Mercurial > repos > astroteam > cta_astro_tool
changeset 0:2f3e314c3dfa draft default tip
planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 4543470805fc78f6cf2604b9d55beb6f06359995
| author | astroteam |
|---|---|
| date | Fri, 19 Apr 2024 10:06:21 +0000 |
| parents | |
| children | |
| files | cta_astro_tool.xml model_cube_file.py pre-defined_model.py |
| diffstat | 3 files changed, 1189 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cta_astro_tool.xml Fri Apr 19 10:06:21 2024 +0000 @@ -0,0 +1,183 @@ +<tool id="cta_astro_tool" name="CTA" version="0.0.1+galaxy0" profile="23.0"> + <requirements> + <requirement type="package" version="6.0">unzip</requirement> + <requirement type="package" version="2.31.0">requests</requirement> + <requirement type="package" version="1.2">gammapy</requirement> + <requirement type="package" version="5.3">astropy</requirement> + <requirement type="package" version="3.8.4">matplotlib</requirement> + <requirement type="package" version="1.11.4">scipy</requirement> + <requirement type="package" version="1.2.15">oda-api</requirement> + <requirement type="package" version="8.22.2">ipython</requirement> + <!--Requirements string 'nb2workflow[cwl,service,rdf,mmoda]>=1.3.30 +' can't be converted automatically. Please add the galaxy/conda requirement manually or modify the requirements file!--> + <requirement type="package" version="7.16.3">nbconvert</requirement> + </requirements> + <command detect_errors="exit_code">ipython '$__tool_directory__/${_data_product._selector}.py'</command> + <configfiles> + <inputs name="inputs" filename="inputs.json" data_style="paths" /> + </configfiles> + <inputs> + <conditional name="_data_product"> + <param name="_selector" type="select" label="Data Product"> + <option value="pre-defined_model" selected="true">pre-defined_model</option> + <option value="model_cube_file" selected="false">model_cube_file</option> + </param> + <when value="pre-defined_model"> + <param name="RA" type="float" value="166.113809" label="RA (unit: deg)" /> + <param name="DEC" type="float" value="38.208833" label="DEC (unit: deg)" /> + <param name="OffAxis_angle" type="float" value="0.78" label="OffAxis_angle (unit: deg)" /> + <param name="Texp" type="float" value="1.0" label="Texp (unit: hour)" /> + <param name="z" type="float" value="0.03" label="z" /> + <param name="F0" type="float" value="1e-11" label="F0" /> + <param name="E0" type="float" value="1.0" label="E0 (unit: TeV)" /> + <param name="Gamma" type="float" value="2.0" label="Gamma" /> + <param name="Radius_spectal_extraction" type="float" value="0.2" label="Radius_spectal_extraction" /> + <param name="Radius_sky_image" type="float" value="2.5" label="Radius_sky_image (unit: deg)" /> + <param name="Site" type="select" label="Site"> + <option value="North" selected="true">North</option> + <option value="South">South</option> + </param> + <param name="Telescope_LST" type="boolean" checked="true" label="Telescope_LST" /> + <param name="Telescope_MST" type="boolean" checked="true" label="Telescope_MST" /> + <param name="Telescope_SST" type="boolean" label="Telescope_SST" /> + </when> + <when value="model_cube_file"> + <param name="data_cube" type="data" label="data_cube" format="data" /> + <param name="F0" type="float" value="1e-11" label="F0" /> + <param name="E0" type="float" value="1.0" label="E0 (unit: TeV)" /> + <param name="OffAxis_angle" type="float" value="0.4" label="OffAxis_angle (unit: deg)" /> + <param name="Radius_spectal_extraction" type="float" value="0.2" label="Radius_spectal_extraction (unit: deg)" /> + <param name="Radius_sky_image" type="float" value="2.5" label="Radius_sky_image (unit: deg)" /> + <param name="Site" type="select" label="Site"> + <option value="North" selected="true">North</option> + <option value="South">South</option> + </param> + <param name="Telescopes_LST" type="boolean" checked="true" label="Telescopes_LST" /> + <param name="Telescopes_MST" type="boolean" checked="true" label="Telescopes_MST" /> + <param name="Telescopes_SST" type="boolean" label="Telescopes_SST" /> + <param name="Texp" type="float" value="1.0" label="Texp (unit: hour)" /> + </when> + </conditional> + </inputs> + <outputs> + <data label="${tool.name} -> pre-defined_model image_png" name="out_pre_defined_model_image_png" format="auto" from_work_dir="image_png_galaxy.output"> + <filter>_data_product['_selector'] == 'pre-defined_model'</filter> + </data> + <data label="${tool.name} -> pre-defined_model theta2_png" name="out_pre_defined_model_theta2_png" format="auto" from_work_dir="theta2_png_galaxy.output"> + <filter>_data_product['_selector'] == 'pre-defined_model'</filter> + </data> + <data label="${tool.name} -> pre-defined_model spectrum_png" name="out_pre_defined_model_spectrum_png" format="auto" from_work_dir="spectrum_png_galaxy.output"> + <filter>_data_product['_selector'] == 'pre-defined_model'</filter> + </data> + <data label="${tool.name} -> pre-defined_model