interfaces.ants.visualization¶
ConvertScalarImageToRGB¶
Wraps the executable 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]
dimension: (3 or 2, nipype default value: 3)
image dimension (2 or 3)
argument: ``%d``, position: 0
input_image: (an existing file name)
Main input is a 3-D grayscale image.
argument: ``%s``, position: 1
colormap: (a unicode string, nipype default value: )
Possible colormaps: grey, red, green, blue, copper, jet, hsv,
spring, summer, autumn, winter, hot, cool, overunder, custom
argument: ``%s``, position: 4
minimum_input: (an integer (int or long))
minimum input
argument: ``%d``, position: 6
maximum_input: (an integer (int or long))
maximum input
argument: ``%d``, position: 7
[Optional]
output_image: (a unicode string, nipype default value: rgb.nii.gz)
rgb output image
argument: ``%s``, position: 2
mask_image: (an existing file name, nipype default value: none)
mask image
argument: ``%s``, position: 3
custom_color_map_file: (a unicode string, nipype default value: none)
custom color map file
argument: ``%s``, position: 5
minimum_RGB_output: (an integer (int or long), nipype default value:
0)
argument: ``%d``, position: 8
maximum_RGB_output: (an integer (int or long), nipype default value:
255)
argument: ``%d``, position: 9
num_threads: (an integer (int or long), nipype default value: 1)
Number of ITK threads to use
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
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', nipype default value: {})
Environment variables
Outputs:
output_image: (an existing file name)
converted RGB image
CreateTiledMosaic¶
Wraps the executable 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.
argument: ``-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.
argument: ``-r %s``
[Optional]
mask_image: (an existing file name)
Specifies the ROI of the RGB voxels used.
argument: ``-x %s``
alpha_value: (a float)
If an Rgb image is provided, render the overlay using the specified
alpha parameter.
argument: ``-a %.2f``
output_image: (a unicode string, nipype default value: output.png)
The output consists of the tiled mosaic image.
argument: ``-o %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.
argument: ``-t %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.
argument: ``-d %d``
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".
argument: ``-p %s``
slices: (a unicode string)
Number of slices to increment Slice1xSlice2xSlice3[numberOfSlicesToI
ncrement,<minSlice=0>,<maxSlice=lastSlice>]
argument: ``-s %s``
flip_slice: (a unicode string)
flipXxflipY
argument: ``-f %s``
permute_axes: (a boolean)
doPermute
argument: ``-g``
num_threads: (an integer (int or long), nipype default value: 1)
Number of ITK threads to use
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
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', nipype default value: {})
Environment variables
Outputs:
output_image: (an existing file name)
image file