Update README.md

README.md

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-# zooms_classifier
+# ZooMS Classifier
+
+## Model Training and Explainability
+
+**Note:** Access to Google Drive is required to utilize this Colab notebook.
+
+[![Open in Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1Ljos45IErs819W3ynY5-u9ach85y9J9G?usp=sharing)

windows_app/README.md

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+# ZooMS Windows Classifer App 
+
+
+Please use pyinstaller to compile the app on a Windows machine. 
+
+
+MyApp/
+|-- model/
+|   |-- weights.pth # 1DCNN weights (PyTorch)
+|-- src/
+|   |-- main.py
+|   |-- model.py
+|   |-- file_ops.py
+|   |-- gui.py
+|-- requirements.txt

windows_app/requirements.txt

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+pandas >= 1.4.4
+torch >= 1.10.2
+pyinstaller >= 5.13.2

windows_app/setup.py

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+from cx_Freeze import setup, Executable
+
+setup(
+    name="AI_ZooMS",
+    version="0.0.1",
+    description="Find homininis with AI",
+    executables=[Executable("src/main.py")]
+)

windows_app/src/file_ops.py

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+import pandas as pd
+import os
+from datetime import datetime
+
+def read_csv_files(directory):
+    file_paths = []
+    file_names = []
+    for filename in os.listdir(directory):
+        if filename.endswith('.csv'):
+            filepath = os.path.join(directory, filename)
+            file_paths.append(filepath)
+            file_names.append(filename)
+    return file_paths, file_names
+
+
+
+def save_results(results, output_directory, file_names, targets):
+    # Column names
+    column_names = [
+        'Canidae', 'Cervidae', 'CervidaeGazellaSaiga', 'Ovis', 'Equidae',
+        'CrocutaPanthera', 'BisonYak', 'Capra', 'Ursidae', 'Vulpes vulpes',
+        'Elephantidae', 'Others', 'Rhinocerotidae', 'Rangifer tarandus', 'Hominins'
+    ]
+
+    # Updated the dataframe creation line to handle numpy arrays
+    concatenated_df = pd.concat([pd.DataFrame(result) for result in results], ignore_index=True)
+
+    concatenated_df.columns = column_names
+    concatenated_df['Most Probable Class'] = [column_names[i] for i in targets]
+
+    # Reorder columns to place 'Most Probable Class' as the second column
+    cols = ['Most Probable Class'] + [col for col in concatenated_df.columns if col != 'Most Probable Class']
+    concatenated_df = concatenated_df[cols]
+
+    # Insert file names as the first column
+    concatenated_df.insert(0, 'File Name', file_names)
+
+    # Get current date and time
+    current_datetime = datetime.now().strftime('%Y-%m-%d_%H-%M-%S')
+
+    # Create a unique filename with current date and time
+    output_path = os.path.join(output_directory, f'results_{current_datetime}.csv')
+
+    # Save the concatenated dataframe to the unique output path
+    concatenated_df.to_csv(output_path, index=False)

windows_app/src/gui.py

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+from PyQt5.QtWidgets import QApplication, QWidget, QVBoxLayout, QHBoxLayout, QLabel, QLineEdit, QPushButton, QFileDialog
+from PyQt5.QtGui import QIcon, QFont
+
+def create_gui(main_func):
+    app = QApplication([])
+
+    window = QWidget()
+    window.setWindowTitle("ML-Based Mass Spectra Species Identifier")
+    window.setWindowIcon(QIcon('icon.png'))
+    window.setFixedSize(700, 350)
+
+    layoutV = QVBoxLayout()
+    font_label = QFont("Arial", 16, QFont.Bold)
+    font_button = QFont("Arial", 14)
+
+    layoutV.setContentsMargins(40, 40, 40, 40)
+
+    layoutH3 = QHBoxLayout()
+    model_file_path = QLineEdit(placeholderText="Select your ML model file...")
+    model_file_path.setFont(font_button)
+    browse_model_btn = QPushButton("Select Model")
+    browse_model_btn.setFont(font_button)
+    label3 = QLabel("Model File:")
+    label3.setFont(font_label)
+    layoutH3.addWidget(label3)
+    layoutH3.addWidget(model_file_path)
+    layoutH3.addWidget(browse_model_btn)
+    layoutV.addLayout(layoutH3)
+
+    layoutH1 = QHBoxLayout()
+    input_directory = QLineEdit(placeholderText="Select a directory with CSV files...")
+    input_directory.setFont(font_button)
+    browse_input_btn = QPushButton("Browse")
+    browse_input_btn.setFont(font_button)
+    label1 = QLabel("Input Directory:")
+    label1.setFont(font_label)
+    layoutH1.addWidget(label1)
+    layoutH1.addWidget(input_directory)
+    layoutH1.addWidget(browse_input_btn)
+    layoutV.addLayout(layoutH1)
+
+    layoutH2 = QHBoxLayout()
+    output_directory = QLineEdit(placeholderText="Select a directory for results...")
+    output_directory.setFont(font_button)
+    browse_output_btn = QPushButton("Browse")
+    browse_output_btn.setFont(font_button)
+    label2 = QLabel("Output Directory:")
+    label2.setFont(font_label)
+    layoutH2.addWidget(label2)
+    layoutH2.addWidget(output_directory)
+    layoutH2.addWidget(browse_output_btn)
+    layoutV.addLayout(layoutH2)
+
+    classify_btn = QPushButton("Classify")
+    classify_btn.setFont(font_button)
+    layoutV.addWidget(classify_btn)
+
+    window.setStyleSheet("""
+        QWidget {
+            background-color: #fafafa;
+            font-size: 18px;
+            color: #333;
+        }
+        QPushButton {
+            background-color: #11a611; /* Green */
+            color: white;
+            border: none;
+            border-radius: 10px;
+            padding: 14px 28px;
+        }
+        QPushButton:pressed {
+            background-color: #005900; /* Darker green on click */
+        }
+        QLineEdit {
+            background-color: #fff;
+            border: 1px solid #ccc;
+            border-radius: 10px;
+            padding: 14px;
+        }
+    """)
+
+    browse_model_btn.clicked.connect(lambda: model_file_path.setText(QFileDialog.getOpenFileName()[0]))
+    browse_input_btn.clicked.connect(lambda: input_directory.setText(QFileDialog.getExistingDirectory()))
+    browse_output_btn.clicked.connect(lambda: output_directory.setText(QFileDialog.getExistingDirectory()))
+    classify_btn.clicked.connect(lambda: main_func(model_file_path.text(), input_directory.text(), output_directory.text()))
+
+    window.setLayout(layoutV)
+    window.show()
+    app.exec_()
+
+if __name__ == "__main__":
+    create_gui(main)

windows_app/src/main.py

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+from file_ops import read_csv_files, save_results
+from gui import create_gui
+import torch
+from PyQt5.QtWidgets import QMessageBox
+import numpy as np
+import pandas as pd
+import os 
+from model import CNN1D
+
+def mean_intensity(temp_df, bin_resolution=0.5):
+    bins = np.arange(899.9, 3500, bin_resolution)
+    temp_df['bin'] = pd.cut(temp_df['mass'], bins=bins)
+    return temp_df.groupby('bin')['intensity'].mean().values
+
+def normalize(tensor):
+    tensor[torch.isnan(tensor)] = 0
+    mean = tensor.mean()
+    std = tensor.std()
+    return (tensor - mean) / (std + torch.finfo(torch.float32).eps)
+
+def load_model(weight_path):
+    model = torch.load(weight_path, map_location=torch.device('cpu'))
+    model.eval()
+    return model
+
+def main(model_file_path, input_directory, output_directory):
+    if not model_file_path or not input_directory or not output_directory:
+        show_missing_paths_message()
+        return
+
+    model = load_model(model_file_path)
+    file_paths, file_names = read_csv_files(input_directory)
+    results, file_names, targets = make_predictions(file_paths, model)
+    save_results(results, output_directory, file_names, targets)
+    show_done_message()
+
+def show_missing_paths_message():
+    msg = QMessageBox()
+    msg.setIcon(QMessageBox.Critical)
+    msg.setWindowTitle("Missing Path")
+    msg.setText("Please provide all required paths (Model, Input Directory, Output Directory).")
+    msg.exec_()
+
+def show_done_message():
+    msg = QMessageBox()
+    msg.setIcon(QMessageBox.Information)
+    msg.setWindowTitle("Process Completed")
+    msg.setText("The classification process is complete.")
+    msg.exec_()
+
+def make_predictions(file_paths, model):
+    results = []
+    file_names = []
+    targets = []
+    for i, file_path in enumerate(file_paths):
+        temp_df = pd.read_csv(file_path)
+        file_name = os.path.basename(file_path)
+        file_names.append(file_name)
+
+        intensities = mean_intensity(temp_df)
+        tensor_data = torch.tensor(intensities, dtype=torch.float32)
+        tensor_data = normalize(tensor_data)
+
+        output = model(tensor_data.unsqueeze(0).unsqueeze(0))
+        probabilities = torch.softmax(output, dim=1).detach().numpy().round(3)
+        results.append(probabilities)
+
+        target = np.argmax(probabilities)
+        targets.append(target)
+
+    return results, file_names, targets
+
+if __name__ == "__main__":
+    create_gui(main)

windows_app/src/model.py

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+import torch
+import torch.nn as nn
+
+class CNN1D(nn.Module):
+    def __init__(self, input_size, num_classes):
+        super(CNN1D, self).__init__()
+
+        self.conv1 = nn.Conv1d(1, 32, kernel_size=5, stride=1)
+
+        self.conv2 = nn.Conv1d(32, 64, kernel_size=5, stride=1)
+        #self.bn2 = nn.BatchNorm1d(32)
+
+        self.pool = nn.AvgPool1d(kernel_size=3)
+
+        output_size = (input_size - 5 + 1) // 3  # After conv1 and pool
+        output_size = (output_size - 5 + 1) // 3  # After conv2 and pool
+
+        self.fc1 = nn.Linear(64 * output_size, 128)
+        self.dropout1 = nn.Dropout(0.25)
+
+        self.fc2 = nn.Linear(128, num_classes)
+
+        self.relu = nn.ReLU()
+
+    def forward(self, x):
+        x = self.pool(self.relu(self.conv1(x)))
+        x = self.pool(self.relu(self.conv2(x)))
+
+        x = x.view(x.size(0), -1)
+
+        x = self.relu(self.fc1(x))
+        x = self.dropout1(x)
+
+        x = self.fc2(x)
+        return x
+
+
+def load_model(weight_path):
+    model = torch.load(weight_path, map_location=torch.device('cpu'))
+    model.eval()
+    return model
+
+

windows_app/test.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "55bd4cb8-4bf1-48f8-bcb3-11375f947e31",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import tkinter as tk\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "ab248bcb-4c77-442b-a12d-9bb89965d029",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from cx_Freeze import setup, Executable\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "bc3e8b53-753d-4d63-9f31-ae485850acbd",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import torch, pandas "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "74fb7e63-4b89-43ce-a98d-06871d43f416",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "('1.12.1+cu116', '1.5.0')"
+      ]
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "torch.__version__, pandas.__version__"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "20a31617-7550-424c-8119-fd76d66c1cfa",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.16"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

windows_app/untitled.md

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+