event_list_fits" name="out_pre_defined_model_event_list_fits" format="auto" from_work_dir="event_list_fits_galaxy.output"> + <filter>_data_product['_selector'] == 'pre-defined_model'</filter> + </data> + <data label="${tool.name} -> model_cube_file spectrum_png" name="out_model_cube_file_spectrum_png" format="auto" from_work_dir="spectrum_png_galaxy.output"> + <filter>_data_product['_selector'] == 'model_cube_file'</filter> + </data> + <data label="${tool.name} -> model_cube_file theta2_png" name="out_model_cube_file_theta2_png" format="auto" from_work_dir="theta2_png_galaxy.output"> + <filter>_data_product['_selector'] == 'model_cube_file'</filter> + </data> + <data label="${tool.name} -> model_cube_file image_png" name="out_model_cube_file_image_png" format="auto" from_work_dir="image_png_galaxy.output"> + <filter>_data_product['_selector'] == 'model_cube_file'</filter> + </data> + <data label="${tool.name} -> model_cube_file event_list_fits" name="out_model_cube_file_event_list_fits" format="auto" from_work_dir="event_list_fits_galaxy.output"> + <filter>_data_product['_selector'] == 'model_cube_file'</filter> + </data> + </outputs> + <tests> + <test expect_num_outputs="4"> + <conditional name="_data_product"> + <param name="_selector" value="pre-defined_model" /> + <param name="RA" value="166.113809" /> + <param name="DEC" value="38.208833" /> + <param name="OffAxis_angle" value="0.78" /> + <param name="Texp" value="1.0" /> + <param name="z" value="0.03" /> + <param name="F0" value="1e-11" /> + <param name="E0" value="1.0" /> + <param name="Gamma" value="2.0" /> + <param name="Radius_spectal_extraction" value="0.2" /> + <param name="Radius_sky_image" value="2.5" /> + <param name="Site" value="North" /> + <param name="Telescope_LST" value="True" /> + <param name="Telescope_MST" value="True" /> + <param name="Telescope_SST" value="False" /> + </conditional> + <assert_stdout> + <has_text text="*** Job finished successfully ***" /> + </assert_stdout> + </test> + <test expect_num_outputs="4"> + <conditional name="_data_product"> + <param name="_selector" value="model_cube_file" /> + <param name="data_cube" location="https://gitlab.renkulab.io/astronomy/mmoda/cta/-/raw/b3f69b091ce942c05ad035220501ea078d54de26/3d.fits" /> + <param name="F0" value="1e-11" /> + <param name="E0" value="1.0" /> + <param name="OffAxis_angle" value="0.4" /> + <param name="Radius_spectal_extraction" value="0.2" /> + <param name="Radius_sky_image" value="2.5" /> + <param name="Site" value="North" /> + <param name="Telescopes_LST" value="True" /> + <param name="Telescopes_MST" value="True" /> + <param name="Telescopes_SST" value="False" /> + <param name="Texp" value="1.0" /> + </conditional> + <assert_stdout> + <has_text text="*** Job finished successfully ***" /> + </assert_stdout> + </test> + </tests> + <help>This service provides simulaiton of observations with `Cherenkov +Telescope Array (CTA) <https://www.cta-observatory.org/>`__ observatory +(now in construction), based on the Instrument Response Funcitons (IRF) +from Monte-Carlo Production 5: |DOI|. The simulation is done using +`Gammapy <https://gammapy.org/>`__ package. + +Two possibilities for defining the sky model are available: +``Simulate_pointing_using_pre-defined_model`` and +``Simulate_pointing_using_model_cube_file``. The “pre-defined model” +option provides a possibility to simulate a source at sky position +``RA``, ``DEC``, with a power-law spectrum, +``dN/dE=F0 (E/E0)^{-\Gamma}``, considering also the effect of absorption +on the Extragalactic Backgorund Light (EBL, based on `Franceschini et +al. (2017) <https://arxiv.org/abs/1705.10256>`__ model. In the “model +cube file” approach, the sky model is loaded from a datacube file (to be +uploaded from an URL to be given in the parameter box). The model cube +describes source counts as a function of ``RA``, ``DEC`` and energy +``E``. Hence, both the source position on the sky and the model source +spectrum are encoded directly in the data cube. + +Parameters that can be adjusted are the source position (``RA``, +``DEC``), the off-axis angle in the telescope field-of-view, ``R_s``, +Radius of the sky image around the source position, ``Radius`` (used in +the image preview), the exposure time in hours, ``Texp``, source +redshift ``z``, the powerlaw flux normalisation ``F0`` and the reference +energy of normalisation ``E0`` (in TeV), the slope of the powerlaw +spectrum ``Gamma``, radius of the spectral extraction region ``R_s`` +used in the count-spectrum preview. + +For the sources visible from both South and North CTA sites, it is +possible to choose between ``South`` and ``North`` sites. It is also +possible to simulate observations with different CTA sub-arrays: Large +Size Telescopes (LST), Medium Size Telescopes (MST), Small Size +Telescopes (SST). Note that in the “Production 5” Monte-Carlo +simulations of the telescope responses it was assumed that the Northern +site will host only LST and MST sub-arrays (no SST available), while the +Southern site will have MST and SST sub-arrays (no LST available). + +Four data products are generated: the Data Level 3 (DL3) event list (a +FITS file), a sky image, a “theta-square plot” showsing distribution of +gamma-like events around the the source position, and the count-spectrum +showing the excess counts as a funciton of energy. The image, spectrum +and theta-square plot are for “preview” of the event set, further +analysis of the simulated events can be done with deticated imaging and +spectral analysis tools. + +.. |DOI| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.5499840.svg + :target: https://doi.org/10.5281/zenodo.5499840 +</help> + <citations> + <citation type="doi">10.1007/s10686-011-9247-0</citation> + </citations> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/model_cube_file.py Fri Apr 19 10:06:21 2024 +0000 @@ -0,0 +1,561 @@ +#!/usr/bin/env python +# coding: utf-8 + +# flake8: noqa + +import json +import os +import shutil + +from oda_api.json import CustomJSONEncoder + +get_ipython().run_cell_magic( # noqa: F821 + "bash", + "", + 'rm -r IRFS | echo "Ok"\nmkdir IRFS\ncd IRFS\nwget https://zenodo.org/records/5499840/files/cta-prod5-zenodo-fitsonly-v0.1.zip\nunzip cta-prod5-zenodo-fitsonly-v0.1.zip\ncd fits\nfor fn in *.gz ; do tar -zxvf $fn; done \n', +) + +import sys + +sys.path.append(".") +from pathlib import Path + +import astropy.units as u +import matplotlib.pyplot as plt +import numpy as np +from astropy import units as u +from astropy import wcs +from astropy.coordinates import SkyCoord +from astropy.io import fits +from gammapy.data import ( + FixedPointingInfo, + Observation, + PointingMode, + observatory_locations, +) +from gammapy.datasets import MapDataset, MapDatasetEventSampler +from gammapy.irf import load_irf_dict_from_file +from gammapy.makers import MapDatasetMaker +from gammapy.maps import Map, MapAxis +from gammapy.modeling.models import ( + FoVBackgroundModel, + Models, + SkyModel, + TemplateSpatialModel, +) +from numpy import cos, pi, sqrt +from oda_api.api import ProgressReporter +from oda_api.data_products import BinaryProduct, PictureProduct + +# not for run on Galaxy +# %%bash +# git lfs install +# git lfs pull + +data_cube = "3d.fits" # http://odahub.io/ontology#POSIXPath + +# Source flux normalisaiton F0 in 1/(TeV cm2 s) at reference energy E0 +F0 = 1e-11 # http://odahub.io/ontology#Float +E0 = 1.0 # http://odahub.io/ontology#Energy_TeV + +OffAxis_angle = 0.4 # http://odahub.io/ontology#AngleDegrees + +Radius_spectal_extraction = 0.2 # http://odahub.io/ontology#AngleDegrees +Radius_sky_image = 2.5 # http://odahub.io/ontology#AngleDegrees + +Site = "North" # http://odahub.io/ontology#String ; oda:allowed_value "North","South" +Telescopes_LST = True # http://odahub.io/ontology#Boolean +Telescopes_MST = True # http://odahub.io/ontology#Boolean +Telescopes_SST = False # http://odahub.io/ontology#Boolean + +Texp = 1.0 # http://odahub.io/ontology#TimeIntervalHours + +_galaxy_wd = os.getcwd() + +with open("inputs.json", "r") as fd: + inp_dic = json.load(fd) +if "_data_product" in inp_dic.keys(): + inp_pdic = inp_dic["_data_product"] +else: + inp_pdic = inp_dic + +for vn, vv in inp_pdic.items(): + if vn != "_selector": + globals()[vn] = type(globals()[vn])(vv) + +R_s = Radius_spectal_extraction +Radius = Radius_sky_image +LSTs = Telescopes_LST +MSTs = Telescopes_MST +SSTs = Telescopes_SST +file_path = data_cube + +pr = ProgressReporter() +pr.report_progress(stage="Progress", progress=10.0) + +print("loading " + file_path) +cube_map = Map.read(file_path) +cube_map.geom + +print("locating source") +# source = SkyCoord.from_name(src_name, frame='icrs', parse=False, cache=True) +source = cube_map.geom.center_skydir +DEC = float(source.dec / u.deg) +RA = float(source.ra / u.deg) + +CTA_south_lat = -25.0 +CTA_north_lat = 18.0 +filename = "" +if Site == "North": + Zd = abs(DEC - CTA_north_lat) + if Zd < 30.0: + Zd = "20deg-" + elif Zd < 50: + Zd = "40deg-" + elif Zd < 70.0: + Zd = "60deg-" + else: + raise RuntimeError("Source not visible from " + Site) + if DEC > CTA_north_lat: + N_S = "NorthAz-" + else: + N_S = "SouthAz-" + if LSTs: + tel = "4LSTs" + if MSTs: + tel += "09MSTs" + if SSTs: + raise RuntimeError("No SSTs on the North site") + filename = "IRFS/fits/Prod5-North-" + Zd + N_S + tel +else: + Zd = abs(DEC - CTA_south_lat) + if Zd < 30.0: + Zd = "20deg-" + elif Zd < 50: + Zd = "40deg-" + elif Zd < 70.0: + Zd = "60deg-" + else: + raise RuntimeError("Source not visible from " + Site) + if DEC > CTA_south_lat: + N_S = "NorthAz-" + else: + N_S = "SouthAz-" + if MSTs: + tel = "14MSTs" + if SSTs: + tel += "37MSTs" + if LSTs: + raise RuntimeError("No LSTs on the South site") + filename = "IRFS/fits/Prod5-South-" + Zd + N_S + tel + +if Texp < 1800: + filename += ".1800s-v0.1.fits.gz" +elif Texp < 18000: + filename += ".18000s-v0.1.fits.gz" +else: + filename += ".180000s-v0.1.fits.gz" + +import os + +print(filename) +if os.path.exists(filename) == False: + raise RuntimeError("No reponse function found") + message = "No reponse