__all__ = ['create_tiled_mosaic']
import os
from tempfile import mktemp
from PIL import Image
from .. import utils
from ..core import ants_image_io as iio2
[docs]def create_tiled_mosaic(image, rgb=None, mask=None, overlay=None,
output=None, alpha=1., direction=0,
pad_or_crop=None, slices=None,
flip_slice=None, permute_axes=False):
"""
Create a tiled mosaic of 2D slice images from a 3D ANTsImage.
ANTsR function : N/A
ANTs function : `createTiledMosaic`
Arguments
---------
image : ANTsImage
base image to visualize
rgb : ANTsImage
optional overlay image to display on top of base image
mask : ANTsImage
optional mask image
alpha : float
alpha value for rgb/overlay image
direction : integer or string
which axis to visualize
options: 0, 1, 2, 'x', 'y', 'z'
pad_or_crop : list of 2-tuples
padding or cropping values for each dimension and each side.
- to crop the X dimension, use the following:
pad_or_crop = [(10,10), 0, 0]
- to pad the X dimension, use the following:
pad_or_crop = [(-10,-10), 0, 0]
slices : list/numpy.ndarray or integer or 3-tuple
if list or numpy.ndarray:
slices to use
if integer:
number of slices to incremenet
if 3-tuple:
(# slices to increment, min slice, max slice)
flip_slice : 2-tuple of boolean
(whether to flip X direction, whether to flip Y direction)
permute_axes : boolean
whether to permute axes
output : string
output filename where mosaic image will be saved.
If not given, this function will save to a temp file,
then return the image as a PIL.Image object
ANTs
----
-i, --input-image inputImageFilename
-r, --rgb-image rgbImageFilename
-x, --mask-image maskImageFilename
-a, --alpha value
-e, --functional-overlay [rgbImageFileName,maskImageFileName,<alpha=1>]
-o, --output tiledMosaicImage
-t, --tile-geometry RxC
-d, --direction 0/1/2/x/y/(z)
-p, --pad-or-crop padVoxelWidth
[padVoxelWidth,<constantValue=0>]
[lowerPadding[0]xlowerPadding[1],upperPadding[0]xupperPadding[1],constantValue]
-s, --slices Slice1xSlice2xSlice3...
numberOfSlicesToIncrement
[numberOfSlicesToIncrement,<minSlice=0>,<maxSlice=lastSlice>]
-f, --flip-slice flipXxflipY
-g, --permute-axes doPermute
-h
CreateTiledMosaic -i OAS1_0457_MR1_mpr_n3_anon_sbj_111BrainSegmentation0N4 . nii . gz \
-r OAS1_0457_MR1_mpr_n3_anon_sbj_111CorticalThickness_hot . nii . gz \
-x OAS1_0457_MR1_mpr_n3_anon_sbj_111CorticalThickness_mask . nii . gz \
-o OAS1_0457_MR1_mpr_n3_anon_sbj_111_tiledMosaic . png \
-a 1.0 -t -1 x8 -d 2 -p [ -15x -50 , -15x -30 ,0] -s [2 ,100 ,160]
Example
-------
>>> import ants
>>> image = ants.image_read(ants.get_ants_data('ch2'))
>>> plt = ants.create_tiled_mosaic(image)
"""
# image needs to be unsigned char
if image.pixeltype != 'unsigned char':
# transform between 0 and 255.
image = (image - image.max()) / (image.max() - image.min())
image = image * 255.
image = image.clone('unsigned char')
output_is_temp = False
if output is None:
output_is_temp = True
output = mktemp(suffix='.jpg')
if rgb is None:
rgb = image.clone()
imagepath = mktemp(suffix='.nii.gz')
iio2.image_write(image, imagepath)
rgbpath = mktemp(suffix='.nii.gz')
iio2.image_write(rgb, rgbpath)
args = {
'i': imagepath,
'r': rgbpath,
'o': output,
'x': mask,
'e': overlay,
'a': alpha,
'd': direction
}
processed_args = utils._int_antsProcessArguments(args)
libfn = utils.get_lib_fn('CreateTiledMosaic')
libfn(processed_args)
outimage = Image.open(output)
if output_is_temp:
os.remove(output)
return outimage
