(https://github.com/fastai/courses)
This is a beginner level code (can be learnt in 2 classes of deep learning taught by Jeremy Howard) and we can get decent results by only tuning learning rate and training until model overfits.
I have used pretrained resnet18 model based on Imagenet data for this
Steps to use fastai library --
This kernel is specifically is for Beginners who want's to experiment building CNN using fastai (on the top of pytorch). By using this kernel, you can expect to get good score and also learn fastai. Fastai has made building deep neural networks very easy.
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# Put these at the top of every notebook, to get automatic reloading and inline plotting
%reload_ext autoreload
%autoreload 2
%matplotlib inline
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# This is required to make fastai library work on ec2-user
# fastai library is not yet available using pip install
# pull it from github using below link
# https://github.com/fastai/courses
import sys
sys.path.append("/home/ec2-user/data/fastai/")
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# This file contains all the main external libs we'll use
import numpy as np
import pandas as pd
from fastai.imports import *
from sklearn.model_selection import train_test_split
from fastai.imports import *
from fastai.transforms import *
from fastai.conv_learner import *
from fastai.model import *
from fastai.dataset import *
from fastai.sgdr import *
from fastai.plots import *
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#! ls /home/ec2-user/data/data/processed
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path = "/home/ec2-user/data/data/processed/"
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train = pd.read_json(f'{path}train.json')
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test = pd.read_json(f'{path}test.json')
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train[:2]
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len(train.iloc[4][1])
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train.inc_angle = train.inc_angle.apply(lambda x: np.nan if x == 'na' else x)
test.inc_angle = test.inc_angle.apply(lambda x: np.nan if x == 'na' else x)
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img1 = train.loc[0,['band_1','band_2']]
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img1
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img1 = np.stack([img1['band_1'], img1['band_2']], -1).reshape(75,75,2)
Below picture is not an iceberg
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plt.imshow(img1[:,:,1])
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Get rgb of image using color composite function
Thanks to MadScientist for color composite. Here is the kernal -- https://www.kaggle.com/keremt/getting-color-composites
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def color_composite(data):
rgb_arrays = []
for i, row in data.iterrows():
band_1 = np.array(row['band_1']).reshape(75, 75)
band_2 = np.array(row['band_2']).reshape(75, 75)
band_3 = band_1 / band_2
r = (band_1 + abs(band_1.min())) / np.max((band_1 + abs(band_1.min())))
g = (band_2 + abs(band_2.min())) / np.max((band_2 + abs(band_2.min())))
b = (band_3 + abs(band_3.min())) / np.max((band_3 + abs(band_3.min())))
# r = ((band_1 - np.mean(band_1)) / (np.max(band_1) - np.min(band_1)))
# g = ((band_2 - np.mean(band_2)) / (np.max(band_2) - np.min(band_2)))
# b = ((band_3 - np.mean(band_3)) / (np.max(band_3) - np.min(band_3)))
rgb = np.dstack((r, g, b))
rgb_arrays.append(rgb)
return np.array(rgb_arrays)
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# Trained with data about rgb
rgb_train = color_composite(train)
rgb_train.shape
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# Test with data about rgb
rgb_test = color_composite(test)
rgb_test.shape
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# look at random ships
print('Looking at random ships')
ships = np.random.choice(np.where(train.is_iceberg ==0)[0], 9)
fig = plt.figure(1,figsize=(12,12))
for i in range(9):
ax = fig.add_subplot(3,3,i+1)
arr = rgb_train[ships[i], :, :]
ax.imshow(arr)
plt.show()
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# look at random iceberges
print('Looking at random icebergs')
ice = np.random.choice(np.where(train.is_iceberg ==1)[0], 9)
fig = plt.figure(200,figsize=(12,12))
for i in range(9):
ax = fig.add_subplot(3,3,i+1)
arr = rgb_train[ice[i], :, :]
ax.imshow(arr)
plt.show()
saving images in directories (train, valid, test)
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# # making directories for training resnet (as it need files to be in right dir)
os.makedirs(f'{path}/composites', exist_ok= True)
os.makedirs(f'{path}/composites/train', exist_ok=True)
os.makedirs(f'{path}/composites/valid', exist_ok=True)
os.makedirs(f'{path}/composites/test', exist_ok=True)
dir_list = [f'{path}/composites/train', f'{path}/composites/valid']
for i in dir_list:
os.makedirs(f'{i}/ship')
os.makedirs(f'{i}/iceberg')
The reason of converting these images to .png is that the pretrained ConvLearner that I am going to call takes image as input
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# split
train_y, valid_y = train_test_split(train.is_iceberg, test_size=0.10)
train_iceberg_index, train_ship_index, valid_iceberg_index, valid_ship_index = train_y[train_y==1].index, train_y[train_y==0].index, valid_y[valid_y==1].index, valid_y[valid_y==0].index
#save train images
for idx in train_iceberg_index:
img = rgb_train[idx]
plt.imsave(f'{path}/composites/train/iceberg/' + str(idx) + '.png', img)
for idx in train_ship_index:
img = rgb_train[idx]
plt.imsave(f'{path}/composites/train/ship/' + str(idx) + '.png', img)
#save valid images
for idx in valid_iceberg_index:
img = rgb_train[idx]
plt.imsave(f'{path}/composites/valid/iceberg/' + str(idx) + '.png', img)
for idx in valid_ship_index:
img = rgb_train[idx]
plt.imsave(f'{path}/composites/valid/ship/' + str(idx) + '.png', img)
#save test images
for idx in range(len(test)):
img = rgb_test[idx]
plt.imsave(f'{path}/composites/test/' + str(idx) + '.png', img)
let's check directory where files are saved. Ok we have train, test and valid directories
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! ls /home/ec2-user/data/data/processed/composites/
let's train first resnet model using fastai
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path2 = '/home/ec2-user/data/data/processed/composites/'
let's look at a random ships now (from png) to make sure images are saved in directory
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files = !ls {path2}valid/ship | head
img = plt.imread(f'{path2}valid/ship/{files[0]}')
plt.imshow(img)
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! ls {path2}
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# only run this if face an error
#! rm -f -R {path2}tmp
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def get_data(sz, bs):
tfms = tfms_from_model(arch, sz, aug_tfms=transforms_top_down, max_zoom=1.00)
data = ImageClassifierData.from_paths(path2, test_name = 'test', bs = bs,
tfms = tfms)
return data
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arch=resnet18
sz = 75 # because our image size is 75*75
bs = 32 # because default batch size of 64 was not giving good converging loss
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data = get_data(sz, bs)
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data = data.resize(int(sz*1.3), 'tmp')
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learn = ConvLearner.pretrained(arch, data, precompute=False)
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lrf = learn.lr_find()
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learn.sched.plot_lr()
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learn.sched.plot()
Now, this plot is important to decide a good learning rate. We will not decide the learning rate at the lowest loss, which might sound confusing. But the catch is that we are going to do differential annealing to activate our layers which take varying learning rates. And the rate we chose here is going to be the maximum rate. So, we will chose some rate just before it bottoms up where loss is still falling.
Minimum is at 10^-1, I would chose 10^-2 is LR
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lr = 0.01
epochs = 3
cycle length = 1
cycle multiple = 2
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learn.fit(lr, 3, cycle_len=1, cycle_mult=2) # precompute was false # first fit
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# stochastic descent with restart
learn.sched.plot_lr()
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learn.sched.plot_loss()
Loss is decreasing with increaseing iterations
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#learn.save('/home/ec2-user/data/data/processed/75_lastlayer_res34_bs28')
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#learn.load('/home/ec2-user/data/data/processed/75_lastlayer')
Since, the images that we have do not have very clear and sharp features which might be present in top layers of our pre-trained neural network. Let's unfreeze our layers and calculate activations
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lr = 0.01
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learn.unfreeze()
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lrs=np.array([lr/9,lr/3,lr]) # use lr/100 and lr/10 respectively if images would have been larger in sizes
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learn.fit(lrs, 3, cycle_len=1, cycle_mult=2)
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learn.sched.plot_loss()
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! ls /home/ec2-user/data/
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#learn.save('/home/ec2-user/data/data/processed/75_all_res18_bs24_4') # save learn
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learn.fit(lr, 3, cycle_len=1, cycle_mult=2) # precompute was false # first fit
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learn.sched.plot_loss()
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#learn.save('/home/ec2-user/data/data/processed/75_all_res18_bs32_2') # save learn
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#learn.load('/home/ec2-user/data/data/processed/75_all_res18_bs32_2')
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# to check validation accuray
log_preds,y = learn.TTA()
accuracy(log_preds,y)
TTA (Test Time Augmentation) simply makes predictions not just on the images in your validation set, but also makes predictions on a number of randomly augmented versions of them
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# from here we know that 'icebergs' is label 0 and 'ships' is label 1.
data.classes
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# this gives prediction for validation set. Predictions are in log scale
log_preds = learn.TTA(is_test=True) # If need TTA
#log_preds = learn.predict(is_test=True) # if don't need TTA
log_preds[0].shape
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probs_submit1 = np.exp(log_preds[0][:,0])
probs_submit1[:10]
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# getting ids from test list
id_raw = data.test_dl.dataset.fnames
id_raw[1]
# using regex to take numbers from ids
id_pro = result_array = np.empty((0, len(id_raw)))
for i in range(len(id_raw)):
stuff = int(re.findall(r'\d+', id_raw[i])[0])
#print(type(str(stuff)))
id_pro = np.append(id_pro,int(stuff))
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id_pro_list = []
for i in id_pro:
id_pro_list.append(int(i))
id_pro_list[:4]
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# joining id and probability
d = {'index': id_pro_list, 'is_iceberg': probs_submit1}
submit1_df = pd.DataFrame(data=d)
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id_ = test['id']
id_pd = pd.DataFrame({'id': id_} )
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submit1_df_sorted = submit1_df.sort_values('index')
submit1_df_sorted2 = pd.concat([id_, submit1_df_sorted.set_index('index')], axis = 1)
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submit1_df_sorted2.dtypes
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submit1_df.dtypes
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#submit1_df.id = submit1_df.id.astype(str)
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submit1_df_sorted2.to_csv('/home/ec2-user/data/submissions/submit6.csv', index = False)
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! head -5 /home/ec2-user/data/submissions/submit7.csv
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submit_check = pd.read_csv("/home/ec2-user/data/submissions/submit6.csv")
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#submit_check.dtypes
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submit_check[:10]
scp submit1 to local machine to upload on kaggle
As well as looking at the overall metrics, it's also a good idea to look at examples of each of:
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log_pred1 = learn.TTA() # If need TTA
preds = np.argmax(log_pred1[0], axis=1) # from log probabilities to 0 or 1
probs = np.exp(log_pred1[0][:,1]) # pr(ship)
#probs = submit_check['is_iceberg']
#submit_check['C'] = np.where(submit_check['is_iceberg'] >= 0.5,1, 0)
#preds = np.array(submit_check['C'])
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def rand_by_mask(mask): return np.random.choice(np.where(mask)[0], 4, replace=False)
def rand_by_correct(is_correct): return rand_by_mask((preds == data.val_y)==is_correct)
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def plot_val_with_title(idxs, title):
imgs = np.stack([data.val_ds[x][0] for x in idxs])
title_probs = [probs[x] for x in idxs]
print(title)
return plots(data.val_ds.denorm(imgs), rows=1, titles=title_probs)
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def plots(ims, figsize=(12,6), rows=1, titles=None):
f = plt.figure(figsize=figsize)
for i in range(len(ims)):
sp = f.add_subplot(rows, len(ims)//rows, i+1)
sp.axis('Off')
if titles is not None: sp.set_title(titles[i], fontsize=16)
plt.imshow(ims[i])
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def load_img_id(ds, idx): return np.array(PIL.Image.open(path2+ds.fnames[idx]))
def plot_val_with_title(idxs, title):
imgs = [load_img_id(data.val_ds,x) for x in idxs]
title_probs = [probs[x] for x in idxs]
print(title)
return plots(imgs, rows=1, titles=title_probs, figsize=(16,8))
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# 1. A few correct labels at random
plot_val_with_title(rand_by_correct(True), "Correctly classified")
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# 2. A few incorrect labels at random
plot_val_with_title(rand_by_correct(False), "Incorrectly classified")
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def most_by_mask(mask, mult):
idxs = np.where(mask)[0]
return idxs[np.argsort(mult * probs[idxs])[:4]]
def most_by_correct(y, is_correct):
mult = -1 if (y==1)==is_correct else 1
return most_by_mask((preds == data.val_y)==is_correct & (data.val_y == y), mult)
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plot_val_with_title(most_by_correct(0, True), "Most correct icebergs")
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plot_val_with_title(most_by_correct(1, True), "Most correct ships")
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