feat(notebook): Add evaluation metrics and confusion matrix visualizations for model predictions on Dataset B. Remove commented-out code and integrate data preparation using create_ready_data function.

Closes #43

.gitignore

@@ -2,3 +2,4 @@
 data/**/*.csv
 .venv/
 *.pyc
+*.egg-info/

.vscode/settings.json

@@ -1,3 +1,4 @@
 {
-  "python.analysis.extraPaths": ["./code/src/features"]
+  "python.analysis.extraPaths": ["./code/src/features"],
+  "jupyter.notebookFileRoot": "${workspaceFolder}/code"
 }

README.md

@@ -16,3 +16,8 @@ The repository is private and access is restricted only to those who have been g
 All contents of this repository, including the thesis idea, code, and associated data, are copyrighted © 2024 by Rifqi Panuluh. Unauthorized use or duplication is prohibited.
 
 [LICENSE](https://github.com/nuluh/thesis?tab=License-1-ov-file#readme)
+
+## How to Run `stft.ipynb`
+
+1. run `pip install -e .` in root project first
+2. run the notebook

code/notebooks/stft.ipynb

@@ -121,8 +121,9 @@
     "signal_sensor2_test1 = []\n",
     "\n",
     "for data in df:\n",
-    "    signal_sensor1_test1.append(data['sensor 1'].values)\n",
-    "    signal_sensor2_test1.append(data['sensor 2'].values)\n",
+    "    if not data.empty and 'sensor 1' in data.columns and 'sensor 2' in data.columns:\n",
+    "        signal_sensor1_test1.append(data['sensor 1'].values)\n",
+    "        signal_sensor2_test1.append(data['sensor 2'].values)\n",
     "\n",
     "print(len(signal_sensor1_test1))\n",
     "print(len(signal_sensor2_test1))"
@@ -154,9 +155,7 @@
     "import pandas as pd\n",
     "import numpy as np\n",
     "from scipy.signal import stft, hann\n",
-    "from multiprocessing import Pool\n",
-    "\n",
-    "\n",
+    "# from multiprocessing import Pool\n",
     "\n",
     "# Function to compute and append STFT data\n",
     "def process_stft(args):\n",
@@ -199,23 +198,22 @@
     "    # Compute STFT\n",
     "    frequencies, times, Zxx = stft(sensor_data, fs=Fs, window=window, nperseg=window_size, noverlap=window_size - hop_size)\n",
     "    magnitude = np.abs(Zxx)\n",
-    "    flattened_stft = magnitude.flatten()\n",
+    "    df_stft = pd.DataFrame(magnitude, index=frequencies, columns=times).T\n",
+    "    df_stft.columns = [f\"Freq_{i}\" for i in frequencies]\n",
     "    \n",
     "    # Define the output CSV file path\n",
     "    stft_file_name = f'stft_data{sensor_num}_{damage_num}.csv'\n",
     "    sensor_output_dir = os.path.join(damage_base_path, sensor_name.lower())\n",
     "    os.makedirs(sensor_output_dir, exist_ok=True)\n",
     "    stft_file_path = os.path.join(sensor_output_dir, stft_file_name)\n",
-    "    print(stft_file_path)\n",
     "    # Append the flattened STFT to the CSV\n",
     "    try:\n",
-    "        flattened_stft_df = pd.DataFrame([flattened_stft])\n",
     "        if not os.path.isfile(stft_file_path):\n",
     "            # Create a new CSV\n",
-    "            flattened_stft_df.to_csv(stft_file_path, index=False, header=False)\n",
+    "            df_stft.to_csv(stft_file_path, index=False, header=False)\n",
     "        else:\n",
     "            # Append to existing CSV\n",
-    "            flattened_stft_df.to_csv(stft_file_path, mode='a', index=False, header=False)\n",
+    "            df_stft.to_csv(stft_file_path, mode='a', index=False, header=False)\n",
     "        print(f\"Appended STFT data to {stft_file_path}\")\n",
     "    except Exception as e:\n",
     "        print(f\"Error writing to {stft_file_path}: {e}\")"
@@ -295,7 +293,7 @@
     "\n",
     "# get current y ticks in list\n",
     "print(len(frequencies))\n",
-    "print(len(times))\n"
+    "print(len(times))"
    ]
   },
   {
@@ -323,10 +321,9 @@
    "source": [
     "import pandas as pd\n",
     "import matplotlib.pyplot as plt\n",
-    "ready_data1 = []\n",
-    "for file in os.listdir('D:/thesis/data/working/sensor1'):\n",
-    "    ready_data1.append(pd.read_csv(os.path.join('D:/thesis/data/working/sensor1', file)))\n",
-    "# ready_data1[1]\n",
+    "ready_data1a = []\n",
+    "for file in os.listdir('D:/thesis/data/converted/raw/sensor1'):\n",
+    "    ready_data1a.append(pd.read_csv(os.path.join('D:/thesis/data/converted/raw/sensor1', file)))\n",
     "# colormesh give title x is frequency and y is time and rotate/transpose the data\n",
     "# Plotting the STFT Data"
    ]
@@ -337,8 +334,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ready_data1[1]\n",
-    "plt.pcolormesh(ready_data1[1])"
+    "len(ready_data1a)\n",
+    "# plt.pcolormesh(ready_data1[0])"
    ]
   },
   {
@@ -348,7 +345,7 @@
    "outputs": [],
    "source": [
     "for i in range(6):\n",
-    "    plt.pcolormesh(ready_data1[i])\n",
+    "    plt.pcolormesh(ready_data1a[i])\n",
     "    plt.title(f'STFT Magnitude for case {i} sensor 1')\n",
     "    plt.xlabel(f'Frequency [Hz]')\n",
     "    plt.ylabel(f'Time [sec]')\n",
@@ -361,10 +358,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ready_data2 = []\n",
-    "for file in os.listdir('D:/thesis/data/working/sensor2'):\n",
-    "    ready_data2.append(pd.read_csv(os.path.join('D:/thesis/data/working/sensor2', file)))\n",
-    "ready_data2[5]"
+    "ready_data2a = []\n",
+    "for file in os.listdir('D:/thesis/data/converted/raw/sensor2'):\n",
+    "    ready_data2a.append(pd.read_csv(os.path.join('D:/thesis/data/converted/raw/sensor2', file)))"
