CNN & NN regressor

src/pitl/examples/demo_pitl_2D_cnn.py

@@ -0,0 +1,95 @@
+import os
+import time
+
+import numpy as np
+from matplotlib import pyplot as plt
+from skimage.data import camera
+from skimage.exposure import rescale_intensity
+from skimage.measure import compare_psnr as psnr
+from skimage.measure import compare_ssim as ssim
+from skimage.util import random_noise
+
+from src.pitl.features.multiscale_convolutions import MultiscaleConvolutionalFeatures
+from src.pitl.pitl_classic import ImageTranslator
+from src.pitl.regression.nn import CNNRegressor, Modeltype
+
+"""
+    Demo for self-supervised denoising using camera image with synthetic noise
+"""
+
+
+def demo_pitl_2D(noisy):
+
+
+    scales = [1, 3, 7, 15, 31, 63, 127]
+    widths = [3, 3, 3,  3,  3,  3,   3]
+
+    start_time = time.time()
+
+    regressor = CNNRegressor(mode=Modeltype.Convolutional,
+                             learning_rate=0.001,
+                             early_stopping_rounds=5)
+
+
+    generator = MultiscaleConvolutionalFeatures(kernel_widths=widths,
+                                                kernel_scales=scales,
+                                                kernel_shapes=['l1'] * len(scales),
+                                                exclude_center=True,
+                                                )
+
+    it = ImageTranslator(feature_generator=generator, regressor=regressor)
+
+    denoised = it.train(noisy, noisy)
+
+    results = [[psnr(noisy, image), ssim(noisy, image)]]
+    results.append([psnr(denoised, image), ssim(denoised, image)])
+    results.append(time.time() - start_time)
+
+    print("noisy ", results[0])
+    print("denoised ", results[1])
+    print("time elapsed: ", results[2])
+
+    #    from napari import ViewerApp
+    #    with app_context():
+    #        viewer = ViewerApp()
+    #        viewer.add_image(rescale_intensity(image, in_range='image', out_range=(0, 1)), name='image')
+    #        viewer.add_image(rescale_intensity(noisy, in_range='image', out_range=(0, 1)), name='noisy')
+
+    #            viewer.add_image(rescale_intensity(denoised, in_range='image', out_range=(0, 1)), name='denoised%d' % param)
+    # viewer.add_image(rescale_intensity(denoised_predict, in_range='image', out_range=(0, 1)), name='denoised_predict%d' % param)
+
+    return denoised, results
+
+
+image = camera().astype(np.float32)  # [:,50:450]
+image = rescale_intensity(image, in_range='image', out_range=(0, 1))
+
+intensity = 5
+np.random.seed(0)
+noisy = np.random.poisson(image * intensity) / intensity
+noisy = random_noise(noisy, mode='gaussian', var=0.01, seed=0)
+noisy = noisy.astype(np.float32)
+
+denoised_cnn, results_cnn = demo_pitl_2D(noisy)
+
+savepath = '/Users/hirofumi.kobayashi/Github_repositories/pitl/output_data'
+plt.figure()
+plt.subplot(221)
+plt.imshow(image, cmap='gray')
+plt.axis('off')
+plt.title('Original')
+plt.subplot(222)
+plt.imshow(noisy, cmap='gray')
+plt.axis('off')
+plt.title('Noisy \nPSNR={:.2f}, SSMI={:.2f}'.format(results_cnn[0][0], results_cnn[0][1]))
+# plt.subplot(223)
+# plt.imshow(denoised_lgbm, cmap='gray')
+# plt.axis('off')
+# plt.title('LGBM {:.2f}sec \nPSNR={:.2f}, SSMI={:.2f}'.format(results_lgbm[2], results_lgbm[1][0], results_lgbm[1][1]))
+plt.subplot(224)
+plt.imshow(denoised_cnn, cmap='gray')
+plt.axis('off')
+plt.title('CNN {:.2f}sec \nPSNR={:.2f}, SSMI={:.2f}'.format(results_cnn[2], results_cnn[1][0], results_cnn[1][1]))
+plt.subplots_adjust(left=0.11, right=0.9, top=0.91, bottom=0.02, hspace=0.25, wspace=0.2)
+plt.savefig(os.path.join(savepath, 'CNN_2D.png'), dpi=300)
+plt.show()

src/pitl/examples/demo_pitl_2D_lgbm.py

@@ -0,0 +1,94 @@
+import os
+import time
+
+import numpy as np
+from matplotlib import pyplot as plt
+from skimage.data import camera
+from skimage.exposure import rescale_intensity
+from skimage.measure import compare_psnr as psnr
+from skimage.measure import compare_ssim as ssim
+from skimage.util import random_noise
+
+from src.pitl.features.multiscale_convolutions import MultiscaleConvolutionalFeatures
+from src.pitl.pitl_classic import ImageTranslator
+from src.pitl.regression.gbm import GBMRegressor
+
+"""
+    Demo for self-supervised denoising using camera image with synthetic noise
+"""
+
+
+def demo_pitl_2D(noisy):
+
+
+    scales = [1, 3, 7, 15, 31, 63, 127]
+    widths = [3, 3, 3,  3,  3,  3,   3]
+
+    start_time = time.time()
+
+    regressor = GBMRegressor(learning_rate=0.001,
+                             early_stopping_rounds=5)
+
+
+    generator = MultiscaleConvolutionalFeatures(kernel_widths=widths,
+                                                kernel_scales=scales,
+                                                kernel_shapes=['l1'] * len(scales),
+                                                exclude_center=True,
+                                                )
+
+    it = ImageTranslator(feature_generator=generator, regressor=regressor)
+
+    denoised = it.train(noisy, noisy)
+
+    results = [[psnr(noisy, image), ssim(noisy, image)]]
+    results.append([psnr(denoised, image), ssim(denoised, image)])
+    results.append(time.time() - start_time)
+
+    print("noisy ", results[0])
+    print("denoised ", results[1])
+    print("time elapsed: ", results[2])
+
+    #    from napari import ViewerApp
+    #    with app_context():
+    #        viewer = ViewerApp()
+    #        viewer.add_image(rescale_intensity(image, in_range='image', out_range=(0, 1)), name='image')
+    #        viewer.add_image(rescale_intensity(noisy, in_range='image', out_range=(0, 1)), name='noisy')
+
+    #            viewer.add_image(rescale_intensity(denoised, in_range='image', out_range=(0, 1)), name='denoised%d' % param)
+    # viewer.add_image(rescale_intensity(denoised_predict, in_range='image', out_range=(0, 1)), name='denoised_predict%d' % param)
+
+    return denoised, results
+
+
+image = camera().astype(np.float32)  # [:,50:450]
+image = rescale_intensity(image, in_range='image', out_range=(0, 1))
+
+intensity = 5
+np.random.seed(0)
+noisy = np.random.poisson(image * intensity) / intensity
+noisy = random_noise(noisy, mode='gaussian', var=0.01, seed=0)
+noisy = noisy.astype(np.float32)
+
+denoised_lgbm, results_lgbm = demo_pitl_2D(noisy)
+
+savepath = '/Users/hirofumi.kobayashi/Github_repositories/pitl/output_data'
+plt.figure()
+plt.subplot(221)
+plt.imshow(image, cmap='gray')
+plt.axis('off')
+plt.title('Original')
+plt.subplot(222)
+plt.imshow(noisy, cmap='gray')
+plt.axis('off')
+plt.title('Noisy \nPSNR={:.2f}, SSMI={:.2f}'.format(results_lgbm[0][0], results_lgbm[0][1]))
+plt.subplot(223)
+plt.imshow(denoised_lgbm, cmap='gray')
+plt.axis('off')
+plt.title('LGBM {:.2f}sec \nPSNR={:.2f}, SSMI={:.2f}'.format(results_lgbm[2], results_lgbm[1][0], results_lgbm[1][1]))
+# plt.subplot(224)
+# plt.imshow(denoised_cnn, cmap='gray')
+# plt.axis('off')
+# plt.title('CNN {:.2f}sec \nPSNR={:.2f}, SSMI={:.2f}'.format(results_cnn[2], results_cnn[1][0], results_cnn[1][1]))
+plt.subplots_adjust(left=0.11, right=0.9, top=0.91, bottom=0.02, hspace=0.25, wspace=0.2)
+plt.savefig(os.path.join(savepath, 'NN_2D.png'), dpi=300)
+plt.show()

src/pitl/examples/demo_pitl_2D_nn.py

@@ -0,0 +1,95 @@
+import os
+import time
+
+import numpy as np
+from matplotlib import pyplot as plt
+from skimage.data import camera
+from skimage.exposure import rescale_intensity
+from skimage.measure import compare_psnr as psnr
+from skimage.measure import compare_ssim as ssim
+from skimage.util import random_noise
+
+from src.pitl.features.multiscale_convolutions import MultiscaleConvolutionalFeatures
+from src.pitl.pitl_classic import ImageTranslator
+from src.pitl.regression.nn import CNNRegressor, Modeltype
+
+"""
+    Demo for self-supervised denoising using camera image with synthetic noise
+"""
+
+
+def demo_pitl_2D(noisy):
+
+
+    scales = [1, 3, 7, 15, 31, 63, 127]
+    widths = [3, 3, 3,  3,  3,  3,   3]
+
+    start_time = time.time()
+
+    regressor = CNNRegressor(mode=Modeltype.Perceptron,
+                             learning_rate=0.001,
+                             early_stopping_rounds=5)
+
+
+    generator = MultiscaleConvolutionalFeatures(kernel_widths=widths,
+                                                kernel_scales=scales,
+                                                kernel_shapes=['l1'] * len(scales),
+                                                exclude_center=True,
+                                                )
+
+    it = ImageTranslator(feature_generator=generator, regressor=regressor)
+
+    denoised = it.train(noisy, noisy)
+
+    results = [[psnr(noisy, image), ssim(noisy, image)]]
+    results.append([psnr(denoised, image), ssim(denoised, image)])
+    results.append(time.time() - start_time)
+
+    print("noisy ", results[0])
+    print("denoised ", results[1])
+    print("time elapsed: ", results[2])
+
+    #    from napari import ViewerApp
+    #    with app_context():
+    #        viewer = ViewerApp()
+    #        viewer.add_image(rescale_intensity(image, in_range='image', out_range=(0, 1)), name='image')
+    #        viewer.add_image(rescale_intensity(noisy, in_range='image', out_range=(0, 1)), name='noisy')
+
+    #            viewer.add_image(rescale_intensity(denoised, in_range='image', out_range=(0, 1)), name='denoised%d' % param)
+    # viewer.add_image(rescale_intensity(denoised_predict, in_range='image', out_range=(0, 1)), name='denoised_predict%d' % param)
+
+    return denoised, results
+
+
+image = camera().astype(np.float32)  # [:,50:450]
+image = rescale_intensity(image, in_range='image', out_range=(0, 1))
+
+intensity = 5
+np.random.seed(0)
+noisy = np.random.poisson(image * intensity) / intensity
+noisy = random_noise(noisy, mode='gaussian', var=0.01, seed=0)
+noisy = noisy.astype(np.float32)
+
+denoised_cnn, results_cnn = demo_pitl_2D(noisy)
+
+savepath = '/Users/hirofumi.kobayashi/Github_repositories/pitl/output_data'
+plt.figure()
+plt.subplot(221)
+plt.imshow(image, cmap='gray')
+plt.axis('off')
+plt.title('Original')
+plt.subplot(222)
+plt.imshow(noisy, cmap='gray')
+plt.axis('off')
+plt.title('Noisy \nPSNR={:.2f}, SSMI={:.2f}'.format(results_cnn[0][0], results_cnn[0][1]))
+# plt.subplot(223)
+# plt.imshow(denoised_lgbm, cmap='gray')
+# plt.axis('off')
+# plt.title('LGBM {:.2f}sec \nPSNR={:.2f}, SSMI={:.2f}'.format(results_lgbm[2], results_lgbm[1][0], results_lgbm[1][1]))
+plt.subplot(224)
+plt.imshow(denoised_cnn, cmap='gray')
+plt.axis('off')
+plt.title('NN {:.2f}sec \nPSNR={:.2f}, SSMI={:.2f}'.format(results_cnn[2], results_cnn[1][0], results_cnn[1][1]))
+plt.subplots_adjust(left=0.11, right=0.9, top=0.91, bottom=0.02, hspace=0.25, wspace=0.2)
+plt.savefig(os.path.join(savepath, 'NN_2D.png'), dpi=300)
+plt.show()

src/pitl/regression/gbm.py

@@ -48,7 +48,7 @@ def __init__(self,
 
     def fit(self, x_train, y_train, x_test, y_test):
         """
-        Fits function y=f(x) goiven training pairs (x_train, y_train).
+        Fits function y=f(x) given training pairs (x_train, y_train).
         Stops when performance stops improving on the test dataset: (x_test, y_test).
 
         :param x_train: