re-architect

Dockerfile

@@ -0,0 +1,142 @@
+FROM ubuntu:20.04
+
+# Set environment variables to make the build non-interactive
+ENV DEBIAN_FRONTEND=noninteractive
+ENV TZ=Etc/UTC
+
+# Update and install prerequisites for adding the PPA
+RUN apt-get update && apt-get install -y \
+    software-properties-common \
+    build-essential \
+    libssl-dev \
+    libffi-dev \
+    curl \
+    lsb-release \
+    && add-apt-repository -y ppa:deadsnakes/ppa \
+    && apt-get update \
+    && apt-get install -y \
+    python3.10 \
+    python3.10-dev \
+    python3.10-venv \
+    python3.10-distutils \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install pip using the official get-pip.py script
+RUN ln -sf /usr/bin/python3.10 /usr/bin/python
+RUN curl -O https://bootstrap.pypa.io/get-pip.py && python get-pip.py 
+
+# Set the working directory in the container
+WORKDIR /app
+
+# Copy the requirements.txt file to the working directory
+COPY requirements.txt .
+
+RUN pip install -r requirements.txt
+
+RUN apt-get update && \
+    # apt-get install -y libx11-dev libgl1-mesa-dev && \
+    apt-get install -y libx11-dev libgl1-mesa-dev libxcomposite-dev libxrandr-dev libxss-dev libxcursor-dev
+
+RUN apt-get install -y libx11-xcb1 libxcb-xinerama0 libxkbcommon0 libglib2.0-0
+
+
+RUN apt-get update && apt-get install -y \
+    libx11-xcb1 \
+    libxcb-util1 \
+    # libxcb-xinerama0 \
+    libxcb-icccm4 \
+    libxcb-image0 \
+    libxcb-keysyms1 \
+    libxcb-randr0 \
+    libxcb-render-util0 \
+    libxcb-render0 \
+    libxcb-shape0 \
+    libxcb-shm0 \
+    libxcb-sync1 \
+    libxcb-xfixes0 \
+    libxcb-xkb1 \
+    x11-utils \
+    libxkbcommon-x11-0
+
+RUN export QT_QPA_PLATFORM_PLUGIN_PATH=/usr/local/lib/python3.10/dist-packages/PyQt5/Qt5/plugins/platforms
+RUN export QT_DEBUG_PLUGINS=1
+
+
+# Copy Cellscanner files to the working directory
+COPY cellscanner ./
+
+# Specify the command to run the application (optional)
+CMD ["python", "Cellscanner.py"]
+
+
+
+# docker run --rm -it --entrypoint /bin/bash cellscanner
+# docker run -e DISPLAY=$DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix -v .:/media cellscanner
+
+
+
+
+# # FROM DEEPSEEK AS ALTERNATIVE -- NOT WORKING MOUHAHA
+# FROM ubuntu:20.04
+
+# # Set environment variables
+# ENV DEBIAN_FRONTEND=noninteractive \
+#     TZ=Etc/UTC \
+#     QT_QPA_PLATFORM_PLUGIN_PATH=/usr/local/lib/python3.10/dist-packages/PyQt5/Qt5/plugins/platforms \
+#     QT_DEBUG_PLUGINS=1
+
+# # Combine all package installations into a single layer
+# RUN apt-get update && apt-get install -y --no-install-recommends \
+#     software-properties-common \
+#     build-essential \
+#     libssl-dev \
+#     libffi-dev \
+#     curl \
+#     lsb-release \
+#     python3.10 \
+#     python3.10-dev \
+#     python3.10-venv \
+#     python3.10-distutils \
+#     libx11-dev \
+#     libgl1-mesa-dev \
+#     libxcomposite-dev \
+#     libxrandr-dev \
+#     libxss-dev \
+#     libxcursor-dev \
+#     libx11-xcb1 \
+#     libxcb-xinerama0 \
+#     libxkbcommon0 \
+#     libglib2.0-0 \
+#     libxcb-util1 \
+#     libxcb-icccm4 \
+#     libxcb-image0 \
+#     libxcb-keysyms1 \
+#     libxcb-randr0 \
+#     libxcb-render-util0 \
+#     libxcb-render0 \
+#     libxcb-shape0 \
+#     libxcb-shm0 \
+#     libxcb-sync1 \
+#     libxcb-xfixes0 \
+#     libxcb-xkb1 \
+#     x11-utils \
+#     libxkbcommon-x11-0 && \
+#     add-apt-repository -y ppa:deadsnakes/ppa && \
+#     apt-get clean && \
+#     rm -rf /var/lib/apt/lists/*
+
+# # Install pip and setup Python
+# RUN ln -sf /usr/bin/python3.10 /usr/bin/python && \
+#     curl -sS https://bootstrap.pypa.io/get-pip.py | python -
+
+# WORKDIR /app
+
+# # Install Python dependencies first (better layer caching)
+# COPY requirements.txt .
+# RUN pip install --no-cache-dir -r requirements.txt
+
+# # Copy application files
+# COPY cellscanner ./
+
+# CMD ["python", "Cellscanner.py"]