    ]
   },
   {
@@ -373,8 +369,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "print(len(ready_data1))\n",
-    "print(len(ready_data2))"
+    "print(len(ready_data1a))\n",
+    "print(len(ready_data2a))"
    ]
   },
   {
@@ -383,28 +379,78 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "x1 = 0\n",
+    "x1a = 0\n",
+    "print(type(ready_data1a[0]))\n",
+    "ready_data1a[0].iloc[:,0]"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### Checking length of the total array"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "x1a = 0\n",
+    "print(type(x1a))\n",
+    "for i in range(len(ready_data1a)):\n",
+    "    print(type(ready_data1a[i].shape[0]))\n",
+    "    x1a = x1a + ready_data1a[i].shape[0]\n",
+    "    print(type(x1a))\n",
     "\n",
-    "for i in range(len(ready_data1)):\n",
-    "    print(ready_data1[i].shape)\n",
-    "    x1 = x1 + ready_data1[i].shape[0]\n",
+    "print(x1a)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "x2a = 0\n",
     "\n",
-    "print(x1)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "x2 = 0\n",
+    "for i in range(len(ready_data2a)):\n",
+    "    print(ready_data2a[i].shape)\n",
+    "    x2a = x2a + ready_data2a[i].shape[0]\n",
     "\n",
-    "for i in range(len(ready_data2)):\n",
-    "    print(ready_data2[i].shape)\n",
-    "    x2 = x2 + ready_data2[i].shape[0]\n",
+    "print(x2a)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Flatten 6 array into one array"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Combine all dataframes in ready_data1a into a single dataframe\n",
+    "if ready_data1a:  # Check if the list is not empty\n",
+    "    # Use pandas concat function instead of iterative concatenation\n",
+    "    combined_data = pd.concat(ready_data1a, axis=0, ignore_index=True)\n",
+    "    \n",
+    "    print(f\"Type of combined data: {type(combined_data)}\")\n",
+    "    print(f\"Shape of combined data: {combined_data.shape}\")\n",
+    "    \n",
+    "    # Display the combined dataframe\n",
+    "    combined_data\n",
+    "else:\n",
+    "    print(\"No data available in ready_data1a list\")\n",
+    "    combined_data = pd.DataFrame()\n",
     "\n",
-    "print(x2)"
+    "# Store the result in x1a for compatibility with subsequent code\n",
+    "x1a = combined_data"
    ]
   },
   {
@@ -413,50 +459,29 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "x1 = ready_data1[0]\n",
-    "# print(x1)\n",
-    "print(type(x1))\n",
-    "for i in range(len(ready_data1) - 1):\n",
-    "    #print(i)\n",
-    "    x1 = np.concatenate((x1, ready_data1[i + 1]), axis=0)\n",
-    "# print(x1)\n",
-    "pd.DataFrame(x1)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "x2 = ready_data2[0]\n",
+    "# Combine all dataframes in ready_data1a into a single dataframe\n",
+    "if ready_data2a:  # Check if the list is not empty\n",
+    "    # Use pandas concat function instead of iterative concatenation\n",
+    "    combined_data = pd.concat(ready_data2a, axis=0, ignore_index=True)\n",
+    "    \n",
+    "    print(f\"Type of combined data: {type(combined_data)}\")\n",
+    "    print(f\"Shape of combined data: {combined_data.shape}\")\n",
+    "    \n",
+    "    # Display the combined dataframe\n",
+    "    combined_data\n",
+    "else:\n",
+    "    print(\"No data available in ready_data1a list\")\n",
+    "    combined_data = pd.DataFrame()\n",
     "\n",
-    "for i in range(len(ready_data2) - 1):\n",
-    "    #print(i)\n",
-    "    x2 = np.concatenate((x2, ready_data2[i + 1]), axis=0)\n",
-    "pd.DataFrame(x2)"
+    "# Store the result in x1a for compatibility with subsequent code\n",
+    "x2a = combined_data"
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": null,
+   "cell_type": "markdown",
    "metadata": {},
-   "outputs": [],
    "source": [
-    "print(x1.shape)\n",
-    "print(x2.shape)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "y_1 = [1,1,1,1]\n",
-    "y_2 = [0,1,1,1]\n",
-    "y_3 = [1,0,1,1]\n",
-    "y_4 = [1,1,0,0]"
+    "### Creating the label"
    ]
   },
   {
@@ -479,7 +504,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "y_data = [y_1, y_2, y_3, y_4, y_5, y_6]"
+    "y_data = [y_1, y_2, y_3, y_4, y_5, y_6]\n",
+    "y_data"
    ]
   },
   {
@@ -489,7 +515,7 @@
    "outputs": [],
    "source": [
     "for i in range(len(y_data)):\n",
-    "    print(ready_data1[i].shape[0])"
+    "    print(ready_data1a[i].shape[0])"
    ]
   },
   {
@@ -498,9 +524,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "import numpy as np\n",
     "for i in range(len(y_data)):\n",
-    "    y_data[i] = [y_data[i]]*ready_data1[i].shape[0]\n",
-    "    y_data[i] = np.array(y_data[i])"
+    "    y_data[i] = [y_data[i]]*ready_data1a[i].shape[0]"
    ]
   },
   {
@@ -509,6 +535,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "# len(y_data[0])\n",
     "y_data"
    ]
   },
@@ -541,10 +568,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from sklearn.model_selection import train_test_split\n",
+    "from src.ml.model_selection import create_ready_data\n",
     "\n",
-    "x_train1, x_test1, y_train, y_test = train_test_split(x1, y, test_size=0.2, random_state=2)\n",
-    "x_train2, x_test2, y_train, y_test = train_test_split(x2, y, test_size=0.2, random_state=2)"
+    "X1a, y = create_ready_data('D:/thesis/data/converted/raw/sensor1')\n",
+    "X2a, y = create_ready_data('D:/thesis/data/converted/raw/sensor2')"
    ]
   },
   {
@@ -554,6 +581,17 @@
    "outputs": [],
    "source": [
     "from sklearn.model_selection import train_test_split\n",
+    "\n",
+    "x_train1, x_test1, y_train, y_test = train_test_split(X1a, y, test_size=0.2, random_state=2)\n",
+    "x_train2, x_test2, y_train, y_test = train_test_split(X2a, y, test_size=0.2, random_state=2)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
     "from sklearn.metrics import accuracy_score\n",
     "from sklearn.ensemble import RandomForestClassifier, BaggingClassifier\n",
     "from sklearn.tree import DecisionTreeClassifier\n",
@@ -586,16 +624,17 @@
     "\n",
     "\n",
     "# 1. Random Forest\n",
-    "rf_model = RandomForestClassifier()\n",
-    "rf_model.fit(x_train1, y_train)\n",
-    "rf_pred1 = rf_model.predict(x_test1)\n",
+    "rf_model1 = RandomForestClassifier()\n",
+    "rf_model1.fit(x_train1, y_train)\n",
+    "rf_pred1 = rf_model1.predict(x_test1)\n",
     "acc1 = accuracy_score(y_test, rf_pred1) * 100\n",
     "accuracies1.append(acc1)\n",
     "# format with color coded if acc1 > 90\n",
     "acc1 = f\"\\033[92m{acc1:.2f}\\033[00m\" if acc1 > 90 else f\"{acc1:.2f}\"\n",
     "print(\"Random Forest Accuracy for sensor 1:\", acc1)\n",
-    "rf_model.fit(x_train2, y_train)\n",
-    "rf_pred2 = rf_model.predict(x_test2)\n",
+    "rf_model2 = RandomForestClassifier()\n",
+    "rf_model2.fit(x_train2, y_train)\n",
+    "rf_pred2 = rf_model2.predict(x_test2)\n",
     "acc2 = accuracy_score(y_test, rf_pred2) * 100\n",
     "accuracies2.append(acc2)\n",
     "# format with color coded if acc2 > 90\n",
@@ -605,16 +644,17 @@
     "# print(y_test)\n",
     "\n",
     "# 2. Bagged Trees\n",
-    "bagged_model = BaggingClassifier(estimator=DecisionTreeClassifier(), n_estimators=10)\n",
-    "bagged_model.fit(x_train1, y_train)\n",
-    "bagged_pred1 = bagged_model.predict(x_test1)\n",
+    "bagged_model1 = BaggingClassifier(estimator=DecisionTreeClassifier(), n_estimators=10)\n",
+    "bagged_model1.fit(x_train1, y_train)\n",
+    "bagged_pred1 = bagged_model1.predict(x_test1)\n",
     "acc1 = accuracy_score(y_test, bagged_pred1) * 100\n",
     "accuracies1.append(acc1)\n",
     "# format with color coded if acc1 > 90\n",
     "acc1 = f\"\\033[92m{acc1:.2f}\\033[00m\" if acc1 > 90 else f\"{acc1:.2f}\"\n",
     "print(\"Bagged Trees Accuracy for sensor 1:\", acc1)\n",
-    "bagged_model.fit(x_train2, y_train)\n",
-    "bagged_pred2 = bagged_model.predict(x_test2)\n",
+    "bagged_model2 = BaggingClassifier(estimator=DecisionTreeClassifier(), n_estimators=10)\n",
+    "bagged_model2.fit(x_train2, y_train)\n",
+    "bagged_pred2 = bagged_model2.predict(x_test2)\n",
     "acc2 = accuracy_score(y_test, bagged_pred2) * 100\n",
     "accuracies2.append(acc2)\n",
     "# format with color coded if acc2 > 90\n",
@@ -630,8 +670,9 @@
     "# format with color coded if acc1 > 90\n",
     "acc1 = f\"\\033[92m{acc1:.2f}\\033[00m\" if acc1 > 90 else f\"{acc1:.2f}\"\n",
     "print(\"Decision Tree Accuracy for sensor 1:\", acc1)\n",
-    "dt_model.fit(x_train2, y_train)\n",
-    "dt_pred2 = dt_model.predict(x_test2)\n",
+    "dt_model2 = DecisionTreeClassifier()\n",
+    "dt_model2.fit(x_train2, y_train)\n",
+    "dt_pred2 = dt_model2.predict(x_test2)\n",
     "acc2 = accuracy_score(y_test, dt_pred2) * 100\n",
     "accuracies2.append(acc2)\n",
     "# format with color coded if acc2 > 90\n",
@@ -647,8 +688,9 @@
     "# format with color coded if acc1 > 90\n",
     "acc1 = f\"\\033[92m{acc1:.2f}\\033[00m\" if acc1 > 90 else f\"{acc1:.2f}\"\n",
     "print(\"KNeighbors Accuracy for sensor 1:\", acc1)\n",
-    "knn_model.fit(x_train2, y_train)\n",
-    "knn_pred2 = knn_model.predict(x_test2)\n",
+    "knn_model2 = KNeighborsClassifier()\n",
+    "knn_model2.fit(x_train2, y_train)\n",
+    "knn_pred2 = knn_model2.predict(x_test2)\n",
     "acc2 = accuracy_score(y_test, knn_pred2) * 100\n",
     "accuracies2.append(acc2)\n",
     "# format with color coded if acc2 > 90\n",
@@ -664,8 +706,9 @@
     "# format with color coded if acc1 > 90\n",
     "acc1 = f\"\\033[92m{acc1:.2f}\\033[00m\" if acc1 > 90 else f\"{acc1:.2f}\"\n",
     "print(\"Linear Discriminant Analysis Accuracy for sensor 1:\", acc1)\n",
-    "lda_model.fit(x_train2, y_train)\n",
-    "lda_pred2 = lda_model.predict(x_test2)\n",
+    "lda_model2 = LinearDiscriminantAnalysis()\n",
+    "lda_model2.fit(x_train2, y_train)\n",
+    "lda_pred2 = lda_model2.predict(x_test2)\n",
     "acc2 = accuracy_score(y_test, lda_pred2) * 100\n",
     "accuracies2.append(acc2)\n",
     "# format with color coded if acc2 > 90\n",
@@ -681,8 +724,9 @@
     "# format with color coded if acc1 > 90\n",
     "acc1 = f\"\\033[92m{acc1:.2f}\\033[00m\" if acc1 > 90 else f\"{acc1:.2f}\"\n",
     "print(\"Support Vector Machine Accuracy for sensor 1:\", acc1)\n",
-    "svm_model.fit(x_train2, y_train)\n",
-    "svm_pred2 = svm_model.predict(x_test2)\n",
+    "svm_model2 = SVC()\n",
+    "svm_model2.fit(x_train2, y_train)\n",
+    "svm_pred2 = svm_model2.predict(x_test2)\n",
     "acc2 = accuracy_score(y_test, svm_pred2) * 100\n",
     "accuracies2.append(acc2)\n",
     "# format with color coded if acc2 > 90\n",
@@ -698,8 +742,9 @@
     "# format with color coded if acc1 > 90\n",
     "acc1 = f\"\\033[92m{acc1:.2f}\\033[00m\" if acc1 > 90 else f\"{acc1:.2f}\"\n",
     "print(\"XGBoost Accuracy:\", acc1)\n",
-    "xgboost_model.fit(x_train2, y_train)\n",
-    "xgboost_pred2 = xgboost_model.predict(x_test2)\n",
+    "xgboost_model2 = XGBClassifier()\n",
+    "xgboost_model2.fit(x_train2, y_train)\n",
+    "xgboost_pred2 = xgboost_model2.predict(x_test2)\n",
     "acc2 = accuracy_score(y_test, xgboost_pred2) * 100\n",
     "accuracies2.append(acc2)\n",
     "# format with color coded if acc2 > 90\n",
@@ -776,51 +821,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "def spectograph(data_dir: str):\n",
-    "    # print(os.listdir(data_dir))\n",
-    "    for damage in os.listdir(data_dir):\n",
-    "        # print(damage)\n",
-    "        d = os.path.join(data_dir, damage)\n",
-    "        # print(d)\n",
-    "        for file in os.listdir(d):\n",
-    "            # print(file)\n",
-    "            f = os.path.join(d, file)\n",
-    "            print(f)\n",
-    "            # sensor1 = pd.read_csv(f, skiprows=1, sep=';')\n",
-    "            # sensor2 = pd.read_csv(f, skiprows=1, sep=';')\n",
+    "from src.ml.model_selection import create_ready_data\n",
     "\n",
-    "            # df1 = pd.DataFrame()\n",
-    "\n",
-    "            # df1['s1'] = sensor1[sensor1.columns[-1]]\n",
-    "            # df1['s2'] = sensor2[sensor2.columns[-1]]\n",
-    "ed\n",
-    "            # # Combined Plot for sensor 1 and sensor 2 from data1 file in which motor is operated at 800 rpm\n",
-    "\n",
-    "            # plt.plot(df1['s2'], label='sensor 2')\n",
-    "            # plt.plot(df1['s1'], label='sensor 1')\n",
-    "            # plt.xlabel(\"Number of samples\")\n",
-    "            # plt.ylabel(\"Amplitude\")\n",
-    "            # plt.title(\"Raw vibration signal\")\n",
-    "            # plt.legend()\n",
-    "            # plt.show()\n",
-    "\n",
-    "            # from scipy import signal\n",
-    "            # from scipy.signal.windows import hann\n",
-    "\n",
-    "            # vibration_data = df1['s1']\n",
-    "\n",
-    "            # # Applying STFT\n",
-    "            # window_size = 1024\n",
-    "            # hop_size = 512\n",
-    "            # window = hann(window_size)  # Creating a Hanning window\n",
-    "            # frequencies, times, Zxx = signal.stft(vibration_data, window=window, nperseg=window_size, noverlap=window_size - hop_size)\n",
-    "\n",
-    "            # # Plotting the STFT Data\n",
-    "            # plt.pcolormesh(times, frequencies, np.abs(Zxx), shading='gouraud')\n",
-    "            # plt.title(f'STFT Magnitude for case 1 signal sensor 1 ')\n",
-    "            # plt.ylabel('Frequency [Hz]')\n",
-    "            # plt.xlabel('Time [sec]')\n",
-    "            # plt.show()"
+    "X1b, y = create_ready_data('D:/thesis/data/converted/raw_B/sensor1')\n",
+    "X2b, y = create_ready_data('D:/thesis/data/converted/raw_B/sensor2')"
    ]
   },
   {
@@ -829,7 +833,115 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "spectograph('D:/thesis/data/converted/raw')"
+    "y.shape"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from sklearn.metrics import accuracy_score, classification_report\n",
+    "# 4. Validate on Dataset B\n",
+    "y_pred_svm = svm_model.predict(X1b)\n",
+    "\n",
+    "# 5. Evaluate\n",
+    "print(\"Accuracy on Dataset B:\", accuracy_score(y, y_pred_svm))\n",
+    "print(classification_report(y, y_pred_svm))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from sklearn.metrics import accuracy_score, classification_report\n",
+    "# 4. Validate on Dataset B\n",
+    "y_pred = rf_model2.predict(X2b)\n",
+    "\n",
+    "# 5. Evaluate\n",
+    "print(\"Accuracy on Dataset B:\", accuracy_score(y, y_pred))\n",
+    "print(classification_report(y, y_pred))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "y_predict = svm_model2.predict(X2b.iloc[[5312],:])\n",
+    "print(y_predict)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "y[5312]"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Confusion Matrix"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import matplotlib.pyplot as plt\n",
+    "from sklearn.metrics import confusion_matrix, ConfusionMatrixDisplay\n",
+    "\n",
+    "\n",
+    "cm = confusion_matrix(y, y_pred_svm) # -> ndarray\n",
+    "\n",
+    "# get the class labels\n",
+    "labels = svm_model.classes_\n",
+    "\n",
+    "# Plot\n",
+    "disp = ConfusionMatrixDisplay(confusion_matrix=cm, display_labels=labels)\n",
+    "disp.plot(cmap=plt.cm.Blues)  # You can change colormap\n",
+    "plt.title(\"SVM Sensor1 CM Train w/ Dataset A Val w/ Dataset B\")\n",
+    "plt.show()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### Self-test CM"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# 1. Predict sensor 1 on Dataset A\n",
+    "y_train_pred = svm_model.predict(x_train1)\n",
+    "\n",
+    "# 2. Import confusion matrix tools\n",
+    "from sklearn.metrics import confusion_matrix, ConfusionMatrixDisplay\n",
+    "import matplotlib.pyplot as plt\n",
+    "\n",
+    "# 3. Create and plot confusion matrix\n",
+    "cm_train = confusion_matrix(y_train, y_train_pred)\n",
+    "labels = svm_model.classes_\n",
+    "\n",
+    "disp = ConfusionMatrixDisplay(confusion_matrix=cm_train, display_labels=labels)\n",
+    "disp.plot(cmap=plt.cm.Blues)\n",
+    "plt.title(\"Confusion Matrix: Train & Test on Dataset A\")\n",
+    "plt.show()\n"
    ]
   }
  ],

code/src/ml/model_selection.py

@@ -0,0 +1,57 @@
+import numpy as np
+import pandas as pd
+import os
+from sklearn.model_selection import train_test_split as sklearn_split
+
+
+def create_ready_data(
+    stft_data_path: str,
+    stratify: np.ndarray = None,
+) -> tuple:
+    """
+    Create a stratified train-test split from STFT data.
+
+    Parameters:
+    -----------
+    stft_data_path : str
+        Path to the directory containing STFT data files (e.g. 'data/converted/raw/sensor1')
+    stratify : np.ndarray, optional
+        Labels to use for stratified sampling
+
+    Returns:
+    --------
+    tuple
+        (X_train, X_test, y_train, y_test) - Split datasets
+    """
+    ready_data = []
+    for file in os.listdir(stft_data_path):
+        ready_data.append(pd.read_csv(os.path.join(stft_data_path, file)))
+
+    y_data = [i for i in range(len(ready_data))]
+
+    # Combine all dataframes in ready_data into a single dataframe
+    if ready_data:  # Check if the list is not empty
+        # Use pandas concat function instead of iterative concatenation
+        combined_data = pd.concat(ready_data, axis=0, ignore_index=True)
+
+        print(f"Type of combined data: {type(combined_data)}")
+        print(f"Shape of combined data: {combined_data.shape}")
+    else:
+        print("No data available in ready_data list")
+        combined_data = pd.DataFrame()
+
+    # Store the result in x1a for compatibility with subsequent code
+    X = combined_data
+
+    for i in range(len(y_data)):
+        y_data[i] = [y_data[i]] * ready_data[i].shape[0]
+        y_data[i] = np.array(y_data[i])
+
+    if y_data:
+        # Use numpy concatenate function instead of iterative concatenation
+        y = np.concatenate(y_data, axis=0)
+    else:
+        print("No labels available in y_data list")
+        y = np.array([])
+
+    return X, y

data/QUGS/convert.py

@@ -1,25 +1,307 @@
 import pandas as pd
 import os
+import re
 import sys
+import numpy as np
 from colorama import Fore, Style, init
+from typing import TypedDict, Dict, List
+from joblib import load
+from pprint import pprint
+
+# class DamageFilesIndices(TypedDict):
+#     damage_index: int
+#     files: list[int]
+OriginalSingleDamageScenarioFilePath = str
+DamageScenarioGroupIndex = int
+OriginalSingleDamageScenario = pd.DataFrame
+SensorIndex = int
+VectorColumnIndex = List[SensorIndex]
+VectorColumnIndices = List[VectorColumnIndex]
+DamageScenarioGroup = List[OriginalSingleDamageScenario]
+GroupDataset = List[DamageScenarioGroup]
+
+
+class DamageFilesIndices(TypedDict):
+    damage_index: int
+    files: List[str]
+
+
+def generate_damage_files_index(**kwargs) -> DamageFilesIndices:
+    prefix: str = kwargs.get("prefix", "zzzAD")
+    extension: str = kwargs.get("extension", ".TXT")
+    num_damage: int = kwargs.get("num_damage")
+    file_index_start: int = kwargs.get("file_index_start")
+    col: int = kwargs.get("col")
+    base_path: str = kwargs.get("base_path")
+
+    damage_scenarios = {}
+    a = file_index_start
+    b = col + 1
+    for i in range(1, num_damage + 1):
+        damage_scenarios[i] = range(a, b)
+        a += col
+        b += col
+
+    # return damage_scenarios
+
+    x = {}
+    for damage, files in damage_scenarios.items():
+        x[damage] = []  # Initialize each key with an empty list
+        for i, file_index in enumerate(files, start=1):
+            if base_path:
+                x[damage].append(
+                    os.path.normpath(
+                        os.path.join(base_path, f"{prefix}{file_index}{extension}")
+                    )
+                )
+                # if not os.path.exists(file_path):
+                #     print(Fore.RED + f"File {file_path} does not exist.")
+                #     continue
+            else:
+                x[damage].append(f"{prefix}{file_index}{extension}")
+    return x
+
+    # file_path = os.path.join(base_path, f"zzz{prefix}D{file_index}.TXT")
+    # df = pd.read_csv( file_path, sep="\t", skiprows=10)  # Read with explicit column names
+
+
+class DataProcessor:
+    def __init__(self, file_index: DamageFilesIndices, cache_path: str = None):
+        self.file_index = file_index
+        if cache_path:
+            self.data = load(cache_path)
+        else:
+            self.data = self._load_all_data()
+
+    def _extract_column_names(self, file_path: str) -> List[str]:
+        """
+        Extracts column names from the header of the given file.
+        Assumes the 6th line contains column names.
+
+        :param file_path: Path to the data file.
+        :return: List of column names.
+        """
+        with open(file_path, "r") as f:
+            header_lines = [next(f) for _ in range(12)]
+
+        # Extract column names from the 6th line
+        channel_line = header_lines[10].strip()
+        tokens = re.findall(r'"([^"]+)"', channel_line)
+        if not channel_line.startswith('"'):
+            first_token = channel_line.split()[0]
+            tokens = [first_token] + tokens
+
+        return tokens  # Prepend 'Time' column if applicable
+
+    def _load_dataframe(self, file_path: str) -> OriginalSingleDamageScenario:
+        """
+        Loads a single data file into a pandas DataFrame.
+
+        :param file_path: Path to the data file.
+        :return: DataFrame containing the numerical data.
+        """
+        col_names = self._extract_column_names(file_path)
+        df = pd.read_csv(
+            file_path, delim_whitespace=True, skiprows=11, header=None, memory_map=True
+        )
+        df.columns = col_names
+        return df
+
+    def _load_all_data(self) -> GroupDataset:
+        """
+        Loads all data files based on the grouping dictionary and returns a nested list.
+
+        :return: A nested list of DataFrames where the outer index corresponds to group_idx - 1.
+        """
+        data = []
+        # Find the maximum group index to determine the list size
+        max_group_idx = max(self.file_index.keys()) if self.file_index else 0
+
+        # Initialize empty lists
+        for _ in range(max_group_idx):
+            data.append([])
+
+        # Fill the list with data
+        for group_idx, file_list in self.file_index.items():
+            # Adjust index to be 0-based
+            list_idx = group_idx - 1
+            data[list_idx] = [self._load_dataframe(file) for file in file_list]
+
+        return data
+
+    def get_group_data(self, group_idx: int) -> List[pd.DataFrame]:
+        """
+        Returns the list of DataFrames for the given group index.
+
+        :param group_idx: Index of the group.
+        :return: List of DataFrames.
+        """
+        return self.data.get([group_idx, []])
+
+    def get_column_names(self, group_idx: int, file_idx: int = 0) -> List[str]:
+        """
+        Returns the column names for the given group and file indices.
+
+        :param group_idx: Index of the group.
+        :param file_idx: Index of the file in the group.
+        :return: List of column names.
+        """
+        if group_idx in self.data and len(self.data[group_idx]) > file_idx:
+            return self.data[group_idx][file_idx].columns.tolist()
+        return []
+
+    def get_data_info(self):
+        """
+        Print information about the loaded data structure.
+        Adapted for when self.data is a List instead of a Dictionary.
+        """
+        if isinstance(self.data, list):
+            # For each sublist in self.data, get the type names of all elements
+            pprint(
+                [
+                    (
+                        [type(item).__name__ for item in sublist]
+                        if isinstance(sublist, list)
+                        else type(sublist).__name__
+                    )
+                    for sublist in self.data
+                ]
+            )
+        else:
+            pprint(
+                {
+                    key: [type(df).__name__ for df in value]
+                    for key, value in self.data.items()
+                }
+                if isinstance(self.data, dict)
+                else type(self.data).__name__
+            )
+
+    def _create_vector_column_index(self) -> VectorColumnIndices:
+        vector_col_idx: VectorColumnIndices = []
+        y = 0
+        for data_group in self.data:  # len(data_group[i]) = 5
+            for j in data_group:  # len(j[i]) =
+                c: VectorColumnIndex = []  # column vector c_{j}
+                x = 0
+                for _ in range(6):  # TODO: range(6) should be dynamic and parameterized
+                    c.append(x + y)
+                    x += 5
+                vector_col_idx.append(c)
+                y += 1
+            return vector_col_idx
+
+    def create_vector_column(self, overwrite=True) -> List[List[List[pd.DataFrame]]]:
+        """
+        Create a vector column from the loaded data.
+
+        :param overwrite: Overwrite the original data with vector column-based data.
+        """
+        idx = self._create_vector_column_index()
+        # if overwrite:
+        for i in range(len(self.data)):
+            for j in range(len(self.data[i])):
+                # Get the appropriate indices for slicing from idx
+                indices = idx[j]
+
+                # Get the current DataFrame
+                df = self.data[i][j]
+
+                # Keep the 'Time' column and select only specified 'Real' columns
+                # First, we add 1 to all indices to account for 'Time' being at position 0
+                real_indices = [index + 1 for index in indices]
+
+                # Create list with Time column index (0) and the adjusted Real indices
+                all_indices = [0] + real_indices
+
+                # Apply the slicing
+                self.data[i][j] = df.iloc[:, all_indices]
+        # TODO: if !overwrite:
+
+    def create_limited_sensor_vector_column(self, overwrite=True):
+        """
+        Create a vector column from the loaded data.
+
+        :param overwrite: Overwrite the original data with vector column-based data.
+        """
+        idx = self._create_vector_column_index()
+        # if overwrite:
+        for i in range(len(self.data)):  # damage(s)
+            for j in range(len(self.data[i])):  # col(s)
+                # Get the appropriate indices for slicing from idx
+                indices = idx[j]
+
+                # Get the current DataFrame
+                df = self.data[i][j]
+
+                # Keep the 'Time' column and select only specifid 'Real' colmns
+                # First, we add 1 to all indices to acount for 'Time' being at positiion 0
+                real_indices = [index + 1 for index in indices]
+
+                # Create list with Time column index (0) and the adjustedd Real indices
+                all_indices = [0] + [real_indices[0]] + [real_indices[-1]]
+
+                # Apply the slicing
+                self.data[i][j] = df.iloc[:, all_indices]
+        # TODO: if !overwrite:
+
+    def export_to_csv(self, output_dir: str, file_prefix: str = "DAMAGE"):
+        """
+        Export the processed data to CSV files in the required folder structure.
+
+        :param output_dir: Directory to save the CSV files.
+        :param file_prefix: Prefix for the output filenames.
+        """
+        for group_idx, group in enumerate(self.data, start=1):
+            group_folder = os.path.join(output_dir, f"{file_prefix}_{group_idx}")
+            os.makedirs(group_folder, exist_ok=True)
+            for test_idx, df in enumerate(group, start=1):
+                # Ensure columns are named uniquely if duplicated
+                df = df.copy()
+                df.columns = ["Time", "Real_0", "Real_1"]  # Rename
+
+                # Export first Real column
+                out1 = os.path.join(
+                    group_folder, f"{file_prefix}_{group_idx}_TEST{test_idx}_01.csv"
+                )
+                df[["Time", "Real_0"]].rename(columns={"Real_0": "Real"}).to_csv(
+                    out1, index=False
+                )
+
+                # Export last Real column
+                out2 = os.path.join(
+                    group_folder, f"{file_prefix}_{group_idx}_TEST{test_idx}_02.csv"
+                )
+                df[["Time", "Real_1"]].rename(columns={"Real_1": "Real"}).to_csv(
+                    out2, index=False
+                )
+
 
 def create_damage_files(base_path, output_base, prefix):
     # Initialize colorama
     init(autoreset=True)
 
     # Generate column labels based on expected duplication in input files
-    columns = ['Real'] + [f'Real.{i}' for i in range(1, 30)]  # Explicitly setting column names
+    columns = ["Real"] + [
+        f"Real.{i}" for i in range(1, 30)
+    ]  # Explicitly setting column names
 
-    sensor_end_map = {1: 'Real.25', 2: 'Real.26', 3: 'Real.27', 4: 'Real.28', 5: 'Real.29'}
+    sensor_end_map = {
+        1: "Real.25",
+        2: "Real.26",
+        3: "Real.27",
+        4: "Real.28",
+        5: "Real.29",
+    }
 
     # Define the damage scenarios and the corresponding original file indices
     damage_scenarios = {
         1: range(1, 6),  # Damage 1 files from zzzAD1.csv to zzzAD5.csv
         2: range(6, 11),  # Damage 2 files from zzzAD6.csv to zzzAD10.csv
-        3: range(11, 16), # Damage 3 files from zzzAD11.csv to zzzAD15.csvs
-        4: range(16, 21), # Damage 4 files from zzzAD16.csv to zzzAD20.csv
+        3: range(11, 16),  # Damage 3 files from zzzAD11.csv to zzzAD15.csvs
+        4: range(16, 21),  # Damage 4 files from zzzAD16.csv to zzzAD20.csv
         5: range(21, 26),  # Damage 5 files from zzzAD21.csv to zzzAD25.csv
-        6: range(26, 31)  # Damage 6 files from zzzAD26.csv to zzzAD30.csv
+        6: range(26, 31),  # Damage 6 files from zzzAD26.csv to zzzAD30.csv
     }
     damage_pad = len(str(len(damage_scenarios)))
     test_pad = len(str(30))
@@ -27,29 +309,36 @@ def create_damage_files(base_path, output_base, prefix):
     for damage, files in damage_scenarios.items():
         for i, file_index in enumerate(files, start=1):
             # Load original data file
-            file_path = os.path.join(base_path, f'zzz{prefix}D{file_index}.TXT')
-            df = pd.read_csv(file_path, sep='\t', skiprows=10)  # Read with explicit column names
+            file_path = os.path.join(base_path, f"zzz{prefix}D{file_index}.TXT")
+            df = pd.read_csv(
+                file_path, sep="\t", skiprows=10
+            )  # Read with explicit column names
 
-            top_sensor = columns[i-1]
+            top_sensor = columns[i - 1]
             print(top_sensor, type(top_sensor))
-            output_file_1 = os.path.join(output_base, f'DAMAGE_{damage}', f'DAMAGE{damage}_TEST{i}_01.csv')
+            output_file_1 = os.path.join(
+                output_base, f"DAMAGE_{damage}", f"DAMAGE{damage}_TEST{i}_01.csv"
+            )
             print(f"Creating {output_file_1} from taking zzz{prefix}D{file_index}.TXT")
             print("Taking datetime column on index 0...")
             print(f"Taking `{top_sensor}`...")
             os.makedirs(os.path.dirname(output_file_1), exist_ok=True)
-            df[['Time', top_sensor]].to_csv(output_file_1, index=False)
+            df[["Time", top_sensor]].to_csv(output_file_1, index=False)
             print(Fore.GREEN + "Done")
 
             bottom_sensor = sensor_end_map[i]
-            output_file_2 = os.path.join(output_base, f'DAMAGE_{damage}', f'DAMAGE{damage}_TEST{i}_02.csv')
+            output_file_2 = os.path.join(
+                output_base, f"DAMAGE_{damage}", f"DAMAGE{damage}_TEST{i}_02.csv"
+            )
             print(f"Creating {output_file_2} from taking zzz{prefix}D{file_index}.TXT")
             print("Taking datetime column on index 0...")
             print(f"Taking `{bottom_sensor}`...")
             os.makedirs(os.path.dirname(output_file_2), exist_ok=True)
-            df[['Time', bottom_sensor]].to_csv(output_file_2, index=False)
+            df[["Time", bottom_sensor]].to_csv(output_file_2, index=False)
             print(Fore.GREEN + "Done")
             print("---")
 
+
 def main():
     if len(sys.argv) < 2:
         print("Usage: python convert.py <path_to_csv_files>")
@@ -66,5 +355,6 @@ def main():
     create_damage_files(base_path, output_base, prefix)
     print(Fore.YELLOW + Style.BRIGHT + "All files have been created successfully.")
 
+
 if __name__ == "__main__":
     main()

data/QUGS/test.py

@@ -0,0 +1,25 @@
+from convert import *
+from joblib import dump, load
+
+# a = generate_damage_files_index(
+#     num_damage=6, file_index_start=1, col=5, base_path="D:/thesis/data/dataset_A"
+# )
+
+b = generate_damage_files_index(
+    num_damage=6,
+    file_index_start=1,
+    col=5,
+    base_path="D:/thesis/data/dataset_B",
+    prefix="zzzBD",
+)
+# data_A = DataProcessor(file_index=a)
+# # data.create_vector_column(overwrite=True)
+# data_A.create_limited_sensor_vector_column(overwrite=True)
+# data_A.export_to_csv("D:/thesis/data/converted/raw")
+
+data_B = DataProcessor(file_index=b)
+# data.create_vector_column(overwrite=True)
+data_B.create_limited_sensor_vector_column(overwrite=True)
+data_B.export_to_csv("D:/thesis/data/converted/raw_B")
+# a = load("D:/cache.joblib")
+# breakpoint()

setup.py

@@ -0,0 +1,8 @@
+from setuptools import setup, find_packages
+
+setup(
+    name="thesisrepo",
+    version="0.1",
+    packages=find_packages(where="code"),
+    package_dir={"": "code"},
+)