From cb48427837b79ec0ab7306b2e893feab7c1db9c5 Mon Sep 17 00:00:00 2001
From: "Jangberry (Nomad-Debian)" <matt2001@hotmail.fr>
Date: Fri, 27 Oct 2023 15:49:29 +0200
Subject: [PATCH] Read cifar file

---
 .gitignore         | 161 +++++++++++++++++++++++++++
 README-tutorial.md | 270 +++++++++++++++++++++++++++++++++++++++++++++
 read_cifar.py      |  91 +++++++++++++++
 requirements.txt   |   1 +
 4 files changed, 523 insertions(+)
 create mode 100644 .gitignore
 create mode 100644 README-tutorial.md
 create mode 100644 read_cifar.py
 create mode 100644 requirements.txt

diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..708bba6
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,161 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+data
\ No newline at end of file
diff --git a/README-tutorial.md b/README-tutorial.md
new file mode 100644
index 0000000..abc9128
--- /dev/null
+++ b/README-tutorial.md
@@ -0,0 +1,270 @@
+# Tutorial 1 : Image Classification
+
+MOD 4.6 Deep Learning & Artificial Intelligence: an introduction
+
+## Introduction
+
+The objective of this tutorial is to write a complete image classification program in Python.
+Two classification models will be successively developed and tested: k-nearest neighbors (KNN) and neural networks (NN).
+
+### Before you start
+
+In this tutorial we use Python 3.7 or higher. Make sure it is properly installed. Make sure `numpy` is installed.
+
+We assume that `git` is installed, and that you are familiar with the basic `git` commands. (Optionnaly, you can use GitHub Desktop.)
+We also assume that you have access to the [ECL GitLab](https://gitlab.ec-lyon.fr/). If necessary, please consult [this tutorial](https://gitlab.ec-lyon.fr/edelland/inf_tc2/-/blob/main/Tutoriel_gitlab/tutoriel_gitlab.md).
+
+**Important note**: In this tutorial, you will be asked to write functions. If you want to test the correct operation of your functions in the same file, you must use the statement `if __name__ == "__main__":`:
+
+```python
+def func():
+    ...
+
+if __name__ == "__main__":
+    func()
+```
+
+### README
+
+Your repository must contain a text file `README.md` that introduces the project in a **short way**. To learn how to write a readme, visit <https://www.makeareadme.com>. We recommend that you include at least the sections _Description_ and _Usage_.
+
+### Code style
+
+Your code must follow the [PEP8 recommendations](https://peps.python.org/pep-0008/). To help you format your code properly, you can use [Black](https://black.readthedocs.io/en/stable/). To help you sort your imports, you can use [isort](https://pycqa.github.io/isort/).
+
+### Docstring
+
+Your code must be properly documented. It must follow the [PEP257 recommendations](https://peps.python.org/pep-0257/). To help you document your code properly, you can use [pydocstyle](http://www.pydocstyle.org/en/stable/).
+
+### Prepare your directory
+
+1. Create a new blank project on the ECL GitLab (`New project` then `Create blank project`).
+2. Fill in the form as follows.
+   - Project name: `Image classification`.
+   - Project slug: `image-classification`.
+   - Visibility Level: public
+   - Project Configuration: Initialize repository with a README
+3. Clone the repository.
+
+    ```bash
+    git clone https://gitlab.ec-lyon.fr/<user>/image-classification
+    ```
+
+4. In this tutorial you will use files that should not be pushed to the remote repository. To ignore them when committing, you can put their path in a file named `.gitignore`. For simplicity, we use the [`.gitignore` file](https://github.com/github/gitignore/blob/main/Python.gitignore) recommended by GitHub for Python projects.
+
+## Prepare the CIFAR dataset
+
+The image database used for the experiments is CIFAR-10 which consists of 60 000 color images of size 32x32 divided into 10 classes (plane, car, bird, cat, ...).
+This database can be obtained at the address <https://www.cs.toronto.edu/~kriz/cifar.html> where are also given the indications to read the data.
+
+1. Create a folder named `data` in which you move the downloaded `cifar-10-batches-py` folder. Make sure that the `data` folder is ignored when commiting.
