3 d@sdZddlZddlmZmZmZddlmZmZGdddeZGd d d eZ Gd d d eZ Gd ddeZ GdddeZ GdddeZ dS)zEThe ants visualisation module provides basic functions based on ITK. N) TraitedSpecFiletraits) ANTSCommandANTSCommandInputSpecc@seZdZejddddddddZeddd dd d Zejd ddd ddZ ej dejddddddddZ ejdddddddddddddd d!dd"dd#d$Z ejdddd%d&dZ ejdd'dd(d$Zejdd)dd*d$Zejdddd+d,Zejd-ddd.d,Zd/S)0 ConvertScalarImageToRGBInputSpecrz%dTzimage dimension (2 or 3)r)argstr usedefaultdesc mandatorypositionz%sz$Main input is a 3-D grayscale image.r)r existsr rrz rgb.nii.gzzrgb output image)r r r rnone)rz mask image)r r rdefaultr ZgreyZredZgreenZblueZcopperZjetZhsvZspringZsummerZautumnZwinterZhotZcoolZ overunderZcustomzSelect a colormap)r r rrzcustom color map filez minimum inputz maximum input)r r r N)__name__ __module__ __qualname__rEnumZ dimensionr input_imageStr output_imageZEither mask_imageZcolormapZcustom_color_map_fileIntZ minimum_inputZ maximum_inputZminimum_RGB_outputZmaximum_RGB_outputr#r#F/tmp/pip-build-7vycvbft/nipype/nipype/interfaces/ants/visualization.pyr sh r c@seZdZedddZdS)!ConvertScalarImageToRGBOutputSpecTzconverted RGB image)rr N)rrrrr r#r#r#r$r%Jsr%cs4eZdZdZdZeZeZfddZ ddZ Z S)ConvertScalarImageToRGBa Convert scalar images to RGB. Examples -------- >>> from nipype.interfaces.ants.visualization import ConvertScalarImageToRGB >>> converter = ConvertScalarImageToRGB() >>> converter.inputs.dimension = 3 >>> converter.inputs.input_image = 'T1.nii.gz' >>> converter.inputs.colormap = 'jet' >>> converter.inputs.minimum_input = 0 >>> converter.inputs.maximum_input = 6 >>> converter.cmdline 'ConvertScalarImageToRGB 3 T1.nii.gz rgb.nii.gz none jet none 0 6 0 255' cstt|j|||S)N)superr& _format_arg)selfoptspecval) __class__r#r$r(dsz#ConvertScalarImageToRGB._format_argcCs*|jj}tjjtj|jj|d<|S)Nr )_outputsgetospathjoingetcwdinputsr )r)outputsr#r#r$ _list_outputsgs z%ConvertScalarImageToRGB._list_outputs) rrr__doc___cmdr input_specr% output_specr(r6 __classcell__r#r#)r-r$r&Ns  r&c@seZdZedddddZedddddZedddd Zejd d d Z ej d ddddZ ej ddd Z ej ddd Zej ddd Zej ddd Zej ddd Zejddd ZdS)CreateTiledMosaicInputSpecz-i %sTz$Main input is a 3-D grayscale image.)r rr rz-r %szrAn optional Rgb image can be added as an overlay.It must have the same imagegeometry as the input grayscale image.z-x %sz)Specifies the ROI of the RGB voxels used.)r rr z-a %.2fzTIf an Rgb image is provided, render the overlay using the specified alpha parameter.)r r z output.pngz-o %sz.The output consists of the tiled mosaic image.)r r r z-t %saThe tile geometry specifies the number of rows and columnsin the output image. For example, if the user specifies "5x10", then 5 rows by 10 columns of slices are rendered. If R < 0 and C > 0 (or vice versa), the negative value is selectedbased on direction.z-d %dzwSpecifies the direction of the slices. If no direction is specified, the direction with the coarsest spacing is chosen.z-p %saargument passed to -p flag:[padVoxelWidth,][lowerPadding[0]xlowerPadding[1],upperPadding[0]xupperPadding[1],constantValue]The user can specify whether to pad or crop a specified voxel-width boundary of each individual slice. For this program, cropping is simply padding with negative voxel-widths.If one pads (+), the user can also specify a constant pad value (default = 0). If a mask is specified, the user can use the mask to define the region, by using the keyword "mask" plus an offset, e.g. "-p mask+3".z-s %szoNumber of slices to increment Slice1xSlice2xSlice3[numberOfSlicesToIncrement,,]z-f %sZ flipXxflipYz-gZ doPermuteN)rrrrrZ rgb_imager!rZFloatZ alpha_valuerr Z tile_geometryr" directionZ pad_or_cropZslicesZ flip_sliceZBoolZ permute_axesr#r#r#r$r<msD  r<c@seZdZedddZdS)CreateTiledMosaicOutputSpecTz image file)rr N)rrrrr r#r#r#r$r>sr>c@s$eZdZdZdZeZeZddZ dS)CreateTiledMosaicaThe program CreateTiledMosaic in conjunction with ConvertScalarImageToRGB provides useful functionality for common image analysis tasks. The basic usage of CreateTiledMosaic is to tile a 3-D image volume slice-wise into a 2-D image. Examples -------- >>> from nipype.interfaces.ants.visualization import CreateTiledMosaic >>> mosaic_slicer = CreateTiledMosaic() >>> mosaic_slicer.inputs.input_image = 'T1.nii.gz' >>> mosaic_slicer.inputs.rgb_image = 'rgb.nii.gz' >>> mosaic_slicer.inputs.mask_image = 'mask.nii.gz' >>> mosaic_slicer.inputs.output_image = 'output.png' >>> mosaic_slicer.inputs.alpha_value = 0.5 >>> mosaic_slicer.inputs.direction = 2 >>> mosaic_slicer.inputs.pad_or_crop = '[ -15x -50 , -15x -30 ,0]' >>> mosaic_slicer.inputs.slices = '[2 ,100 ,160]' >>> mosaic_slicer.cmdline 'CreateTiledMosaic -a 0.50 -d 2 -i T1.nii.gz -x mask.nii.gz -o output.png -p [ -15x -50 , -15x -30 ,0] -r rgb.nii.gz -s [2 ,100 ,160]' cCs*|jj}tjjtj|jj|d<|S)Nr )r.r/r0r1r2r3r4r )r)r5r#r#r$r6s zCreateTiledMosaic._list_outputsN) rrrr7r8r<r9r>r:r6r#r#r#r$r?s r?)r7r0baserrrrrr r%r&r<r>r?r#r#r#r$s?L