.gitignore

@@ -2,5 +2,6 @@
 */.ipynb_checkpoints/*
 __pycache__
 */__pycache__/*
-/run/**
+run/
 */data/*
+!/GTSRB/data/dataset.tar.gz

GTSRB/01-Preparation-of-data.ipynb

+%% Cell type:markdown id: tags:
+
+German Traffic Sign Recognition Benchmark (GTSRB)
+=================================================
+---
+Introduction au Deep Learning  (IDLE) - S. Arias, E. Maldonado, JL. Parouty - CNRS/SARI/DEVLOG - 2020
+Version: 1.12
+
+## Episode 1 : Preparation of data
+
+ - Understanding the dataset
+ - Preparing and formatting enhanced data
+ - Save enhanced datasets in h5 file format
+
+%% Cell type:markdown id: tags:
+
+## 1/ Import and init
+
+%% Cell type:code id: tags:
+
+``` python
+import os, time, sys
+import csv
+import math, random
+
+import numpy as np
+import matplotlib.pyplot as plt
+import h5py
+
+from skimage.morphology import disk
+from skimage.filters import rank
+from skimage import io, color, exposure, transform
+
+import idle.pwk as ooo
+from importlib import reload
+
+ooo.init()
+```
+
+%% Cell type:markdown id: tags:
+
+## 2/ Read the dataset
+Description is available there : http://benchmark.ini.rub.de/?section=gtsrb&subsection=dataset
+ - Each directory contains one CSV file with annotations ("GT-<ClassID>.csv") and the training images
+ - First line is fieldnames: Filename;Width;Height;Roi.X1;Roi.Y1;Roi.X2;Roi.Y2;ClassId
+
+### 2.1/ Usefull functions
+
+%% Cell type:code id: tags:
+
+``` python
+def read_dataset_dir(csv_filename):
+    '''Reads traffic sign data from German Traffic Sign Recognition Benchmark dataset.
+
+    Arguments:  csv filename
+                Example /data/GTSRB/Train.csv
+    Returns:   np array of images, np array of corresponding labels'''
+
+    # ---- csv filename and path
+    #
+    name=os.path.basename(csv_filename)
+    path=os.path.dirname(csv_filename)
+
+    # ---- Read csv file
+    #
+    f,x,y = [],[],[]
+    with open(csv_filename) as csv_file:
+        reader = csv.DictReader(csv_file, delimiter=',')
+        for row in reader:
+            f.append( path+'/'+row['Path'] )
+            y.append( int(row['ClassId'])  )
+        csv_file.close()
+    nb_images = len(f)
+
+    # ---- Read images
+    #
+    for filename in f:
+        image=io.imread(filename)
+        x.append(image)
+        ooo.update_progress(name,len(x),nb_images)
+    # ---- Return
+    #
+    return np.array(x),np.array(y)
+```
+
+%% Cell type:markdown id: tags:
+
+### 2.2/ Read the data
+We will read the following datasets:
+ - **x_train, y_train** : Learning data
+ - **x_test, y_test** : Validation or test data
+ - x_meta, y_meta : Illustration data
+
+The learning data will be randomly mixted and the illustration data sorted.
+Will take about 2-3'
+
+%% Cell type:code id: tags:
+
+``` python
+%%time
+
+# ---- Read datasets
+(x_train,y_train) = read_dataset_dir('./data/origine/Train.csv')
+(x_test ,y_test)  = read_dataset_dir('./data/origine/Test.csv')
+(x_meta ,y_meta)  = read_dataset_dir('./data/origine/Meta.csv')
+
+# ---- Shuffle train set
+combined = list(zip(x_train,y_train))
+random.shuffle(combined)
+x_train,y_train = zip(*combined)
+
+# ---- Sort Meta
+combined = list(zip(x_meta,y_meta))
+combined.sort(key=lambda x: x[1])
+x_meta,y_meta = zip(*combined)
+```
+
+%% Cell type:markdown id: tags:
+
+## 3/ Few statistics about train dataset
+We want to know if our images are homogeneous in terms of size, ratio, width or height.
+
+### 3.1/ Do statistics
+
+%% Cell type:code id: tags:
+
+``` python
+train_size  = []
+train_ratio = []
+train_lx    = []
+train_ly    = []
+
+test_size   = []
+test_ratio  = []
+test_lx     = []
+test_ly     = []
+
+for image in x_train:
+    (lx,ly,lz) = image.shape
+    train_size.append(lx*ly/1024)
+    train_ratio.append(lx/ly)
+    train_lx.append(lx)
+    train_ly.append(ly)
+
+for image in x_test:
+    (lx,ly,lz) = image.shape
+    test_size.append(lx*ly/1024)
+    test_ratio.append(lx/ly)
+    test_lx.append(lx)
+    test_ly.append(ly)
+```
+
+%% Cell type:markdown id: tags:
+
+### 3.2/ Show statistics
+
+%% Cell type:code id: tags:
+
+``` python
+# ------ Global stuff
+print("x_train size : ",len(x_train))
+print("y_train size : ",len(y_train))
+print("x_test size  : ",len(x_test))
+print("y_test size  : ",len(y_test))
+
+# ------ Statistics / sizes
+plt.figure(figsize=(16,6))
+plt.hist([train_size,test_size], bins=100)
+plt.gca().set(title='Sizes in Kpixels - Train=[{:5.2f}, {:5.2f}]'.format(min(train_size),max(train_size)),
+              ylabel='Population',
+              xlim=[0,30])
+plt.legend(['Train','Test'])
+plt.show()
+
+# ------ Statistics / ratio lx/ly
+plt.figure(figsize=(16,6))
+plt.hist([train_ratio,test_ratio], bins=100)
+plt.gca().set(title='Ratio lx/ly - Train=[{:5.2f}, {:5.2f}]'.format(min(train_ratio),max(train_ratio)),
+              ylabel='Population',
+              xlim=[0.8,1.2])
+plt.legend(['Train','Test'])
+plt.show()
+
+# ------ Statistics / lx
+plt.figure(figsize=(16,6))
+plt.hist([train_lx,test_lx], bins=100)
+plt.gca().set(title='Images lx - Train=[{:5.2f}, {:5.2f}]'.format(min(train_lx),max(train_lx)),
+              ylabel='Population',
+              xlim=[20,150])
+plt.legend(['Train','Test'])
+plt.show()
+
+# ------ Statistics / ly
+plt.figure(figsize=(16,6))
+plt.hist([train_ly,test_ly], bins=100)
+plt.gca().set(title='Images ly - Train=[{:5.2f}, {:5.2f}]'.format(min(train_ly),max(train_ly)),
+              ylabel='Population',
+              xlim=[20,150])
+plt.legend(['Train','Test'])
+plt.show()
+
+# ------ Statistics / classId
+plt.figure(figsize=(16,6))
+plt.hist([y_train,y_test], bins=43)
+plt.gca().set(title='ClassesId',
+              ylabel='Population',
+              xlim=[0,43])
+plt.legend(['Train','Test'])
+plt.show()
+```
+
+%% Cell type:markdown id: tags:
+
+## 4/ List of classes
+What are the 43 classes of our images...
+
+%% Cell type:code id: tags:
+
+``` python
+ooo.plot_images(x_meta,y_meta, range(43), columns=8, x_size=2, y_size=2,
+                                colorbar=False, y_pred=None, cm='binary')
+```
+
+%% Cell type:markdown id: tags:
+
+## 5/ What does it really look like
+
+%% Cell type:code id: tags:
+
+``` python
+# ---- Get and show few images
+
+samples = [ random.randint(0,len(x_train)-1) for i in range(32)]
+ooo.plot_images(x_train,y_train, samples, columns=8, x_size=2, y_size=2, colorbar=False, y_pred=None, cm='binary')
+```
+
+%% Cell type:markdown id: tags:
+
+## 6/ dataset cooking...
+
+Images must have the **same size** to match the size of the network.
+It is possible to work on **rgb** or **monochrome** images and **equalize** the histograms.
+The data must be **normalized**.
+
+See : [Exposure with scikit-image](https://scikit-image.org/docs/dev/api/skimage.exposure.html)
+See : [Local histogram equalization](https://scikit-image.org/docs/dev/api/skimage.filters.rank.html#skimage.filters.rank.equalize)
+See : [Histogram equalization](https://scikit-image.org/docs/dev/api/skimage.exposure.html#skimage.exposure.equalize_hist)
+
+### 6.1/ Enhancement cook
+
+%% Cell type:code id: tags:
+
+``` python
+def images_enhancement(images, width=25, height=25, mode='RGB'):
+    '''
+    Resize and convert images - doesn't change originals.
+    input images must be RGBA or RGB.
+    args:
+        images :         images list
+        width,height :   new images size (25,25)
+        mode :           RGB | RGB-HE | L | L-HE | L-LHE | L-CLAHE
+    return:
+        numpy array of enhanced images
+    '''
+    modes = { 'RGB':3, 'RGB-HE':3, 'L':1, 'L-HE':1, 'L-LHE':1, 'L-CLAHE':1}
+    lz=modes[mode]
+
+    out=[]
+    for img in images:
+
+        # ---- if RGBA, convert to RGB
+        if img.shape[2]==4:
+            img=color.rgba2rgb(img)
+
+        # ---- Resize
+        img = transform.resize(img, (width,height))
+
+        # ---- RGB / Histogram Equalization
+        if mode=='RGB-HE':
+            hsv = color.rgb2hsv(img.reshape(width,height,3))
+            hsv[:, :, 2] = exposure.equalize_hist(hsv[:, :, 2])
+            img = color.hsv2rgb(hsv)
+
+        # ---- Grayscale
+        if mode=='L':
+            img=color.rgb2gray(img)
+
+        # ---- Grayscale / Histogram Equalization
+        if mode=='L-HE':
+            img=color.rgb2gray(img)
+            img=exposure.equalize_hist(img)
+
+        # ---- Grayscale / Local Histogram Equalization
+        if mode=='L-LHE':
+            img=color.rgb2gray(img)
+            img=rank.equalize(img, disk(10))/255.
+
+        # ---- Grayscale / Contrast Limited Adaptive Histogram Equalization (CLAHE)
+        if mode=='L-CLAHE':
+            img=color.rgb2gray(img)
+            img=exposure.equalize_adapthist(img)
+
+        # ---- Add image in list of list
+        out.append(img)
+        ooo.update_progress('Enhancement: ',len(out),len(images))
+
+    # ---- Reshape images
+    #     (-1, width,height,1) for L
+    #     (-1, width,height,3) for RGB
+    #
+    out = np.array(out,dtype='float64')
+    out = out.reshape(-1,width,height,lz)
+    return out
+```
+
+%% Cell type:markdown id: tags:
+
+### 6.2/ To get an idea of the different recipes
+
+%% Cell type:code id: tags:
+
+``` python
+i=random.randint(0,len(x_train)-16)
+x_samples = x_train[i:i+16]
+y_samples = y_train[i:i+16]
+
+datasets  = {}
+
+datasets['RGB']      = images_enhancement( x_samples, width=25, height=25, mode='RGB'  )
+datasets['RGB-HE']   = images_enhancement( x_samples, width=25, height=25, mode='RGB-HE'  )
+datasets['L']        = images_enhancement( x_samples, width=25, height=25, mode='L'  )
+datasets['L-HE']     = images_enhancement( x_samples, width=25, height=25, mode='L-HE'  )
+datasets['L-LHE']    = images_enhancement( x_samples, width=25, height=25, mode='L-LHE'  )
+datasets['L-CLAHE']  = images_enhancement( x_samples, width=25, height=25, mode='L-CLAHE'  )
+
+print('\nEXPECTED (Meta) :\n')
+x_expected=[ x_meta[i] for i in y_samples]
+ooo.plot_images(x_expected, y_samples, range(16), columns=16, x_size=1, y_size=1, colorbar=False, y_pred=None, cm='binary')
+
+print('\nORIGINAL IMAGES :\n')
+ooo.plot_images(x_samples,  y_samples, range(16), columns=16, x_size=1, y_size=1, colorbar=False, y_pred=None, cm='binary')
+
+print('\nENHANCED :\n')
+for k,d in datasets.items():
+    print("dataset : {}  min,max=[{:.3f},{:.3f}]  shape={}".format(k,d.min(),d.max(), d.shape))
+    ooo.plot_images(d, y_samples, range(16), columns=16, x_size=1, y_size=1, colorbar=False, y_pred=None, cm='binary')
+```
+
+%% Cell type:markdown id: tags:
+
+### 6.3/ Cook and save
+A function to save a dataset
+
+%% Cell type:code id: tags:
+
+``` python
+def save_h5_dataset(x_train, y_train, x_test, y_test, x_meta,y_meta, h5name):
+
+    # ---- Filename
+    filename='./data/'+h5name
+
+    # ---- Create h5 file
+    with h5py.File(filename, "w") as f:
+        f.create_dataset("x_train", data=x_train)
+        f.create_dataset("y_train", data=y_train)
+        f.create_dataset("x_test",  data=x_test)
+        f.create_dataset("y_test",  data=y_test)
+        f.create_dataset("x_meta",  data=x_meta)
+        f.create_dataset("y_meta",  data=y_meta)
+
+    # ---- done
+    size=os.path.getsize(filename)/(1024*1024)
+    print('Dataset : {:24s}  shape : {:22s} size : {:6.1f} Mo   (saved)\n'.format(filename, str(x_train.shape),size))
+```
+
+%% Cell type:markdown id: tags:
+
+Create enhanced datasets, and save them...
+Will take about 7-8'
+
+%% Cell type:code id: tags:
+
+``` python
+%%time
+
+for s in [24, 48]:
+    for m in ['RGB', 'RGB-HE', 'L', 'L-LHE']:
+        # ---- A nice dataset name
+        name='set-{}x{}-{}.h5'.format(s,s,m)
+        print("\nDataset : ",name)
+        # ---- Enhancement
+        x_train_new = images_enhancement( x_train, width=s, height=s, mode=m )
+        x_test_new  = images_enhancement( x_test,  width=s, height=s, mode=m )
+        x_meta_new  = images_enhancement( x_meta,  width=s, height=s, mode='RGB' )
+        # ---- Save
+        save_h5_dataset( x_train_new, y_train, x_test_new, y_test, x_meta_new,y_meta, name)
+
+x_train_new,x_test_new=0,0
+```
+
+%% Cell type:markdown id: tags:
+
+## 7/ Reload data to be sure ;-)
+
+%% Cell type:code id: tags:
+
+``` python
+%%time
+
+dataset='set-48x48-L'
+samples=range(24)
+
+with  h5py.File('./data/'+dataset+'.h5') as f:
+    x_tmp = f['x_train'][:]
+    y_tmp = f['y_train'][:]
+    print("dataset loaded from h5 file.")
+
+ooo.plot_images(x_tmp,y_tmp, samples, columns=8, x_size=2, y_size=2, colorbar=False, y_pred=None, cm='binary')
+x_tmp,y_tmp=0,0
+```
+
+%% Cell type:markdown id: tags:
+
+----
+That's all folks !

GTSRB/07-Full-convolutions.ipynb

+%% Cell type:markdown id: tags:
+
+German Traffic Sign Recognition Benchmark (GTSRB)
+=================================================
+---
+Introduction au Deep Learning  (IDLE) - S. Arias, E. Maldonado, JL. Parouty - CNRS/SARI/DEVLOG - 2020
+Vesion : 1.2.1
+
+## Episode 7 : Full Convolutions
+
+Our main steps:
+ - Try n models with n datasets
+
+## 1/ Import and init
+
+%% Cell type:code id: tags:
+
+``` python
+import tensorflow as tf
+from tensorflow import keras
+from tensorflow.keras.callbacks import TensorBoard
+
+import numpy as np
+import matplotlib.pyplot as plt
+import h5py
+import os,time
+
+import pandas as pd
+import idle.pwk as ooo
+from importlib import reload
+from IPython.display import display
+
+ooo.init()
+```
+
+%% Output
+
+    IDLE 2020 - Practical Work Module
+      Version            : 0.1.4
+      Run time           : Friday 17 January 2020, 21:38:34
+      Matplotlib style   : idle/talk.mplstyle
+      TensorFlow version : 2.0.0
+      Keras version      : 2.2.4-tf
+
+%% Cell type:markdown id: tags:
+
+## 2/ Load dataset functions
+
+%% Cell type:code id: tags:
+
+``` python
+def read_dataset(name):
+    '''Reads h5 dataset from ./data
+
+    Arguments:  dataset name, without .h5
+    Returns:    x_train,y_train,x_test,y_test data'''
+    # ---- Read dataset
+    filename='./data/'+name+'.h5'
+    with  h5py.File(filename) as f:
+        x_train = f['x_train'][:]
+        y_train = f['y_train'][:]
+        x_test  = f['x_test'][:]
+        y_test  = f['y_test'][:]
+
+    return x_train,y_train,x_test,y_test
+```
+
+%% Cell type:markdown id: tags:
+
+## 3/ Models collection
+
+%% Cell type:code id: tags:
+
+``` python
+
+# A basic model
+#
+def get_model_v1(lx,ly,lz):
+
+    model = keras.models.Sequential()
+
+    model.add( keras.layers.Conv2D(96, (3,3), activation='relu', input_shape=(lx,ly,lz)))
+    model.add( keras.layers.MaxPooling2D((2, 2)))
+    model.add( keras.layers.Dropout(0.2))
+
+    model.add( keras.layers.Conv2D(192, (3, 3), activation='relu'))
+    model.add( keras.layers.MaxPooling2D((2, 2)))
+    model.add( keras.layers.Dropout(0.2))
+
+    model.add( keras.layers.Flatten())
+    model.add( keras.layers.Dense(1500, activation='relu'))
+    model.add( keras.layers.Dropout(0.5))
+
+    model.add( keras.layers.Dense(43, activation='softmax'))
+    return model
+
+# A more sophisticated model
+#
+def get_model_v2(lx,ly,lz):
+    model = keras.models.Sequential()
+
+    model.add( keras.layers.Conv2D(64, (3, 3), padding='same', input_shape=(lx,ly,lz), activation='relu'))
+    model.add( keras.layers.Conv2D(64, (3, 3), activation='relu'))
+    model.add( keras.layers.MaxPooling2D(pool_size=(2, 2)))
+    model.add( keras.layers.Dropout(0.2))
+
+    model.add( keras.layers.Conv2D(128, (3, 3), padding='same', activation='relu'))
+    model.add( keras.layers.Conv2D(128, (3, 3), activation='relu'))
+    model.add( keras.layers.MaxPooling2D(pool_size=(2, 2)))
+    model.add( keras.layers.Dropout(0.2))
+
+    model.add( keras.layers.Conv2D(256, (3, 3), padding='same',activation='relu'))
+    model.add( keras.layers.Conv2D(256, (3, 3), activation='relu'))
+    model.add( keras.layers.MaxPooling2D(pool_size=(2, 2)))
+    model.add( keras.layers.Dropout(0.2))
+
+    model.add( keras.layers.Flatten())
+    model.add( keras.layers.Dense(512, activation='relu'))
+    model.add( keras.layers.Dropout(0.5))
+    model.add( keras.layers.Dense(43, activation='softmax'))
+    return model
+
+# My sphisticated model, but small and fast
+#
+def get_model_v3(lx,ly,lz):
+    model = keras.models.Sequential()
+    model.add( keras.layers.Conv2D(32, (3,3),   activation='relu', input_shape=(lx,ly,lz)))
+    model.add( keras.layers.MaxPooling2D((2, 2)))
+    model.add( keras.layers.Dropout(0.5))
+
+    model.add( keras.layers.Conv2D(64, (3, 3), activation='relu'))
+    model.add( keras.layers.MaxPooling2D((2, 2)))
+    model.add( keras.layers.Dropout(0.5))
+
+    model.add( keras.layers.Conv2D(128, (3, 3), activation='relu'))
+    model.add( keras.layers.MaxPooling2D((2, 2)))
+    model.add( keras.layers.Dropout(0.5))
+
+    model.add( keras.layers.Conv2D(256, (3, 3), activation='relu'))
+    model.add( keras.layers.MaxPooling2D((2, 2)))
+    model.add( keras.layers.Dropout(0.5))
+
+    model.add( keras.layers.Flatten())
+    model.add( keras.layers.Dense(1152, activation='relu'))
+    model.add( keras.layers.Dropout(0.5))
+
+    model.add( keras.layers.Dense(43, activation='softmax'))
+    return model
+```
+
+%% Cell type:markdown id: tags:
+
+## 4/ Callbacks
+
+%% Cell type:code id: tags:
+
+``` python
+%%bash
+# To clean old logs and saved model, run this cell
+#
+/bin/rm -r ./run/logs 2>/dev/null
+/bin/rm -r ./run/models 2>/dev/null
+/bin/ls -l ./run  2>/dev/null
+```
+
+%% Output
+
+    total 0
+
+%% Cell type:code id: tags:
+
+``` python
+ooo.mkdir('./run/models')
+ooo.mkdir('./run/logs')
+
+# ---- Callback tensorboard
+log_dir = "./run/logs/tb_" + ooo.tag_now()
+tensorboard_callback = tf.keras.callbacks.TensorBoard(log_dir=log_dir, histogram_freq=1)
+
+# ---- Callback ModelCheckpoint - Save best model
+save_dir = "./run/models/best-model.h5"
+bestmodel_callback = tf.keras.callbacks.ModelCheckpoint(filepath=save_dir, verbose=0, monitor='accuracy', save_best_only=True)
+
+# ---- Callback ModelCheckpoint - Save model each epochs
+save_dir = "./run/models/model-{epoch:04d}.h5"
+savemodel_callback = tf.keras.callbacks.ModelCheckpoint(filepath=save_dir, verbose=0, save_freq=2000*5)
+```
+
+%% Cell type:markdown id: tags:
+
+## 6/ Multiple datasets, multiple models ;-)
+
+%% Cell type:code id: tags:
+
+``` python
+def multi_run(datasets, models, batch_size=64, epochs=16):
+
+    # ---- Columns of report
+    #
+    report={}
+    report['Dataset']=[]
+    report['Size']   =[]
+    for m in models:
+        report[m+' Accuracy'] = []
+        report[m+' Duration'] = []
+
+    # ---- Let's go
+    #
+    for dname in datasets:
+        print("\nDataset : ",dname)
+
+        # ---- Read dataset
+        x_train,y_train,x_test,y_test = read_dataset(dname)
+        dsize=os.path.getsize('./data/'+dname+'.h5')/(1024*1024)
+        report['Dataset'].append(dname)
+        report['Size'].append(dname)
+
+        # ---- Get the shape
+        (n,lx,ly,lz) = x_train.shape
+
+        # ---- For each model
+        for kmodel,fmodel in models.items():
+            print("    Run model {}  : ".format(kmodel), end='')
+            # ---- get model
+            try:
+                model=fmodel(lx,ly,lz)
+                # ---- Compile it
+                model.compile(optimizer='adam', loss='sparse_categorical_crossentropy', metrics=['accuracy'])
+                # ---- Train
+                start_time = time.time()
+                history = model.fit(  x_train[:1000], y_train[:1000],
+                                    batch_size      = batch_size,
+                                    epochs          = epochs,
+                                    verbose         = 0,
+                                    validation_data = (x_test, y_test),
+                                    callbacks       = [tensorboard_callback, bestmodel_callback, savemodel_callback])
+                # ---- Result
+                end_time = time.time()
+                duration = end_time-start_time
+                accuracy = max(history.history["val_accuracy"])*100
+                #
+                report[kmodel+' Accuracy'].append(accuracy)
+                report[kmodel+' Duration'].append(duration)
+                print("Accuracy={:.2f} and Duration={:.2f})".format(accuracy,duration))
+            except:
+                report[kmodel+' Accuracy'].append('-')
+                report[kmodel+' Duration'].append('-')
+                print('-')
+    print("\n")
+    return report
+```
+
+%% Cell type:code id: tags:
+
+``` python
+%%time
+
+# datasets = ['set-24x24-L', 'set-24x24-RGB', 'set-48x48-L', 'set-48x48-RGB', 'set-24x24-L-LHE', 'set-24x24-RGB-HE', 'set-48x48-L-LHE', 'set-48x48-RGB-HE']
+# models   = {'v1':get_model_v1, 'v2':get_model_v2, 'v3':get_model_v3}
+
+datasets = ['set-24x24-L', 'set-24x24-RGB']
+models   = {'v1':get_model_v1, 'v3':get_model_v3}
+
+out    = multi_run(datasets, models, batch_size=64, epochs=2)
+report = pd.DataFrame (out)
+```
+
+%% Output
+
+    
+    Dataset :  set-24x24-L
+        Run model v1  : Accuracy=9.46 and Duration=7.51)
+        Run model v3  : -
+    
+    Dataset :  set-24x24-RGB
+        Run model v1  : Accuracy=15.95 and Duration=7.95)
+        Run model v3  : -
+    
+    
+    CPU times: user 1min 35s, sys: 3.31 s, total: 1min 38s
+    Wall time: 17 s
+
+%% Cell type:code id: tags:
+
+``` python
+display(report)
+df.to_hdf('foo.h5', 'df')
+```
+
+%% Output
+
+
+%% Cell type:code id: tags:
+
+``` python
+df=pd.read_hdf('foo.h5', 'df')
+display(df)
+```
+
+%% Output
+
+
+%% Cell type:markdown id: tags:
+
+---
+
+
+### Some results :
+
+
+%% Cell type:markdown id: tags:
+
+|         Datasets         |       Size      |     Model : v1     |    Model : v2      |     Model : v3     |
+|:------------------------:|:---------------:|:------------------:|:------------------:|:------------------:|
+| set-24x24-L              |          229 Mo |   95.91%  75.04s   |   96.86% 102.28s   |   -      -         |
+| set-24x24-RGB            |          684 Mo |   96.60%  77.24s   |   97.32% 103.93s   |   -      -         |
+| set-48x48-L              |          914 Mo | **96.71%** 123.94s |   97.68% 149.57s   |  97.60%  91.53s    |
+| set-48x48-RGB            |         2736 Mo |   96.36% 117.74s   | **98.20%** 142.63s |  97.28%  91.29s    |
+| set-24x24-L-LHE          |          229 Mo |   95.95%  66.12s   |   96.75%  89.45s   |   -      -         |
+| set-24x24-RGB-HE         |          684 Mo |   95.30%  68.89s   |   96.28%  92.15s   |   -      -         |
+| set-48x48-L-LHE          |          914 Mo |   96.69% 109.28s   |   97.94% 135.17s   | **97.97%** 83.80s  |
+| set-48x48-RGB-HE         |         2736 Mo |   95.29% 117.70s   | **98.13%** 141.56s |  97.00%  89.38s    |
+
+%% Cell type:code id: tags:
+
+``` python
+```

GTSRB/99 Scripts-Tensorboard.ipynb

+%% Cell type:markdown id: tags:
+
+Running Tensorboard from Jupyter lab
+====================================
+---
+Introduction au Deep Learning  (IDLE) - S. Arias, E. Maldonado, JL. Parouty - CNRS/SARI/DEVLOG - 2020
+Vesion : 1.0
+
+%% Cell type:markdown id: tags:
+
+## 1/ Méthode 1 : Shell execute
+### 1.1/ Start/stop
+
+%% Cell type:code id: tags:
+
+``` python
+%%bash
+tensorboard_start --logdir ./run/logs
+```
+
+%% Output
+
+    Tensorbord started - pid is  211387
+
+%% Cell type:code id: tags:
+
+``` python
+%%bash
+tensorboard_status
+```
+
+%% Output
+
+    Tensorboard status - pid is  214798
+
+%% Cell type:code id: tags:
+
+``` python
+%%bash
+tensorboard_stop
+```
+
+%% Output
+
+    Tensorboard process not found...
+
+%% Cell type:markdown id: tags:
+
+### 1.3/ Scripts
+
+%% Cell type:code id: tags:
+
+``` python
+%%writefile "~/bin/tensorboard_start"
+
+#!/bin/bash
+#
+# -----------------------------------------------------------
+#  _____                         _                         _
+# |_   _|__ _ __  ___  ___  _ __| |__   ___   __ _ _ __ __| |
+#   | |/ _ \ '_ \/ __|/ _ \| '__| '_ \ / _ \ / _` | '__/ _` |
+#   | |  __/ | | \__ \ (_) | |  | |_) | (_) | (_| | | | (_| |
+#   |_|\___|_| |_|___/\___/|_|  |_.__/ \___/ \__,_|_|  \__,_|
+#                                                       Start
+# -----------------------------------------------------------
+# Start tensorboard, with calculate port number and good host
+# -----------------------------------------------------------
+# Jean-Luc Parouty CNRS/SIMaP Janvier 2020 - version 1.02
+
+VERSION='1.02'
+
+# ---- Usage
+#
+if [ "$1" == "-?" ] || [ $# -eq 0 ]; then
+        echo -e "Start tensorboard in GRICAD environment. (v$VERSION)"
+        echo -e "Usage: $(basename $0) -h | --logdir <logdir> [tensorboard args]"
+        echo -e "Exemple :  $(basename $0) --logdir ./run/logs\n"
+        exit
+fi
+
+# ---- Port number
+#
+PORT_JPY="$(/usr/bin/id -u)"
+PORT_TSB="$(( $PORT_JPY + 10000 ))"
+
+# ---- tmpdir (tmp bug)
+#
+export TMPDIR="/tmp/$(/usr/bin/id -un)"
+/bin/mkdir -p "$TMPDIR"
+
+# ---- Start it
+#
+tensorboard --port $PORT_TSB --host 0.0.0.0 $@  &>/dev/null &
+
+# ---- Where is it ?
+#
+sleep 5
+p="$(/bin/ps ax | /bin/grep "tensorboard --port $PORT_TSB" | /bin/grep -v grep | awk '{print $1}')"
+if [ -z "$p" ]; then
+        echo "Tensorboard didn't start... check your parameters !"
+else
+        echo "Tensorbord started - pid is  $p"
+fi
+```
+
+%% Output
+
+    Overwriting /home/paroutyj/bin/tensorboard_start
+
+%% Cell type:code id: tags:
+
+``` python
+%%writefile "~/bin/tensorboard_status"
+
+#!/bin/bash
+#
+# -----------------------------------------------------------
+#  _____                         _                         _
+# |_   _|__ _ __  ___  ___  _ __| |__   ___   __ _ _ __ __| |
+#   | |/ _ \ '_ \/ __|/ _ \| '__| '_ \ / _ \ / _` | '__/ _` |
+#   | |  __/ | | \__ \ (_) | |  | |_) | (_) | (_| | | | (_| |
+#   |_|\___|_| |_|___/\___/|_|  |_.__/ \___/ \__,_|_|  \__,_|
+#                                                      Status
+# -----------------------------------------------------------
+# Stop tensorboard previously started with tensorboard_start
+# -----------------------------------------------------------
+# Jean-Luc Parouty CNRS/SIMaP Janvier 2020
+
+VERSION="1.02"
+
+# ---- Usage
+#
+if [ "$1" == "-?" ] ; then
+        echo -e "Tensorboard status in GRICAD environment. (v$VERSION)"
+        echo -e "Usage: $(basename $0) [-h ]"
+        echo -e "Exemple :  $(basename $0)\n"
+        exit
+fi
+
+# ---- Process id
+#
+PORT_JPY="$(id -u)"
+PORT_TSB="$(( $PORT_JPY + 10000 ))"
+
+# ---- Where is it ?
+#
+p="$(ps ax | grep "tensorboard --port $PORT_TSB" | grep -v grep | awk '{print $1}')"
+if [ -z "$p" ]; then
+        echo "Tensorboard status - not found..."
+else
+        echo "Tensorboard status - pid is  $p"
+fi
+```
+
+%% Output
+
+    Writing /home/paroutyj/bin/tensorboard_status
+
+%% Cell type:code id: tags:
+
+``` python
+%%writefile "~/bin/tensorboard_stop"
+
+#!/bin/bash
+#
+# -----------------------------------------------------------
+#  _____                         _                         _
+# |_   _|__ _ __  ___  ___  _ __| |__   ___   __ _ _ __ __| |
+#   | |/ _ \ '_ \/ __|/ _ \| '__| '_ \ / _ \ / _` | '__/ _` |
+#   | |  __/ | | \__ \ (_) | |  | |_) | (_) | (_| | | | (_| |
+#   |_|\___|_| |_|___/\___/|_|  |_.__/ \___/ \__,_|_|  \__,_|
+#                                                       Stop
+# -----------------------------------------------------------
+# Stop tensorboard previously started with tensorboard_start
+# -----------------------------------------------------------
+# Jean-Luc Parouty CNRS/SIMaP Janvier 2020
+
+VERSION="1.02"
+
+# ---- Usage
+#
+if [ "$1" == "-?" ] ; then
+        echo -e "Stop tensorboard in GRICAD environment. (v$VERSION)"
+        echo -e "Usage: $(basename $0) [-h ]"
+        echo -e "Exemple :  $(basename $0)\n"
+        exit
+fi
+
+# ---- Process id
+#
+PORT_JPY="$(id -u)"
+PORT_TSB="$(( $PORT_JPY + 10000 ))"
+
+# ---- Where is it ?
+#
+p="$(ps ax | grep "tensorboard --port $PORT_TSB" | grep -v grep | awk '{print $1}')"
+if [ -z "$p" ]; then
+        echo "Tensorboard process not found..."
+else
+        kill $p
+        echo "Tensorbord stopped - pid was $p"
+fi
+```
+
+%% Output
+
+    Overwriting /home/paroutyj/bin/tensorboard_stop
+
+%% Cell type:markdown id: tags:
+
+**Set scripts privileges :**
+
+%% Cell type:code id: tags:
+
+``` python
+%%bash
+/bin/chmod 755 ~/bin/tensorboard_*  2>/dev/null
+/bin/ls -l ~/bin/tensorboard_*      2>/dev/null
+```
+
+%% Output
+
+    -rwxr-xr-x 1 paroutyj l-simap 1560 Jan 14 15:41 /home/paroutyj/bin/tensorboard_start
+    -rwxr-xr-x 1 paroutyj l-simap 1227 Jan 14 15:52 /home/paroutyj/bin/tensorboard_status
+    -rwxr-xr-x 1 paroutyj l-simap 1239 Jan 14 15:40 /home/paroutyj/bin/tensorboard_stop
+
+%% Cell type:markdown id: tags:
+
+**Check**
+
+%% Cell type:markdown id: tags:
+
+## Méthode 2 : Magic command
+**Start**
+
+%% Cell type:code id: tags:
+
+``` python
+%load_ext tensorboard
+```
+
+%% Cell type:code id: tags:
+
+``` python
+%tensorboard --port 21277 --host 0.0.0.0 --logdir ./run/logs
+```
+
+%% Output
+
+
+%% Cell type:markdown id: tags:
+
+**Stop**
+No way... use bash method
+
+## Methode 3  : Tensorboard module
+
+**Start**
+
+%% Cell type:code id: tags:
+
+``` python
+import tensorboard.notebook as tsb
+```
+
+%% Cell type:code id: tags:
+
+``` python
+tsb.start('--port 21277 --host 0.0.0.0 --logdir ./run/logs')
+```
+
+%% Output
+
+
+%% Cell type:markdown id: tags:
+
+**Check**
+
+%% Cell type:code id: tags:
+
+``` python
+a=tsb.list()
+```
+
+%% Output
+
+    No known TensorBoard instances running.
+
+%% Cell type:markdown id: tags:
+
+**Stop**
+No way... use bash method
+
+%% Cell type:code id: tags:
+
+``` python
+!kill 214798
+```
+
+%% Cell type:code id: tags:
+
+``` python
+```

GTSRB/README.ipynb

+%% Cell type:markdown id: tags:
+
+German Traffic Sign Recognition Benchmark (GTSRB)
+=================================================
+
+---
+Introduction au Deep Learning  (IDLE)
+S. Aria, E. Maldonado, JL. Parouty
+CNRS/SARI/DEVLOG - 2020
+
+Objectives of this practical work
+---------------------------------
+
+Traffic sign classification with **CNN**, using Tensorflow and **Keras**
+
+
+Prerequisite
+------------
+
+Environment, with the following packages :
+ - Python 3.6
+ - numpy
+ - Tensorflow 2.0
+ - scikit-image
+ - scikit-learn
+ - Matplotlib
+ - seaborn
+
+You can create it from the `environment.yml` file :
+```
+# conda env create -f environment.yml
+```
+To manage conda environment see [there](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#)
+
+About the dataset
+-----------------
+
+Name : [German Traffic Sign Recognition Benchmark (GTSRB)](http://benchmark.ini.rub.de/?section=gtsrb)
+Available [here](https://sid.erda.dk/public/archives/daaeac0d7ce1152aea9b61d9f1e19370/published-archive.html)
+or on **[kaggle](https://www.kaggle.com/meowmeowmeowmeowmeow/gtsrb-german-traffic-sign)**
+
+A nice example from : [Alex Staravoitau](https://navoshta.com/traffic-signs-classification/)
+
+In few words :
+ - Images : Variable dimensions, rgb
+ - Train set : 39209 images
+ - Test set : 12630 images
+ - Classes : 0 to 42
+
+Episodes
+--------
+
+**[01 - Preparation of data](01-Preparation-of-data.ipynb)**
+ - Understanding the dataset
+ - Preparing and formatting data
+ - Organize and backup data
+
+**[02 - First convolutions](02-First-convolutions.ipynb)**
+ - Read dataset
+ - Build a model
+ - Train the model
+ - Model evaluation
+
+
+%% Cell type:code id: tags:
+
+``` python
+```

GTSRB/idle/__init__.py

+
+VERSION='0.1a'
\ No newline at end of file

GTSRB/idle/pwk.py

+
+# ==================================================================
+#  ____                 _   _           _  __        __         _
+# |  _ \ _ __ __ _  ___| |_(_) ___ __ _| | \ \      / /__  _ __| | __
+# | |_) | '__/ _` |/ __| __| |/ __/ _` | |  \ \ /\ / / _ \| '__| |/ /
+# |  __/| | | (_| | (__| |_| | (_| (_| | |   \ V  V / (_) | |  |   <
+# |_|   |_|  \__,_|\___|\__|_|\___\__,_|_|    \_/\_/ \___/|_|  |_|\_\
+#                                                        module pwk                                   
+# ==================================================================
+# A simple module to host some common functions for practical work
+# pjluc 2019
+
+import os
+import glob
+from datetime import datetime
+import itertools
+import datetime
+
+import math
+import numpy as np
+
+import tensorflow as tf
+from tensorflow import keras
+
+import matplotlib
+import matplotlib.pyplot as plt
+import seaborn as sn
+
+VERSION='0.1.4'
+
+
+# -------------------------------------------------------------
+# init_all
+# -------------------------------------------------------------
+#
+def init(mplstyle='idle/talk.mplstyle'):
+    global VERSION
+    # ---- matplotlib
+    matplotlib.style.use(mplstyle)
+    # ---- Hello world
+    now = datetime.datetime.now()
+    print('IDLE 2020 - Practical Work Module')
+    print('  Version            :', VERSION)
+    print('  Run time           : {}'.format(now.strftime("%A %-d %B %Y, %H:%M:%S")))
+    print('  Matplotlib style   :', mplstyle)
+    print('  TensorFlow version :',tf.__version__)
+    print('  Keras version      :',tf.keras.__version__)
+          
+# -------------------------------------------------------------
+# Folder cooking
+# -------------------------------------------------------------
+#
+def tag_now():
+    return datetime.datetime.now().strftime("%Y-%m-%d_%Hh%Mm%Ss")
+
+def mkdir(path):
+    os.makedirs(path, mode=0o750, exist_ok=True)
+      
+def get_directory_size(path):
+    """
+    Return the directory size, but only 1 level
+    args:
+        path : directory path
+    return:
+        size in Mo
+    """
+    size=0
+    for f in os.listdir(path):
+        if os.path.isfile(path+'/'+f):
+            size+=os.path.getsize(path+'/'+f)
+    return size/(1024*1024)
+
+# -------------------------------------------------------------
+# shuffle_dataset
+# -------------------------------------------------------------
+#
+def shuffle_np_dataset(x, y):
+    assert (len(x) == len(y)), "x and y must have same size"
+    p = np.random.permutation(len(x))
+    return x[p], y[p]
+
+
+def update_progress(what,i,imax):
+    bar_length = min(40,imax)
+    if (i%int(imax/bar_length))!=0 and i<imax:
+        return
+    progress  = float(i/imax)
+    block     = int(round(bar_length * progress))
+    endofline = '\r' if progress<1 else '\n'
+    text = "{:16s} [{}] {:>5.1f}% of {}".format( what, "#"*block+"-"*(bar_length-block), progress*100, imax)
+    print(text, end=endofline)
+
+
+# -------------------------------------------------------------
+# show_images
+# -------------------------------------------------------------
+#
+def plot_images(x,y, indices, columns=12, x_size=1, y_size=1, colorbar=False, y_pred=None, cm='binary'):
+    """
+    Show some images in a grid, with legends
+    args:
+        X: images - Shapes must be (-1 lx,ly,1) or (-1 lx,ly,3)
+        y: real classes
+        indices: indices of images to show
+        columns: number of columns (12)
+        x_size,y_size: figure size
+        colorbar: show colorbar (False)
+        y_pred: predicted classes (None)
+        cm: Matplotlib olor map
+    returns: 
+        nothing
+    """
+    rows    = math.ceil(len(indices)/columns)
+    fig=plt.figure(figsize=(columns*x_size, rows*(y_size+0.35)))
+    n=1
+    errors=0 
+    if np.any(y_pred)==None:
+        y_pred=y
+    for i in indices:
+        axs=fig.add_subplot(rows, columns, n)
+        n+=1
+        # Shapes must be differents for RGB and L
+        (lx,ly,lz)=x[i].shape
+        if lz==1:
+            img=axs.imshow(x[i].reshape(lx,ly),   cmap = cm, interpolation='lanczos')
+        else:
+            img=axs.imshow(x[i].reshape(lx,ly,lz),cmap = cm, interpolation='lanczos')
+        axs.spines['right'].set_visible(True)
+        axs.spines['left'].set_visible(True)
+        axs.spines['top'].set_visible(True)
+        axs.spines['bottom'].set_visible(True)
+        axs.set_yticks([])
+        axs.set_xticks([])
+        if y[i]!=y_pred[i]:
+            axs.set_xlabel('{} ({})'.format(y_pred[i],y[i]))
+            axs.xaxis.label.set_color('red')
+            errors+=1
+        else:
+            axs.set_xlabel(y[i])
+        if colorbar:
+            fig.colorbar(img,orientation="vertical", shrink=0.65)
+    plt.show()
+
+def plot_image(x,cm='binary', figsize=(4,4)):
+    (lx,ly,lz)=x.shape
+    plt.figure(figsize=figsize)
+    if lz==1:
+        plt.imshow(x.reshape(lx,ly),   cmap = cm, interpolation='lanczos')
+    else:
+        plt.imshow(x.reshape(lx,ly,lz),cmap = cm, interpolation='lanczos')
+    plt.show()
+
+
+# -------------------------------------------------------------
+# show_history
+# -------------------------------------------------------------
+#
+def plot_history(history, figsize=(8,6)):
+    """
+    Show history
+    args:
+        history: history
+        save_as: filename to save or None
+    """
+    # Accuracy 
+    plt.figure(figsize=figsize)
+    plt.plot(history.history['accuracy'])
+    plt.plot(history.history['val_accuracy'])
+    plt.title('Model accuracy')
+    plt.ylabel('Accuracy')
+    plt.xlabel('Epoch')
+    plt.legend(['Train', 'Test'], loc='upper left')
+    plt.show()
+
+    # Loss values
+    plt.figure(figsize=figsize)
+    plt.plot(history.history['loss'])
+    plt.plot(history.history['val_loss'])
+    plt.title('Model loss')
+    plt.ylabel('Loss')
+    plt.xlabel('Epoch')
+    plt.legend(['Train', 'Test'], loc='upper left')
+    plt.show()    
+
+
+# -------------------------------------------------------------
+# plot_confusion_matrix
+# -------------------------------------------------------------
+#
+def plot_confusion_matrix(cm,
+                          title='Confusion matrix',
+                          figsize=(12,8),
+                          cmap="gist_heat_r",
+                          vmin=0,
+                          vmax=1,
+                          xticks=5,yticks=5):
+    """
+    given a sklearn confusion matrix (cm), make a nice plot
+
+    Args:
+        cm:           confusion matrix from sklearn.metrics.confusion_matrix
+        title:        the text to display at the top of the matrix
+        figsize:      Figure size (12,8)
+        cmap:         color map (gist_heat_r)
+        vmi,vmax:     Min/max 0 and 1
+        
+    """
+ 
+    accuracy = np.trace(cm) / float(np.sum(cm))
+    misclass = 1 - accuracy
+
+    plt.figure(figsize=figsize)
+    sn.heatmap(cm, linewidths=1, linecolor="#ffffff",square=True, 
+               cmap=cmap, xticklabels=xticks, yticklabels=yticks,
+               vmin=vmin,vmax=vmax)
+    plt.ylabel('True label')
+    plt.xlabel('Predicted label\naccuracy={:0.4f}; misclass={:0.4f}'.format(accuracy, misclass))
+
+    plt.show()

GTSRB/idle/talk.mplstyle

+
+# See : https://matplotlib.org/users/customizing.html
+
+axes.titlesize : 24
+axes.labelsize : 20
+axes.edgecolor      : dimgrey
+axes.labelcolor     : dimgrey
+axes.linewidth      : 2
+axes.grid           : False
+
+axes.prop_cycle    : cycler('color', ['steelblue', 'tomato', '2ca02c', 'd62728', '9467bd', '8c564b', 'e377c2', '7f7f7f', 'bcbd22', '17becf'])
+
+lines.linewidth     : 3
+lines.markersize    : 10
+
+xtick.color         : black
+xtick.labelsize     : 18
+ytick.color         : black
+ytick.labelsize     : 18
+
+axes.spines.left   : True
+axes.spines.bottom : True
+axes.spines.top    : False
+axes.spines.right  : False
+
+savefig.dpi         : 300      # figure dots per inch or 'figure'
+savefig.facecolor   : white    # figure facecolor when saving
+savefig.edgecolor   : white    # figure edgecolor when saving
+savefig.format      : svg
+savefig.bbox        : tight
+savefig.pad_inches  : 0.1
+savefig.transparent : True
+savefig.jpeg_quality: 95

environment.yml

+name: deeplearning2
+channels:
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1=main
+  - _tflow_select=2.1.0=gpu
+  - absl-py=0.8.1=py37_0
+  - astor=0.8.0=py37_0
+  - attrs=19.3.0=py_0
+  - backcall=0.1.0=py37_0
+  - blas=1.0=mkl
+  - bleach=3.1.0=py_0
+  - blosc=1.16.3=hd408876_0
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+