpdZrgbz-%s)rrz-out %s)rZgenfileN) rrrrrrr.in_flagrr r r r!r7sr7c@seZdZeZdS)TVtoolOutputSpecN)rrrrrr r r r!r?sr?c@s,eZdZdZeZeZdZddZ ddZ dS)TVtoolaV Calculates a tensor metric volume from a tensor volume. Example ------- >>> from nipype.interfaces import dtitk >>> node = dtitk.TVtool() >>> node.inputs.in_file = 'im1.nii' >>> node.inputs.in_flag = 'fa' >>> node.cmdline 'TVtool -in im1.nii -fa -out im1_fa.nii' >>> node.run() # doctest: +SKIP cCs:|jj}|jj}t|s&|jd}tjj||d<|S)Nr) Z_outputsgetinputsrr _gen_filenameospathabspath)selfoutputsrr r r! _list_outputs7s   zTVtool._list_outputscCs,|dkr dSttjj|jjd|jjdS)Nr_)suffix)rrDrEbasenamerBrr>)rGnamer r r!rC?szTVtool._gen_filenameN) rrrr$r7r%r?r&r'rIrCr r r r!r@#s r@c@seZdZeddddddZedddddd d Zejd dd d dddZejdddd dddZ ejddd ddddZ ejddd ddddZ dS)BinThreshInputSpeczImage to threshold/binarizeTr z%s)rrpositionrrz output pathr rz %s_thrbin)rrOrrrrg{Gz?rz%gz!lower bound of binarization range) usedefaultrOrrrdrz!upper bound of binarization rangez&value for voxels in binarization range)rOrrPrrz-value for voxelsoutside of binarization rangeN) rrrrrrrrZ lower_boundZ upper_boundZ inside_valueZ outside_valuer r r r!rNJsRrNc@seZdZeddZdS)BinThreshOutputSpecT)rN)rrrrrr r r r!rT|srTc@seZdZdZeZeZdZdS) BinThresha Binarizes an image. Example ------- >>> from nipype.interfaces import dtitk >>> node = dtitk.BinThresh() >>> node.inputs.in_file = 'im1.nii' >>> node.inputs.lower_bound = 0 >>> node.inputs.upper_bound = 100 >>> node.inputs.inside_value = 1 >>> node.inputs.outside_value = 0 >>> node.cmdline 'BinaryThresholdImageFilter im1.nii im1_thrbin.nii 0 100 1 0' >>> node.run() # doctest: +SKIP ZBinaryThresholdImageFilterN) rrrr$rNr%rTr&r'r r r r!rUsrUc@s eZdZdS) BinThreshTaskN)rrrr r r r!rVsrVc@s eZdZdS)SVAdjustVoxSpTaskN)rrrr r r r!rWsrWc@s eZdZdS)SVResampleTaskN)rrrr r r r!rXsrXc@s eZdZdS)TVAdjustOriginTaskN)rrrr r r r!rYsrYc@s eZdZdS)TVAdjustVoxSpTaskN)rrrr r r r!rZsrZc@s eZdZdS)TVResampleTaskN)rrrr r r r!r[sr[c@s eZdZdS) TVtoolTaskN)rrrr r r r!r\sr\)&r$baserrrrrZutils.filemaniprr r rDZ __docformat__r r"r#r(r)r*r+r2r3r4r5r6r7r?r@rNrTrUrVrWrXrYrZr[r\r r r r!s< -* '2