+2. Create a Python file named `read_cifar.py`. Write the function `read_cifar_batch` taking as parameter the path of a single batch as a string, and returning:
+      - a matrix `data` of size (`batch_size` x `data_size`) where `batch_size` is the number of available data in the batch, and `data_size` the dimension of these data (number of numerical values describing the data), and
+      - a vector `labels` of size `batch_size` whose values correspond to the class code of the data of the same index in `data`.
+
+    `data` must be `np.float32` array and `labels` must be `np.int64` array.
+3. Write the function `read_cifar` taking as parameter the path of the directory containing the six batches (five `data_batch` and one `test_batch`) as a string, and returning
+      - a matrix `data` of shape (`batch_size` x `data_size`) where `batch_size` is the number of available data in all batches (including `test_batch`), and
+      - a vector `labels` of size `batch_size` whose values correspond to the class code of the data of the same index in `data`.
+    `data` must be `np.float32` array and `labels` must be `np.int64` array.
+4. Write the function `split_dataset` which splits the dataset into a training set and a test set. The data must be shuffled, so that two successive calls shouldn't give the same output. This function takes as parameter
+      - `data` and `labels`, two arrays that have the same size in the first dimension.
+      - `split`, a float between 0 and 1 which determines the split factor of the training set with respect to the test set.
+
+    This function must return
+      - `data_train` the training data,
+      - `labels_train` the corresponding labels,
+      - `data_test` the testing data, and
+      - `labels_test` the corresponding labels.
+
+## k-nearest neighbors
+
+1. Create a Python fil named `knn.py`. Write the function `distance_matrix` taking as parameters two matrices and returns `dists`, the L2 Euclidean distance matrix. The computation must be done only with matrix manipulation (no loops).
+    Hint: $`(a-b)^2 = a^2 + b^2 - 2 ab`$
+2. Write the function `knn_predict` taking as parameters:
+      - `dists` the distance matrix between the train set and the test set,
+      - `labels_train` the training labels, and
+      - `k` the number of of neighbors.
+    This function must return the predicted labels for the elements of `data_test`.
+
+    **Note:** if the memory occupation is too important, you can use several batches for the calculation of the distance matrix (loop on sub-batches of test data).
+3. Write the function `evaluate_knn` taking as parameters:
+      - `data_train` the training data,
+      - `labels_train` the corresponding labels,
+      - `data_test` the testing data,
+      - `labels_test` the corresponding labels, and
+      - `k` the number of of neighbors.
+    This function must return the classification rate (accuracy).
+4. For `split_factor=0.9`, plot the variation of the accuracy as a function of `k` (from 1 to 20). Save the plot as an image named `knn.png` in the directory `results`.
+
+## Artificial Neural Network
+
+The objective here is to develop a classifier based on a multilayer perceptron (MLP) neural network.
+
+First of all, let's focus on the backpropagation of the gradient with an example. If you still have trouble understanding the intuition behind the back propagation of the gradient, check out this video: [3Blue1Brown/Backpropagation calculus | Chapter 4, Deep learning](https://www.youtube.com/watch?v=tIeHLnjs5U8).
+
+The weight matrix of the layer $`L`$ is denoted $`W^{(L)}`$. The bias vector of the layer $`L`$ is denoted $`B^{(L)}`$. We choose the sigmoid function, denoted $`\sigma`$, as the activation function. The output vector of the layer $`L`$ before activation is denoted $`Z^{(L)}`$. The output vector of the layer $`L`$ after activation is denoted $`A^{(L)}`$. By convention, we note $`A^{(0)}`$ the network input vector. Thus $`Z^{(L+1)} = W^{(L+1)}A^{(L)} + B^{(L+1)}`$ and $`A^{(L+1)} = \sigma\left(Z^{(L+1)}\right)`$. Let's consider a network with one hidden layer. Thus, the output is $`\hat{Y} = A^{(2)}`$.
+Let $`Y`$ be the target (desired output). We use mean squared error (MSE) as the cost function. Thus, the cost is $`C = \frac{1}{N_{out}}\sum_{i=1}^{N_{out}} (\hat{y_i} - y_i)^2`$.
