From 8a3363aa2a7f8fe5a0f5291d7872f01b513a05c8 Mon Sep 17 00:00:00 2001 From: robvanholstein Date: Sun, 6 Jun 2021 20:26:45 -0400 Subject: [PATCH] Updated code so that it correctly handles the change of the header names INS4 DROT2 BEGIN and INS4 DROT3 BEGIN to INS4 DROT2 START and INS4 DROT3 START in the FITS files --- docs/build/doctrees/changelog.doctree | Bin 43220 -> 45043 bytes docs/build/doctrees/environment.pickle | Bin 27479 -> 27661 bytes docs/build/html/.buildinfo | 2 +- docs/build/html/_sources/changelog.rst.txt | 4 +++ .../html/_static/documentation_options.js | 2 +- docs/build/html/acknowledgements.html | 4 +-- docs/build/html/changelog.html | 10 +++++-- docs/build/html/citing.html | 4 +-- docs/build/html/configfile.html | 4 +-- docs/build/html/contributing.html | 4 +-- docs/build/html/example.html | 4 +-- docs/build/html/genindex.html | 4 +-- docs/build/html/index.html | 4 +-- docs/build/html/installation.html | 4 +-- docs/build/html/instructions.html | 4 +-- docs/build/html/mailinglist.html | 4 +-- docs/build/html/objects.inv | Bin 1057 -> 1057 bytes docs/build/html/search.html | 4 +-- docs/build/html/searchindex.js | 2 +- docs/source/changelog.rst | 4 +++ irdap/irdap.py | 28 ++++++++++++++---- irdap/version.py | 2 +- 22 files changed, 64 insertions(+), 34 deletions(-) diff --git a/docs/build/doctrees/changelog.doctree b/docs/build/doctrees/changelog.doctree index 55c5c1588989a08527260dde94e6156a7548c461..c030dd33ca3523117911aea7cc4f57f6e9938184 100644 GIT binary patch delta 5635 zcmd6rdr(x@8NfZ4z02JtDGy!V$`t}Eua#F+KoAr~G-41$4DwiDarcTmcQI-d69qNm z^IMG?OYyBSjxjqiFCCl2q+`d%m?k!jlT;^TCK~f$Zy)bzAudA6y@BzKux4!Om=2*t%EWtno}>{;dM@}wz6#ib=O>J9d0u-+2c-a6QqE|--T%r3td zj$ zZ{zL$1@StqzST}^K;N$!a?OxA^z&-`3qpnh?f0PbIYJ(RQ$7kzmTKX7O*dKU$`|h= z;%ioe^$e71jj&38+Lhxg5%F{Ex(;cwQ4Gbuu7O#OhJY$R*IwyG;-e4(-xw2_=nj07 z8zWe6qk81lu>q{_J1D5ezH5*_)<{Aj-(+wV`1Sbc6%!dY%xX}Qsd_ZjO_H=Dv1ugm zb^I7toc~vZOmYPW<`Gf|bAqx-32Y9Eksjhoh45-nlvIcfN4+u={$WTUW-2#%OrO2oHPj=-isE_`iF5+jkz0y!a`W2Yl`kqQ_U zT_faDTcdD3F;m&tDvuLzo|t13$w)S#W{kQ_q?O#*3N#i&r;`|s2A9HD@oBJ0KC5?9 zFc6EYJvq}QMmcUsi<4?L|KEG?re-;^Rqi@7leQ>Uvq1;KV7T*awy zDfI)g9*(DdB(3Mv2GwN}QtMQgy>K(VjO>N{jA_zdj_y~{WJCu%sML#MN4?b!`C^po zH<_ITPG{AUUby<;7?B!Xg=9Qw$95F7Wow{rtOWbB4X)*5V+rI=$RMfEJ|ThaU;6Pb zBHiWg?s(k6_1tu*$PUM$gpmA7#OapxO7<$EOVF?y$7|FbD-#{YXjrZXC-exp8c4}q zr_1HsM9L*iE|E%`*3%Bgft z;nhy%Eg+R6JawuQ)jCZ?r}N!TT_PYA66y{chmyXbZ@f) zVqvg=uyJ0n>s+}+bS|!Sf@<+Ia5A#TM4V9%uqm2VF_}o`JaMj`yCC@8{}`v_9?x?y zvT}=XZZKME^Gz15@VbaQJljiY=NV*hFGYVesx8$9*S>iH1e$9z$W$1pO>hNN?IKdN zmW`bZS8YjPXiA4J3tJtB7E~feSI431H;MER$EG93_FwIE^e|OR7l-TpS`8s}@L`=( zsz;0++Fj;}M1gjTdZ^dKRrAO}xwd`=Sw2+mZwVdVC$gKe6OF5;4%g2in}?za4PK^7 z8q&zVq4J{*S%a=_HcTWZsodXv^l{790C>DH93E|q8$=H_=8|(mP5E2G{5SFB)riJf zvdHD3*lx>ApNVJgI_7O_zjWzHr%AEmTp04iEz>X)(1nUP!w1rf;?W zT}t$217ZZSDjFV^b=ndH9`I$`P?c?hkmn0KZTV6j$MPB0rqziv5u3nT0ePa3HFciCDN$Y#0G*3@L_K$%=vTu$F% z`~lQjui!h(LmO=-i%B*+?5&H;c3XqF86Rk!_=9hPgPjIqv**ZmOQ&6CvEt*x%RUkVITk#mm?arM-m;~GG8>BGKMX20d3q@$MaxR1K8|hlU@-86hCJ!U zZY^uaZBcowN!rJ;10GDQMr(WASnBe6{VNpU`Al412v?TtCDvt7PN_OIsPmFrXZnga z$VK=~_e;`6Zu-wER*TpLj=ADi775Z#PTWw5IwU@&gs_M1GHf@b^Q|8TH%8jc$9+8{ zuUbe-AxjtqCs$?ph3ME28}NtjL7_?z?HJsH8t~BhEviDAEfH+17Ya!_xU{-eO5%Dc zaCL2xXhAOt_*V?QD+qBqIM{Pan52Wo-V@R!4i+-73Bi1CuxrgpG7nPLJ}b@RTovOM zAUD^W%U<_8(gq){+a|Sfu7hz_anJ44kXzo|VW%Pl>S4sT z23??@jpcAXyDhe&Z+|_zK;wvfux*QA)WgE z_~35F1O}ymE4HIzuB!O1`9+G#K>MFSXN{)3PR<2?n@0>vvLE^3g-6Br4a;g)l zg(~HqymVT{V6M@6#XWn2bda(t3<{r~MH*brr#l4ln#;Gpf|jIa?*;st_SNY$eyj|{ z4@?JB;Sc*vy1U%h_jr?FGnK|gD8r71o13A3VyoQIcYjlBtG&hb@}UUwFL8L#jsO4v delta 4201 zcmai%c~n$K7RIedFZCLY7;F)gW)qr40VPaSKtv%ZyNVlww2gp|hlm7lBg73QL6U$M zGow)v9pbKs^Bgsa8Z{Z0nd4D&lA}(RnV5`8CQ8U;CML(IbE}H(1~TW&AH1gP{=VmU9meRxCCuhnh6vcFTWb0h6=jD|pY+#raeHSoEcCmf}A$ksKHm2hsn83vgO zVWZwpdmy_Ja5r{q|8O@F7%bbg^g$TCX)?|tmtjldv?Hd6g?ymgO(ga%2< zL$Lb&BK=Gt*#8ImvoLyy+Cb>G%6f0SeGm9I|4w!To=N^Xce+7Y9R$4_tR2stpPHgvgVGI$nbIyl{gb%Ex12d844YXdui9 zexJ;Q5g}LTOo8RHBrq*-G|7Zy>vNe{)EJD+epiiOjkZe{ zBuE=mOfJBZumW-h21nYY+qldlXVKe2`Y|sp2$eT^X=flP>LsaLf+JBc&~Cx}i!-B; 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When it is not found, a full rebuild will be done. -config: ced7332a251a8231d0a8b9c93920bc51 +config: c3324f68be465bb2ffcd7003b9cac817 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/docs/build/html/_sources/changelog.rst.txt b/docs/build/html/_sources/changelog.rst.txt index 078ea00..f7fc34a 100644 --- a/docs/build/html/_sources/changelog.rst.txt +++ b/docs/build/html/_sources/changelog.rst.txt @@ -14,6 +14,9 @@ Changelog & to-do Changelog --------- +v1.3.3 June 2021, R.G. van Holstein + - Updated code so that it correctly handles the change of the header names INS4 DROT2 BEGIN and INS4 DROT3 BEGIN to INS4 DROT2 START and INS4 DROT3 START in the FITS files + v1.3.2 January 2021, R.G. van Holstein - Corrected a bug that prevented reductions to be performed when dark and flat files are included in the raw subdirectory @@ -76,6 +79,7 @@ v0.1.2 June 2019, R.G. van Holstein: To-do high priority ------------------- + - Add possibility to reduce data with center frames having a different DIT than the object frames (i.e. automatically scale object frames to DIT and ND filter of center frames before subtracting it; test with data of HD142527) - Automatically optimize the annulus for star polarization subtraction by iterativey updating the annulus by excluding disk signal and companions etc. - Improve computation of stellar DoLP and AoLP and corresponding uncertainties (standard error of mean) by sampling from Gaussian distributions with Monte Carlo - Correct error in computation of photon noise for Q and U images that uses signal in Q and U rather than I_Q and I_U. diff --git a/docs/build/html/_static/documentation_options.js b/docs/build/html/_static/documentation_options.js index c276d44..2107abe 100644 --- a/docs/build/html/_static/documentation_options.js +++ b/docs/build/html/_static/documentation_options.js @@ -1,6 +1,6 @@ var DOCUMENTATION_OPTIONS = { URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'), - VERSION: '1.3.2', + VERSION: '1.3.3', LANGUAGE: 'None', COLLAPSE_INDEX: false, FILE_SUFFIX: '.html', diff --git a/docs/build/html/acknowledgements.html b/docs/build/html/acknowledgements.html index 7792315..d628dfb 100644 --- a/docs/build/html/acknowledgements.html +++ b/docs/build/html/acknowledgements.html @@ -8,7 +8,7 @@ - Acknowledgements — IRDAP 1.3.2 documentation + Acknowledgements — IRDAP 1.3.3 documentation @@ -60,7 +60,7 @@
- 1.3.2 + 1.3.3
diff --git a/docs/build/html/changelog.html b/docs/build/html/changelog.html index 8d84a27..9101a30 100644 --- a/docs/build/html/changelog.html +++ b/docs/build/html/changelog.html @@ -8,7 +8,7 @@ - Changelog & to-do — IRDAP 1.3.2 documentation + Changelog & to-do — IRDAP 1.3.3 documentation @@ -61,7 +61,7 @@
- 1.3.2 + 1.3.3
@@ -171,6 +171,11 @@

Changelog & to-do

Changelog

+
v1.3.3 June 2021, R.G. van Holstein
+
    +
  • Updated code so that it correctly handles the change of the header names INS4 DROT2 BEGIN and INS4 DROT3 BEGIN to INS4 DROT2 START and INS4 DROT3 START in the FITS files
    • +
+
v1.3.2 January 2021, R.G. van Holstein
  • Corrected a bug that prevented reductions to be performed when dark and flat files are included in the raw subdirectory
    • @@ -265,6 +270,7 @@

    Changelog

      +
    • Add possibility to reduce data with center frames having a different DIT than the object frames (i.e. automatically scale object frames to DIT and ND filter of center frames before subtracting it; test with data of HD142527)
    • Automatically optimize the annulus for star polarization subtraction by iterativey updating the annulus by excluding disk signal and companions etc.
    • Improve computation of stellar DoLP and AoLP and corresponding uncertainties (standard error of mean) by sampling from Gaussian distributions with Monte Carlo
    • Correct error in computation of photon noise for Q and U images that uses signal in Q and U rather than I_Q and I_U.
      • diff --git a/docs/build/html/citing.html b/docs/build/html/citing.html index 486f215..ea385cf 100644 --- a/docs/build/html/citing.html +++ b/docs/build/html/citing.html @@ -8,7 +8,7 @@ - Citing IRDAP — IRDAP 1.3.2 documentation + Citing IRDAP — IRDAP 1.3.3 documentation @@ -61,7 +61,7 @@
      - 1.3.2 + 1.3.3
      diff --git a/docs/build/html/configfile.html b/docs/build/html/configfile.html index 29ca58d..84992ca 100644 --- a/docs/build/html/configfile.html +++ b/docs/build/html/configfile.html @@ -8,7 +8,7 @@ - Configuration file — IRDAP 1.3.2 documentation + Configuration file — IRDAP 1.3.3 documentation @@ -61,7 +61,7 @@
      - 1.3.2 + 1.3.3
      diff --git a/docs/build/html/contributing.html b/docs/build/html/contributing.html index 795ae82..cf30dc8 100644 --- a/docs/build/html/contributing.html +++ b/docs/build/html/contributing.html @@ -8,7 +8,7 @@ - Contributing & issues — IRDAP 1.3.2 documentation + Contributing & issues — IRDAP 1.3.3 documentation @@ -61,7 +61,7 @@
      - 1.3.2 + 1.3.3
      diff --git a/docs/build/html/example.html b/docs/build/html/example.html index 9e238d1..b536f1a 100644 --- a/docs/build/html/example.html +++ b/docs/build/html/example.html @@ -8,7 +8,7 @@ - Example reduction — IRDAP 1.3.2 documentation + Example reduction — IRDAP 1.3.3 documentation @@ -61,7 +61,7 @@
      - 1.3.2 + 1.3.3
      diff --git a/docs/build/html/genindex.html b/docs/build/html/genindex.html index f285a29..d22e0a6 100644 --- a/docs/build/html/genindex.html +++ b/docs/build/html/genindex.html @@ -9,7 +9,7 @@ - Index — IRDAP 1.3.2 documentation + Index — IRDAP 1.3.3 documentation @@ -60,7 +60,7 @@
      - 1.3.2 + 1.3.3
      diff --git a/docs/build/html/index.html b/docs/build/html/index.html index 5a18904..9f3d899 100644 --- a/docs/build/html/index.html +++ b/docs/build/html/index.html @@ -8,7 +8,7 @@ - IRDAP — IRDAP 1.3.2 documentation + IRDAP — IRDAP 1.3.3 documentation @@ -60,7 +60,7 @@
      - 1.3.2 + 1.3.3
      diff --git a/docs/build/html/installation.html b/docs/build/html/installation.html index 82cd7bf..3f59638 100644 --- a/docs/build/html/installation.html +++ b/docs/build/html/installation.html @@ -8,7 +8,7 @@ - Installation — IRDAP 1.3.2 documentation + Installation — IRDAP 1.3.3 documentation @@ -61,7 +61,7 @@
      - 1.3.2 + 1.3.3
      diff --git a/docs/build/html/instructions.html b/docs/build/html/instructions.html index 410689a..05ed3c9 100644 --- a/docs/build/html/instructions.html +++ b/docs/build/html/instructions.html @@ -8,7 +8,7 @@ - Usage instructions — IRDAP 1.3.2 documentation + Usage instructions — IRDAP 1.3.3 documentation @@ -61,7 +61,7 @@
      - 1.3.2 + 1.3.3
      diff --git a/docs/build/html/mailinglist.html b/docs/build/html/mailinglist.html index ebbc7b1..b75d0bb 100644 --- a/docs/build/html/mailinglist.html +++ b/docs/build/html/mailinglist.html @@ -8,7 +8,7 @@ - Mailing list — IRDAP 1.3.2 documentation + Mailing list — IRDAP 1.3.3 documentation @@ -61,7 +61,7 @@
