Chemometric Studio

Chemometric Studio is a desktop application for chemometric workflow design, execution, interpretation, and reporting. It combines a visual methodology builder with configurable analysis pages, advanced routing, and PDF reporting.

Project Status

• Active development. Open beta, still with missing features and known issues. You may encounter unfinished features, UI adjustments, or behavior changes in upcoming versions.
• Still in construction end-user documentation is available in the built-in User Manual under Manual/ (index.html).

What the Application Currently Supports

The current feature includes:

• Visual Setup tab for building methodology pipelines (function library, ordered task list, per-function parameter panels).
• Automatic output-to-input routing, with optional manual routing overrides in the Routing tab.
• Execution controls for full runs and partial runs (for example, run to a selected node).
• Analysis tab with method-specific pages/sections (plots, tables, text summaries, and per-section controls).
• Custom Analysis tab for composing a consolidated interpretation workspace from existing analysis sections.
• Report workflow for assembling report content and exporting PDF output.
• Config-driven GUI definitions (gui_configs/) with conditional visibility and dynamic section behavior.
• Data input/validation split for calibration and validation workflows.
• Workflow-control functions for loops, parallel branches, and ensembles.

Function Coverage

• Data Input and Validation:
  • Load Data
  • Validation Data
• Preprocessing:
  • Baseline Correction
  • Smoothing
  • Center and Scale
  • Blank Subtraction
• Calibration and Modeling:
  • First-Order Calibration
  • N-PLS / U-PLS Multiway Regression
• Classification and Novelty Detection:
  • N-class methods (for example Logistic Regression, Random Forest, SVC, KNN, LDA, QDA, PLS-DA)
  • One-class/novelty methods (for example SIMCA, DD-SIMCA, One-Class SVM, Isolation Forest, LOF)
• Exploratory Analysis:
  • PCA Analysis
  • MCR-ALS Analysis
  • PARAFAC Analysis
• Workflow Control:
  • Loop Start/End
  • Parallel Start/Branch/End
  • Ensemble Start/Member/End
• Cross-Validation Configuration:
  • CV Configuration

User GUI (Guided Use of Saved Models)

Chemometric Studio includes a simplified User GUI flow for guided operation of saved models.

• Source entry point: python user.py.
• Packaged app entry point: ChemometricStudioUser / ChemometricStudioUser.exe.

Saved model formats supported by Load Model:

• .mdfd (Full Model): packaged model with calibration/validation-related file paths and data artifacts.
• .mdcd (Model With Calibration): packaged model containing calibration context; user is prompted to provide validation data after loading.
• .mdon (Method Only): packaged method without embedded file paths; user is prompted to provide calibration and validation data.

Guided behavior in User GUI:

• Start screen focuses on loading a model, then running it.
• For .mdcd and .mdon, guided setup steps direct the user to required input functions before execution.
• After a successful run, the interface switches to simplified post-run controls (Analysis, Custom Analysis, Report, Save/Load, Run).
• Report action generates and opens PDF directly when report elements are available.

Supported Runtime

• Python 3.11+
• Tkinter (bundled with standard Python installers on Windows)

Installation

Install Chemometric Studio using the pre-built release packages. This is the easiest and recommended option for most users.

1. Download the latest release for your operating system.
2. Follow the platform-specific steps below.

Windows:

1. Download ChemometricStudio-*-Windows-*-x86_64.zip.
2. Extract the archive to your desired location.
3. Open ChemometricStudio.exe for the full interface, or ChemometricStudioUser.exe for the simplified interface.

macOS:

1. Identify your processor and download the matching package:
   • Apple Silicon (M1, M2, M3, ...): ChemometricStudio-*-macOS.AppleSilicon-*-arm64.tar.gz
   • Intel: ChemometricStudio-*-macOS.Intel-*-x86_64.tar.gz
2. Extract the archive.
3. Open the extracted ChemometricStudio folder and run ChemometricStudio (full interface) or ChemometricStudioUser (simplified interface).
4. On first launch, you may need to allow the app in macOS Security & Privacy settings or run chmod +x on the executable.

Linux:

Release packages are available for both x86_64 and ARM64 architectures. Choose the package that matches your system.

Debian/Ubuntu:

1. Download ChemometricStudio-*-Linux.Debian-based-*-<arch>.deb.
2. Install with:

sudo dpkg -i ChemometricStudio-*-Linux.Debian-based-*-<arch>.deb

3. Launch from your app menu, or run ChemometricStudio (full interface) or ChemometricStudioUser (simplified interface).

Fedora/RHEL/CentOS:

1. Download ChemometricStudio-*-Linux.Fedora-*-<arch>.rpm.
2. Install with:

sudo dnf install ChemometricStudio-*-Linux.Fedora-*-<arch>.rpm

For older systems, use:

sudo yum install ChemometricStudio-*-Linux.Fedora-*-<arch>.rpm

3. Launch from your app menu, or run ChemometricStudio or ChemometricStudioUser.

Arch Linux:

1. Download ChemometricStudio-*-Linux.Arch-based-*-<arch>.pkg.tar.zst.
2. Install with:

sudo pacman -U ChemometricStudio-*-Linux.Arch-based-*-<arch>.pkg.tar.zst

3. Launch from your app menu, or run ChemometricStudio or ChemometricStudioUser.

Installation (Source)

Windows PowerShell:

py -3.11 -m venv .venv
.\.venv\Scripts\Activate.ps1
.\.venv\Scripts\python.exe -m pip install --upgrade pip
.\.venv\Scripts\python.exe -m pip install -r requirements.txt

macOS/Linux:

python3.11 -m venv .venv
source .venv/bin/activate
python -m pip install --upgrade pip
python -m pip install -r requirements.txt

If PowerShell blocks script execution, run once:

Set-ExecutionPolicy -Scope CurrentUser -ExecutionPolicy RemoteSigned -Force

Run

Standard GUI:

python launcher.py

Alternative direct entry point:

python main_gui.py

User GUI:

python user.py

Dependency Set

Pinned in requirements.txt:

• numpy==2.4.2
• scipy==1.17.1
• scikit-learn==1.8.0
• matplotlib==3.10.8
• tensorly==0.9.0
• pylatex==1.4.2
• pandas==3.0.1
• pyMCR==0.5.1
• ddsimca==1.0.3
• prcv==1.2.1
• sv-ttk==2.6.1
• Pillow==12.3.0

User Manual

The end-user manual is available in Manual/. Useful starting pages:

• Manual/index.html
• Manual/getting-started.html
• Manual/workflow-guide.html
• Manual/analysis-reporting.html
• Manual/functions-reference.html

Repository Layout

Top-level areas:

• chemometrics/: core analysis and processing modules.
• app_services/: orchestration and runtime service layers.
• gui_configs/: JSON-driven UI definitions for setup and analysis rendering.
• Manual/: user manual pages and media assets.
• scripts/: development helpers and utility scripts.
• Graphics/, Fonts/, languages/, Settings/: UI assets and configuration.

License

Licensed under Apache-2.0. See LICENSE.

Additional distribution and third-party notices:

• EULA.md
• NOTICE
• Licenses/