init

Q1/code.py

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+# code.py
+# This is an image preprocessing code for HandBoneXRay data, please adopt env.yaml to
+# create conda env to run this script
+#
+# author  : deng
+# date    : 20230919
+# platform: MacBook Pro 14 2021
+
+import os
+from shutil import rmtree
+
+import cv2
+import pydicom
+import numpy as np
+import matplotlib.pyplot as plt
+
+
+if __name__ == '__main__':
+
+    xray_dir = 'HandBoneXRay/'
+    result_dir = 'results'
+    plot = False
+
+    # Create result dir to save processed images
+    if os.path.isdir(result_dir):
+        rmtree(result_dir)
+    os.makedirs(result_dir)
+
+    # Get xray dicom paths
+    dicom_paths = [os.path.join(xray_dir, file_name)
+                  for file_name in os.listdir(xray_dir)
+                  if file_name.endswith('dcm')]
+
+    for dicom_path in dicom_paths:
+        print(f'Start to process {dicom_path}')
+
+        # Read image
+        ds = pydicom.dcmread(dicom_path)
+        pixel_array = ds.pixel_array
+        orig_pixel_array = pixel_array.copy()
+        if plot:
+            plt.title('Raw image')
+            plt.imshow(pixel_array, cmap='gray')
+            plt.show()
+
+        # Thresholding
+        pixel_array[pixel_array < 1] = 0
+        pixel_array[pixel_array >= 1] = 1
+        pixel_array = pixel_array.astype(np.uint8)
+        if plot:
+            plt.title('Thresholding')
+            plt.imshow(pixel_array, cmap='gray')
+            plt.show()
+
+        # Calculate rotation angle by minAreaRect method
+        contours, _ = cv2.findContours(pixel_array, cv2.RETR_TREE, cv2.CHAIN_APPROX_SIMPLE)
+        contour_w_max_area = max(contours, key = cv2.contourArea)
+        rect = cv2.minAreaRect(contour_w_max_area)
+        angle = rect[2]
+        if angle > 45:
+            angle -= 90
+
+        # Rotate image
+        h, w = orig_pixel_array.shape[:2]
+        center = rect[0]
+        matrix = cv2.getRotationMatrix2D(center, angle, 1.0)
+        rotated = cv2.warpAffine(orig_pixel_array, matrix, (w, h), flags=cv2.INTER_CUBIC, borderMode=cv2.BORDER_CONSTANT)
+        if plot:
+            plt.title('Rotated image')
+            plt.imshow(rotated, cmap='gray')
+            plt.show()
+
+        # Crop edge
+        xs, ys = np.nonzero(rotated)
+        x_min,x_max = xs.min(), xs.max()
+        y_min, y_max = ys.min(), ys.max()
+        cropped = rotated[x_min:x_max+1, y_min:y_max+1]
+        cropped = cropped.astype(np.uint16)
+        if plot:
+            plt.title('Cropped image')
+            plt.imshow(cropped, cmap='gray')
+            plt.show()
+
+        # Save it
+        save_path = os.path.join(result_dir, os.path.basename(dicom_path))
+        ds.PixelData = cropped
+        ds.Rows = cropped.shape[0]
+        ds.Columns = cropped.shape[1]
+        pydicom.filewriter.dcmwrite(save_path, ds)
+        if plot:
+            ds = pydicom.dcmread(save_path)
+            pixel_array = ds.pixel_array
+            plt.title('Saved image')
+            plt.imshow(pixel_array, cmap='gray')
+            plt.show()
+
+        print('done.')

