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SpecProc: PyQt GUI for Echelle Spectrograph FITS Data Reduction

A complete PyQt-based graphical interface for reducing echelle spectrograph FITS data.

Table of Contents

Features

Complete Reduction Pipeline

8-stage automated spectral reduction:

  1. Overscan Correction - Overscan correction (all images)
  2. Bias Subtraction - Bias subtraction (combined using mean/median)
  3. Flat Fielding & Order Tracing - Flat field correction and order tracing
  4. Background Subtraction - Background removal
  5. Cosmic Ray Correction - Cosmic ray removal (science images only)
  6. 1D Spectrum Extraction - 1D spectrum extraction
  7. Wavelength Calibration - Wavelength calibration (applied to extracted 1D spectra)
  8. De-blazing - Blaze function correction

Interactive GUI

PyQt5-based user interface with:

  • File management for bias, flat, and science frames
  • Real-time progress tracking
  • Processing logs and diagnostics
  • One-click pipeline execution or step-by-step processing

Key Features

  • Configuration-Driven: INI-format configuration files for easy parameter adjustment
  • Generic Spectrograph Support: Configurable for different echelle spectrographs
  • Flexible Output: Control which intermediate results to save
  • Command Line Interface: Alternative to GUI for batch processing

Installation

Choose one of the following installation methods:

Method 1: Using pip

Install SpecProc directly from PyPI.

# Install SpecProc
pip install specproc

# Launch application
specproc

Notes:

  • Requires Python 3.7+
  • Dependencies will be automatically installed from PyPI
  • Installation is permanent; uninstall with pip uninstall specproc

Method 2: Using conda

Conda provides a complete environment with all dependencies. Two installation options:

Option 2.1: Install in existing conda environment

# Activate your conda environment
conda activate your_environment

# Install SpecProc from conda-forge
conda install -c conda-forge specproc

# Launch application
specproc

Option 2.2: Create new conda environment

# Create new conda environment for SpecProc
conda create -n specproc python=3.8
conda activate specproc

# Install SpecProc and all dependencies
conda install -c conda-forge specproc

# Launch application
specproc

Notes:

  • Recommended for users who want an isolated environment
  • All dependencies are managed by conda
  • Python 3.7-3.11 are supported

Method 3: Installing from Source

Run the installation script to install SpecProc and all dependencies from local source.

# Navigate to SpecProc directory
cd /path/to/SpecProc

# Make the script executable (if needed)
chmod +x install.sh

# Run installation script
./install.sh

# Launch application
specproc

Notes:

  • Installation script handles all dependencies automatically
  • Detects available package manager (pip or conda)
  • Installs SpecProc to your system
  • Use this method for automated setup from local source

Quick Start

Working Directory Setup

Important: SpecProc should be run in your working directory, NOT in the source code directory.

Correct Workflow

# 1. Create your working directory (e.g., for an observation project)
mkdir -p /myworkspace
cd /myworkspace

# 2. Create subdirectories for data processing
mkdir -p 20241102_hrs output

# 3. Copy/move FITS data files to 20241102_hrs directory
cp /somewhere/bias_*.fits ./20241102_hrs/
cp /somewhere/flat_*.fits ./20241102_hrs/
cp /somewhere/thar_*.fits ./20241102_hrs/
cp /somewhere/science_*.fits ./20241102_hrs/

# 4. Create user config file (optional)
cp /path/to/SpecProc/default_config.cfg ./specproc.cfg

# 5. Run SpecProc in your working directory
specproc --config ./specproc.cfg

Directory Structure

Working directory (where you process data):

/myworkspace/                  # Your working directory
├── 20241102_hrs/              # Input FITS files
│   ├── bias_*.fits
│   ├── flat_*.fits
│   ├── thar_*.fits      # ThAr lamp spectrum
│   └── science_*.fits   # Science images
├── output/                    # Processing results (auto-created)
│   ├── step0_overscan/         # Step 0: Overscan-corrected images and diagnostic plots
│   ├── step1_bias/             # Step 1: Master bias frame and diagnostic plots
│   ├── step2_flat/             # Step 2: Master flat field, blaze profiles, and diagnostic plots
│   ├── step3_background/       # Step 3: Background model and diagnostic plots
│   ├── step4_cosmic/           # Step 4: Cosmic ray corrected images and diagnostic plots (if enabled)
│   ├── step5_extraction/       # Step 5: Extracted 1D spectra and diagnostic plots
│   ├── step6_wavelength/       # Step 6: Wavelength calibration solution and diagnostic plots
│   ├── step7_deblazing/        # Step 7: De-blazed spectra and diagnostic plots (if saved)
│   └── step8_final_spectra/    # Step 8: Final 1D spectra and diagnostic plots for science frames
├── specproc.cfg              # User config file (optional)
└── ...

Note:

  • ❌ Do NOT run specproc in SpecProc source directory (/path/to/SpecProc)
  • ✅ Run specproc in your working directory
  • ✅ rawdata and output will be created in your working directory

Configuration

Config File Types

Default Configuration

Location: SpecProc/default_config.cfg Purpose: Provides default parameter values Modification: Not recommended to modify directly

User Configuration

Location: specproc.cfg in working directory Purpose: Override default configuration, customize parameters Priority: User config > Default config

Path Configuration

Data Paths

[data]
# Raw FITS data directory path
# Example: If running in /myworkspace/ and rawdata_path=20241102_hrs,
# data will be loaded from /myworkspace/20241102_hrs/
#
# Path behavior:
# - rawdata_path = /data/20241102_hrs  → Absolute path, loads from /data/20241102_hrs/
# - rawdata_path = ./20241102_hrs       → Relative path, loads from working_directory/20241102_hrs/
# - rawdata_path = 20241102_hrs         → Same as above, also relative to working directory
#   (e.g., if working in /myworkspace/, loads from /myworkspace/20241102_hrs/)
#
# Examples (assuming working directory is /myworkspace/):
#   rawdata_path = ./20241102_hrs      → Data from /myworkspace/20241102_hrs/
#   rawdata_path = 20241102_hrs        → Same as above, data from /myworkspace/20241102_hrs/
#   rawdata_path = /data/20241102_hrs  → Data from /data/20241102_hrs/
rawdata_path = ./20241102_hrs

Output Path

[reduce]
# Output directory path for all processing results
# Example: If running in /myworkspace/ and output=output,
# results will be saved in /myworkspace/output/
#
# Path behavior:
# - output_path = /data/output      → Absolute path, saves to /data/output/
# - output_path = ./output          → Relative path, saves to working_directory/output/
# - output_path = output            → Same as above, also relative to working directory
#   (e.g., if working in /myworkspace/, saves to /myworkspace/output/)
#
# Examples (assuming working directory is /myworkspace/):
#   output_path = ./output          → Results to /myworkspace/output/
#   output_path = output            → Same as above, results to /myworkspace/output/
#   output_path = /data/output      → Results to /data/output/
#
# Output directory structure (corresponds to 9 processing steps):
# output/
#   ├── step0_overscan/         # Step 0: Overscan-corrected images (all frames)
#   ├── step1_bias/             # Step 1: Master bias frame
#   ├── step2_flat/             # Step 2: Master flat field with blaze profiles
#   ├── step3_background/       # Step 3: Background model
#   ├── step4_cosmic/           # Step 4: Cosmic ray corrected science images (if enabled)
#   ├── step5_extraction/       # Step 5: Extracted 1D spectra (pixel space)
#   ├── step6_wavelength/       # Step 6: Wavelength calibration solution
#   ├── step7_deblazing/        # Step 7: De-blazed calibrated spectra (if saved)
#   ├── step8_final_spectra/    # Step 8: Final 1D spectra for science frames
#   └── step8_final_spectra/    # Diagnostic plots for each step
output_path = output

