def main():
parser = argparse.ArgumentParser(
description='Run preprocess on in data folder')
parser.add_argument('--in-folder',
type=str,
help='Folder of input data',
required=True)
parser.add_argument('--out-folder',
type=str,
help='Output location for preprocessed images',
required=True)
parser.add_argument(
'--average-img',
type=str,
help='Use this average image to impute the missing voxels in targets')
parser.add_argument('--file-list-txt', type=str)
parser.add_argument('--num-process', type=int, default=10)
args = parser.parse_args()
in_folder_obj = DataFolder(args.in_folder, args.file_list_txt)
out_folder_obj = DataFolder(args.out_folder, args.file_list_txt)
average_img_obj = ScanWrapper(args.average_img)
preprocess_obj = PreprocessAverageImputation(in_folder_obj, out_folder_obj,
average_img_obj,
args.num_process)
preprocess_obj.run_parallel()
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--in-folder', type=str)
# parser.add_argument(
# '--in-mask',
# type=str,
# default=None,
# help='If is none, the orignal input images will be used'
# )
parser.add_argument('--file-list', type=str)
parser.add_argument('--out-png-folder', type=str)
parser.add_argument('--offset-axial', type=int, default=0)
parser.add_argument('--offset-sagittal', type=int, default=0)
parser.add_argument('--offset-coronal', type=int, default=0)
parser.add_argument('--vmin', type=float, default=-1000)
parser.add_argument('--vmax', type=float, default=500)
parser.add_argument('--unit-label',
type=str,
default=None,
help='If none, the color bar will be omitted.')
parser.add_argument('--num-process', type=str, default=10)
args = parser.parse_args()
in_folder_obj = DataFolder(args.in_folder, args.file_list)
out_folder_obj = DataFolder(args.out_png_folder, args.file_list)
out_folder_obj.change_suffix('')
mkdir_p(args.out_png_folder)
plot_obj = ParalClipPlot(in_folder_obj, out_folder_obj, args.offset_axial,
args.offset_sagittal, args.offset_coronal,
args.vmin, args.vmax, args.unit_label,
args.num_process)
plot_obj.run_parallel()
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--in-folder', type=str)
parser.add_argument('--in-effective-mask-folder', type=str)
parser.add_argument('--file-list-txt', type=str)
parser.add_argument('--gt-mask', type=str)
parser.add_argument('--out-csv', type=str)
parser.add_argument('--num-process', type=int, default=25)
args = parser.parse_args()
in_folder_obj = DataFolder(args.in_folder, args.file_list_txt)
in_effective_mask_folder_obj = DataFolder(args.in_effective_mask_folder, args.file_list_txt)
dice_cal = GetMeanSurfaceDist(in_folder_obj, in_effective_mask_folder_obj, args.num_process, args.gt_mask)
dice_cal.get_surface_metric()
dice_cal.save_csv(args.out_csv)
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--in-ori-folder', type=str)
parser.add_argument('--out-folder', type=str)
parser.add_argument('--file-list-txt', type=str)
parser.add_argument('--val', type=float)
parser.add_argument('--num-process', type=int, default=10)
args = parser.parse_args()
in_ori_folder_obj = DataFolder(args.in_ori_folder, args.file_list_txt)
out_folder_obj = DataFolder(args.out_folder, args.file_list_txt)
exe_obj = ParaReplaceNan(in_ori_folder_obj, out_folder_obj, args.val,
args.num_process)
exe_obj.run_parallel()
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--in-mask-folder1', type=str)
parser.add_argument('--in-mask-folder2', type=str)
parser.add_argument('--out-folder', type=str)
parser.add_argument('--file-list-txt', type=str)
parser.add_argument('--num-process', type=int, default=10)
args = parser.parse_args()
in_folder1_obj = DataFolder(args.in_mask_folder1, args.file_list_txt)
in_folder2_obj = DataFolder(args.in_mask_folder2, args.file_list_txt)
out_folder_obj = DataFolder(args.out_folder, args.file_list_txt)
exe_obj = Union2Masks(in_folder1_obj, in_folder2_obj, out_folder_obj, args.num_process)
exe_obj.run_parallel()
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--in-folder', type=str)
parser.add_argument('--out-mask-folder', type=str)
parser.add_argument('--out-label-folder', type=str)
parser.add_argument('--out-clip-png-folder', type=str)
parser.add_argument('--file-list-txt', type=str)
parser.add_argument('--num-process', type=int, default=10)
args = parser.parse_args()
in_folder_obj = DataFolder(args.in_folder, args.file_list_txt)
out_mask_folder_obj = DataFolder(args.out_mask_folder, args.file_list_txt)
out_label_folder_obj = DataFolder(args.out_label_folder, args.file_list_txt)
out_clip_png_folder_obj = DataFolder(args.out_clip_png_folder, args.file_list_txt)
out_clip_png_folder_obj.change_suffix('.png')
exe_obj = ParalPPVMask(
in_folder_obj,
out_mask_folder_obj,
out_label_folder_obj,
out_clip_png_folder_obj,
args.num_process
)
exe_obj.run_parallel()
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--in-ori-folder', type=str)
parser.add_argument('--in-affine-folder')
parser.add_argument('--in-warped-folder', type=str)
parser.add_argument('--ref-img', type=str)
parser.add_argument('--file-list-txt', type=str)
parser.add_argument('--out-png-folder', type=str)
parser.add_argument('--step-axial', type=int, default=50)
parser.add_argument('--step-sagittal', type=int, default=75)
parser.add_argument('--step-coronal', type=int, default=30)
parser.add_argument('--num-process', type=int, default=10)
args = parser.parse_args()
in_ori_folder_obj = DataFolder(args.in_ori_folder, args.file_list_txt)
in_affine_folder_obj = DataFolder(args.in_affine_folder,
args.file_list_txt)
in_warped_folder_obj = DataFolder(args.in_warped_folder,
args.file_list_txt)
out_png_folder_obj = DataFolder(args.out_png_folder, args.file_list_txt)
out_png_folder_obj.change_suffix('.png')
ref_img = ScanWrapper(args.ref_img)
exe_obj = Overlay3Views(in_ori_folder_obj, in_affine_folder_obj,
in_warped_folder_obj, out_png_folder_obj, ref_img,
args.step_axial, args.step_sagittal,
args.step_coronal, args.num_process)
exe_obj.run_parallel()
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--in-ori-folder', type=str)
parser.add_argument('--file-list-txt', type=str)
parser.add_argument('--in-ref-valid-mask', type=str)
parser.add_argument('--out-folder', type=str)
parser.add_argument('--etch-radius', type=int)
parser.add_argument('--num-process', type=int, default=10)
args = parser.parse_args()
in_folder_obj = DataFolder(args.in_ori_folder, args.file_list_txt)
out_folder_obj = DataFolder(args.out_folder, args.file_list_txt)
effect_region = GetDiceEffectiveRegion(in_folder_obj,
args.in_ref_valid_mask,
args.num_process, out_folder_obj,
args.etch_radius)
effect_region.run_parallel()
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--in-mask-folder', type=str)
parser.add_argument('--in-ref-mask', type=str, default=None)
parser.add_argument('--out-folder', type=str)
parser.add_argument('--file-list-txt', type=str)
parser.add_argument('--num-process', type=int, default=10)
args = parser.parse_args()
in_folder_obj = DataFolder(args.in_mask_folder, args.file_list_txt)
out_folder_obj = DataFolder(args.out_folder, args.file_list_txt)
ref_mask_obj = ScanWrapper(args.in_ref_mask)
exe_obj = GetDiffMask(in_folder_obj, out_folder_obj, ref_mask_obj,
args.num_process)
exe_obj.run_parallel()
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--in-folder', type=str)
