nipype.interfaces.ants.visualization module

The ants visualisation module provides basic functions based on ITK.

ConvertScalarImageToRGB

Link to code

Bases: ANTSCommand

Wrapped executable: ConvertScalarImageToRGB.

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'
colormap‘grey’ or ‘red’ or ‘green’ or ‘blue’ or ‘copper’ or ‘jet’ or ‘hsv’ or ‘spring’ or ‘summer’ or ‘autumn’ or ‘winter’ or ‘hot’ or ‘cool’ or ‘overunder’ or ‘custom’

Select a colormap. Maps to a command-line argument: %s (position: 4).

dimension3 or 2

Image dimension (2 or 3). Maps to a command-line argument: %d (position: 0). (Nipype default value: 3)

input_imagea pathlike object or string representing an existing file

Main input is a 3-D grayscale image. Maps to a command-line argument: %s (position: 1).

maximum_inputan integer (int or long)

Maximum input. Maps to a command-line argument: %d (position: 7).

minimum_inputan integer (int or long)

Minimum input. Maps to a command-line argument: %d (position: 6).

argsa unicode string

Additional parameters to the command. Maps to a command-line argument: %s.

custom_color_map_filea unicode string

Custom color map file. Maps to a command-line argument: %s (position: 5). (Nipype default value: none)

environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

Environment variables. (Nipype default value: {})

mask_imagea pathlike object or string representing an existing file

Mask image. Maps to a command-line argument: %s (position: 3). (Nipype default value: none)

maximum_RGB_outputan integer (int or long)

Maps to a command-line argument: %d (position: 9). (Nipype default value: 255)

minimum_RGB_outputan integer (int or long)

Maps to a command-line argument: %d (position: 8). (Nipype default value: 0)

num_threadsan integer (int or long)

Number of ITK threads to use. (Nipype default value: 1)

output_imagea unicode string

Rgb output image. Maps to a command-line argument: %s (position: 2). (Nipype default value: rgb.nii.gz)

output_imagea pathlike object or string representing an existing file

Converted RGB image.

CreateTiledMosaic

Link to code

Bases: ANTSCommand

Wrapped executable: CreateTiledMosaic.

The 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]'
input_imagea pathlike object or string representing an existing file

Main input is a 3-D grayscale image. Maps to a command-line argument: -i %s.

rgb_imagea pathlike object or string representing an existing file

An optional Rgb image can be added as an overlay.It must have the same imagegeometry as the input grayscale image. Maps to a command-line argument: -r %s.

alpha_valuea float

If an Rgb image is provided, render the overlay using the specified alpha parameter. Maps to a command-line argument: -a %.2f.

argsa unicode string

Additional parameters to the command. Maps to a command-line argument: %s.

directionan integer (int or long)

Specifies the direction of the slices. If no direction is specified, the direction with the coarsest spacing is chosen. Maps to a command-line argument: -d %d.

environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

Environment variables. (Nipype default value: {})

flip_slicea unicode string

FlipXxflipY. Maps to a command-line argument: -f %s.

mask_imagea pathlike object or string representing an existing file

Specifies the ROI of the RGB voxels used. Maps to a command-line argument: -x %s.

num_threadsan integer (int or long)

Number of ITK threads to use. (Nipype default value: 1)

output_imagea unicode string

The output consists of the tiled mosaic image. Maps to a command-line argument: -o %s. (Nipype default value: output.png)

pad_or_cropa unicode string

Argument passed to -p flag:[padVoxelWidth,<constantValue=0>][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”. Maps to a command-line argument: -p %s.

permute_axesa boolean

DoPermute. Maps to a command-line argument: -g.

slicesa unicode string

Number of slices to increment Slice1xSlice2xSlice3[numberOfSlicesToIncrement,<minSlice=0>,<maxSlice=lastSlice>]. Maps to a command-line argument: -s %s.

tile_geometrya unicode string

The 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. Maps to a command-line argument: -t %s.

output_imagea pathlike object or string representing an existing file

Image file.