#### Path Examples

```bash
# Assume working directory is /myworkspace/
cd /myworkspace/

# Config file (relative path example):
[data]
rawdata_path = ./20241102_hrs
[reduce]
output_path = ./output

# Actual paths used:
# Input:  /myworkspace/20241102_hrs/
# Output: /myworkspace/output/

# Config file (absolute path example):
[data]
rawdata_path = /data/20241102_hrs
[reduce]
output_path = /data/output

# Actual paths used:
# Input:  /data/20241102_hrs/
# Output: /data/output/

Intermediate Results Saving

Control which processing steps to save intermediate results:

[reduce.save_intermediate]
# Whether to save intermediate results for each step
# Set to 'yes' or 'no' for each step independently
# Default is 'yes' for all steps
save_overscan = yes        # Step 0: Overscan correction (saves to output/step0_overscan/)
save_bias = yes             # Step 1: Bias correction (saves master bias to output/step1_bias/)
save_flat = yes              # Step 2: Flat fielding (saves master flat to output/step2_flat/)
save_background = yes        # Step 3: Background subtraction (saves model to output/step3_background/)
save_cosmic = yes           # Step 4: Cosmic ray correction (saves corrected images to output/step4_cosmic/)
save_extraction = yes       # Step 5: Spectrum extraction (saves to output/step5_extraction/)
save_wlcalib = yes          # Step 6: Wavelength calibration (saves solution to output/step6_wavelength/)
save_deblaze = yes          # Step 7: De-blazing (saves to output/step7_deblazing/)

Effect:

  • If a step is set to no, the corresponding output subdirectory will NOT be created
  • Final spectra are always saved to output/step8_final_spectra/ regardless of these settings
  • Diagnostic plots can be saved in corresponding step subdirectories
  • In GUI, there should be corresponding checkboxes to enable/disable saving
  • Default: All steps save intermediate results

Telescope and Calibration Configuration

[telescope]
# Telescope name for calibration lookup
name = xinglong216hrs

# Spectrograph instrument name
instrument = hrs

[telescope.linelist]
# Lamp linelist type
linelist_type = ThAr

# Path to linelist files
linelist_path = calib_data/linelists/

# Specific linelist file to use (optional)
# For Xinglong 2.16m HRS: thar-noao.dat is recommended
linelist_file = thar-noao.dat

# Use pre-identified calibration files (optional)
use_precomputed_calibration = yes
calibration_path = calib_data/telescopes/xinglong216hrs/

# Specific calibration file to use (optional)
# Use latest: wlcalib_20211123011_A.fits
calibration_file = wlcalib_20211123011_A.fits

Processing Pipeline

Complete 8-Stage Pipeline

SpecProc Processing Pipeline

Figure: SpecProc 8-stage spectral reduction pipeline

Alternative (for environments that support mermaid): flowchart TD Start([Start]) --> Stage0 subgraph Stage0 [STAGE 0: Overscan Correction] A0[Read raw FITS files] --> A1[Extract overscan region] A1 --> A2[Calculate median or polynomial fit] A2 --> A3[Subtract overscan bias from image] A3 --> End0[Output: Overscan corrected image] end End0 --> Stage1

subgraph Stage1 [STAGE 1: Bias Subtraction]
    B0[Read overscan corrected images] --> B1[Combine bias frames]
    B1 --> B2[Generate master bias]
    B2 --> B3[Subtract master bias from images]
    B3 --> End1[Output: Bias corrected image]
end
End1 --> Stage2

subgraph Stage2 [STAGE 2: Flat Fielding & Order Tracing]
    C0[Read bias corrected flat frames] --> C1[Combine flat frames]
    C1 --> C2[Generate master flat]
    C2 --> C3[Detect echelle orders]
    C3 --> C4[Fit polynomial traces for each order]
    C4 --> C5[Extract blaze profiles]
    C5 --> End2[Output: Master flat and apertures]
end
End2 --> Stage3

subgraph Stage3 [STAGE 3: Background Subtraction]
    D0[Read bias corrected image] --> D1[Estimate background]
    D1 --> D2[Fit 2D polynomial]
    D2 --> D3a[Median filter]
    D2 --> D3b[Apply 2D polynomial]
    D3a --> End3a[Output: Background subtracted image]
    D3b --> End3b[Continue to stage 4]
end
End3a --> Stage4
End3b --> Stage4

subgraph Stage4 [STAGE 4: Cosmic Ray Correction]
    E0[Read background subtracted image] --> E1[Detect cosmic rays]
    E1 --> E2[Identify cosmic ray pixels]
    E2 --> E3[Interpolate with median filter]
    E3 --> End4[Output: Cosmic ray corrected image]
end
End4 --> Stage5

subgraph Stage5 [STAGE 5: 1D Spectrum Extraction]
    F0[Read cosmic ray corrected image] --> F1[Select extraction method]
    F1 --> F2a[Sum extraction]
    F1 --> F2b[Optimal extraction Horne 1986]
    F2a --> F3[Extract 1D spectrum for each order]
    F2b --> F4[Calculate extraction errors]
    F4 --> End5[Output: SpectraSet pixel space]
end
End5 --> Stage6

subgraph Stage6 [STAGE 6: Wavelength Calibration]
    G0[Step 1: ThAr lamp calibration] --> G1[Extract ThAr 1D spectrum]
    G1 --> G2[Identify emission lines]
    G2 --> G3[Fit 2D wavelength polynomial]
    G3 --> G4[Establish pixel to wavelength mapping]
    G4 --> G5[Step 2: Apply to science spectrum]
    G5 --> G6[Convert pixel coordinates to wavelength units]
    G6 --> End6[Output: Wavelength calibrated 1D spectrum]
end
End6 --> Stage7

subgraph Stage7 [STAGE 7: De-blazing]
    H0[Read wavelength calibrated spectrum] --> H1[Read flat spectrum blaze function]
    H1 --> H2{Order matching}
    H2 --> H3[Match corresponding orders]
    H3 --> H4[Divide by blaze function]
    H4 --> H5[Normalize to unit continuum]
    H5 --> End7[Output: Final calibrated spectrum]
end

End7 --> Final

Final([End]) --> Output[Output files]

style Stage0 fill:#e1f5ff
style Stage1 fill:#fff4e1
style Stage2 fill:#e8f5e9
style Stage3 fill:#fce4ec
style Stage4 fill:#f3e5f5
style Stage5 fill:#fff9c4
style Stage6 fill:#ffccbc
style Stage7 fill:#d1c4e9

flowchart TD
    Start([Start]) --> Stage0
    subgraph Stage0 [STAGE 0: Overscan Correction]
        A0[Read raw FITS files] --> A1[Extract overscan region]
        A1 --> A2[Calculate median or polynomial fit]
        A2 --> A3[Subtract overscan bias from image]
        A3 --> End0[Output: Overscan corrected image]
    end
    End0 --> Stage1

    subgraph Stage1 [STAGE 1: Bias Subtraction]
        B0[Read overscan corrected images] --> B1[Combine bias frames]
        B1 --> B2[Generate master bias]
        B2 --> B3[Subtract master bias from images]
        B3 --> End1[Output: Bias corrected image]
    end
    End1 --> Stage2

    subgraph Stage2 [STAGE 2: Flat Fielding & Order Tracing]
        C0[Read bias corrected flat frames] --> C1[Combine flat frames]
        C1 --> C2[Generate master flat]
        C2 --> C3[Detect echelle orders]
        C3 --> C4[Fit polynomial traces for each order]
        C4 --> C5[Extract blaze profiles]
        C5 --> End2[Output: Master flat and apertures]
    end
    End2 --> Stage3

    subgraph Stage3 [STAGE 3: Background Subtraction]
        D0[Read bias corrected image] --> D1[Estimate background]
        D1 --> D2[Fit 2D polynomial]
        D2 --> D3a[Median filter]
        D2 --> D3b[Apply 2D polynomial]
        D3a --> End3a[Output: Background subtracted image]
        D3b --> End3b[Continue to stage 4]
    end
    End3a --> Stage4
    End3b --> Stage4

    subgraph Stage4 [STAGE 4: Cosmic Ray Correction]
        E0[Read background subtracted image] --> E1[Detect cosmic rays]
        E1 --> E2[Identify cosmic ray pixels]
        E2 --> E3[Interpolate with median filter]
        E3 --> End4[Output: Cosmic ray corrected image]
    end
    End4 --> Stage5

    subgraph Stage5 [STAGE 5: 1D Spectrum Extraction]
        F0[Read cosmic ray corrected image] --> F1[Select extraction method]
        F1 --> F2a[Sum extraction]
        F1 --> F2b[Optimal extraction Horne 1986]
        F2a --> F3[Extract 1D spectrum for each order]
        F2b --> F4[Calculate extraction errors]
        F4 --> End5[Output: SpectraSet pixel space]
    end
    End5 --> Stage6

    subgraph Stage6 [STAGE 6: Wavelength Calibration]
        G0[Step 1: ThAr lamp calibration] --> G1[Extract ThAr 1D spectrum]
        G1 --> G2[Identify emission lines]
        G2 --> G3[Fit 2D wavelength polynomial]
        G3 --> G4[Establish pixel to wavelength mapping]
        G4 --> G5[Step 2: Apply to science spectrum]
        G5 --> G6[Convert pixel coordinates to wavelength units]
        G6 --> End6[Output: Wavelength calibrated 1D spectrum]
    end
    End6 --> Stage7

    subgraph Stage7 [STAGE 7: De-blazing]
        H0[Read wavelength calibrated spectrum] --> H1[Read flat spectrum blaze function]
        H1 --> H2{Order matching}
        H2 --> H3[Match corresponding orders]
        H3 --> H4[Divide by blaze function]
        H4 --> H5[Normalize to unit continuum]
        H5 --> End7[Output: Final calibrated spectrum]
    end
    End7 --> Final

    Final([End]) --> Output[Output files]

    style Stage0 fill:#e1f5ff
    style Stage1 fill:#fff4e1
    style Stage2 fill:#e8f5e9
    style Stage3 fill:#fce4ec
    style Stage4 fill:#f3e5f5
    style Stage5 fill:#fff9c4
    style Stage6 fill:#ffccbc
    style Stage7 fill:#d1c4e9
Loading

Stage Descriptions

STAGE 0: Overscan Correction

  • Input: Raw FITS files (bias, flat, ThAr, science)
  • Processing:
    • Extract overscan region (readout bias area)
    • Calculate median or polynomial fit
    • Subtract overscan bias from image
  • Output: Overscan corrected image
  • Note: Must be first step, applied to all image types

STAGE 1: Bias Subtraction

  • Input: Overscan corrected images
  • Processing:
    • Combine multiple bias frames (mean/median)
    • Generate master bias
    • Subtract master bias from science/flat/ThAr images
  • Output: Bias corrected image
  • Note: Bias is 0s exposure, no cosmic ray correction needed

STAGE 2: Flat Fielding & Order Tracing

  • Input: Bias corrected flat frames
  • Processing:
    • Combine flat frames
    • Generate master flat
    • Detect echelle orders
    • Fit polynomial traces for each order
    • Extract blaze profiles
  • Output: Master flat, apertures, and blaze profiles
  • Note: Provides apertures and blaze profiles for later stages

STAGE 3: Background Subtraction

  • Input: Bias corrected image
  • Processing:
    • Estimate background using 2D polynomial or median filter
    • Subtract background from image
  • Output: Background subtracted image
  • Note: Applied to science images after cosmic ray correction

STAGE 4: Cosmic Ray Correction

  • Input: Background subtracted image (science only)
  • Processing:
    • Detect cosmic rays using sigma-threshold
    • Interpolate with median filter
  • Output: Cosmic ray corrected image
  • Note: Applied to science images only (long exposure)

STAGE 5: 1D Spectrum Extraction

  • Input: Cosmic ray corrected image
  • Processing:
    • Extract 1D spectrum for each echelle order
    • Method: Sum extraction or Optimal extraction (Horne 1986)
    • Calculate extraction errors
  • Output: SpectraSet (pixel space)
  • Note: Depends on apertures from Stage 2

STAGE 6: Wavelength Calibration

  • Input: Extracted 1D spectra (pixel space)
  • Processing:
    • Step 1: Calibrate ThAr lamp spectrum
      • Extract 1D spectrum
      • Identify emission lines
      • Fit 2D wavelength polynomial: λ(x,y) = Σ p_ij·x^i·y^j
    • Step 2: Apply to science spectra
      • Convert pixel coordinates to wavelength units
  • Output: Wavelength calibrated 1D spectra
  • Note: Must be after spectrum extraction

STAGE 7: De-blazing

  • Input: Wavelength calibrated 1D spectra
  • Processing:
    • Read flat spectrum blaze function
    • Match orders
    • Divide by blaze function: F_corrected(λ) = F_observed(λ) / B(λ)
    • Normalize to unit continuum
  • Output: Final calibrated spectra
  • Note: Must be after wavelength calibration

Usage

GUI Mode (Default)

# Launch GUI (default mode)
specproc

# Or explicitly specify GUI mode
specproc --mode gui

# With custom config file
specproc --config /path/to/config.cfg

GUI Workflow:

  1. Select bias files
  2. Select flat files
  3. Select calibration files (ThAr lamp)
  4. Select science files
  5. Click "Run Full Pipeline" or execute stages step-by-step
  6. View progress in real-time
  7. Check results in output directory

CLI Mode (Command Line)

