sample ugly csv to nifti

foobar.py

import time
import sys
import pandas as pd
import numpy as np
import SimpleITK as sitk


def foobar_np(source_nifti_file,source_csv_file,target_nifti_file):
    
    df = pd.read_csv(source_csv_file) # columns,x,y,z,foo

    source_obj = sitk.ReadImage(source_nifti_file)
    source = sitk.GetArrayFromImage(source_obj)

    arr = np.zeros_like(source)
    multi_index = df.apply(lambda row: [int(row.z),int(row.y),int(row.x)], axis=1)
    multi_index = np.array(multi_index.to_list()).T

    ind = np.ravel_multi_index(multi_index, arr.shape)
    v = df.apply(lambda row: [row.foo], axis=1).to_list()
    np.put(arr,ind,v)

    target_obj = sitk.GetImageFromArray(arr)
    target_obj.CopyInformation(source_obj)
    sitk.WriteImage(target_obj,target_nifti_file)

    # confirm values are same
    target = sitk.GetArrayFromImage(target_obj)
    
    print(np.mean(np.abs(target-source)))

def foobar_itk(source_nifti_file,source_csv_file,target_nifti_file):
    
    df = pd.read_csv(source_csv_file) # columns,x,y,z,foo
    foo_series = df.apply(lambda row: [int(row.x),int(row.y),int(row.z),row.foo], axis=1)
    
    source_obj = sitk.ReadImage(source_nifti_file)

    arr = np.zeros_like(sitk.GetArrayFromImage(source_obj))
    target_obj = sitk.GetImageFromArray(arr)
    for item in foo_series:
        target_obj.SetPixel(*item)
    target_obj.CopyInformation(source_obj)
    sitk.WriteImage(target_obj,target_nifti_file)

    # confirm values are same
    target = sitk.GetArrayFromImage(target_obj)
    source = sitk.GetArrayFromImage(source_obj)
    print(np.mean(np.abs(target-source)))

def gen_mock_data():
    foo = np.round(np.random.rand(16,16,16),2)
    z,y,x = np.indices(foo.shape)  # NOTE the ordering between numpy vs SimpleITK
    df=pd.DataFrame()
    df['x']=pd.Series(x.ravel())
    df['y']=pd.Series(y.ravel())
    df['z']=pd.Series(z.ravel())
    df['foo']=pd.Series(foo.ravel())
    df.to_csv("foo.csv",index=False)
    foo_obj = sitk.GetImageFromArray(foo)
    sitk.WriteImage(foo_obj,'foo.nii.gz')

if __name__ == "__main__":

    gen_mock_data()

    template_nifti_file = sys.argv[1]
    source_csv_file = sys.argv[2]
    target_nifti_file = sys.argv[3]
    
    s=time.time()
    foobar_itk(template_nifti_file,source_csv_file,target_nifti_file)
    e=time.time()
    print(e-s)
    s=time.time()
    foobar_np(template_nifti_file,source_csv_file,target_nifti_file)
    e=time.time()
    print(e-s)

"""
docker run -it -u $(id -u):$(id -g) \
    -w $PWD -v $PWD:$PWD \
    pangyuteng/dcm:latest bash
python csv2nifti.py foo.nii.gz foo.csv bar.nii.gz
"""

sample_crop.py

import sys
import SimpleITK as sitk

original_image_file = sys.argv[1]
original_mask_file = sys.argv[2]
cropped_image_file = sys.argv[3]
cropped_mask_file = sys.argv[4]

img_obj = sitk.ReadImage(original_image_file)
mask_obj = sitk.ReadImage(original_mask_file)

lower_threshold, upper_threshold = 1,2
inside_val, outside_val = 1,0
roi_obj = sitk.BinaryThreshold( mask_obj, lower_threshold, upper_threshold, inside_val, outside_val)

print("mask_obj")
print("GetSize",mask_obj.GetSize())
print("GetSpacing",mask_obj.GetSpacing())
print("GetDirection",mask_obj.GetDirection())
print("GetOrigin",mask_obj.GetOrigin())

label_shape_filter = sitk.LabelShapeStatisticsImageFilter()    
label_shape_filter.Execute(roi_obj)
bounding_box = label_shape_filter.GetBoundingBox(1)
cropped_size = bounding_box[int(len(bounding_box)/2):]
cropped_start = bounding_box[0:int(len(bounding_box)/2)]

cropped_img_obj = sitk.RegionOfInterest(img_obj,cropped_size,cropped_start)
cropped_mask_obj = sitk.RegionOfInterest(mask_obj,cropped_size,cropped_start)
print("cropped_mask_obj")
print("GetSize",cropped_mask_obj.GetSize())
print("GetSpacing",cropped_mask_obj.GetSpacing())
print("GetDirection",cropped_mask_obj.GetDirection())
print("GetOrigin",cropped_mask_obj.GetOrigin())


sitk.WriteImage(cropped_img_obj,cropped_image_file)
sitk.WriteImage(cropped_mask_obj,cropped_mask_file)


"""

for binary thresholding  you can use:

+ `binary_obj = mask_obj > 0`
+ BinaryThreshold 
+ or ConnectedThresholdImageFilter https://stackoverflow.com/a/76256678/868736

"""

"""
python sample_crop.py tmp/img.nii.gz tmp/mask.nii.gz tmp/cropped_img.nii.gz tmp/cropped_mask.nii.gz
"""