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visualization.py
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visualization.py
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# -*- coding: utf-8 -*-
"""The ants visualisation module provides basic functions based on ITK.
"""
import os
from ..base import TraitedSpec, File, traits
from .base import ANTSCommand, ANTSCommandInputSpec
class ConvertScalarImageToRGBInputSpec(ANTSCommandInputSpec):
dimension = traits.Enum(
3,
2,
argstr="%d",
usedefault=True,
desc="image dimension (2 or 3)",
mandatory=True,
position=0,
)
input_image = File(
argstr="%s",
exists=True,
desc="Main input is a 3-D grayscale image.",
mandatory=True,
position=1,
)
output_image = traits.Str(
"rgb.nii.gz", argstr="%s", usedefault=True, desc="rgb output image", position=2
)
mask_image = traits.Either(
"none",
traits.File(exists=True),
argstr="%s",
desc="mask image",
position=3,
default="none",
usedefault=True,
)
colormap = traits.Enum(
"grey",
"red",
"green",
"blue",
"copper",
"jet",
"hsv",
"spring",
"summer",
"autumn",
"winter",
"hot",
"cool",
"overunder",
"custom",
argstr="%s",
desc="Select a colormap",
mandatory=True,
position=4,
)
custom_color_map_file = traits.Str(
"none", argstr="%s", usedefault=True, desc="custom color map file", position=5
)
minimum_input = traits.Int(
argstr="%d", desc="minimum input", mandatory=True, position=6
)
maximum_input = traits.Int(
argstr="%d", desc="maximum input", mandatory=True, position=7
)
minimum_RGB_output = traits.Int(0, usedefault=True, argstr="%d", position=8)
maximum_RGB_output = traits.Int(255, usedefault=True, argstr="%d", position=9)
class ConvertScalarImageToRGBOutputSpec(TraitedSpec):
output_image = File(exists=True, desc="converted RGB image")
class ConvertScalarImageToRGB(ANTSCommand):
"""
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'
"""
_cmd = "ConvertScalarImageToRGB"
input_spec = ConvertScalarImageToRGBInputSpec
output_spec = ConvertScalarImageToRGBOutputSpec
def _format_arg(self, opt, spec, val):
return super(ConvertScalarImageToRGB, self)._format_arg(opt, spec, val)
def _list_outputs(self):
outputs = self._outputs().get()
outputs["output_image"] = os.path.join(os.getcwd(), self.inputs.output_image)
return outputs
class CreateTiledMosaicInputSpec(ANTSCommandInputSpec):
input_image = File(
argstr="-i %s",
exists=True,
desc="Main input is a 3-D grayscale image.",
mandatory=True,
)
rgb_image = File(
argstr="-r %s",
exists=True,
desc=(
"An optional Rgb image can be added as an overlay."
"It must have the same image"
"geometry as the input grayscale image."
),
mandatory=True,
)
mask_image = File(
argstr="-x %s", exists=True, desc="Specifies the ROI of the RGB voxels used."
)
alpha_value = traits.Float(
argstr="-a %.2f",
desc=(
"If an Rgb image is provided, render the overlay "
"using the specified alpha parameter."
),
)
output_image = traits.Str(
"output.png",
argstr="-o %s",
desc="The output consists of the tiled mosaic image.",
usedefault=True,
)
tile_geometry = traits.Str(
argstr="-t %s",
desc=(
"The tile geometry specifies the number of rows and columns"
'in 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 selected"
"based on direction."
),
)
direction = traits.Int(
argstr="-d %d",
desc=(
"Specifies the direction of "
"the slices. If no direction is specified, the "
"direction with the coarsest spacing is chosen."
),
)
pad_or_crop = traits.Str(
argstr="-p %s",
desc="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".',
)
slices = traits.Str(
argstr="-s %s",
desc=(
"Number of slices to increment Slice1xSlice2xSlice3"
"[numberOfSlicesToIncrement,<minSlice=0>,<maxSlice=lastSlice>]"
),
)
flip_slice = traits.Str(argstr="-f %s", desc="flipXxflipY")
permute_axes = traits.Bool(argstr="-g", desc="doPermute")
class CreateTiledMosaicOutputSpec(TraitedSpec):
output_image = File(exists=True, desc="image file")
class CreateTiledMosaic(ANTSCommand):
"""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]'
"""
_cmd = "CreateTiledMosaic"
input_spec = CreateTiledMosaicInputSpec
output_spec = CreateTiledMosaicOutputSpec
def _list_outputs(self):
outputs = self._outputs().get()
outputs["output_image"] = os.path.join(os.getcwd(), self.inputs.output_image)
return outputs