peterkamphuis / fat Goto Github PK

FAT is now surpassed by pyFAT (https://github.com/PeterKamphuis/pyFAT-astro) a much more flexible and hopefully more accurate version of the code. The IDL/GDL wrapper is merely retained for historical purposes. FAT is an IDL/GDL wrapper to automate TiRiFiC

License: MIT License

Prolog 23.60% IDL 76.40%

gdl fat

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fat's Issues

Make paper reference more accurate

@PeterKamphuis Could you make add the paper reference in the README a bit more accuratey (i.e. the arXiv reference?

Create Data Testset

Create a test set that people can use to check wether FAT is working after installation.

Look at weighing of the outer ring when applying polynomials.

The fit to the outer ring of the models in the final fit is not optimal this should be re-investigated.

Overview plot of fit

Produce as output a single png file that gives an overview of parameters, PV-diagrams and moment maps. This should be uniform/similar as output overview from 2DBAT.

I think that for starters this file should have the radial profiles for SBR, VROT, INC, and PA. The moment0, 1, 2 maps with contours of model and data. In case of FAT a PV-diagram along the major axis comparing model and data.

Renaming of files produces error

Whenever the rename command is called by FAT.pro, e.g.

line 2852:  spawn,'rename 1stfit. 1stfitold. 1stfit.*',isthere

I get error messages similar to the following one:

Bareword found where operator expected at (eval 1) line 1, near "1stfit"
    (Missing operator before stfit?)

The files are not renamed. If I replace the above mentioned line in FAT.pro by e.g.

spawn,"rename 's/1stfit./1stfitold./' 1stfit.*",isthere

the files are properly renamed. I am running FAT on a Linux system.

Rebin not working in GDL 0.9.7

Rebin is not working in GDL 0.9.7. This messes up the creation of the intensity weighted velocity fields. It is fixed in the FAT-GDL-Beta Branch but not yet in the master.

Getting warnings on running `FAT`

Hi,

I get some warnings on trying to run FAT installation check. Just wanted to make sure that it is not something too important probably there can be something which the developers can suggest to fix this.

I have also created a public Docker repository where FAT is setup for public use. One can just download the docker image and get FAT running right away as all libraries and environment has been checked and pre-set. I thought about sharing that as well.
Here's the link: https://hub.docker.com/r/alankardutta/fat_gdl

WARNING: Ignoring unknown parameter: parameters.dilateChan = 1
WARNING: Converting '/S' to '/s' in CUNIT3.
WARNING: FITSFixedWarning: DATE-OBS= 1994.884
a string value was expected. [astropy.wcs.wcs]
WARNING: WCS conversion of parameters failed with the following error:
WARNING:   (<class 'astropy.wcs._wcs.InvalidTransformError'>, InvalidTransformError("ERROR 6 in wcs_units() at line 2582 of file wcs.c:\nIn CUNIT1 : Invalid symbol in EXPON context in 'DEGREE'.\n",), <traceback object at 0x7f753c919f38>)
WARNING:   at line 165 of wcs_coordinates.py
%

ls: cannot access '*_opt*': No such file or directory
ls: cannot access 'Optimized': No such file or directory
ls: cannot access 'No_Warp': No such file or directory
mv: cannot stat 'Overview.png': No such file or directory
% Compiled module: LOADCT.
% DATE_CONV: Invalid input date specified

*** PLPLOT ERROR, ABORTING OPERATION ***
UTF-8 string is malformed: 21!9�!X25', aborting operation
% Compiled module: TO_HEX.

*** PLPLOT ERROR, ABORTING OPERATION ***
UTF-8 string is malformed: 21!9�!X25', aborting operation
% DATE_CONV: Invalid input date specified
%

*** PLPLOT ERROR, ABORTING OPERATION ***
UTF-8 string is malformed: 21!9�!X25', aborting operation

*** PLPLOT ERROR, ABORTING OPERATION ***
UTF-8 string is malformed: 21!9�!X25', aborting operation
% DATE_CONV: Invalid input date specified
% DATE_CONV: Invalid input date specified
GPL Ghostscript 9.26 (2018-11-20)
Copyright (C) 2018 Artifex Software, Inc.  All rights reserved.
This software comes with NO WARRANTY: see the file PUBLIC for details.
Loading NimbusSans-Regular font from /usr/share/ghostscript/9.26/Resource/Font/NimbusSans-Regular... 4425900 2899258 2037672 733360 4 done.
mv: cannot stat 'No_Warp/*.def': No such file or directory
mv: cannot stat 'Optimized/*.def': No such file or directory

