slicersim 1.0.0__tar.gz

slicersim-1.0.0/LICENSE

@@ -0,0 +1,201 @@
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slicersim-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: slicersim
+Version: 1.0.0
+Summary: Simulating Transient in the sky and how to observe them
+Author-email: Mickael Rigault <m.rigault@ipnl.in2p3.fr>
+License-Expression: Apache-2.0
+Project-URL: Homepage, https://github.com/MickaelRigault/slicersim
+Keywords: astronomy,astrophysics
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Astronomy
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: astropy
+Requires-Dist: extinction
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: requests
+Requires-Dist: scipy
+Requires-Dist: sep
+Requires-Dist: shapely
+Requires-Dist: sncosmo
+Provides-Extra: docs
+Requires-Dist: matplotlib; extra == "docs"
+Requires-Dist: myst-nb; extra == "docs"
+Requires-Dist: nbsphinx; extra == "docs"
+Requires-Dist: numpydoc; extra == "docs"
+Requires-Dist: pandas-sphinx; extra == "docs"
+Requires-Dist: sphinx-book-theme; extra == "docs"
+Requires-Dist: sphinx_copybutton; extra == "docs"
+Requires-Dist: sphinx-design; extra == "docs"
+Provides-Extra: tests
+Requires-Dist: pytest; extra == "tests"
+Requires-Dist: pytest-doctestplus; extra == "tests"
+Requires-Dist: pytest-cov; extra == "tests"
+Dynamic: license-file
+
+[![codecov](https://codecov.io/github/MickaelRigault/slicersim/graph/badge.svg?token=A78ZDQQ9N3)](https://codecov.io/github/MickaelRigault/slicersim)
+[![Run unit tests](https://github.com/MickaelRigault/slicersim/actions/workflows/ci.yml/badge.svg)](https://github.com/MickaelRigault/slicersim/actions/workflows/ci.yml)
+
+# slicersim
+Simulation of Slicer observations
+
+
+
+***
+# Installation
+```bash
+git clone https://github.com/MickaelRigault/slicersim.git
+cd slicersim
+pip install .
+```
+or
+```bash
+pip install git+https://github.com/MickaelRigault/slicersim.git
+```
+***
+# Top level ETC
+
+```python
+>>> import slicersim
+>>> import numpy as np
+
+```
+
+## Any spectra
+
+Compute the exposure time needed any input spectrum:
+
+```python
+>>> lbda_ref = np.linspace(3000, 20_000, 500) # larger than lazuli bandpass
+>>> flux_ref = np.ones(lbda_ref.shape) # flat spectrum
+>>> exptime, lazulitarget = slicersim.lazuli_etc(lbda_ref, flux_ref, snr=20, mag=21, band="bessellb")
+>>> print(exptime)
+237.72
+
+```
+
+## Supernova
+
+Compute the exposure time needed to observe a Supernovae:
+
+```python
+>>> exptime, snia_target = slicersim.lazuli_sn_etc(snr=20, model="salt", redshift=1.2, x1=1.5, c=0.2, phase=-2.2)
+>>> print(exptime)
+5795.84
+
+```
+
+***
+# Quick look
+
+```python
+import slicersim
+# load a SN Ia (see also: `slicersim.LazuliTarget(lbda, flux)`)
+snia = slicersim.LazuliSN(redshift=0.8, c=0.2, x1=-1.2, phase=1.5)
+
+# update configuration to reach a signal-to-noise of 20
+_ = snia.setup_to_snr(20)
+
+# grab the expected observed spectrum
+lbda, flux_1, variance_1 = snia.get_spectrum(unit="adu")
+
+# change the target property
+# warning: without updating the setting, this new target won't have a snr=20
+snia.set_properties(redshift=1.2)
+lbda, flux_2, variance_2 = snia.get_spectrum(unit="adu")
+```
+
+and show your simulated spectra
+```python
+import matplotlib.pyplot as plt
+import numpy as np
+fig, ax = plt.subplots(figsize=[7,3])
+
+ax.plot(lbda, flux_1)
+ax.fill_between(lbda, 
+                flux_1-np.sqrt(variance_1),
+                flux_1+np.sqrt(variance_1), alpha=0.3,
+               label="z=0.8")
+
+ax.plot(lbda, flux_2)
+ax.fill_between(lbda, 
+                flux_2-np.sqrt(variance_2),
+                flux_2+np.sqrt(variance_2), alpha=0.3,
+               label="z=1.2")
+ax.legend(frameon=False, fontsize="small")
+ax.set(xlabel=r"wavelength [$\AA$]", ylabel="flux [ADU]")
+```
+![readme example](docs/gallery/spectra_examples.png)
+  
+***
+# Tutorials
+
+## Beginner
+- [ETC and simuated spectra: top level function](docs/notebooks/beginner_ETC_lazulitarget.ipynb)
+  - Exposure time calculator for any target or a supernovae
+  - get the simulated spectrum and variance
+- [LazuliTarget (Any target, Type Ia Supernovae, CalSpec)](docs/notebooks/beginner_LazuliTargets.ipynb):
+  - Specify the desired signal to noise
+  - get exposure time, and read-mode
+  - get simulated spectra
+- [Check the origin of the variance sources](docs/notebooks/beginner_variancesource.ipynb)
+  - origin of variance (read-out noise, target poisson noise, dark-current etc)
+  - switch off any contribution and see resulting variance
+  - scan all variance contributions, get the resulting dataframe and plot the result.
