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).
dimension : 3 or 2
Image dimension (2 or 3). Maps to a command-line argument: %d (position: 0). (Nipype default value: 3)
input_image : a 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_input : an integer (int or long)
Maximum input. Maps to a command-line argument: %d (position: 7).
minimum_input : an integer (int or long)
Minimum input. Maps to a command-line argument: %d (position: 6).
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %s.
custom_color_map_file : a unicode string
Custom color map file. Maps to a command-line argument: %s (position: 5). (Nipype default value: none)
environ : a 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_image : a 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_output : an integer (int or long)
Maps to a command-line argument: %d (position: 9). (Nipype default value: 255)
minimum_RGB_output : an integer (int or long)
Maps to a command-line argument: %d (position: 8). (Nipype default value: 0)
num_threads : an integer (int or long)
Number of ITK threads to use. (Nipype default value: 1)
output_image : a unicode string
Rgb output image. Maps to a command-line argument: %s (position: 2). (Nipype default value: rgb.nii.gz)
output_image : a 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_image : a 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_image : a 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_value : a float
If an Rgb image is provided, render the overlay using the specified alpha parameter. Maps to a command-line argument: -a %.2f.
args : a unicode string
Additional parameters to the command. Maps to a command-line argument: %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. Maps to a command-line argument: -d %d.
environ : a 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_slice : a unicode string
FlipXxflipY. Maps to a command-line argument: -f %s.
mask_image : a 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_threads : an integer (int or long)
Number of ITK threads to use. (Nipype default value: 1)
output_image : a 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_crop : a 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_axes : a boolean
DoPermute. Maps to a command-line argument: -g.
slices : a unicode string
Number of slices to increment Slice1xSlice2xSlice3[numberOfSlicesToIncrement,<minSlice=0>,<maxSlice=lastSlice>]. Maps to a command-line argument: -s %s.
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. Maps to a command-line argument: -t %s.
output_image : a pathlike object or string representing an existing file
Image file.