editeodoro / bbarolo Goto Github PK

Thanks for providing this software. Is it able to decompose the rotation curves into baryons vs dark matter from FITS files? If not, can you suggest software that does decompose from FITS files?

Thanks!

I noticed a possible bug during configure on my system. It complained of being unable to find wcslib (specifically when it tests whether -lwcs finds wcss2p). I explicitly stated --with-wcslib=/home/koman (the library is at /astro/koman/lib), which failed again. Setting LDFLAGS=-L/astro/koman/lib AND specifying --with-wcslib=/astro/koman resolved the issue. Even though configure succeeded with this, the subsequent make failed in linking when unable to find a bunch of wcs library functions.

Here is the attempted linking step:

g++ -O2 -ftree-vectorize -fPIC -Wuninitialized -std=c++11 -fopenmp -flto -o BBarolo /astro/koman/code/Bbarolo/src/Build/bbarolo.o /astro/koman/code/Bbarolo/src/Build/header.o /astro/koman/code/Bbarolo/src/Build/param.o /astro/koman/code/Bbarolo/src/Build/stats.o /astro/koman/code/Bbarolo/src/Build/cube.o /astro/koman/code/Bbarolo/src/Build/search.o /astro/koman/code/Bbarolo/src/Build/image.o /astro/koman/code/Bbarolo/src/Build/object2D.o /astro/koman/code/Bbarolo/src/Build/object3D.o /astro/koman/code/Bbarolo/src/Build/objectgrower.o /astro/koman/code/Bbarolo/src/Build/utils.o /astro/koman/code/Bbarolo/src/Build/conv2D.o /astro/koman/code/Bbarolo/src/Build/smooth3D.o /astro/koman/code/Bbarolo/src/Build/galmod.o /astro/koman/code/Bbarolo/src/Build/galwind.o /astro/koman/code/Bbarolo/src/Build/galfit.o /astro/koman/code/Bbarolo/src/Build/galfit_min.o /astro/koman/code/Bbarolo/src/Build/galfit_errors.o /astro/koman/code/Bbarolo/src/Build/galfit_out.o /astro/koman/code/Bbarolo/src/Build/slitfit.o /astro/koman/code/Bbarolo/src/Build/spacepar.o /astro/koman/code/Bbarolo/src/Build/ringmodel.o /astro/koman/code/Bbarolo/src/Build/progressbar.o /astro/koman/code/Bbarolo/src/Build/ellprof.o /astro/koman/code/Bbarolo/src/Build/allocator.o /astro/koman/code/Bbarolo/src/Build/string.o /astro/koman/code/Bbarolo/src/Build/statistics.o /astro/koman/code/Bbarolo/src/Build/interpolation.o /astro/koman/code/Bbarolo/src/Build/converter.o /astro/koman/code/Bbarolo/src/Build/wcsUtils.o /astro/koman/code/Bbarolo/src/Build/BB_interface.o -L/usr/local/lib -lfftw3 -L/usr/local/lib -lcfitsio -L/astro/koman/lib -lwcs -lm -DHAVE_GNUPLOT -DHAVE_FFTW3 -DHAVE_PYTHON
I experimented a bit and found that simply deleting the two -L/usr/local/lib arguments ended in a successful linking:

g++ -O2 -ftree-vectorize -fPIC -Wuninitialized -std=c++11 -fopenmp -flto -o BBarolo /astro/koman/code/Bbarolo/src/Build/bbarolo.o /astro/koman/code/Bbarolo/src/Build/header.o /astro/koman/code/Bbarolo/src/Build/param.o /astro/koman/code/Bbarolo/src/Build/stats.o /astro/koman/code/Bbarolo/src/Build/cube.o /astro/koman/code/Bbarolo/src/Build/search.o /astro/koman/code/Bbarolo/src/Build/image.o /astro/koman/code/Bbarolo/src/Build/object2D.o /astro/koman/code/Bbarolo/src/Build/object3D.o /astro/koman/code/Bbarolo/src/Build/objectgrower.o /astro/koman/code/Bbarolo/src/Build/utils.o /astro/koman/code/Bbarolo/src/Build/conv2D.o /astro/koman/code/Bbarolo/src/Build/smooth3D.o /astro/koman/code/Bbarolo/src/Build/galmod.o /astro/koman/code/Bbarolo/src/Build/galwind.o /astro/koman/code/Bbarolo/src/Build/galfit.o /astro/koman/code/Bbarolo/src/Build/galfit_min.o /astro/koman/code/Bbarolo/src/Build/galfit_errors.o /astro/koman/code/Bbarolo/src/Build/galfit_out.o /astro/koman/code/Bbarolo/src/Build/slitfit.o /astro/koman/code/Bbarolo/src/Build/spacepar.o /astro/koman/code/Bbarolo/src/Build/ringmodel.o /astro/koman/code/Bbarolo/src/Build/progressbar.o /astro/koman/code/Bbarolo/src/Build/ellprof.o /astro/koman/code/Bbarolo/src/Build/allocator.o /astro/koman/code/Bbarolo/src/Build/string.o /astro/koman/code/Bbarolo/src/Build/statistics.o /astro/koman/code/Bbarolo/src/Build/interpolation.o /astro/koman/code/Bbarolo/src/Build/converter.o /astro/koman/code/Bbarolo/src/Build/wcsUtils.o /astro/koman/code/Bbarolo/src/Build/BB_interface.o -lfftw3 -lcfitsio -L/astro/koman/lib -lwcs -lm -DHAVE_GNUPLOT -DHAVE_FFTW3 -DHAVE_PYTHON

A look at the ld docs was not illuminating as to why this would matter...

My environment in case it is relevant:
env.log

ello, i am using Bbarolo for my master thesis and it works great so far! I was just wondering how Barolo converts the radii to Kpc without having any information about the distance of the galaxies? The radii in kpc seem very of for my calculations. Or is there an option to set the distance?
Thanks in advance!

Hello,

Thanks for BBarolo, a really randomAdjective(1) piece of software!

We have stumbled upon what could be a mismatch of assumed units between the code and the docs in the beam area computation function. It looks like calcArea expects bmaj and bmin in degrees (because CDELTis are usually degrees per pixel), while the docs explicitly state that they should be in arcseconds.

So, could you please clarify, is it an intended behavior and we are missing something important or is it just a typo?

ERROR: Mismatch in the version of the fitsio.h include file used to build
the CFITSIO library, and the version included by the application program:
Version used to build the CFITSIO library = 3.250000
Version included by the application program = 0.000000
Segmentation fault (core dumped)

running on ubuntu 16.04

I don't see the 3DFit code using the 4 threads as specified in the parameters files (ubuntu 17.10).

Screenshot running meanwhile running 3DFIt (using the fits and par files from example)

configure output
out.txt

When I run:
make gui
I get an error message:
In file included from bbarolowindow_run.cpp:29:
./../Arrays/header.hh:31:10: fatal error: 'fitsio.h' file not found
#include <fitsio.h>
^~~~~~~~~~
1 error generated.
make[1]: *** [../Build/bbarolowindow_run.o] Error 1
make: *** [gui] Error 2

Thank you for any hint!

Hello, i have been trying to install PyBarolo using the wget command. The link from the documentation leads to a 404 error. Is there a up to date link somewhere?
Thanks in advance

After I gave BBarolo my initial guesses of PA and inclination, BBarolo gave me a result that the PA of the outmost ring is approximately -280(which I gave 80). Then BBarolo tried to fit -280 into the whole bezier function and made the output pdf look strange. I wonder how to solve the problem.
maps_local.pdf
parameters.pdf

compiled on ubuntu 17.10. when running -f option it will generate only moment maps in the folder output (3DFIT terminal output never starts)

Hi EdT,

I switched from the pre-compiled binary (OSX) to the version I compiled myself on my MacOS 10.14.6 (default configuration). I found the latter is very slow and only using half of my CPU, while the pre-compiled version (https://github.com/editeodoro/Bbarolo/releases/tag/1.4) is using the full CPU.

Do you have any idea why this is happening?

Many thanks!!

Dear Enrico,

I have noticed a strange behavior of the code (the GUI version) in the case no file par is furnished and the WCSlib return an error.
My installation is running on ubuntu 14.04 64bit and I compiled the source using the following version of the prerequisites:
-cfitsio3370
-wcslib5.5
-fftw3.3.4
-Qt4.8.5
-gnuplot 4.6 patchlevel 5
-python2.7.8 with astropy

Here is an output of the log file using this datacube:
https://www.dropbox.com/s/1qf2xkf78lji86c/N2403.fits?dl=0
(wcsgrid5.5 doesn't complain using this datacube)

BaroloGUI log:

///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-------------------------- Parameters -------------------------

Image to be analysed..............................[FitsFile] = /media/Storage/PhD_Groningen/Slicer_data/prova12/N2403.fits

Checking for bad channels in the cube........[checkChannels] = false
Using Robust statistics?...................[flagRobustStats] = true
Searching for sources in cube?..................[flagSearch] = false
Fitting velocity field with a ring model?.........[flagRing] = false
Saving the global profile?...................[globalProfile] = false
Saving 0th moment map to FITS file?...............[totalMap] = false
Saving 1th moment map to FITS file?............[velocityMap] = false
Saving 2th moment map to FITS file?..........[dispersionMap] = false
Smoothing the datacube?.............................[SMOOTH] = false
Fitting a 3D model to the datacube?.................[GALFIT] = true
Sub-region to be used?..............................[BOX] = NONE
Number of radii..................................[NRADII] = 0
Separation between radii (arcsec)................[RADSEP] = 29.66
X center of the galaxy (pixel).....................[XPOS] = 150.00
Y center of the galaxy (pixel).....................[YPOS] = 150.00
Systemic velocity of the galaxy (km/s).............[VSYS] = 0
Initial global rotation velocity (km/s)............[VROT] = 0
Initial global velocity dispersion (km/s).........[VDISP] = 0
Initial global inclination (degrees)................[INC] = 0
Initial global position angle (degrees)..............[PA] = 0
Scale height of the disk (arcsec)....................[Z0] = 0
Global column density of gas (atoms/cm2)...........[DENS] = 1
Parameters to be minimized.........................[FREE] = VROT VDISP INC PA
Type of mask?......................................[MASK] = SMOOTH
What side of the galaxy to be used.................[SIDE] = B
Layer type along z direction......................[LTYPE] = gaussian
Function to be minimized..........................[FTYPE] = |m-o|
Weighting function................................[WFUNC] = cos(θ)^2
Minimization tolerance..............................[TOL] = 0.001
Two stages minimization?.......................[TWOSTAGE] = true
Degree of polynomial fitting angles?............[POLYN] = bezier
Estimating errors?...........................[flagErrors] = false

Opening file /media/Storage/PhD_Groningen/Slicer_data/prova12/N2403.fits
Reading 300 x 300 x 62 pixels FITS file... Done.

Cannot convert to wcs. WCS error code = 9: stat=3 : One or more of the world coordinates were invalid
Creating mask for the fit (SMOOTH) ... Done.

///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////

at this point seems to be stacked, no step further is done, but a huge amount of ram start to be used (16 GB in few seconds).

Inserting a par file (even a "wrong" one) seems that fix the memory allocation problem.

I experienced the issue with also others datacube (like with NAXIS=4) for which WCSlib complain (I think WCS error code =4).

Of course, I think is not your job fixing the datacubes automatically (it is apt to the user to give the proper header following the WCS "rules"), however you can fix the strange memory allocation behavior if it is something not related only to my installation.

Thanks,

Cheers,

Davide.

Hi @editeodoro and @kyleaoman!

This program is fantastic!

I found a tiny problem though. The output stage fails if the path has spaces in it. For example:
/home/me/this path has spaces/output/galaxy_files

Here is a screenshot of the error:
Something went wrong! Check plotting scripts in the output folder

I fixed it by adding escaped quotation marks around the paths. Now, it works with no errors:

I made a new github branch called "bugfix/spaces_in_path". May I submit it to your repository as a Pull Request?

Hey, i want to use a function that was found as a regularization for the PA while i held the inclination at a constant value in another run where i define the PA as this function and now fit only the inc to give more room in the parameter space. Is this a possibility in Barolo?
Basically i just want to reuse a found regularization for further runs, not just in the second run

Hi,
I have installed 3DBarolo on Mac and it appears the installation worked correctly; when I type 'bbarolo' in terminal the quick start guide appears as expected. However when I attempt to run it, whether with or without a parameter file, including on the example data, the parameters are printed out in the terminal and then the error 'zsh: abort' immediately appears before any fitting is performed. Do you have any idea why this might be happening and what I can do to solve the issue? Thanks.

Hello Enrico,

I just started using Bbarolo with some ALMA data. After figuring out that the codes expects velocities in the spectral axis instead of frequencies I managed to obtain some successful fits.
I have the problem that all the mod_local files are empty, full of Nans or zeros. What could be the problem?

About the plots:
I can run the gnuplot script and obtain the plots but the python script fails.
The spectral axis indexes generated by the code are wrong and fail to select a correct subcube from the original ALMA cube. I fixed this manually in the script.

The second problem is that the python scripts fails at:
norm0 = ImageNormalize(np.nanmin(mom0), np.nanmax(mom0), stretch=LinearStretch())
returning:
AttributeError: 'numpy.float32' object has no attribute 'get_limits'

I am using the binaries for mac,

any advice?

Jorge

I noticed that there are many parameters settings in the file ".par".

First, what is the principle of "BMAJ" and "BMIN" settings? Their changes have a significant impact on the results!

And, how can I set up a mask according to my own needs? If I mask the value of the unwanted place, and then give the mask fits file to ".par" file, I will get the following error:
Creating mask (SMOOTH) ... SMOOTH error: new beam smaller than old beam
old beam: mm x nn
new beam: mm x nn
terminate called without an active exception
Aborted (core dumped)

Hi Enrico,

new linux distros (e.g., ubuntu 17.10) do not have anymore libpng12 required from the linux binaries.

Would be great to have input mask FITS file support in pyBBarolo. Currently exits with an error:

if key=='mask' and op[key][0].upper() not in ['SMOOTH','SEARCH','THRESHOLD','NEGATIVE','SMOOTH&SEARCH','NONE']:
raise ValueError("%s ERROR: %s can only 'SMOOTH','SEARCH','THRESHOLD','NEGATIVE', 'SMOOTH&SEARCH' or 'NONE'."%(self.taskname,key))

I can still run with the regular executable (outside of Python) but let me know if this support may be added soon.

Hello and thank you for this amazing code and effort.
So this is a feature request, or a question if I didn't read the documentation very well.
In case the user provides a Vrot (a value or a model from a file) the code should support some boundaries so it fits for every ring a value within (Vrot-DELTAV,Vrot+DELTAV).
Thanks again!

Hey there,
I am a master's student and I am using your code to analyse intensity profiles of my sources (ALMA datacubes). I have so far managed to make the code work for 3 of my cubes (spatially the largest sources in my dataset) successfully, however the consequent sources absolutely refuse to run.
I run the code in the command line using a parameter file, a sample of the one that does not work is here (it does have spaces everywhere, the formatting here is a bit off):

###############################################################
##INPUT AND OUTPUT PARAMETERS##
###############################################################

FITSFILE /msn2e2/avenkat/thesis/subimg-CII/SPT2349-CII_C4.fits
OUTFOLDER /msn2e2/avenkat/thesis/bbarolo-outputs/C4
THREADS 8
PLOTS true
SHOWBAR true
VERBOSE true

###############################################################
##SEARCH TOOL##
###############################################################

SEARCH true
FLAGROBUSTSTATS false
SEARCHTYPE spatial
SNRCUT 0
THRESHOLD 0.00212965
FLAGGROWTH true
GROWTHCUT 0
GROWTHTHRESHOLD 0.00085186
MINPIX 1
MINCHANNELS 5
FLAGADJACENT true
THRESHSPATIAL 1
THRESHVELOCITY 1
REJECTBEFOREMERGE true
TWOSTAGEMERGING true

###############################################################
##3D FITTING TOOL##
###############################################################

3DFIT true
NRADII 6
RADSEP 0.08
XPOS 13
YPOS 13
VSYS -145.1
VROT 490.7
VRAD 0
VDISP 150
INC 65.1
PA 324.2
Z0 0

DELTAINC 3
DELTAPA 3
FREE VROT VDISP
FTYPE 1
WFUNC 2
LTYPE 1
CDENS 10
SIDE B
MAKEMASK true
MASK SEARCH
NORM LOCAL
TWOSTAGE true
POLYN 1
BIWEIGHT 1
FLAGERRORS true
STARTRAD 0
LINEAR 0.42466
ADRIFT false
PLOTMASK false
NOISERMS 0
TOL 0.0001

Once this is done, the program searches the datacube successfully (I get the appropriate results) and later after the fitting, this is what happens:

Starting research for possible sources in the cube...
Intermediate list has 30 objects.
Merging and Rejecting... Done.
... All done.

Final object count = 1

Done.

Starting research for possible sources in the cube...
Searching in progress... Found 93 items.
Updating detection map... Done.
Intermediate list has 35 objects.
Merging and Rejecting... Done.
... All done.

Final object count = 1

Extracting maps... OK. s

======================== Initial parameters ========================
(i) input by the user (d) default (e) estimated by me

Fitting #6(i) rings of width 0.080000(i) arcsec

Xpos (i) =     13.00  pix            Ypos (i) =    13.00  pix    
Vsys (i) =   -145.10  km/s           Vrot (i) =   490.70  km/s   
Inc (i)  =     65.10  deg            PA (i)   =   324.20  deg    
Z0 (i)   =      0.00  arcs           Disp (i) =   200.00  km/s   
Vrad (i) =      0.00  km/s   

================================= 3DFIT =================================

Ring #1 at radius 0.04 arcsec (0.00 Kpc)...
Best parameters for ring #1 (fmin = 1.862e-05):
Vrot = 166.62 km/s Disp = 287.63 km/s
Vrad(f) = 0.00 km/s Vsys(f) = -145.10 km/s
Inc(f) = 65.10 deg PA(f) = 324.20 deg
Xpos(f) = 13.00 pix Ypos(f) = 13.00 pix
Z0(f) = 0.00 Kpc

Ring #2 at radius 0.12 arcsec (0.00 Kpc)...
Best parameters for ring #2 (fmin = 1.456e-05):
Vrot = 286.71 km/s Disp = 189.85 km/s
Vrad(f) = 0.00 km/s Vsys(f) = -145.10 km/s
Inc(f) = 65.10 deg PA(f) = 324.20 deg
Xpos(f) = 13.00 pix Ypos(f) = 13.00 pix
Z0(f) = 0.00 Kpc

Ring #3 at radius 0.20 arcsec (0.00 Kpc)...
Best parameters for ring #3 (fmin = 2.150e-05):
Vrot = 321.77 km/s Disp = 172.24 km/s
Vrad(f) = 0.00 km/s Vsys(f) = -145.10 km/s
Inc(f) = 65.10 deg PA(f) = 324.20 deg
Xpos(f) = 13.00 pix Ypos(f) = 13.00 pix
Z0(f) = 0.00 Kpc

