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b6deff2 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 | # -*- coding: utf-8 -*-
import os
join = os.path.join
import random
import numpy as np
from skimage import io
import SimpleITK as sitk
def dcm2nii(dcm_path, nii_path):
"""
Convert dicom files to nii files
"""
reader = sitk.ImageSeriesReader()
dicom_names = reader.GetGDCMSeriesFileNames(dcm_path)
reader.SetFileNames(dicom_names)
image = reader.Execute()
sitk.WriteImage(image, nii_path)
def mhd2nii(mhd_path, nii_path):
"""
Convert mhd files to nii files
"""
image = sitk.ReadImage(mhd_path)
sitk.WriteImage(image, nii_path)
def nii2nii(nii_path, nii_gz_path):
"""
Convert nii files to nii.gz files, which can reduce the file size
"""
image = sitk.ReadImage(nii_path)
sitk.WriteImage(image, nii_gz_path)
def nrrd2nii(nrrd_path, nii_path):
"""
Convert nrrd files to nii files
"""
image = sitk.ReadImage(nrrd_path)
sitk.WriteImage(image, nii_path)
def jpg2png(jpg_path, png_path):
"""
Convert jpg files to png files
"""
image = io.imread(jpg_path)
io.imsave(png_path, image)
def patchfy(img, mask, outpath, basename):
"""
Patchfy the image and mask into 1024x1024 patches
"""
image_patch_dir = join(outpath, "images")
mask_patch_dir = join(outpath, "labels")
os.makedirs(image_patch_dir, exist_ok=True)
os.makedirs(mask_patch_dir, exist_ok=True)
assert img.shape[:2] == mask.shape
patch_height = 1024
patch_width = 1024
img_height, img_width = img.shape[:2]
mask_height, mask_width = mask.shape
if img_height % patch_height != 0:
img = np.pad(img, ((0, patch_height - img_height % patch_height), (0, 0), (0, 0)), mode="constant")
if img_width % patch_width != 0:
img = np.pad(img, ((0, 0), (0, patch_width - img_width % patch_width), (0, 0)), mode="constant")
if mask_height % patch_height != 0:
mask = np.pad(mask, ((0, patch_height - mask_height % patch_height), (0, 0)), mode="constant")
if mask_width % patch_width != 0:
mask = np.pad(mask, ((0, 0), (0, patch_width - mask_width % patch_width)), mode="constant")
assert img.shape[:2] == mask.shape
assert img.shape[0] % patch_height == 0
assert img.shape[1] % patch_width == 0
assert mask.shape[0] % patch_height == 0
assert mask.shape[1] % patch_width == 0
height_steps = (img_height // patch_height) if img_height % patch_height == 0 else (img_height // patch_height + 1)
width_steps = (img_width // patch_width) if img_width % patch_width == 0 else (img_width // patch_width + 1)
for i in range(height_steps):
for j in range(width_steps):
img_patch = img[i * patch_height:(i + 1) * patch_height, j * patch_width:(j + 1) * patch_width, :]
mask_patch = mask[i * patch_height:(i + 1) * patch_height, j * patch_width:(j + 1) * patch_width]
assert img_patch.shape[:2] == mask_patch.shape
assert img_patch.shape[0] == patch_height
assert img_patch.shape[1] == patch_width
print(f"img_patch.shape: {img_patch.shape}, mask_patch.shape: {mask_patch.shape}")
img_patch_path = join(image_patch_dir, f"{basename}_{i}_{j}.png")
mask_patch_path = join(mask_patch_dir, f"{basename}_{i}_{j}.png")
io.imsave(img_patch_path, img_patch)
io.imsave(mask_patch_path, mask_patch)
def rle_decode(mask_rle, img_shape):
"""
#functions to convert encoding to mask and mask to encoding
mask_rle: run-length as string formated (start length)
shape: (height,width) of array to return
Returns numpy array, 1 - mask, 0 - background
"""
seq = mask_rle.split()
starts = np.array(list(map(int, seq[0::2])))
lengths = np.array(list(map(int, seq[1::2])))
assert len(starts) == len(lengths)
ends = starts + lengths
img = np.zeros((np.product(img_shape),), dtype=np.uint8)
for begin, end in zip(starts, ends):
img[begin:end] = 255
# https://stackoverflow.com/a/46574906/4521646
img.shape = img_shape
return img.T |