API
===

Primary Interface
'''''''''''''''''

hustle_tools.run_pipeline
----------------------------
.. automodule:: hustle_tools.run_pipeline
    :members:
    :undoc-members:
    :show-inheritance:


Stage 0: Data Handling
'''''''''''''''''

Get Files From MAST
----------------------------
.. automodule:: hustle_tools.stage_0.get_files_from_mast
    :members:
    :undoc-members:
    :show-inheritance:

Collect And Move Files
----------------------------
.. automodule:: hustle_tools.stage_0.collect_and_move_files
    :members:
    :undoc-members:
    :show-inheritance:

Locate Target
----------------------------
.. automodule:: hustle_tools.stage_0.locate_target
    :members:
    :undoc-members:
    :show-inheritance:


Stage 1: Reduction
'''''''''''''''''

Temporal Outlier Rejection
----------------------------
.. automodule:: hustle_tools.stage_1.temporal_outlier_rejection
    :members:
    :undoc-members:
    :show-inheritance:

Spatial Outlier Rejection
----------------------------
.. automodule:: hustle_tools.stage_1.spatial_outlier_rejection
    :members:
    :undoc-members:
    :show-inheritance:

Background Subtraction
----------------------------
.. automodule:: hustle_tools.stage_1.bckg_subtract
    :members:
    :undoc-members:
    :show-inheritance:

Displacement Estimation
----------------------------
.. automodule:: hustle_tools.stage_1.compute_displacements
    :members:
    :undoc-members:
    :show-inheritance:


Stage 2: Extraction
'''''''''''''''''

Trace Fitting
----------------------------
.. automodule:: hustle_tools.stage_2.trace_fitting
    :members:
    :undoc-members:
    :show-inheritance:

Time And Relative Detrending In Space (TARDIS)
----------------------------
.. automodule:: hustle_tools.stage_2.tardis
    :members:
    :undoc-members:
    :show-inheritance:

Extraction
----------------------------
.. automodule:: hustle_tools.stage_2.standard_extraction
    :members:
    :undoc-members:
    :show-inheritance:


.. automodule:: hustle_tools.stage_2.optimal_extraction
    :members:
    :undoc-members:
    :show-inheritance:

1D Spectral Alignment
----------------------------
.. automodule:: hustle_tools.stage_2.align_spectra
    :members:
    :undoc-members:
    :show-inheritance:

1D Spectral Cleaning
----------------------------
.. automodule:: hustle_tools.stage_2.clean_spectra
    :members:
    :undoc-members:
    :show-inheritance:


Plotting Backend
'''''''''''''''''

Plotting Background Subtraction
----------------------------
.. automodule:: hustle_tools.plotting.plot_bkgsubtraction
    :members:
    :undoc-members:
    :show-inheritance:

Plotting Displacements
----------------------------
.. automodule:: hustle_tools.plotting.plot_displacements
    :members:
    :undoc-members:
    :show-inheritance:

Plotting Exposures
----------------------------
.. automodule:: hustle_tools.plotting.plot_exposures
    :members:
    :undoc-members:
    :show-inheritance:

Plotting Quicklooks
----------------------------
.. automodule:: hustle_tools.plotting.plot_quicklook
    :members:
    :undoc-members:
    :show-inheritance:

Plotting Spectra
----------------------------
.. automodule:: hustle_tools.plotting.plot_spectra
    :members:
    :undoc-members:
    :show-inheritance:

Plotting Time Series
----------------------------
.. automodule:: hustle_tools.plotting.plot_timeseries
    :members:
    :undoc-members:
    :show-inheritance:

Plotting Traces
----------------------------
.. automodule:: hustle_tools.plotting.plot_traces
    :members:
    :undoc-members:
    :show-inheritance:


Configuration File Backend
'''''''''''''''''

Config Parser
----------------------------
.. automodule:: hustle_tools.read_and_write_config.parser
    :members:
    :undoc-members:
    :show-inheritance:

Config Writer
----------------------------
.. automodule:: hustle_tools.read_and_write_config.writer
    :members:
    :undoc-members:
    :show-inheritance: