Thesis-NoiseDetection-attributes/others/save_model_result_in_md_maxwell.py

# main imports
import numpy as np
import pandas as pd

import sys, os, argparse
import subprocess
import time
import json

# models imports
from sklearn.utils import shuffle
from sklearn.externals import joblib
from sklearn.metrics import accuracy_score, f1_score, recall_score, roc_auc_score
from sklearn.model_selection import cross_val_score
from sklearn.model_selection import StratifiedKFold
from sklearn.model_selection import train_test_split

from keras.models import Sequential
from keras.layers import Conv1D, MaxPooling1D
from keras.layers import Activation, Dropout, Flatten, Dense, BatchNormalization
from keras.wrappers.scikit_learn import KerasClassifier
from keras import backend as K
from keras.models import model_from_json

# image processing imports
from ipfml import processing
from PIL import Image

# modules imports
sys.path.insert(0, '') # trick to enable import of main folder module

import custom_config as cfg

# variables and parameters
threshold_map_folder        = cfg.threshold_map_folder
threshold_map_file_prefix   = cfg.threshold_map_folder + "_"

markdowns_folder            = cfg.models_information_folder
final_csv_model_comparisons = cfg.csv_model_comparisons_filename
models_name                 = cfg.models_names_list

zones                       = cfg.zones_indices

current_dirpath = os.getcwd()


def main():

    kind_model = 'keras'
    model_ext = ''
    
    parser = argparse.ArgumentParser(description="Display SVD data of scene zone")

    parser.add_argument('--interval', type=str, help='Interval value to keep from svd', default='"0, 200"')
    parser.add_argument('--model', type=str, help='.joblib or .json file (sklearn or keras model)')
    parser.add_argument('--feature', type=str, help='Metric data choice', choices=cfg.feature_choices_labels)
    parser.add_argument('--mode', type=str, help='Kind of normalization level wished', choices=cfg.normalization_choices)

    args = parser.parse_args()

    p_interval   = list(map(int, args.interval.split(',')))
    p_model_file = args.model
    p_feature    = args.feature
    p_mode       = args.mode


    # call model and get global result in scenes
    begin, end = p_interval

    bash_cmd = "bash others/testModelByScene_maxwell.sh '" + str(begin) + "' '" + str(end) + "' '" + p_model_file + "' '" + p_mode + "' '" + p_feature + "'"

    print(bash_cmd)

    ## call command ##
    p = subprocess.Popen(bash_cmd, stdout=subprocess.PIPE, shell=True)

    (output, err) = p.communicate()

    ## Wait for result ##
    p_status = p.wait()

    if not os.path.exists(markdowns_folder):
        os.makedirs(markdowns_folder)

    # get model name to construct model

    if '.joblib' in p_model_file:
        kind_model = 'sklearn'
        model_ext = '.joblib'

    if '.json' in p_model_file:
        kind_model = 'keras'
        model_ext = '.json'

    md_model_path = os.path.join(markdowns_folder, p_model_file.split('/')[-1].replace(model_ext, '.md'))

    with open(md_model_path, 'w') as f:
        f.write(output.decode("utf-8"))

        # read each threshold_map information if exists
        model_map_info_path = os.path.join(threshold_map_folder, p_model_file.replace('saved_models/', ''))

        if not os.path.exists(model_map_info_path):
            f.write('\n\n No threshold map information')
        else:
            maps_files = os.listdir(model_map_info_path)

            # get all map information
            for t_map_file in maps_files:

                file_path = os.path.join(model_map_info_path, t_map_file)
                with open(file_path, 'r') as map_file:

                    title_scene =  t_map_file.replace(threshold_map_file_prefix, '')
                    f.write('\n\n## ' + title_scene + '\n')
                    content = map_file.readlines()

                    # getting each map line information
                    for line in content:
                        f.write(line)

        f.close()

    # Keep model information to compare
    current_model_name = p_model_file.split('/')[-1].replace(model_ext, '')

    # Prepare writing in .csv file into results folder
    output_final_file_path = os.path.join(cfg.results_information_folder, final_csv_model_comparisons)
    output_final_file = open(output_final_file_path, "a")

    print(current_model_name)
    # reconstruct data filename
    for name in models_name:
        if name in current_model_name:
            data_filename = current_model_name
            current_data_file_path = os.path.join('data', data_filename)

    print("Current data file ")
    print(current_data_file_path)
    model_scores = []

    ########################
    # 1. Get and prepare data
    ########################
    dataset_train = pd.read_csv(current_data_file_path + '.train', header=None, sep=";")
    dataset_test = pd.read_csv(current_data_file_path + '.test', header=None, sep=";")

    # default first shuffle of data
    dataset_train = shuffle(dataset_train)
    dataset_test = shuffle(dataset_test)

    # get dataset with equal number of classes occurences
    noisy_df_train = dataset_train[dataset_train.ix[:, 0] == 1]
    not_noisy_df_train = dataset_train[dataset_train.ix[:, 0] == 0]
    nb_noisy_train = len(noisy_df_train.index)

    noisy_df_test = dataset_test[dataset_test.ix[:, 0] == 1]
    not_noisy_df_test = dataset_test[dataset_test.ix[:, 0] == 0]
    nb_noisy_test = len(noisy_df_test.index)

    final_df_train = pd.concat([not_noisy_df_train[0:nb_noisy_train], noisy_df_train])
    final_df_test = pd.concat([not_noisy_df_test[0:nb_noisy_test], noisy_df_test])

    # shuffle data another time
    final_df_train = shuffle(final_df_train)
    final_df_test = shuffle(final_df_test)

    final_df_train_size = len(final_df_train.index)
    final_df_test_size = len(final_df_test.index)

    # use of the whole data set for training
    x_dataset_train = final_df_train.ix[:,1:]
    x_dataset_test = final_df_test.ix[:,1:]

    y_dataset_train = final_df_train.ix[:,0]
    y_dataset_test = final_df_test.ix[:,0]

    #######################
    # 2. Getting model
    #######################

    if kind_model == 'keras':
        with open(p_model_file, 'r') as f:
            json_model = json.load(f)
            model = model_from_json(json_model)
            model.load_weights(p_model_file.replace('.json', '.h5'))

            model.compile(loss='binary_crossentropy',
                        optimizer='adam',
                        features=['accuracy'])

        # reshape all input data
        x_dataset_train = np.array(x_dataset_train).reshape(len(x_dataset_train), end, 1)
        x_dataset_test = np.array(x_dataset_test).reshape(len(x_dataset_test), end, 1)


    if kind_model == 'sklearn':
        model = joblib.load(p_model_file)

    #######################
    # 3. Fit model : use of cross validation to fit model
    #######################

    if kind_model == 'keras':
        model.fit(x_dataset_train, y_dataset_train, validation_split=0.20, epochs=cfg.keras_epochs, batch_size=cfg.keras_batch)

    if kind_model == 'sklearn':
        model.fit(x_dataset_train, y_dataset_train)

        train_accuracy = cross_val_score(model, x_dataset_train, y_dataset_train, cv=5)

    ######################
    # 4. Test : Validation and test dataset from .test dataset
    ######################

    # we need to specify validation size to 20% of whole dataset
    val_set_size = int(final_df_train_size/3)
    test_set_size = val_set_size

    total_validation_size = val_set_size + test_set_size

    if final_df_test_size > total_validation_size:
        x_dataset_test = x_dataset_test[0:total_validation_size]
        y_dataset_test = y_dataset_test[0:total_validation_size]

    X_test, X_val, y_test, y_val = train_test_split(x_dataset_test, y_dataset_test, test_size=0.5, random_state=1)

    if kind_model == 'keras':
        y_test_model = model.predict_classes(X_test)
        y_val_model = model.predict_classes(X_val)

        y_train_model = model.predict_classes(x_dataset_train)

        train_accuracy = accuracy_score(y_dataset_train, y_train_model)

    if kind_model == 'sklearn':
        y_test_model = model.predict(X_test)
        y_val_model = model.predict(X_val)

        y_train_model = model.predict(x_dataset_train)

    val_accuracy = accuracy_score(y_val, y_val_model)
    test_accuracy = accuracy_score(y_test, y_test_model)

    train_f1 = f1_score(y_dataset_train, y_train_model)
    train_recall = recall_score(y_dataset_train, y_train_model)
    train_roc_auc = roc_auc_score(y_dataset_train, y_train_model)

    val_f1 = f1_score(y_val, y_val_model)
    val_recall = recall_score(y_val, y_val_model)
    val_roc_auc = roc_auc_score(y_val, y_val_model)

    test_f1 = f1_score(y_test, y_test_model)
    test_recall = recall_score(y_test, y_test_model)
    test_roc_auc = roc_auc_score(y_test, y_test_model)

    if kind_model == 'keras':
        # stats of all dataset
        all_x_data = np.concatenate([x_dataset_train, X_test, X_val])
        all_y_data = np.concatenate([y_dataset_train, y_test, y_val])
        all_y_model = model.predict_classes(all_x_data)

    if kind_model == 'sklearn':
        # stats of all dataset
        all_x_data = pd.concat([x_dataset_train, X_test, X_val])
        all_y_data = pd.concat([y_dataset_train, y_test, y_val])
        all_y_model = model.predict(all_x_data)

    all_accuracy = accuracy_score(all_y_data, all_y_model)
    all_f1_score = f1_score(all_y_data, all_y_model)
    all_recall_score = recall_score(all_y_data, all_y_model)
    all_roc_auc_score = roc_auc_score(all_y_data, all_y_model)

    # stats of dataset sizes
    total_samples = final_df_train_size + val_set_size + test_set_size

    model_scores.append(final_df_train_size)
    model_scores.append(val_set_size)
    model_scores.append(test_set_size)

    model_scores.append(final_df_train_size / total_samples)
    model_scores.append(val_set_size / total_samples)
    model_scores.append(test_set_size / total_samples)

    # add of scores
    model_scores.append(train_accuracy)
    model_scores.append(val_accuracy)
    model_scores.append(test_accuracy)
    model_scores.append(all_accuracy)

    model_scores.append(train_f1)
    model_scores.append(train_recall)
    model_scores.append(train_roc_auc)

    model_scores.append(val_f1)
    model_scores.append(val_recall)
    model_scores.append(val_roc_auc)

    model_scores.append(test_f1)
    model_scores.append(test_recall)
    model_scores.append(test_roc_auc)

    model_scores.append(all_f1_score)
    model_scores.append(all_recall_score)
    model_scores.append(all_roc_auc_score)

    # TODO : improve...
    # check if it's always the case...
    nb_zones = current_data_file_path.split('_')[7]

    final_file_line = current_model_name + '; ' + str(end - begin) + '; ' + str(begin) + '; ' + str(end) + '; ' + str(nb_zones) + '; ' + p_feature + '; ' + p_mode

    for s in model_scores:
        final_file_line += '; ' + str(s)

    output_final_file.write(final_file_line + '\n')


if __name__== "__main__":
    main()