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# 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

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

> minimum_inputan integer

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

> argsa string

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

> custom_color_map_filea 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 string or os.PathLike object referring to an existing file or ‘none’

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

> maximum_RGB_outputan integer

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

> minimum_RGB_outputan integer

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

> num_threadsan integer

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

> output_imagea 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 string

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

> directionan integer

>   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 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

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

> output_imagea 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 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 string

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

> tile_geometrya 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.