Q1/env.yaml

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+name: Q1
+channels:
+  - conda-forge
+dependencies:
+  - aom=3.5.0
+  - brotli=1.1.0
+  - brotli-bin=1.1.0
+  - bzip2=1.0.8
+  - c-ares=1.19.1
+  - ca-certificates=2023.7.22
+  - cairo=1.16.0
+  - certifi=2023.7.22
+  - contourpy=1.1.1
+  - cycler=0.11.0
+  - dav1d=1.2.1
+  - expat=2.5.0
+  - ffmpeg=6.0.0
+  - font-ttf-dejavu-sans-mono=2.37
+  - font-ttf-inconsolata=3.000
+  - font-ttf-source-code-pro=2.038
+  - font-ttf-ubuntu=0.83
+  - fontconfig=2.14.2
+  - fonts-conda-ecosystem=1
+  - fonts-conda-forge=1
+  - fonttools=4.42.1
+  - freetype=2.12.1
+  - fribidi=1.0.10
+  - gettext=0.21.1
+  - gmp=6.2.1
+  - gnutls=3.7.8
+  - graphite2=1.3.13
+  - harfbuzz=8.2.0
+  - hdf5=1.14.2
+  - icu=73.2
+  - jasper=4.0.0
+  - kiwisolver=1.4.5
+  - krb5=1.21.2
+  - lame=3.100
+  - lcms2=2.15
+  - lerc=4.0.0
+  - libabseil=20230802.1
+  - libaec=1.0.6
+  - libass=0.17.1
+  - libblas=3.9.0
+  - libbrotlicommon=1.1.0
+  - libbrotlidec=1.1.0
+  - libbrotlienc=1.1.0
+  - libcblas=3.9.0
+  - libcurl=8.3.0
+  - libcxx=16.0.6
+  - libdeflate=1.19
+  - libedit=3.1.20191231
+  - libev=4.33
+  - libexpat=2.5.0
+  - libffi=3.4.2
+  - libgfortran=5.0.0
+  - libgfortran5=13.2.0
+  - libglib=2.78.0
+  - libiconv=1.17
+  - libidn2=2.3.4
+  - libjpeg-turbo=2.1.5.1
+  - liblapack=3.9.0
+  - liblapacke=3.9.0
+  - libnghttp2=1.52.0
+  - libopenblas=0.3.24
+  - libopencv=4.8.0
+  - libopenvino=2023.0.2
+  - libopenvino-arm-cpu-plugin=2023.0.2
+  - libopenvino-auto-batch-plugin=2023.0.2
+  - libopenvino-auto-plugin=2023.0.2
+  - libopenvino-hetero-plugin=2023.0.2
+  - libopenvino-ir-frontend=2023.0.2
+  - libopenvino-onnx-frontend=2023.0.2
+  - libopenvino-paddle-frontend=2023.0.2
+  - libopenvino-pytorch-frontend=2023.0.2
+  - libopenvino-tensorflow-frontend=2023.0.2
+  - libopenvino-tensorflow-lite-frontend=2023.0.2
+  - libopus=1.3.1
+  - libpng=1.6.39
+  - libprotobuf=4.23.4
+  - libsqlite=3.43.0
+  - libssh2=1.11.0
+  - libtasn1=4.19.0
+  - libtiff=4.6.0
+  - libunistring=0.9.10
+  - libvpx=1.13.0
+  - libwebp-base=1.3.2
+  - libxcb=1.15
+  - libxml2=2.11.5
+  - libzlib=1.2.13
+  - llvm-openmp=16.0.6
+  - matplotlib=3.8.0
+  - matplotlib-base=3.8.0
+  - munkres=1.1.4
+  - ncurses=6.4
+  - nettle=3.8.1
+  - numpy=1.26.0
+  - opencv=4.8.0
+  - openh264=2.3.1
+  - openjpeg=2.5.0
+  - openssl=3.1.2
+  - p11-kit=0.24.1
+  - packaging=23.1
+  - pcre2=10.40
+  - pillow=10.0.1
+  - pip=23.2.1
+  - pixman=0.40.0
+  - pthread-stubs=0.4
+  - pugixml=1.13
+  - py-opencv=4.8.0
+  - pydicom=2.4.3
+  - pyparsing=3.1.1
+  - python=3.10.12
+  - python-dateutil=2.8.2
+  - python_abi=3.10
+  - readline=8.2
+  - setuptools=68.2.2
+  - six=1.16.0
+  - snappy=1.1.10
+  - svt-av1=1.7.0
+  - tbb=2021.10.0
+  - tk=8.6.12
+  - tornado=6.3.3
+  - tzdata=2023c
+  - unicodedata2=15.0.0
+  - wheel=0.41.2
+  - x264=1!164.3095
+  - x265=3.5
+  - xorg-libxau=1.0.11
+  - xorg-libxdmcp=1.1.3
+  - xz=5.2.6
+  - zlib=1.2.13
+  - zstd=1.5.5
+prefix: /Users/xiao_deng/miniforge3/envs/Q1