Full log:

fat_user@9545768d14ac:~/FAT$ gdl

 GDL - GNU Data Language, Version 0.9.6

- For basic information type HELP,/INFO
- Please report bugs, feature or help requests and patches at:
 http://sourceforge.net/projects/gnudatalanguage/

GDL> .r FAT.pro
% Compiled module: FAT.
GDL> FAT, /installation_check
% Compiled module: STR_SEP.
% Compiled module: BEAM_PLOT.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/beam_plot.pro
% Compiled module: BOOK_KEEPING.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/book_keeping.pro
% Compiled module: BUILDAXII.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/buildaxii.pro
% Compiled module: CALC_EDGE.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/calc_edge.pro
% Compiled module: CHANGERADII.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/changeradii.pro
% Compiled module: CHECK_CFLUX.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/check_cflux.pro
% Compiled module: CLEANUP.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/cleanup.pro
% Compiled module: CLEAN_HEADER.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/clean_header.pro
% Compiled module: COLOUR_BAR.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/colour_bar.pro
% Compiled module: COLORMAPS.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/colormaps.pro
% Compiled module: COLUMNDENSITY.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/columndensity.pro
% Compiled module: CONVERTRADEC.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/convertradec.pro
% Compiled module: CONVERTSKYANGLEFUNCTION.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/convertskyanglefunction.pro
% Compiled module: CREATE_RESIDUAL_FILE.
% Compiled module: CREATE_RESIDUALS.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/create_residuals.pro
% Compiled module: DEC_NAMES.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/dec_names.pro
% Compiled module: EXTRACT_PV.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/extract_pv.pro
% Compiled module: FAT_ARCTAN.
% Compiled module: FATARCTAN.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/fat_arctan.pro
% Compiled module: FATARCTAN.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/fatarctan.pro
% Compiled module: FAT_FIT.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/fat_fit.pro
% Warning: Keyword parameter COMPILE_FULL_FILE not supported in call to: RESOLVE_ROUTINE. Ignored.
% Compiled module: FAT_GDLGAUSS.
% Compiled module: FATGAUSS.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/fat_gdlgauss.pro
% Compiled module: FAT_SAVGOL.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/fat_savgol.pro
% Compiled module: FAT_PLOTERROR.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/fat_ploterror.pro
% Compiled module: FAT_SMOOTH.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/fat_smooth.pro
% Compiled module: FAT_SPLINE.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/fat_spline.pro
% Compiled module: GETDHI.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/getdhi.pro
% Compiled module: GET_FIXEDRINGSV9.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/get_fixedringsv9.pro
% Compiled module: GET_NEWRINGSV9.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/get_newringsv9.pro
% Compiled module: GET_PROGRESS.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/get_progress.pro
% Compiled module: INT_PROFILEV2.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/int_profilev2.pro
% Compiled module: INTERPOLATE.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/interpolate.pro
% Compiled module: INSTALL_CHECK.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/install_check.pro
% Compiled module: ISNUMERIC.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/isnumeric.pro
% Compiled module: LINENUMBER.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/linenumber.pro
% Compiled module: MOMENTSV2.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/momentsv2.pro
% Compiled module: OBTAIN_PA_INCL.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/obtain_pa_incl.pro
% Compiled module: OBTAIN_RATIOS.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/obtain_ratios.pro
% Compiled module: OBTAIN_VELPA.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/obtain_velpa.pro
% Compiled module: OBTAIN_W50.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/obtain_w50.pro
% Compiled module: ORGANIZE_OUTPUT.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/organize_output.pro
% Compiled module: OVERVIEW_PLOT.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/overview_plot.pro
% Compiled module: PRE_RAN_SOFIA.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/pre_ran_sofia.pro
% Compiled module: PREPROCESSING.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/preprocessing.pro
% Compiled module: RA_NAMES.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/ra_names.pro
% Compiled module: READ_TEMPLATE.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/read_template.pro
% Compiled module: REGULARISATION_SDIS.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/regularisation_sdis.pro
% Compiled module: RENAME.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/rename.pro
% Compiled module: REVISED_REGULARISATION_COM.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/revised_regularisation_com.pro
% Compiled module: REVISED_REGULARISATION_ROT.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/revised_regularisation_rot.pro
% Compiled module: ROTTAB.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/rottab.pro
% Compiled module: RUN_SOFIA.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/run_sofia.pro
% Compiled module: SBR_CHECK.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/sbr_check.pro
% Compiled module: SET_SBR.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/set_sbr.pro
% Compiled module: SET_SDIS.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/set_sdis.pro
% Compiled module: SET_VROTV6.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/set_vrotv6.pro
% Compiled module: SET_WARP_SLOPEV3.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/set_warp_slopev3.pro
% Compiled module: SHOWPIXELSMAP.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/showpixelsmap.pro
% Compiled module: WRITEFITTINGVARIABLES.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/writefittingvariables.pro
% Compiled module: WRITENEWTOTEMPLATE.
% RESOLVE_ROUTINE: Compiled file: /home/fat_user/FAT/Support/writenewtotemplate.pro
% Compiled module: FILE_LINES.
% Compiled module: STRSPLIT.
(629) This is version V2.0.2 of the program
(864) We're at galaxy number 0. Which is catalogue id number 0
% Compiled module: READFITS.
% Compiled module: SXPAR.
% Compiled module: GETTOK.
% Compiled module: VALID_NUM.
% Compiled module: SXADDPAR.
% Compiled module: SXDELPAR.
% Compiled module: STDDEV.
% Compiled module: MOMENT.
% Compiled module: WRITEFITS.
% Compiled module: CHECK_FITS.
% Compiled module: FXPAR.
(1126) We have started from the original cube.
(1160) RUN_SOFIA: Running SoFiA.
WARNING: Ignoring unknown parameter: parameters.dilateChan = 1
WARNING: Converting '/S' to '/s' in CUNIT3.
WARNING: FITSFixedWarning: DATE-OBS= 1994.884
a string value was expected. [astropy.wcs.wcs]
WARNING: WCS conversion of parameters failed with the following error:
WARNING:   (<class 'astropy.wcs._wcs.InvalidTransformError'>, InvalidTransformError("ERROR 6 in wcs_units() at line 2582 of file wcs.c:\nIn CUNIT1 : Invalid symbol in EXPON context in 'DEGREE'.\n",), <traceback object at 0x7f753c919f38>)
WARNING:   at line 165 of wcs_coordinates.py
% Compiled module: XYAD.
% Compiled module: EXTAST.
% Compiled module: REMCHAR.
% Compiled module: ZPARCHECK.
% Compiled module: REPSTR.
% Compiled module: GET_EQUINOX.
% Compiled module: DATE_CONV.
% DATE_CONV: Invalid input date specified
% Compiled module: TAG_EXIST.
% Compiled module: XY2AD.
% DATE_CONV: Invalid input date specified
% DATE_CONV: Invalid input date specified
(1283) MOMENTSV2: We have converted the units to Jy/Beam x Km/s
% DATE_CONV: Invalid input date specified
(1319) MOMENTSV2: We are converting to KM/S
% DATE_CONV: Invalid input date specified
(1355) MOMENTSV2: We are converting to KM/S
% Compiled module: ROT.
% Compiled module: MPFITFUN.
% Compiled module: MPFIT.
% Compiled module: MEAN.
% DATE_CONV: Invalid input date specified
% DATE_CONV: Invalid input date specified
% Compiled module: ADXY.
% DATE_CONV: Invalid input date specified
% Compiled module: AD2XY.
(2096) EXTRACT_PV: We are converting to KM/S
(2920) Starting tirific SBR estimate in  ./ which is galaxy # 0 at Sat Jul 22 04:39:49 2023
% Compiled module: LA_INVERT.
(3204) Starting tirific first estimate in  ./  which is galaxy #  0 at Sat Jul 22 04:41:44 2023
(3251) The first estimate is accepted.
(3204) Starting tirific first estimate in  ./  which is galaxy #  0 at Sat Jul 22 04:44:53 2023
(3251) The first estimate is accepted.
(3204) Starting tirific first estimate in  ./  which is galaxy #  0 at Sat Jul 22 04:58:47 2023
(3251) The first estimate is accepted.
(3204) Starting tirific first estimate in  ./  which is galaxy #  0 at Sat Jul 22 05:13:46 2023
(3251) The first estimate is accepted.
(3204) Starting tirific first estimate in  ./  which is galaxy #  0 at Sat Jul 22 05:27:22 2023
(3251) The first estimate is accepted.
(3204) Starting tirific first estimate in  ./  which is galaxy #  0 at Sat Jul 22 05:43:11 2023
(3251) The first estimate is accepted.
% DATE_CONV: Invalid input date specified
(4002) EXTRACT_PV: We are converting to KM/S
% EXTAST: Unrecognized distortion acronym: / P
(4005) EXTRACT_PV: We are converting to KM/S
(4033) MOMENTSV2: We have converted the units to Jy/Beam x Km/s
% EXTAST: Unrecognized distortion acronym: / P
(4036) MOMENTSV2: We are converting to KM/S
% EXTAST: Unrecognized distortion acronym: / P
(4039) MOMENTSV2: We are converting to KM/S
% EXTAST: Unrecognized distortion acronym: / P
ls: cannot access '*_opt*': No such file or directory
ls: cannot access 'Optimized': No such file or directory
ls: cannot access 'No_Warp': No such file or directory
mv: cannot stat 'Overview.png': No such file or directory
% Compiled module: LOADCT.
% DATE_CONV: Invalid input date specified