+
+1. Prove that $`\sigma' = \sigma \times (1-\sigma)`$
+2. Express $`\frac{\partial C}{\partial A^{(2)}}`$, i.e. the vector of $`\frac{\partial C}{\partial a^{(2)}_i}`$ as a function of $`A^{(2)}`$ and $`Y`$.
+3. Using the chaining rule, express $`\frac{\partial C}{\partial Z^{(2)}}`$, i.e. the vector of $`\frac{\partial C}{\partial z^{(2)}_i}`$ as a function of $`\frac{\partial C}{\partial A^{(2)}}`$ and $`A^{(2)}`$.
+4. Similarly, express $`\frac{\partial C}{\partial W^{(2)}}`$, i.e. the matrix of $`\frac{\partial C}{\partial w^{(2)}_{i,j}}`$ as a function of $`\frac{\partial C}{\partial Z^{(2)}}`$ and $`A^{(1)}`$.
+5. Similarly, express $`\frac{\partial C}{\partial B^{(2)}}`$ as a function of $`\frac{\partial C}{\partial Z^{(2)}}`$.
+6. Similarly, express $`\frac{\partial C}{\partial A^{(1)}}`$ as a function of $`\frac{\partial C}{\partial Z^{(2)}}`$ and $`W^{(2)}`$.
+7. Similarly, express $`\frac{\partial C}{\partial Z^{(1)}}`$ as a function of $`\frac{\partial C}{\partial A^{(1)}}`$ and $`A^{(1)}`$.
+8. Similarly, express $`\frac{\partial C}{\partial W^{(1)}}`$ as a function of $`\frac{\partial C}{\partial Z^{(1)}}`$ and $`A^{(0)}`$.
+9. Similarly, express $`\frac{\partial C}{\partial B^{(1)}}`$ as a function of $`\frac{\partial C}{\partial Z^{(1)}}`$.
+
+Below is a Python code performing a forward pass and computing the cost in a network containing one hidden layer for the regression task. It uses  the sigmoid function as the activation function:
+
+```python
+import numpy as np
+
+N = 30  # number of input data
+d_in = 3  # input dimension
+d_h = 3  # number of neurons in the hidden layer
+d_out = 2  # output dimension (number of neurons of the output layer)
+
+# Random initialization of the network weights and biaises
+w1 = 2 * np.random.rand(d_in, d_h) - 1  # first layer weights
+b1 = np.zeros((1, d_h))  # first layer biaises
+w2 = 2 * np.random.rand(d_h, d_out) - 1  # second layer weights
+b2 = np.zeros((1, d_out))  # second layer biaises
+
+data = np.random.rand(N, d_in)  # create a random data
+targets = np.random.rand(N, d_out)  # create a random targets
+
+# Forward pass
+a0 = data # the data are the input of the first layer
+z1 = np.matmul(a0, w1) + b1  # input of the hidden layer
+a1 = 1 / (1 + np.exp(-z1))  # output of the hidden layer (sigmoid activation function)
+z2 = np.matmul(a1, w2) + b2  # input of the output layer
+a2 = 1 / (1 + np.exp(-z2))  # output of the output layer (sigmoid activation function)
+predictions = a2  # the predicted values are the outputs of the output layer
+
+# Compute loss (MSE)
+loss = np.mean(np.square(predictions - targets))
+print(loss)
+```
+
+10. Create a Python file named `mlp.py`. Use the above code to write the function `learn_once_mse` taking as parameters:
+      - `w1`, `b1`, `w2` and `b2` the weights and biases of the network,
+      - `data` a matrix of shape (`batch_size` x `d_in`),
+      - `targets` a matrix of shape (`batch_size` x `d_out`),
+      - `learning_rate` the learning rate,
+
+    that perform one gradient descent step, and returns:
+      - `w1`, `b1`, `w2` and `b2` the updated weights and biases of the network,
+      - `loss` the loss, for monitoring purpose.
+
+MSE loss is not well suited for a classification task. Instead, we want to use the binary cross-entropy loss. To use this loss, we need the target to be is the one-hot encoding of the desired labels. Example:
+
+```python
+one_hot(labels=[1 2 0]) = [[0 1 0]
+                           [0 0 1]
+                           [1 0 0]]
+```
+
+We also need that the last activation layer of the network to be a softmax layer.
