PISCAL

PISCAL is a Fortran-based photosynthesis calculation tool for analyzing leaf-level gas exchange data. It supports C3, C4, and CAM photosynthetic pathways and provides parameter optimization for photosynthesis models.

Quick Start with Docker

Build the Docker Image

Windows (PowerShell):

.\build-docker.ps1

Linux/Mac (Bash):

./build-docker.sh

Run the Container

# Start container
docker run -d -p 2222:22 --name piscal-server piscal:latest

# SSH into container
ssh -p 2222 piscaladmin@localhost
# Password: piscaladmin

Full Docker Documentation

See README-Docker.md for complete Docker build and deployment documentation, including:

• Container configuration
• Security best practices
• Troubleshooting
• CI/CD integration examples

Project Structure

piscal/
├── Dockerfile                    # Multi-stage Docker build configuration
├── build-docker.ps1              # Build script (Windows/PowerShell)
├── build-docker.sh               # Build script (Linux/Mac/Bash)
├── README-Docker.md              # Comprehensive Docker documentation
│
├── leafres/                      # Leaf response calculation modules
│   ├── testarea/                 # Test area source files
│   └── testrun/                  # Test run configuration and Makefile
│
├── dataassim/                    # Data assimilation and optimization
│   └── math/                     # Mathematical libraries
│       ├── optimization/         # Optimization algorithms
│       ├── othersupmath/         # Supporting mathematical functions
│       ├── algebra/              # Linear algebra routines
│       ├── specialfuncs/         # Special mathematical functions
│       └── nonlinsystems/        # Nonlinear system solvers
│
└── piscal-manager/               # Container management scripts
    ├── piscal_manager.sh         # Job orchestration script
    ├── piscal_launcher.sh        # Execution wrapper
    ├── subdir_year.sh            # Output organization utility
    ├── piscal_launcher.cfg       # Configuration (reference for non-Docker)
    └── README.txt                # Manager scripts documentation

Building from Source (Non-Docker)

PISCAL is written in Fortran and requires:

• gfortran (GNU Fortran compiler)
• make
• xutils-dev

To build manually:

cd leafres/testrun
make clean
make

The compiled executable will be located at leafres/testrun/piscal.

Photosynthetic Pathway Support

PISCAL supports three photosynthetic pathway types:

• C3_photosynthesis_leafweb - C3 pathway (default)
• C4_photosynthesis_leafweb - C4 pathway
• CAM_photosynthesis_leafweb - CAM pathway

Specify the pathway type in the piscal.cfg configuration file.

Input and Output

Input Files

Place leaf gas exchange data files (CSV format) in the input/ directory. See piscal-manager/README.txt for input file format details.

Output Structure

PISCAL generates organized output in the following structure:

output/
├── clninput/                     # Cleaned input data
└── fitresult/                    # Optimization results
    ├── touser/                   # User-facing results
    │   ├── cntrlbestparameters.csv
    │   ├── errormessage
    │   └── warningmessage
    └── nottouser/                # Internal/storage results

Usage with piscal-manager Scripts

The container includes management scripts for job orchestration:

# Start a job
./piscal_manager.sh -d /path/to/workdir -s -p C3_photosynthesis_leafweb

# Check job status
./piscal_manager.sh -d /path/to/workdir

# Cleanup completed job
./piscal_manager.sh -d /path/to/workdir -c

See piscal-manager/README.txt for detailed script usage.

Version History

Images are automatically tagged with:

• piscal:YYYYMMDD-gitsha - Date and commit-based version
• piscal:latest - Latest build
• piscal:dev - Development alias

Security Notes

Default Credentials:

• Username: piscaladmin
• Password: piscaladmin

Important: Always change the default password after deployment:

ssh -p 2222 piscaladmin@localhost
passwd piscaladmin

See README-Docker.md for comprehensive security best practices.

License

[Add license information here]

Contributing

[Add contribution guidelines here]

Support

For Docker-related issues, see the troubleshooting section in README-Docker.md.

For PISCAL algorithm or calculation issues, refer to piscal-manager/README.txt.