医学图像预处理----RandomCrop（随机剪裁）

class RandomCrop(object):
	"""
	Crop randomly the image in a sample. This is usually used for data augmentation.
	Drop ratio is implemented for randomly dropout crops with empty label. (Default to be 0.2)
	This transformation only applicable in train mode

	Args:
	output_size (tuple or int): Desired output size. If int, cubic crop is made.
	"""

	def __init__(self, output_size, drop_ratio=0.1, min_pixel=1):
		self.name = 'Random Crop'

		assert isinstance(output_size, (int, tuple, list))
		if isinstance(output_size, int):
			self.output_size = (output_size, output_size, output_size)
		else:
			assert len(output_size) == 2
			self.output_size = output_size

		assert isinstance(drop_ratio, (int,float))
		if drop_ratio >=0 and drop_ratio<=1:
			self.drop_ratio = drop_ratio
		else:
			raise RuntimeError('Drop ratio should be between 0 and 1')

		assert isinstance(min_pixel, int)
		if min_pixel >=0 :
			self.min_pixel = min_pixel
		else:
			raise RuntimeError('Min label pixel count should be integer larger than 0')

	def __call__(self,sample):
		image, label = sample['image'], sample['label']
		size_old = image[0].GetSize()
		size_new = self.output_size

		contain_label = False

		roiFilter = sitk.RegionOfInterestImageFilter()
		roiFilter.SetSize([size_new[0],size_new[1]])

		# statFilter = sitk.StatisticsImageFilter()
		# statFilter.Execute(label)
		# print(statFilter.GetMaximum(), statFilter.GetSum())

		binaryThresholdFilter = sitk.BinaryThresholdImageFilter()
		binaryThresholdFilter.SetLowerThreshold(1)
		binaryThresholdFilter.SetUpperThreshold(255)
		binaryThresholdFilter.SetInsideValue(1)
		binaryThresholdFilter.SetOutsideValue(0)
		label_ = binaryThresholdFilter.Execute(label)

		# check if the whole slice contain label > minimum pixel
		statFilter = sitk.StatisticsImageFilter()
		statFilter.Execute(label_)
		if statFilter.GetSum() < self.min_pixel:
			contain_label = True

		while not contain_label: 
			# get the start crop coordinate in ijk
			if size_old[0] <= size_new[0]:
				start_i = 0
			else:
				start_i = np.random.randint(0, size_old[0]-size_new[0])

			if size_old[1] <= size_new[1]:
				start_j = 0
			else:
				start_j = np.random.randint(0, size_old[1]-size_new[1])

			roiFilter.SetIndex([start_i,start_j])

			label_crop = roiFilter.Execute(label_)

			statFilter.Execute(label_crop)

			# will iterate until a sub volume containing label is extracted
			# pixel_count = seg_crop.GetHeight()*seg_crop.GetWidth()*seg_crop.GetDepth()
			# if statFilter.GetSum()/pixel_count<self.min_ratio:
			if statFilter.GetSum()<self.min_pixel:
				contain_label = self.drop(self.drop_ratio) # has some probabilty to contain patch with empty label
			else:
				contain_label = True

		for image_channel in range(len(image)):
			image[image_channel] = roiFilter.Execute(image[image_channel])
		label = roiFilter.Execute(label)

		return {'image': image, 'label': label}

	def drop(self,probability):
		return random.random() <= probability