Ring #4 at radius 0.28 arcsec (0.00 Kpc)...
Best parameters for ring #4 (fmin = 2.473e-05):
Vrot = 346.50 km/s Disp = 205.90 km/s
Vrad(f) = 0.00 km/s Vsys(f) = -145.10 km/s
Inc(f) = 65.10 deg PA(f) = 324.20 deg
Xpos(f) = 13.00 pix Ypos(f) = 13.00 pix
Z0(f) = 0.00 Kpc

Ring #6 at radius 0.44 arcsec (0.00 Kpc)...
Best parameters for ring #6 (fmin = 3.009e-05):
Vrot = 472.50 km/s Disp = 78.53 km/s
Vrad(f) = 0.00 km/s Vsys(f) = -145.10 km/s
Inc(f) = 65.10 deg PA(f) = 324.20 deg
Xpos(f) = 13.00 pix Ypos(f) = 13.00 pix
Z0(f) = 0.00 Kpc

Ring #5 at radius 0.36 arcsec (0.00 Kpc)...
Best parameters for ring #5 (fmin = 2.376e-05):
Vrot = 419.60 km/s Disp = 101.98 km/s
Vrad(f) = 0.00 km/s Vsys(f) = -145.10 km/s
Inc(f) = 65.10 deg PA(f) = 324.20 deg
Xpos(f) = 13.00 pix Ypos(f) = 13.00 pix
Z0(f) = 0.00 Kpc

Preparing a bunch of cool outputs...
Extracting execrable 2D maps... Done.
Deriving illuminating radial profile... Done.
Calculating the very last model...*** Error in `./BBarolo': double free or corruption (!prev): 0x0000562aa7f7d990 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x70bfb)[0x7f98b03a7bfb]
/lib/x86_64-linux-gnu/libc.so.6(+0x76fc6)[0x7f98b03adfc6]
/lib/x86_64-linux-gnu/libc.so.6(+0x7780e)[0x7f98b03ae80e]
./BBarolo(+0xda1a4)[0x562aa73d51a4]
./BBarolo(+0xd22f4)[0x562aa73cd2f4]
./BBarolo(+0xf532a)[0x562aa73f032a]
./BBarolo(+0x110290)[0x562aa740b290]
./BBarolo(+0x15f5bb)[0x562aa745a5bb]
./BBarolo(+0xd083)[0x562aa7308083]
./BBarolo(+0x9d68)[0x562aa7304d68]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf1)[0x7f98b03572e1]
./BBarolo(+0xa7ca)[0x562aa73057ca]
======= Memory map: ========
562aa72fb000-562aa74eb000 r-xp 00000000 00:27 1151054122620 /msn2e2/avenkat/thesis/softwares/Bbarolo-1.5/soft/bin/BBarolo-1.5
562aa76ea000-562aa76ec000 r--p 001ef000 00:27 1151054122620 /msn2e2/avenkat/thesis/softwares/Bbarolo-1.5/soft/bin/BBarolo-1.5
562aa76ec000-562aa76ed000 rw-p 001f1000 00:27 1151054122620 /msn2e2/avenkat/thesis/softwares/Bbarolo-1.5/soft/bin/BBarolo-1.5
562aa76ed000-562aa76f1000 rw-p 00000000 00:00 0
562aa7f45000-562aa80bd000 rw-p 00000000 00:00 0 [heap]
7f9878000000-7f98780a5000 rw-p 00000000 00:00 0
7f98780a5000-7f987c000000 ---p 00000000 00:00 0
7f987c000000-7f987c021000 rw-p 00000000 00:00 0
7f987c021000-7f9880000000 ---p 00000000 00:00 0
7f9880000000-7f98800a4000 rw-p 00000000 00:00 0
7f98800a4000-7f9884000000 ---p 00000000 00:00 0
7f9888000000-7f9888022000 rw-p 00000000 00:00 0
7f9888022000-7f988c000000 ---p 00000000 00:00 0
7f9890000000-7f989006c000 rw-p 00000000 00:00 0
7f989006c000-7f9894000000 ---p 00000000 00:00 0
7f9898000000-7f9898022000 rw-p 00000000 00:00 0
7f9898022000-7f989c000000 ---p 00000000 00:00 0
7f98a0000000-7f98a00ba000 rw-p 00000000 00:00 0
7f98a00ba000-7f98a4000000 ---p 00000000 00:00 0
7f98a8000000-7f98a8087000 rw-p 00000000 00:00 0
7f98a8087000-7f98ac000000 ---p 00000000 00:00 0
7f98ac301000-7f98ac502000 rw-p 00000000 00:00 0
7f98ac502000-7f98ac503000 ---p 00000000 00:00 0
7f98ac503000-7f98acd03000 rw-p 00000000 00:00 0
7f98acd03000-7f98acd04000 ---p 00000000 00:00 0
7f98acd04000-7f98ad504000 rw-p 00000000 00:00 0
7f98ad504000-7f98ad505000 ---p 00000000 00:00 0
7f98ad505000-7f98add05000 rw-p 00000000 00:00 0
7f98add05000-7f98add06000 ---p 00000000 00:00 0
7f98add06000-7f98ae506000 rw-p 00000000 00:00 0
7f98ae506000-7f98ae507000 ---p 00000000 00:00 0
7f98ae507000-7f98aed07000 rw-p 00000000 00:00 0
7f98aed07000-7f98aed08000 ---p 00000000 00:00 0
7f98aed08000-7f98af508000 rw-p 00000000 00:00 0
7f98af508000-7f98af509000 ---p 00000000 00:00 0
7f98af509000-7f98afd09000 rw-p 00000000 00:00 0
7f98afd09000-7f98afd0c000 r-xp 00000000 fe:00 33822335 /lib/x86_64-linux-gnu/libdl-2.24.so
7f98afd0c000-7f98aff0b000 ---p 00003000 fe:00 33822335 /lib/x86_64-linux-gnu/libdl-2.24.so
7f98aff0b000-7f98aff0c000 r--p 00002000 fe:00 33822335 /lib/x86_64-linux-gnu/libdl-2.24.so
7f98aff0c000-7f98aff0d000 rw-p 00003000 fe:00 33822335 /lib/x86_64-linux-gnu/libdl-2.24.so
7f98aff0d000-7f98aff1c000 r-xp 00000000 fe:00 37183546 /lib/x86_64-linux-gnu/libbz2.so.1.0.4
7f98aff1c000-7f98b011b000 ---p 0000f000 fe:00 37183546 /lib/x86_64-linux-gnu/libbz2.so.1.0.4
7f98b011b000-7f98b011c000 r--p 0000e000 fe:00 37183546 /lib/x86_64-linux-gnu/libbz2.so.1.0.4
7f98b011c000-7f98b011d000 rw-p 0000f000 fe:00 37183546 /lib/x86_64-linux-gnu/libbz2.so.1.0.4
7f98b011d000-7f98b0136000 r-xp 00000000 fe:00 37564716 /lib/x86_64-linux-gnu/libz.so.1.2.8
7f98b0136000-7f98b0335000 ---p 00019000 fe:00 37564716 /lib/x86_64-linux-gnu/libz.so.1.2.8
7f98b0335000-7f98b0336000 r--p 00018000 fe:00 37564716 /lib/x86_64-linux-gnu/libz.so.1.2.8
7f98b0336000-7f98b0337000 rw-p 00019000 fe:00 37564716 /lib/x86_64-linux-gnu/libz.so.1.2.8
7f98b0337000-7f98b04cc000 r-xp 00000000 fe:00 33822332 /lib/x86_64-linux-gnu/libc-2.24.so
7f98b04cc000-7f98b06cc000 ---p 00195000 fe:00 33822332 /lib/x86_64-linux-gnu/libc-2.24.so
7f98b06cc000-7f98b06d0000 r--p 00195000 fe:00 33822332 /lib/x86_64-linux-gnu/libc-2.24.so
7f98b06d0000-7f98b06d2000 rw-p 00199000 fe:00 33822332 /lib/x86_64-linux-gnu/libc-2.24.so
7f98b06d2000-7f98b06d6000 rw-p 00000000 00:00 0
7f98b06d6000-7f98b06ee000 r-xp 00000000 fe:00 33822383 /lib/x86_64-linux-gnu/libpthread-2.24.so
7f98b06ee000-7f98b08ed000 ---p 00018000 fe:00 33822383 /lib/x86_64-linux-gnu/libpthread-2.24.so
7f98b08ed000-7f98b08ee000 r--p 00017000 fe:00 33822383 /lib/x86_64-linux-gnu/libpthread-2.24.so
7f98b08ee000-7f98b08ef000 rw-p 00018000 fe:00 33822383 /lib/x86_64-linux-gnu/libpthread-2.24.so
7f98b08ef000-7f98b08f3000 rw-p 00000000 00:00 0
7f98b08f3000-7f98b0909000 r-xp 00000000 fe:00 33699333 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f98b0909000-7f98b0b08000 ---p 00016000 fe:00 33699333 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f98b0b08000-7f98b0b09000 r--p 00015000 fe:00 33699333 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f98b0b09000-7f98b0b0a000 rw-p 00016000 fe:00 33699333 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f98b0b0a000-7f98b0b36000 r-xp 00000000 fe:00 17667477 /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f98b0b36000-7f98b0d35000 ---p 0002c000 fe:00 17667477 /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f98b0d35000-7f98b0d36000 r--p 0002b000 fe:00 17667477 /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f98b0d36000-7f98b0d37000 rw-p 0002c000 fe:00 17667477 /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f98b0d37000-7f98b0e3a000 r-xp 00000000 fe:00 33822368 /lib/x86_64-linux-gnu/libm-2.24.so
7f98b0e3a000-7f98b1039000 ---p 00103000 fe:00 33822368 /lib/x86_64-linux-gnu/libm-2.24.so
7f98b1039000-7f98b103a000 r--p 00102000 fe:00 33822368 /lib/x86_64-linux-gnu/libm-2.24.so
7f98b103a000-7f98b103b000 rw-p 00103000 fe:00 33822368 /lib/x86_64-linux-gnu/libm-2.24.so
7f98b103b000-7f98b11ad000 r-xp 00000000 fe:00 18225260 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.22
7f98b11ad000-7f98b13ad000 ---p 00172000 fe:00 18225260 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.22
7f98b13ad000-7f98b13b7000 r--p 00172000 fe:00 18225260 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.22
7f98b13b7000-7f98b13b9000 rw-p 0017c000 fe:00 18225260 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.22
7f98b13b9000-7f98b13bd000 rw-p 00000000 00:00 0
7f98b13bd000-7f98b1510000 r-xp 00000000 fe:00 16835475 /usr/lib/x86_64-linux-gnu/libwcs.so.5.16
7f98b1510000-7f98b170f000 ---p 00153000 fe:00 16835475 /usr/lib/x86_64-linux-gnu/libwcs.so.5.16
7f98b170f000-7f98b1710000 r--p 00152000 fe:00 16835475 /usr/lib/x86_64-linux-gnu/libwcs.so.5.16
7f98b1710000-7f98b1713000 rw-p 00153000 fe:00 16835475 /usr/lib/x86_64-linux-gnu/libwcs.so.5.16
7f98b1713000-7f98b1714000 rw-p 00000000 00:00 0
7f98b1714000-7f98b1872000 r-xp 00000000 fe:00 16835237 /usr/lib/x86_64-linux-gnu/libcfitsio.so.5.3.41
7f98b1872000-7f98b1a71000 ---p 0015e000 fe:00 16835237 /usr/lib/x86_64-linux-gnu/libcfitsio.so.5.3.41
7f98b1a71000-7f98b1a72000 r--p 0015d000 fe:00 16835237 /usr/lib/x86_64-linux-gnu/libcfitsio.so.5.3.41
7f98b1a72000-7f98b1a76000 rw-p 0015e000 fe:00 16835237 /usr/lib/x86_64-linux-gnu/libcfitsio.so.5.3.41
7f98b1a76000-7f98b1aed000 rw-p 00000000 00:00 0
7f98b1aed000-7f98b1cd9000 r-xp 00000000 fe:00 21498975 /usr/lib/x86_64-linux-gnu/libfftw3.so.3.5.5
7f98b1cd9000-7f98b1ed8000 ---p 001ec000 fe:00 21498975 /usr/lib/x86_64-linux-gnu/libfftw3.so.3.5.5
7f98b1ed8000-7f98b1ee9000 r--p 001eb000 fe:00 21498975 /usr/lib/x86_64-linux-gnu/libfftw3.so.3.5.5
7f98b1ee9000-7f98b1eea000 rw-p 001fc000 fe:00 21498975 /usr/lib/x86_64-linux-gnu/libfftw3.so.3.5.5
7f98b1eea000-7f98b1f0d000 r-xp 00000000 fe:00 33822328 /lib/x86_64-linux-gnu/ld-2.24.so
7f98b209c000-7f98b20ea000 rw-p 00000000 00:00 0
7f98b210c000-7f98b210d000 rw-p 00000000 00:00 0
7f98b210d000-7f98b210e000 r--p 00023000 fe:00 33822328 /lib/x86_64-linux-gnu/ld-2.24.so
7f98b210e000-7f98b210f000 rw-p 00024000 fe:00 33822328 /lib/x86_64-linux-gnu/ld-2.24.so
7f98b210f000-7f98b2110000 rw-p 00000000 00:00 0
7ffc2e8d0000-7ffc2e8f1000 rw-p 00000000 00:00 0 [stack]
7ffc2e93b000-7ffc2e93d000 r--p 00000000 00:00 0 [vvar]
7ffc2e93d000-7ffc2e93f000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
Abort

