Initial Merge Pull Request #2

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MishaSavchenko wants to merge 33 commits into Phys767-Spring17:master from MishaSavchenko:master

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MishaSavchenko commented Mar 29, 2017

No description provided.

MishaSavchenko added 12 commits

March 22, 2017 13:14


          new fork

1262d02


          updating the new fork

89b3d7b


          i dont even at this point

7641e25


          fixing the incorect matrix multiplication)

8a53534


          understanding the use of bounds in the minimization function

7d6ddba


          temp to high mistakes in the code are still to be found

ff198ff


          RuntimeWarning errors appear, possible bug in the code

a77c2df


          RuntimeWarning errors appear, possible bug in the code

00add82


          minor cleanup prefomed

767374e


          mimicing the model of mcmc.py

abd1504


          ValueError: setting an array element with a sequence is fixed

98b7dad


          separate folders, addition of the test files, __init__.py are present

e5d3263

MishaSavchenko requested a review from drewjrosen

March 29, 2017 15:15


          separete folders, testing files creation, pytest operation

0c34dc2

drewjrosen suggested changes

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drewjrosen left a comment

Basically you need to comment more on everything.

Log_of_planck_function.py Outdated

+                  # So logflux (which is what we want) is just the log of this
+                  logflux[i] = logfactor + np.log10(flux[i])
+                return logflux

drewjrosen Mar 29, 2017

You should comment on everything below. Explain more what is going on.

Spectral_Radiance.py Outdated

		@@ -0,0 +1,54 @@
		from __future__ import print_function

drewjrosen Mar 29, 2017

Add comments to everything.

MishaSavchenko added 15 commits

March 29, 2017 12:03


          functional py.test

441caac


          addition of a vary through description

55813dc


          addition of MHSampler into clone code

fccd882


          ordered savefig

37e688c


          clone emcee working

626d052


          addition of a class version

3ce7393


          test file

77ff7fa


          working timeit script, almost no difference between class or no class…

e929aea

… runtime


          clone_emceee and clone_emceee_class both show the log factor calculat…

8eca441

…ion from the MCMC calculation


          addition of initial guess plot

522e64f


          extra commit

4e9e719


          better plots

e9ec10f


          addition of more graphs

391203b


          addition of more graphs

cfae021


          mcmc_clone_emcee now makes a new folder and saves figures inside of it

07f9291

MishaSavchenko added 4 commits

April 10, 2017 18:10


          clone emceee now ptakes the data from SED.dat file and runs calculati…

da1112d

…ons with an arbitrary and a calculated burn point


          oh boy, mcmc_clone_emcee_class up to date, mcmc_clone saes the last r…

70f5d30

…esult int results.dat, Spectral_radiance uses results.dat to plot last estimate, spectral_radiance.py does the same with some issues


          pytest includes two more tests, more annotated mcmc_clone_emcee.py

ad3b9c7


          deleted unnecessary files

4be1f49

MishaSavchenko self-assigned this

MishaSavchenko requested a review from kelle

April 13, 2017 20:32

MishaSavchenko changed the title ~~General Pull Request~~ Initial Merge Pull Request

kelle requested changes

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Member

kelle left a comment

I made several comments in line.
also, files in pycache should not be here. Several other students have had all these extra files in their repos as well. Consider asking David for help.

.cache/v/cache/lastfailed Outdated

    
            @@ -0,0 +1 @@
          
              {}

  No newline at end of file

Member

kelle Apr 13, 2017

this file should not be tracked by github. (Nothing in the .cache directory should be.)

.ipynb_checkpoints/mcmc-checkpoint.ipynb Outdated

    
            @@ -0,0 +1,474 @@
          
              {

Member

kelle Apr 13, 2017

Pretty sure this file shouldn't be tracked either.

mcmc_test/Log_of_planck_function.py Outdated

+                flux=np.empty([len(wavelength)])
+                logflux=np.empty([len(wavelength)])
+                for i in range(len(wavelength)):
+                  # Flux is just the Planck function

Member

kelle Apr 13, 2017

delete "just".

mcmc_test/Log_of_planck_function.py Outdated

+                for i in range(len(wavelength)):
+                  # Flux is just the Planck function
+                  flux[i] = ( (2.0*con.h*con.c**2)/(wavelength[i]**5) )/( np.exp( (con.h*con.c)/(con.k*Teff*wavelength[i]) ) - 1.0 )
+                  # So logflux (which is what we want) is just the log of this

Member

kelle Apr 13, 2017

delete "just". logflux is the log of the Planck function.

mcmc_test/Log_of_planck_function.py Outdated


		results = ascii.read("results.dat")

		T1 = 100

Member

kelle Apr 13, 2017

T is ambigiusous. temp?

mcmc_test/Log_of_planck_function.py Outdated

+              T3 = 300
+              MCMC_Temp = results[0][0]
+              Y1_B = (np.log10(planck(X*10**-6,T1)))

Member

kelle Apr 13, 2017

I dont know what the code is doing here. what does Y1_B mean?

mcmc_test/Log_of_planck_function.py Outdated

		Y4_B = (np.log10(planck(X10*-6,T3)))


		x = np.asarray([3.368,4.618,12.082,22.194,3.6,4.5])

Member

kelle Apr 13, 2017

where do these numbers come from?


          pull request modifications

0f190bd

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