      - 1.3.2 + 1.3.3
      diff --git a/docs/build/html/objects.inv b/docs/build/html/objects.inv index 267cc33ddafb16ea742b5602a5624e1698c4854f..10b84429551b850c15710c95e4e2f073a8a69cce 100644 GIT binary patch delta 12 TcmZ3;v5;eeEu-;9yT{A`8u - Search — IRDAP 1.3.2 documentation + Search — IRDAP 1.3.3 documentation @@ -59,7 +59,7 @@
      - 1.3.2 + 1.3.3
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& to-do","Citing IRDAP","Configuration file","Contributing & issues","Example reduction","IRDAP","Installation","Usage instructions","Mailing list"],titleterms:{acknowledg:0,adi:[3,8],advanc:3,basic:3,changelog:1,cite:2,combin:8,configur:3,content:6,contribut:4,data:8,differenti:[],exampl:5,file:3,high:1,hint:8,imag:[],instal:7,instruct:8,irdap:[2,6,7,8],issu:4,list:9,low:1,mail:9,multipl:8,nutshel:8,option:3,pdi:[3,8],polarimetr:[],post:[],pre:[3,8],prioriti:1,process:[3,8],reduct:5,run:8,set:8,test:7,usag:8}}) \ No newline at end of file diff --git a/docs/source/changelog.rst b/docs/source/changelog.rst index 078ea00..f7fc34a 100644 --- a/docs/source/changelog.rst +++ b/docs/source/changelog.rst @@ -14,6 +14,9 @@ Changelog & to-do Changelog --------- +v1.3.3 June 2021, R.G. van Holstein + - Updated code so that it correctly handles the change of the header names INS4 DROT2 BEGIN and INS4 DROT3 BEGIN to INS4 DROT2 START and INS4 DROT3 START in the FITS files + v1.3.2 January 2021, R.G. van Holstein - Corrected a bug that prevented reductions to be performed when dark and flat files are included in the raw subdirectory @@ -76,6 +79,7 @@ v0.1.2 June 2019, R.G. van Holstein: To-do high priority ------------------- + - Add possibility to reduce data with center frames having a different DIT than the object frames (i.e. automatically scale object frames to DIT and ND filter of center frames before subtracting it; test with data of HD142527) - Automatically optimize the annulus for star polarization subtraction by iterativey updating the annulus by excluding disk signal and companions etc. - Improve computation of stellar DoLP and AoLP and corresponding uncertainties (standard error of mean) by sampling from Gaussian distributions with Monte Carlo - Correct error in computation of photon noise for Q and U images that uses signal in Q and U rather than I_Q and I_U. diff --git a/irdap/irdap.py b/irdap/irdap.py index 7a22757..06658db 100644 --- a/irdap/irdap.py +++ b/irdap/irdap.py @@ -363,8 +363,15 @@ def create_overview_headers(path_raw_dir, path_overview, log=True): # If header exists, include it in overview print_array[i+1, j+2] = header_sel[header_name_sel] else: - # If header does note exist, keep element of overview empty - print_array[i+1, j+2] = '' + if header_name_sel == 'ESO INS4 DROT2 BEGIN' and 'ESO INS4 DROT2 START' in header_sel: + # If header is derotator angle at start, try alternative name as implemented in 2021 + print_array[i+1, j+2] = header_sel['ESO INS4 DROT2 START'] + elif header_name_sel == 'ESO INS4 DROT3 BEGIN' and 'ESO INS4 DROT3 START' in header_sel: + # If header is HWP angle