getDist contour plt do not appear

Use of Cobaya. camb, CLASS, cosmomc, compilers, etc.
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Ira *Wolfson
Posts: 69
Joined: January 24 2013
Affiliation: MPA
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getDist contour plt do not appear

Post by Ira *Wolfson » November 19 2015

Hi all,

I recently was able to compile the new (July15 version).
I ran a test, using test.ini, producing chanis.

However trying to make the graphs yielded blank contour graphs.
No errors were communicated from python.

here is a link to my result triangle graph

test_tri.pdf

thanks

-- Ira


Antony Lewis
Posts: 1941
Joined: September 23 2004
Affiliation: University of Sussex
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Re: getDist contour plt do not appear

Post by Antony Lewis » November 19 2015

Really need more detail to have a chance of helping with this.

Ira *Wolfson
Posts: 69
Joined: January 24 2013
Affiliation: MPA
Contact:

getDist contour plt do not appear

Post by Ira *Wolfson » November 19 2015

Thanks for the swift reply,

I'll try to supply some more detail:
the cosmomc test.ini file I ran:

Image

the getdist .ini file I'm using is the distparams.ini:

Code: Select all

#sample params for "getdist" - for processing .txt chain information
#not required if you just want to run with defaults to produce .margestats etc

#set to true if you want to produce plot.py files for various standard plots
no_tests = F

file_root = chains/test
out_root = 
out_dir = 
plot_data_dir = ./plot_data/

#If 0 assume 1 and no chain filename prefixes; if -1 read as many as exist
chain_num = -1
first_chain = 
exclude_chain = 

#For disgarding burn-in if using raw chains. Set to zero if already removed or you have independent samples.
#if < 1 interpreted as a fraction of the total number of rows &#40;0.3 ignores first 30% of lines&#41;
ignore_rows = 0.3

#plot_ext = m

#include defaults settings for kernel densitiy estimates etc, can also be specified in this file if you want to override
DEFAULT&#40;python/getdist/analysis_defaults.ini&#41;

#samples_are_chains = F can be useful for other samples when first two columns not present
samples_are_chains = T

#if no_plots =F, produce plot script files for specific plots producing ./plot_data/ density files
no_plots = F

#if we only want 2D plots agains a particular variable
plot_2D_param = 0

#if above zero, instead plot just these combinations&#58;
#if both zero it will plot most correlated variables
plot_2D_num = 1
plot1 = ns omegabh2
#plot2 =

#number of sample plots, colored by third parameter
#if last parameter is 0 or -1 colored by the parameter most correlated
#with one of the eigenvector directions &#40;e.g. parallel or orthogonal to degeneracy&#41;
num_3D_plots = 1
3D_plot1 = H0 omegam tau

#Output 2D plots for param combos with 1D marginalized plots along the diagonal
triangle_plot = T
triangle_params = omegabh2 omegach2 tau omegak mnu nnu yhe Alens ns nrun logA r H0 omegam omegal sigma8 r02

#Parameters to use. If not specified use all parameters which have lables.
#plot_params = omegabh2 omegach2 tau ns

#Get set label to empty to not include a parameter in the parameter_names file
#lab&#91;asz&#93;=

#marker&#91;x&#93; adds vertical line to MatLab 1D plot
marker&#91;nrun&#93; = 0

# if non-zero, output _thin file, thinned by thin_factor
thin_factor = 0
#Do probabilistic importance sampling to single samples
make_single_samples = F
single_thin = 4

#Need to give limits if prior cuts off distribution where not very small
limits&#91;r02&#93;= 0 N
limits&#91;r10&#93;= 0 N

#all_limits sets all limitsxx for all variables to the same; can be useful for bins
all_limits = 

#compute two-tail marginalized limits irrespective of limits settings above
#&#40;otherwise limits are two-tail only for those parameters without limits&#41;
force_twotail = F

#PCA - analysis output in file file_root.PCA
#number of parameter to do PCA for
PCA_num = 0
PCA_normparam = omegam
#The parameters to use
PCA_params = omegam H0 tau
#L for log&#40;x&#41;, M for log&#40;-x&#41;, N for no log
PCA_func   = LLL

#If generated chain at higher temperature can cool for computing results
cool = 1
I'm sorry to sorta "dump" this on your doorstep, but The last working version I used was a while ago, and I couldn't find the problem on my own :(


thanks!!!

-- Ira

Antony Lewis
Posts: 1941
Joined: September 23 2004
Affiliation: University of Sussex
Contact:

Re: getDist contour plt do not appear

Post by Antony Lewis » November 21 2015

Are you using python getdist or fortran getdist? Can you view the triangle plot OK in the GetDist Gui using the same chains?

Ira *Wolfson
Posts: 69
Joined: January 24 2013
Affiliation: MPA
Contact:

getDist contour plt do not appear

Post by Ira *Wolfson » November 22 2015

So,
I tried first to use the fortran getdist.

Fortarn getdis:

This yielded the expected python scripts for graphs.
(later I tried also the matlab option)
However, the scripts exited with no errors, but did not produce the 2D contour graphs.
i.e. in the triangle graph one gets the diagonal graphs correct, but the 'lower triangle'
graphs are simply blank. (frames exist, but no graph).

I later tried to use the python version:
GetDist.py:

After specifying :

Code: Select all

plot_meanlikes = T
shade_meanlikes = T
as well as

Code: Select all

 
triangle_plot = T
triangle_params = omegabh2 omegach2 tau omegak mnu nnu yhe Alens ns nrun logA r H0 omegam omegal sigma8 r02
I get this triangle graph:
test_tri.pdf
Which is shown to have no coloured graphs.

as for GetDistGui.py:
The GUI will not open, and exits with an error message as follows:

Code: Select all

Traceback &#40;most recent call last&#41;&#58;
  File "./python/GetDistGUI.py", line 16, in <module>
    from getdist.gui.mainwindow import MainWindow
  File "/home/spawn/CosmoMC/cosmomc/python/getdist/gui/mainwindow.py", line 1134
    if isinstance&#40;self.iniFile, six.string_types&#41; and self.iniFile <> getdist.default_getdist_settings&#58;
                                                                    ^
SyntaxError&#58; invalid syntax
Thanks again for the swift reply

-- Ira

Antony Lewis
Posts: 1941
Joined: September 23 2004
Affiliation: University of Sussex
Contact:

Re: getDist contour plt do not appear

Post by Antony Lewis » November 22 2015

I suggest you pull the latest changes from

http://github.com/cmbant/cosmomc

- the getdist gui error you report is at least fixed I think.

Ira *Wolfson
Posts: 69
Joined: January 24 2013
Affiliation: MPA
Contact:

getDist contour plt do not appear

Post by Ira *Wolfson » November 23 2015

Thanks!!!

The GUI works great, and it really is a great tool :)

--Ira

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