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# interfaces.ants.visualization

## ConvertScalarImageToRGB

Link to code

Wraps command ConvertScalarImageToRGB

### 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'

Inputs:

    [Mandatory]
    colormap: (a unicode string, nipype default value: )
            Possible colormaps: grey, red, green, blue, copper, jet, hsv,
            spring, summer, autumn, winter, hot, cool, overunder, custom
            flag: %s, position: 4
    dimension: (3 or 2, nipype default value: 3)
            image dimension (2 or 3)
            flag: %d, position: 0
    input_image: (an existing file name)
            Main input is a 3-D grayscale image.
            flag: %s, position: 1
    maximum_input: (an integer (int or long))
            maximum input
            flag: %d, position: 7
    minimum_input: (an integer (int or long))
            minimum input
            flag: %d, position: 6

    [Optional]
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    custom_color_map_file: (a unicode string, nipype default value: none)
            custom color map file
            flag: %s, position: 5
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    mask_image: (an existing file name, nipype default value: none)
            mask image
            flag: %s, position: 3
    maximum_RGB_output: (an integer (int or long), nipype default value:
             255)
            flag: %d, position: 9
    minimum_RGB_output: (an integer (int or long), nipype default value:
             0)
            flag: %d, position: 8
    num_threads: (an integer (int or long), nipype default value: 1)
            Number of ITK threads to use
    output_image: (a unicode string, nipype default value: rgb.nii.gz)
            rgb output image
            flag: %s, position: 2
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored

Outputs:

    output_image: (an existing file name)
            converted RGB image

## CreateTiledMosaic

Link to code

Wraps command 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]'

Inputs:

    [Mandatory]
    input_image: (an existing file name)
            Main input is a 3-D grayscale image.
            flag: -i %s
    rgb_image: (an existing file name)
            An optional Rgb image can be added as an overlay.It must have the
            same imagegeometry as the input grayscale image.
            flag: -r %s

    [Optional]
    alpha_value: (a float)
            If an Rgb image is provided, render the overlay using the specified
            alpha parameter.
            flag: -a %.2f
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    direction: (an integer (int or long))
            Specifies the direction of the slices. If no direction is specified,
            the direction with the coarsest spacing is chosen.
            flag: -d %d
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    flip_slice: (a unicode string)
            flipXxflipY
            flag: -f %s
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    mask_image: (an existing file name)
            Specifies the ROI of the RGB voxels used.
            flag: -x %s
    num_threads: (an integer (int or long), nipype default value: 1)
            Number of ITK threads to use
    output_image: (a unicode string, nipype default value: output.png)
            The output consists of the tiled mosaic image.
            flag: -o %s
    pad_or_crop: (a unicode string)
            argument passed to -p flag:[padVoxelWidth,<constantValue=0>][lowerPa
            dding[0]xlowerPadding[1],upperPadding[0]xupperPadding[1],constantVal
            ue]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".
            flag: -p %s
    permute_axes: (a boolean)
            doPermute
            flag: -g
    slices: (a unicode string)
            Number of slices to increment Slice1xSlice2xSlice3[numberOfSlicesToI
            ncrement,<minSlice=0>,<maxSlice=lastSlice>]
            flag: -s %s
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    tile_geometry: (a 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.
            flag: -t %s

Outputs:

    output_image: (an existing file name)
            image file