def fbresnet_augmentor(isTrain): """ Augmentor used in fb.resnet.torch, for BGR images in range [0,255]. """ if isTrain: augmentors = [ GoogleNetResize(), imgaug.Flip(horiz=True), imgaug.ToFloat32(), imgaug.RandomOrderAug([ imgaug.BrightnessScale((0.6, 1.4), clip=False), imgaug.Contrast((0.6, 1.4), rgb=False, clip=False), imgaug.Saturation(0.4, rgb=False), # rgb-bgr conversion for the constants copied from fb.resnet.torch imgaug.Lighting( 0.1, eigval=np.asarray([0.2175, 0.0188, 0.0045][::-1]) * 255.0, eigvec=np.array([[-0.5675, 0.7192, 0.4009], [-0.5808, -0.0045, -0.8140], [-0.5836, -0.6948, 0.4203]], dtype='float32')[::-1, ::-1]) ]), ] else: augmentors = [ imgaug.ResizeShortestEdge(256, cv2.INTER_LINEAR), imgaug.CenterCrop((224, 224)), imgaug.ToFloat32(), ] return augmentors
def test_dataloader(self): """Summary Returns: TYPE: Description """ ds_test = MultiLabelDataset(folder=self.hparams.data_path, is_train='test', fname='test.csv', types=self.hparams.types, pathology=self.hparams.pathology, resize=int(self.hparams.shape)) ds_test.reset_state() ag_test = [ imgaug.Albumentations( AB.SmallestMaxSize(self.hparams.shape, p=1.0)), iimgaug.ColorSpace(mode=cv2.COLOR_GRAY2RGB), imgaug.Albumentations(AB.CLAHE(p=1)), imgaug.ToFloat32(), ] ds_test = AugmentImageComponent(ds_test, ag_test, 0) ds_test = BatchData(ds_test, self.hparams.batch, remainder=True) # ds_test = MultiProcessRunner(ds_test, num_proc=4, num_prefetch=16) ds_test = PrintData(ds_test) ds_test = MapData(ds_test, lambda dp: [torch.tensor(np.transpose(dp[0], (0, 3, 1, 2))), torch.tensor(dp[1]).float()]) return ds_test
def test_dataloader(self): """Summary Returns: TYPE: Description """ ds_test = CustomDataSet(folder=self.hparams.data, train_or_valid='test', size=np.inf, hparams=self.hparams) ds_test.reset_state() ag_test = [ imgaug.Resize(self.hparams.shape, interp=cv2.INTER_NEAREST), imgaug.ToFloat32(), ] # ds_test = AugmentImageComponent(ds_test, [imgaug.Albumentations(AB.CLAHE(tile_grid_size=(32, 32), always_apply=True, p=1)),], 0) ds_test = AugmentImageComponents(ds_test, ag_test, [0, 1]) ds_test = BatchData(ds_test, self.hparams.batch, remainder=True) ds_test = MultiProcessRunner(ds_test, num_proc=4, num_prefetch=16) ds_test = PrintData(ds_test) ds_test = MapData( ds_test, lambda dp: [ torch.tensor(dp[0][:, np.newaxis, :, :]).float(), torch.tensor(dp[1][:, np.newaxis, :, :]).float(), ]) return ds_test
def test_dataloader(self): ds_test = MultiLabelDataset(folder=self.hparams.data, is_train='valid', fname='covid_test_v5.csv', types=self.hparams.types, pathology=self.hparams.pathology, resize=int(self.hparams.shape), fold_idx=None, n_folds=1) ds_test.reset_state() ag_test = [ imgaug.Resize(self.hparams.shape, interp=cv2.INTER_AREA), imgaug.ToFloat32(), ] ds_test = AugmentImageComponent(ds_test, ag_test, 0) ds_test = BatchData(ds_test, self.hparams.batch, remainder=True) ds_test = MultiProcessRunner(ds_test, num_proc=4, num_prefetch=16) ds_test = PrintData(ds_test) ds_test = MapData( ds_test, lambda dp: [ torch.tensor(np.transpose(dp[0], (0, 3, 1, 2))), torch.tensor(dp[1]).float() ]) return ds_test
def val_dataloader(self): """Summary Returns: TYPE: Description """ ds_valid = MultiLabelDataset( folder=self.hparams.data, is_train='valid', fname='covid_test_v5.csv', types=self.hparams.types, pathology=self.hparams.pathology, resize=int(self.hparams.shape), ) ds_valid.reset_state() ag_valid = [ imgaug.Resize(self.hparams.shape, interp=cv2.INTER_AREA), imgaug.ToFloat32(), ] ds_valid = AugmentImageComponent(ds_valid, ag_valid, 0) ds_valid = BatchData(ds_valid, self.hparams.batch, remainder=True) ds_valid = MultiProcessRunner(ds_valid, num_proc=4, num_prefetch=16) ds_valid = PrintData(ds_valid) ds_valid = MapData( ds_valid, lambda dp: [ torch.tensor(np.transpose(dp[0], (0, 3, 1, 2))), torch.tensor(dp[1]).float() ]) return ds_valid
def train_dataloader(self): ds_train = MultiLabelDataset(folder=self.hparams.data, is_train='train', fname='covid_train_v5.csv', types=self.hparams.types, pathology=self.hparams.pathology, resize=int(self.hparams.shape), balancing=None) ds_train.reset_state() ag_train = [ # imgaug.Albumentations( # AB.SmallestMaxSize(self.hparams.shape, p=1.0)), imgaug.ColorSpace(mode=cv2.COLOR_GRAY2RGB), # imgaug.Affine(shear=10), imgaug.RandomChooseAug([ imgaug.Albumentations(AB.Blur(blur_limit=4, p=0.25)), imgaug.Albumentations(AB.MotionBlur(blur_limit=4, p=0.25)), imgaug.Albumentations(AB.MedianBlur(blur_limit=4, p=0.25)), ]), imgaug.Albumentations(AB.CLAHE(tile_grid_size=(32, 32), p=0.5)), imgaug.RandomOrderAug([ imgaug.Affine(shear=10, border=cv2.BORDER_CONSTANT, interp=cv2.INTER_AREA), imgaug.Affine(translate_frac=(0.01, 0.02), border=cv2.BORDER_CONSTANT, interp=cv2.INTER_AREA), imgaug.Affine(scale=(0.5, 1.0), border=cv2.BORDER_CONSTANT, interp=cv2.INTER_AREA), ]), imgaug.RotationAndCropValid(max_deg=10, interp=cv2.INTER_AREA), imgaug.GoogleNetRandomCropAndResize( crop_area_fraction=(0.8, 1.0), aspect_ratio_range=(0.8, 1.2), interp=cv2.INTER_AREA, target_shape=self.hparams.shape), imgaug.ColorSpace(mode=cv2.COLOR_RGB2GRAY), imgaug.ToFloat32(), ] ds_train = AugmentImageComponent(ds_train, ag_train, 0) # Label smoothing ag_label = [ imgaug.BrightnessScale((0.8, 1.2), clip=False), ] # ds_train = AugmentImageComponent(ds_train, ag_label, 1) ds_train = BatchData(ds_train, self.hparams.batch, remainder=True) if self.hparams.debug: ds_train = FixedSizeData(ds_train, 2) ds_train = MultiProcessRunner(ds_train, num_proc=4, num_prefetch=16) ds_train = PrintData(ds_train) ds_train = MapData( ds_train, lambda dp: [ torch.tensor(np.transpose(dp[0], (0, 3, 1, 2))), torch.tensor(dp[1]).float() ]) return ds_train
def get_moco_v1_augmentor(): augmentors = [ TorchvisionCropAndResize(crop_area_fraction=(0.2, 1.)), RandomGrayScale(0.2), imgaug.ToFloat32(), imgaug.RandomOrderAug([ imgaug.BrightnessScale((0.6, 1.4)), imgaug.Contrast((0.6, 1.4), rgb=False), imgaug.Saturation(0.4, rgb=False), # 72 = 180*0.4 imgaug.Hue(range=(-72, 72), rgb=False) ]), imgaug.ToUint8(), imgaug.Flip(horiz=True), ] return augmentors
def get_moco_v1_augmentor(): augmentors = [ imgaug.GoogleNetRandomCropAndResize(crop_area_fraction=(0.2, 1.)), imgaug.RandomApplyAug(imgaug.Grayscale(rgb=False, keepshape=True), 0.2), imgaug.ToFloat32(), imgaug.RandomOrderAug( [imgaug.BrightnessScale((0.6, 1.4)), imgaug.Contrast((0.6, 1.4), rgb=False), imgaug.Saturation(0.4, rgb=False), # 72 = 180*0.4 imgaug.Hue(range=(-72, 72), rgb=False) ]), imgaug.ToUint8(), imgaug.Flip(horiz=True), ] return augmentors
def val_dataloader(self): """Summary Returns: TYPE: Description """ ds_valid = CustomDataSet(folder=self.hparams.data, train_or_valid='valid', size=np.inf, hparams=self.hparams) ds_valid.reset_state() ag_valid = [ imgaug.Resize(self.hparams.shape, interp=cv2.INTER_NEAREST), imgaug.ToFloat32(), ] ds_valid = AugmentImageComponent(ds_valid, [ imgaug.Albumentations(AB.CLAHE(p=1)), ], 0) if self.hparams.types == 6: ds_valid = AugmentImageComponents(ds_valid, ag_valid, [0, 1, 2, 3, 4, 5, 6]) elif self.hparams.types == 1: ds_valid = AugmentImageComponents(ds_valid, ag_valid, [0, 1]) ds_valid = BatchData(ds_valid, self.hparams.batch, remainder=True) ds_valid = MultiProcessRunner(ds_valid, num_proc=4, num_prefetch=16) ds_valid = PrintData(ds_valid) if self.hparams.types == 6: ds_valid = MapData( ds_valid, lambda dp: [ torch.tensor(dp[0][:, np.newaxis, :, :]).float(), torch.tensor(dp[1][:, np.newaxis, :, :]).float(), torch.tensor(dp[2][:, np.newaxis, :, :]).float(), torch.tensor(dp[3][:, np.newaxis, :, :]).float(), torch.tensor(dp[4][:, np.newaxis, :, :]).float(), torch.tensor(dp[5][:, np.newaxis, :, :]).float(), torch.tensor(dp[6][:, np.newaxis, :, :]).float(), ]) elif self.hparams.types == 1: ds_valid = MapData( ds_valid, lambda dp: [ torch.tensor(dp[0][:, np.newaxis, :, :]).float(), torch.tensor(dp[1][:, np.newaxis, :, :]).float(), ]) return ds_valid
def get_moco_v2_augmentor(): augmentors = [ TorchvisionCropAndResize(crop_area_fraction=(0.2, 1.)), imgaug.ToFloat32(), imgaug.RandomApplyAug( imgaug.RandomOrderAug([ imgaug.BrightnessScale((0.6, 1.4)), imgaug.Contrast((0.6, 1.4), rgb=False), imgaug.Saturation(0.4, rgb=False), # 18 = 180*0.1 imgaug.Hue(range=(-18, 18), rgb=False) ]), 0.8), RandomGrayScale(0.2), imgaug.RandomApplyAug(RandomGaussionBlur([0.1, 2.0], 0.1), 0.5), imgaug.ToUint8(), imgaug.Flip(horiz=True), ] return augmentors
def get_moco_v2_augmentor(): augmentors = [ imgaug.GoogleNetRandomCropAndResize(crop_area_fraction=(0.2, 1.)), imgaug.ToFloat32(), imgaug.RandomApplyAug( imgaug.RandomOrderAug( [imgaug.BrightnessScale((0.6, 1.4)), imgaug.Contrast((0.6, 1.4), rgb=False), imgaug.Saturation(0.4, rgb=False), # 18 = 180*0.1 imgaug.Hue(range=(-18, 18), rgb=False) ]), 0.8), imgaug.RandomApplyAug(imgaug.Grayscale(rgb=False, keepshape=True), 0.2), imgaug.RandomApplyAug( # 11 = 0.1*224//2 imgaug.GaussianBlur(size_range=(11, 12), sigma_range=[0.1, 2.0]), 0.5), imgaug.ToUint8(), imgaug.Flip(horiz=True), ] return augmentors
def fbresnet_augmentor(isTrain): """ Augmentor used in fb.resnet.torch, for BGR images in range [0,255]. """ interpolation = cv2.INTER_CUBIC # linear seems to have more stable performance. # but we keep cubic for compatibility with old models if isTrain: augmentors = [ imgaug.GoogleNetRandomCropAndResize(interp=interpolation), imgaug.ToFloat32(), # avoid frequent casting in each color augmentation # It's OK to remove the following augs if your CPU is not fast enough. # Removing brightness/contrast/saturation does not have a significant effect on accuracy. # Removing lighting leads to a tiny drop in accuracy. imgaug.RandomOrderAug( [imgaug.BrightnessScale((0.6, 1.4)), imgaug.Contrast((0.6, 1.4), rgb=False), imgaug.Saturation(0.4, rgb=False), # rgb-bgr conversion for the constants copied from fb.resnet.torch imgaug.Lighting(0.1, eigval=np.asarray( [0.2175, 0.0188, 0.0045][::-1]) * 255.0, eigvec=np.array( [[-0.5675, 0.7192, 0.4009], [-0.5808, -0.0045, -0.8140], [-0.5836, -0.6948, 0.4203]], dtype='float32')[::-1, ::-1] )]), imgaug.ToUint8(), imgaug.Flip(horiz=True), ] else: augmentors = [ imgaug.ResizeShortestEdge(256, interp=interpolation), imgaug.CenterCrop((224, 224)), ] return augmentors
def train_dataloader(self): """Summary Returns: TYPE: Description """ ds_train = CustomDataSet(folder=self.hparams.data, train_or_valid='train', size=np.inf, hparams=self.hparams) ds_train.reset_state() ag_train = [ imgaug.Affine(shear=10, interp=cv2.INTER_NEAREST), imgaug.Affine(translate_frac=(0.01, 0.02), interp=cv2.INTER_NEAREST), imgaug.Affine(scale=(0.25, 1.0), interp=cv2.INTER_NEAREST), imgaug.RotationAndCropValid(max_deg=10, interp=cv2.INTER_NEAREST), imgaug.GoogleNetRandomCropAndResize( crop_area_fraction=(0.8, 1.0), aspect_ratio_range=(0.8, 1.2), interp=cv2.INTER_NEAREST, target_shape=self.hparams.shape), imgaug.Resize(self.hparams.shape, interp=cv2.INTER_NEAREST), imgaug.Flip(horiz=True, vert=False, prob=0.5), imgaug.Flip(horiz=False, vert=True, prob=0.5), imgaug.Transpose(prob=0.5), imgaug.Albumentations(AB.RandomRotate90(p=1)), imgaug.ToFloat32(), ] ds_train = AugmentImageComponent( ds_train, [ # imgaug.Float32(), # imgaug.RandomChooseAug([ # imgaug.Albumentations(AB.IAAAdditiveGaussianNoise(p=0.25)), # imgaug.Albumentations(AB.GaussNoise(p=0.25)), # ]), # imgaug.ToUint8(), imgaug.RandomChooseAug([ imgaug.Albumentations(AB.Blur(blur_limit=4, p=0.25)), imgaug.Albumentations(AB.MotionBlur(blur_limit=4, p=0.25)), imgaug.Albumentations(AB.MedianBlur(blur_limit=4, p=0.25)), ]), imgaug.RandomChooseAug([ # imgaug.Albumentations(AB.IAASharpen(p=0.5)), # imgaug.Albumentations(AB.IAAEmboss(p=0.5)), imgaug.Albumentations(AB.RandomBrightnessContrast(p=0.5)), ]), imgaug.ToUint8(), imgaug.Albumentations(AB.CLAHE(tile_grid_size=(32, 32), p=0.5)), ], 0) ds_train = AugmentImageComponents(ds_train, ag_train, [0, 1]) ds_train = BatchData(ds_train, self.hparams.batch, remainder=True) if self.hparams.debug: ds_train = FixedSizeData(ds_train, 2) ds_train = MultiProcessRunner(ds_train, num_proc=4, num_prefetch=16) ds_train = PrintData(ds_train) ds_train = MapData( ds_train, lambda dp: [ torch.tensor(dp[0][:, np.newaxis, :, :]).float(), torch.tensor(dp[1][:, np.newaxis, :, :]).float(), ]) return ds_train