[英]Resize a DICOM image in python
I am trying to resize DICOM images of different dimensions into a common dimension size for training my neural.network.我正在尝试将不同尺寸的 DICOM 图像调整为通用尺寸大小以训练我的神经网络。 I thought that cv2 could solve my problem.
我认为 cv2 可以解决我的问题。 But I am getting a 'datatype not understood error' in my jupyter notebook
但是我的 jupyter notebook 中出现“数据类型不理解错误”
I am trying to create a tensorflow neural.network that could predict the class of the image.我正在尝试创建一个 tensorflow 神经网络,它可以预测图像的 class。 Thus, I need images of a common dimension size for the first layer training
因此,我需要用于第一层训练的通用尺寸的图像
Here is the function I have created:这是我创建的 function:
IMG_PX_SIZE = 224
def resize(img_dcm):
return cv2.resize(np.array(img_dcm.pixel_array, (IMG_PX_SIZE,IMG_PX_SIZE)))
This is how I read the dcm files and pass it to the function:这就是我读取 dcm 文件并将其传递给 function 的方式:
img = pydi.dcmread(PATH)
image = resize(img)
I expected it to output a 224*224 sized image.我希望它是 output 一个 224*224 大小的图像。 But I am getting the following error:
但我收到以下错误:
<ipython-input-66-3cf283042491> in resize(img_dcm)
1 IMG_PX_SIZE = 224
2 def resize(img_dcm):
----> 3 return cv2.resize(np.array(image.pixel_array, (IMG_PX_SIZE,IMG_PX_SIZE)))
TypeError: data type not understood
Here's an alternative way to resize the images using Scikit-Image:这是使用 Scikit-Image 调整图像大小的另一种方法:
In [105]: from pydicom.data import get_testdata_files
# read a sample image
In [106]: filename = get_testdata_files('MR_small.dcm')[0]
...: ds = pydicom.dcmread(filename)
In [107]: data = ds.pixel_array
In [108]: type(data)
Out[108]: numpy.ndarray
In [109]: data.shape
Out[109]: (64, 64)
In [111]: from skimage.transform import resize
In [114]: IMG_PX_SIZE = 32
# resize to new size
In [115]: resized_img = resize(data, (IMG_PX_SIZE, IMG_PX_SIZE), anti_aliasing=True)
In [116]: resized_img.shape
Out[116]: (32, 32)
DICOM is not supported in OpenCV, see here . OpenCV 不支持DICOM ,请参见此处。 You will have to convert all of your images into a suitable format (eg jpg or png) before you are able to resize them with OpenCV:
您必须先将所有图像转换为合适的格式(例如 jpg 或 png),然后才能使用 OpenCV 调整它们的大小:
OpenCV does not support DICOM images so that you will have to find a suitable libary (like http://dicom.offis.de/dcmtk.php.en ) and convert the loaded image to a cv::Mat.
OpenCV 不支持 DICOM 图像,因此您必须找到合适的库(如http://dicom.offis.de/dcmtk.php.en )并将加载的图像转换为 cv::Mat。
Then again you may want to use a different library for re-sizing as well, it is probably not worth the effort to:再说一次,您可能还想使用不同的库来调整大小,这样做可能不值得:
I'd recommend you instead look into a library or tool specifically designed to work with DICOM images.我建议您转而查看专门设计用于处理 DICOM 图像的库或工具。
You can use this functions from here您可以从这里使用此功能
You need to first read your dicom/Niftii files你需要先阅读你的 dicom/Niftii 文件
def read_nifti_file(filepath):
"""Read and load volume"""
# Read file
scan = nib.load(filepath)
# Get raw data
scan = scan.get_fdata()
return scan
then you can resize your volume:然后你可以调整你的音量:
def resize_volume(img):
"""Resize across z-axis"""
# Set the desired depth
desired_depth = 64
desired_width = 128
desired_height = 128
# Get current depth
current_depth = img.shape[-1]
current_width = img.shape[0]
current_height = img.shape[1]
# Compute depth factor
depth = current_depth / desired_depth
width = current_width / desired_width
height = current_height / desired_height
depth_factor = 1 / depth
width_factor = 1 / width
height_factor = 1 / height
# Resize across z-axis
img = ndimage.zoom(img, (width_factor, height_factor, depth_factor), order=1)
return img
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