README.md

@@ -28,7 +28,7 @@ To run CellScanner with its GUI, you may now run:
 # Always remember to activate your conda environment, if you set one for CellScanner
 conda activate cellscanner
 # If `python` returns an error message that is not there, try with `python3` instead
-python Cellscanner.py
+python cellscanner/Cellscanner.py
 ```
 
 This will pop-up CellScanner where you can now import your data, fill in your training parameters and 
@@ -90,7 +90,7 @@ Once your configuration file is ready, you may run CellScanner CLI :
 
 ```bash
 conda activate cellscanner
-python CellscannerCLI.py --config config.yml
+python cellscanner/CellscannerCLI.py --config config.yml
 ```
 
 
@@ -107,5 +107,22 @@ For the new features that have been added, a manuscript is in process. :pencil:
 
 
 
+## Docker 
+
+In linux, remember to disable access control for local connections first:
+
+  ```bash
+  xhost +local:
+  ```
+
+  then, you need to run something line:
+
+  ```bash
+  docker run -e DISPLAY=$DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix -v ./Testfiles:/csFiles  hariszaf/cell_scanner
+  ```
+
+  where `Testfiles` is the directory where you have you input data, and also, where CellScanner will return its findings, on your local machine. 
+
+  `csFiles` is the output directory of CellScanner within the container, so make sure you always keep it like that in your command. 
 
 

Cellscanner.py → cellscanner/Cellscanner.py

@@ -1,21 +1,5 @@
-# CellScanner.py
-import os
-import sys
-
-from PyQt5.QtCore import Qt
-from PyQt5.QtGui import QPixmap, QFont
-from PyQt5.QtWidgets import QApplication, QMainWindow, QVBoxLayout, QHBoxLayout,\
-    QPushButton, QWidget, QLabel, QScrollArea
-
-from scripts.helpers import button_style, get_app_dir
-from scripts.ImportFiles import  ImportFilePanel
-from scripts.TrainingModel import TrainModelPanel
-from scripts.Prediction import PredictionPanel
-
-
+#!/usr/bin/env python
 """
-CellScanner - A Comprehensive Flow Cytometry Data Analysis Tool
-
 ==========================================
 Overview
 ==========================================
@@ -36,78 +20,52 @@
 - **Heterogeneity Analysis**: Perform heterogeneity assessments using both simple range-based methods and MiniBatchKMeans clustering.
 - **Interactive Visualizations**: Generate and save interactive 3D scatter plots, pie charts, and bar charts to visualize predictions, gating results, and heterogeneity measures.
 
-
 ==========================================
-Modules and Functions
+Cellscanner.py
 ==========================================
 
-1. **get_app_dir()**:
-    - **Description**: Determines the base path of the application, accommodating both development and bundled executable environments (e.g., PyInstaller).
-    - **Returns**: Absolute path to the directory where the script or executable is located.
-
-2. **get_abs_path(relative_path)**:
-    - **Description**: Converts a relative file path to an absolute path based on the application's base directory.
-    - **Parameters**:
-        - `relative_path` (str): The relative path of the resource.
-    - **Returns**: Absolute path to the specified resource.
-
-3. **NeuralNetworkGUI (class)**:
-    - **Description**: The primary GUI class inheriting from `QMainWindow`. It orchestrates the layout, user interactions, and integrates various panels for data importation, model training, prediction, and analysis.
-    - **Attributes**:
-        - `model`: Trained neural network model.
-        - `scaler`: Scaler object for data preprocessing.
-        - `label_encoder`: Encoder for translating model predictions into readable labels.
-    - **Methods**:
-        - `__init__()`: Initializes the GUI components, including title, logo, buttons, and panels.
-        - `init_predict_panel()`: Configures the prediction panel with options for selecting coculture files, axis channels, gating parameters, and initiating predictions.
-        - `toggle_file_panel()`: Shows or hides the data import panel based on user interaction.
-        - `toggle_train_panel()`: Shows or hides the model training panel.
-        - `toggle_gating_options()`: Displays or conceals gating options contingent on the gating checkbox state.
-        - `toggle_predict_panel()`: Shows or hides the prediction panel.
-        - `choose_coculture_file()`: Facilitates the selection of coculture files and populates axis selection dropdowns with appropriate channels.
-        - `run_prediction()`: Executes the prediction workflow, including loading models, predicting species, applying gating, performing heterogeneity analysis, and generating visualizations.
-        - `open_documentation()`: Opens the application's documentation webpage in the user's default web browser.
-
-4. **Main Application Loop**:
-    - **Description**: Initializes the QApplication, instantiates the main GUI window, and executes the application loop to render the GUI.
+Initializes the QApplication, instantiates the main GUI window, and executes the application loop to render the GUI.
+
 Usage:
 - Import Files: Allows users to import monoculture and blank files for analysis.
 - Train Neural Network: Provides an interface to train a neural network model on the imported data.
 - Predict Coculture: Allows users to select a coculture file, predict species within the sample, and optionally apply gating and heterogeneity analysis.
+"""
+import os
+import sys
 
-Dependencies:
-- Python 3.x
-- PyQt5
-- TensorFlow
-- fcsparser
-- joblib
-- numpy
-- shutil
-- atexit
+from PyQt5.QtCore import Qt
+from PyQt5.QtGui import QPixmap, QFont
+from PyQt5.QtWidgets import QApplication, QMainWindow, QVBoxLayout, QHBoxLayout,\
+    QPushButton, QWidget, QLabel, QScrollArea
 
+from scripts.helpers import get_app_dir
+from scripts.GUIhelpers import button_style
+from scripts.ImportFiles import  ImportFilePanel
+from scripts.TrainingModel import TrainModelPanel
+from scripts.Prediction import PredictionPanel
+
+"""
 Authors:
     - Ermis Ioannis Michail Delopoulos
     - Haris Zafeiropoulos
 
 Date: 2024-2025
-
 """
 
 class NeuralNetworkGUI(QMainWindow):
     """
     Main class of the CellScanner GUI.
     It builds a PyQT app with 3 main panels:
-    - Importing files
-    - Training
-    - Prediction
-
-    NOTE: The Training panel is delivered thanks to the TrainModelPanel class of the TrainingModel.py
-    The Importing files and the Predictions panels though, they are described as features of the NeuralNetworkGUI class.
+    - Importing files (:class:`scripts.ImportFiles.ImportFilePanel`)
+    - Training (:class:`scripts.TrainingModel.TrainModelPanel`)
+    - Prediction (:class:`scripts.Prediction.PredictionPanel`)
     """
     def __init__(self):
         super().__init__()
         self.setWindowTitle("CellScanner")
-        self.setGeometry(100, 100, 850, 1800)
+        # setGeometry(x, y, width, height) x, y stand for top-left corner
+        self.setGeometry(100, 100, 950, 2100)
 
         # Initialize model-related attributes
         self.model = None
@@ -207,21 +165,21 @@ def __init__(self):
         self.setCentralWidget(scroll_area)
 
     def toggle_file_panel(self):
-        # Toggle the visibility of the file import panel
+        """Shows or hides the data import panel based on user interaction."""
         if self.file_panel.isVisible():
             self.file_panel.hide()
         else:
             self.file_panel.show()
 
     def toggle_train_panel(self):
-        # Toggle the visibility of the train model panel
+        """Shows or hides the model training panel."""
         if self.train_panel.isVisible():
             self.train_panel.hide()
         else:
             self.train_panel.show()
 
     def toggle_predict_panel(self):
-        # Toggle the visibility of the predict panel
+        """Shows or hides the predict panel"""
         if self.predict_panel.isVisible():
             self.predict_panel.hide()
         else: