sarthakpati

import SimpleITK as sitk

# read image
inputImage = sitk.ReadImage('/path/to/input.nii.gz')

# get result in the form of a numpy array
npa_res = my_algorithm(sitk.GetArrayFromImage(inputImage)) # my_algorithm does something fancy

# Converting back to SimpleITK (assumes we didn't move the image in space as we copy the information from the original)
result_image = sitk.GetImageFromArray(npa_res)

sarthakpati

import SimpleITK as sitk

image_file = '/path/to/image.nii.gz'
mask_file = '/path/to/image.nii.gz'

image = sitk.ReadImage(image_file)
mask = sitk.ReadImage(mask_file)

bb_filter = sitk.LabelStatisticsImageFilter()
bb_filter.Execute(image, mask)

sarthakpati

import os
import SimpleITK as sitk

input_dicom = '/path/to/input/dicom'
output_dicom_dir = '/path/to/output'
# create the folder output_dicom_dir
series_IDs = sitk.ImageSeriesReader.GetGDCMSeriesIDs(input_dicom)
if not series_IDs:
  print("ERROR: given directory \"" + input_dicom + "\" does not contain a valid DICOM series.")
  sys.exit(1)

sarthakpati

## Ref: https://github.com/razorx89/pydicom-seg#getting-started

import pydicom
import pydicom_seg
import SimpleITK as sitk

dcm_path = pydicom.dcmread('/path/to/segmentation.dcm')

reader = pydicom_seg.MultiClassReader()
result = reader.read(dcm_path)

sarthakpati

import SimpleITK as sitk
import numpy as np


def sanity_checker_with_files(
    image_file_baseline: str, image_file_compare: str, threshold: float = 1e-5
) -> bool:
    """
    This function performs sanity check on 2 image files WITHOUT loading images into memory.
    Supported image formats: https://simpleitk.readthedocs.io/en/master/IO.html

sarthakpati

import SimpleITK as sitk

# read image to copy information from
image_reference = sitk.ReadImage('/path/to/reference.nii.gz')
image_to_copy_from = sitk.ReadImage('/path/to/image_to_change.nii.gz')

image_to_copy_from.CopyInformation(image_reference)

# write the image
sitk.WriteImage(image_to_copy_from, '/path/to/result.nii.gz')

sarthakpati

from typing import Union, OrderedDict
import SimpleITK as sitk
import numpy as np


def one_hot_encode(
    input_mask: Union[str, sitk.Image],
    encoding_logic: dict = {"NET": [1], "TC": [1, 4], "WT": [1, 2, 4]},
) -> dict:
    """

sarthakpati

import os
import SimpleITK as sitk

input_directory = os.path.join(os.getcwd(), "data")

for filename in os.listdir(input_directory):
    if filename.endswith(".nii.gz"):
        image = sitk.ReadImage(os.path.join(input_directory, filename))

        # properties

sarthakpati

import os, time, traceback, pathlib
import SimpleITK as sitk


def downsample_dicom(
    dicom_path: str, output_path: str, downsample_factor: int = 0.5
) -> None:
    """
    Downsample DICOM images and save them to the output path.

sarthakpati

import SimpleITK as sitk

image_to_cast = sitk.ReadImage("/path/to/image.nii.gz")
options_for_casting = {
    "int64": sitk.sitkInt64,
    "int32": sitk.sitkInt32,
    "int16": sitk.sitkInt16,
    "int8": sitk.sitkInt8,
    "uint64": sitk.sitkUInt64,
    "uint32": sitk.sitkUInt32,