# Run CLI mode
specproc --mode cli

# Or with custom config file
specproc --mode cli --config /path/to/config.cfg

CLI Workflow:

  1. Follow prompts to select files
  2. Select processing stages (0-7, or Enter for all)
  3. Monitor console progress
  4. Check results in output directory

Calibration Data

Directory Structure

calib_data/
├── linelists/              # Lamp emission line catalogs
│   ├── thar-noao.dat      # ThAr lamp lines (Xinglong 2.16m HRS recommended)
│   ├── thar.dat           # Standard ThAr lamp lines
│   ├── FeAr.dat           # FeAr lamp lines
└── ...
└── telescopes/             # Telescope-specific calibration files
    ├── generic/           # Generic configuration template
    └── xinglong216hrs/    # Xinglong 2.16m telescope
        ├── wlcalib_20141103049.fits
        ├── wlcalib_20171202012.fits
        ├── wlcalib_20190905028_A.fits
        └── wlcalib_20211123011_A.fits

Lamp Line Lists

Available linelist files:

  • thar-noao.dat - ThAr lamp lines (Xinglong 2.16m HRS recommended)
  • thar.dat - Standard ThAr lamp lines
  • FeAr.dat - FeAr lamp lines

Supported lamp types:

  • ThAr - Thorium-Argon (most common for echelle spectrographs)
  • FeAr - Iron-Argon
  • Ar - Argon
  • Ne - Neon
  • He - Helium
  • Fe - Iron

Telescope Calibrations

Available calibration files for Xinglong 2.16m HRS:

  • wlcalib_20141103049.fits - 2014-11-03 04:50
  • wlcalib_20171202012.fits - 2017-12-02 01:20
  • wlcalib_20190905028_A.fits - 2019-09-05 02:50 (version A)
  • wlcalib_20211123011_A.fits - 2021-11-23 01:10 (version A) - Latest

Configuration

[telescope]
name = xinglong216hrs
instrument = hrs

[telescope.linelist]
linelist_type = ThAr
linelist_path = calib_data/linelists/
linelist_file = thar-noao.dat
use_precomputed_calibration = yes
calibration_path = calib_data/telescopes/xinglong216hrs/
calibration_file = wlcalib_20211123011_A.fits

Troubleshooting

ImportError: No module named 'PyQt5'

# Install PyQt5
pip install PyQt5

specproc command not found

conda activate specproc
pip install -e .

Configuration file not found

# Copy default config
cp /path/to/SpecProc/default_config.cfg ./specproc.cfg

Large file errors on GitHub

Error: File exceeds GitHub's file size limit of 100.00 MB

Solution: Large FITS files should not be committed. Use .gitignore to exclude them.

Prevent future additions:

  • Add output directories to .gitignore
  • Run SpecProc in separate working directory, not in source directory

Documentation

Project Structure

SpecProc/
├── README.md                    # Main documentation
├── README_CN.md                # Main documentation (Chinese)
├── default_config.cfg           # Default configuration
├── specproc.cfg.example         # Example user configuration
├── install.sh                   # Installation script
├── requirements.txt              # Python dependencies
├── run.py                      # Main entry point
├── setup.py                     # Installation configuration
├── LICENSE                      # License
├── .gitignore                  # Git ignore rules
├── calib_data/                 # Calibration data
│   ├── README.md
│   ├── linelists/
│   └── telescopes/
├── src/                         # Source code
│   ├── gui/                     # GUI modules
│   ├── core/                    # Core processing
│   ├── config/                  # Configuration management
│   ├── utils/                   # Utility functions
│   └── plotting/                # Plotting functions
└── test_*.py                    # Test files

License

See LICENSE file for details.

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

Acknowledgments

  • Inspired by gamse package
  • Built with PyQt5, NumPy, SciPy and Astropy

Support

For issues and questions, please open an issue on GitHub.

About

This is a PyQt-based graphical tool for the reduction of echelle spectrograph raw FITS data.

Topics

astronomy-software

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Readme

License

GPL-3.0 license
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