parser.add_argument('--inverse-label', action='store_true')
parser.add_argument('--out-mask-folder', type=str)
parser.add_argument('--file-list-txt', type=str)
parser.add_argument('--num-process', type=int, default=10)
args = parser.parse_args()
in_folder_obj = DataFolder(args.in_folder, args.file_list_txt)
out_mask_folder_obj = DataFolder(args.out_mask_folder, args.file_list_txt)
logger.info(f'Get non-nan mask in folder from {args.in_folder}')
exe_obj = NonNanRegionMask(in_folder_obj, out_mask_folder_obj,
args.num_process, args.inverse_label)
exe_obj.run_parallel()
def main():
parser = argparse.ArgumentParser(description='Run preprocess on in data folder')
parser.add_argument('--in-folder', type=str,
help='Folder of input data', required=True)
parser.add_argument('--out-folder', type=str,
help='Output location for preprocessed images', required=True)
parser.add_argument('--c3d-path', type=str)
parser.add_argument('--file-list-txt', type=str)
parser.add_argument('--num-process', type=int, default=10)
args = parser.parse_args()
in_folder_obj = DataFolder(args.in_folder, args.file_list_txt)
out_folder_obj = DataFolder(args.out_folder, args.file_list_txt)
preprocess_obj = PreprocessTrimROI(
in_folder_obj,
out_folder_obj,
args.c3d_path,
args.num_process
)
preprocess_obj.run_parallel()
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--in-folder', type=str)
parser.add_argument('--out-folder', type=str)
parser.add_argument('--file-list-txt', type=str)
parser.add_argument('--num-clip', type=int)
parser.add_argument('--vmin', type=float)
parser.add_argument('--vmax', type=float)
parser.add_argument('--num-process', type=int, default=10)
args = parser.parse_args()
in_folder_obj = DataFolder(args.in_folder, args.file_list_txt)
out_folder_obj = DataFolder(args.out_folder, args.file_list_txt)
out_folder_obj.change_suffix('.png')
exe_obj = ParalClipMontagePlotNII(in_folder_obj, out_folder_obj,
args.num_clip, args.vmin, args.vmax,
args.num_process)
exe_obj.run_parallel()
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--in-folder', type=str)
parser.add_argument('--in-mask-folder', type=str, default=None)
parser.add_argument('--in-mask-file', type=str, default=None)
parser.add_argument('--out-folder', type=str)
parser.add_argument('--file-list-txt', type=str)
parser.add_argument('--ambient-val', type=str)
parser.add_argument('--num-process', type=int, default=10)
args = parser.parse_args()
in_folder_obj = DataFolder(args.in_folder, args.file_list_txt)
out_folder_obj = DataFolder(args.out_folder, args.file_list_txt)
in_mask_folder_obj = None
in_mask_file_obj = None
if args.in_mask_folder is not None:
logger.info(f'Create in_mask_folder_obj with {args.in_mask_folder}')
in_mask_folder_obj = DataFolder(args.in_mask_folder,
args.file_list_txt)
logger.info(
f'Apply mask in folder {args.in_mask_folder} to {args.in_folder}')
if args.in_mask_file is not None:
logger.info(f'Create in_mask_file_obj with {args.in_mask_file}')
in_mask_file_obj = ScanWrapper(args.in_mask_file)
ambient_val = None
ambient_val_str = args.ambient_val
if ambient_val_str is 'nan':
ambient_val = np.nan
else:
ambient_val = float(args.ambient_val)
exe_obj = ApplyMask(in_folder_obj,
out_folder_obj,
ambient_val,
args.num_process,
in_mask_folder_obj=in_mask_folder_obj,
in_mask_file_obj=in_mask_file_obj)
exe_obj.run_parallel()
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--in-jac-det-folder', type=str)
parser.add_argument('--file-list-txt', type=str)
parser.add_argument('--out-csv', type=str)
parser.add_argument('--num-process', type=int, default=10)
args = parser.parse_args()
in_folder_obj = DataFolder(args.in_jac_det_folder, args.file_list_txt)
dice_cal = JacobianDetStatics(in_folder_obj, args.num_process)
dice_cal.get_jac_statics()
dice_cal.save_csv(args.out_csv)
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--in-ori-folder', type=str)
parser.add_argument('--in-ref-folder', type=str)
parser.add_argument('--out-folder', type=str)
parser.add_argument('--file-list-txt', type=str)
parser.add_argument('--niftyreg-path', type=str, default=reg_resample_path)
parser.add_argument('--int-order', type=int, default=3)
parser.add_argument('--pad-val', type=str, default='NaN')
parser.add_argument('--num-process', type=int, default=10)
args = parser.parse_args()
in_ori_folder_obj = DataFolder(args.in_ori_folder, args.file_list_txt)
in_ref_folder_obj = DataFolder(args.in_ref_folder, args.file_list_txt)
out_folder_obj = DataFolder(args.out_folder, args.file_list_txt)
exe_obj = ParalResampleNiftyReg(in_ori_folder_obj, in_ref_folder_obj,
out_folder_obj, args.niftyreg_path,
args.int_order, args.num_process,
args.pad_val)
exe_obj.run_parallel()
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--in-ori-folder', type=str)
parser.add_argument('--out-folder', type=str)
parser.add_argument('--file-list-txt', type=str)
parser.add_argument('--c3d-path', type=str)
parser.add_argument('--command-str', type=str)
parser.add_argument('--num-process', type=int, default=10)
args = parser.parse_args()
in_ori_folder_obj = DataFolder(args.in_ori_folder, args.file_list_txt)
out_folder_obj = DataFolder(args.out_folder, args.file_list_txt)
exe_obj = ParalC3DCommand(
in_ori_folder_obj,
out_folder_obj,
args.c3d_path,
args.command_str,
args.num_process
)
exe_obj.run_parallel()
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--in-folder', type=str,
default='/nfs/masi/xuk9/SPORE/data/data_flat')
parser.add_argument('--in-mask-folder', type=str,
default='/nfs/masi/xuk9/src/lungmask/SPORE/lung_mask_nii')
parser.add_argument('--out-clip-png-folder', type=str,
default='/nfs/masi/xuk9/src/lungmask/SPORE/lung_mask_nii_clip_png')
parser.add_argument('--file-list-txt', type=str,
default='/nfs/masi/xuk9/SPORE/data/vlsp_data_list.txt')
parser.add_argument('--num-process', type=int, default=1)
args = parser.parse_args()
mkdir_p(args.in_mask_folder)
mkdir_p(args.out_clip_png_folder)
in_folder_obj = DataFolder(args.in_folder, args.file_list_txt)
out_mask_folder_obj = DataFolder(args.in_mask_folder, args.file_list_txt)
out_clip_png_folder_obj = DataFolder(args.out_clip_png_folder, args.file_list_txt)
out_clip_png_folder_obj.change_suffix('.png')
exe_obj = ParalPPVMask(
in_folder_obj,
out_mask_folder_obj,
out_clip_png_folder_obj,
args.num_process
)
exe_obj.run_parallel()
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--in-folder', type=str)
parser.add_argument('--out-average-path', type=str)
parser.add_argument('--file-list-txt', type=str)
parser.add_argument('--num-process', type=int, default=10)
args = parser.parse_args()
in_folder_obj = DataFolder(args.in_folder, args.file_list_txt)
exe_obj = AverageValidRegion(in_folder_obj, args.num_process)
exe_obj.run_get_average()
exe_obj.output_result_average(args.out_average_path, ambient_val=np.nan)
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--in-folder', type=str)
parser.add_argument('--out-folder', type=str)
parser.add_argument('--inter', type=int, default=3)
parser.add_argument('--file-list-txt', type=str)
parser.add_argument('--dim', type=str)
parser.add_argument('--num-process', type=int, default=10)
args = parser.parse_args()
dim_list = args.dim.split('x')
logger.info(
f'Resample image to dimension {dim_list[0]}x{dim_list[1]}x{dim_list[2]}'
)
in_folder_obj = DataFolder(args.in_folder, args.file_list_txt)
out_folder_obj = DataFolder(args.out_folder, args.file_list_txt)
exe_obj = C3DResample(in_folder_obj, out_folder_obj, dim_list, args.inter,
args.num_process)
exe_obj.run_parallel()
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--in-ori-folder', type=str)
parser.add_argument('--out-folder', type=str)
parser.add_argument('--file-list-txt', type=str)
parser.add_argument('--c3d-path', type=str)
parser.add_argument('--res-val', type=float)
parser.add_argument('--int-order', type=int, default=3)
parser.add_argument('--num-process', type=int, default=10)
args = parser.parse_args()
in_ori_folder_obj = DataFolder(args.in_ori_folder, args.file_list_txt)
out_folder_obj = DataFolder(args.out_folder, args.file_list_txt)
exe_obj = ParalResample(
in_ori_folder_obj,
out_folder_obj,
args.c3d_path,
args.res_val,
args.int_order,
args.num_process
)
exe_obj.run_parallel()
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--in-folder', type=str)
parser.add_argument('--mask-img', type=str)
parser.add_argument('--file-list-txt', type=str)
parser.add_argument('--out-bin-path', type=str)
args = parser.parse_args()
in_folder_obj = DataFolder(args.in_folder, args.file_list_txt)
mask_img = ScanWrapper(args.mask_img)
creator_obj = CreateMaskedFeatureMatrix(in_folder_obj, mask_img)
creator_obj.load_data()
creator_obj.save_to_bin(args.out_bin_path)
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--in-folder', type=str, help='Folder of NIFTI files')
parser.add_argument('--out-folder', type=str, help='Output folder')
parser.add_argument('--file-list-txt', type=str, help='List of filename in plain txt (ls ${in_folder} > file_list)')
parser.add_argument('--num-clip', type=int, help='Number of clip on each direction')
parser.add_argument('--vmin', type=float, default=-1000)
parser.add_argument('--vmax', type=float, default=600)
parser.add_argument('--num-process', type=int, default=10, help='Number of cores')
args = parser.parse_args()
in_folder_obj = DataFolder(args.in_folder, args.file_list_txt)
out_folder_obj = DataFolder(args.out_folder, args.file_list_txt)
out_folder_obj.change_suffix('.png')
exe_obj = ParalClipMontagePlotNII(
in_folder_obj,
out_folder_obj,
args.num_clip,
args.vmin, args.vmax,
args.num_process
)
exe_obj.run_parallel()
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--in-folder', type=str)
parser.add_argument('--ref-img', type=str)
parser.add_argument('--file-list-txt', type=str)
parser.add_argument('--niftyreg-root', type=str)
parser.add_argument('--out-csv', type=str)
parser.add_argument('--num-process', type=int, default=10)
args = parser.parse_args()
in_folder_obj = DataFolder(args.in_folder, args.file_list_txt)
ref_img = ScanWrapper(args.ref_img)
exe_obj = MetricNMI(in_folder_obj, ref_img, args.niftyreg_root,
args.num_process)
exe_obj.get_nmi()
exe_obj.save_csv(args.out_csv)
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--in-folder', type=str)
parser.add_argument('--in-omat-folder', type=str)
parser.add_argument('--out-folder', type=str)
parser.add_argument('--out-corrected-folder')
parser.add_argument('--file-list-txt', type=str)
parser.add_argument('--num-process', type=int, default=10)
args = parser.parse_args()
in_folder_obj = DataFolder(args.in_folder, args.file_list_txt)
in_omat_obj = DataFolder(args.in_omat_folder, args.file_list_txt)
in_omat_obj.change_suffix('.txt')
out_corrected_folder_obj = DataFolder(args.out_corrected_folder,
args.file_list_txt)
exe_obj = AverageValidRegion(in_folder_obj, in_omat_obj,
out_corrected_folder_obj, args.num_process)
exe_obj.run_get_average()
exe_obj.run_get_variance()
exe_obj.output_result_folder(args.out_folder, np.nan)