nipype.interfaces.ants.visualization module¶
The ants visualisation module provides basic functions based on ITK.
ConvertScalarImageToRGB¶
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'
- Mandatory Inputs
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) – Maximum input. Maps to a command-line argument:
%d
(position: 7).minimum_input (an integer) – Minimum input. Maps to a command-line argument:
%d
(position: 6).- Optional Inputs
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s
.custom_color_map_file (a 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) – Maps to a command-line argument:
%d
(position: 9). (Nipype default value:255
)minimum_RGB_output (an integer) – Maps to a command-line argument:
%d
(position: 8). (Nipype default value:0
)num_threads (an integer) – Number of ITK threads to use. (Nipype default value:
1
)output_image (a string) – Rgb output image. Maps to a command-line argument:
%s
(position: 2). (Nipype default value:rgb.nii.gz
)- Outputs
output_image (a pathlike object or string representing an existing file) – Converted RGB image.
CreateTiledMosaic¶
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]'
- Mandatory Inputs
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
.- Optional Inputs
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 string) – Additional parameters to the command. Maps to a command-line argument:
%s
.direction (an 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
.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 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) – Number of ITK threads to use. (Nipype default value:
1
)output_image (a 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 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 string) – Number of slices to increment Slice1xSlice2xSlice3[numberOfSlicesToIncrement,<minSlice=0>,<maxSlice=lastSlice>]. Maps to a command-line argument:
-s %s
.tile_geometry (a 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
.- Outputs
output_image (a pathlike object or string representing an existing file) – Image file.