diff --git a/.gitignore b/.gitignore index 6f96f7faac16fc23364231c0e49dd03cbbd77adb..6fe12c4bb68f8569b8f1945d8df2436732470308 100644 --- a/.gitignore +++ b/.gitignore @@ -6,3 +6,5 @@ pcigale/data/data.db pcigale.egg-info docs/_build docs/api +dist/ +build/ diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml new file mode 100644 index 0000000000000000000000000000000000000000..3aa5ef19dc6e8913fbbd5d3f0857d17bc906d65c --- /dev/null +++ b/.gitlab-ci.yml @@ -0,0 +1,16 @@ +stages: + - build + +build_wheel: + stage: build + image: python:latest + variables: + PIP_CACHE_DIR: "$CI_PROJECT_DIR/.cache/pip" + cache: + paths: + - .cache/pip + script: + - python setup.py sdist bdist_wheel + - pip install twine + - twine upload --verbose --disable-progress-bar --repository-url $TWINE_URL -u $TWINE_USER -p $TWINE_PASS dist/pcigale*.whl + when: manual diff --git a/CHANGELOG.md b/CHANGELOG.md index 68632458acca5a7309453f6ddd5e9c07e7129c83..7007be268de1f76d807d8db5616572687e383ee2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,22 @@ ## Unreleased ### Added - The (1+z1)/(1+z2) factor between observed and grid flux densities caused by the differential redshifting is now taken into account. With a default grid redshift rounding of two decimals this yields a difference of at most 0.5% in the estimated physical properties at z=0 and even less at higher z. (Médéric Boquien) +- The list of bands for which to carry out a Bayesian flux estimate is now configurable. By default this corresponds to the fitted bands but it also supports bands that are not included in the fit. This can be set in the `fluxes` parameter of the `pdf\_analysis` module. (Médéric Boquien) +- Implementation of the auto-detection of lines in the input flux file so they are automatically added to the list of bands in `pcigale.ini`. (Médéric Boquien) +- The `dl2007` and `dl2014` modules now provide \. (Médéric Boquien) +- Saving the χ² is now a bit more fine-grained. It is possible to save none, all, only the properties, or only the fluxes. (Médéric Boquien) +- The database now includes the JWST MIRI and NIRCam filters. (Médéric Boquien) ### Changed +- Python 3.6 is now the minimum required version. (Médéric Boquien) +- The logo has now been moved to the lower-right corner of the figure so that it does not overlap with any information and it has been updated for a less pixelated version. (Médéric Boquien & Rodrigo González Castillo) +- The wavelength range in SED plots is now dynamically adapted to cover the observed wavelengths. (Médéric Boquien) +- The uncertainties on the SED plots now correspond only to 1σ rather than 3σ so they do not appear exceedingly large. (Médéric Boquien) +- The lines linking the different bands in the residual SED plot have been eliminated to improve the readability. (Médéric Boquien) +- Some lines have been made slightly thicker in SED plots so the different components are more visible. (Médéric Boquien) +- The colours in the SED plots have been tweaked for aesthetic reasons. (Médéric Boquien) +- The markers for the observed fluxes in the SED plots have been tweaked to improve readability. (Médéric Boquien) +- The computation of all the cosmology-dependent quantities has been consolidated in pcigale/utils/cosmology.py and optimised. This leads to a slightly faster startup, in particular when there are many objects to fit, and it makes it easier to change the cosmology. (Médéric Boquien) +- The time spent computing is now displayed in hours, minutes, and seconds rather than just seconds to improve legibility. (Médéric Boquien) ### Fixed - Make sure we can plot the PDF of equivalent widths. (Médéric Boquien) - Fix a crash when generating a mock catalogue containing intensive properties. (Médéric Boquien) @@ -13,8 +28,18 @@ - Fix the pip install by making pcigale.managers discoverable. (Yannick Roehlly) - When using a parameters file, Boolean values were not correctly interpreted. (Médéric Boquien, reported by Eric Martínez, INAOE) - Make sure that the best-fit models are stored with the correct scaling factor when the distance is given explicitly (Médéric Boquien) +- Some labels and the title for the SED plots has been improved to avoid overlaps and overflows. (Médéric Boquien) +- Ensure that best models are properly computed when models are computed by blocks and that no fit could be made in one or more blocks. This can be case if all the models in the block are older than the age of the universe. (Médéric) +- Make sure that the parameters are saved with the proper scale (linear or logarithmic) in the χ² files. (Médéric Boquien) +- Some math libraries such as MKL or OpenBLAS sometime try to be (too) smart, starting computation threads on their own. As cigale is already parallel, this just oversubscribes the CPU and can lead to important slowdowns. An environment variable could be set by the user to disable this, but this is cumbersome. Rather, we set these variables directly in the code at the startup of cigale. (Yannick Roehlly & Médéric Boquien) ### Optimised -- Slight speedup of the computation of the likelihood from the χ² (Médéric Boquien) +- Slight speedup of the computation of the likelihood from the χ² using a multiplication rather than a division. (Médéric Boquien) +- Speedup of the computation of the χ² by ~10% taking the opposite of a scalar rather than of an array. (Médéric Boquien) +- Thanks to a change in the layout of the models storage in RAM, the computation of the χ² is now massively faster when the run contains multiple redshifts. (Médéric Boquien) +- The computation of the weighted means and standard deviations has been made ~50% faster by normalising the likelihood. (Médéric Boquien) +- The the fritz2006 module should now run faster thanks to an optimisation of the computation of the luminosity of the various AGN components (Médéric Boquien & Guang Yang) +- Various optimisations have been made regarding shared arrays to make their access faster. The overall effect is a speedup of 3-4% for the computation of the models. (Médéric Boquien) +- All the cores should now be used over the entire duration of the computation of the Bayesian and best-fit estimates. Before the number of active cores could drop towards the end of the computation. (Médéric Boquien) ## 2018.0 (2018-11-06) ### Added diff --git a/database_builder/__init__.py b/database_builder/__init__.py index f4cc6ccc2200d062c78d27316fd651d834a0538b..92b6f14ff35e3c33fecbb53a99162e69025a102e 100644 --- a/database_builder/__init__.py +++ b/database_builder/__init__.py @@ -141,11 +141,16 @@ def read_bc03_ssp(filename): def build_filters(base): filters = [] filters_dir = os.path.join(os.path.dirname(__file__), 'filters/') - for filter_file in glob.glob(filters_dir + '*.dat'): + for filter_file in glob.glob(filters_dir + '**/*.dat', recursive=True): with open(filter_file, 'r') as filter_file_read: filter_name = filter_file_read.readline().strip('# \n\t') filter_type = filter_file_read.readline().strip('# \n\t') filter_description = filter_file_read.readline().strip('# \n\t') + + # Make the name dynamic for filters in subdirectories + tmp_name = filter_file.replace(filters_dir, '')[:-4] + if '/' in tmp_name: + filter_name = tmp_name.replace('/', '.') filter_table = np.genfromtxt(filter_file) # The table is transposed to have table[0] containing the wavelength # and table[1] containing the transmission. diff --git a/database_builder/filters/jwst/miri/F1000W.dat b/database_builder/filters/jwst/miri/F1000W.dat new file mode 100644 index 0000000000000000000000000000000000000000..d4a3639f4968ef43e65753a949a2f992030832cd --- /dev/null +++ b/database_builder/filters/jwst/miri/F1000W.dat @@ -0,0 +1,482 @@ +# F1000W +# photon +# Includes Nominal transmission of the JWST OTE is not included. Source: http://svo2.cab.inta-csic.es/svo/theory/fps3/index.php?mode=browse&gname=JWST&gname2=MIRI +87430 0.0004 +87490 0.0012 +87550 0.002 +87600 0.0029 +87660 0.0056 +87720 0.0082 +87780 0.0109 +87840 0.0127 +87890 0.0139 +87950 0.0151 +88010 0.0156 +88070 0.013 +88130 0.0104 +88180 0.0078 +88240 0.0062 +88300 0.005 +88360 0.0038 +88420 0.0029 +88470 0.0029 +88530 0.0029 +88590 0.0029 +88650 0.0033 +88710 0.0038 +88760 0.0043 +88820 0.0052 +88880 0.0065 +88940 0.0078 +89000 0.0092 +89050 0.0119 +89110 0.0147 +89170 0.0174 +89230 0.0211 +89290 0.0258 +89340 0.0305 +89400 0.0352 +89460 0.0416 +89520 0.0481 +89580 0.0545 +89630 0.0623 +89690 0.0711 +89750 0.0799 +89810 0.0894 +89870 0.1029 +89920 0.1163 +89980 0.1298 +90040 0.1482 +90100 0.1687 +90160 0.1893 +90210 0.2109 +90270 0.2357 +90330 0.2605 +90390 0.2853 +90450 0.3036 +90500 0.3202 +90560 0.3369 +90620 0.3482 +90680 0.3494 +90740 0.3506 +90790 0.3518 +90850 0.347 +90910 0.3414 +90970 0.3358 +91030 0.3312 +91080 0.3277 +91140 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0.0001 +115100 0.0001 +115150 0.0001 diff --git a/database_builder/filters/jwst/miri/F1130W.dat b/database_builder/filters/jwst/miri/F1130W.dat new file mode 100644 index 0000000000000000000000000000000000000000..9f82d288a854e061a2d7147aedf7e54450a5e660 --- /dev/null +++ b/database_builder/filters/jwst/miri/F1130W.dat @@ -0,0 +1,345 @@ +# F1130W +# photon +# Includes Nominal transmission of the JWST OTE is not included. 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0.0003 +121530 0.0002 +121590 0.0002 +121650 0.0002 +121710 0.0002 +121770 0.0001 +121820 0.0001 +121880 0.0001 +121940 0.0001 +122000 0.0001 +122060 0.0001 +122110 0.0001 +122170 0.0001 +122230 0.0001 +122290 0.0001 diff --git a/database_builder/filters/jwst/miri/F1280W.dat b/database_builder/filters/jwst/miri/F1280W.dat new file mode 100644 index 0000000000000000000000000000000000000000..0f78087790a5b0d5300bb55702c5c2f6351cfad7 --- /dev/null +++ b/database_builder/filters/jwst/miri/F1280W.dat @@ -0,0 +1,612 @@ +# F1280W +# photon +# Includes Nominal transmission of the JWST OTE is not included. Source: http://svo2.cab.inta-csic.es/svo/theory/fps3/index.php?mode=browse&gname=JWST&gname2=MIRI +110860 0.0001 +110920 0.0001 +110980 0.0001 +111040 0.0001 +111090 0.0002 +111150 0.0002 +111210 0.0003 +111270 0.0003 +111330 0.0004 +111380 0.0005 +111440 0.0005 +111500 0.0006 +111560 0.0007 +111620 0.0008 +111670 0.001 +111730 0.0011 +111790 0.0012 +111850 0.0014 +111910 0.0015 +111960 0.0017 +112020 0.0019 +112080 0.0021 +112140 0.0022 +112200 0.0024 +112250 0.0026 +112310 0.0028 +112370 0.003 +112430 0.0032 +112490 0.0034 +112540 0.0036 +112600 0.0038 +112660 0.004 +112720 0.0042 +112780 0.0044 +112830 0.0045 +112890 0.0047 +112950 0.0049 +113010 0.0051 +113070 0.0053 +113120 0.0056 +113180 0.0058 +113240 0.006 +113300 0.0062 +113360 0.0065 +113410 0.0067 +113470 0.007 +113530 0.0073 +113590 0.0077 +113650 0.0081 +113700 0.0085 +113760 0.0089 +113820 0.0094 +113880 0.01 +113940 0.0106 +113990 0.0112 +114050 0.0119 +114110 0.0127 +114170 0.0135 +114230 0.0144 +114280 0.0155 +114340 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+145490 0.0002 +145550 0.0002 +145600 0.0002 +145660 0.0002 +145720 0.0002 +145780 0.0001 +145840 0.0001 +145890 0.0001 +145950 0.0001 +146010 0.0001 +146070 0.0001 +146130 0.0001 diff --git a/database_builder/filters/jwst/miri/F1500W.dat b/database_builder/filters/jwst/miri/F1500W.dat new file mode 100644 index 0000000000000000000000000000000000000000..443cc94273a7e898174713f80c52732f21d410bb --- /dev/null +++ b/database_builder/filters/jwst/miri/F1500W.dat @@ -0,0 +1,820 @@ +# F1500W +# photon +# Includes Nominal transmission of the JWST OTE is not included. Source: http://svo2.cab.inta-csic.es/svo/theory/fps3/index.php?mode=browse&gname=JWST&gname2=MIRI +127740 0.0001 +127800 0.0001 +127860 0.0001 +127910 0.0001 +127970 0.0001 +128030 0.0002 +128090 0.0002 +128150 0.0002 +128200 0.0002 +128260 0.0002 +128320 0.0002 +128380 0.0003 +128440 0.0003 +128490 0.0003 +128550 0.0003 +128610 0.0003 +128670 0.0003 +128730 0.0003 +128780 0.0004 +128840 0.0004 +128900 0.0004 +128960 0.0004 +129020 0.0005 +129070 0.0005 +129130 0.0005 +129190 0.0006 +129250 0.0006 +129310 0.0007 +129360 0.0007 +129420 0.0007 +129480 0.0008 +129540 0.0008 +129600 0.0009 +129650 0.0009 +129710 0.001 +129770 0.001 +129830 0.0011 +129890 0.0011 +129940 0.0012 +130000 0.0012 +130060 0.0013 +130120 0.0014 +130180 0.0015 +130230 0.0015 +130290 0.0016 +130350 0.0017 +130410 0.0018 +130470 0.0019 +130520 0.002 +130580 0.0021 +130640 0.0023 +130700 0.0024 +130760 0.0025 +130810 0.0026 +130870 0.0028 +130930 0.0029 +130990 0.0031 +131050 0.0032 +131100 0.0034 +131160 0.0036 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0000000000000000000000000000000000000000..bdf30e6d44d7ded5165b9664eb3a0c8cac6c5d8c --- /dev/null +++ b/database_builder/filters/jwst/miri/F2550W.dat @@ -0,0 +1,1485 @@ +# F2550W +# photon +# Includes Nominal transmission of the JWST OTE is not included. 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Source: http://svo2.cab.inta-csic.es/svo/theory/fps3/index.php?mode=browse&gname=JWST&gname2=MIRI +47530 0.0001 +47580 0.0001 +47640 0.0001 +47700 0.0001 +47760 0.0001 +47820 0.0001 +47870 0.0001 +47930 0.0001 +47990 0.0001 +48050 0.0002 +48110 0.0002 +48160 0.0003 +48220 0.0003 +48280 0.0004 +48340 0.0005 +48400 0.0006 +48450 0.0009 +48510 0.0011 +48570 0.0014 +48630 0.0017 +48690 0.0022 +48740 0.0026 +48800 0.0031 +48860 0.0035 +48920 0.004 +48980 0.0044 +49030 0.0047 +49090 0.005 +49150 0.0053 +49210 0.0056 +49270 0.006 +49320 0.0064 +49380 0.0068 +49440 0.0075 +49500 0.0083 +49560 0.0092 +49610 0.0103 +49670 0.0121 +49730 0.0139 +49790 0.0158 +49850 0.0194 +49900 0.0234 +49960 0.0274 +50020 0.0332 +50080 0.0421 +50140 0.0511 +50190 0.0601 +50250 0.0764 +50310 0.0935 +50370 0.1107 +50430 0.1302 +50480 0.1525 +50540 0.1749 +50600 0.1974 +50660 0.2123 +50720 0.2273 +50770 0.2424 +50830 0.2507 +50890 0.2536 +50950 0.2565 +51010 0.2589 +51060 0.2568 +51120 0.2547 +51180 0.2525 +51240 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/dev/null +++ b/database_builder/filters/jwst/miri/F770W.dat @@ -0,0 +1,542 @@ +# F770W +# photon +# Includes Nominal transmission of the JWST OTE is not included. Source: http://svo2.cab.inta-csic.es/svo/theory/fps3/index.php?mode=browse&gname=JWST&gname2=MIRI +62080 0.0001 +62140 0.0001 +62200 0.0001 +62260 0.0001 +62320 0.0002 +62370 0.0002 +62430 0.0003 +62490 0.0005 +62550 0.0007 +62610 0.0009 +62660 0.0008 +62720 0.0007 +62780 0.0007 +62840 0.0006 +62900 0.0005 +62950 0.0004 +63010 0.0003 +63070 0.0002 +63130 0.0002 +63190 0.0001 +63240 0.0001 +63300 0.0001 +63360 0.0001 +63420 0.0001 +63480 0.0001 +63530 0.0001 +63590 0.0002 +63650 0.0002 +63710 0.0002 +63770 0.0002 +63820 0.0002 +63880 0.0002 +63940 0.0003 +64000 0.0003 +64060 0.0004 +64110 0.0004 +64170 0.0005 +64230 0.0005 +64290 0.0007 +64350 0.0008 +64400 0.001 +64460 0.0013 +64520 0.0015 +64580 0.0018 +64640 0.0025 +64690 0.0033 +64750 0.0041 +64810 0.0052 +64870 0.0079 +64930 0.0105 +64980 0.0131 +65040 0.0194 +65100 0.0272 +65160 0.0349 +65220 0.0455 +65270 0.0637 +65330 0.0818 +65390 0.0999 +65450 0.1192 +65510 0.1388 +65560 0.1584 +65620 0.1734 +65680 0.1812 +65740 0.1889 +65800 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Element. 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Telescope Element. 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mode 100644 index 0000000000000000000000000000000000000000..ed8aec546e031ac5551214a75673484d8ac95f4e --- /dev/null +++ b/database_builder/filters/jwst/nircam/F150W.dat @@ -0,0 +1,448 @@ +# F150W +# photon +# Includes NIRCam optics, DBS, QE and JWST Optical Telescope Element. Source: http://svo2.cab.inta-csic.es/svo/theory/fps3/index.php?mode=browse&gname=JWST&gname2=NIRCam +12797.9 0.000114018 +12807.9 0.000130904 +12817.9 0.000150553 +12827.9 0.00017276 +12837.9 0.000198265 +12847.9 0.000227338 +12857.9 0.000261516 +12867.9 0.000302631 +12877.9 0.000346276 +12887.9 0.00040194 +12897.9 0.000466704 +12907.9 0.000539474 +12917.9 0.000625161 +12927.9 0.000738185 +12937.9 0.000860926 +12947.9 0.00100688 +12957.9 0.00120139 +12967.9 0.00142181 +12977.9 0.00169382 +12987.9 0.00204397 +12997.9 0.00246139 +13007.9 0.00297229 +13017.9 0.00361802 +13027.9 0.00441297 +13037.9 0.00535765 +13047.9 0.00649437 +13057.9 0.00780339 +13067.9 0.00902663 +13077.9 0.00989439 +13087.9 0.0109851 +13097.9 0.0119422 +13107.9 0.0130791 +13117.9 0.0145165 +13127.9 0.0162748 +13137.9 0.0181405 +13147.9 0.020708 +13157.9 0.0228907 +13167.9 0.0262277 +13177.9 0.0297241 +13187.9 0.0346917 +13197.9 0.040074 +13207.9 0.0475486 +13217.9 0.0556905 +13227.9 0.0659581 +13237.9 0.0769476 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0.000109001 diff --git a/database_builder/filters/jwst/nircam/F164N.dat b/database_builder/filters/jwst/nircam/F164N.dat new file mode 100644 index 0000000000000000000000000000000000000000..ca1b21bbdc7211615b6a9e2345e97b10bd68fd35 --- /dev/null +++ b/database_builder/filters/jwst/nircam/F164N.dat @@ -0,0 +1,75 @@ +# F164N +# photon +# Includes NIRCam optics, DBS, QE and JWST Optical Telescope Element. Source: http://svo2.cab.inta-csic.es/svo/theory/fps3/index.php?mode=browse&gname=JWST&gname2=NIRCam +16094 0.000131894 +16104 0.000180643 +16114 0.000282778 +16124 0.000391389 +16134 0.000634029 +16144 0.00103662 +16154 0.00181898 +16164 0.00297595 +16174 0.00487449 +16184 0.00817524 +16194 0.0107449 +16204 0.0130522 +16214 0.0152163 +16224 0.0186037 +16234 0.0208216 +16244 0.0202447 +16254 0.024827 +16264 0.0285572 +16274 0.0354254 +16284 0.0371807 +16294 0.0474915 +16304 0.0600472 +16314 0.071285 +16324 0.0916878 +16334 0.119545 +16344 0.160767 +16354 0.213657 +16364 0.272929 +16374 0.336978 +16384 0.370779 +16394 0.397567 +16404 0.420973 +16414 0.420406 +16424 0.419744 +16434 0.417256 +16444 0.421542 +16454 0.43078 +16464 0.424106 +16474 0.416873 +16484 0.417405 +16494 0.382757 +16504 0.362442 +16514 0.317987 +16524 0.27084 +16534 0.210229 +16544 0.1666 +16554 0.132709 +16564 0.100947 +16574 0.0825025 +16584 0.0666722 +16594 0.0567399 +16604 0.0506122 +16614 0.0435872 +16624 0.0349235 +16634 0.0296522 +16644 0.0297128 +16654 0.0249716 +16664 0.0218161 +16674 0.0181107 +16684 0.0132569 +16694 0.0106076 +16704 0.00709955 +16714 0.00499041 +16724 0.00297306 +16734 0.00183477 +16744 0.00111767 +16754 0.000633319 +16764 0.000433937 +16774 0.000283229 +16784 0.000214783 +16794 0.000149246 +16804 0.00011478 diff --git a/database_builder/filters/jwst/nircam/F182M.dat b/database_builder/filters/jwst/nircam/F182M.dat new file mode 100644 index 0000000000000000000000000000000000000000..94c2460db364fff02d94c62155f8c51d58298700 --- /dev/null +++ b/database_builder/filters/jwst/nircam/F182M.dat @@ -0,0 +1,385 @@ +# F182M +# photon +# Includes NIRCam optics, DBS, QE and JWST Optical Telescope Element. 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Source: http://svo2.cab.inta-csic.es/svo/theory/fps3/index.php?mode=browse&gname=JWST&gname2=NIRCam +18342 0.000103148 +18352 0.000131861 +18362 0.000171293 +18372 0.000219328 +18382 0.000298494 +18392 0.000421847 +18402 0.000622217 +18412 0.000949507 +18422 0.00151122 +18432 0.00244918 +18442 0.00390198 +18452 0.00606737 +18462 0.00905615 +18472 0.0126345 +18482 0.0163208 +18492 0.0200583 +18502 0.023646 +18512 0.0276377 +18522 0.0316866 +18532 0.0359896 +18542 0.0396152 +18552 0.0464873 +18562 0.053833 +18572 0.0638679 +18582 0.0754185 +18592 0.0917678 +18602 0.112155 +18612 0.140973 +18622 0.176981 +18632 0.221948 +18642 0.278332 +18652 0.3304 +18662 0.378472 +18672 0.413302 +18682 0.434989 +18692 0.44549 +18702 0.452087 +18712 0.453965 +18722 0.453915 +18732 0.454272 +18742 0.453325 +18752 0.452206 +18762 0.449517 +18772 0.445449 +18782 0.437419 +18792 0.425541 +18802 0.404255 +18812 0.373641 +18822 0.332361 +18832 0.284807 +18842 0.23679 +18852 0.193285 +18862 0.157641 +18872 0.128755 +18882 0.107033 +18892 0.0891157 +18902 0.0760267 +18912 0.0650723 +18922 0.0569369 +18932 0.049413 +18942 0.0433947 +18952 0.0373836 +18962 0.0317836 +18972 0.0266474 +18982 0.0216912 +18992 0.0170193 +19002 0.0125226 +19012 0.00889334 +19022 0.00608921 +19032 0.00406114 +19042 0.00261502 +19052 0.0016935 +19062 0.00111099 +19072 0.000741078 +19082 0.000508555 +19092 0.000362592 +19102 0.000260952 +19112 0.00019614 +19122 0.000149173 +19132 0.000115321 diff --git a/database_builder/filters/jwst/nircam/F200W.dat b/database_builder/filters/jwst/nircam/F200W.dat new file mode 100644 index 0000000000000000000000000000000000000000..0a77bb47f4cdc6a1987686b0a6c3abe68489e01b --- /dev/null +++ b/database_builder/filters/jwst/nircam/F200W.dat @@ -0,0 +1,612 @@ +# F200W +# photon +# Includes NIRCam optics, DBS, QE and JWST Optical Telescope Element. 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+22964 0.000122147 +22974 0.000113735 +22984 0.000106439 diff --git a/database_builder/filters/jwst/nircam/F210M.dat b/database_builder/filters/jwst/nircam/F210M.dat new file mode 100644 index 0000000000000000000000000000000000000000..d97bd910d64f590f7ce607827ec6d9cc7214a0f7 --- /dev/null +++ b/database_builder/filters/jwst/nircam/F210M.dat @@ -0,0 +1,338 @@ +# F210M +# photon +# Includes NIRCam optics, DBS, QE and JWST Optical Telescope Element. 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optics, DBS, QE and JWST Optical Telescope Element. Source: http://svo2.cab.inta-csic.es/svo/theory/fps3/index.php?mode=browse&gname=JWST&gname2=NIRCam +20793 0.000107469 +20803 0.000140004 +20813 0.000184095 +20823 0.00024885 +20833 0.000342441 +20843 0.000474071 +20853 0.000677728 +20863 0.000983255 +20873 0.00147884 +20883 0.00222807 +20893 0.00342182 +20903 0.005295 +20913 0.00797616 +20923 0.0119179 +20933 0.017092 +20943 0.0237052 +20953 0.0317775 +20963 0.0413422 +20973 0.0521817 +20983 0.0634178 +20993 0.074177 +21003 0.0832909 +21013 0.0919438 +21023 0.102108 +21033 0.113692 +21043 0.126681 +21053 0.143502 +21063 0.161998 +21073 0.184937 +21083 0.209318 +21093 0.240102 +21103 0.272345 +21113 0.307939 +21123 0.344436 +21133 0.37728 +21143 0.409575 +21153 0.433287 +21163 0.451935 +21173 0.466291 +21183 0.475341 +21193 0.477677 +21203 0.4818 +21213 0.481406 +21223 0.483143 +21233 0.48312 +21243 0.479361 +21253 0.475957 +21263 0.46871 +21273 0.45536 +21283 0.435291 +21293 0.408469 +21303 0.374007 +21313 0.339505 +21323 0.30041 +21333 0.264397 +21343 0.229902 +21353 0.198308 +21363 0.170701 +21373 0.147237 +21383 0.128825 +21393 0.111996 +21403 0.0979074 +21413 0.0847365 +21423 0.0719702 +21433 0.0604536 +21443 0.0499166 +21453 0.0409578 +21463 0.0326772 +21473 0.0256806 +21483 0.0197729 +21493 0.0147751 +21503 0.0107322 +21513 0.00751351 +21523 0.00511303 +21533 0.00337217 +21543 0.00221793 +21553 0.00145375 +21563 0.000965096 +21573 0.000658268 +21583 0.0004605 +21593 0.000325462 +21603 0.000239286 +21613 0.000176958 +21623 0.000132413 +21633 0.000103486 diff --git a/database_builder/filters/jwst/nircam/F250M.dat b/database_builder/filters/jwst/nircam/F250M.dat new file mode 100644 index 0000000000000000000000000000000000000000..0dcc56f688898fbaa765b28c7c30964dad7c9118 --- /dev/null +++ b/database_builder/filters/jwst/nircam/F250M.dat @@ -0,0 +1,238 @@ +# F250M +# photon +# Includes NIRCam optics, DBS, QE and JWST Optical Telescope Element. Source: http://svo2.cab.inta-csic.es/svo/theory/fps3/index.php?mode=browse&gname=JWST&gname2=NIRCam +23755.1 0.000107045 +23767.1 0.000145178 +23779.1 0.000185769 +23791.1 0.00024084 +23803.1 0.000312019 +23815.2 0.000398983 +23827.2 0.000506634 +23839.2 0.00064075 +23851.2 0.000809355 +23863.2 0.001017 +23875.2 0.00128451 +23887.2 0.00162052 +23899.2 0.00204708 +23911.2 0.00259079 +23923.2 0.00328686 +23935.3 0.00419312 +23947.3 0.0053728 +23959.3 0.00691475 +23971.3 0.00895136 +23983.3 0.0116533 +23995.3 0.0152514 +24007.3 0.0200345 +24019.3 0.0263824 +24031.3 0.0347689 +24043.3 0.0457316 +24055.3 0.0598474 +24067.4 0.0776469 +24079.4 0.0995236 +24091.4 0.125582 +24103.4 0.155405 +24115.4 0.187978 +24127.4 0.221705 +24139.4 0.25457 +24151.4 0.284486 +24163.4 0.309842 +24175.4 0.329849 +24187.5 0.344519 +24199.5 0.354576 +24211.5 0.361288 +24223.5 0.365878 +24235.5 0.368541 +24247.5 0.370314 +24259.5 0.371653 +24271.5 0.372821 +24283.5 0.373969 +24295.5 0.375193 +24307.6 0.376513 +24319.6 0.377895 +24331.6 0.379286 +24343.6 0.38064 +24355.6 0.381931 +24367.6 0.383136 +24379.6 0.384285 +24391.6 0.38529 +24403.6 0.386145 +24415.6 0.386837 +24427.6 0.387415 +24439.7 0.387864 +24451.7 0.388204 +24463.7 0.388444 +24475.7 0.388357 +24487.7 0.388259 +24499.7 0.388088 +24511.7 0.387843 +24523.7 0.387571 +24535.7 0.387272 +24547.7 0.386963 +24559.8 0.386806 +24571.8 0.386651 +24583.8 0.386512 +24595.8 0.386392 +24607.8 0.386257 +24619.8 0.386125 +24631.8 0.386038 +24643.8 0.386001 +24655.8 0.386005 +24667.8 0.38605 +24679.8 0.386159 +24691.9 0.386439 +24703.9 0.38671 +24715.9 0.387099 +24727.9 0.387563 +24739.9 0.388512 +24751.9 0.389231 +24763.9 0.389949 +24775.9 0.390717 +24787.9 0.391508 +24799.9 0.392366 +24812 0.393029 +24824 0.393499 +24836 0.394308 +24848 0.395018 +24860 0.395722 +24872 0.396382 +24884 0.396948 +24896 0.397422 +24908 0.397814 +24920 0.398099 +24932.1 0.398377 +24944.1 0.398617 +24956.1 0.398741 +24968.1 0.398799 +24980.1 0.398731 +24992.1 0.398555 +25004.1 0.398328 +25016.1 0.398025 +25028.1 0.397631 +25040.1 0.397208 +25052.1 0.396743 +25064.2 0.396238 +25076.2 0.395731 +25088.2 0.395237 +25100.2 0.394727 +25112.2 0.394248 +25124.2 0.393876 +25136.2 0.393604 +25148.2 0.393369 +25160.2 0.393194 +25172.2 0.393052 +25184.3 0.392945 +25196.3 0.392896 +25208.3 0.392899 +25220.3 0.392929 +25232.3 0.393004 +25244.3 0.393107 +25256.3 0.393218 +25268.3 0.39336 +25280.3 0.393524 +25292.3 0.39366 +25304.4 0.393821 +25316.4 0.394028 +25328.4 0.394315 +25340.4 0.3946 +25352.4 0.394874 +25364.4 0.395095 +25376.4 0.395297 +25388.4 0.395485 +25400.4 0.395623 +25412.4 0.395719 +25424.4 0.395792 +25436.5 0.395815 +25448.5 0.395803 +25460.5 0.395773 +25472.5 0.395685 +25484.5 0.395567 +25496.5 0.395422 +25508.5 0.395191 +25520.5 0.394974 +25532.5 0.394782 +25544.5 0.394463 +25556.6 0.39406 +25568.6 0.393571 +25580.6 0.392954 +25592.6 0.392239 +25604.6 0.391434 +25616.6 0.390512 +25628.6 0.389524 +25640.6 0.388517 +25652.6 0.387437 +25664.6 0.386403 +25676.7 0.385458 +25688.7 0.384588 +25700.7 0.383973 +25712.7 0.383967 +25724.7 0.383839 +25736.7 0.384132 +25748.7 0.384719 +25760.7 0.385522 +25772.7 0.386444 +25784.7 0.38709 +25796.7 0.387614 +25808.8 0.387396 +25820.8 0.385817 +25832.8 0.382365 +25844.8 0.376469 +25856.8 0.367363 +25868.8 0.354829 +25880.8 0.3386 +25892.8 0.318626 +25904.8 0.295261 +25916.8 0.269093 +25928.9 0.240771 +25940.9 0.211495 +25952.9 0.181672 +25964.9 0.153537 +25976.9 0.127952 +25988.9 0.105071 +26000.9 0.0852662 +26012.9 0.0685904 +26024.9 0.0548441 +26036.9 0.0437742 +26049 0.0349595 +26061 0.0278677 +26073 0.0223317 +26085 0.0179562 +26097 0.0144816 +26109 0.0117388 +26121 0.00955625 +26133 0.00780662 +26145 0.00641752 +26157 0.00529072 +26169 0.00438844 +26181.1 0.00365894 +26193.1 0.00305666 +26205.1 0.00257316 +26217.1 0.00217032 +26229.1 0.00183642 +26241.1 0.00157054 +26253.1 0.00134532 +26265.1 0.00115871 +26277.1 0.0010035 +26289.1 0.000866369 +26301.2 0.000757953 +26313.2 0.000664461 +26325.2 0.000581108 +26337.2 0.000521327 +26349.2 0.000459942 +26361.2 0.000407772 +26373.2 0.000366687 +26385.2 0.000328487 +26397.2 0.000302875 +26409.2 0.000274869 +26421.3 0.000247124 +26433.3 0.000231262 +26445.3 0.00021102 +26457.3 0.000192723 +26469.3 0.0001792 +26481.3 0.00016312 +26493.3 0.000153746 +26505.3 0.00013872 +26517.3 0.0001302 +26529.3 0.000126668 +26541.3 0.000112803 +26553.4 0.000106621 +26565.4 0.000101511 diff --git a/database_builder/filters/jwst/nircam/F277W.dat b/database_builder/filters/jwst/nircam/F277W.dat new file mode 100644 index 0000000000000000000000000000000000000000..4ca225e4f723264cca4637e729050e697e697952 --- /dev/null +++ b/database_builder/filters/jwst/nircam/F277W.dat @@ -0,0 +1,807 @@ +# F277W +# photon +# Includes NIRCam optics, DBS, QE and JWST Optical Telescope Element. Source: http://svo2.cab.inta-csic.es/svo/theory/fps3/index.php?mode=browse&gname=JWST&gname2=NIRCam +23370.8 0.000102131 +23382.8 0.000116982 +23394.8 0.000133638 +23406.8 0.000152799 +23418.8 0.000174244 +23430.8 0.000198711 +23442.9 0.000226746 +23454.9 0.000259659 +23466.9 0.000298134 +23478.9 0.000342796 +23490.9 0.00039695 +23502.9 0.000462159 +23514.9 0.000541808 +23526.9 0.000638213 +23538.9 0.000756321 +23550.9 0.000900023 +23563 0.00107562 +23575 0.00128856 +23587 0.00154269 +23599 0.00184674 +23611 0.0022055 +23623 0.00261881 +23635 0.00309215 +23647 0.00362388 +23659 0.00420953 +23671 0.00484633 +23683 0.00552886 +23695.1 0.00625344 +23707.1 0.00700609 +23719.1 0.00778862 +23731.1 0.00859829 +23743.1 0.00942745 +23755.1 0.0102371 +23767.1 0.0111128 +23779.1 0.0120649 +23791.1 0.0131103 +23803.1 0.0142788 +23815.2 0.015599 +23827.2 0.0170858 +23839.2 0.018787 +23851.2 0.0207372 +23863.2 0.0229977 +23875.2 0.025646 +23887.2 0.0287399 +23899.2 0.0323427 +23911.2 0.036561 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b/database_builder/filters/jwst/nircam/F300M.dat @@ -0,0 +1,458 @@ +# F300M +# photon +# Includes NIRCam optics, DBS, QE and JWST Optical Telescope Element. 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b/database_builder/filters/jwst/nircam/F323N.dat @@ -0,0 +1,92 @@ +# F323N +# photon +# Includes NIRCam optics, DBS, QE and JWST Optical Telescope Element. Source: http://svo2.cab.inta-csic.es/svo/theory/fps3/index.php?mode=browse&gname=JWST&gname2=NIRCam +31862 0.000103353 +31875.5 0.000141048 +31889.1 0.000173732 +31902.6 0.000221757 +31916.1 0.000261402 +31929.6 0.000318318 +31943.1 0.000385079 +31956.6 0.00048122 +31970.1 0.000608597 +31983.6 0.000782358 +31997.2 0.00102994 +32010.7 0.00136456 +32024.2 0.00185483 +32037.7 0.00254774 +32051.2 0.00359682 +32064.7 0.00517129 +32078.2 0.00769131 +32091.7 0.0117243 +32105.3 0.0185748 +32118.8 0.0302582 +32132.3 0.0502025 +32145.8 0.0825821 +32159.3 0.129635 +32172.8 0.186164 +32186.3 0.234506 +32199.8 0.265164 +32213.4 0.27598 +32226.9 0.275376 +32240.4 0.272539 +32253.9 0.272296 +32267.4 0.276237 +32280.9 0.283768 +32294.4 0.293617 +32307.9 0.30361 +32321.5 0.311909 +32335 0.316933 +32348.5 0.318519 +32362 0.317344 +32375.5 0.314337 +32389 0.310972 +32402.5 0.308443 +32416 0.307638 +32429.6 0.308758 +32443.1 0.311246 +32456.6 0.313695 +32470.1 0.312941 +32483.6 0.306665 +32497.1 0.291244 +32510.6 0.266751 +32524.1 0.235325 +32537.7 0.199068 +32551.2 0.162578 +32564.7 0.129232 +32578.2 0.100591 +32591.7 0.0772336 +32605.2 0.0589332 +32618.7 0.0448286 +32632.2 0.0341186 +32645.8 0.0260284 +32659.3 0.0199105 +32672.8 0.0153232 +32686.3 0.0118317 +32699.8 0.00919106 +32713.3 0.00715808 +32726.8 0.00562149 +32740.3 0.00442694 +32753.9 0.00352015 +32767.4 0.00281439 +32780.9 0.00226202 +32794.4 0.00183535 +32807.9 0.00148646 +32821.4 0.00122302 +32834.9 0.00099546 +32848.4 0.000827934 +32861.9 0.000681361 +32875.5 0.000573942 +32889 0.000478431 +32902.5 0.000404438 +32916 0.000344458 +32929.5 0.000288623 +32943 0.000253235 +32956.5 0.000215668 +32970 0.000197984 +32983.6 0.000167749 +32997.1 0.000152558 +33010.6 0.000132001 +33024.1 0.000119889 +33037.6 0.000112309 +33051.1 0.000100132 diff --git a/database_builder/filters/jwst/nircam/F335M.dat b/database_builder/filters/jwst/nircam/F335M.dat new file mode 100644 index 0000000000000000000000000000000000000000..c089e42c3653992547941f53acf983b8e9bc1521 --- /dev/null +++ b/database_builder/filters/jwst/nircam/F335M.dat @@ -0,0 +1,560 @@ +# F335M +# photon +# Includes NIRCam optics, DBS, QE and JWST Optical Telescope Element. Source: http://svo2.cab.inta-csic.es/svo/theory/fps3/index.php?mode=browse&gname=JWST&gname2=NIRCam +30281.1 0.000103407 +30294.6 0.000109283 +30308.1 0.000113567 +30321.6 0.000115691 +30335.1 0.000118311 +30348.7 0.000122004 +30362.2 0.000126757 +30375.7 0.000132526 +30389.2 0.000135679 +30402.7 0.000141945 +30416.2 0.000146414 +30429.7 0.000154716 +30443.2 0.000161179 +30456.8 0.000171459 +30470.3 0.000181116 +30483.8 0.000192842 +30497.3 0.000201595 +30510.8 0.000211621 +30524.3 0.000223182 +30537.8 0.000236563 +30551.3 0.000250351 +30564.9 0.000262829 +30578.4 0.000276805 +30591.9 0.000293885 +30605.4 0.00031204 +30618.9 0.00033038 +30632.4 0.000351539 +30645.9 0.000373864 +30659.4 0.00039822 +30673 0.000419386 +30686.5 0.000443469 +30700 0.000466322 +30713.5 0.000493477 +30727 0.000521088 +30740.5 0.000551405 +30754 0.00058025 +30767.5 0.000615582 +30781.1 0.000649162 +30794.6 0.000686516 +30808.1 0.000724162 +30821.6 0.000764462 +30835.1 0.000804225 +30848.6 0.00085235 +30862.1 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b/database_builder/filters/jwst/nircam/F360M.dat new file mode 100644 index 0000000000000000000000000000000000000000..18c503f01faf6ff704b9882e3b19865fabe9e554 --- /dev/null +++ b/database_builder/filters/jwst/nircam/F360M.dat @@ -0,0 +1,556 @@ +# F360M +# photon +# Includes NIRCam optics, DBS, QE and JWST Optical Telescope Element. 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0000000000000000000000000000000000000000..199806b7ab95e2f28fac26e399f1cc33bc3ae445 --- /dev/null +++ b/database_builder/filters/jwst/nircam/F430M.dat @@ -0,0 +1,334 @@ +# F430M +# photon +# Includes NIRCam optics, DBS, QE and JWST Optical Telescope Element. Source: http://svo2.cab.inta-csic.es/svo/theory/fps3/index.php?mode=browse&gname=JWST&gname2=NIRCam +40645 0.00010441 +40658.6 0.000109859 +40672.1 0.000115742 +40685.6 0.000123582 +40699.1 0.000133835 +40712.6 0.000145404 +40726.1 0.000156864 +40739.6 0.000168961 +40753.1 0.000183428 +40766.7 0.000200091 +40780.2 0.000218099 +40793.7 0.000236722 +40807.2 0.000256702 +40820.7 0.000279759 +40834.2 0.000305825 +40847.7 0.000334594 +40861.2 0.000365645 +40874.8 0.000399003 +40888.3 0.000435705 +40901.8 0.000477724 +40915.3 0.000523979 +40928.8 0.000574129 +40942.3 0.000628849 +40955.8 0.000688882 +40969.3 0.000754612 +40982.8 0.000827087 +40996.4 0.000908089 +41009.9 0.000997032 +41023.4 0.00109434 +41036.9 0.00120264 +41050.4 0.00132376 +41063.9 0.00146053 +41077.4 0.00161304 +41090.9 0.00178197 +41104.5 0.00196905 +41118 0.00217693 +41131.5 0.00240906 +41145 0.00267081 +41158.5 0.0029651 +41172 0.00329488 +41185.5 0.00366692 +41199 0.00408485 +41212.6 0.00455418 +41226.1 0.00508497 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0.000252883 +44928.4 0.000233556 +44942 0.000215098 +44955.5 0.00019906 +44969 0.0001856 +44982.5 0.000175881 +44996 0.000166653 +45009.5 0.000156813 +45023 0.000145719 +45036.5 0.000136946 +45050.1 0.000129661 +45063.6 0.000123821 +45077.1 0.000116252 +45090.6 0.000109436 +45104.1 0.000103411 diff --git a/database_builder/filters/jwst/nircam/F444W.dat b/database_builder/filters/jwst/nircam/F444W.dat new file mode 100644 index 0000000000000000000000000000000000000000..5d46be858712dde57d1ef35a79f997b630fe911f --- /dev/null +++ b/database_builder/filters/jwst/nircam/F444W.dat @@ -0,0 +1,1030 @@ +# F444W +# photon +# Includes NIRCam optics, DBS, QE and JWST Optical Telescope Element. Source: http://svo2.cab.inta-csic.es/svo/theory/fps3/index.php?mode=browse&gname=JWST&gname2=NIRCam +37131.8 0.000105079 +37145.4 0.000111043 +37158.9 0.000117881 +37172.4 0.000125669 +37185.9 0.000134103 +37199.4 0.000142807 +37212.9 0.00015187 +37226.4 0.000162043 +37239.9 0.000173402 +37253.5 0.000185178 +37267 0.000197201 +37280.5 0.000209706 +37294 0.00022309 +37307.5 0.000238074 +37321 0.000254511 +37334.5 0.000271741 +37348 0.000289914 +37361.5 0.000309707 +37375.1 0.000330673 +37388.6 0.000353334 +37402.1 0.000377173 +37415.6 0.000402053 +37429.1 0.000427952 +37442.6 0.00045533 +37456.1 0.000484329 +37469.6 0.000515273 +37483.2 0.000547963 +37496.7 0.000582708 +37510.2 0.000620142 +37523.7 0.000659979 +37537.2 0.000701959 +37550.7 0.000746257 +37564.2 0.000792952 +37577.7 0.000842476 +37591.3 0.000895015 +37604.8 0.000950179 +37618.3 0.00100817 +37631.8 0.00106941 +37645.3 0.00113391 +37658.8 0.00120198 +37672.3 0.00127372 +37685.8 0.0013491 +37699.4 0.00142862 +37712.9 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+48901.1 0.000167768 +48914.6 0.000159696 +48928.1 0.000152587 +48941.6 0.000146305 +48955.1 0.000140665 +48968.6 0.00013512 +48982.1 0.000129657 +48995.7 0.000123708 +49009.2 0.000117984 +49022.7 0.000112548 +49036.2 0.000107727 +49049.7 0.000103278 diff --git a/database_builder/filters/jwst/nircam/F466N.dat b/database_builder/filters/jwst/nircam/F466N.dat new file mode 100644 index 0000000000000000000000000000000000000000..b8658e4abf99faa5e73bc87f0ddef212ac6baac6 --- /dev/null +++ b/database_builder/filters/jwst/nircam/F466N.dat @@ -0,0 +1,138 @@ +# F466N +# photon +# Includes NIRCam optics, DBS, QE and JWST Optical Telescope Element. Source: http://svo2.cab.inta-csic.es/svo/theory/fps3/index.php?mode=browse&gname=JWST&gname2=NIRCam +45658.1 0.000107229 +45671.6 0.00014 +45685.1 0.000181014 +45698.6 0.000231183 +45712.2 0.000291353 +45725.7 0.000364578 +45739.2 0.000452281 +45752.7 0.000546802 +45766.2 0.000648996 +45779.7 0.000756019 +45793.2 0.000842916 +45806.7 0.000918859 +45820.3 0.000980502 +45833.8 0.00100989 +45847.3 0.00103247 +45860.8 0.00104946 +45874.3 0.00107545 +45887.8 0.00111628 +45901.3 0.00117287 +45914.8 0.00125862 +45928.4 0.00136785 +45941.9 0.00150418 +45955.4 0.00168509 +45968.9 0.00190269 +45982.4 0.00216516 +45995.9 0.00249768 +46009.4 0.00290064 +46022.9 0.00339197 +46036.5 0.00401061 +46050 0.00476937 +46063.5 0.00570727 +46077 0.00689024 +46090.5 0.00834957 +46104 0.0101613 +46117.5 0.0124356 +46131 0.0152531 +46144.6 0.0187596 +46158.1 0.0231345 +46171.6 0.0285685 +46185.1 0.0353462 +46198.6 0.0437771 +46212.1 0.0542423 +46225.6 0.0671992 +46239.1 0.0829122 +46252.7 0.101938 +46266.2 0.124099 +46279.7 0.14864 +46293.2 0.176046 +46306.7 0.203573 +46320.2 0.230262 +46333.7 0.256599 +46347.2 0.277555 +46360.8 0.294905 +46374.3 0.309127 +46387.8 0.316772 +46401.3 0.321937 +46414.8 0.324769 +46428.3 0.325076 +46441.8 0.32505 +46455.3 0.324641 +46468.8 0.32451 +46482.4 0.324664 +46495.9 0.325236 +46509.4 0.326164 +46522.9 0.327525 +46536.4 0.328523 +46549.9 0.329221 +46563.4 0.329675 +46576.9 0.329557 +46590.5 0.329002 +46604 0.328181 +46617.5 0.327024 +46631 0.325821 +46644.5 0.324583 +46658 0.323349 +46671.5 0.321848 +46685 0.320015 +46698.6 0.316137 +46712.1 0.310488 +46725.6 0.3019 +46739.1 0.288052 +46752.6 0.271514 +46766.1 0.249493 +46779.6 0.223638 +46793.1 0.197241 +46806.7 0.167728 +46820.2 0.139876 +46833.7 0.114643 +46847.2 0.0912094 +46860.7 0.071923 +46874.2 0.0560259 +46887.7 0.0433102 +46901.2 0.0334431 +46914.8 0.025846 +46928.3 0.0200907 +46941.8 0.0156812 +46955.3 0.0123675 +46968.8 0.00982738 +46982.3 0.00786661 +46995.8 0.00637428 +47009.3 0.00519345 +47022.9 0.00426389 +47036.4 0.00353504 +47049.9 0.00294523 +47063.4 0.00247473 +47076.9 0.00209268 +47090.4 0.00177692 +47103.9 0.00152243 +47117.4 0.00130943 +47131 0.00113057 +47144.5 0.000978761 +47158 0.000848912 +47171.5 0.000738611 +47185 0.000645273 +47198.5 0.000564872 +47212 0.00049577 +47225.5 0.000436712 +47239.1 0.00038582 +47252.6 0.000343503 +47266.1 0.000307624 +47279.6 0.000278045 +47293.1 0.000256427 +47306.6 0.000238426 +47320.1 0.000223968 +47333.6 0.000210647 +47347.1 0.000198489 +47360.7 0.000188464 +47374.2 0.000178337 +47387.7 0.000167811 +47401.2 0.000155645 +47414.7 0.000143847 +47428.2 0.000132978 +47441.7 0.000123031 +47455.2 0.000113945 +47468.8 0.000105791 diff --git a/database_builder/filters/jwst/nircam/F470N.dat b/database_builder/filters/jwst/nircam/F470N.dat new file mode 100644 index 0000000000000000000000000000000000000000..16f832dbf93877d6a54feb4195b1f7103e65a763 --- /dev/null +++ b/database_builder/filters/jwst/nircam/F470N.dat @@ -0,0 +1,134 @@ +# F470N +# photon +# Includes NIRCam optics, DBS, QE and JWST Optical Telescope Element. Source: http://svo2.cab.inta-csic.es/svo/theory/fps3/index.php?mode=browse&gname=JWST&gname2=NIRCam +46198.6 0.000105082 +46212.1 0.000111768 +46225.6 0.000119298 +46239.1 0.000128891 +46252.7 0.000139871 +46266.2 0.000152236 +46279.7 0.000166345 +46293.2 0.000182483 +46306.7 0.000202077 +46320.2 0.00022358 +46333.7 0.000247444 +46347.2 0.000274629 +46360.8 0.000306904 +46374.3 0.000344836 +46387.8 0.000392118 +46401.3 0.000450875 +46414.8 0.000523499 +46428.3 0.000616008 +46441.8 0.000726451 +46455.3 0.000858879 +46468.8 0.00102229 +46482.4 0.00121874 +46495.9 0.00145535 +46509.4 0.00173404 +46522.9 0.00206656 +46536.4 0.00245724 +46549.9 0.00291514 +46563.4 0.00345337 +46576.9 0.00408025 +46590.5 0.00481797 +46604 0.00568643 +46617.5 0.006705 +46631 0.00790399 +46644.5 0.00931658 +46658 0.0110092 +46671.5 0.0130398 +46685 0.015491 +46698.6 0.0185317 +46712.1 0.0222828 +46725.6 0.0270064 +46739.1 0.0330727 +46752.6 0.0407568 +46766.1 0.0507279 +46779.6 0.0634849 +46793.1 0.079677 +46806.7 0.0997065 +46820.2 0.123537 +46833.7 0.151693 +46847.2 0.180004 +46860.7 0.209472 +46874.2 0.23715 +46887.7 0.258311 +46901.2 0.276415 +46914.8 0.287648 +46928.3 0.294246 +46941.8 0.298276 +46955.3 0.299158 +46968.8 0.299545 +46982.3 0.299858 +46995.8 0.300184 +47009.3 0.300758 +47022.9 0.301693 +47036.4 0.302782 +47049.9 0.303789 +47063.4 0.304413 +47076.9 0.304384 +47090.4 0.303943 +47103.9 0.302553 +47117.4 0.300861 +47131 0.298839 +47144.5 0.296876 +47158 0.295183 +47171.5 0.294019 +47185 0.293503 +47198.5 0.293199 +47212 0.292714 +47225.5 0.290678 +47239.1 0.287438 +47252.6 0.278164 +47266.1 0.265547 +47279.6 0.248039 +47293.1 0.224041 +47306.6 0.198798 +47320.1 0.16983 +47333.6 0.141538 +47347.1 0.115985 +47360.7 0.0919123 +47374.2 0.0722363 +47387.7 0.0560776 +47401.2 0.0433395 +47414.7 0.0334854 +47428.2 0.0259764 +47441.7 0.0202779 +47455.2 0.0159046 +47468.8 0.0126395 +47482.3 0.0101008 +47495.8 0.00814595 +47509.3 0.00663449 +47522.8 0.00543138 +47536.3 0.00449631 +47549.8 0.0037456 +47563.3 0.00313822 +47576.9 0.00265276 +47590.4 0.00225104 +47603.9 0.00192354 +47617.4 0.00165303 +47630.9 0.00142477 +47644.4 0.00123253 +47657.9 0.00106805 +47671.4 0.000927506 +47685 0.000807287 +47698.5 0.000703241 +47712 0.000613333 +47725.5 0.000537816 +47739 0.000473594 +47752.5 0.000421701 +47766 0.000377045 +47779.5 0.000339478 +47793.1 0.00030924 +47806.6 0.000283385 +47820.1 0.000262023 +47833.6 0.000242267 +47847.1 0.00022397 +47860.6 0.0002071 +47874.1 0.000191178 +47887.6 0.000174663 +47901.2 0.000158565 +47914.7 0.000143122 +47928.2 0.000129159 +47941.7 0.000116253 +47955.2 0.000103776 diff --git a/database_builder/filters/jwst/nircam/F480M.dat b/database_builder/filters/jwst/nircam/F480M.dat new file mode 100644 index 0000000000000000000000000000000000000000..b146097e6a264e0a65b605d4458abb468dc7399a --- /dev/null +++ b/database_builder/filters/jwst/nircam/F480M.dat @@ -0,0 +1,456 @@ +# F480M +# photon +# Includes NIRCam optics, DBS, QE and JWST Optical Telescope Element. Source: http://svo2.cab.inta-csic.es/svo/theory/fps3/index.php?mode=browse&gname=JWST&gname2=NIRCam +44887.9 0.00010321 +44901.4 0.000108246 +44914.9 0.000111698 +44928.4 0.000113345 +44942 0.000117792 +44955.5 0.000118586 +44969 0.000118236 +44982.5 0.000119574 +44996 0.000127985 +45009.5 0.000135586 +45023 0.000136602 +45036.5 0.000140817 +45050.1 0.000147789 +45063.6 0.000156993 +45077.1 0.000159127 +45090.6 0.000164739 +45104.1 0.000174889 +45117.6 0.000186217 +45131.1 0.000193053 +45144.6 0.000199964 +45158.2 0.000215071 +45171.7 0.00022813 +45185.2 0.000237456 +45198.7 0.000241592 +45212.2 0.000256138 +45225.7 0.000273841 +45239.2 0.000289596 +45252.7 0.000301911 +45266.3 0.000319682 +45279.8 0.00034535 +45293.3 0.000364302 +45306.8 0.000383932 +45320.3 0.000405663 +45333.8 0.000440335 +45347.3 0.000470473 +45360.8 0.000496685 +45374.4 0.00052314 +45387.9 0.000559658 +45401.4 0.000601727 +45414.9 0.000638258 +45428.4 0.000678743 +45441.9 0.000725015 +45455.4 0.000780971 +45468.9 0.000831432 +45482.5 0.000883381 +45496 0.000942023 +45509.5 0.00100739 +45523 0.00107346 +45536.5 0.00113477 +45550 0.00120832 +45563.5 0.00128897 +45577 0.00137575 +45590.5 0.00145551 +45604.1 0.00154388 +45617.6 0.00164718 +45631.1 0.00175522 +45644.6 0.00186423 +45658.1 0.00197293 +45671.6 0.00210288 +45685.1 0.00223888 +45698.6 0.0023796 +45712.2 0.00251784 +45725.7 0.00267575 +45739.2 0.00285228 +45752.7 0.00303272 +45766.2 0.00321888 +45779.7 0.00341092 +45793.2 0.00363421 +45806.7 0.00386795 +45820.3 0.00411229 +45833.8 0.0043684 +45847.3 0.00465099 +45860.8 0.0049621 +45874.3 0.00528023 +45887.8 0.00561861 +45901.3 0.00597886 +45914.8 0.00638184 +45928.4 0.00680343 +45941.9 0.00724389 +45955.4 0.00772049 +45968.9 0.00823957 +45982.4 0.00880557 +45995.9 0.00939197 +46009.4 0.0100218 +46022.9 0.0106996 +46036.5 0.0114418 +46050 0.0122278 +46063.5 0.013057 +46077 0.0139609 +46090.5 0.014936 +46104 0.0159905 +46117.5 0.0171028 +46131 0.018299 +46144.6 0.0195937 +46158.1 0.0209916 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0.156059 +49968.5 0.152069 +49982.1 0.147897 +49995.6 0.143773 +50009.1 0.139351 +50022.6 0.135002 +50036.1 0.130514 +50049.6 0.126039 +50063.1 0.121538 +50076.6 0.116964 +50090.1 0.112563 +50103.7 0.10797 +50117.2 0.103517 +50130.7 0.0990158 +50144.2 0.0946428 +50157.7 0.0902711 +50171.2 0.0860186 +50184.7 0.0818767 +50198.2 0.0778333 +50211.8 0.0739453 +50225.3 0.0701088 +50238.8 0.0664489 +50252.3 0.0629004 +50265.8 0.0595217 +50279.3 0.0562688 +50292.8 0.0531509 +50306.3 0.0501596 +50319.9 0.0473218 +50333.4 0.0446384 +50346.9 0.0420821 +50360.4 0.0396671 +50373.9 0.037344 +50387.4 0.0351591 +50400.9 0.0331047 +50414.4 0.0311671 +50428 0.0293382 +50441.5 0.0276046 +50455 0.0259666 +50468.5 0.0244427 +50482 0.0230131 +50495.5 0.0216617 +50509 0.020388 +50522.5 0.0191786 +50536.1 0.0180506 +50549.6 0.0170063 +50563.1 0.0160215 +50576.6 0.0150931 +50590.1 0.0142142 +50603.6 0.0133851 +50617.1 0.0126264 +50630.6 0.0119146 +50644.2 0.0112428 +50657.7 0.0106084 +50671.2 0.0100076 +50684.7 0.00944902 +50698.2 0.0089349 +50711.7 0.00844477 +50725.2 0.00797823 +50738.7 0.0075383 +50752.3 0.00712316 +50765.8 0.00674796 +50779.3 0.00640168 +50792.8 0.00605772 +50806.3 0.00573237 +50819.8 0.00542654 +50833.3 0.00514279 +50846.8 0.00488468 +50860.4 0.00463419 +50873.9 0.00439114 +50887.4 0.00416401 +50900.9 0.00395035 +50914.4 0.00375778 +50927.9 0.00357732 +50941.4 0.00339398 +50954.9 0.00322009 +50968.4 0.00306027 +50982 0.0029107 +50995.5 0.00277536 diff --git a/docs/Makefile b/docs/Makefile deleted file mode 100644 index 15122473a187c7a218f3b5bc47c3dcbf88379277..0000000000000000000000000000000000000000 --- a/docs/Makefile +++ /dev/null @@ -1,178 +0,0 @@ -# Makefile for Sphinx documentation -# - -# You can set these variables from the command line. -SPHINXOPTS = -SPHINXBUILD = sphinx-build -PAPER = -BUILDDIR = _build - -# User-friendly check for sphinx-build -ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1) -$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. 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The pseudo-XML files are in $(BUILDDIR)/pseudoxml." diff --git a/docs/_templates/autosummary/base.rst b/docs/_templates/autosummary/base.rst deleted file mode 100644 index 9cabaf5238d62b16f3ff3c1fd828130815f33324..0000000000000000000000000000000000000000 --- a/docs/_templates/autosummary/base.rst +++ /dev/null @@ -1,2 +0,0 @@ -{% extends "autosummary_core/base.rst" %} -{# The template this is inherited from is in astropy/sphinx/ext/templates/autosummary_core. If you want to modify this template, it is strongly recommended that you still inherit from the astropy template. #} \ No newline at end of file diff --git a/docs/_templates/autosummary/class.rst b/docs/_templates/autosummary/class.rst deleted file mode 100644 index 6b214a5c09d3a2ed5399a65ba6100bdfd0b070ca..0000000000000000000000000000000000000000 --- a/docs/_templates/autosummary/class.rst +++ /dev/null @@ -1,2 +0,0 @@ -{% extends "autosummary_core/class.rst" %} -{# The template this is inherited from is in astropy/sphinx/ext/templates/autosummary_core. If you want to modify this template, it is strongly recommended that you still inherit from the astropy template. #} \ No newline at end of file diff --git a/docs/_templates/autosummary/module.rst b/docs/_templates/autosummary/module.rst deleted file mode 100644 index f38315b22a4929c146aebfb5f2671bb16c003fd7..0000000000000000000000000000000000000000 --- a/docs/_templates/autosummary/module.rst +++ /dev/null @@ -1,2 +0,0 @@ -{% extends "autosummary_core/module.rst" %} -{# The template this is inherited from is in astropy/sphinx/ext/templates/autosummary_core. If you want to modify this template, it is strongly recommended that you still inherit from the astropy template. #} \ No newline at end of file diff --git a/docs/conf.py b/docs/conf.py deleted file mode 100644 index bf8594cb5b13dec9ffea75405c8e1bdcefb1dd4d..0000000000000000000000000000000000000000 --- a/docs/conf.py +++ /dev/null @@ -1,228 +0,0 @@ -# -*- coding: utf-8 -*- - -# Adjust Python path to load the module -import os -import sys -sys.path.insert(0, os.path.abspath('..')) - -# Use astropy Sphinx configuration -from astropy.sphinx.conf import * - -# -- General configuration ---------------------------------------------------- - -# If your documentation needs a minimal Sphinx version, state it here. -#needs_sphinx = '1.1' - -# List of patterns, relative to source directory, that match files and -# directories to ignore when looking for source files. -exclude_patterns.append('_templates') - -# This is added to the end of RST files - a good place to put substitutions to -# be used globally. -rst_epilog += """ -""" - -# -- Project information ---------------------------------------------------- -project = u'pcigale' -author = u'The pcigale team' -copyright = u'2013, Laboratoire d\'Astrophysique de Marseille' - -# The version info for the project you're documenting, acts as replacement for -# |version| and |release|, also used in various other places throughout the -# built documents. - -import pcigale -# The short X.Y version. -version = pcigale.__version__.split('-', 1)[0] -# The full version, including alpha/beta/rc tags. -release = pcigale.__version__ - -# -- Options for HTML output -------------------------------------------------- - -# A NOTE ON HTML THEMES -# The global astropy configuration uses a custom theme, 'bootstrap-astropy', -# which is installed along with astropy. A different theme can be used or -# the options for this theme can be modified by overriding some of the -# variables set in the global configuration. The variables set in the -# global configuration are listed below, commented out. - -# Add any paths that contain custom themes here, relative to this directory. -# To use a different custom theme, add the directory containing the theme. -#html_theme_path = [] - -# The theme to use for HTML and HTML Help pages. See the documentation for -# a list of builtin themes. To override the custom theme, set this to the -# name of a builtin theme or the name of a custom theme in html_theme_path. -#html_theme = None - -# Custom sidebar templates, maps document names to template names. -#html_sidebars = {} - -# The name of an image file (within the static path) to use as favicon of the -# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 -# pixels large. -#html_favicon = '' - -# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, -# using the given strftime format. -#html_last_updated_fmt = '' - -# The name for this set of Sphinx documents. If None, it defaults to -# " v documentation". -html_title = '{0} v{1}'.format(project, release) - -# Output file base name for HTML help builder. -htmlhelp_basename = project + 'doc' - - -# -- Options for LaTeX output ------------------------------------------------- - -latex_elements = { - # The paper size ('letterpaper' or 'a4paper'). - #'papersize': 'letterpaper', - - # The font size ('10pt', '11pt' or '12pt'). - #'pointsize': '10pt', - - # Additional stuff for the LaTeX preamble. - #'preamble': '', -} - -# Grouping the document tree into LaTeX files. List of tuples -# (source start file, target name, title, author, documentclass -# [howto/manual]). -latex_documents = [ - ('index', 'pcigale.tex', u'pcigale Documentation', - u'pcigale team', 'manual'), - ] - -# The name of an image file (relative to this directory) to place at the top of -# the title page. -#latex_logo = None - -# For "manual" documents, if this is true, then toplevel headings are parts, -# not chapters. -#latex_use_parts = False - -# If true, show page references after internal links. -#latex_show_pagerefs = False - -# If true, show URL addresses after external links. -#latex_show_urls = False - -# Documents to append as an appendix to all manuals. -#latex_appendices = [] - -# If false, no module index is generated. -#latex_domain_indices = True - - -# -- Options for manual page output ------------------------------------------- - -# One entry per manual page. List of tuples -# (source start file, name, description, authors, manual section). -man_pages = [ - ('index', 'pcigale', u'pcigale Documentation', - [u'pcigale team'], 1) -] - -# If true, show URL addresses after external links. -#man_show_urls = False - - -# -- Options for Texinfo output ----------------------------------------------- - -# Grouping the document tree into Texinfo files. List of tuples -# (source start file, target name, title, author, -# dir menu entry, description, category) -texinfo_documents = [ - ('index', 'pcigale', u'pcigale Documentation', - u'pcigale team', 'pcigale', 'One line description of project.', - 'Miscellaneous'), - ] - -# Documents to append as an appendix to all manuals. -#texinfo_appendices = [] - -# If false, no module index is generated. -#texinfo_domain_indices = True - -# How to display URL addresses: 'footnote', 'no', or 'inline'. -#texinfo_show_urls = 'footnote' - -# If true, do not generate a @detailmenu in the "Top" node's menu. -#texinfo_no_detailmenu = False - - -# -- Options for Epub output -------------------------------------------------- - -# Bibliographic Dublin Core info. -epub_title = u'pcigale documentation' -epub_author = u'pcigale team' -epub_publisher = u'Laboratoire d\'Astrophysique de Marseille' -epub_copyright = u'Laboratoire d\'Astrophysique de Marseille' - -# The language of the text. It defaults to the language option -# or en if the language is not set. -#epub_language = '' - -# The scheme of the identifier. Typical schemes are ISBN or URL. -#epub_scheme = '' - -# The unique identifier of the text. This can be a ISBN number -# or the project homepage. -#epub_identifier = '' - -# A unique identification for the text. -#epub_uid = '' - -# A tuple containing the cover image and cover page html template filenames. -#epub_cover = () - -# A sequence of (type, uri, title) tuples for the guide element of content.opf. -#epub_guide = () - -# HTML files that should be inserted before the pages created by sphinx. -# The format is a list of tuples containing the path and title. -#epub_pre_files = [] - -# HTML files shat should be inserted after the pages created by sphinx. -# The format is a list of tuples containing the path and title. -#epub_post_files = [] - -# A list of files that should not be packed into the epub file. -#epub_exclude_files = [] - -# The depth of the table of contents in toc.ncx. -#epub_tocdepth = 3 - -# Allow duplicate toc entries. -#epub_tocdup = True - -# Fix unsupported image types using the PIL. -#epub_fix_images = False - -# Scale large images. -#epub_max_image_width = 0 - -# If 'no', URL addresses will not be shown. -#epub_show_urls = 'inline' - -# If false, no index is generated. -#epub_use_index = True - -## -- Options for the edit_on_github extension -------------------------------- -# -#extensions += ['astropy.sphinx.ext.edit_on_github'] -# -## Don't import the module as "version" or it will override the -## "version" configuration parameter -#from packagename import version as versionmod -#edit_on_github_project = "astropy/reponame" -#if versionmod.release: -# edit_on_github_branch = "v" + versionmod.version -#else: -# edit_on_github_branch = "master" -# -#edit_on_github_source_root = "" -#edit_on_github_doc_root = "docs" diff --git a/docs/database/filters.rst b/docs/database/filters.rst deleted file mode 100644 index 3593c070617687266a4d1b7bfa0c6c22a411ff2b..0000000000000000000000000000000000000000 --- a/docs/database/filters.rst +++ /dev/null @@ -1,3 +0,0 @@ -#################### -Filter transmissions -#################### diff --git a/docs/database/index.rst b/docs/database/index.rst deleted file mode 100644 index a65e03cdbc05789c986222bc78d0b7195c524704..0000000000000000000000000000000000000000 --- a/docs/database/index.rst +++ /dev/null @@ -1,8 +0,0 @@ -##################################### -The database distributed with pcigale -##################################### - -.. toctree:: - :maxdepth: 2 - - filters diff --git a/docs/index.rst b/docs/index.rst deleted file mode 100644 index 960517c28aa35c23322ad08007466a0af211f0f4..0000000000000000000000000000000000000000 --- a/docs/index.rst +++ /dev/null @@ -1,26 +0,0 @@ -.. pcigale documentation master file, created by - sphinx-quickstart on Wed Sep 11 16:32:56 2013. - You can adapt this file completely to your liking, but it should at least - contain the root `toctree` directive. - -Welcome to pcigale's documentation! -=================================== - -Contents: - -.. toctree:: - :maxdepth: 2 - - usage/index - creation_modules/index - stat_modules/index - database/index - programmer/index - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/programmer/index.rst b/docs/programmer/index.rst deleted file mode 100644 index 55826446083e42f019c8c0ff1e52164da8819a9a..0000000000000000000000000000000000000000 --- a/docs/programmer/index.rst +++ /dev/null @@ -1,3 +0,0 @@ -######################## -Programmer documentation -######################## diff --git a/docs/sed_modules/bc03.rst b/docs/sed_modules/bc03.rst deleted file mode 100644 index 48ac1607c356d86fd2f839341f18a5f1310b9946..0000000000000000000000000000000000000000 --- a/docs/sed_modules/bc03.rst +++ /dev/null @@ -1,3 +0,0 @@ -########################################################### -*bc03* - Bruzual & Charlot (2003) Single Stellar Population -########################################################### diff --git a/docs/sed_modules/dh2002.rst b/docs/sed_modules/dh2002.rst deleted file mode 100644 index 96b49b78169c6f2d4e666d12ceb7fcadc4b196ed..0000000000000000000000000000000000000000 --- a/docs/sed_modules/dh2002.rst +++ /dev/null @@ -1,3 +0,0 @@ -################################################################# -*dh2002* - Infra-red re-emission using Dale & Helou (2002) models -################################################################# diff --git a/docs/sed_modules/dl2007.rst b/docs/sed_modules/dl2007.rst deleted file mode 100644 index 96b49b78169c6f2d4e666d12ceb7fcadc4b196ed..0000000000000000000000000000000000000000 --- a/docs/sed_modules/dl2007.rst +++ /dev/null @@ -1,3 +0,0 @@ -################################################################# -*dh2002* - Infra-red re-emission using Dale & Helou (2002) models -################################################################# diff --git a/docs/sed_modules/dustatt_calzleit.rst b/docs/sed_modules/dustatt_calzleit.rst deleted file mode 100644 index 46e02351ebe2aa8dcff645ef0f5449020bb1b52f..0000000000000000000000000000000000000000 --- a/docs/sed_modules/dustatt_calzleit.rst +++ /dev/null @@ -1,3 +0,0 @@ -################################################################################################## -*dustatt_calzleit* - Attenuation using Calzetti *et al.* (2000) and Leitherer *et al.* (2002) laws -################################################################################################## diff --git a/docs/sed_modules/dustatt_powerlaw.rst b/docs/sed_modules/dustatt_powerlaw.rst deleted file mode 100644 index 5f256e29f9e77b148119451de2389c9036d25c72..0000000000000000000000000000000000000000 --- a/docs/sed_modules/dustatt_powerlaw.rst +++ /dev/null @@ -1,3 +0,0 @@ -###################################################### -*dustatt_powerlaw* - Simple power law dust attenuation -###################################################### diff --git a/docs/sed_modules/igmattenuation.rst b/docs/sed_modules/igmattenuation.rst deleted file mode 100644 index 798c61c40350c3d6fca726480079d93a11ec603b..0000000000000000000000000000000000000000 --- a/docs/sed_modules/igmattenuation.rst +++ /dev/null @@ -1,3 +0,0 @@ -############################################### -*igmattenuation* - Redshift and IGM attenuation -############################################### diff --git a/docs/sed_modules/index.rst b/docs/sed_modules/index.rst deleted file mode 100644 index 464166e2dec0ebd21eaaad0dc6d8e3191241e2d4..0000000000000000000000000000000000000000 --- a/docs/sed_modules/index.rst +++ /dev/null @@ -1,17 +0,0 @@ -################################## -SED creation modules documentation -################################## - -.. toctree:: - :maxdepth: 2 - - sfh2exp - sfhfromfile - m2005 - bc03 - dustatt_calzleit - dustatt_powerlaw - dh2002 - dl2007 - lines - igmattenuation diff --git a/docs/sed_modules/lines.rst b/docs/sed_modules/lines.rst deleted file mode 100644 index 894ee2c3d6035694f56aaf2c6fbd477ddc0d34b2..0000000000000000000000000000000000000000 --- a/docs/sed_modules/lines.rst +++ /dev/null @@ -1,3 +0,0 @@ -############################ -*lines* - Add emission lines -############################ diff --git a/docs/sed_modules/m2005.rst b/docs/sed_modules/m2005.rst deleted file mode 100644 index 5b91c65f8a6a6e4ed733b4b2a87e874ea0704153..0000000000000000000000000000000000000000 --- a/docs/sed_modules/m2005.rst +++ /dev/null @@ -1,3 +0,0 @@ -#################################################### -*m2005* - Maraston (2005) Single Stellar Populations -#################################################### diff --git a/docs/sed_modules/sfh2exp.rst b/docs/sed_modules/sfh2exp.rst deleted file mode 100644 index 0dc11c1ae64d7206a97069d37b28a0669989e4b6..0000000000000000000000000000000000000000 --- a/docs/sed_modules/sfh2exp.rst +++ /dev/null @@ -1,3 +0,0 @@ -################################################## -*sfh2exp* - Two exponential Star Formation History -################################################## diff --git a/docs/sed_modules/sfhfromfile.rst b/docs/sed_modules/sfhfromfile.rst deleted file mode 100644 index 5354e1b0f095c8c8f5ac783fd00371cce38312b1..0000000000000000000000000000000000000000 --- a/docs/sed_modules/sfhfromfile.rst +++ /dev/null @@ -1,3 +0,0 @@ -########################################################### -*sfhfromfile* - Read the Star Formation History from a file -########################################################### diff --git a/docs/stat_modules/index.rst b/docs/stat_modules/index.rst deleted file mode 100644 index 6029dfd3f41c8957c231ee2c40e056a5628bc76b..0000000000000000000000000000000000000000 --- a/docs/stat_modules/index.rst +++ /dev/null @@ -1,9 +0,0 @@ -################################# -Statistical modules documentation -################################# - -.. toctree:: - :maxdepth: 2 - :glob: - - * diff --git a/docs/stat_modules/psum.rst b/docs/stat_modules/psum.rst deleted file mode 100644 index 342b651649dcac5091d78c61ece329426a939172..0000000000000000000000000000000000000000 --- a/docs/stat_modules/psum.rst +++ /dev/null @@ -1,3 +0,0 @@ -#################################### -*psum* - The PSUM statistical method -#################################### diff --git a/docs/usage/index.rst b/docs/usage/index.rst deleted file mode 100644 index c0631385bdcbfbc25499656413ef49d6f240ef69..0000000000000000000000000000000000000000 --- a/docs/usage/index.rst +++ /dev/null @@ -1,11 +0,0 @@ -################## -How to use pcigale -################## - - -.. toctree:: - :maxdepth: 2 - - installation - script_usage - programming diff --git a/docs/usage/installation.rst b/docs/usage/installation.rst deleted file mode 100644 index 7ede50e92bead23753f8294574046fcfe92bab8a..0000000000000000000000000000000000000000 --- a/docs/usage/installation.rst +++ /dev/null @@ -1,3 +0,0 @@ -############ -Installation -############ diff --git a/docs/usage/programming.rst b/docs/usage/programming.rst deleted file mode 100644 index 62501b699f875d79b0afb523653c43877230a4dd..0000000000000000000000000000000000000000 --- a/docs/usage/programming.rst +++ /dev/null @@ -1,3 +0,0 @@ -############################# -How to programme with pcigale -############################# diff --git a/docs/usage/script_usage.rst b/docs/usage/script_usage.rst deleted file mode 100644 index a6fa2940b7bbebdb096551c3ae136ea22ff343a4..0000000000000000000000000000000000000000 --- a/docs/usage/script_usage.rst +++ /dev/null @@ -1,242 +0,0 @@ -######################### -How to use pcigale script -######################### - -pcigale comes with a script (a programme callable from the command line) that -will help you to run the complete analysis of a set of galaxy with known -redshift and fluxes in various filters. - -Generation of a minimal configuration files -=========================================== - -First, you need a minimal configuration file. Create a directory where you -will proceed with your analysis. In a shell, go inside this directory and -launch ``pcigale init``. This will create a *pcigale.ini* file in the -directory with that content: - -.. code-block:: cfg - :emphasize-lines: 4,9,14,17 - - # File containing the observation data to be fitted. Each flux column - # must have the name of the corresponding filter, the error columns are - # suffixed with '_err'. The values must be in mJy. - data_file = - - # Order of the modules use for SED creation. Available modules : bc03, - # dh2002, dl2007, dustatt_calzleit, dustatt_powerlaw, igmattenuation, - # lines, loadfile, m2005, sfh2exp, sfhfromfile. - creation_modules = , - - # Module used to redshift the SED before the integration in the filters. - # This is a SED creation module that accepts a 'redshift' parameter (see - # the documentation). - redshift_module = - - # Method used for statistical analysis. Available methods: psum. - analysis_method = - -You need to edit this file to complete: - -* *data_file* is the name of the file containing you observations. This is a - FITS or VO-Table file containing the observations to be analysed. It must - contain a column named *id* with an identifier for each source, a column - named *redshift* and columns containing the fluxes in *mJy* in various - filters. The flux columns must be named exactly as the corresponding filters - in the pcigale database. When a column is the error associated with a - filter, its name must prefix the filter name with *_err*. - -* *creation_modules* is the list of pcigale SED creation modules, **in the right - order**, that will be used to create the theoretical SED (see the various - module documentations). The comments above the entry list the available - modules. - -* *redshift_module* is the name of the module that will be used to redshift - and add IGM attenuation to the SED before computing the fluxes that will be - compared to observed ones. - -* *analysis_method* is the name of the statistical analysis module that will - be used. Here again, the comments list the available modules. - -Here is a sample completed minimal configuration file: - -.. code-block:: cfg - - # File containing the observation data to be fitted. Each flux column - # must have the name of the corresponding filter, the error columns are - # suffixed with '_err'. The values must be in mJy. - data_file = data.fits - - # Order of the modules use for SED creation. Available modules : bc03, - # dh2002, dl2007, dustatt_calzleit, dustatt_powerlaw, igmattenuation, - # lines, loadfile, m2005, sfh2exp, sfhfromfile. - creation_modules = sfh2exp, m2005, dustatt_calzleit, dh2002 - - # Module used to redshift the SED before the integration in the filters. - # This is a SED creation module that accepts a 'redshift' parameter (see - # the documentation). - redshift_module = igmattenuation - - # Method used for statistical analysis. Available methods: psum. - analysis_method = psum - -Generation of the main configuration file -========================================= - -You can now run the ``pcigale genconf`` command. pcigale will read the data -file to identify which columns contain filter fluxes and errors. It will then -pick each module and add their configuration section to the ini file, that -will become something like this: - -.. code-block:: cfg - - # File containing the observation data to be fitted. Each flux column - # must have the name of the corresponding filter, the error columns are - # suffixed with '_err'. The values must be in mJy. - data_file = data.fits - - # Order of the modules use for SED creation. Available modules : bc03, - # dh2002, dl2007, dustatt_calzleit, dustatt_powerlaw, igmattenuation, - # lines, loadfile, m2005, sfh2exp, sfhfromfile. - creation_modules = sfh2exp, m2005, dustatt_calzleit, dh2002 - - # Module used to redshift the SED before the integration in the filters. - # This is a SED creation module that accepts a 'redshift' parameter (see - # the documentation). - redshift_module = igmattenuation - - # Method used for statistical analysis. Available methods: psum. - analysis_method = psum - - # List of the columns in the observation data file to use for the - # fitting. - column_list = WFI_U38, WFI_U38_err, WFI_U, WFI_U_err, WFI_B, WFI_B_err, - WFI_V, WFI_V_err, WFI_R, WFI_R_err, WFI_I, WFI_I_err, WFI_z, - WFI_z_err, IRAC1, IRAC1_err, IRAC2, IRAC2_err, IRAC3, - IRAC3_err, IRAC4, IRAC4_err, MIPS1, MIPS1_err, PACS_green, - PACS_green_err - - - # Configuration of the SED creation modules. - [sed_creation_modules] - - [[sfh2exp]] - # Age of the oldest stars in the galaxy in Myr. The precision is 1 Myr. - age = - # e-folding time of the late starburst population model in Myr. - tau_burst = - # Mass fraction of the late burst population. - f_burst = - # e-folding time of the main stellar population model in Myr. - tau_main = - # Age of the late burst in Myr. Precision is 1 Myr. - burst_age = - - [[m2005]] - # Metallicity Z. - metallicity = - # Age [Myr] of the separation between the young and the old star - # populations. The default value in 10^7 years (10 Myr). Set to 0 not to - # differentiate ages (only an old population). - separation_age = 10 - # Initial mass function: salp (Salpeter) or krou (Krupa) - imf = - - [[dustatt_calzleit]] - # Width (FWHM) of the UV bump in nm. - uv_bump_width = - # Reduction factor for the E(B-V)* of the old population compared to the - # young one (<1). - E_BVs_old_factor = - # Central wavelength of the UV bump in nm. - uv_bump_wavelength = 217.5 - # Slope delta of the power law modifying the attenuation curve. - powerlaw_slope = - # E(B-V)*, the colour excess of the stellar continuum light for the - # young population. - E_BVs_young = - # Name of the contribution containing the spectrum of the young - # population. - young_contribution_name = m2005_young - # List of the filters for which the attenuation will be computed. - filters = V_B90, FUV - # Name of the contribution containing the spectrum of the old - # population. If it is set to 'None', only one population is considered. - old_contribution_name = m2005_old - # Amplitude of the UV bump in nm. - uv_bump_amplitude = - - [[dh2002]] - # List of attenuation value names (in the SED's info dictionary). A new - # re-emission contribution will be added for each one. - attenuation_value_names = - # Alpha slope. - alpha = - - - # Set the 'redshift' parameter to None (or delete the line). If there - # are other parameters, you must give only one value for each. - [redshift_configuration] - # If set to true, the cosmological dimming is applied to the fluxes. - dimming = True - # Parameter which scales the tau value at each wavelength. - rtau = 1.0 - # Redshift to apply to the galaxy. - redshift = 0.0 - - - # Configuration of the statistical analysis method. - [analysis_configuration] - # If true, save the best SED for each observation to a file. - save_best_sed = False - # List of the variables (in the SEDs info dictionaries) for which the - # statistical analysis will be done. - analysed_variables = (sfr, average_sfr) - # If true, for each observation and each analysed variable plot the - # probability density function. - plot_pdf = False - # Maximum number of bins used to compute the probability density - # function. This is only used when saving or printing the PDF. If there - # are less values, the probability is given for each one. - pdf_max_bin_number = 50 - # If true, for each observation save a plot of the best SED and the - # observed fluxes. - plot_best_sed = False - # If true, for each observation and each analysed variable plot the - # value vs reduced chi-square distribution. - plot_chi2_distribution = False - # If true, for each observation and each analysed variable save the - # probability density function. - save_pdf = False - # Type of storage used to cache the generate SED. - storage_type = memory - -If you don't want to use all the filters present in you data file, delete the -name of their columns (and error columns) from the *column_list* entry. Also, -if you want to use some filters but not the error, delete the error column -names. - -To each module is associated a set of parameters (see -:doc:`/creation_modules/index`). You may give a list of possible values for each -one, separated by commas. pcigale will compute all the possible combination of -parameter values and create the corresponding SED that will be compared to -your observations. - -.. warning:: - - For some parameters, a *single value* is in fact a list, for instance the - *analysed_variables*; in that case, use the *tuple* notation, between - parenthesis. - -.. todo:: - - In fact the parenthesis notation needs to be implemented. - -.. note:: - - You may also want to evaluate Python code to generate the list of values. You - can use a string (between quotation marks) beginning with *eval*. In this - string, you can use *numpy* with *np*. For instance, if a parameter is set to - "eval np.arange(100)", its possible will be from 0 to 99 every 1. - -Once the configuration is complete, `pcigale check` will give you the number -of SED that will be computed. You can run the analysis with `pcigale run`. diff --git a/pcigale/__init__.py b/pcigale/__init__.py index d27187488f9231e7cd2dbb3affff871e14f8805d..979bf6e2bc7d771b9a5940be6d94dd571461a4bc 100644 --- a/pcigale/__init__.py +++ b/pcigale/__init__.py @@ -3,6 +3,15 @@ # Licensed under the CeCILL-v2 licence - see Licence_CeCILL_V2-en.txt # Author: Yannick Roehlly +import os +# Set environment variables to disable multithreading as users will probably +# want to set the number of cores to the max of their computer. +os.environ["OMP_NUM_THREADS"] = "1" +os.environ["OPENBLAS_NUM_THREADS"] = "1" +os.environ["MKL_NUM_THREADS"] = "1" +os.environ["VECLIB_MAXIMUM_THREADS"] = "1" +os.environ["NUMEXPR_NUM_THREADS"] = "1" + import argparse import multiprocessing as mp import sys @@ -11,8 +20,6 @@ from .session.configuration import Configuration from .analysis_modules import get_module from .managers.parameters import ParametersManager -__version__ = "0.10.0" - def init(config): """Create a blank configuration file. @@ -39,8 +46,8 @@ def check(config): configuration = config.configuration if configuration: - print("With this configuration cigale will compute {} " - "models.".format(ParametersManager(configuration).size)) + print(f"With this configuration cigale will compute " + f"{ParametersManager(configuration).size} models.") def run(config): @@ -54,12 +61,9 @@ def run(config): def main(): - if sys.version_info[:2] < (3, 5): - raise Exception("Python {}.{} is unsupported. Please upgrade to " - "Python 3.5 or later.".format(*sys.version_info[:2])) if sys.version_info[:2] < (3, 6): - print("Python {}.{} detected. For better performance we recommend " - "Python 3.6 or later.".format(*sys.version_info[:2])) + raise Exception(f"Python {sys.version_info[0]}.{sys.version_info[1]} is" + f" unsupported. Please upgrade to Python 3.6 or later.") # We set the sub processes start method to spawn because it solves # deadlocks when a library cannot handle being used on two sides of a diff --git a/pcigale/analysis_modules/__init__.py b/pcigale/analysis_modules/__init__.py index bf1d3c1b3429ef78b9bc9ca1db0d14d1cd63719d..3112ddbd216e7f499a704a28f833535a42707f26 100644 --- a/pcigale/analysis_modules/__init__.py +++ b/pcigale/analysis_modules/__init__.py @@ -54,7 +54,7 @@ class AnalysisModule(object): if os.path.exists('out/'): name = datetime.now().strftime("%Y-%m-%d_%H:%M:%S") + '_out/' os.rename('out/', name) - print("The out/ directory was renamed to {}".format(name)) + print(f"The out/ directory was renamed to {name}") os.mkdir('out/') shutil.copy('pcigale.ini', 'out/') diff --git a/pcigale/analysis_modules/pdf_analysis/__init__.py b/pcigale/analysis_modules/pdf_analysis/__init__.py index 4305d420b1e01fe7f70c489496fe0e7aca0a0250..6436691a8394e4555e729d1f9f8ad693eaef4040 100644 --- a/pcigale/analysis_modules/pdf_analysis/__init__.py +++ b/pcigale/analysis_modules/pdf_analysis/__init__.py @@ -31,7 +31,7 @@ import multiprocessing as mp import numpy as np from .. import AnalysisModule -from ..utils import Counter +from utils.counter import Counter from .workers import sed as worker_sed from .workers import init_sed as init_worker_sed from .workers import init_analysis as init_worker_analysis @@ -55,16 +55,23 @@ class PdfAnalysis(AnalysisModule): "are many models).", ["sfh.sfr", "sfh.sfr10Myrs", "sfh.sfr100Myrs"] )), + ("bands", ( + "cigale_string_list()", + "List of bands for which to estimate the fluxes. Note that this is " + "independent from the fluxes actually fitted to estimate the " + "physical properties.", + None + )), ("save_best_sed", ( "boolean()", "If true, save the best SED for each observation to a file.", False )), ("save_chi2", ( - "boolean()", - "If true, for each observation and each analysed property, save " - "the raw chi2. It occupies ~15 MB/million models/variable.", - False + "option('all', 'none', 'properties', 'fluxes')", + "Save the raw chi2. It occupies ~15 MB/million models/variable. " + "Allowed values are 'all', 'none', 'properties', and 'fluxes'.", + "none" )), ("lim_flag", ( "boolean()", @@ -114,16 +121,17 @@ class PdfAnalysis(AnalysisModule): initargs = (models, results, Counter(len(obs))) self._parallel_job(worker_analysis, obs, initargs, - init_worker_analysis, conf['cores']) + init_worker_analysis, conf['cores'], 1) return results def _compute_best(self, conf, obs, params, results): initargs = (conf, params, obs, results, Counter(len(obs))) self._parallel_job(worker_bestfit, obs, initargs, - init_worker_bestfit, conf['cores']) + init_worker_bestfit, conf['cores'], 1) - def _parallel_job(self, worker, items, initargs, initializer, ncores): + def _parallel_job(self, worker, items, initargs, initializer, ncores, + chunksize=None): if ncores == 1: # Do not create a new process initializer(*initargs) for idx, item in enumerate(items): @@ -131,13 +139,13 @@ class PdfAnalysis(AnalysisModule): else: # run in parallel with mp.Pool(processes=ncores, initializer=initializer, initargs=initargs) as pool: - pool.starmap(worker, enumerate(items)) + pool.starmap(worker, enumerate(items), chunksize) def _compute(self, conf, obs, params): results = [] nblocks = len(params.blocks) for iblock in range(nblocks): - print('\nProcessing block {}/{}...'.format(iblock + 1, nblocks)) + print(f"\nProcessing block {iblock + 1}/{nblocks}...") # We keep the models if there is only one block. This allows to # avoid recomputing the models when we do a mock analysis if not hasattr(self, '_models'): @@ -195,6 +203,7 @@ class PdfAnalysis(AnalysisModule): obs.save('observations') results = self._compute(conf, obs, params) + print("\nSanity check of the analysis results...") results.best.analyse_chi2() print("\nSaving the analysis results...") @@ -205,7 +214,7 @@ class PdfAnalysis(AnalysisModule): # For the mock analysis we do not save the ancillary files. for k in ['best_sed', 'chi2']: - conf['analysis_params']["save_{}".format(k)] = False + conf['analysis_params'][f"save_{k}"] = False # We replace the observations with a mock catalogue.. obs.generate_mock(results) diff --git a/pcigale/analysis_modules/pdf_analysis/utils.py b/pcigale/analysis_modules/pdf_analysis/utils.py index 59c33aada1964647eeabe1e459ef2e80dd877644..7c5ff717d1a0350c08f6f25deea0bdc343c052b0 100644 --- a/pcigale/analysis_modules/pdf_analysis/utils.py +++ b/pcigale/analysis_modules/pdf_analysis/utils.py @@ -8,7 +8,7 @@ from functools import lru_cache from astropy import log -from astropy.cosmology import WMAP7 as cosmo +from ...utils.cosmology import luminosity_distance import numpy as np from scipy import optimize from scipy.constants import parsec @@ -21,8 +21,8 @@ def save_chi2(obs, variable, models, chi2, values): """Save the chi² and the associated physocal properties """ - fname = 'out/{}_{}_chi2-block-{}.npy'.format(obs.id, variable.replace('/', - '_'), models.iblock) + fname = f"out/{obs.id}_{variable.replace('/', '_')}_chi2-block-" \ + f"{models.iblock}.npy" data = np.memmap(fname, dtype=np.float64, mode='w+', shape=(2, chi2.size)) data[0, :] = chi2 @@ -48,11 +48,7 @@ def compute_corr_dz(model_z, obs): Object containing the distance and redshift of an object """ - if model_z == 0.: - mod_distance = 10. * parsec - else: - mod_distance = cosmo.luminosity_distance(model_z).value * 1e6 * parsec - return (obs.distance / mod_distance) ** 2. * \ + return (obs.distance / luminosity_distance(model_z)) ** 2. * \ (1. + model_z) / (1. + obs.redshift) @@ -256,12 +252,12 @@ def compute_chi2(models, obs, corr_dz, wz, lim_flag): # inverse error inv_flux_err = 1. / obs.flux_err[band] model = models.flux[band][wz] - chi2 += ((flux - model * scaling) * inv_flux_err) ** 2. + chi2 += ((model * scaling - flux) * inv_flux_err) ** 2. # Computation of the χ² from intensive properties for name, prop in obs.intprop.items(): model = models.intprop[name][wz] - chi2 += ((prop - model) * (1. / obs.intprop_err[name])) ** 2. + chi2 += ((model - prop) * (1. / obs.intprop_err[name])) ** 2. # Computation of the χ² from extensive properties for name, prop in obs.extprop.items(): @@ -269,7 +265,7 @@ def compute_chi2(models, obs, corr_dz, wz, lim_flag): # inverse error inv_prop_err = 1. / obs.extprop_err[name] model = models.extprop[name][wz] - chi2 += ((prop - (scaling * model) * corr_dz) * inv_prop_err) ** 2. + chi2 += (((scaling * model) * corr_dz - prop) * inv_prop_err) ** 2. # Finally take the presence of upper limits into account if limits is True: @@ -289,13 +285,15 @@ def compute_chi2(models, obs, corr_dz, wz, lim_flag): def weighted_param(param, weights): """Compute the weighted mean and standard deviation of an array of data. + Note that here we assume that the sum of the weights is normalised to 1. + This simplifies and accelerates the computation. Parameters ---------- param: array Values of the parameters for the entire grid of models weights: array - Weights by which to weight the parameter values + Weights by which to weigh the parameter values Returns ------- @@ -306,7 +304,7 @@ def weighted_param(param, weights): """ - mean = np.average(param, weights=weights) - std = np.sqrt(np.average((param-mean)**2, weights=weights)) + mean = np.sum(param * weights) + std = np.sqrt(np.sum((param - mean)**2 * weights)) return (mean, std) diff --git a/pcigale/analysis_modules/pdf_analysis/workers.py b/pcigale/analysis_modules/pdf_analysis/workers.py index cb09e8f853a948f35657e04201f39f4a60ecb752..95981dc332d6e2f8c1f635027246be79ec2964e3 100644 --- a/pcigale/analysis_modules/pdf_analysis/workers.py +++ b/pcigale/analysis_modules/pdf_analysis/workers.py @@ -10,7 +10,6 @@ from copy import deepcopy import numpy as np -from ..utils import nothread from .utils import save_chi2, compute_corr_dz, compute_chi2, weighted_param from ...warehouse import SedWarehouse @@ -28,10 +27,6 @@ def init_sed(models, counter): """ global gbl_warehouse, gbl_models, gbl_counter - # Limit the number of threads to 1 if we use MKL in order to limit the - # oversubscription of the CPU/RAM. - nothread() - gbl_warehouse = SedWarehouse() gbl_models = models @@ -103,6 +98,9 @@ def sed(idx, midx): sed = gbl_warehouse.get_sed(gbl_models.params.modules, gbl_models.params.from_index(midx)) + # The redshift is the fastest varying variable but we want to store it + # as the slowest one so that models at a given redshift are contiguous + idx = (idx % gbl_models.nz) * gbl_models.nm + idx // gbl_models.nz if 'sfh.age' in sed.info and sed.info['sfh.age'] > sed.info['universe.age']: for band in gbl_models.flux: gbl_models.flux[band][idx] = np.nan @@ -117,6 +115,7 @@ def sed(idx, midx): gbl_models.extprop[prop][idx] = sed.info[prop] for prop in gbl_models.intprop: gbl_models.intprop[prop][idx] = sed.info[prop] + gbl_models.index[idx] = midx gbl_counter.inc() @@ -141,8 +140,10 @@ def analysis(idx, obs): # work on views of the arrays and not on copies to save on RAM. z = np.array( gbl_models.conf['sed_modules_params']['redshifting']['redshift']) - wz = slice(np.abs(obs.redshift-z).argmin(), None, z.size) - corr_dz = compute_corr_dz(z[wz.start], obs) + length = gbl_models.nm + zidx = np.abs(obs.redshift-z).argmin() + wz = slice(zidx * length, (zidx + 1) * length, 1) + corr_dz = compute_corr_dz(z[zidx], obs) else: # We do not know the redshift so we use the full grid wz = slice(0, None, 1) corr_dz = 1. @@ -162,6 +163,7 @@ def analysis(idx, obs): scaling_l = scaling[wlikely] gbl_results.bayes.weight[idx] = np.nansum(likelihood) + likelihood *= 1. / gbl_results.bayes.weight[idx] # We compute the weighted average and standard deviation using the # likelihood as weight. @@ -175,8 +177,9 @@ def analysis(idx, obs): mean, std = weighted_param(_(values[wlikely]), likelihood) gbl_results.bayes.intmean[prop][idx] = mean gbl_results.bayes.interror[prop][idx] = std - if gbl_models.conf['analysis_params']['save_chi2'] is True: - save_chi2(obs, prop, gbl_models, chi2, values) + if (gbl_models.conf['analysis_params']['save_chi2'] in + ['all', 'properties']): + save_chi2(obs, prop, gbl_models, chi2, _(values)) for prop in gbl_results.bayes.extmean: if prop.endswith('_log'): @@ -189,9 +192,10 @@ def analysis(idx, obs): likelihood) gbl_results.bayes.extmean[prop][idx] = mean gbl_results.bayes.exterror[prop][idx] = std - if gbl_models.conf['analysis_params']['save_chi2'] is True: + if (gbl_models.conf['analysis_params']['save_chi2'] in + ['all', 'properties']): save_chi2(obs, prop, gbl_models, chi2, - values * scaling * corr_dz) + _(values * scaling * corr_dz)) for band in gbl_results.bayes.fluxmean: values = gbl_models.flux[band][wz] @@ -199,19 +203,14 @@ def analysis(idx, obs): likelihood) gbl_results.bayes.fluxmean[band][idx] = mean gbl_results.bayes.fluxerror[band][idx] = std - if gbl_models.conf['analysis_params']['save_chi2'] is True: + if (gbl_models.conf['analysis_params']['save_chi2'] in + ['all', 'fluxes']): save_chi2(obs, band, gbl_models, chi2, values * scaling) best_idx_z = np.nanargmin(chi2) gbl_results.best.chi2[idx] = chi2[best_idx_z] gbl_results.best.scaling[idx] = scaling[best_idx_z] - gbl_results.best.index[idx] = (wz.start + best_idx_z*wz.step + - gbl_models.block.start) - else: - # It sometimes happens because models are older than the Universe's age - print("No suitable model found for the object {}. It may be that " - "models are older than the Universe or that your chi² are very " - "large.".format(obs.id)) + gbl_results.best.index[idx] = gbl_models.index[wz][best_idx_z] gbl_counter.inc() diff --git a/pcigale/analysis_modules/savefluxes/__init__.py b/pcigale/analysis_modules/savefluxes/__init__.py index 4ff65b273783744dc084d402c327f73b536a38f8..d449c639ec27e15075481d689df40aeccc2bac8c 100644 --- a/pcigale/analysis_modules/savefluxes/__init__.py +++ b/pcigale/analysis_modules/savefluxes/__init__.py @@ -19,7 +19,7 @@ from collections import OrderedDict import multiprocessing as mp from .. import AnalysisModule -from ..utils import Counter +from utils.counter import Counter from .workers import init_fluxes as init_worker_fluxes from .workers import fluxes as worker_fluxes from ...managers.models import ModelsManager @@ -71,8 +71,7 @@ class SaveFluxes(AnalysisModule): def _compute_models(self, conf, obs, params): nblocks = len(params.blocks) for iblock in range(nblocks): - print('Computing models for block {}/{}...'.format(iblock + 1, - nblocks)) + print(f"Computing models for block {iblock + 1}/{nblocks}...") models = ModelsManager(conf, obs, params, iblock) counter = Counter(len(params.blocks[iblock]), 50, 250) @@ -86,7 +85,7 @@ class SaveFluxes(AnalysisModule): counter.pprint(len(params.blocks[iblock])) print("Saving the models ....") - models.save('models-block-{}'.format(iblock)) + models.save(f"models-block-{iblock}") def process(self, conf): diff --git a/pcigale/analysis_modules/savefluxes/workers.py b/pcigale/analysis_modules/savefluxes/workers.py index c8790f3a856e73eb32193e2db8f4cab77ccdde75..f413d8a1251456ccce31d4d5b7239929b119e1ca 100644 --- a/pcigale/analysis_modules/savefluxes/workers.py +++ b/pcigale/analysis_modules/savefluxes/workers.py @@ -8,7 +8,6 @@ import numpy as np from ...warehouse import SedWarehouse -from ..utils import nothread def init_fluxes(models, counter): @@ -26,10 +25,6 @@ def init_fluxes(models, counter): """ global gbl_warehouse, gbl_models, gbl_obs, gbl_save, gbl_counter - # Limit the number of threads to 1 if we use MKL in order to limit the - # oversubscription of the CPU/RAM. - nothread() - gbl_warehouse = SedWarehouse() gbl_models = models @@ -67,6 +62,6 @@ def fluxes(idx, midx): gbl_models.intprop[prop][idx] = sed.info[prop] if gbl_save is True: - sed.to_fits("out/{}".format(midx)) + sed.to_fits(f"out/{midx}") gbl_counter.inc() diff --git a/pcigale/data/__init__.py b/pcigale/data/__init__.py index 30ca6a76e982bb0c1e7c4c94af0e751af43bdc60..09db1022ee0e87e8ce643d6f2a1090135b79231c 100644 --- a/pcigale/data/__init__.py +++ b/pcigale/data/__init__.py @@ -413,8 +413,8 @@ class Database(object): result.spec_table) else: raise DatabaseLookupError( - "The M2005 SSP for imf <{0}> and metallicity <{1}> is not in " - "the database.".format(imf, metallicity)) + f"The M2005 SSP for imf <{imf}> and metallicity <{metallicity}>" + f" is not in the database.") def get_m2005_parameters(self): """Get parameters for the Maraston 2005 stellar models. @@ -477,8 +477,8 @@ class Database(object): result.spec_table) else: raise DatabaseLookupError( - "The BC03 SSP for imf <{0}> and metallicity <{1}> is not in " - "the database.".format(imf, metallicity)) + f"The BC03 SSP for imf <{imf}> and metallicity <{metallicity}> " + f"is not in the database.") def get_bc03_parameters(self): """Get parameters for the Bruzual & Charlot 2003 stellar models. @@ -647,8 +647,8 @@ class Database(object): result.lumin) else: raise DatabaseLookupError( - "The DL2007 model for qpah <{0}>, umin <{1}>, and umax <{2}> " - "is not in the database.".format(qpah, umin, umax)) + f"The DL2007 model for qpah <{qpah}>, umin <{umin}>, and umax " + f"<{umax}> is not in the database.") def get_dl2007_parameters(self): """Get parameters for the DL2007 models. @@ -718,9 +718,8 @@ class Database(object): result.wave, result.lumin) else: raise DatabaseLookupError( - "The DL2014 model for qpah <{0}>, umin <{1}>, umax <{2}>, and " - "alpha <{3}> is not in the database." - .format(qpah, umin, umax, alpha)) + f"The DL2014 model for qpah <{qpah}>, umin <{umin}>, umax " + f"<{umax}>, and alpha <{alpha}> is not in the database.") def get_dl2014_parameters(self): """Get parameters for the DL2014 models. @@ -786,8 +785,8 @@ class Database(object): result.lumin) else: raise DatabaseLookupError( - "The Dale2014 template for frac_agn <{0}> and alpha <{1}> " - "is not in the database.".format(frac_agn, alpha)) + f"The Dale2014 template for frac_agn <{frac_agn}> and alpha " + f"<{alpha}> is not in the database.") def get_dale2014_parameters(self): """Get parameters for the Dale 2014 models. @@ -1032,8 +1031,8 @@ class Database(object): result.lumin) else: raise DatabaseLookupError( - "The Schreiber2016 template for type <{0}> and tdust <{1}> " - "is not in the database.".format(type, tdust)) + f"The Schreiber2016 template for type <{type}> and tdust " + f"<{tdust}> is not in the database.") def get_schreiber2016_parameters(self): """Get parameters for the Scnreiber 2016 models. @@ -1104,9 +1103,8 @@ class Database(object): result.wave, result.lumin) else: raise DatabaseLookupError( - "The THEMIS model for qhac <{0}>, umin <{1}>, umax <{2}>, and " - "alpha <{3}> is not in the database." - .format(qhac, umin, umax, alpha)) + f"The THEMIS model for qhac <{qhac}>, umin <{umin}>, umax " + f"<{umax}>, and alpha <{alpha}> is not in the database.") def _get_parameters(self, schema): """Generic function to get parameters from an arbitrary schema. @@ -1186,7 +1184,7 @@ class Database(object): raise Exception('The database is not writable.') else: raise DatabaseLookupError( - "The filter <{0}> is not in the database".format(name)) + f"The filter <{name}> is not in the database") def get_filter(self, name): """ @@ -1215,7 +1213,7 @@ class Database(object): result.pivot_wavelength) else: raise DatabaseLookupError( - "The filter <{0}> is not in the database".format(name)) + f"The filter <{name}> is not in the database") def get_filter_names(self): """Get the list of the name of the filters in the database. diff --git a/pcigale/managers/models.py b/pcigale/managers/models.py index 9b8fc6dfb65345b9495123e351e09b1eeef02bfd..15af9de1353120818da2dc084e9e7b25ab4086cf 100644 --- a/pcigale/managers/models.py +++ b/pcigale/managers/models.py @@ -9,6 +9,8 @@ compute them, such as the configuration, the observations, and the parameters of the models. """ +import ctypes + from astropy.table import Table, Column from .utils import SharedArray, get_info @@ -37,11 +39,20 @@ class ModelsManager(object): self.allintpropnames & props_nolog) self.extpropnames = (self.allextpropnames & set(obs.extprops) | self.allextpropnames & props_nolog) + if 'bands' in conf['analysis_params']: + bandnames = set(obs.bands+conf['analysis_params']['bands']) + else: + bandnames = obs.bands + size = len(params.blocks[iblock]) + if conf['parameters_file'] is "": + self.nz = len(conf['sed_modules_params']['redshifting']['redshift']) + self.nm = size // self.nz - self.flux = {band: SharedArray(size) for band in obs.bands} + self.flux = {band: SharedArray(size) for band in bandnames} self.intprop = {prop: SharedArray(size) for prop in self.intpropnames} self.extprop = {prop: SharedArray(size) for prop in self.extpropnames} + self.index = SharedArray(size, ctypes.c_uint32) def save(self, filename): """Save the fluxes and properties of all the models into a table. @@ -66,6 +77,6 @@ class ModelsManager(object): for prop in sorted(self.intprop.keys()): table.add_column(Column(self.intprop[prop], name=prop)) - table.write("out/{}.fits".format(filename)) - table.write("out/{}.txt".format(filename), format='ascii.fixed_width', + table.write(f"out/{filename}.fits") + table.write(f"out/{filename}.txt", format='ascii.fixed_width', delimiter=None) diff --git a/pcigale/managers/observations.py b/pcigale/managers/observations.py index 6ce52ddf187492277a243e931b94977536adc614..c429b20d9fe34f2e64106d133280c604329f4bce 100644 --- a/pcigale/managers/observations.py +++ b/pcigale/managers/observations.py @@ -3,12 +3,12 @@ # Licensed under the CeCILL-v2 licence - see Licence_CeCILL_V2-en.txt # Author: Médéric Boquien -from astropy.cosmology import WMAP7 as cosmo from astropy.table import Column import numpy as np from scipy.constants import parsec -from ..utils import read_table +from ..utils.cosmology import luminosity_distance +from utils.io import read_table from .utils import get_info @@ -103,15 +103,15 @@ class ObservationsManagerPassbands(object): """ for item in self.tofit + self.tofit_err: if item not in self.table.colnames: - raise Exception("{} to be taken in the fit but not present " - "in the observation table.".format(item)) + raise Exception(f"{item} to be taken in the fit but not present" + f" in the observation table.") for item in self.table.colnames: if (item != 'id' and item != 'redshift' and item != 'distance' and item not in self.tofit + self.tofit_err): self.table.remove_column(item) - print("Warning: {} in the input file but not to be taken into" - " account in the fit.".format(item)) + print(f"Warning: {item} in the input file but not to be taken " + f"into account in the fit.") def _check_errors(self, defaulterror=0.1): """Check whether the error columns are present. If not, add them. @@ -148,9 +148,8 @@ class ObservationsManagerPassbands(object): name=error) self.table.add_column(colerr, index=self.table.colnames.index(item)+1) - print("Warning: {}% of {} taken as errors.".format(defaulterror * - 100., - item)) + print(f"Warning: {defaulterror * 100}% of {item} taken as " + f"errors.") def _check_invalid(self, upperlimits=False, threshold=-9990.): """Check whether invalid data are correctly marked as such. @@ -194,8 +193,7 @@ class ObservationsManagerPassbands(object): self.extprops.remove(item) self.extprops_err.remove(item + '_err') self.table.remove_columns([item, item + '_err']) - print("Warning: {} removed as no valid data was found.".format( - allinvalid)) + print(f"Warning: {allinvalid} removed as no valid data was found.") def _add_model_error(self, modelerror=0.1): """Add in quadrature the error of the model to the input error. @@ -256,9 +254,9 @@ class ObservationsManagerPassbands(object): Root of the filename where to save the observations. """ - self.table.write('out/{}.fits'.format(filename)) - self.table.write('out/{}.txt'.format(filename), - format='ascii.fixed_width', delimiter=None) + self.table.write(f'out/{filename}.fits') + self.table.write(f'out/{filename}.txt', format='ascii.fixed_width', + delimiter=None) class ObservationsManagerVirtual(object): @@ -301,11 +299,8 @@ class Observation(object): if 'distance' in row.colnames and np.isfinite(row['distance']): self.distance = row['distance'] * parsec * 1e6 else: - if self.redshift == 0.: - self.distance = 10. * parsec - elif self.redshift > 0.: - self.distance = cosmo.luminosity_distance(self.redshift).value \ - * 1e6 * parsec + if self.redshift >= 0.: + self.distance = luminosity_distance(self.redshift) else: self.distance = np.nan self.flux = {k: row[k] for k in cls.bands diff --git a/pcigale/managers/parameters.py b/pcigale/managers/parameters.py index 0306a603442ede8a627256396883d951de74f655..67c7d35ddb1f8a5bfe6570f64f29c8eccc966cb4 100644 --- a/pcigale/managers/parameters.py +++ b/pcigale/managers/parameters.py @@ -8,7 +8,7 @@ import collections import itertools import numpy as np -from ..utils import read_table +from utils.io import read_table class ParametersManager(object): diff --git a/pcigale/managers/results.py b/pcigale/managers/results.py index 923f94b617c0e8e011316ce36d86f6e772334fd6..24fdd6819dac94b4c69ac0299a3dc9d66013bef0 100644 --- a/pcigale/managers/results.py +++ b/pcigale/managers/results.py @@ -10,6 +10,7 @@ along with the names of the parameters, which are proportional to the mass, etc. Each of these classes contain a merge() method that allows to combine results of the analysis with different blocks of models. """ +import ctypes from astropy.table import Table, Column import numpy as np @@ -36,6 +37,7 @@ class BayesResultsManager(object): intpropnames = [prop for prop in models.obs.conf['analysis_params']['variables'] if (prop in models.allintpropnames or prop[:-4] in models.allintpropnames)] + fluxnames = [name for name in models.conf['analysis_params']['bands']] self.nproperties = len(intpropnames) + len(extpropnames) # Arrays where we store the data related to the models. For memory @@ -47,8 +49,8 @@ class BayesResultsManager(object): self.interror = {prop: SharedArray(nobs) for prop in intpropnames} self.extmean = {prop: SharedArray(nobs) for prop in extpropnames} self.exterror = {prop: SharedArray(nobs) for prop in extpropnames} - self.fluxmean = {band: SharedArray(nobs) for band in models.flux} - self.fluxerror = {band: SharedArray(nobs) for band in models.flux} + self.fluxmean = {band: SharedArray(nobs) for band in fluxnames} + self.fluxerror = {band: SharedArray(nobs) for band in fluxnames} self.weight = SharedArray(nobs) @property @@ -112,10 +114,10 @@ class BayesResultsManager(object): for band in merged.fluxerror} weight = np.array([result.weight for result in results]) - totweight = np.sum(weight, axis=0) + totweight = np.nansum(weight, axis=0) for prop in merged.intmean: - merged.intmean[prop][:] = np.sum( + merged.intmean[prop][:] = np.nansum( intmean[prop] * weight, axis=0) / totweight # We compute the merged standard deviation by combining the @@ -123,11 +125,11 @@ class BayesResultsManager(object): # http://stats.stackexchange.com/a/10445 where the number of # datapoints has been substituted with the weights. In short we # exploit the fact that Var(X) = E(Var(X)) + Var(E(X)). - merged.interror[prop][:] = np.sqrt(np.sum( + merged.interror[prop][:] = np.sqrt(np.nansum( weight * (interror[prop]**2. + (intmean[prop]-merged.intmean[prop])**2), axis=0) / totweight) for prop in merged.extmean: - merged.extmean[prop][:] = np.sum( + merged.extmean[prop][:] = np.nansum( extmean[prop] * weight, axis=0) / totweight # We compute the merged standard deviation by combining the @@ -135,7 +137,7 @@ class BayesResultsManager(object): # http://stats.stackexchange.com/a/10445 where the number of # datapoints has been substituted with the weights. In short we # exploit the fact that Var(X) = E(Var(X)) + Var(E(X)). - merged.exterror[prop][:] = np.sqrt(np.sum( + merged.exterror[prop][:] = np.sqrt(np.nansum( weight * (exterror[prop]**2. + (extmean[prop]-merged.extmean[prop])**2), axis=0) / totweight) for prop in merged.extmean: @@ -148,7 +150,7 @@ class BayesResultsManager(object): merged.exterror[prop]) for band in merged.fluxmean: - merged.fluxmean[band][:] = np.sum( + merged.fluxmean[band][:] = np.nansum( fluxmean[band] * weight, axis=0) / totweight # We compute the merged standard deviation by combining the @@ -156,7 +158,7 @@ class BayesResultsManager(object): # http://stats.stackexchange.com/a/10445 where the number of # datapoints has been substituted with the weights. In short we # exploit the fact that Var(X) = E(Var(X)) + Var(E(X)). - merged.fluxerror[band][:] = np.sqrt(np.sum( + merged.fluxerror[band][:] = np.sqrt(np.nansum( weight * (fluxerror[band]**2. + (fluxmean[band]-merged.fluxmean[band])**2), axis=0) / totweight) @@ -189,9 +191,7 @@ class BestResultsManager(object): for prop in allextpropnames} self.chi2 = SharedArray(nobs) self.scaling = SharedArray(nobs) - - # We store the index as a float to work around python issue #10746 - self.index = SharedArray(nobs) + self.index = SharedArray(nobs, ctypes.c_uint32) @property def flux(self): @@ -284,22 +284,22 @@ class BestResultsManager(object): if len(results) == 1: return results[0] - best = np.argmin([result.chi2 for result in results], axis=0) - + chi2 = np.array([result.chi2 for result in results]) merged = results[0] - for iobs, bestidx in enumerate(best): - for band in merged.flux: - merged.flux[band][iobs] = \ - results[bestidx].flux[band][iobs] - for prop in merged.intprop: - merged.intprop[prop][iobs] = \ - results[bestidx].intprop[prop][iobs] - for prop in merged.extprop: - merged.extprop[prop][iobs] = \ - results[bestidx].extprop[prop][iobs] - merged.chi2[iobs] = results[bestidx].chi2[iobs] - merged.scaling[iobs] = results[bestidx].scaling[iobs] - merged.index[iobs] = results[bestidx].index[iobs] + for iobs, bestidx in enumerate(np.argsort(chi2, axis=0)[0, :]): + if np.isfinite(bestidx): + for band in merged.flux: + merged.flux[band][iobs] = \ + results[bestidx].flux[band][iobs] + for prop in merged.intprop: + merged.intprop[prop][iobs] = \ + results[bestidx].intprop[prop][iobs] + for prop in merged.extprop: + merged.extprop[prop][iobs] = \ + results[bestidx].extprop[prop][iobs] + merged.chi2[iobs] = results[bestidx].chi2[iobs] + merged.scaling[iobs] = results[bestidx].scaling[iobs] + merged.index[iobs] = results[bestidx].index[iobs] return merged @@ -308,14 +308,23 @@ class BestResultsManager(object): objects seems to be overconstrainted. """ + # If no best model has been found, it means none could be properly + # fitted. We warn the user in that case + bad = [str(id_) for id_ in self.obs.table['id'][np.isnan(self.chi2)]] + if len(bad) > 0: + print(f"No suitable model found for {', '.join(bad)}. It may be " + f"that models are older than the universe or that your χ² are" + f" very large.") + obs = [self.obs.table[obs].data for obs in self.obs.tofit] nobs = np.count_nonzero(np.isfinite(obs), axis=0) chi2_red = self.chi2 / (nobs - 1) # If low values of reduced chi^2, it means that the data are overfitted # Errors might be under-estimated or not enough valid data. - print("\n{}% of the objects have chi^2_red~0 and {}% chi^2_red<0.5" - .format(np.round((chi2_red < 1e-12).sum() / chi2_red.size, 1), - np.round((chi2_red < 0.5).sum() / chi2_red.size, 1))) + print(f"{np.round((chi2_red < 1e-12).sum() / chi2_red.size, 1)}% of " + f"the objects have χ²_red~0 and " + f"{np.round((chi2_red < 0.5).sum() / chi2_red.size, 1)}% " + f"χ²_red<0.5") class ResultsManager(object): @@ -405,6 +414,6 @@ class ResultsManager(object): name="best."+band, unit=unit)) - table.write("out/{}.txt".format(filename), format='ascii.fixed_width', + table.write(f"out/{filename}.txt", format='ascii.fixed_width', delimiter=None) - table.write("out/{}.fits".format(filename), format='fits') + table.write(f"out/{filename}.fits", format='fits') diff --git a/pcigale/managers/utils.py b/pcigale/managers/utils.py index 7b32de5a1dff3c76992f7029bc5a786a3fda7c8f..ed20d945254759c76c6339fa66d8132be0584ad6 100644 --- a/pcigale/managers/utils.py +++ b/pcigale/managers/utils.py @@ -37,7 +37,7 @@ class SharedArray(object): implementation and if new operations are done on these arrays, it may be necessary to define them here. """ - def __init__(self, size): + def __init__(self, size, dtype=ctypes.c_double): """The RawArray is stored in raw, which is protected by a setter and a getter. The array property returns raw as a regular Numpy array. It is important to access both the RawArray and the Numpy array forms. The @@ -47,29 +47,30 @@ class SharedArray(object): issue we selectively work with array or raw depending on whether the operation is done with a slice or not. """ - self.raw = RawArray(ctypes.c_double, size) + self.raw = RawArray(dtype, size) self.size = size + # By default RawArray initialises all the elements to 0. Setting them to + # np.nan is preferanble to in case for a reason some elements are never + # assigned a value during a run + self.array[:] = np.nan def __setitem__(self, idx, data): - if isinstance(idx, slice): - self.array[idx] = data - else: - self._raw[idx] = data + self._raw[idx] = data def __getitem__(self, idx): - if isinstance(idx, slice): - return self.array[idx] - return self._raw[idx] + if isinstance(idx, int): + return self._raw[idx] + return self.array[idx] def __len__(self): return self.size def __rmul__(self, other): - return other * self.array + return other * self._array @property def array(self): - return np.ctypeslib.as_array(self._raw) + return self._array @property def raw(self): @@ -79,5 +80,6 @@ class SharedArray(object): def raw(self, raw): if isinstance(raw, ctypes.Array): self._raw = raw + self._array = np.ctypeslib.as_array(self._raw) else: raise TypeError("Type must be RawArray.") diff --git a/pcigale/sed/__init__.py b/pcigale/sed/__init__.py index 5ad006e439424e9785ca5a5e311f11ca02a5050e..1ba116873cfe210001e2a0cf8cd091160a9e78b7 100644 --- a/pcigale/sed/__init__.py +++ b/pcigale/sed/__init__.py @@ -220,9 +220,6 @@ class SED(object): def get_lumin_contribution(self, name): """Get the luminosity vector of a given contribution - If the name of the contribution is not unique in the SED, the flux of - the last one is returned. - Parameters ---------- name: string @@ -235,10 +232,7 @@ class SED(object): wavelength grid. """ - # Find the index of the _last_ name element - idx = (len(self.contribution_names) - 1 - - self.contribution_names[::-1].index(name)) - return self.luminosities[idx] + return self.luminosities[self.contribution_names.index(name)] def compute_fnu(self, filter_name): """ diff --git a/pcigale/sed/io/fits.py b/pcigale/sed/io/fits.py index 529ad8f56a3224a0c8b66fb001962fa45030e13f..7f295c2a328b778f594cbe5c93dc3040dbe14e2a 100644 --- a/pcigale/sed/io/fits.py +++ b/pcigale/sed/io/fits.py @@ -37,10 +37,10 @@ def save_sed_to_fits(sed, prefix, norm=1.): for name in sed.contribution_names: table[name] = Column(norm * sed.get_lumin_contribution(name), unit="W/nm") - table.write("{}_best_model.fits".format(prefix)) + table.write(f"{prefix}_best_model.fits") if sed.sfh is not None: table = Table(meta=info) table["time"] = Column(np.arange(sed.sfh.size), unit="Myr") table["SFR"] = Column(norm * sed.sfh, unit="Msun/yr") - table.write("{}_SFH.fits".format(prefix)) + table.write(f"{prefix}_SFH.fits") diff --git a/pcigale/sed_modules/bc03.py b/pcigale/sed_modules/bc03.py index 78bb2588d38ccd8dfb47ff918159341a9517e597..0fa0268b90a0eca10b9d7d29e9fe775c93f89506 100644 --- a/pcigale/sed_modules/bc03.py +++ b/pcigale/sed_modules/bc03.py @@ -63,7 +63,7 @@ class BC03(SedModule): elif self.imf == 1: self.ssp = database.get_bc03('chab', self.metallicity) else: - raise Exception("IMF #{} unknown".format(self.imf)) + raise Exception(f"IMF #{self.imf} unknown") def process(self, sed): """Add the convolution of a Bruzual and Charlot SSP to the SED diff --git a/pcigale/sed_modules/dl2007.py b/pcigale/sed_modules/dl2007.py index 4a51bd1cad50766064c5f0187bc57338e5dae2b3..be4026ba7f785e9a86981f72b097e284c0f68223 100644 --- a/pcigale/sed_modules/dl2007.py +++ b/pcigale/sed_modules/dl2007.py @@ -71,6 +71,11 @@ class DL2007(SedModule): self.umax = float(self.parameters["umax"]) self.gamma = float(self.parameters["gamma"]) + # We also compute + self.umean = (1. - self.gamma) * self.umin + \ + self.gamma * np.log(self.umax / self.umin) / \ + (1. / self.umin - 1. / self.umax) + with Database() as database: self.model_minmin = database.get_dl2007(self.qpah, self.umin, self.umin) @@ -110,6 +115,7 @@ class DL2007(SedModule): sed.add_info('dust.qpah', self.qpah) sed.add_info('dust.umin', self.umin) sed.add_info('dust.umax', self.umax) + sed.add_info('dust.umean', self.umean) sed.add_info('dust.gamma', self.gamma) # To compute the dust mass we simply divide the luminosity in W by the # emissivity in W/kg of dust. diff --git a/pcigale/sed_modules/dl2014.py b/pcigale/sed_modules/dl2014.py index 5ee4c8194ae365354dede78c1962eba383f645fa..340b6e71e76e483067ddcddb01080ff414f1a650 100644 --- a/pcigale/sed_modules/dl2014.py +++ b/pcigale/sed_modules/dl2014.py @@ -77,7 +77,24 @@ class DL2014(SedModule): self.umin = float(self.parameters["umin"]) self.alpha = float(self.parameters["alpha"]) self.gamma = float(self.parameters["gamma"]) + + # We also compute . For this we consider Eq. 6 and 15 of Draine & Li + # (2007) taking into account that α can be different from 2. We then + # just compute the integral. We have two specific cases, α=1 and α=2. self.umax = 1e7 + self.umean = (1. - self.gamma) * self.umin + if self.alpha == 1.0: + self.umean += self.gamma * (self.umax - self.umin) / \ + np.log(self.umax / self.umin) + elif self.alpha == 2.0: + self.umean += self.gamma * np.log(self.umax / self.umin) / \ + (1. / self.umin - 1. / self.umax) + else: + oma = 1. - self.alpha + tma = 2. - self.alpha + self.umean += self.gamma * oma / tma * \ + (self.umin**tma - self.umax**tma) / \ + (self.umin**oma - self.umax**oma) with Database() as database: self.model_minmin = database.get_dl2014(self.qpah, self.umin, @@ -117,6 +134,7 @@ class DL2014(SedModule): sed.add_module(self.name, self.parameters) sed.add_info('dust.qpah', self.qpah) sed.add_info('dust.umin', self.umin) + sed.add_info('dust.umean', self.umean) sed.add_info('dust.alpha', self.alpha) sed.add_info('dust.gamma', self.gamma) # To compute the dust mass we simply divide the luminosity in W by the diff --git a/pcigale/sed_modules/fluxes.py b/pcigale/sed_modules/fluxes.py index 2dbc74d96b0a5459a3a1af5cce22c80bcef4fd8a..4a553dc77dcd897945abc3c2850de5806fa28e83 100644 --- a/pcigale/sed_modules/fluxes.py +++ b/pcigale/sed_modules/fluxes.py @@ -56,7 +56,7 @@ class Fluxes(SedModule): for filter_ in filter_list: sed.add_info( - "param.{}".format(filter_), + f"param.{filter_}", sed.compute_fnu(filter_), True ) diff --git a/pcigale/sed_modules/fritz2006.py b/pcigale/sed_modules/fritz2006.py index 69208311796d85459a4dc1458577f43b45ad4e50..4aa8b55b90adaa31bd1f92fd190f025e1a2fc6a6 100644 --- a/pcigale/sed_modules/fritz2006.py +++ b/pcigale/sed_modules/fritz2006.py @@ -100,6 +100,10 @@ class Fritz2006(SedModule): self.fritz2006 = base.get_fritz2006(self.r_ratio, self.tau, self.beta, self.gamma, self.opening_angle, self.psy) + self.l_agn_scatt = np.trapz(self.fritz2006.lumin_scatt, + x=self.fritz2006.wave) + self.l_agn_agn = np.trapz(self.fritz2006.lumin_agn, + x=self.fritz2006.wave) def process(self, sed): """Add the IR re-emission contributions @@ -128,10 +132,8 @@ class Fritz2006(SedModule): if self.fracAGN < 1.: agn_power = luminosity * (1./(1.-self.fracAGN) - 1.) l_agn_therm = agn_power - l_agn_scatt = np.trapz(agn_power * self.fritz2006.lumin_scatt, - x=self.fritz2006.wave) - l_agn_agn = np.trapz(agn_power * self.fritz2006.lumin_agn, - x=self.fritz2006.wave) + l_agn_scatt = agn_power * self.l_agn_scatt + l_agn_agn = agn_power * self.l_agn_agn l_agn_total = l_agn_therm + l_agn_scatt + l_agn_agn else: diff --git a/pcigale/sed_modules/loadfile.py b/pcigale/sed_modules/loadfile.py index cc5da2c349db8e06b05ec0ea26861324b409bb39..4594ad7bac7e9b778f9655770ca3aae100a8d13d 100644 --- a/pcigale/sed_modules/loadfile.py +++ b/pcigale/sed_modules/loadfile.py @@ -13,7 +13,7 @@ This module reads a SED spectrum from a file. from collections import OrderedDict -from ..utils import read_table +from utils.io import read_table from . import SedModule diff --git a/pcigale/sed_modules/m2005.py b/pcigale/sed_modules/m2005.py index 3daf68f8c5cb2980439b8c4dbe92092ddf73492c..5090f27b1a9efa4573ced0e4ba0476fc1879965b 100644 --- a/pcigale/sed_modules/m2005.py +++ b/pcigale/sed_modules/m2005.py @@ -61,7 +61,7 @@ class M2005(SedModule): with Database() as database: self.ssp = database.get_m2005('krou', self.metallicity) else: - raise Exception("IMF #{} unknown".format(self.imf)) + raise Exception(f"IMF #{self.imf} unknown") def process(self, sed): """Add the convolution of a Maraston 2005 SSP to the SED diff --git a/pcigale/sed_modules/redshifting.py b/pcigale/sed_modules/redshifting.py index a209a5a706c083435c27fc01997888c2f4ed03fd..5b8dfa4a05944166c6b11a5d181a91097cfd2db3 100644 --- a/pcigale/sed_modules/redshifting.py +++ b/pcigale/sed_modules/redshifting.py @@ -23,7 +23,7 @@ from collections import OrderedDict import numpy as np from scipy.constants import parsec from scipy.special import factorial -from astropy.cosmology import WMAP7 as cosmology +from ..utils.cosmology import age, luminosity_distance from . import SedModule @@ -160,16 +160,11 @@ class Redshifting(SedModule): # Raise an error when applying a negative redshift. This module is # not for blue-shifting. if self.redshift < 0.: - raise Exception("The redshift provided is negative <{}>." - .format(self.redshift)) + raise Exception(f"The redshift provided is negative " + f"({self.redshift}).") - self.universe_age = cosmology.age(self.redshift).value * 1000. - if self.redshift == 0.: - self.luminosity_distance = 10. * parsec - else: - self.luminosity_distance = ( - cosmology.luminosity_distance(self.redshift).value * 1e6 * - parsec) + self.universe_age = age(self.redshift) + self.luminosity_distance = luminosity_distance(self.redshift) # We do not define the values of the IGM attenuation component yet. # This is because we need the wavelength grid for that first. This # will be assigned on the first call. @@ -188,8 +183,8 @@ class Redshifting(SedModule): # If the SED is already redshifted, raise an error. if ('universe.redshift' in sed.info and sed.info['universe.redshift'] > 0.): - raise Exception("The SED is already redshifted ." - .format(sed.info['universe.redshift'])) + raise Exception(f"The SED is already redshifted (z=" + f"{sed.info['universe.redshift']}).") if redshift > 0.: # We redshift directly the SED wavelength grid diff --git a/pcigale/sed_modules/restframe_parameters.py b/pcigale/sed_modules/restframe_parameters.py index 9bf6daa4dd880c9fbb9f2e53a26c82db15f46c4c..b531ab77c9a9580e99e9b5ada5db71339e185dd8 100644 --- a/pcigale/sed_modules/restframe_parameters.py +++ b/pcigale/sed_modules/restframe_parameters.py @@ -220,14 +220,14 @@ class RestframeParam(SedModule): if 'nebular.lines_young' in sed.contribution_names: for line, EW in self.EW(sed).items(): - sed.add_info("param.EW({}/{})".format(*line), EW) + sed.add_info(f"param.EW({line[0]}/{line[1]})", EW) for filt in self.lumin_filters: - sed.add_info("param.restframe_Lnu({})".format(filt), + sed.add_info(f"param.restframe_Lnu({filt})", fluxes[filt] * self.to_lumin, True) for filt1, filt2 in self.colours: - sed.add_info("param.restframe_{}-{}".format(filt1, filt2), + sed.add_info(f"param.restframe_{filt1}-{filt2}", 2.5 * np.log10(fluxes[filt2]/fluxes[filt1])) diff --git a/pcigale/sed_modules/sfhfromfile.py b/pcigale/sed_modules/sfhfromfile.py index 818e369885e5b4c07688f452d6f792f8bbe95059..8ad8170d446c47b0bb638ebf6ada3cd0f2f370a3 100644 --- a/pcigale/sed_modules/sfhfromfile.py +++ b/pcigale/sed_modules/sfhfromfile.py @@ -15,7 +15,7 @@ from collections import OrderedDict import numpy as np -from ..utils import read_table +from utils.io import read_table from . import SedModule diff --git a/pcigale/sed_modules/sfhperiodic.py b/pcigale/sed_modules/sfhperiodic.py index ae041364e9132beb36c20692332ae86ef9dc834c..5eeb39da8e8be5ae1c3283028f62f29d15838239 100644 --- a/pcigale/sed_modules/sfhperiodic.py +++ b/pcigale/sed_modules/sfhperiodic.py @@ -90,7 +90,7 @@ class SfhPeriodic(SedModule): burst = np.zeros_like(time_grid) burst[:int(self.tau_bursts)+1] = 1. else: - raise Exception("Burst type {} unknown.".format(self.type_bursts)) + raise Exception(f"Burst type {self.type_bursts} unknown.") for t_burst in np.arange(0, age, self.delta_bursts): self.sfr += burst diff --git a/pcigale/session/configuration.py b/pcigale/session/configuration.py index 4b9fbd1d02acf0f8b223ce85ea1da33e3d332af6..517e220daa53a8e55fdb0d6a1c451b1345a0476d 100644 --- a/pcigale/session/configuration.py +++ b/pcigale/session/configuration.py @@ -16,12 +16,12 @@ import validate from ..managers.parameters import ParametersManager from ..data import Database -from ..utils import read_table +from utils.io import read_table from .. import sed_modules from .. import analysis_modules from ..warehouse import SedWarehouse from . import validation - +from pcigale.sed_modules.nebular import default_lines class Configuration(object): """This class manages the configuration of pcigale. @@ -139,8 +139,8 @@ class Configuration(object): self.config['cores'] = "" self.config.comments['cores'] = [""] + wrap( - "Number of CPU cores available. This computer has {} cores." - .format(mp.cpu_count())) + f"Number of CPU cores available. This computer has " + f"{mp.cpu_count()} cores.") self.spec['cores'] = "integer(min=1)" self.config.write() @@ -161,6 +161,7 @@ class Configuration(object): # Getting the list of the filters available in pcigale database with Database() as base: filter_list = base.get_filter_names() + filter_list += [f'line.{line}' for line in default_lines] if self.config['data_file'] != '': obs_table = read_table(self.config['data_file']) @@ -187,9 +188,8 @@ class Configuration(object): # band for band in bands: if band.endswith('_err') and (band[:-4] not in bands): - raise Exception("The observation table as a {} column " - "but no {} column.".format(band, - band[:-4])) + raise Exception(f"The observation table as a {band} column " + f"but no {band[:-4]} column.") self.config['bands'] = bands else: @@ -248,6 +248,11 @@ class Configuration(object): self.config['analysis_params'].comments[name] = wrap(desc) self.spec['analysis_params'][name] = typ + if 'pdf_analysis' == module_name: + bands = [band for band in self.config['bands'] + if not band.endswith('_err')] + self.config['analysis_params']['bands'] = bands + self.config.write() self.spec.write() @@ -276,10 +281,10 @@ class Configuration(object): for module, param, message in configobj.flatten_errors(self.config, validity): if len(module) > 0: - print("Module {}, parameter {}: {}".format('/'.join(module), - param, message)) + print(f"Module {'/'.join(module)}, parameter {param}: " + f"{message}") else: - print("Parameter {}: {}".format(param, message)) + print(f"Parameter {param}: {message}") print("Run the same command after having fixed pcigale.ini.") return None @@ -327,8 +332,8 @@ class Configuration(object): for module in modules: if all([user_module not in modules[module] for user_module in self.config['sed_modules']]): - print("{} Options are: {}.". - format(comments[module], ', '.join(modules[module]))) + print(f"{comments[module]} Options are: " + f"{', '.join(modules[module])}.") def complete_redshifts(self): """Complete the configuration when the redshifts are missing from the diff --git a/pcigale/session/validation.py b/pcigale/session/validation.py index a4adc8b46ebe8e4bc2ae4eff357002b1595d0f95..02b32b14c7bcd6391b03d0fd0c3138fef5b8bd60 100644 --- a/pcigale/session/validation.py +++ b/pcigale/session/validation.py @@ -17,7 +17,7 @@ class VdtValueRepeatedError(vdt.VdtValueError): Traceback (most recent call last): VdtValueRepeatedError: the value "jedie" is too long. """ - vdt.ValidateError.__init__(self, 'the value {} is repeated.'.format(value)) + vdt.ValidateError.__init__(self, f"the value {value} is repeated.") def is_cigale_list(inobject, dtype='float', minvalue=None, maxvalue=None, diff --git a/pcigale/utils/__init__.py b/pcigale/utils/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/pcigale/utils/cosmology.py b/pcigale/utils/cosmology.py new file mode 100644 index 0000000000000000000000000000000000000000..5e6f3ca7ba281d4fd070585b666487e21534e49a --- /dev/null +++ b/pcigale/utils/cosmology.py @@ -0,0 +1,44 @@ +# -*- coding: utf-8 -*- +# Licensed under the CeCILL-v2 licence - see Licence_CeCILL_V2-en.txt + +from functools import lru_cache + +from astropy.cosmology import WMAP7 as _cosmo +from scipy.constants import parsec + + +@lru_cache(maxsize=None) +def luminosity_distance(redshift): + """Computes the luminosity distance in m for a given redshift. If the + redshift is 0, then we assume a distance of 10 pc. + + Parameter + --------- + redshift: scalar + Redshift of the object + + Returns + ------- + luminosity_distance: scalar + Luminosity distance to the object in m + """ + if redshift > 0: + return _cosmo.luminosity_distance(redshift).value * 1e6 * parsec + return 10. * parsec + + +@lru_cache(maxsize=None) +def age(redshift): + """Computes the age of the universe in Myr at a given redshift. + + Parameter + --------- + redshift: scalar + Redshift of the object + + Returns + ------- + age: float + Age of the universe in Myr at the corresponding redshift + """ + return _cosmo.age(redshift).value * 1000. diff --git a/pcigale_filters/__init__.py b/pcigale_filters/__init__.py index d080ea5fd9e75f0ec08fdd9b2a81e0fd9dc36ab5..9daef4cc3ce4938746aea7c1426bb5e1ff9c8a3e 100644 --- a/pcigale_filters/__init__.py +++ b/pcigale_filters/__init__.py @@ -14,8 +14,6 @@ import numpy as np from pcigale.data import Database, Filter -__version__ = "0.1-alpha" - def list_filters(): """Print the list of filters in the pcigale database. @@ -62,8 +60,8 @@ def add_filters(fnames): raise ValueError("Filter transmission type can only be " "'energy' or 'photon'.") - print("Importing {}... ({} points)".format(filter_name, - filter_table.shape[1])) + print(f"Importing {filter_name}... " + f"({filter_table.shape[1]} points)") new_filter = Filter(filter_name, filter_description, filter_table) @@ -89,9 +87,9 @@ def del_filters(fnames): for fname in fnames: if fname in names: base.del_filter(fname) - print("Removing filter {}".format(fname)) + print(f"Removing filter {fname}") else: - print("Filter {} not in the database".format(fname)) + print("Filter {fname} not in the database") def worker_plot(fname): @@ -110,9 +108,9 @@ def worker_plot(fname): plt.minorticks_on() plt.xlabel('Wavelength [nm]') plt.ylabel('Relative transmission') - plt.title("{} filter".format(fname)) + plt.title(f"{fname} filter") plt.tight_layout() - plt.savefig("{}.pdf".format(fname)) + plt.savefig(f"{fname}.pdf") def plot_filters(fnames): diff --git a/pcigale_plots/__init__.py b/pcigale_plots/__init__.py index 9c24548921d130ecca470bbd69b044c9491f207b..822d918b5b8540cb0825d4299d951bb860ffab29 100644 --- a/pcigale_plots/__init__.py +++ b/pcigale_plots/__init__.py @@ -6,488 +6,44 @@ # Licensed under the CeCILL-v2 licence - see Licence_CeCILL_V2-en.txt # Author: Yannick Roehlly, Médéric Boquien & Denis Burgarella +import os +# Set environment variables to disable multithreading as users will probably +# want to set the number of cores to the max of their computer. +os.environ["OMP_NUM_THREADS"] = "1" +os.environ["OPENBLAS_NUM_THREADS"] = "1" +os.environ["MKL_NUM_THREADS"] = "1" +os.environ["VECLIB_MAXIMUM_THREADS"] = "1" +os.environ["NUMEXPR_NUM_THREADS"] = "1" + import argparse -import glob -from itertools import product, repeat -from collections import OrderedDict import sys - -from astropy.table import Table -import matplotlib - -matplotlib.use('Agg') -import matplotlib.pyplot as plt +from os import path import multiprocessing as mp -import numpy as np -import os -import pkg_resources -from scipy.constants import c -from scipy import stats -from pcigale.data import Database -from pcigale.utils import read_table -from pcigale.session.configuration import Configuration -import matplotlib.gridspec as gridspec - -__version__ = "0.1-alpha" - - -# Name of the file containing the best models information -BEST_RESULTS = "results.fits" -MOCK_RESULTS = "results_mock.fits" -# Wavelength limits (restframe) when plotting the best SED. -PLOT_L_MIN = 0.1 -PLOT_L_MAX = 5e5 - - -def _chi2_worker(obj_name, var_name): - """Plot the reduced χ² associated with a given analysed variable - - Parameters - ---------- - obj_name: string - Name of the object. - var_name: string - Name of the analysed variable.. - - """ - figure = plt.figure() - ax = figure.add_subplot(111) - - var_name = var_name.replace('/', '_') - fnames = glob.glob("out/{}_{}_chi2-block-*.npy".format(obj_name, var_name)) - for fname in fnames: - data = np.memmap(fname, dtype=np.float64) - data = np.memmap(fname, dtype=np.float64, shape=(2, data.size // 2)) - ax.scatter(data[1, :], data[0, :], color='k', s=.1) - ax.set_xlabel(var_name) - ax.set_ylabel("Reduced $\chi^2$") - ax.set_ylim(0., ) - ax.minorticks_on() - figure.suptitle("Reduced $\chi^2$ distribution of {} for {}." - .format(var_name, obj_name)) - figure.savefig("out/{}_{}_chi2.pdf".format(obj_name, var_name)) - plt.close(figure) - - -def _pdf_worker(obj_name, var_name): - """Plot the PDF associated with a given analysed variable - - Parameters - ---------- - obj_name: string - Name of the object. - var_name: string - Name of the analysed variable.. - - """ - var_name = var_name.replace('/', '_') - if var_name.endswith('_log'): - fnames = glob.glob("out/{}_{}_chi2-block-*.npy".format(obj_name, - var_name[:-4])) - log = True - else: - fnames = glob.glob("out/{}_{}_chi2-block-*.npy".format(obj_name, - var_name)) - log = False - likelihood = [] - model_variable = [] - for fname in fnames: - data = np.memmap(fname, dtype=np.float64) - data = np.memmap(fname, dtype=np.float64, shape=(2, data.size // 2)) - - likelihood.append(np.exp(-data[0, :] / 2.)) - model_variable.append(data[1, :]) - likelihood = np.concatenate(likelihood) - model_variable = np.concatenate(model_variable) - if log is True: - model_variable = np.log10(model_variable) - w = np.where(np.isfinite(likelihood) & np.isfinite(model_variable)) - likelihood = likelihood[w] - model_variable = model_variable[w] - - Npdf = 100 - min_hist = np.min(model_variable) - max_hist = np.max(model_variable) - Nhist = min(Npdf, len(np.unique(model_variable))) - - if min_hist == max_hist: - pdf_grid = np.array([min_hist, max_hist]) - pdf_prob = np.array([1., 1.]) - else: - pdf_prob, pdf_grid = np.histogram(model_variable, Nhist, - (min_hist, max_hist), - weights=likelihood, density=True) - pdf_x = (pdf_grid[1:]+pdf_grid[:-1]) / 2. - - pdf_grid = np.linspace(min_hist, max_hist, Npdf) - pdf_prob = np.interp(pdf_grid, pdf_x, pdf_prob) - - figure = plt.figure() - ax = figure.add_subplot(111) - ax.plot(pdf_grid, pdf_prob, color='k') - ax.set_xlabel(var_name) - ax.set_ylabel("Probability density") - ax.minorticks_on() - figure.suptitle("Probability distribution function of {} for {}" - .format(var_name, obj_name)) - figure.savefig("out/{}_{}_pdf.pdf".format(obj_name, var_name)) - plt.close(figure) - - -def _sed_worker(obs, mod, filters, sed_type, nologo): - """Plot the best SED with the associated fluxes in bands - - Parameters - ---------- - obs: Table row - Data from the input file regarding one object. - mod: Table row - Data from the best model of one object. - filters: ordered dictionary of Filter objects - The observed fluxes in each filter. - sed_type: string - Type of SED to plot. It can either be "mJy" (flux in mJy and observed - frame) or "lum" (luminosity in W and rest frame) - nologo: boolean - Do not add the logo when set to true. - - """ - - if os.path.isfile("out/{}_best_model.fits".format(obs['id'])): - - sed = Table.read("out/{}_best_model.fits".format(obs['id'])) - - filters_wl = np.array([filt.pivot_wavelength - for filt in filters.values()]) - wavelength_spec = sed['wavelength'] - obs_fluxes = np.array([obs[filt] for filt in filters.keys()]) - obs_fluxes_err = np.array([obs[filt+'_err'] - for filt in filters.keys()]) - mod_fluxes = np.array([mod["best."+filt] for filt in filters.keys()]) - if obs['redshift'] >= 0: - z = obs['redshift'] - else: # Redshift mode - z = mod['best.universe.redshift'] - DL = mod['best.universe.luminosity_distance'] - - if sed_type == 'lum': - xmin = PLOT_L_MIN - xmax = PLOT_L_MAX - - k_corr_SED = 1e-29 * (4.*np.pi*DL*DL) * c / (filters_wl*1e-9) - obs_fluxes *= k_corr_SED - obs_fluxes_err *= k_corr_SED - mod_fluxes *= k_corr_SED - - for cname in sed.colnames[1:]: - sed[cname] *= wavelength_spec - - filters_wl /= 1. + z - wavelength_spec /= 1. + z - elif sed_type == 'mJy': - xmin = PLOT_L_MIN * (1. + z) - xmax = PLOT_L_MAX * (1. + z) - k_corr_SED = 1. - - for cname in sed.colnames[1:]: - sed[cname] *= (wavelength_spec * 1e29 / - (c / (wavelength_spec * 1e-9)) / - (4. * np.pi * DL * DL)) - else: - print("Unknown plot type") - - filters_wl /= 1000. - wavelength_spec /= 1000. - wsed = np.where((wavelength_spec > xmin) & (wavelength_spec < xmax)) - figure = plt.figure() - gs = gridspec.GridSpec(2, 1, height_ratios=[3, 1]) - if (sed.columns[1][wsed] > 0.).any(): - ax1 = plt.subplot(gs[0]) - ax2 = plt.subplot(gs[1]) - - # Stellar emission - if 'nebular.absorption_young' in sed.columns: - ax1.loglog(wavelength_spec[wsed], - (sed['stellar.young'][wsed] + - sed['attenuation.stellar.young'][wsed] + - sed['nebular.absorption_young'][wsed] + - sed['stellar.old'][wsed] + - sed['attenuation.stellar.old'][wsed] + - sed['nebular.absorption_old'][wsed]), - label="Stellar attenuated ", color='orange', - marker=None, nonposy='clip', linestyle='-', - linewidth=0.5) - else: - ax1.loglog(wavelength_spec[wsed], - (sed['stellar.young'][wsed] + - sed['attenuation.stellar.young'][wsed] + - sed['stellar.old'][wsed] + - sed['attenuation.stellar.old'][wsed]), - label="Stellar attenuated ", color='orange', - marker=None, nonposy='clip', linestyle='-', - linewidth=0.5) - ax1.loglog(wavelength_spec[wsed], - (sed['stellar.old'][wsed] + - sed['stellar.young'][wsed]), - label="Stellar unattenuated", color='b', marker=None, - nonposy='clip', linestyle='--', linewidth=0.5) - # Nebular emission - if 'nebular.lines_young' in sed.columns: - ax1.loglog(wavelength_spec[wsed], - (sed['nebular.lines_young'][wsed] + - sed['nebular.lines_old'][wsed] + - sed['nebular.continuum_young'][wsed] + - sed['nebular.continuum_old'][wsed] + - sed['attenuation.nebular.lines_young'][wsed] + - sed['attenuation.nebular.lines_old'][wsed] + - sed['attenuation.nebular.continuum_young'][wsed] + - sed['attenuation.nebular.continuum_old'][wsed]), - label="Nebular emission", color='y', marker=None, - nonposy='clip', linewidth=.5) - # Dust emission Draine & Li - if 'dust.Umin_Umin' in sed.columns: - ax1.loglog(wavelength_spec[wsed], - (sed['dust.Umin_Umin'][wsed] + - sed['dust.Umin_Umax'][wsed]), - label="Dust emission", color='r', marker=None, - nonposy='clip', linestyle='-', linewidth=0.5) - # Dust emission Dale - if 'dust' in sed.columns: - ax1.loglog(wavelength_spec[wsed], sed['dust'][wsed], - label="Dust emission", color='r', marker=None, - nonposy='clip', linestyle='-', linewidth=0.5) - # AGN emission Fritz - if 'agn.fritz2006_therm' in sed.columns: - ax1.loglog(wavelength_spec[wsed], - (sed['agn.fritz2006_therm'][wsed] + - sed['agn.fritz2006_scatt'][wsed] + - sed['agn.fritz2006_agn'][wsed]), - label="AGN emission", color='g', marker=None, - nonposy='clip', linestyle='-', linewidth=0.5) - # Radio emission - if 'radio_nonthermal' in sed.columns: - ax1.loglog(wavelength_spec[wsed], - sed['radio_nonthermal'][wsed], - label="Radio nonthermal", color='brown', - marker=None, nonposy='clip', linestyle='-', - linewidth=0.5) - - ax1.loglog(wavelength_spec[wsed], sed['L_lambda_total'][wsed], - label="Model spectrum", color='k', nonposy='clip', - linestyle='-', linewidth=1.5) - - ax1.set_autoscale_on(False) - s = np.argsort(filters_wl) - filters_wl = filters_wl[s] - mod_fluxes = mod_fluxes[s] - obs_fluxes = obs_fluxes[s] - obs_fluxes_err = obs_fluxes_err[s] - ax1.scatter(filters_wl, mod_fluxes, marker='o', color='r', s=8, - zorder=3, label="Model fluxes") - mask_ok = np.logical_and(obs_fluxes > 0., obs_fluxes_err > 0.) - ax1.errorbar(filters_wl[mask_ok], obs_fluxes[mask_ok], - yerr=obs_fluxes_err[mask_ok]*3, ls='', marker='s', - label='Observed fluxes', markerfacecolor='None', - markersize=6, markeredgecolor='b', capsize=0.) - mask_uplim = np.logical_and(np.logical_and(obs_fluxes > 0., - obs_fluxes_err < 0.), - obs_fluxes_err > -9990. * k_corr_SED) - if not mask_uplim.any() == False: - ax1.errorbar(filters_wl[mask_uplim], obs_fluxes[mask_uplim], - yerr=obs_fluxes_err[mask_uplim]*3, ls='', - marker='v', label='Observed upper limits', - markerfacecolor='None', markersize=6, - markeredgecolor='g', capsize=0.) - mask_noerr = np.logical_and(obs_fluxes > 0., - obs_fluxes_err < -9990. * k_corr_SED) - if not mask_noerr.any() == False: - ax1.errorbar(filters_wl[mask_noerr], obs_fluxes[mask_noerr], - ls='', marker='s', markerfacecolor='None', - markersize=6, markeredgecolor='r', - label='Observed fluxes, no errors', capsize=0.) - mask = np.where(obs_fluxes > 0.) - ax2.errorbar(filters_wl[mask], - (obs_fluxes[mask]-mod_fluxes[mask])/obs_fluxes[mask], - yerr=obs_fluxes_err[mask]/obs_fluxes[mask]*3, - marker='_', label="(Obs-Mod)/Obs", color='k', - capsize=0.) - ax2.plot([xmin, xmax], [0., 0.], ls='--', color='k') - ax2.set_xscale('log') - ax2.minorticks_on() - - figure.subplots_adjust(hspace=0., wspace=0.) - - ax1.set_xlim(xmin, xmax) - ymin = min(np.min(obs_fluxes[mask_ok]), - np.min(mod_fluxes[mask_ok])) - if not mask_uplim.any() == False: - ymax = max(max(np.max(obs_fluxes[mask_ok]), - np.max(obs_fluxes[mask_uplim])), - max(np.max(mod_fluxes[mask_ok]), - np.max(mod_fluxes[mask_uplim]))) - else: - ymax = max(np.max(obs_fluxes[mask_ok]), - np.max(mod_fluxes[mask_ok])) - ax1.set_ylim(1e-1*ymin, 1e1*ymax) - ax2.set_xlim(xmin, xmax) - ax2.set_ylim(-1.0, 1.0) - if sed_type == 'lum': - ax2.set_xlabel("Rest-frame wavelength [$\mu$m]") - ax1.set_ylabel("Luminosity [W]") - ax2.set_ylabel("Relative residual luminosity") - else: - ax2.set_xlabel("Observed wavelength [$\mu$m]") - ax1.set_ylabel("Flux [mJy]") - ax2.set_ylabel("Relative residual flux") - ax1.legend(fontsize=6, loc='best', fancybox=True, framealpha=0.5) - ax2.legend(fontsize=6, loc='best', fancybox=True, framealpha=0.5) - plt.setp(ax1.get_xticklabels(), visible=False) - plt.setp(ax1.get_yticklabels()[1], visible=False) - figure.suptitle("Best model for {} at z = {}. Reduced $\chi^2$={}". - format(obs['id'], np.round(z, decimals=3), - np.round(mod['best.reduced_chi_square'], - decimals=2))) - if nologo is False: - image = plt.imread(pkg_resources.resource_filename(__name__, - "data/CIGALE.png")) - figure.figimage(image, 75, 330, origin='upper', zorder=10, - alpha=1) - figure.savefig("out/{}_best_model.pdf".format(obs['id'])) - plt.close(figure) - else: - print("No valid best SED found for {}. No plot created.". - format(obs['id'])) - else: - print("No SED found for {}. No plot created.".format(obs['id'])) - - -def _mock_worker(exact, estimated, param, nologo): - """Plot the exact and estimated values of a parameter for the mock analysis - - Parameters - ---------- - exact: Table column - Exact values of the parameter. - estimated: Table column - Estimated values of the parameter. - param: string - Name of the parameter - nologo: boolean - Do not add the logo when set to true. - - """ - - range_exact = np.linspace(np.min(exact), np.max(exact), 100) - - # We compute the linear regression - if (np.min(exact) < np.max(exact)): - slope, intercept, r_value, p_value, std_err = stats.linregress(exact, - estimated) - else: - slope = 0.0 - intercept = 1.0 - r_value = 0.0 - - plt.errorbar(exact, estimated, marker='.', label=param, color='k', - linestyle='None', capsize=0.) - plt.plot(range_exact, range_exact, color='r', label='1-to-1') - plt.plot(range_exact, slope * range_exact + intercept, color='b', - label='exact-fit $r^2$ = {:.2f}'.format(r_value**2)) - plt.xlabel('Exact') - plt.ylabel('Estimated') - plt.title(param) - plt.legend(loc='best', fancybox=True, framealpha=0.5, numpoints=1) - plt.minorticks_on() - if nologo is False: - image = plt.imread(pkg_resources.resource_filename(__name__, - "data/CIGALE.png")) - plt.figimage(image, 510, 55, origin='upper', zorder=10, alpha=1) - - plt.tight_layout() - plt.savefig('out/mock_{}.pdf'.format(param.replace('/', '_'))) - - plt.close() - - -def chi2(config): - """Plot the χ² values of analysed variables. - """ - input_data = read_table(config.configuration['data_file']) - chi2_vars = config.configuration['analysis_params']['variables'] - chi2_vars += [band for band in config.configuration['bands'] - if band.endswith('_err') is False] - - with mp.Pool(processes=config.configuration['cores']) as pool: - items = product(input_data['id'], chi2_vars) - pool.starmap(_chi2_worker, items) - pool.close() - pool.join() - - -def pdf(config): - """Plot the PDF of analysed variables. - """ - input_data = read_table(config.configuration['data_file']) - pdf_vars = config.configuration['analysis_params']['variables'] - pdf_vars += [band for band in config.configuration['bands'] - if band.endswith('_err') is False] +from pcigale.session.configuration import Configuration +from .plot_types.chi2 import chi2 as chi2_action +from .plot_types.pdf import pdf as pdf_action +from .plot_types.sed import sed as sed_action, AVAILABLE_SERIES +from .plot_types.mock import mock as mock_action - with mp.Pool(processes=config.configuration['cores']) as pool: - items = product(input_data['id'], pdf_vars) - pool.starmap(_pdf_worker, items) - pool.close() - pool.join() +__version__ = "0.2-alpha" -def sed(config, sed_type, nologo): - """Plot the best SED with associated observed and modelled fluxes. +def parser_range(range_str): """ - obs = read_table(config.configuration['data_file']) - mod = Table.read('out/' + BEST_RESULTS) - - with Database() as base: - filters = OrderedDict([(name, base.get_filter(name)) - for name in config.configuration['bands'] - if not (name.endswith('_err') or name.startswith('line')) ]) - - with mp.Pool(processes=config.configuration['cores']) as pool: - pool.starmap(_sed_worker, zip(obs, mod, repeat(filters), - repeat(sed_type), repeat(nologo))) - pool.close() - pool.join() - - -def mock(config, nologo): - """Plot the comparison of input/output values of analysed variables. + Auxiliary parser for plot X and Y ranges + :param range_str: a string like []:[] + :return: """ - - try: - exact = Table.read('out/' + BEST_RESULTS) - except FileNotFoundError: - print("Best models file {} not found.".format('out/' + BEST_RESULTS)) - sys.exit(1) - + rmin, rmax = range_str.split(':') try: - estimated = Table.read('out/' + MOCK_RESULTS) - except FileNotFoundError: - print("Mock models file {} not found.".format('out/' + MOCK_RESULTS)) - sys.exit(1) - - params = config.configuration['analysis_params']['variables'] - - for param in params: - if param.endswith('_log'): - param = "best."+param - exact[param] = np.log10(exact[param[:-4]]) - - arguments = ((exact["best."+param], estimated["bayes."+param], param, nologo) - for param in params) - - with mp.Pool(processes=config.configuration['cores']) as pool: - pool.starmap(_mock_worker, arguments) - pool.close() - pool.join() + rmin = float(rmin) if rmin else False + rmax = float(rmax) if rmax else False + except ValueError: + msg = '{} has not the format []:[], where ' \ + 'min and max are either float or empty'.format(range_str) + raise argparse.ArgumentTypeError(msg) + return rmin, rmax def main(): @@ -505,36 +61,69 @@ def main(): subparsers = parser.add_subparsers(help="List of commands") - pdf_parser = subparsers.add_parser('pdf', help=pdf.__doc__) + fmtstr = 'format of the output files, for instance pdf or png.' + pdf_parser = subparsers.add_parser('pdf', help=pdf_action.__doc__) + pdf_parser.add_argument('--format', default='pdf', help=fmtstr) + pdf_parser.add_argument('--outdir', default='out') pdf_parser.set_defaults(parser='pdf') - chi2_parser = subparsers.add_parser('chi2', help=chi2.__doc__) + chi2_parser = subparsers.add_parser('chi2', help=chi2_action.__doc__) + chi2_parser.add_argument('--format', default='pdf', help=fmtstr) + chi2_parser.add_argument('--outdir', default='out') chi2_parser.set_defaults(parser='chi2') - sed_parser = subparsers.add_parser('sed', help=sed.__doc__) - sed_parser.add_argument('--type', default='mJy') - sed_parser.add_argument('--nologo', action="store_true") + sed_parser = subparsers.add_parser('sed', help=sed_action.__doc__) + sed_parser.add_argument('--type', default='mJy', + help='type of plot. Options are mJy (observed ' + 'frame in flux) and lum (rest-frame in ' + 'lumunosity).') + sed_parser.add_argument('--nologo', action='store_true') + sed_parser.add_argument('--format', default='pdf', help=fmtstr) + sed_parser.add_argument('--outdir', default='out') + sed_parser.add_argument('--xrange', default=':', type=parser_range, + help='Wavelength range []:[] in nm.') + sed_parser.add_argument('--yrange', default=':', type=parser_range, + help='y-axis range []:[].') + sed_parser.add_argument('--series', nargs='*', + help='components to plot. Options are: ' + + ', '.join(AVAILABLE_SERIES) + '.') + sed_parser.add_argument('--seriesdisabled', + help='components not to plot. Options are: ' + + ', '.join(AVAILABLE_SERIES) + '.', + action='store_true') sed_parser.set_defaults(parser='sed') - sed_parser = subparsers.add_parser('mock', help=mock.__doc__) - sed_parser.add_argument('--nologo', action="store_true") - sed_parser.set_defaults(parser='mock') + mock_parser = subparsers.add_parser('mock', help=mock_action.__doc__) + mock_parser.add_argument('--nologo', action='store_true') + mock_parser.add_argument('--format', default='pdf', help=fmtstr) + mock_parser.add_argument('--outdir', default='out') + mock_parser.set_defaults(parser='mock') args = parser.parse_args() + outdir = path.abspath(args.outdir) if args.config_file: config = Configuration(args.config_file) else: - config = Configuration() + config = Configuration(path.join(path.dirname(outdir), 'pcigale.ini')) if len(sys.argv) == 1: parser.print_usage() else: if args.parser == 'chi2': - chi2(config) + chi2_action(config, args.format, outdir) elif args.parser == 'pdf': - pdf(config) + pdf_action(config, args.format, outdir) elif args.parser == 'sed': - sed(config, args.type, args.nologo) + if not args.series: + series = AVAILABLE_SERIES + else: + if args.seriesdisabled: + series = [series for series in AVAILABLE_SERIES + if series not in args.series] + else: + series = args.series + sed_action(config, args.type, args.nologo, args.xrange, args.yrange, + series, args.format, outdir) elif args.parser == 'mock': - mock(config, args.nologo) + mock_action(config, args.nologo, outdir) diff --git a/pcigale_plots/data/CIGALE.png b/pcigale_plots/data/CIGALE.png deleted file mode 100644 index 19f82b1a1f271dd5c4a3695c5b210c076744bec6..0000000000000000000000000000000000000000 Binary files a/pcigale_plots/data/CIGALE.png and /dev/null differ diff --git a/pcigale_plots/plot_types/chi2.py b/pcigale_plots/plot_types/chi2.py new file mode 100644 index 0000000000000000000000000000000000000000..d913d3831594610a3f18fec61484d171656979f2 --- /dev/null +++ b/pcigale_plots/plot_types/chi2.py @@ -0,0 +1,82 @@ +# -*- coding: utf-8 -*- +# Copyright (C) 2013 Centre de données Astrophysiques de Marseille +# Copyright (C) 2013-2014 Yannick Roehlly +# Copyright (C) 2013 Institute of Astronomy +# Copyright (C) 2014 Laboratoire d'Astrophysique de Marseille +# Licensed under the CeCILL-v2 licence - see Licence_CeCILL_V2-en.txt +# Author: Yannick Roehlly, Médéric Boquien & Denis Burgarella + +import glob +from itertools import product +from os import path + +import matplotlib + +matplotlib.use('Agg') +import matplotlib.pyplot as plt +import multiprocessing as mp +import numpy as np +from utils.io import read_table +from utils.counter import Counter + + +def pool_initializer(counter): + """Initializer of the pool of processes to share variables between workers. + Parameters + ---------- + :param counter: Counter class object for the number of models plotted + """ + global gbl_counter + + gbl_counter = counter + + +def chi2(config, format, outdir): + """Plot the χ² values of analysed variables. + """ + file = path.join(path.dirname(outdir), config.configuration['data_file']) + input_data = read_table(file) + chi2_vars = config.configuration['analysis_params']['variables'] + chi2_vars += [band for band in config.configuration['bands'] + if band.endswith('_err') is False] + + items = list(product(input_data['id'], chi2_vars, [format], [outdir])) + counter = Counter(len(items)) + with mp.Pool(processes=config.configuration['cores'], initializer=pool_initializer, + initargs=(counter,)) as pool: + pool.starmap(_chi2_worker, items) + pool.close() + pool.join() + + +def _chi2_worker(obj_name, var_name, format, outdir): + """Plot the reduced χ² associated with a given analysed variable + + Parameters + ---------- + obj_name: string + Name of the object. + var_name: string + Name of the analysed variable.. + outdir: string + The absolute path to outdir + + """ + gbl_counter.inc() + figure = plt.figure() + ax = figure.add_subplot(111) + + var_name = var_name.replace('/', '_') + fnames = glob.glob(f"{outdir}/{obj_name}_{var_name}_chi2-block-*.npy") + for fname in fnames: + data = np.memmap(fname, dtype=np.float64) + data = np.memmap(fname, dtype=np.float64, shape=(2, data.size // 2)) + ax.scatter(data[1, :], data[0, :], color='k', s=.1) + ax.set_xlabel(var_name) + ax.set_ylabel("Reduced $\chi^2$") + ax.set_ylim(0., ) + ax.minorticks_on() + figure.suptitle(f"Reduced $\chi^2$ distribution of {var_name} for " + f"{obj_name}.") + figure.savefig(f"{outdir}/{obj_name}_{var_name}_chi2.{format}") + plt.close(figure) diff --git a/pcigale_plots/plot_types/mock.py b/pcigale_plots/plot_types/mock.py new file mode 100644 index 0000000000000000000000000000000000000000..3fadebf176e266e2f76f79fbf19ef39d0e9fffbe --- /dev/null +++ b/pcigale_plots/plot_types/mock.py @@ -0,0 +1,123 @@ +# -*- coding: utf-8 -*- +# Copyright (C) 2013 Centre de données Astrophysiques de Marseille +# Copyright (C) 2013-2014 Yannick Roehlly +# Copyright (C) 2013 Institute of Astronomy +# Copyright (C) 2014 Laboratoire d'Astrophysique de Marseille +# Licensed under the CeCILL-v2 licence - see Licence_CeCILL_V2-en.txt +# Author: Yannick Roehlly, Médéric Boquien & Denis Burgarella + +from astropy.table import Table +import matplotlib +import sys +from os import path + +matplotlib.use('Agg') +import matplotlib.pyplot as plt +import multiprocessing as mp +import numpy as np +import pkg_resources +from scipy import stats +from utils.counter import Counter + +# Name of the file containing the best models information +BEST_RESULTS = "results.fits" +MOCK_RESULTS = "results_mock.fits" + + +def pool_initializer(counter): + """Initializer of the pool of processes to share variables between workers. + Parameters + ---------- + :param counter: Counter class object for the number of models plotted + """ + global gbl_counter + + gbl_counter = counter + + +def mock(config, nologo, outdir): + """Plot the comparison of input/output values of analysed variables. + """ + best_results_file = path.abspath(path.join(outdir, BEST_RESULTS)) + mock_results_file = path.abspath(path.join(outdir, MOCK_RESULTS)) + + try: + exact = Table.read(best_results_file) + except FileNotFoundError: + print(f"Best models file {best_results_file} not found.") + sys.exit(1) + + try: + estimated = Table.read(mock_results_file) + except FileNotFoundError: + print(f"Mock models file {mock_results_file} not found.") + sys.exit(1) + + params = config.configuration['analysis_params']['variables'] + + for param in params: + if param.endswith('_log'): + param = "best."+param + exact[param] = np.log10(exact[param[:-4]]) + + logo = False if nologo else plt.imread(pkg_resources.resource_filename(__name__, + "../resources/CIGALE.png")) + + arguments = [(exact["best."+param], estimated["bayes."+param], param, logo, outdir) + for param in params] + + counter = Counter(len(arguments)) + with mp.Pool(processes=config.configuration['cores'], initializer=pool_initializer, + initargs=(counter,)) as pool: + pool.starmap(_mock_worker, arguments) + pool.close() + pool.join() + + +def _mock_worker(exact, estimated, param, logo, outdir): + """Plot the exact and estimated values of a parameter for the mock analysis + + Parameters + ---------- + exact: Table column + Exact values of the parameter. + estimated: Table column + Estimated values of the parameter. + param: string + Name of the parameter + nologo: boolean + Do not add the logo when set to true. + outdir: string + The absolute path to outdir + + """ + gbl_counter.inc() + range_exact = np.linspace(np.min(exact), np.max(exact), 100) + + # We compute the linear regression + if np.min(exact) < np.max(exact): + slope, intercept, r_value, p_value, std_err = stats.linregress(exact, + estimated) + else: + slope = 0.0 + intercept = 1.0 + r_value = 0.0 + + plt.errorbar(exact, estimated, marker='.', label=param, color='k', + linestyle='None', capsize=0.) + plt.plot(range_exact, range_exact, color='r', label='1-to-1') + plt.plot(range_exact, slope * range_exact + intercept, color='b', + label=f'exact-fit $r^2$ = {r_value**2:.2f}') + plt.xlabel('Exact') + plt.ylabel('Estimated') + plt.title(param) + plt.legend(loc='best', fancybox=True, framealpha=0.5, numpoints=1) + plt.minorticks_on() + + if logo is not False: + plt.figimage(logo, 510, 55, origin='upper', zorder=10, alpha=1) + + plt.tight_layout() + plt.savefig(f'{outdir}/mock_{param}.pdf') + + plt.close() diff --git a/pcigale_plots/plot_types/pdf.py b/pcigale_plots/plot_types/pdf.py new file mode 100644 index 0000000000000000000000000000000000000000..db3b2672a60791dbd0d4ae2ba51cd86022f7b8f2 --- /dev/null +++ b/pcigale_plots/plot_types/pdf.py @@ -0,0 +1,114 @@ +# -*- coding: utf-8 -*- +# Copyright (C) 2013 Centre de données Astrophysiques de Marseille +# Copyright (C) 2013-2014 Yannick Roehlly +# Copyright (C) 2013 Institute of Astronomy +# Copyright (C) 2014 Laboratoire d'Astrophysique de Marseille +# Licensed under the CeCILL-v2 licence - see Licence_CeCILL_V2-en.txt +# Author: Yannick Roehlly, Médéric Boquien & Denis Burgarella + +import glob +from itertools import product +import matplotlib +from os import path + +matplotlib.use('Agg') +import matplotlib.pyplot as plt +import multiprocessing as mp +import numpy as np +from utils.io import read_table +from utils.counter import Counter + + +def pool_initializer(counter): + """Initializer of the pool of processes to share variables between workers. + Parameters + ---------- + :param counter: Counter class object for the number of models plotted + """ + global gbl_counter + + gbl_counter = counter + + +def pdf(config, format, outdir): + """Plot the PDF of analysed variables. + """ + input_data = read_table(path.join(path.dirname(outdir), config.configuration['data_file'])) + pdf_vars = config.configuration['analysis_params']['variables'] + pdf_vars += [band for band in config.configuration['bands'] + if band.endswith('_err') is False] + + items = list(product(input_data['id'], pdf_vars, [format], [outdir])) + counter = Counter(len(items)) + with mp.Pool(processes=config.configuration['cores'], initializer=pool_initializer, + initargs=(counter,)) as pool: + pool.starmap(_pdf_worker, items) + pool.close() + pool.join() + + +def _pdf_worker(obj_name, var_name, format, outdir): + """Plot the PDF associated with a given analysed variable + + Parameters + ---------- + obj_name: string + Name of the object. + var_name: string + Name of the analysed variable.. + outdir: string + The absolute path to outdir + + """ + gbl_counter.inc() + var_name = var_name.replace('/', '_') + if var_name.endswith('_log'): + fnames = glob.glob(f"{outdir}/{obj_name}_{var_name[:-4]}_chi2-block-" + f"*.npy") + log = True + else: + fnames = glob.glob(f"{outdir}/{obj_name}_{var_name}_chi2-block-*.npy") + log = False + likelihood = [] + model_variable = [] + for fname in fnames: + data = np.memmap(fname, dtype=np.float64) + data = np.memmap(fname, dtype=np.float64, shape=(2, data.size // 2)) + + likelihood.append(np.exp(-data[0, :] / 2.)) + model_variable.append(data[1, :]) + likelihood = np.concatenate(likelihood) + model_variable = np.concatenate(model_variable) + if log is True: + model_variable = np.log10(model_variable) + w = np.where(np.isfinite(likelihood) & np.isfinite(model_variable)) + likelihood = likelihood[w] + model_variable = model_variable[w] + + Npdf = 100 + min_hist = np.min(model_variable) + max_hist = np.max(model_variable) + Nhist = min(Npdf, len(np.unique(model_variable))) + + if min_hist == max_hist: + pdf_grid = np.array([min_hist, max_hist]) + pdf_prob = np.array([1., 1.]) + else: + pdf_prob, pdf_grid = np.histogram(model_variable, Nhist, + (min_hist, max_hist), + weights=likelihood, density=True) + pdf_x = (pdf_grid[1:]+pdf_grid[:-1]) / 2. + + pdf_grid = np.linspace(min_hist, max_hist, Npdf) + pdf_prob = np.interp(pdf_grid, pdf_x, pdf_prob) + + figure = plt.figure() + ax = figure.add_subplot(111) + ax.plot(pdf_grid, pdf_prob, color='k') + ax.set_xlabel(var_name) + ax.set_ylabel("Probability density") + ax.minorticks_on() + figure.suptitle(f"Probability distribution function of {var_name} for " + f"{obj_name}") + figure.savefig(f"{outdir}/{obj_name}_{var_name}_pdf.{format}") + plt.close(figure) diff --git a/pcigale_plots/plot_types/sed.py b/pcigale_plots/plot_types/sed.py new file mode 100644 index 0000000000000000000000000000000000000000..a6dfb16e13c190fb474c14f099125def7524a8a3 --- /dev/null +++ b/pcigale_plots/plot_types/sed.py @@ -0,0 +1,352 @@ +# -*- coding: utf-8 -*- +# Copyright (C) 2013 Centre de données Astrophysiques de Marseille +# Copyright (C) 2013-2014 Yannick Roehlly +# Copyright (C) 2013 Institute of Astronomy +# Copyright (C) 2014 Laboratoire d'Astrophysique de Marseille +# Licensed under the CeCILL-v2 licence - see Licence_CeCILL_V2-en.txt +# Author: Yannick Roehlly, Médéric Boquien & Denis Burgarella + +from itertools import repeat +from collections import OrderedDict + +from astropy.table import Table +import matplotlib + +matplotlib.use('Agg') +import matplotlib.pyplot as plt +import multiprocessing as mp +import numpy as np +from os import path +import pkg_resources +from scipy.constants import c +from pcigale.data import Database +from utils.io import read_table +import matplotlib.gridspec as gridspec +from utils.counter import Counter + +# Name of the file containing the best models information +BEST_RESULTS = "results.fits" +MOCK_RESULTS = "results_mock.fits" + +AVAILABLE_SERIES = [ + 'stellar_attenuated', + 'stellar_unattenuated', + 'nebular', + 'dust', + 'agn', + 'radio', + 'model' +] + + +def pool_initializer(counter): + """Initializer of the pool of processes to share variables between workers. + Parameters + ---------- + :param counter: Counter class object for the number of models plotted + """ + global gbl_counter + + gbl_counter = counter + + +def sed(config, sed_type, nologo, xrange, yrange, series, format, outdir): + """Plot the best SED with associated observed and modelled fluxes. + """ + obs = read_table(path.join(path.dirname(outdir), + config.configuration['data_file'])) + mod = Table.read(path.join(outdir, BEST_RESULTS)) + + with Database() as base: + filters = OrderedDict([(name, base.get_filter(name)) + for name in config.configuration['bands'] + if not (name.endswith('_err') or name.startswith('line'))]) + + if nologo is True: + logo = False + else: + logo = plt.imread(pkg_resources.resource_filename(__name__, + "../resources/CIGALE.png")) + + counter = Counter(len(obs)) + with mp.Pool(processes=config.configuration['cores'], + initializer=pool_initializer, initargs=(counter,)) as pool: + pool.starmap(_sed_worker, zip(obs, mod, repeat(filters), + repeat(sed_type), repeat(logo), + repeat(xrange), repeat(yrange), + repeat(series), repeat(format), + repeat(outdir))) + pool.close() + pool.join() + + +def _sed_worker(obs, mod, filters, sed_type, logo, xrange, yrange, series, + format, outdir): + """Plot the best SED with the associated fluxes in bands + + Parameters + ---------- + obs: Table row + Data from the input file regarding one object. + mod: Table row + Data from the best model of one object. + filters: ordered dictionary of Filter objects + The observed fluxes in each filter. + sed_type: string + Type of SED to plot. It can either be "mJy" (flux in mJy and observed + frame) or "lum" (luminosity in W and rest frame) + logo: numpy.array | boolean + The readed logo image data. Has shape + (M, N) for grayscale images. + (M, N, 3) for RGB images. + (M, N, 4) for RGBA images. + Do not add the logo when set to False. + xrange: tuple(float|boolean, float|boolean) + yrange: tuple(float|boolean, float|boolean) + series: list + format: string + One of png, pdf, ps, eps or svg. + outdir: string + The absolute path to outdir + + """ + gbl_counter.inc() + + id_best_model_file = path.join(outdir, f"{obs['id']}_best_model.fits") + if path.isfile(id_best_model_file): + sed = Table.read(id_best_model_file) + + filters_wl = np.array([filt.pivot_wavelength + for filt in filters.values()]) * 1e-3 + wavelength_spec = sed['wavelength'] * 1e-3 + obs_fluxes = np.array([obs[filt] for filt in filters.keys()]) + obs_fluxes_err = np.array([obs[filt+'_err'] + for filt in filters.keys()]) + mod_fluxes = np.array([mod["best."+filt] for filt in filters.keys()]) + if obs['redshift'] >= 0: + z = obs['redshift'] + else: # Redshift mode + z = mod['best.universe.redshift'] + zp1 = 1. + z + surf = 4. * np.pi * mod['best.universe.luminosity_distance'] ** 2 + + xmin = 0.9 * np.min(filters_wl) if xrange[0] is False else xrange[0] + xmax = 1.1 * np.max(filters_wl) if xrange[1] is False else xrange[1] + + if sed_type == 'lum': + k_corr_SED = 1e-29 * surf * c / (filters_wl * 1e-6) + obs_fluxes *= k_corr_SED + obs_fluxes_err *= k_corr_SED + mod_fluxes *= k_corr_SED + + for cname in sed.colnames[1:]: + sed[cname] *= wavelength_spec * 1e3 + + filters_wl /= zp1 + wavelength_spec /= zp1 + xmin /= zp1 + xmax /= zp1 + elif sed_type == 'mJy': + k_corr_SED = 1. + + fact = 1e29 * 1e-3 * wavelength_spec**2 / c / surf + for cname in sed.colnames[1:]: + sed[cname] *= fact + else: + print("Unknown plot type") + + wsed = np.where((wavelength_spec > xmin) & (wavelength_spec < xmax)) + figure = plt.figure() + gs = gridspec.GridSpec(2, 1, height_ratios=[3, 1]) + if (sed.columns[1][wsed] > 0.).any(): + ax1 = plt.subplot(gs[0]) + ax2 = plt.subplot(gs[1]) + + # Stellar emission + if 'stellar_attenuated' in series: + if 'nebular.absorption_young' in sed.columns: + ax1.loglog(wavelength_spec[wsed], + (sed['stellar.young'][wsed] + + sed['attenuation.stellar.young'][wsed] + + sed['nebular.absorption_young'][wsed] + + sed['stellar.old'][wsed] + + sed['attenuation.stellar.old'][wsed] + + sed['nebular.absorption_old'][wsed]), + label="Stellar attenuated", color='gold', + marker=None, nonposy='clip', linestyle='-', + linewidth=1.0) + else: + ax1.loglog(wavelength_spec[wsed], + (sed['stellar.young'][wsed] + + sed['attenuation.stellar.young'][wsed] + + sed['stellar.old'][wsed] + + sed['attenuation.stellar.old'][wsed]), + label="Stellar attenuated", color='gold', + marker=None, nonposy='clip', linestyle='-', + linewidth=1.0) + + if 'stellar_unattenuated' in series: + ax1.loglog(wavelength_spec[wsed], + (sed['stellar.old'][wsed] + + sed['stellar.young'][wsed]), + label="Stellar unattenuated", + color='xkcd:deep sky blue', marker=None, + nonposy='clip', linestyle='--', linewidth=1.0) + + # Nebular emission + if 'nebular' in series and 'nebular.lines_young' in sed.columns: + ax1.loglog(wavelength_spec[wsed], + (sed['nebular.lines_young'][wsed] + + sed['nebular.lines_old'][wsed] + + sed['nebular.continuum_young'][wsed] + + sed['nebular.continuum_old'][wsed] + + sed['attenuation.nebular.lines_young'][wsed] + + sed['attenuation.nebular.lines_old'][wsed] + + sed['attenuation.nebular.continuum_young'][wsed] + + sed['attenuation.nebular.continuum_old'][wsed]), + label="Nebular emission", color='xkcd:true green', + marker=None, nonposy='clip', linewidth=1.0) + + # Dust emission Draine & Li + if 'dust' in series and 'dust.Umin_Umin' in sed.columns: + ax1.loglog(wavelength_spec[wsed], + (sed['dust.Umin_Umin'][wsed] + + sed['dust.Umin_Umax'][wsed]), + label="Dust emission", color='xkcd:bright red', + marker=None, nonposy='clip', linestyle='-', + linewidth=1.0) + + # Dust emission Dale + if 'dust' in series and 'dust' in sed.columns: + ax1.loglog(wavelength_spec[wsed], sed['dust'][wsed], + label="Dust emission", color='xkcd:bright red', + marker=None, nonposy='clip', linestyle='-', + linewidth=1.0) + + # AGN emission Fritz + if 'agn' in series and 'agn.fritz2006_therm' in sed.columns: + ax1.loglog(wavelength_spec[wsed], + (sed['agn.fritz2006_therm'][wsed] + + sed['agn.fritz2006_scatt'][wsed] + + sed['agn.fritz2006_agn'][wsed]), + label="AGN emission", color='xkcd:apricot', + marker=None, nonposy='clip', linestyle='-', + linewidth=1.0) + + # Radio emission + if 'radio' in series and 'radio_nonthermal' in sed.columns: + ax1.loglog(wavelength_spec[wsed], + sed['radio_nonthermal'][wsed], + label="Radio nonthermal", color='brown', + marker=None, nonposy='clip', linestyle='-', + linewidth=1.0) + + if 'model' in series: + ax1.loglog(wavelength_spec[wsed], sed['L_lambda_total'][wsed], + label="Model spectrum", color='k', nonposy='clip', + linestyle='-', linewidth=1.5) + + ax1.set_autoscale_on(False) + s = np.argsort(filters_wl) + filters_wl = filters_wl[s] + mod_fluxes = mod_fluxes[s] + obs_fluxes = obs_fluxes[s] + obs_fluxes_err = obs_fluxes_err[s] + ax1.scatter(filters_wl, mod_fluxes, marker='o', + color='xkcd:strawberry', s=8, zorder=3, + label="Model fluxes") + mask_ok = np.logical_and(obs_fluxes > 0., obs_fluxes_err > 0.) + ax1.errorbar(filters_wl[mask_ok], obs_fluxes[mask_ok], + yerr=obs_fluxes_err[mask_ok], ls='', marker='o', + label='Observed fluxes', markerfacecolor='None', + markersize=5, markeredgecolor='xkcd:pastel purple', + color='xkcd:light indigo', capsize=0., zorder=3, lw=1) + mask_uplim = np.logical_and(np.logical_and(obs_fluxes > 0., + obs_fluxes_err < 0.), + obs_fluxes_err > -9990. * k_corr_SED) + if not mask_uplim.any() == False: + ax1.errorbar(filters_wl[mask_uplim], obs_fluxes[mask_uplim], + yerr=obs_fluxes_err[mask_uplim], ls='', marker='v', + label='Observed upper limits', + markerfacecolor='None', markersize=6, + markeredgecolor='g', capsize=0.) + mask_noerr = np.logical_and(obs_fluxes > 0., + obs_fluxes_err < -9990. * k_corr_SED) + if not mask_noerr.any() == False: + ax1.errorbar(filters_wl[mask_noerr], obs_fluxes[mask_noerr], + ls='', marker='p', markerfacecolor='None', + markersize=5, markeredgecolor='r', + label='Observed fluxes, no errors', capsize=0.) + mask = np.where(obs_fluxes > 0.) + ax2.errorbar(filters_wl[mask], + (obs_fluxes[mask]-mod_fluxes[mask])/obs_fluxes[mask], + yerr=obs_fluxes_err[mask]/obs_fluxes[mask], + marker='_', label="(Obs-Mod)/Obs", color='k', + capsize=0., ls='None', lw=1) + ax2.plot([xmin, xmax], [0., 0.], ls='--', color='k') + ax2.set_xscale('log') + ax2.minorticks_on() + + ax1.tick_params(direction='in', axis='both', which='both', top=True, + left=True, right=True, bottom=False) + ax2.tick_params(direction='in', axis='both', which='both', + right=True) + + figure.subplots_adjust(hspace=0., wspace=0.) + + ax1.set_xlim(xmin, xmax) + + if yrange[0] is not False: + ymin = yrange[0] + else: + ymin = min(np.min(obs_fluxes[mask_ok]), + np.min(mod_fluxes[mask_ok])) + ymin *= 1e-1 + + if yrange[1] is not False: + ymax = yrange[1] + else: + if not mask_uplim.any() == False: + ymax = max(max(np.max(obs_fluxes[mask_ok]), + np.max(obs_fluxes[mask_uplim])), + max(np.max(mod_fluxes[mask_ok]), + np.max(mod_fluxes[mask_uplim]))) + else: + ymax = max(np.max(obs_fluxes[mask_ok]), + np.max(mod_fluxes[mask_ok])) + ymax *= 1e1 + + xmin = xmin if xmin < xmax else xmax - 1e1 + ymin = ymin if ymin < ymax else ymax - 1e1 + + ax1.set_ylim(ymin, ymax) + ax2.set_xlim(xmin, xmax) + ax2.set_ylim(-1.0, 1.0) + if sed_type == 'lum': + ax2.set_xlabel(r"Rest-frame wavelength [$\mu$m]") + ax1.set_ylabel("Luminosity [W]") + else: + ax2.set_xlabel(r"Observed $\lambda$ ($\mu$m)") + ax1.set_ylabel(r"S$_\nu$ (mJy)") + ax2.set_ylabel("Relative\nresidual") + ax1.legend(fontsize=6, loc='best', frameon=False) + ax2.legend(fontsize=6, loc='best', frameon=False) + plt.setp(ax1.get_xticklabels(), visible=False) + plt.setp(ax1.get_yticklabels()[1], visible=False) + figure.suptitle(f"Best model for {obs['id']}\n (z={z:.3}, " + f"reduced χ²={mod['best.reduced_chi_square']:.2})") + if logo is not False: + # Multiplying the dpi by 2 is a hack so the figure is small + # and not too pixelated + figwidth = figure.get_figwidth() * figure.dpi * 2. + figure.figimage(logo, figwidth-logo.shape[0], 0, + origin='upper', zorder=0, alpha=1) + + figure.savefig(path.join(outdir, + f"{obs['id']}_best_model.{format}"), + dpi=figure.dpi * 2.) + plt.close(figure) + else: + print(f"No valid best SED found for {obs['id']}. No plot created.") + else: + print(f"No SED found for {obs['id']}. No plot created.") diff --git a/pcigale_plots/resources/CIGALE.png b/pcigale_plots/resources/CIGALE.png new file mode 100644 index 0000000000000000000000000000000000000000..16aa2f2f8c7c5448e4b8d8e64ed696d9302198cf Binary files /dev/null and b/pcigale_plots/resources/CIGALE.png differ diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index dd55ae2f1f621609aae17f61cdc03d2b22015aec..0000000000000000000000000000000000000000 --- a/setup.cfg +++ /dev/null @@ -1,3 +0,0 @@ -[egg_info] -tag_build = .dev -tag_svn_revision = 1 \ No newline at end of file diff --git a/setup.py b/setup.py index a8e72e2142e4d7e3c59b4d0e032f67eced86b000..ffa2a00dd79cdb3c3388b5919985bb8e428287a4 100755 --- a/setup.py +++ b/setup.py @@ -38,20 +38,22 @@ entry_points = { setup( name="pcigale", - version="2018.0", + version="2018.0.1", packages=find_packages(exclude=["database_builder"]), install_requires=['numpy', 'scipy', 'sqlalchemy', 'matplotlib', 'configobj', 'astropy'], - + setup_requires=['numpy', 'scipy', 'astropy', 'sqlalchemy', 'configobj'], entry_points=entry_points, cmdclass={"build": custom_build}, package_data={'pcigale': ['data/data.db'], - 'pcigale_plots': ['data/CIGALE.png']}, + 'pcigale_plots': ['resources/CIGALE.png']}, + include_package_data=True, author="The CIGALE team", author_email="cigale@lam.fr", + url="https://cigale.lam.fr", description="Python Code Investigating Galaxy Emission", license="CeCILL-V2", keywords="astrophysics, galaxy, SED fitting" diff --git a/pcigale/analysis_modules/utils.py b/utils/counter.py similarity index 72% rename from pcigale/analysis_modules/utils.py rename to utils/counter.py index d8ffad8b7605975939e62d007867e6fb977985a9..c408800b6b579b8d8822c8046d5e43cc064066e8 100644 --- a/pcigale/analysis_modules/utils.py +++ b/utils/counter.py @@ -4,34 +4,14 @@ # Author: Médéric Boquien """ -Various utility functions for pcigale analysis modules +Multiprocessing counter class with utility functions for periodic updating and +printing. """ + import multiprocessing as mp import time -def nothread(): - """Some libraries such as Intel's MKL have automatic threading. This is - good when having only one process. However we already do our own - parallelisation. The additional threads created by the MKL increase in - excess the pressure on the CPU and on the RAM slowing everything down. - - Parameters - ---------- - None - - Returns - ------- - None - - """ - try: - import mkl - mkl.set_num_threads(1) - except ImportError: - pass - - class Counter: """Class to count the number of models computers/objects analysed. It has two internal counters. One is internal to the process and is incremented at @@ -66,6 +46,8 @@ class Counter: def pprint(self, n): dt = time.time() - self.t0 - print("{}/{} computed in {:.1f} seconds ({:.1f}/s)". - format(n, self.nmodels, dt, n / dt), + s = round(dt % 60, 1) + m = round((dt // 60) % 60) + h = round(dt // 3600) + print(f"{n}/{self.nmodels} in {h:02}:{m:02}:{s:04.1f} ({n/dt:.1f}/s)", end="\n" if n == self.nmodels else "\r") diff --git a/pcigale/utils.py b/utils/io.py similarity index 90% rename from pcigale/utils.py rename to utils/io.py index ba1f9c0724ba840b7af1ea8b4f4b39acd854f544..14387c8bc1b2d597fefb976662b08b7faccfb2c5 100644 --- a/pcigale/utils.py +++ b/utils/io.py @@ -39,8 +39,8 @@ def read_table(file_): try: table = Table.read(file_, format="ascii", delimiter='\s') except InconsistentTableError: - raise Exception("The file <{}> can not be parsed as a data " - "table.".format(file_)) + raise Exception(f"The file {file_} can not be parsed as a data " + "table.") # Convert all the integers to floats. return Table([