function found!" + +# telescope pointing will be shifted slightly +cdec = cos(DEC * pi / 180.0) +RA_pnt = RA - OffAxis_angle / cdec +DEC_pnt = DEC +pnt = SkyCoord(RA_pnt, DEC_pnt, unit="degree") + +# telescope is pointing at a fixed position in ICRS for the observation +pointing = FixedPointingInfo(fixed_icrs=pnt, mode=PointingMode.POINTING) + +location = observatory_locations["cta_south"] + +print("loading IRFs") + +# irfs = load_irf_dict_from_file(path / irf_filename) +# filename = "data/Prod5-North-20deg-AverageAz-4LSTs09MSTs.180000s-v0.1.fits.gz" +irfs_filename = ( + "IRFS/fits/Prod5-North-20deg-AverageAz-4LSTs09MSTs.180000s-v0.1.fits.gz" +) +irfs = load_irf_dict_from_file(irfs_filename) + +print("Creating observation") +livetime = Texp * u.hr +observation = Observation.create( + obs_id=1001, + pointing=pointing, + livetime=livetime, + irfs=irfs, + location=location, +) +print(observation) + +def GetBinSpectralModel( + E, bins_per_decade=20, amplitude=1e-12 * u.Unit("cm-2 s-1") +): + # amplitude=1e-12 * u.Unit("cm-2 s-1") * norm + from gammapy.modeling.models import GaussianSpectralModel + + sigma = (10 ** (1 / bins_per_decade) - 1) * E + return GaussianSpectralModel(mean=E, sigma=sigma, amplitude=amplitude) + +print("Calculate energy range") + +# selected_n_bins_per_decade = 20 # n bins per decade +max_rel_energy_error = 3 + +energy_axis = cube_map.geom.axes["energy"] +EminMap = energy_axis.edges[0] +EmaxMap = energy_axis.edges[-1] +stepE = energy_axis.edges[1] / energy_axis.edges[0] +nbins_per_decade = int(np.round(np.log(10) / np.log(stepE))) +Emin = EminMap / max_rel_energy_error +Emax = EmaxMap * max_rel_energy_error +nbins_per_decade, Emin, Emax + +print("Create empty dataset") + +# energy_axis = MapAxis.from_energy_bounds(max_rel_energy_error*Emin*u.TeV, Emax*u.TeV, nbin=selected_n_bins_per_decade, per_decade=True) +energy_axis_true = MapAxis.from_energy_bounds( + Emin, Emax, nbin=nbins_per_decade, per_decade=True, name="energy_true" +) # TODO: get from geom +migra_axis = MapAxis.from_bounds( + 1.0 / max_rel_energy_error, + max_rel_energy_error, + nbin=150, + node_type="edges", + name="migra", +) +# TODO: get from geom + +geom = cube_map.geom + +empty = MapDataset.create( + geom, + energy_axis_true=energy_axis_true, + migra_axis=migra_axis, + name="my-dataset", +) +maker = MapDatasetMaker(selection=["exposure", "background", "psf", "edisp"]) +dataset = maker.run(empty, observation) + +Path("event_sampling").mkdir(exist_ok=True) +dataset.write("./event_sampling/dataset.fits", overwrite=True) + +print("Plotting GaussianSpectralModel") +from gammapy.modeling.models import GaussianSpectralModel + +meanE = 1 * u.TeV +bins_per_decade = 20 +sigma = (10 ** (1 / bins_per_decade) - 1) * meanE +amplitude = 1 * u.Unit("cm-2 s-1") +gm = GaussianSpectralModel(mean=meanE, sigma=sigma, amplitude=amplitude) +ax = gm.plot(energy_bounds=(0.1, 100) * u.TeV) +ax.set_yscale("linear") +gm.integral(meanE - 3 * sigma, meanE + 3 * sigma) + +print("cube_map.get_spectrum()") +spec = cube_map.get_spectrum() +spec + +# print('spec.plot()') +# spec.plot() # this plot shows dN/dE * E + +pr.report_progress(stage="Progress", progress=20.0) + +print("Find norm bin") + +energy_bins = cube_map.geom.axes["energy"].center +len(energy_bins), float(np.max(energy_bins) / u.TeV) +norm_bin = 0 +for i, E in enumerate(energy_bins): + if E > E0 * u.TeV: + norm_bin = i + break +assert norm_bin > 0 +norm_bin + +print("obtain norm_bin_width") +norm_bin_width = cube_map.geom.axes["energy"].bin_width[norm_bin] +norm_bin_width + +print("find norm_flux") +# Npart=5000 # TODO update +# n_events_reduction_factor = 1 # suppress flux factor + +int_bin_flux = ( + spec.data.flatten() +) # we don't have to multiply by energy_bins /u.TeV since spectrum is already multiplied by E (see above) +norm_flux = int_bin_flux[norm_bin] / norm_bin_width +norm_flux +# int_bin_flux /= (Npart/200000 * np.max(int_bin_flux) * n_events_reduction_factor * 20/len(energy_bins)) # roughly 100 events +# int_bin_flux + +print("find mult") +mult = F0 * u.Unit("cm-2 s-1 TeV-1") / norm_flux # .decompose() +mult + +print("find int_bin_flux") +int_bin_flux = mult * int_bin_flux + +int_bin_flux + +pr.report_progress(stage="Progress", progress=30.0) + +print("Creating bin_models") + +bin_models = [] +for i, (flux, E) in enumerate(zip(int_bin_flux, energy_bins)): + # print(i) + if flux == 0: + print("skipping bin ", i) + continue + # print(flux) + spectral_model_delta = GetBinSpectralModel( + E, amplitude=flux + ) # normalizing here + spacial_template_model = TemplateSpatialModel( + cube_map.slice_by_idx({"energy": i}), + filename=f"cube_bin{i}.fit", + normalize=True, + ) + sky_bin_model = SkyModel( + spectral_model=spectral_model_delta, + spatial_model=spacial_template_model, + name=f"bin_{i}", + ) + bin_models.append(sky_bin_model) + +print("Creating bkg_model") +bkg_model = FoVBackgroundModel(dataset_name="my-dataset") +models = Models(bin_models + [bkg_model]) + +print("dataset.models = models") +dataset.models = models + +print("Creating sampler") +sampler = MapDatasetEventSampler(random_state=0) +print("Running sampler") +events = sampler.run(dataset, observation) + +hdul = fits.open(filename) +aeff = hdul["EFFECTIVE AREA"].data +ENERG_LO = aeff["ENERG_LO"][0] +ENERG_HI = aeff["ENERG_HI"][0] +THETA_LO = aeff["THETA_LO"][0] +THETA_HI = aeff["THETA_HI"][0] +EFFAREA = aeff["EFFAREA"][0] +ind_offaxis = len(THETA_LO[THETA_LO < OffAxis_angle] - 1) +EFAREA = EFFAREA[ind_offaxis] +HDU_EFFAREA = hdul["EFFECTIVE AREA"] +HDU_RMF = hdul["ENERGY DISPERSION"] + +pr.report_progress(stage="Progress", progress=80.0) + +print(f"Save events ...") +primary_hdu = fits.PrimaryHDU() +hdu_evt = fits.BinTableHDU(events.table) +hdu_gti = fits.BinTableHDU(dataset.gti.table, name="GTI") +hdu_all = fits.HDUList([primary_hdu, hdu_evt, hdu_gti, HDU_EFFAREA, HDU_RMF]) +hdu_all.writeto(f"./events.fits", overwrite=True) + +print(f"Reading events ...") +hdul = fits.open("events.fits") +ev = hdul["EVENTS"].data +ra = ev["RA"] +dec = ev["DEC"] +en = ev["ENERGY"] + +[cube_map.geom.center_coord[i] / cube_map.geom.data_shape[i] for i in (0, 1)] + +ra_bins, dec_bins = (int(2 * x) for x in cube_map.geom.center_pix[:2]) +ra_bins, dec_bins + +Radius = float(min(cube_map.geom.width / 2 / u.degree).decompose()) + +print(f"Building event image ...") +plt.close() +pixsize = 0.1 +from matplotlib.colors import LogNorm + +cube_map.geom.width[0] + +Nbins = 2 * int(Radius / pixsize) + 1 +ra0 = np.mean(ra) +dec0 = np.mean(dec) +from numpy import cos, pi + +cdec = cos(DEC_pnt * pi / 180.0) +ra_bins = np.linspace(RA - Radius / cdec, RA + Radius / cdec, Nbins + 1) +dec_bins = np.linspace(DEC - Radius, DEC + Radius, Nbins + 1) + +h = plt.hist2d(ra, dec, bins=[ra_bins, dec_bins], norm=LogNorm()) +image = h[0] +plt.colorbar() +plt.xlabel("RA") +plt.ylabel("Dec") + +print(f"Building event image 2 ...") +plt.figure() +# Create a new WCS object. The number of axes must be set +# from the start +w = wcs.WCS(naxis=2) + +w.wcs.ctype = ["RA---CAR", "DEC--CAR"] +# we need a Plate carrée (CAR) projection since histogram is binned by ra-dec +# the peculiarity here is that CAR projection produces rectilinear grid only if CRVAL2==0 +# also, we will follow convention of RA increasing from right to left (CDELT1<0, need to flip an input image) +# otherwise, aladin-lite doesn't show it +w.wcs.crval = [RA_pnt, 0] +w.wcs.crpix = [Nbins / 2.0 + 0.5, 1 - dec_bins[0] / pixsize] +w.wcs.cdelt = np.array([-pixsize / cdec, pixsize]) + +header = w.to_header() + +hdu = fits.PrimaryHDU(np.flip(image.T, axis=1), header=header) +hdu.writeto("Image.fits", overwrite=True) +hdu = fits.open("Image.fits") +im = hdu[0].data +wcs1 = wcs.WCS(hdu[0].header) +ax = plt.subplot(projection=wcs1) +lon = ax.coords["ra"] +lon.set_major_formatter("d.dd") +lat = ax.coords["dec"] +lat.set_major_formatter("d.dd") +plt.imshow(im, origin="lower") +plt.colorbar(label="Counts") + +plt.scatter( + [RA_pnt], + [DEC_pnt], + marker="x", + color="white", + alpha=0.5, + transform=ax.get_transform("world"), +) +plt.scatter( + [RA], + [DEC], + marker="+", + color="red", + alpha=0.5, + transform=ax.get_transform("world"), +) +plt.grid(color="white", ls="solid") +plt.xlabel("RA") +plt.ylabel("Dec") +plt.savefig("Image.png", format="png", bbox_inches="tight") + +print("building event spectrum") +plt.close() +E = (events.energy / u.TeV).decompose() +ras = events.radec.ra.deg +decs = events.radec.dec.deg +# plt.hist(E,bins=np.logspace(-2,2,41)) + +mask = events.table["MC_ID"] > 0 +plt.hist(E[mask], bins=np.logspace(-2, 2, 41), alpha=0.5, label="source") +mask = events.table["MC_ID"] == 0 +plt.hist(E[mask], bins=np.logspace(-2, 2, 41), alpha=0.5, label="background") +plt.xlabel("E, TeV") + +plt.xscale("log") +plt.yscale("log") +plt.legend(loc="upper right") +plt.savefig("event_spectrum.png", format="png") + +coord_s = SkyCoord(RA, DEC, unit="degree") +RA_bkg = RA_pnt - (RA - RA_pnt) +DEC_bkg = DEC_pnt - (DEC - DEC_pnt) +coord_b = SkyCoord(RA_bkg, DEC_bkg, unit="degree") +coords = SkyCoord(ra, dec, unit="degree") + +plt.figure() +ev_src = en[coords.separation(coord_s).deg < R_s] +ev_bkg = en[coords.separation(coord_b).deg < R_s] +ENERG_BINS = np.concatenate((ENERG_LO, [ENERG_HI[-1]])) +ENERG = sqrt(ENERG_LO * ENERG_HI) +h1 = np.histogram(ev_src, bins=ENERG_BINS) +h2 = np.histogram(ev_bkg, bins=ENERG_BINS) +cts_s = h1[0] +cts_b = h2[0] +src = cts_s - cts_b +src_err = sqrt(cts_s + cts_b) +plt.errorbar(ENERG, src, src_err) +plt.axhline(0, linestyle="dashed", color="black") +plt.xscale("log") +plt.xlabel(r"$E$, TeV") +plt.ylabel("Counts") +plt.yscale("log") +plt.ylim(0.1, 2 * max(src)) +plt.savefig("Count_spectrum.png") + +plt.figure() +sep_s = coords.separation(coord_s).deg +sep_b = coords.separation(coord_b).deg +plt.hist(sep_s**2, bins=np.linspace(0, 0.5, 50)) +plt.hist(sep_b**2, bins=np.linspace(0, 0.5, 50)) +plt.axvline(R_s**2, color="black", linestyle="dashed") +plt.xlabel(r"$\theta^2$, degrees") +plt.ylabel("Counts") +plt.savefig("Theta2_plot.png") + +pr.report_progress(stage="Progress", progress=100.0) + +fits_events = BinaryProduct.from_file("events.fits") +bin_image = PictureProduct.from_file("Image.png") +spec_image = PictureProduct.from_file("Count_spectrum.png") +theta2_png = PictureProduct.from_file("Theta2_plot.png") + +spectrum_png = spec_image # http://odahub.io/ontology#ODAPictureProduct +theta2_png = theta2_png # http://odahub.io/ontology#ODAPictureProduct +image_png = bin_image # http://odahub.io/ontology#ODAPictureProduct +event_list_fits = fits_events # http://odahub.io/ontology#ODABinaryProduct + +# output gathering +_galaxy_meta_data = {} +_oda_outs = [] +_oda_outs.append( + ( + "out_model_cube_file_spectrum_png", + "spectrum_png_galaxy.output", + spectrum_png, + ) +) +_oda_outs.append( + ("out_model_cube_file_theta2_png", "theta2_png_galaxy.output", theta2_png) +) +_oda_outs.append( + ("out_model_cube_file_image_png", "image_png_galaxy.output", image_png) +) +_oda_outs.append( + ( + "out_model_cube_file_event_list_fits", + "event_list_fits_galaxy.output", + event_list_fits, + ) +) + +for _outn, _outfn, _outv in _oda_outs: + _galaxy_outfile_name = os.path.join(_galaxy_wd, _outfn) + if isinstance(_outv, str) and os.path.isfile(_outv): + shutil.move(_outv, _galaxy_outfile_name) + _galaxy_meta_data[_outn] = {"ext": "_sniff_"} + elif getattr(_outv, "write_fits_file", None): + _outv.write_fits_file(_galaxy_outfile_name) + _galaxy_meta_data[_outn] = {"ext": "fits"} + elif getattr(_outv, "write_file", None): + _outv.write_file(_galaxy_outfile_name) + _galaxy_meta_data[_outn] = {"ext": "_sniff_"} + else: + with open(_galaxy_outfile_name, "w") as fd: + json.dump(_outv, fd, cls=CustomJSONEncoder) + _galaxy_meta_data[_outn] = {"ext": "json"} + +with open(os.path.join(_galaxy_wd, "galaxy.json"), "w") as fd: + json.dump(_galaxy_meta_data, fd) +print("*** Job finished successfully ***")
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pre-defined_model.py Fri Apr 19 10:06:21 2024 +0000 @@ -0,0 +1,445 @@ +#!/usr/bin/env python +# coding: utf-8 + +# flake8: noqa + +import json +import os +import shutil + +from oda_api.json import CustomJSONEncoder + +get_ipython().run_cell_magic( # noqa: F821 + "bash", + "", + 'wget https://gitlab.renkulab.io/astronomy/mmoda/cta/-/raw/master/Franceschini17.txt\n\nrm -r IRFS | echo "Ok"\nmkdir IRFS\ncd IRFS\nwget https://zenodo.org/records/5499840/files/cta-prod5-zenodo-fitsonly-v0.1.zip\nunzip cta-prod5-zenodo-fitsonly-v0.1.zip\ncd fits\nfor fn in *.gz ; do tar -zxvf $fn; done \n \n', +) + +import astropy.units as u +import matplotlib.pyplot as plt +import numpy as np +from astropy import wcs +from astropy.coordinates import SkyCoord +from astropy.io import fits +from gammapy.data import Observation +from gammapy.datasets import MapDataset, MapDatasetEventSampler +from gammapy.irf import load_irf_dict_from_file +from gammapy.makers import MapDatasetMaker +from gammapy.maps import MapAxis, WcsGeom +from gammapy.modeling.models import FoVBackgroundModel, Models +from numpy import cos, exp, pi, sqrt +from oda_api.api import ProgressReporter +from oda_api.data_products import BinaryProduct, PictureProduct +from regions import CircleSkyRegion + +# from gammapy.irf import load_cta_irfs + +RA = 166.113809 # http://odahub.io/ontology#PointOfInterestRA +DEC = 38.208833 # http://odahub.io/ontology#PointOfInterestDEC + +OffAxis_angle = 0.78 # http://odahub.io/ontology#AngleDegrees +# Exposure time in hours +Texp = 1.0 # http://odahub.io/ontology#TimeIntervalHours +# Source redshift +z = 0.03 # http://odahub.io/ontology#Float +# Source flux normalisaiton F0 in 1/(TeV cm2 s) at reference energy E0 +F0 = 1e-11 # http://odahub.io/ontology#Float +E0 = 1.0 # http://odahub.io/ontology#Energy_TeV +Gamma = 2.0 # http://odahub.io/ontology#Float + +Radius_spectal_extraction = 0.2 # http://odahub.io/ontology#Float +Radius_sky_image = 2.5 # http://odahub.io/ontology#AngleDegrees + +Site = "North" # http://odahub.io/ontology#String ; oda:allowed_value "North","South" +Telescope_LST = True # http://odahub.io/ontology#Boolean +Telescope_MST = True # http://odahub.io/ontology#Boolean +Telescope_SST = False # http://odahub.io/ontology#Boolean + +_galaxy_wd = os.getcwd() + +with open("inputs.json", "r") as fd: + inp_dic = json.load(fd) +if "_data_product" in inp_dic.keys(): + inp_pdic = inp_dic["_data_product"] +else: + inp_pdic = inp_dic + +for vn, vv in inp_pdic.items(): + if vn != "_selector": + globals()[vn] = type(globals()[vn])(vv) + +LSTs = Telescope_LST +MSTs = Telescope_MST +SSTs = Telescope_SST + +Texp = Texp * 3600.0 +DEC_pnt = DEC +cdec = cos(DEC * pi / 180.0) +RA_pnt = RA - OffAxis_angle / cdec +Radius = Radius_sky_image +R_s = Radius_spectal_extraction + +pointing = SkyCoord(RA_pnt, DEC_pnt, unit="deg", frame="icrs") +coord_s = SkyCoord(RA, DEC, unit="deg", frame="icrs") +RA_bkg = RA_pnt - (RA - RA_pnt) +DEC_bkg = DEC_pnt - (DEC - DEC_pnt) +coord_b = SkyCoord(RA_bkg, DEC_bkg, unit="deg", frame="icrs") +offaxis = coord_s.separation(pointing).deg +pr = ProgressReporter() +pr.report_progress(stage="Progress", progress=10.0) + +CTA_south_lat = -25.0 +CTA_north_lat = 18.0 +if Site == "North": + Zd = abs(DEC - CTA_north_lat) + if Zd < 30.0: + Zd = "20deg-" + elif Zd < 50: + Zd = "40deg-" + elif Zd < 70.0: + Zd = "60deg-" + else: + raise RuntimeError("Source not visible from " + Site) + if DEC > CTA_north_lat: + N_S = "NorthAz-" + else: + N_S = "SouthAz-" + if LSTs: + tel = "4LSTs" + if MSTs: + tel += "09MSTs" + if SSTs: + raise RuntimeError("No SSTs on the North site") + filename = "IRFS/fits/Prod5-North-" + Zd + N_S + tel +else: + Zd = abs(DEC - CTA_south_lat) + if Zd < 30.0: + Zd = "20deg-" + elif Zd < 50: + Zd = "40deg-" + elif Zd < 70.0: + Zd = "60deg-" + else: + raise RuntimeError("Source not visible from " + Site) + if DEC > CTA_south_lat: + N_S = "NorthAz-" + else: + N_S = "SouthAz-" + if MSTs: + tel = "14MSTs" + if SSTs: + tel += "37MSTs" + if LSTs: + raise RuntimeError("No LSTs on the South site") + filename = "IRFS/fits/Prod5-South-" + Zd + N_S + tel + +if Texp < 1800: + filename += ".1800s-v0.1.fits.gz" +elif Texp < 18000: + filename += ".18000s-v0.1.fits.gz" +else: + filename += ".180000s-v0.1.fits.gz" +import os + +print(filename) +if os.path.exists(filename) == False: + raise RuntimeError("No reponse function found") + message = "No reponse function found!" + +hdul = fits.open(filename) +aeff = hdul["EFFECTIVE AREA"].data +ENERG_LO = aeff["ENERG_LO"][0] +ENERG_HI = aeff["ENERG_HI"][0] +THETA_LO = aeff["THETA_LO"][0] +THETA_HI = aeff["THETA_HI"][0] +EFFAREA = aeff["EFFAREA"][0] +print(offaxis) +ind_offaxis = len(THETA_LO[THETA_LO < offaxis] - 1) +EFAREA = EFFAREA[ind_offaxis] +HDU_EFFAREA = hdul["EFFECTIVE AREA"] +HDU_RMF = hdul["ENERGY DISPERSION"] + +E = np.logspace(-2, 2, 20) + +d = np.genfromtxt("Franceschini17.txt") +ee = d[:, 0] +z_grid = np.array([0.01, 0.03, 0.1, 0.3, 0.5, 1.0, 1.5, 2.0, 3.0]) +ind = len(z_grid[z > z_grid]) - 1 +coeff = (z - z_grid[ind]) / (z_grid[ind + 1] - z_grid[ind]) +tau = d[:, ind + 1] + coeff * d[:, ind + 2] +tau_interp = np.interp(E, ee, tau) + +def powerlaw_EBL(): + return F0 * (E / E0) ** (-Gamma) * exp(-tau_interp) + +F = powerlaw_EBL() +plt.plot(E, E**2 * F) +plt.xscale("log") +plt.yscale("log") +plt.ylim(1e-14, 1e-10) + +# filename = "IRFS/fits/Prod5-North-20deg-AverageAz-4LSTs09MSTs.180000s-v0.1.fits.gz" +IRFS = load_irf_dict_from_file(filename) +dic = { + "components": [ + { + "name": "Source1", + "type": "SkyModel", + "spectral": { + "type": "TemplateSpectralModel", + "parameters": [{"name": "norm", "value": 1.0}], + "energy": {"data": E.tolist(), "unit": "TeV"}, + "values": {"data": F.tolist(), "unit": "1 / (cm2 TeV s)"}, + }, + "spatial": { + "type": "PointSpatialModel", + "frame": "icrs", + "parameters": [ + {"name": "lon_0", "value": RA, "unit": "deg"}, + {"name": "lat_0", "value": DEC, "unit": "deg"}, + ], + }, + }, + { + "type": "FoVBackgroundModel", + "datasets_names": ["my-dataset"], + "spectral": { + "type": "PowerLawNormSpectralModel", + "parameters": [ + {"name": "norm", "value": 1.0}, + {"name": "tilt", "value": 0.0}, + {"name": "reference", "value": 1.0, "unit": "TeV"}, + ], + }, + }, + ] +} +modelsky = Models.from_dict(dic) + +bkg_model = FoVBackgroundModel(dataset_name="my-dataset") + +observation = Observation.create( + obs_id="0", pointing=pointing, livetime=str(Texp) + " s", irfs=IRFS +) + +print(f"Create the dataset for {pointing}") +energy_axis = MapAxis.from_energy_bounds( + "0.012 TeV", "100 TeV", nbin=10, per_decade=True +) +energy_axis_true = MapAxis.from_energy_bounds( + "0.001 TeV", "300 TeV", nbin=20, per_decade=True, name="energy_true" +) +migra_axis = MapAxis.from_bounds( + 0.5, 2, nbin=150, node_type="edges", name="migra" +) + +geom = WcsGeom.create( + skydir=pointing, + width=(2 * Radius, 2 * Radius), + binsz=0.02, + frame="icrs", + axes=[energy_axis], +) + +empty = MapDataset.create( + geom, + energy_axis_true=energy_axis_true, + migra_axis=migra_axis, + name="my-dataset", +) +maker = MapDatasetMaker(selection=["exposure", "background", "psf", "edisp"]) +dataset = maker.run(empty, observation) + +region_sky = CircleSkyRegion(center=pointing, radius=Radius * u.deg) +mask_map = dataset.geoms["geom"].region_mask(region_sky) +mod = modelsky.select_mask(mask_map) + +bkg_idx = np.where(np.array(modelsky.names) == "my-dataset-bkg") +mod.append(modelsky[int(bkg_idx[0][0])]) + +dataset.models = mod + +for m in dataset.models[:-1]: + sep = m.spatial_model.position.separation(pointing).deg + print( + f"This is the spatial separation of {m.name} from the pointing direction: {sep}" + ) +pr.report_progress(stage="Progress", progress=50.0) +print("Simulate...") +sampler = MapDatasetEventSampler() +events = sampler.run(dataset, observation) + +pr.report_progress(stage="Progress", progress=90.0) +print(f"Save events ...") +primary_hdu = fits.PrimaryHDU() +hdu_evt = fits.BinTableHDU(events.table) +hdu_gti = fits.BinTableHDU(dataset.gti.table, name="GTI") +hdu_all = fits.HDUList([primary_hdu, hdu_evt, hdu_gti, HDU_EFFAREA, HDU_RMF]) +hdu_all.writeto(f"./events.fits", overwrite=True) + +hdul = fits.open("events.fits") +ev = hdul["EVENTS"].data +ra = ev["RA"] +dec = ev["DEC"] +coords = SkyCoord(ra, dec, unit="degree") +en = ev["ENERGY"] + +from matplotlib.colors import LogNorm + +plt.figure() +pixsize = 0.1 +Nbins = 2 * int(Radius / pixsize) + 1 +ra0 = np.mean(ra) +dec0 = np.mean(dec) +from numpy import cos, pi + +cdec = cos(DEC_pnt * pi / 180.0) +ra_bins = np.linspace( + RA_pnt - Radius / cdec, RA_pnt + Radius / cdec, Nbins + 1 +) +dec_bins = np.linspace(DEC_pnt - Radius, DEC_pnt + Radius, Nbins + 1) + +h = plt.hist2d(ra, dec, bins=[ra_bins, dec_bins], norm=LogNorm()) +image = h[0] +plt.colorbar() +plt.xlabel("RA") +plt.ylabel("Dec") + +plt.figure() +ev_src = en[coords.separation(coord_s).deg < R_s] +ev_bkg = en[coords.separation(coord_b).deg < R_s] +ENERG_BINS = np.concatenate((ENERG_LO, [ENERG_HI[-1]])) +ENERG = sqrt(ENERG_LO * ENERG_HI) +h1 = np.histogram(ev_src, bins=ENERG_BINS) +h2 = np.histogram(ev_bkg, bins=ENERG_BINS) +cts_s = h1[0] +cts_b = h2[0] +src = cts_s - cts_b +src_err = sqrt(cts_s + cts_b) +plt.errorbar(ENERG, src, src_err) +plt.axhline(0, linestyle="dashed", color="black") +plt.xscale("log") +plt.xlabel(r"$E$, TeV") +plt.ylabel("Counts") +plt.yscale("log") +plt.ylim(0.1, 2 * max(src)) +plt.savefig("Count_spectrum.png") + +plt.figure() +sep_s = coords.separation(coord_s).deg +sep_b = coords.separation(coord_b).deg +plt.hist(sep_s**2, bins=np.linspace(0, 0.5, 50)) +plt.hist(sep_b**2, bins=np.linspace(0, 0.5, 50)) +plt.axvline(R_s**2, color="black", linestyle="dashed") +plt.xlabel(r"$\theta^2$, degrees") +plt.ylabel("Counts") +plt.savefig("Theta2_plot.png") + +# Create a new WCS object. The number of axes must be set +# from the start +plt.figure() +w = wcs.WCS(naxis=2) + +w.wcs.ctype = ["RA---CAR", "DEC--CAR"] +# we need a Plate carrée (CAR) projection since histogram is binned by ra-dec +# the peculiarity here is that CAR projection produces rectilinear grid only if CRVAL2==0 +# also, we will follow convention of RA increasing from right to left (CDELT1<0, need to flip an input image) +# otherwise, aladin-lite doesn't show it +w.wcs.crval = [RA_pnt, 0] +w.wcs.crpix = [Nbins / 2.0 + 0.5, 1 - dec_bins[0] / pixsize] +w.wcs.cdelt = np.array([-pixsize / cdec, pixsize]) + +header = w.to_header() + +hdu = fits.PrimaryHDU(np.flip(image.T, axis=1), header=header) +hdu.writeto("Image.fits", overwrite=True) +hdu = fits.open("Image.fits") +im = hdu[0].data +wcs1 = wcs.WCS(hdu[0].header) +ax = plt.subplot(projection=wcs1) +lon = ax.coords["ra"] +lon.set_major_formatter("d.dd") +lat = ax.coords["dec"] +lat.set_major_formatter("d.dd") +plt.imshow(im, origin="lower") +plt.colorbar(label="Counts") + +plt.scatter( + [RA_pnt], + [DEC_pnt], + marker="x", + color="white", + alpha=0.5, + transform=ax.get_transform("world"), +) +plt.scatter( + [RA], + [DEC], + marker="+", + color="red", + alpha=0.5, + transform=ax.get_transform("world"), +) +plt.grid(color="white", ls="solid") +plt.xlabel("RA") +plt.ylabel("Dec") +plt.savefig("Image.png", format="png", bbox_inches="tight") + +fits_events = BinaryProduct.from_file("events.fits") +bin_image1 = PictureProduct.from_file("Image.png") +bin_image2 = PictureProduct.from_file("Theta2_plot.png") +bin_image3 = PictureProduct.from_file("Count_spectrum.png") +pr.report_progress(stage="Progress", progress=100.0) + +image_png = bin_image1 # http://odahub.io/ontology#ODAPictureProduct +theta2_png = bin_image2 # http://odahub.io/ontology#ODAPictureProduct +spectrum_png = bin_image3 # http://odahub.io/ontology#ODAPictureProduct +event_list_fits = fits_events # http://odahub.io/ontology#ODABinaryProduct + +# output gathering +_galaxy_meta_data = {} +_oda_outs = [] +_oda_outs.append( + ("out_pre_defined_model_image_png", "image_png_galaxy.output", image_png) +) +_oda_outs.append( + ( + "out_pre_defined_model_theta2_png", + "theta2_png_galaxy.output", + theta2_png, + ) +) +_oda_outs.append( + ( + "out_pre_defined_model_spectrum_png", + "spectrum_png_galaxy.output", + spectrum_png, + ) +) +_oda_outs.append( + ( + "out_pre_defined_model_event_list_fits", + "event_list_fits_galaxy.output", + event_list_fits, + ) +) + +for _outn, _outfn, _outv in _oda_outs: + _galaxy_outfile_name = os.path.join(_galaxy_wd, _outfn) + if isinstance(_outv, str) and os.path.isfile(_outv): + shutil.move(_outv, _galaxy_outfile_name) + _galaxy_meta_data[_outn] = {"ext": "_sniff_"} + elif getattr(_outv, "write_fits_file", None): + _outv.write_fits_file(_galaxy_outfile_name) + _galaxy_meta_data[_outn] = {"ext": "fits"} + elif getattr(_outv, "write_file", None): + _outv.write_file(_galaxy_outfile_name) + _galaxy_meta_data[_outn] = {"ext": "_sniff_"} + else: + with open(_galaxy_outfile_name, "w") as fd: + json.dump(_outv, fd, cls=CustomJSONEncoder) + _galaxy_meta_data[_outn] = {"ext": "json"} + +with open(os.path.join(_galaxy_wd, "galaxy.json"), "w") as fd: + json.dump(_galaxy_meta_data, fd) +print("*** Job finished successfully ***")