Tgs salt example (#286)

* TGS salt example

* updates

* updates

examples/trials/kaggle-tgs-salt/README.md

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+## 33rd place solution code for Kaggle [TGS Salt Identification Chanllenge](https://www.kaggle.com/c/tgs-salt-identification-challenge)
+
+This example shows how to enable AutoML for competition code by running it on NNI without any code change. 
+To run this code on NNI, firstly you need to run it standalone, then configure the config.yml and:
+```
+nnictl create --config config.yml
+```
+
+This code can still run standalone, the code is for reference, it requires at least one week effort to reproduce the competition result.
+
+[Solution summary](https://www.kaggle.com/c/tgs-salt-identification-challenge/discussion/69593)
+
+Preparation:
+
+Download competition data, run preprocess.py to prepare training data.
+
+Stage 1:
+
+Train fold 0-3 for 100 epochs, for each fold, train 3 models:
+```
+python3 train.py --ifolds 0 --epochs 100 --model_name UNetResNetV4 
+python3 train.py --ifolds 0 --epochs 100 --model_name UNetResNetV5 --layers 50
+python3 train.py --ifolds 0 --epochs 100 --model_name UNetResNetV6
+```
+
+Stage 2:
+
+Fine tune stage 1 models for 300 epochs with cosine annealing lr scheduler:
+
+```
+python3 train.py --ifolds 0 --epochs 300 --lrs cosine --lr 0.001 --min_lr 0.0001 --model_name UNetResNetV4 
+```
+
+Stage 3:
+
+Fine tune Stage 2 models with depths channel:
+
+```
+python3 train.py --ifolds 0 --epochs 300 --lrs cosine --lr 0.001 --min_lr 0.0001 --model_name UNetResNetV4 --depths
+```
+
+Stage 4:
+
+Make prediction for each model,  then ensemble the result to generate peasdo labels.
+
+Stage 5:
+
+Fine tune stage 3 models with pseudo labels
+
+```
+python3 train.py --ifolds 0 --epochs 300 --lrs cosine --lr 0.001 --min_lr 0.0001 --model_name UNetResNetV4 --depths --pseudo
+```
+
+Stage 6:
+Ensemble all stage 3 and stage 5 models.
+

examples/trials/kaggle-tgs-salt/augmentation.py

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+# Copyright (c) Microsoft Corporation
+# All rights reserved.
+#
+# MIT License
+#
+# Permission is hereby granted, free of charge,
+# to any person obtaining a copy of this software and associated
+# documentation files (the "Software"),
+# to deal in the Software without restriction, including without limitation
+# the rights to use, copy, modify, merge, publish, distribute, sublicense,
+# and/or sell copies of the Software, and
+# to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+# The above copyright notice and this permission notice shall be included
+# in all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED *AS IS*, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING
+# BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
+# DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+import os
+import cv2
+import numpy as np
+import random
+import torchvision.transforms.functional as F
+from torchvision.transforms import RandomResizedCrop, ColorJitter, RandomAffine
+import PIL
+from PIL import Image
+import collections
+
+import settings
+
+
+class RandomHFlipWithMask(object):
+    def __init__(self, p=0.5):
+        self.p = p
+    def __call__(self, *imgs):
+        if random.random() < self.p:
+            return map(F.hflip, imgs)
+        else:
+            return imgs
+
+class RandomVFlipWithMask(object):
+    def __init__(self, p=0.5):
+        self.p = p
+    def __call__(self, *imgs):
+        if random.random() < self.p:
+            return map(F.vflip, imgs)
+        else:
+            return imgs
+
+class RandomResizedCropWithMask(RandomResizedCrop):
+    def __init__(self, size, scale=(0.08, 1.0), ratio=(3. / 4., 4. / 3.), interpolation=Image.BILINEAR):
+        super(RandomResizedCropWithMask, self).__init__(size, scale, ratio, interpolation)
+    def __call__(self, *imgs):
+        i, j, h, w = self.get_params(imgs[0], self.scale, self.ratio)
+        #print(i,j,h,w)
+        return map(lambda x: F.resized_crop(x, i, j, h, w, self.size, self.interpolation), imgs)
+
+class RandomAffineWithMask(RandomAffine):
+    def __init__(self, degrees, translate=None, scale=None, shear=None, resample='edge'):
+        super(RandomAffineWithMask, self).__init__(degrees, translate, scale, shear, resample)
+    def __call__(self, *imgs):
+        ret = self.get_params(self.degrees, self.translate, self.scale, self.shear, imgs[0].size)
+        w, h = imgs[0].size
+        imgs = map(lambda x: F.pad(x, w//2, 0, self.resample), imgs)
+        imgs = map(lambda x: F.affine(x, *ret, resample=0), imgs)
+        imgs = map(lambda x: F.center_crop(x, (w, h)), imgs)
+        return imgs
+
+class RandomRotateWithMask(object):
+    def __init__(self, degrees, pad_mode='reflect', expand=False, center=None):
+        self.pad_mode = pad_mode
+        self.expand = expand
+        self.center = center
+        self.degrees = degrees
+
+    def __call__(self, *imgs):
+        angle = self.get_angle()
+        if angle == int(angle) and angle % 90 == 0:
+            if angle == 0:
+                return imgs
+            else:
+                #print(imgs)
+                return map(lambda x: F.rotate(x, angle, False, False, None), imgs)
+        else:
+            return map(lambda x: self._pad_rotate(x, angle), imgs)
+
+    def get_angle(self):
+        if isinstance(self.degrees, collections.Sequence):
+            index = int(random.random() * len(self.degrees))
+            return self.degrees[index]
+        else:
+            return random.uniform(-self.degrees, self.degrees)
+
+    def _pad_rotate(self, img, angle):
+        w, h = img.size
+        img = F.pad(img, w//2, 0, self.pad_mode)
+        img = F.rotate(img, angle, False, self.expand, self.center)
+        img = F.center_crop(img, (w, h))
+        return img
+
+class CropWithMask(object):
+    def __init__(self, i, j, h, w):
+        self.i = i
+        self.j = j
+        self.h = h
+        self.w = w
+    def __call__(self, *imgs):
+        return map(lambda x: F.crop(x, self.i, self.j, self.h, self.w), imgs)
+
+class PadWithMask(object):
+    def __init__(self, padding, padding_mode):
+        self.padding = padding
+        self.padding_mode = padding_mode
+    def __call__(self, *imgs):
+        return map(lambda x: F.pad(x, self.padding, padding_mode=self.padding_mode), imgs)
+
+class Compose(object):
+    def __init__(self, transforms):
+        self.transforms = transforms
+
+    def __call__(self, *imgs):
+        for t in self.transforms:
+            imgs = t(*imgs)
+        return imgs
+    def __repr__(self):
+        format_string = self.__class__.__name__ + '('
+        for t in self.transforms:
+            format_string += '\n'
+            format_string += '    {0}'.format(t)
+        format_string += '\n)'
+        return format_string
+
+def get_img_mask_augments(train_mode, pad_mode):
+    if pad_mode == 'resize':
+        img_mask_aug_train = Compose([
+            RandomHFlipWithMask(),
+            RandomAffineWithMask(10, translate=(0.1, 0.1), scale=(0.9, 1.1), shear=None)
+        ])
+        img_mask_aug_val = None
+    else:
+        img_mask_aug_train = Compose([
+            PadWithMask((28, 28), padding_mode=pad_mode),
+            RandomHFlipWithMask(),
+            RandomAffineWithMask(10, translate=(0.1, 0.1), scale=(0.9, 1.1), shear=None),
+            RandomResizedCropWithMask(128, scale=(1., 1.), ratio=(1., 1.))
+        ])
+        img_mask_aug_val = PadWithMask((13, 14), padding_mode=pad_mode)
+
+    return img_mask_aug_train, img_mask_aug_val
+
+
+def test_transform():
+    img_id = '0b73b427d1.png'
+    img = Image.open(os.path.join(settings.TRAIN_IMG_DIR, img_id)).convert('RGB')
+    mask = Image.open(os.path.join(settings.TRAIN_MASK_DIR, img_id)).convert('L').point(lambda x: 0 if x < 128 else 1, 'L')
+
+    img_id = '0a1ea1af4.jpg'
+    img = Image.open(os.path.join(r'D:\data\ship\train_v2', img_id)).convert('RGB')
+    mask = Image.open(os.path.join(r'D:\data\ship\train_masks', img_id)).convert('L').point(lambda x: 0 if x < 128 else 1, 'L')
+
+    trans = Compose([
+        RandomHFlipWithMask(),
+        RandomVFlipWithMask(),
+        RandomRotateWithMask([0, 90, 180, 270]),
+        #RandomRotateWithMask(15), 
+        RandomResizedCropWithMask(768, scale=(0.81, 1))
+    ])
+
+    trans2 = RandomAffineWithMask(45, (0.2,0.2), (0.9, 1.1))
+    trans3, trans4 = get_img_mask_augments(True, 'edge')
+
+    img, mask = trans4(img, mask)
+
+    img.show()
+    mask.point(lambda x: x*255).show()
+
+def test_color_trans():
+    img_id = '00abc623a.jpg'
+    img = Image.open(os.path.join(settings.TRAIN_IMG_DIR, img_id)).convert('RGB')
+    trans = ColorJitter(0.1, 0.1, 0.1, 0.1)
+
+    img2 = trans(img)
+    img.show()
+    img2.show()
+
+
+class TTATransform(object):
+    def __init__(self, index):
+        self.index = index
+    def __call__(self, img):
+        trans = {
+            0: lambda x: x,
+            1: lambda x: F.hflip(x),
+            2: lambda x: F.vflip(x),
+            3: lambda x: F.vflip(F.hflip(x)),
+            4: lambda x: F.rotate(x, 90, False, False),
+            5: lambda x: F.hflip(F.rotate(x, 90, False, False)),
+            6: lambda x: F.vflip(F.rotate(x, 90, False, False)),
+            7: lambda x: F.vflip(F.hflip(F.rotate(x, 90, False, False)))
+        }
+        return trans[self.index](img)
+
+# i is tta index, 0: no change, 1: horizon flip, 2: vertical flip, 3: do both
+def tta_back_mask_np(img, index):
+    print(img.shape)
+    trans = {
+        0: lambda x: x,
+        1: lambda x: np.flip(x, 2),
+        2: lambda x: np.flip(x, 1),
+        3: lambda x: np.flip(np.flip(x, 2), 1),
+        4: lambda x: np.rot90(x, 3, axes=(1,2)),
+        5: lambda x: np.rot90(np.flip(x, 2), 3, axes=(1,2)),
+        6: lambda x: np.rot90(np.flip(x, 1), 3, axes=(1,2)),
+        7: lambda x: np.rot90(np.flip(np.flip(x,2), 1), 3, axes=(1,2))
+    }
+
+    return trans[index](img)
+
+def test_tta():
+    img_f = os.path.join(settings.TEST_IMG_DIR, '0c2637aa9.jpg')
+    img = Image.open(img_f)
+    img = img.convert('RGB')
+
+    tta_index = 7
+    trans1 = TTATransform(tta_index)
+    img = trans1(img)
+    #img.show()
+
+    img_np = np.array(img)
+    img_np = np.expand_dims(img_np, 0)
+    print(img_np.shape)
+    img_np = tta_back_mask_np(img_np, tta_index)
+    img_np = np.reshape(img_np, (768, 768, 3))
+    img_back = F.to_pil_image(img_np)
+    img_back.show()
+
+if __name__ == '__main__':
+    test_transform()

examples/trials/kaggle-tgs-salt/config.yml

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+authorName: default
+experimentName: example_tgs
+trialConcurrency: 2
+maxExecDuration: 10h
+maxTrialNum: 10
+#choice: local, remote, pai
+trainingServicePlatform: local
+#choice: true, false
+useAnnotation: true
+tuner:
+  #choice: TPE, Random, Anneal, Evolution, BatchTuner
+  #SMAC (SMAC should be installed through nnictl)
+  builtinTunerName: TPE
+  classArgs:
+    #choice: maximize, minimize
+    optimize_mode: maximize
+trial:
+  command: python3 train.py
+  codeDir: .
+  gpuNum: 1

examples/trials/kaggle-tgs-salt/focal_loss.py

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+# Copyright (c) Microsoft Corporation
+# All rights reserved.
+#
+# MIT License
+#
+# Permission is hereby granted, free of charge,
+# to any person obtaining a copy of this software and associated
+# documentation files (the "Software"),
+# to deal in the Software without restriction, including without limitation
+# the rights to use, copy, modify, merge, publish, distribute, sublicense,
+# and/or sell copies of the Software, and
+# to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+# The above copyright notice and this permission notice shall be included
+# in all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED *AS IS*, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING
+# BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
+# DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+import torch
+import torch.nn as nn
+import torch.nn.functional as F
+
+class FocalLoss2d(nn.Module):
+
+    def __init__(self, gamma=2, size_average=True):
+        super(FocalLoss2d, self).__init__()
+        self.gamma = gamma
+        self.size_average = size_average
+
+
+    def forward(self, logit, target, class_weight=None, type='sigmoid'):
+        target = target.view(-1, 1).long()
+
+        if type=='sigmoid':
+            if class_weight is None:
+                class_weight = [1]*2 #[0.5, 0.5]
+
+            prob   = torch.sigmoid(logit)
+            prob   = prob.view(-1, 1)
+            prob   = torch.cat((1-prob, prob), 1)
+            select = torch.FloatTensor(len(prob), 2).zero_().cuda()
+            select.scatter_(1, target, 1.)
+
+        elif  type=='softmax':
+            B,C,H,W = logit.size()
+            if class_weight is None:
+                class_weight =[1]*C #[1/C]*C
+
+            logit   = logit.permute(0, 2, 3, 1).contiguous().view(-1, C)
+            prob    = F.softmax(logit,1)
+            select  = torch.FloatTensor(len(prob), C).zero_().cuda()
+            select.scatter_(1, target, 1.)
+
+        class_weight = torch.FloatTensor(class_weight).cuda().view(-1,1)
+        class_weight = torch.gather(class_weight, 0, target)
+
+        prob       = (prob*select).sum(1).view(-1,1)
+        prob       = torch.clamp(prob,1e-8,1-1e-8)
+        batch_loss = - class_weight *(torch.pow((1-prob), self.gamma))*prob.log()
+
+        if self.size_average:
+            loss = batch_loss.mean()
+        else:
+            loss = batch_loss
+
+        return loss
+
+
+if __name__ == '__main__':
+    L = FocalLoss2d()
+    out = torch.randn(2, 3, 3).cuda()
+    target = (torch.sigmoid(out) > 0.5).float()
+    loss = L(out, target)
+    print(loss)