*** PLPLOT ERROR, ABORTING OPERATION ***
UTF-8 string is malformed: 21!9�!X25', aborting operation
% Compiled module: TO_HEX.

*** PLPLOT ERROR, ABORTING OPERATION ***
UTF-8 string is malformed: 21!9�!X25', aborting operation
% DATE_CONV: Invalid input date specified
% Compiled module: INTERPOL.
% Compiled module: FINDEX.

*** PLPLOT ERROR, ABORTING OPERATION ***
UTF-8 string is malformed: 21!9�!X25', aborting operation

*** PLPLOT ERROR, ABORTING OPERATION ***
UTF-8 string is malformed: 21!9�!X25', aborting operation
% DATE_CONV: Invalid input date specified
% DATE_CONV: Invalid input date specified
GPL Ghostscript 9.26 (2018-11-20)
Copyright (C) 2018 Artifex Software, Inc.  All rights reserved.
This software comes with NO WARRANTY: see the file PUBLIC for details.
Loading NimbusSans-Regular font from /usr/share/ghostscript/9.26/Resource/Font/NimbusSans-Regular... 4425900 2899258 2037672 733360 4 done.
mv: cannot stat 'No_Warp/*.def': No such file or directory
mv: cannot stat 'Optimized/*.def': No such file or directory

!!!!--------------------------------------------!!!!!
!!!! As far as we can tell FAT is installed     !!!!!
!!!! properly and runs smoothly.                !!!!!
!!!!--------------------------------------------!!!!!

FAT not compatible with current SoFiA version

The current version of SoFiA only returns certain source parameters when doParameterise=true in the SoFiA input parameter file. The flux related parameters ('f_int', 'f_peak', 'f_wm50' - names might have changed compared to previous versions) belong to this particular group. This is important because FAT needs these parameters (e.g. in line 1076) and terminates if they are not present and the array holding the source parameters is too short for the provided index (17 in the following error message):

% Attempt to subscript VALS with <LONG     (          17)> is out of range.

The indices of source parameters that are used are hard coded in FAT. Even if doParameterise is set to 'true', the wrong source parameter values will be used in some cases, e.g.

line 1076: Totflux=[double(vals[17])]

The parameter index of the total flux in the catalogue that is returned by SoFiA is 18, the index of 17 corresponds to the position angle that has been determined by ellipse fitting. Thus, the wrong value is used. It might be better to get the parameter index from the name in the catalogue file ('f_int' in this case).

Base D_HI on the de-convolved SBR profile.

After the fit, D_HI should be based on the SBR profile such that we get deconvolved sizes.

Subscript out of range [s:e]

Error message:

Subscript out of range [s:e]
Execution halted at: FAT 1991 /home/colin/Documents/Work/PhD/Codes/FAT/FAT/FAT.pro

In the galaxy(files.tar.gz) I'm trying to fit, norings[0] = 9 (and therefore rings[0:8] is the array I think?), but the following line tries to place a vector with length 10 into a vector with length 9

rings[0:9]=(findgen(10))*catmajbeam[i]+catmajbeam[i]/5.

when I work around there is an error on line 1992:

rings[10:norings[0]-1]=(findgen(fix(tmpring)))*catmajbeam[i]*2+catmajbeam[i]/5.+11.*catmajbeam[i]

where tmpring=norings[0]-10. If tmpring = -1, then findgen(fix(tmpring)) returns an error

Outdated Installation Check

The installation check fails due to updated sofia and tirific.

Implement proper error handling through CATCH use.

The main routine now use a CATCH to deal with errors and to remind users to submit bug reports here. However whenever the code breaks in a subroutine this will not be caught.

Implement the CATCH routine in all subroutine such that proper handling occurs.

Additionally in GDL currently it is impossible to get a decent trace back with catch. Find a solution for this.

Study use of new spline interpolation of Tirific on small sources.

Create a working GDL version

Create a working version of FAT that works under GDL such that IDL licences are no longer required.

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