interfaces.ants.visualization¶
ConvertScalarImageToRGB¶
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 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 string)
Additional parameters to the command
flag: %s
custom_color_map_file: (a string, nipype default value: none)
custom color map file
flag: %s, position: 5
environ: (a dictionary with keys which are a value of type 'str' and
with values which are a value of type 'str', 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 string, nipype default value: rgb.nii.gz)
rgb output image
flag: %s, position: 2
terminal_output: ('stream' or 'allatonce' or 'file' or '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¶
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 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 value of type 'str' and
with values which are a value of type 'str', nipype default value:
{})
Environment variables
flip_slice: (a 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 string, nipype default value: output.png)
The output consists of the tiled mosaic image.
flag: -o %s
pad_or_crop: (a 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 string)
Number of slices to increment Slice1xSlice2xSlice3[numberOfSlicesToI
ncrement,<minSlice=0>,<maxSlice=lastSlice>]
flag: -s %s
terminal_output: ('stream' or 'allatonce' or 'file' or '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 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