I am not running this on a personal computer or laptop, this is run in a powerful machine at my institute with plenty of memory capacity. I tried changing the number of threads to a higher value, still nothing. The parameters that change between the first 3 sources and the rest are the filenames and their corresponding estimates in order to maintain consistency in evaluation. What am i doing wrong here?

Hello Enrico!

Thank you for the updated version of Barolo - I am keen on trying it out soon!
I have questions about the S/N maps constructed in the moment map task. You once pointed out that it is a non-trivial operation to determine the contours on a moment 0 map based on the S/N cuts we apply to a datacube. I read your references, but unfortunately, I kept going in circles due to my specific case.

I obtained my datacube using the CASA task tclean using a robust weighting parameter of +0.5, i.e., favouring resolution over sensitivity. Is using "UNIFORM" in the TAPER parameter correct in my case? I did not smooth the datacube in the analysis, so the other two keywords seem inappropriate. Furthermore, would it be possible to know the sigma/noise value at the end of the task so I can use it to apply contours to my maps directly?

Cheers, and thanks for all the work you do!

Hi there,

I'm trying to replicate an analysis done by one of my collaborators using pyBBarolo in a python script. I've been able to install the command-line BBarolo tool via Homebrew without issue, but I am having trouble installing pyBBarolo. In particular, I'm getting the following message:

  ------ Installing pyBBarolo v1.2.3 ------
  Checking numpy... OK.
  Checking astropy... OK.
  Running BBarolo configure... configure: WARNING: No MPI compiler found, won't use MPI.
  configure: error:
      -------------------------------------------------------------
      Could not find the CFITSIO library.
  
      ERROR: BBarolo configuration failure. If you have the libra-
             ry in non ordinary path, try to run ./configure with
             --with-cfitsio=<dir> option
      -------------------------------------------------------------

I'm not sure how to resolve this issue. I do have the dependencies installed (which I did with Conda) - after all, Homebrew was able to find them. I've tried manually adding CFITSIO to $PATH, but this doesn't seem to have changed anything. Do you have any suggestions?

Hi,

I'm impressed by the results of this code - thanks! I just have (hopefully!) a minor clarification to ask.

I am currently using Bbarolo to fit a ringmodel to some ALMA data of a T Tauri star. I am getting reasonable results, except for Vdisp. It seems like the returned value for Vdisp is just the input value, and this parameter is not being included in the minimisation. Looking at the following code: ringmodel.cpp, it seems like VDISP is not considered a model parameter that can be minimised for a ringmodel - is that true? Also, I noticed a VEXP variable in the above code, but I could not find what this variable means in the documentation.

Any help on either of these points would be greatly appreciated!

Many thanks,
Ryan.

After compiling the latest git version of Bbarolo the code cannot achieve convergence where with the same configuration file/data and the stable version it can.

Tried with the DELTAVROT option on and off. Both examples tried to fit VROT VRAD INC VDISP PA

Michalis

After doing 'make mpi' I get a program 'BBarolo_MPI' instead of the usual 'BBarolo'. 'make install' is unaware of the alternate name, however, and crashes after failing to find 'BBarolo'. Trivial to fix by hand and get the install to work, but also easy to fix upstream!

Could you please clarify in the docs whether this package can run under python3, or must use python2

I think we may need a clarification in the documentation. The PA is not defined in terms of receding or approaching side, where the convention is receding. The figure with PA=124 does seem to suggest this is indeed receding, but I didn't see it mention. I'm surprised i'm only noticing this ambiguity now.

I am trying to install the BBarolo in my computer.
Its requirements are available in my machine.
However, I got the following error when I ran the command "./congifure" .

Could not find the FFTW3 library

ERROR: BBarolo configuration failure. If you have the library in non ordinary path, try to run ./configure with --whih-fftw3= option.

When I manually added the path according to the prompts of the script, I got the same error alert.

Hi, I'm a new user of Bbarolo. There is an example of 3D fit of a galaxy on the website, but I didn't see an example of fitting, e.g. two interacting galaxies. I wonder if Bbarolo has the ability of 3D fitting two mergering/interacting galaxies ? If not, could you recommend any tools that may do such a fitting ? I find the HI interacting galaxies in my data cube are close and hard to be separated visually, thanks.

Hi,

I'm trying to use 3DBbarolo to fit simulated high-redshift galaxy data cubes. I have been able to successfully do this with one datacube, but with another the fitting errors out with this message:

Preparing a bunch of cool outputs...
Extracting guileless 2D maps... Done.
Deriving sublime radial profile... Done.
Calculating the very last model...corrupted size vs. prev_size
Aborted (core dumped)

I have tried to investigate this error but I don't recognise it and couldn't find any useful information on how to deal with it. Do you have any idea what could have caused this error? I was running 3DBbarolo with a .par file, where the .par file has this structure:

FITSFILE Opuntia_bbarolo.fits
OUTFOLDER Opuntia
3DFIT true
NRADII 2
RADSEP 0.16
VSYS 161.673
XPOS 6.5
YPOS 6.5
INC 60.0
Z0 0.001
FREE VROT VDISP
TWOSTAGE True
NORM AZIM
MASK SEARCH
SNRCUT 3
GROWTHCUT 2.8
NORMALCUBE True

Many thanks, Sian