+
+11. Write the function `one_hot` taking a (n)-D array as parameters and returning the corresponding (n+1)-D one-hot matrix.
+12. Write the function `learn_once_cross_entropy` taking as parameters:
+      - `w1`, `b1`, `w2` and `b2` the weights and biases of the network,
+      - `data` a matrix of shape (`batch_size` x `d_in`),
+      - `labels_train` a vector of size `batch_size`, and
+      - `learning_rate` the learning rate,
+
+    that perform one gradient descent step using a binary cross-entropy loss.
+    We admit that $`\frac{\partial C}{\partial Z^{(2)}} = A^{(2)} - Y`$, where $`Y`$ is a one-hot vector encoding the label.
+    The function must return:
+      - `w1`, `b1`, `w2` and `b2` the updated weights and biases of the network,
+      - `loss` the loss, for monitoring purpose.
+13. Write the function `train_mlp` taking as parameters:
+      - `w1`, `b1`, `w2` and `b2` the weights and biases of the network,
+      - `data_train` a matrix of shape (`batch_size` x `d_in`),
+      - `labels_train` a vector of size `batch_size`,
+      - `learning_rate` the learning rate, and
+      - `num_epoch` the number of training epoch,
+
+    that perform `num_epoch` of training steps and returns:
+      - `w1`, `b1`, `w2` and `b2` the updated weights and biases of the network,
+      - `train_accuracies` the list of train accuracies across epochs as a list of floats.
+14. Write the function `test_mlp` taking as parameters:
+      - `w1`, `b1`, `w2` and `b2` the weights and biases of the network,
+      - `data_test` a matrix of shape (`batch_size` x `d_in`), and
+      - `labels_test` a vector of size `batch_size`,
+
+    testing the network on the test set and returns:
+      - `test_accuracy` the testing accuracy.
+15. Write the function `run_mlp_training` taking as parameter:
+      - `data_train`, `labels_train`, `data_test`, `labels_test`, the training and testing data,
+      - `d_h` the number of neurons in the hidden layer
+      - `learning_rate` the learning rate, and
+      - `num_epoch` the number of training epoch,
+
+    that train an MLP classifier and return the training accuracies across epochs as a list of floats and the final testing accuracy as a float.
+16. For `split_factor=0.9`, `d_h=64`, `learning_rate=0.1` and `num_epoch=100`, plot the evolution of learning accuracy across learning epochs. Save the graph as an image named `mlp.png` in the `results` directory.
+
+## To go further
+
+### Unittest
+
+Your code should contain unit tests. All unit tests should be contained in the `tests` directory located at the root of the directory.
+We choose to use [pytest](https://docs.pytest.org/en/7.1.x/). To help you write unit tests, you can consult the pytest documentation.
+
+### License
+
+Your project should be properly licensed. Since it is your project, it is up to you to choose your license. In general, the license consists of a file named LICENSE in the root directory. A useful resource to help you choose: <https://choosealicense.com/>
+
+### Deep dive into the classifier
+
+Experiments will have to be carried out by studying the following variations:
+
+- use image representation by descriptors (LBP, HOG, ...) instead of raw pixels using the `scikit-image` module.
+- use of N-fold cross-validation instead of a fixed learning and testing subset.
+
+## To be handed in
+
+This work must be done individually. The expected output is a repository on <https://gitlab.ec-lyon.fr>. It must contain the complete, minimal and functional code corresponding to this tutorial.
+To see the details of the expected, see the Evaluation section.
+
+The last commit is due before 11:59 pm on Sunday, November 6, 2022. Subsequent commits will not be considered.
+
+## Evaluation
+
+In this section, we present all the items on which the work is evaluated.
+
+- ( /1) The function `read_cifar_batch` works as described
+- ( /1) The function `read_cifar` works as described
+- ( /1) The `split_dataset` works as described
+- ( /1) The function `distance_matrix` works as described
+- ( /1) The function `knn_predict` works as described
+- ( /1) The function `evaluate_knn` works as described
+- ( /1) The graph `knn.png` shows the results obtained
+- ( /1) The function `learn_once_mse` works as described
+- ( /1) The function `one_hot` works as described
+- ( /1) The function `learn_once_cross_entropy` works as described
+- ( /1) The function `train_mlp` works as described
+- ( /1) The function `test_mlp` works as described
+- ( /1) The function `run_mlp_training` works as described
+- ( /1) The graph `mlp.png` shows the results obtained
+- ( /1) The project has a good README.
+- ( /2) The guidlines about the project structure are all followed
+- ( /1) All functions are documented
+- ( /1) All functions are documented clearly and follow the PEP257 recommendations
+- ( /1) The code is properly formatted, i.e. follow the PEP8 recommendations
+
+**Bonus**
+
+- ( /1) Project has a license
+- ( /2) Unitest coverage
+- ( /2) Deep dive into the classifier
+
+## Contribute
+
+This tutorial may contain errors, inaccuracies, typos or areas for improvement. Feel free to contribute to its improvement by [opening an issue](https://gitlab.ec-lyon.fr/qgalloue/image_classification_instructions/-/issues).
+
+## Author
+
+- Quentin Gallouédec
diff --git a/read_cifar.py b/read_cifar.py
new file mode 100644
index 0000000..86d78f2
--- /dev/null
+++ b/read_cifar.py
@@ -0,0 +1,91 @@
+import os
+import numpy as np
+
+def unpickle(file: str):
+    """Returns an unpickled object from a file
+
+    Arguments:
+        file -- path to the file
+
+    Returns:
+        dict -- unpickled object
+    """    
+    import pickle
+    with open(file, 'rb') as fo:
+        dict = pickle.load(fo, encoding='bytes')
+    return dict
+
+def read_cifar_batch(path: str):
+    """Reads a cifar batch file and outputs the images and labels
+
+    Arguments:
+        path (str) -- path to the cifar file
+    Returns:
+        tuple[data (np.Array), labels (np.Array)] -- images and labels
+    """
+    batch = unpickle(path)
+    data = np.array(batch[b'data'], np.float32)
+    labels = np.array(batch[b'labels'], np.int64)
+    return data, labels
+
+def read_cifar(path: str):
+    """Reads all the cifar files and outputs the images and labels
+
+    Arguments:
+        path -- directory where the cifar files are located
+    Returns:
+        tuple[data (np.Array), labels (np.Array)] -- images and labels
+    """
+    dirs = os.listdir(path)
+    data = np.array([[]], dtype=np.float32)
+    labels = np.array([], dtype=np.int64)
+    for file in dirs:
+        if file.startswith("data_batch") or file.startswith("test_batch"):
+            d, l = read_cifar_batch(os.path.join(path, file))
+            if data.size == 0:
+                data = d
+                labels = l
+            else:
+                data = np.concatenate((data, d), axis=0)
+                labels = np.concatenate((labels, l), axis=0)
+    return data, labels
+
+def split_dataset(data: np.array, labels: np.array, split: float):
+    """Shuffles and splits the dataset into train and test sets
+
+    Arguments:
+        data -- data to be split
+        labels -- labels related to the data
+        split -- split factor (0 <= split <= 1)
+    """
+    assert 0 <= split <= 1
+    
+    p = np.random.permutation(data.shape[0])
+    
+    d = data[p]
+    l = labels[p]
+    
+    split_index = int(data.shape[0] * split)
+    
+    data_train = d[:split_index]
+    labels_train = l[:split_index]
+    
+    data_test = d[split_index:]
+    labels_test = l[split_index:]
+    
+    return data_train, labels_train, data_test, labels_test
+
+if __name__ == "__main__":
+    images, labels = read_cifar("data/cifar-10-batches-py/")
+    print(images.shape)
+    print(labels.shape)
+    data_train, labels_train, data_test, labels_test = split_dataset(images, labels, 0.8)
+    print(data_train.shape)
+    print(labels_train.shape)
+    print(data_test.shape)
+    print(labels_test.shape)
+    print(data_train[0])
+    print(labels_train[0])
+    print(data_test[0])
+    print(labels_test[0])
+    
\ No newline at end of file
diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 0000000..296d654
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1 @@
+numpy
\ No newline at end of file
-- 
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