def main(args):
parser = parsefn()
subj_dir, img, seg, gap, tile, alpha, ax, roi, flip, min_sl, out = parse_inputs(
parser, args)
# pred preprocess dir
pred_dir = '%s/pred_process' % os.path.abspath(subj_dir)
if not os.path.exists(pred_dir):
os.mkdir(pred_dir)
# trim seg to focus
c3 = C3d()
mosaic_slicer = CreateTiledMosaic()
if seg:
c3.inputs.in_file = seg
c3.inputs.args = "-trim %sx%sx%svox" % (roi, roi, roi)
seg_trim_file = "%s/%s_trim_mosaic.nii.gz" % (
pred_dir, os.path.basename(seg).split('.')[0])
# seg_trim_file = "seg_trim.nii.gz"
c3.inputs.out_file = seg_trim_file
c3.run()
# trim struct like seg
c3.inputs.in_file = seg_trim_file
c3.inputs.args = "%s -reslice-identity" % img
struct_trim_file = "%s/%s_trim_mosaic.nii.gz" % (
pred_dir, os.path.basename(img).split('.')[0])
# struct_trim_file = "struct_trim.nii.gz"
c3.inputs.out_file = struct_trim_file
c3.run()
# create rgb image from seg
converter = ConvertScalarImageToRGB()
converter.inputs.dimension = 3
converter.inputs.input_image = seg_trim_file
converter.inputs.colormap = 'jet'
converter.inputs.minimum_input = 0
converter.inputs.maximum_input = 10
out_rgb = "%s/%s_trim_rgb.nii.gz" % (
pred_dir, os.path.basename(seg).split('.')[0])
converter.inputs.output_image = out_rgb
converter.run()
mosaic_slicer.inputs.rgb_image = out_rgb
mosaic_slicer.inputs.mask_image = seg_trim_file
mosaic_slicer.inputs.alpha_value = alpha
else:
struct_trim_file = img
mosaic_slicer.inputs.rgb_image = struct_trim_file
# stretch and clip intensities
c3.inputs.in_file = struct_trim_file
c3.inputs.args = "-stretch 2% 98% 0 255 -clip 0 255"
c3.inputs.out_file = struct_trim_file
c3.run()
# slices to show
if gap == 1:
max_sl = 100
elif gap == 2:
max_sl = 220
elif gap == 5:
max_sl = 275
else:
max_sl = 300
slices = '[%s,%s,%s]' % (gap, min_sl, max_sl)
mosaic_slicer.inputs.input_image = struct_trim_file
mosaic_slicer.inputs.output_image = out
mosaic_slicer.inputs.direction = ax
# mosaic_slicer.inputs.pad_or_crop = '[ -15x -50 , -15x -30 ,0]'
mosaic_slicer.inputs.tile_geometry = tile
mosaic_slicer.inputs.slices = slices
mosaic_slicer.inputs.flip_slice = flip
mosaic_slicer.terminal_output = "none"
mosaic_slicer.run()
