Sunpy Python for Solar Physics Juan Carlos Martínez Oliveros

Transcription

1 Sunpy Python for Solar Physics Juan Carlos Martínez Oliveros

2 In the beginning (ENIAC)

3 Evolution

4 Evolution

5 Evolution

6 Introduction The SunPy project is an effort to create an opensource software library for solar physics using the Python programming language. SunPy was started little over a year ago, but already much progress has been made. Initial efforts have focused on core functionality relating to acquiring and reading in data and plotting.

7 Goals of this talk The goal of this talk is to introduce you to a new different platform to make solar physics. Hopefully after this talk you will decide to try, use and abuse Sunpy.

8 Goals of this talk In the words of Anakin Skywalker: Turn to the dark side

9 Outline What is Python? Python in Science Numpy Scipy Matplotlib Sunpy

10 What is Python? First we should ask: Why python? Each programming language has disadvantages. Python was chosen because it excels above other languages for scientific applications such as SunPy. Some of its advantages are: Easy Free and open source Large following in the scientific community

11 What is Python? o o o o o o o o o Python is an interpreted, object-oriented, high-level programming language with dynamic semantics. Python is simple and easy to learn. Python is open source, free and cross-platform. Python provides high-level built in data structures. Python is useful for rapid application development. Python can be used as a scripting or glue language. Python emphasizes readability. Python supports modules and packages. Python bugs or bad inputs will never cause a segmentation fault.

12 Basic Syntaxis o comments are indicated with # o o o o o two statements on the same line are separated with a semicolon ; no semicolon at the end of lines a long line continue on next with \ (it is not always needed) grouping is obtained through indentation one Python script is considered a module that can be run or imported by other modules

13 Assignments o Assignment creates references, not values: tmp = "hello"; tmp = 10 # the first string will be deallocated o Contrary to C, assignment do not have value: y = (x = x + 1) is invalid o o o o o As in C: x += 1 is valid Note that pre/post increment/decrement: x++; ++x; x--; --x are invalid Multiple assignment (references to a unique object): x=y=z=1 Multiple assignments: (x,y,z)=(3.5,5.5, string ) Example of swaping variables value: (x,y)=(y,x)

14 Type of Objects Numbers : , 1234, 999L, 3+4j Strings : spam, "guido s" Lists : [1, [2, three ], 4] Dictionaries : { food : spam, taste : yum } Tuples : (1, spam, 4, U ) Files : text = open( eggs, r ).read()

15 Control Flow if/elif/else for-loop break continue else while-loop pass

16 Hello, World! #!/usr/bin/env python import sys, math # load system and math module r = float(sys.argv[1]) # extract the 1st command-line arg. s = math.sin(r) comp:user$ python hw.py 15 Hello, World! sin(15.0)=

17 Loops (Hello World!) Nested loops for x in xrange(1,3): for y in xrange(1,3): print '%d * %d = %d' % (x,y,x*y) Early exit 1 * 1 = 1 1 * 2 = 2 2 * 1 = 2 2 * 2 = 4 for x in xrange(3): if x==1: print x 1 break

18 Loops (Hello World!) Strings as an iterable string = "Hello World" for x in string: print x Lists as an iterable collection = ['hey',5,'d'] for x in collection: print x H e l l o W o r l d

19 Hello, World! # At the interpreter print "Hello World!" # Note that the "\n" is automagic after each print. # As a function def hello(): print "Hello World!" return # This is optional, since you aren't returning anything. # From the command line (A one liner, immediate execution) import os os.popen("python -c \"print 'Hello World!'\"") # Just python -c "print 'hello world!'" at the command line.

20 Python in sciences Astronomy Artificial intelligence & machine learning Bayesian Statistics Biology (including Neuroscience) Dynamical systems Economics and Econometrics Electromagnetism Electrical Engineering Geosciences Molecular modeling Signal processing Symbolic math, number theory

21 Python in Astronomy pyfits read FITS files pyraf run IRAF tasks pywcs pyephem compute positions of objects in space spacepy (space sciences, just released) Planned standard library AstroPy

22 numpy NumPy is an open source extension module for Python. The module NumPy provides fast precompiled functions for numerical routines. It adds support to Python for large, multidimensional arrays and matrices. Besides that it supplies a large library of high-level mathematical functions to operate on these

23 numpy powerful N-dimensional array object sophisticated functions basic linear algebra functions basic Fourier transforms sophisticated random number capabilities tools for integrating Fortran code. tools for integrating C/C++ code.

