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Implement
EmissionAbsorptionMismatchedModel (#10)
* rework matched/mismatched models
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,6 @@ | ||
| """ | ||
| emission_absorption_ff_model.py | ||
| EmissionAbsorptionFFModel definition | ||
| emission_absorption_matched_model.py | ||
| EmissionAbsorptionMatchedModel definition | ||
| Copyright(C) 2024 by | ||
| Trey V. Wenger; [email protected] | ||
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@@ -28,11 +28,11 @@ | |
| from caribou_hi import physics | ||
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| class EmissionAbsorptionFFModel(HIModel): | ||
| """Definition of the EmissionAbsorptionFFModel model. SpecData keys must be "emission" and "absorption".""" | ||
| class EmissionAbsorptionMatchedModel(HIModel): | ||
| """Definition of the EmissionAbsorptionMatchedModel model. SpecData keys must be "emission" and "absorption".""" | ||
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| def __init__(self, *args, bg_temp: float = 3.77, **kwargs): | ||
| """Initialize a new EmissionAbsorptionFFModel instance | ||
| """Initialize a new EmissionAbsorptionMatchedModel instance | ||
| Parameters | ||
| ---------- | ||
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@@ -48,7 +48,7 @@ def __init__(self, *args, bg_temp: float = 3.77, **kwargs): | |
| # Define TeX representation of each parameter | ||
| self.var_name_map.update( | ||
| { | ||
| "filling_factor": r"f", | ||
| "filling_factor": r"$f$", | ||
| } | ||
| ) | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,111 @@ | ||
| """ | ||
| emission_absorption_mismatched_model.py | ||
| EmissionAbsorptionMismatchedModel definition | ||
| Copyright(C) 2024 by | ||
| Trey V. Wenger; [email protected] | ||
| GNU General Public License v3 (GNU GPLv3) | ||
| 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 the Free Software Foundation, either version 3 of the License, | ||
| or (at your option) any later version. | ||
| This program is distributed in the hope that it will be useful, | ||
| but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| GNU General Public License for more details. | ||
| You should have received a copy of the GNU General Public License | ||
| along with this program. If not, see <http://www.gnu.org/licenses/>. | ||
| """ | ||
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| import pymc as pm | ||
| import pytensor.tensor as pt | ||
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| from caribou_hi.hi_model import HIModel | ||
| from caribou_hi import physics | ||
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| class EmissionAbsorptionMismatchedModel(HIModel): | ||
| """Definition of the EmissionAbsorptionMismatchedModel model. SpecData keys must be "emission" and "absorption".""" | ||
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| def __init__(self, *args, bg_temp: float = 3.77, **kwargs): | ||
| """Initialize a new EmissionAbsorptionMismatchedModel instance | ||
| Parameters | ||
| ---------- | ||
| bg_temp : float, optional | ||
| Assumed background temperature (K), by default 3.77 | ||
| """ | ||
| # Initialize HIModel | ||
| super().__init__(*args, **kwargs) | ||
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| # Save inputs | ||
| self.bg_temp = bg_temp | ||
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| # Define TeX representation of each parameter | ||
| self.var_name_map.update( | ||
| { | ||
| "filling_factor": r"$f$", | ||
| "absorption_weight": r"$w_\tau$", | ||
| } | ||
| ) | ||
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| def add_priors(self, *args, **kwargs): | ||
| """Add priors and deterministics to the model""" | ||
| super().add_priors(*args, **kwargs) | ||
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| with self.model: | ||
| # Filling factor | ||
| _ = pm.Uniform("filling_factor", lower=0.0, upper=1.0, dims="cloud") | ||
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| # Absorption weight | ||
| _ = pm.Uniform("absorption_weight", lower=0.0, upper=1.0, dims="cloud") | ||
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| def add_likelihood(self): | ||
| """Add likelihood to the model. SpecData key must be "emission".""" | ||
| # Predict optical depth spectrum (shape: spectral, clouds) | ||
| absorption_optical_depth = self.model["absorption_weight"] * physics.calc_optical_depth( | ||
| self.data["absorption"].spectral, | ||
| self.model["velocity"], | ||
| 10.0 ** self.model["log10_NHI"], | ||
| self.model["tspin"], | ||
| self.model["fwhm"], | ||
| ) | ||
| emission_optical_depth = physics.calc_optical_depth( | ||
| self.data["emission"].spectral, | ||
| self.model["velocity"], | ||
| 10.0 ** self.model["log10_NHI"], | ||
| self.model["tspin"], | ||
| self.model["fwhm"], | ||
| ) | ||
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| # Sum over clouds | ||
| predicted_absorption = 1.0 - pt.exp(-absorption_optical_depth.sum(axis=1)) | ||
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| # Evaluate radiative transfer | ||
| predicted_emission = physics.radiative_transfer( | ||
| emission_optical_depth, self.model["tspin"], self.model["filling_factor"], self.bg_temp | ||
| ) | ||
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| # Add baseline models | ||
| baseline_models = self.predict_baseline() | ||
| predicted_absorption = predicted_absorption + baseline_models["absorption"] | ||
| predicted_emission = predicted_emission + baseline_models["emission"] | ||
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| with self.model: | ||
| # Evaluate likelihood | ||
| _ = pm.Normal( | ||
| "absorption", | ||
| mu=predicted_absorption, | ||
| sigma=self.data["absorption"].noise, | ||
| observed=self.data["absorption"].brightness, | ||
| ) | ||
| _ = pm.Normal( | ||
| "emission", | ||
| mu=predicted_emission, | ||
| sigma=self.data["emission"].noise, | ||
| observed=self.data["emission"].brightness, | ||
| ) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,9 @@ | ||
| {%- if show_headings %} | ||
| {{- [basename] | join(' ') | e | heading }} | ||
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| {% endif -%} | ||
| .. automodule:: {{ qualname }} | ||
| {%- for option in automodule_options %} | ||
| :{{ option }}: | ||
| {%- endfor %} | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,57 @@ | ||
| {%- macro automodule(modname, options) -%} | ||
| .. automodule:: {{ modname }} | ||
| {%- for option in options %} | ||
| :{{ option }}: | ||
| {%- endfor %} | ||
| {%- endmacro %} | ||
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| {%- macro toctree(docnames) -%} | ||
| .. toctree:: | ||
| :maxdepth: {{ maxdepth }} | ||
| {% for docname in docnames %} | ||
| {{ docname }} | ||
| {%- endfor %} | ||
| {%- endmacro %} | ||
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| {%- if is_namespace %} | ||
| {{- [pkgname] | join(" ") | e | heading }} | ||
| {% else %} | ||
| {{- [pkgname] | join(" ") | e | heading }} | ||
| {% endif %} | ||
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| {%- if is_namespace %} | ||
| .. py:module:: {{ pkgname }} | ||
| {% endif %} | ||
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| {%- if modulefirst and not is_namespace %} | ||
| {{ automodule(pkgname, automodule_options) }} | ||
| {% endif %} | ||
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| {%- if subpackages %} | ||
| Subpackages | ||
| ----------- | ||
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| {{ toctree(subpackages) }} | ||
| {% endif %} | ||
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| {%- if submodules %} | ||
| Submodules | ||
| ---------- | ||
| {% if separatemodules %} | ||
| {{ toctree(submodules) }} | ||
| {% else %} | ||
| {%- for submodule in submodules %} | ||
| {% if show_headings %} | ||
| {{- [submodule] | join(" ") | e | heading(2) }} | ||
| {% endif %} | ||
| {{ automodule(submodule, automodule_options) }} | ||
| {% endfor %} | ||
| {%- endif %} | ||
| {%- endif %} | ||
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| {%- if not modulefirst and not is_namespace %} | ||
| Module contents | ||
| --------------- | ||
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| {{ automodule(pkgname, automodule_options) }} | ||
| {% endif %} |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,8 @@ | ||
| {{ header | heading }} | ||
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| .. toctree:: | ||
| :maxdepth: {{ maxdepth }} | ||
| {% for docname in docnames %} | ||
| {{ docname }} | ||
| {%- endfor %} | ||
|
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