gattia

import SimpleITK as sitk
import numpy as np
import os
import matplotlib.pyplot as plt

folder_dicom = 'FILL THIS PATH IN'
where_to_save = 'PATH_TO_SAVE/filename.nrrd'


# read in the dicom series as an image

gattia

import os
import json
import subprocess


def python_submit(command, 
                  out='./slurm-%j.out', 
                  gpu='2080ti', 
                  node='any', 
                  memory=24, 

gattia

import torch 
import numpy as np
from typing import Callable, Sequence, Union

arr_type = Union[np.ndarray, torch.Tensor]

def flatten_other_dims(
    xs: Union[arr_type, Sequence[arr_type]], dim: Union[int, Sequence[int]] = None
):
    """Flattens all dimensions other than the specified dimension(s).

gattia

imoport numpy as np
import SimpleITK as sitk

def get_maps(binary_seg):
    dist_map = sitk.Abs(sitk.SignedMaurerDistanceMap(binary_seg,
                                                     squaredDistance=False,
                                                     useImageSpacing=True))
    surface_map = sitk.LabelContour(binary_seg)

    return (dist_map, surface_map)

gattia

apt-get update
apt-get install --yes \
    build-essential \
    cmake \
    libtool \
    autoconf \
    pkg-config \
    gfortran \
    libopenblas-dev \
    liblapack-dev \

gattia

import numpy as np
from pycpd import RigidRegistration

# Based off of this example: https://github.com/siavashk/pycpd/blob/master/examples/bunny_rigid_3D.py

X = np.loadtxt('data/bunny_target.txt')
# synthetic data, equaivalent to X + 1
Y = np.loadtxt('data/bunny_source.txt')

reg = RigidRegistration(**{'X': X, 'Y': Y})

gattia

/* ----------------------------------------------------------------------------
 * This file was automatically generated by SWIG (http://www.swig.org).
 * Version 4.0.2
 *
 * Do not make changes to this file unless you know what you are doing--modify
 * the SWIG interface file instead.
 * ----------------------------------------------------------------------------- */

package org.opensim.modeling;

gattia

/* ----------------------------------------------------------------------------
 * This file was automatically generated by SWIG (http://www.swig.org).
 * Version 4.0.2
 *
 * Do not make changes to this file unless you know what you are doing--modify
 * the SWIG interface file instead.
 * ----------------------------------------------------------------------------- */

package org.opensim.modeling;

gattia

/* ----------------------------------------------------------------------------
 * This file was automatically generated by SWIG (http://www.swig.org).
 * Version 4.0.2
 *
 * Do not make changes to this file unless you know what you are doing--modify
 * the SWIG interface file instead.
 * ----------------------------------------------------------------------------- */

package org.opensim.modeling;

gattia

# This file was automatically generated by SWIG (http://www.swig.org).
# Version 4.0.2
#
# Do not make changes to this file unless you know what you are doing--modify
# the SWIG interface file instead.

from sys import version_info as _swig_python_version_info
if _swig_python_version_info < (2, 7, 0):
    raise RuntimeError("Python 2.7 or later required")