+- [Change properties of the target](beginner_change_properties.ipynb):
+  - change any supernovae properties
+  - change the magnitude of a loaded target
+
+## Advanced
+- [Change the detector read-out mode or spectrograph spatial sampling](advanced_change_detector_and_spectrograph.ipynb)
+  - change the detector mode: max-group, n-frames per group
+  - force the read-our mode (and see which SNR you eventually get)
+  - change the spectrograph sampling (fine and medium grid)
+- [Access the detector QE, throughtput, effective spectral resolution...](advanced_access_qe_spectral_resolution_etc.ipynb) 
+- Access any property of any simulation element, and change them !
+
+  
+## Experts
+- Noise Equivalent area
+- Build you own “scene” 
+- Build your own configuration
+***
+# Lower-level: Simulator & config.
+
+Example: Study origin of variance
+
+You can load a slicersim object at a lower level than an lazuli object: a Simulator. This object is at the core of slicersim and combines information of all sources needed to simulate our observations: a scene (what is observed), a mirror, a spectrograph and a detector.
+
+The Simulator combine these to be able to generate a datacube with realistic noise, and extract a realistic spectrum from it.
+
+Once your simulator is loaded, you have several method to check the variance origin. 
+- `estimate_variance_contribution`: that probe the variance origin for a given wavelength rate
+- `estimate_variance_contribution_spectra`: similar but for whole spectrum
+- `show_variance_sources`: plotting function associated to `estimate_variance_contribution_spectra`
+
+```python
+import slicersim
+# load the correct simulator
+config = slicersim.iotools.get_config(instrument='lazuli.toml')
+sim = slicersim.Simulation.from_config(config)
+
+# Set the target you want
+sim.update(target__redshift=1., target__x1=0, target__c=0)
+
+# look for the config needed to get an average SNR of 20 in [4000, 6800] rest-frame
+new_config, snr, integration_time = sim.fetch_snr(20, lbda_range=[4000, 6800], frame='rest')
+sim.update(**new_config) # let's set it
+
+# get the expected spectrum (in ADU)
+lbda, flux, variance = sim.get_spectrum()
+
+# Show details
+fig = sim.show_variance_sources(flux_calibrated=False)
+```
+![readme example](docs/gallery/spectra_variance.png)
+
+***
+# PSF & Noise equivalent area
+
+by default, the code assumes gaussian PSF both for spatial (at the slicer/mla) and cross-dispersion (at pixels) level.
+
+`slicersim.profiles` contains additional PSF model (from [astropy.modeling](https://docs.astropy.org/en/latest/modeling/predef_models2D.html) 
+that can be used to build 2D model or estimate the PSF noise equivalent area (nea).
+
+*(more to come..., see: `slicersim.profiles.get_2dpsf_nea()`)*
+
+
+
+
+***
+# Credits
+Developped by M. Rigault ; _adapted from the original MLAPerf v:0.18.0 developed by Y. Copin and M. Rigault_

slicersim-1.0.0/README.md

@@ -0,0 +1,177 @@
+[![codecov](https://codecov.io/github/MickaelRigault/slicersim/graph/badge.svg?token=A78ZDQQ9N3)](https://codecov.io/github/MickaelRigault/slicersim)
+[![Run unit tests](https://github.com/MickaelRigault/slicersim/actions/workflows/ci.yml/badge.svg)](https://github.com/MickaelRigault/slicersim/actions/workflows/ci.yml)
+
+# slicersim
+Simulation of Slicer observations
+
+
+
+***
+# Installation
+```bash
+git clone https://github.com/MickaelRigault/slicersim.git
+cd slicersim
+pip install .
