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| @@ -1,3 +1,6 @@ | ||
| # Skip __init__.py setting | ||
| __init__.py | ||
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| # Skip vscode setting | ||
| .vscode | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,6 +1,6 @@ | ||
| """ | ||
| This file is part of the METIS Pipeline. | ||
| Copyright (C) 2024 European Southern Observatory | ||
| Copyright (C) 2025 European Southern Observatory | ||
| This program is free software; you can redistribute it and/or modify | ||
| it under the terms of the GNU General Public License as published by | ||
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@@ -18,74 +18,115 @@ | |
| """ | ||
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| import re | ||
| from typing import Dict | ||
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| import cpl | ||
| from typing import Dict | ||
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| from pymetis.base import MetisRecipe, MetisRecipeImpl | ||
| from pymetis.base.product import PipelineProduct | ||
| from pymetis.inputs import SinglePipelineInput | ||
| from pymetis.inputs.mixins import PersistenceInputSetMixin | ||
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| from pymetis.inputs import SinglePipelineInput, PipelineInputSet | ||
| from pymetis.inputs.common import FluxTableInput, LsfKernelInput, AtmProfileInput | ||
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| class ProductTelluric(PipelineProduct): | ||
| level = cpl.ui.Frame.FrameLevel.FINAL | ||
| frame_type = cpl.ui.Frame.FrameType.IMAGE | ||
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| # The aim of this recipe is twofold, | ||
| # (a) to determine the transmission function for telluric absorption correction | ||
| # (b) determination of the response function for the flux calibration | ||
| # | ||
| # Note that there will be most probably a redesign / split into more recipes to follow the approach | ||
| # implemented already in other ESO pipelines | ||
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| class MetisIfuTelluricImpl(MetisRecipeImpl): | ||
| detector = '2RG' | ||
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| class InputSet(PersistenceInputSetMixin): | ||
| class CombinedInput(SinglePipelineInput): | ||
| _title = "combined science and standard frames" | ||
| """Implementation class for metis_ifu_telluric""" | ||
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| # Defining detector name | ||
| @property | ||
| def detector_name(self) -> str | None: | ||
| return "IFU" | ||
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| # ++++++++++++++ Defining input +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ | ||
| # Define molecfit main input class as one 1d spectrum, either Science or Standard spectrum | ||
| class InputSet(PipelineInputSet): | ||
| """Inputs for metis_ifu_telluric""" | ||
| class Reduced1DInput(SinglePipelineInput): | ||
| _tags = re.compile(rf"IFU_(?P<target>SCI|STD)_1D") | ||
| _group = cpl.ui.Frame.FrameGroup.CALIB | ||
| _tags = re.compile(r"IFU_(?P<target>SCI|STD)_COMBINED") | ||
| _title = "uncorrected mf input spectrum" | ||
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| class LsfKernelInput(SinglePipelineInput): | ||
| _title = "LSF kernel" | ||
| _group = cpl.ui.Frame.FrameGroup.CALIB | ||
| _tags = re.compile(r"LSF_KERNEL") | ||
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| class AtmProfileInput(SinglePipelineInput): | ||
| _title = "atmospheric profile" | ||
| _group = cpl.ui.Frame.FrameGroup.CALIB | ||
| _tags = re.compile(r"ATM_PROFILE") | ||
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| class FluxStdCatalogInput(SinglePipelineInput): | ||
| _title = "flux std catalog" | ||
| class CombinedInput(SinglePipelineInput): | ||
| _tags = re.compile(rf"IFU_(?P<target>SCI|STD)_COMBINED") | ||
| _group = cpl.ui.Frame.FrameGroup.CALIB | ||
| _tags = re.compile(r"FLUXSTD_CATALOG") | ||
| _title = "spectral cube of science object" | ||
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| def __init__(self, frameset: cpl.ui.FrameSet): | ||
| super().__init__(frameset) | ||
| self.combined = self.CombinedInput(frameset) | ||
| self.lsf_kernel = self.LsfKernelInput(frameset) | ||
| self.atmospheric_profile = self.AtmProfileInput(frameset) | ||
| self.fluxstd_catalog = self.FluxStdCatalogInput(frameset) | ||
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| self.inputs |= {self.combined, self.lsf_kernel, self.atmospheric_profile, self.fluxstd_catalog} | ||
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| class ProductSciReduced1D(ProductTelluric): | ||
| tag = rf"IFU_SCI_REDUCED_1D" | ||
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| class ProductIfuTelluric(ProductTelluric): | ||
| tag = "IFU_TELLURIC" | ||
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| class ProductFluxcalTab(ProductTelluric): | ||
| tag = "FLUXCAL_TAB" | ||
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| self.fluxstd_catalog = FluxTableInput(frameset) | ||
| self.atm_profile = AtmProfileInput(frameset) | ||
| self.lsf_kernel = LsfKernelInput(frameset) | ||
| self.inputs |= {self.combined, self.fluxstd_catalog, self.atm_profile, self.lsf_kernel} | ||
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| # ++++++++++++++ Defining ouput +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ | ||
| # Recipe is foreseen to do both, create transmission and response functions | ||
| # We therefore need to define transmission spectrum and response curve class | ||
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| # Tranmission spectrum | ||
| class ProductTelluricTransmission(PipelineProduct): | ||
| """ | ||
| Final product: Transmission function for the telluric correction | ||
| """ | ||
| level = cpl.ui.Frame.FrameLevel.FINAL | ||
| tag = r"IFU_TELLURIC" | ||
| frame_type = cpl.ui.Frame.FrameType.IMAGE | ||
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| # Response curve | ||
| class ProductResponseFunction(PipelineProduct): | ||
| """ | ||
| Final product: response curve for the flux calibration | ||
| """ | ||
| level = cpl.ui.Frame.FrameLevel.FINAL | ||
| tag = r"IFU_TELLURIC" | ||
| frame_type = cpl.ui.Frame.FrameType.IMAGE | ||
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| # TODO: Define input type for the paramfile in common.py | ||
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| # ++++++++++++++ Defining functions +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ | ||
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| # Invoke molecfit | ||
| def mf_model(self): | ||
| """ | ||
| Purpose: invoke molecfit to achieve a best-fit in the fitting regions | ||
| """ | ||
| pass # do nothing in the meanwhile | ||
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| # Invoke Calctrans | ||
| def mf_calctrans(self): | ||
| """ | ||
| Purpose: invoke calctrans to calculate transmission over the whole wavelength range | ||
| """ | ||
| pass # do nothing in the meanwhile | ||
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| # Recipe is in the moment also foreseen to create the response curve for the flux calibration | ||
| # Response determination | ||
| def determine_response(self): | ||
| """ | ||
| Purpose: determine response function, i.e. compare observed standard star spectrum with the model in REF_STD_CAT | ||
| """ | ||
| pass # do nothing in the meanwhile | ||
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| # Function to process everything? | ||
| def process_images(self) -> Dict[str, PipelineProduct]: | ||
| # self.correct_telluric() | ||
| # self.apply_fluxcal() | ||
| self.mf_model() | ||
| self.mf_calctrans() | ||
| self.determine_response() | ||
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| header = cpl.core.PropertyList() | ||
| image = cpl.core.Image.load(self.inputset.combined.frame.file) | ||
| header = self._create_dummy_header() | ||
| image = self._create_dummy_image() | ||
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| self.products = { | ||
| str(product.category): product(self, header, image) | ||
| for product in [self.ProductSciReduced1D, self.ProductIfuTelluric, self.ProductFluxcalTab] | ||
| product.category: product(self, header, image) | ||
| for product in [self.ProductTelluricTransmission, self.ProductResponseFunction] | ||
| } | ||
| return self.products | ||
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@@ -97,13 +138,20 @@ class MetisIfuTelluric(MetisRecipe): | |
| _email = "[email protected]" | ||
| _copyright = "GPL-3.0-or-later" | ||
| _synopsis = "Derive telluric absorption correction and optionally flux calibration" | ||
| _description = ( | ||
| "Currently just a skeleton prototype." | ||
| ) | ||
| _description = """ | ||
| Recipe to derive the atmospheric transmission and the response function. | ||
| implementation_class = MetisIfuTelluricImpl | ||
| Inputs | ||
| IFU_SCI|STD_1D: 1d spectrum either from science target or standard star | ||
| Outputs | ||
| IFU_TELLURIC: Tranmission of the Earth#s atmosphere | ||
| FLUXCAL_TAB: Response function | ||
| Algorithm | ||
| *TBwritten* | ||
| """ | ||
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| # Dummy parameter to circumvent a potential bug in `pyesorex` | ||
| parameters = cpl.ui.ParameterList([ | ||
| cpl.ui.ParameterValue( | ||
| name=f"{_name}.dummy", | ||
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@@ -112,3 +160,5 @@ class MetisIfuTelluric(MetisRecipe): | |
| default="dummy", | ||
| ) | ||
| ]) | ||
| implementation_class = MetisIfuTelluricImpl | ||
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