at start, try alternative name as implemented in 2021 + print_array[i+1, j+2] = header_sel['ESO INS4 DROT3 START'] + else: + # If header does note exist, keep element of overview empty + print_array[i+1, j+2] = '' if type(print_array[i+1, j+2]) is float: # Include string with 4 decimal places @@ -3526,7 +3533,7 @@ def preprocess_data(frames_to_remove=[], printandlog('\nWrote file ' + os.path.join(path_flux_dir, name_file_root + 'reference_flux.csv') + ' showing for each FLUX-file the ratios of the transmission and DIT of the OBJECT- and FLUX-files, and the measured' + - ' star total flux in ADU of the left and right frame halves and the left + right frame halves. The file ' + + ' star total flux in ADU of the left and right frame halves and the left + right frame halves. The file' + ' also shows the reference fluxes which are the products star_total_flux * transmission_ratio * dit_ratio.' + ' To express the final images produced by IRDAP (e.g. the I_Q-, Qphi- or summed ADI images) in Jansky per arcsec^2,' + ' determine the star flux in Jansky in the corresponding filter, and multiply the final images by the factor' + @@ -4204,11 +4211,20 @@ def correct_instrumental_polarization_effects(cube_I_Q_double_sum, for i, header_sel in enumerate(header): p[i] = compute_mean_angle([header_sel['ESO TEL PARANG START'], header_sel['ESO TEL PARANG END']]) a_start[i] = header_sel['ESO TEL ALT'] - theta_hwp[i] = np.mod(compute_mean_angle([np.mod(header_sel['ESO INS4 DROT3 BEGIN'] - 152.15, 360), np.mod(header_sel['ESO INS4 DROT3 END'] - 152.15, 360)]), 180) + try: + theta_hwp[i] = np.mod(compute_mean_angle([np.mod(header_sel['ESO INS4 DROT3 BEGIN'] - 152.15, 360), np.mod(header_sel['ESO INS4 DROT3 END'] - 152.15, 360)]), 180) + except: + theta_hwp[i] = np.mod(compute_mean_angle([np.mod(header_sel['ESO INS4 DROT3 START'] - 152.15, 360), np.mod(header_sel['ESO INS4 DROT3 END'] - 152.15, 360)]), 180) if tracking_mode_used == 'FIELD': - theta_der[i] = np.mod(compute_mean_angle([header_sel['ESO INS4 DROT2 BEGIN'], header_sel['ESO INS4 DROT2 END']]), 360) + try: + theta_der[i] = np.mod(compute_mean_angle([header_sel['ESO INS4 DROT2 BEGIN'], header_sel['ESO INS4 DROT2 END']]), 360) + except: + theta_der[i] = np.mod(compute_mean_angle([header_sel['ESO INS4 DROT2 START'], header_sel['ESO INS4 DROT2 END']]), 360) elif tracking_mode_used == 'PUPIL': - theta_der[i] = np.mod(compute_mean_angle([header_sel['ESO INS4 DROT2 BEGIN'], header_sel['ESO INS4 DROT2 END']]) + 0.5*pupil_offset, 360) + try: + theta_der[i] = np.mod(compute_mean_angle([header_sel['ESO INS4 DROT2 BEGIN'], header_sel['ESO INS4 DROT2 END']]) + 0.5*pupil_offset, 360) + except: + theta_der[i] = np.mod(compute_mean_angle([header_sel['ESO INS4 DROT2 START'], header_sel['ESO INS4 DROT2 END']]) + 0.5*pupil_offset, 360) mjd[i] = header_sel['MJD-OBS'] exposure_time[i] = header_sel['ESO DET SEQ1 DIT'] NDIT[i] = header_sel['ESO DET NDIT'] diff --git a/irdap/version.py b/irdap/version.py index bd18148..1930276 100644 --- a/irdap/version.py +++ b/irdap/version.py @@ -1 +1 @@ -__version__ = '1.3.2' \ No newline at end of file +__version__ = '1.3.3' \ No newline at end of file