+```
+or
+```bash
+pip install git+https://github.com/MickaelRigault/slicersim.git
+```
+***
+# Top level ETC
+
+```python
+>>> import slicersim
+>>> import numpy as np
+
+```
+
+## Any spectra
+
+Compute the exposure time needed any input spectrum:
+
+```python
+>>> lbda_ref = np.linspace(3000, 20_000, 500) # larger than lazuli bandpass
+>>> flux_ref = np.ones(lbda_ref.shape) # flat spectrum
+>>> exptime, lazulitarget = slicersim.lazuli_etc(lbda_ref, flux_ref, snr=20, mag=21, band="bessellb")
+>>> print(exptime)
+237.72
+
+```
+
+## Supernova
+
+Compute the exposure time needed to observe a Supernovae:
+
+```python
+>>> exptime, snia_target = slicersim.lazuli_sn_etc(snr=20, model="salt", redshift=1.2, x1=1.5, c=0.2, phase=-2.2)
+>>> print(exptime)
+5795.84
+
+```
+
+***
+# Quick look
+
+```python
+import slicersim
+# load a SN Ia (see also: `slicersim.LazuliTarget(lbda, flux)`)
+snia = slicersim.LazuliSN(redshift=0.8, c=0.2, x1=-1.2, phase=1.5)
+
+# update configuration to reach a signal-to-noise of 20
+_ = snia.setup_to_snr(20)
+
+# grab the expected observed spectrum
+lbda, flux_1, variance_1 = snia.get_spectrum(unit="adu")
+
+# change the target property
+# warning: without updating the setting, this new target won't have a snr=20
+snia.set_properties(redshift=1.2)
+lbda, flux_2, variance_2 = snia.get_spectrum(unit="adu")
+```
+
+and show your simulated spectra
+```python
+import matplotlib.pyplot as plt
+import numpy as np
+fig, ax = plt.subplots(figsize=[7,3])
+
+ax.plot(lbda, flux_1)
+ax.fill_between(lbda, 
+                flux_1-np.sqrt(variance_1),
+                flux_1+np.sqrt(variance_1), alpha=0.3,
+               label="z=0.8")
+
+ax.plot(lbda, flux_2)
+ax.fill_between(lbda, 
+                flux_2-np.sqrt(variance_2),
+                flux_2+np.sqrt(variance_2), alpha=0.3,
+               label="z=1.2")
+ax.legend(frameon=False, fontsize="small")
+ax.set(xlabel=r"wavelength [$\AA$]", ylabel="flux [ADU]")
+```
+![readme example](docs/gallery/spectra_examples.png)
+  
+***
+# Tutorials
+
+## Beginner
+- [ETC and simuated spectra: top level function](docs/notebooks/beginner_ETC_lazulitarget.ipynb)
+  - Exposure time calculator for any target or a supernovae
+  - get the simulated spectrum and variance
+- [LazuliTarget (Any target, Type Ia Supernovae, CalSpec)](docs/notebooks/beginner_LazuliTargets.ipynb):
+  - Specify the desired signal to noise
+  - get exposure time, and read-mode
+  - get simulated spectra
+- [Check the origin of the variance sources](docs/notebooks/beginner_variancesource.ipynb)
+  - origin of variance (read-out noise, target poisson noise, dark-current etc)
+  - switch off any contribution and see resulting variance
+  - scan all variance contributions, get the resulting dataframe and plot the result.
+- [Change properties of the target](beginner_change_properties.ipynb):
+  - change any supernovae properties
+  - change the magnitude of a loaded target
+
+## Advanced
+- [Change the detector read-out mode or spectrograph spatial sampling](advanced_change_detector_and_spectrograph.ipynb)
+  - change the detector mode: max-group, n-frames per group
+  - force the read-our mode (and see which SNR you eventually get)
+  - change the spectrograph sampling (fine and medium grid)
+- [Access the detector QE, throughtput, effective spectral resolution...](advanced_access_qe_spectral_resolution_etc.ipynb) 
+- Access any property of any simulation element, and change them !
+
+  
+## Experts
+- Noise Equivalent area
+- Build you own “scene” 
+- Build your own configuration
+***
+# Lower-level: Simulator & config.
+
+Example: Study origin of variance
+
+You can load a slicersim object at a lower level than an lazuli object: a Simulator. This object is at the core of slicersim and combines information of all sources needed to simulate our observations: a scene (what is observed), a mirror, a spectrograph and a detector.
+
+The Simulator combine these to be able to generate a datacube with realistic noise, and extract a realistic spectrum from it.
+
+Once your simulator is loaded, you have several method to check the variance origin. 
+- `estimate_variance_contribution`: that probe the variance origin for a given wavelength rate
+- `estimate_variance_contribution_spectra`: similar but for whole spectrum
+- `show_variance_sources`: plotting function associated to `estimate_variance_contribution_spectra`
+
+```python
+import slicersim
+# load the correct simulator
+config = slicersim.iotools.get_config(instrument='lazuli.toml')
+sim = slicersim.Simulation.from_config(config)
+
+# Set the target you want
+sim.update(target__redshift=1., target__x1=0, target__c=0)
+
+# look for the config needed to get an average SNR of 20 in [4000, 6800] rest-frame
+new_config, snr, integration_time = sim.fetch_snr(20, lbda_range=[4000, 6800], frame='rest')
+sim.update(**new_config) # let's set it
+
+# get the expected spectrum (in ADU)
+lbda, flux, variance = sim.get_spectrum()
+
+# Show details
+fig = sim.show_variance_sources(flux_calibrated=False)
+```
+![readme example](docs/gallery/spectra_variance.png)
+
+***
+# PSF & Noise equivalent area
+
+by default, the code assumes gaussian PSF both for spatial (at the slicer/mla) and cross-dispersion (at pixels) level.
+
+`slicersim.profiles` contains additional PSF model (from [astropy.modeling](https://docs.astropy.org/en/latest/modeling/predef_models2D.html) 
+that can be used to build 2D model or estimate the PSF noise equivalent area (nea).
+
+*(more to come..., see: `slicersim.profiles.get_2dpsf_nea()`)*
+
+
+
+
+***
+# Credits
+Developped by M. Rigault ; _adapted from the original MLAPerf v:0.18.0 developed by Y. Copin and M. Rigault_