24 numpy In [1]: import numpy as np In [2]: x = np.array([42,47,11], int) In [3]: x Out[3]: array([42, 47, 11] In [1]: import numpy as np In [2]: x = np.array( ((11,12,13), (21,22,23), (31,32,33)) ) In [3]: print x [[ ] [ ]

25 numpy Print elements in first column In [5]: print x[:, 0] [ ] Print elements in first row In [6]: print x[0,:] [ ]

26 SciPy SciPy (Scientific Python) extends the functionalities of NumPy with further useful functions for minimization, regression, Fouriertransformation and many others. Gathers a variety of high level science and engineering modules together: fftpack discrete fourier transform algorithms Integrate integration routines Interpolate interpolation tools Linalg linear algebra routines Optimize optimization tools Signal signal processing tools Sparse sparse matrices Stats statistical functions Io data input and output

27 SciPy Matplotlib is a object oriented plotting library. SciPy make use of matplotlib to generate high resolution plots and images. You can use latex expressions to add math to your plot.

28 SciPy Example 1

29 SciPy Example 1 $ python example_lsq.py [ ] [ ] [ ]

30 SciPy Example 2

31 SciPy Example 2

32 SciPy Example 3 In [1]: from scipy import * In [2]: p = poly1d([3,4,5]) In [3]: print p 2 3 x + 4 x + 5 In [4]: print p*p x + 24 x + 46 x + 40 x + 25 In [5]: print p.integ(k=6) x + 2 x + 5 x + 6 In [6]: print p.deriv() 6 x + 4

33 SciPy More examples!

34 SciPy More examples!

35 SciPy More examples!

36 Sunpy: Python for Solar Spatially aware maps Read FITS files RHESSI SDO/AIA EIT TRACE LASCO Physics Standard color tables and histogram equalization Basic image co-alignment VSO (Virtual Solar Observtory) HEK

37 Sunpy: Python for Solar Physics 1. Rotate the image. 2. Crop the are you are studying. 3. Overlay the HXR

38 import pylab as pl import sunpy import numpy as np Sunpy: Python for Solar mdi_map = sunpy.make_map('fd_mdi.fits ) mdiarr = np.array(mdi_map) mhdr = mdi_map.get_header() # rotation 180 degrees NO arbitrary rmdiarr = np.rot90(mdiarr,2) Physics #Create a map with the rotated data rmdi_map = sunpy.make_map(rmdiarr, mhdr) #sub_map smap_mdi = rmdi_map.submap((-250, -50), (200, 400), units='data') mdi_map = sunpy.make_map([smap_mdi,'im_ _clean_ _40-100kev_peak40s_t0.fits'] ) mdi_map.set_levels(1,[50,60,70,80,90], percent = True) #save to eps import matplotlib.pyplot as plt fig = mdi_map.plot()

39 Sunpy: Python for Solar Physics

40 import pylab as pl import sunpy import numpy as np Sunpy: Python for Solar mdi_map = sunpy.make_map('fd_mdi.fits ) mdiarr = np.array(mdi_map) mhdr = mdi_map.get_header() # rotation 180 degrees NO arbitrary rmdiarr = np.rot90(mdiarr,2) Physics #Create a map with the rotated data rmdi_map = sunpy.make_map(rmdiarr, mhdr) #sub_map smap_mdi = rmdi_map.submap((-250, -50), (200, 400), units='data') mdi_map = sunpy.make_map([smap_mdi,'im_ _clean_ _40-100kev_peak40s_t0.fits'] ) mdi_map.set_levels(1,[50,60,70,80,90], percent = True) #save to eps import matplotlib.pyplot as plt fig = mdi_map.plot()

41 Sunpy: Python for Solar Physics

42 import pylab as pl import sunpy import numpy as np Sunpy: Python for Solar mdi_map = sunpy.make_map('fd_mdi.fits ) mdiarr = np.array(mdi_map) mhdr = mdi_map.get_header() # rotation 180 degrees NO arbitrary rmdiarr = np.rot90(mdiarr,2) Physics #Create a map with the rotated data rmdi_map = sunpy.make_map(rmdiarr, mhdr) #sub_map smap_mdi = rmdi_map.submap((-250, -50), (200, 400), units='data') mdi_map = sunpy.make_map([smap_mdi,'im_ _clean_ _40-100kev_peak40s_t0.fits'] ) mdi_map.set_levels(1,[50,60,70,80,90], percent = True) #save to eps import matplotlib.pyplot as plt fig = mdi_map.plot()

43 Sunpy: Python for Solar Physics

44 Sunpy: Python for Solar Physics

45 Sunpy: Python for Solar Physics Use it! File feature requests Express opinion on the mailing list / in IRC File bug reports Contribute documentation Contribute code

46 Sunpy: Python for Solar Physics Website: Mailing list: IRC: #sunpy on irc.freenode.net Git code repository: