pyKOSMOS++

User Guide

  • Installation
    • Requirements
    • Quick Install (pip)
    • Development Install
    • Conda Environment (Recommended)
    • Virtual Environment (Alternative)
    • Dependencies
    • Verify Installation
    • Platform-Specific Notes
      • macOS
      • Linux
      • Windows
    • Troubleshooting
    • Upgrading
    • Uninstalling
    • Next Steps
  • Quick Start Guide
    • Prerequisites
    • Step 1: Organize Your Data
    • Step 2: Run the Pipeline
    • Step 3: Examine Outputs
    • Step 4: Inspect Results
    • Common Adjustments
    • Troubleshooting
    • Next Steps
    • Need Help?
  • CLI Reference
    • Main Command
      • kosmos-reduce
    • Subcommands
      • calibrate
      • wavelength
      • combine
    • Exit Codes
    • Output Products
    • Configuration Files
    • Performance Tips
    • Troubleshooting
    • See Also
  • Python API
    • Overview
    • Installation
    • Basic Usage
      • Simple Pipeline Execution
      • Custom Configuration
    • PipelineRunner Class
      • PipelineRunner
        • PipelineRunner.run()
    • Module-Level API
      • Calibration Module
      • Wavelength Module
      • Extraction Module
      • Quality Module
    • Data Models
      • Raw Frame Classes
      • Calibration Classes
      • Spectroscopic Data
    • Advanced Examples
      • Custom Processing Workflow
      • Batch Processing Multiple Nights
      • Integration with Astropy
    • Error Handling
    • Configuration via Python
    • See Also
  • Configuration Reference
    • Configuration File Format
    • Loading Configuration
    • Default Configuration
    • Parameter Reference
      • Detector Section
      • Calibration Section
      • Wavelength Section
      • Trace Detection Section
      • Extraction Section
      • Cosmic Ray Section
      • Quality Section
      • Binning Section (Optional)
      • AB Subtraction Section (Optional)
    • Example Configurations
      • Faint Galaxy Configuration
      • High-Resolution Wavelength Config
      • Multi-Slit Configuration
    • Configuration Validation
    • See Also
  • Output Products
    • Directory Structure
    • Calibration Products
      • master_bias.fits
      • master_flat.fits
      • bad_pixel_mask.fits
    • Reduced 2D Spectra
      • science_NNN_2d.fits
    • Extracted 1D Spectra
      • science_NNN_traceM.fits
    • Wavelength Solutions
      • wavelength_solution_arcNNN.fits
    • Quality Reports
      • science_NNN_quality.yaml
      • summary_report.txt
    • Diagnostic Plots
      • wavelength_solution.png
      • science_NNN_2d.png
      • science_NNN_traceM_profile.png
      • science_NNN_traceM_1d.png
    • Logs
      • reduction_log.txt
    • Reading Output Products
      • Python Example
    • See Also

Tutorials

  • Interactive Tutorial Notebook
    • Tutorial Notebook
    • Additional Resources
    • Download
    • Requirements

API Reference

  • Calibration Module
    • Combine Submodule
    • Bias Submodule
    • Flat Submodule
    • Cosmic Ray Submodule
  • Wavelength Module
    • Identify Submodule
    • Match Submodule
    • Fit Submodule
    • Apply Submodule
  • Extraction Module
    • Trace Submodule
    • Profile Submodule
    • Sky Submodule
    • Extract Submodule
  • Quality Module
    • Validate Submodule
    • Metrics Submodule
    • Plots Submodule
  • Data Models
    • RawFrame
      • RawFrame.__init__()
      • RawFrame.from_fits()
      • RawFrame.validate_header()
      • RawFrame.detect_saturation()
    • BiasFrame
      • BiasFrame.__init__()
      • BiasFrame.validate_header()
    • FlatFrame
      • FlatFrame.__init__()
      • FlatFrame.validate_header()
    • ArcFrame
      • ArcFrame.__init__()
      • ArcFrame.validate_header()
    • ScienceFrame
      • ScienceFrame.__init__()
      • ScienceFrame.validate_header()
    • MasterBias
      • MasterBias.data
      • MasterBias.n_combined
      • MasterBias.bias_level
      • MasterBias.bias_stdev
      • MasterBias.provenance
      • MasterBias.validate()
      • MasterBias.__init__()
    • MasterFlat
      • MasterFlat.data
      • MasterFlat.n_combined
      • MasterFlat.normalization_region
      • MasterFlat.bad_pixel_fraction
      • MasterFlat.provenance
      • MasterFlat.validate()
      • MasterFlat.__init__()
    • CalibrationSet
      • CalibrationSet.master_bias
      • CalibrationSet.master_flat
      • CalibrationSet.bad_pixel_mask
      • CalibrationSet.apply_to_frame()
      • CalibrationSet.validate()
      • CalibrationSet.__init__()
    • Spectrum2D
      • Spectrum2D.__init__()
      • Spectrum2D.detect_traces()
      • Spectrum2D.subtract_sky()
      • Spectrum2D.extract_spectrum()
    • Trace
      • Trace.__init__()
      • Trace.fit_profile()
      • Trace.apply_wavelength_solution()
      • Trace.extract_optimal()
    • SpatialProfile
      • SpatialProfile.__init__()
      • SpatialProfile.evaluate()
    • WavelengthSolution
      • WavelengthSolution.__init__()
      • WavelengthSolution.wavelength()
      • WavelengthSolution.inverse()
      • WavelengthSolution.validate()
    • Spectrum1D
    • QualityMetrics
      • QualityMetrics.__init__()
      • QualityMetrics.compute()
      • QualityMetrics.generate_report()
    • PipelineConfig
    • ObservationSet
      • ObservationSet.observation_date
      • ObservationSet.target_name
      • ObservationSet.bias_frames
      • ObservationSet.flat_frames
      • ObservationSet.arc_frames
      • ObservationSet.science_frames
      • ObservationSet.calibration_set
      • ObservationSet.from_directory()
      • ObservationSet.group_ab_pairs()
      • ObservationSet.validate_completeness()
      • ObservationSet.__init__()
    • ReducedData
      • ReducedData.__init__()
      • ReducedData.source_frame
      • ReducedData.spectrum_2d
      • ReducedData.spectra_1d
      • ReducedData.diagnostic_plots
      • ReducedData.processing_log
      • ReducedData.reduction_timestamp
      • ReducedData.quality_metrics
      • ReducedData.save_to_disk()
      • ReducedData.generate_summary_report()
    • InteractiveSelection
    • ProcessingLog

Algorithms

  • Trace Detection Algorithm
    • Overview
    • Method: Cross-Correlation with Gaussian Templates
      • Algorithm Steps
      • Implementation
      • Advantages
    • Parameters
      • expected_fwhm
      • min_snr
      • min_separation
    • Trace Position Fitting
    • Performance
    • References
    • See Also
  • Wavelength Fitting Algorithm
    • Overview
    • Method
    • Chebyshev Polynomials
    • BIC Order Selection
    • Iterative Sigma-Clipping
    • Parameters
    • Performance
    • References
    • See Also
  • Optimal Extraction Algorithm
    • Overview
    • Method: Horne 1986 Algorithm
    • Algorithm Steps
    • Advantages Over Aperture Extraction
    • Comparison: Optimal vs Boxcar
    • When to Use Boxcar Instead
    • Spatial Profile Fitting
    • Variance Propagation
    • Parameters
    • Performance
    • References
    • See Also
  • Cosmic Ray Detection Algorithm
    • Overview
    • Method: L.A.Cosmic Algorithm
    • Parameters
    • Implementation
    • Performance
    • Integration with Pipeline
    • Impact on Extraction
    • Limitations
    • References
    • See Also

Additional Resources

  • Troubleshooting
    • Installation Issues
      • ImportError: No module named ‘pykosmospp’
      • ModuleNotFoundError: No module named ‘astropy’
      • Version conflicts with existing packages
    • Data Loading Issues
      • “No FITS files found”
      • “IMAGETYP keyword not found”
    • Calibration Errors
      • “Insufficient calibration frames”
      • “Bias level variation too high”
      • “Flat field saturation”
    • Wavelength Calibration Issues
      • “Wavelength solution failed to converge”
      • “Wavelength RMS too high”
    • Trace Detection Issues
      • “No traces detected”
      • “Too many false trace detections”
    • Extraction Issues
      • “Negative flux values in extracted spectrum”
      • “Low flux conservation”
    • Quality Issues
      • “Low SNR warning”
      • “Poor wavelength calibration grade”
    • Performance Issues
      • “Pipeline runs very slowly”
      • “Out of memory errors”
    • Debugging Tips
      • Enable Verbose Logging
      • Check Intermediate Products
      • Use Python Interactively
      • Examine FITS Headers
      • Validate FITS Files
    • Getting Help
    • See Also
  • Contributing Guide
    • Development Philosophy
    • Getting Started
      • Fork and Clone
      • Development Environment
    • Development Workflow
      • Feature Branch Workflow
    • Code Standards
      • Style Guide
      • Type Hints
      • Imports
    • Testing
      • Test Structure
      • Running Tests
      • Writing Tests
      • Test Data
    • Documentation
      • Building Documentation
      • Documentation Standards
      • API Documentation
    • Pull Request Process
      • Before Submitting
      • PR Template
      • Review Process
    • Issue Guidelines
      • Reporting Bugs
      • Feature Requests
    • Project Structure
    • Code of Conduct
    • License
    • Questions?
    • See Also
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