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1. HELLO WORLD gt gt gt s hello world gt gt gt s find world 6 gt gt gt s endwith 1d True gt gt gt s split hello world 1 5 2 Lists gt gt gt mylist gt gt gt mylist J Lists also have several methods 1 hello 2 3 HH H HF HHHH HHHH return string left justified within string of specified width convert to lower case strip leading whitespace and optional characters specified substitute old substring with new string return position of rightmost match of substring like rfind but raises exception on failure like ljust but right justified instead Similar to split see documentation return list of words delimited by whitespace or optional sep string returns list of lines within string true if string begins with prefix strip leading and trailing whitespace switch lower to upper case and visa versa return title cased version maps characters using table convert to upper case left fill string with zeros to given width Think of lists as one dimensional arrays that can contain anything for its elements Unlike arrays the elements of a list can be different kinds of objects including other lists and the list can change in size Lists are created using simple brackets e g This particular list contains 3 objects the integer value 1 the string hello and the list 2 3 Emp2. k gt black w gt white Style 2 standard color string eg yellow wheat Style 3 grayscale intensity between 0 and 1 inclusive Style 4 RGB hex color triple eg 2F4F4F Style 5 RGB tuple e g 0 18 0 31 0 31 all values be tween 0 and 1 data_ clipping Clip data before plotting if the great majority of points will fall outside the plot window this may be much faster True or False label A string optionally used for legend linestyle ls One of dashed dotted dashed dot solid linewidth lw width of line in points nonzero float value marker symbol o gt circle OW lt gt triangles up down left right respectively s gt square 7 gt plus x gt cross D gt diamond d gt thin diamond T 2 3 2 tripods down up left right h gt hexagon p gt pentagon gt vertical line _ gt horizontal line steps keyword arg only markeredgewidth mew width in points nonzero float value markeredgecolor mec color value markerfacecolor mef color value markersize ms size in points nonzero float value 18 The following describes text attributes those shared with lines are not detailed Property Value alpha color As with Lin
3. lower gt gt gt contour pixdata levels colors 1 1 1 0 500 400 300 200 100 0 100 200 300 400 500 1 7 7 subplot example You aren t limited to having one plot per page The subplot command will divide the page into a user specified number of plots gt gt gt err err 1 0e12 gt gt gt flux flux 1 0e12 There s a bug in the axes code of Matplotlib that causes an exception when the upper and lower limits of the plot are too close to each other so we multiply the data by 1 0e12 to guard against this gt gt gt subplot 211 Divide area into 2 vertically 1 horizontally and select the first plot gt gt gt plot wavelength flux 23 gt gt gt subplot 212 Select second plot gt gt gt plot wavelength error gt e a Q 1 980 1000 1020 1040 1060 1080 1100 0 1 0 05 5 meee 980 1000 1020 1040 1060 1080 1100 1 7 8 readcursor example Finally it is possible to set up functions to interact with a plot using the event handling capabilities of Matplotlib Like many other GUIs Matplotlib provides an interface to the underlying GUI event handling mechanism This is achieved using a callback function that is activated when a certain prescribed action is performed The prescribed action could be a mouse button click key press or mouse movement You can set up a handler function to handle the event by registering the event you want to detect and connecting your callbac
4. suberror error flat 100 gt gt gt errorbar subwave subflux suberror fmt k hold True lt matplotlib lines Line2D instance at Ox046EBEEO gt lt a list of 204 Line2D errorbar objects gt Adding legends is simple gt gt gt legend unsmoothed smoothed every 100 lt matplotlib legend Legend instance at 0x04978D28 gt As is adding arbitrary text gt gt gt text 1007 0 5e 12 Hi There lt matplotlib text Text instance at 0x04B27328 gt le 12 unsmoothed smoothed every 100 4e 13 2e 13 1006 1008 1010 1012 1014 1016 1018 1020 AA Matplotlib uses a very different style from IDL regarding how different devices are handled Underneath the hood matplotlib saves all the information to make the plot as a result it is simple to regenerate the plot for other devices without having to regenerate the plotting commands themselves it s also why the figures can be interactive The following saves the figure to a png and postscript file gt gt gt savefig fuse png gt gt gt savefig fuse ps 1 5 A little background on Python sequences Python has a few powerful built in sequence data types that are widely used You have already encountered 3 of them 1 5 1 Strings Strings are so ubiquitous that it may seem strange treating them as a spe
5. get the STScI default matplotlibre from one of the Unix systems or from the web imshow will resample the data to fit into the figure using a defined interpolation scheme The default is set by the image interpolation parameter in the matplotlibre file bilinear on STScI systems but this can be set to one of bicubic bilinear blackman100 blackman256 blackman64 nearest sincl144 sinc256 sinc64 splinel6 and spline36 Most astronomers are used to blocky pixels that come from using the nearest pixel so we can get this at run time by doing gt gt gt imshow pixdata vmin 0 vmax 1000 interpolation nearest 21 1 7 4 figimage figimage is like imshow except no spatial resampling is performed It also allows displaying RGB or RGB alpha images This function behaves more like the IDL TVSCL command See the manual for more details 1 7 5 Histogram example Histograms can be plotted using the hist command gt gt gt pixdata pixdata gt 256 256 gt gt gt hist pixdata bins 256 Duplicating the functionality of for example the IRAF imhistogram task will take a bit more work 8000 7000 6000 5000 4000 3000 2000 1000 50 0 50 100 150 200 250 300 1 7 6 contour example Contour plotting was added by Nadia Dencheva So to overplot green contours at levels of 100 200 400 and 800 we can do 22 gt gt gt levels 100 200 400 800 gt gt gt imshow pixdata vmin 0 vmax 1000 origin
6. translation from common IDL plotting functionality and mentions a few of the additional capabilities provided by pylab For a more complete discussion you will eventually want to see the tutorial and the documentation for the pylab interface http matplotlib sourceforge net tutorial html http matplotlib sourceforge net matplotlib pylab html This document also makes use of the PyFITS and numarray packages in its examples Separate documentation packages exist for these as well http www stsci edu resources software_hardware pyfits http www stsci edu resources software_hardware numarray Setting up and customizing your Python environment Whether you use PyRAF ipython or the default python interpreter there are ways to automatically import your favorite modules at startup using a configuration file See the documentation for those packages for details The examples in this document will explicitly import all packages used Setting up and customizing matplotlib You will want to modify your matplotlibrc plot to use the correct backend for plotting and to set some default behaviors The STScI versions of the default matplotlibrc have already been modified to incorporate many of these changes If there is a matplotlibrc file in your current directory it will be used instead of the file in your home directory This permits setting up different default environments for different purposes You may also want to change the d
7. use Details on their use can be found in the Python library documentation the references in Appendix A or any introductory Python book capitalize capitalize first character center width fillchar return string centered in string of width specified with optional fill char count sub start end return number of occurences of substring decode encodingL errors see documentation encode encoding errors see documentation endswith suffix start end True if string ends with suffix expandtabs tabsize defaults to 8 spaces find substring start end returns position of substring found index substring start end like find but raises exception on failure isalnum true if all characters are alphanumeric isdigit true if all characters are digits islower true if all characters are lowercase isspace true if all characters are whitespace istitle true if titlecased isupper true if all characters are uppercase join seq use string to join strings in the seq ljust width fillchar lower lstrip chars replace old new count rfind substring start edn rindex substring start end rjust width fillchar rsplit sep maxsplit split sep maxsplit splitlines keepends startswith prefix start end strip chars swapcase title translate table deletechars upper zfill width gt gt gt hello world upper
8. Setup none needed if your paths are correct from numarray import from pylab import import pyfits Or none needed if you set up your favorite modules in the configuration file for the Python environment you re using Some data sets foo indgen 20 bar foo 2 foo arange 20 bar foox 2 Basic plotting plot foo plot foo plot foo bar plot foo bar plot foo bar line 1 thick 2 plot foo bar lw 2 kkor spell out linewidth 2 plot foo bar ticklen 1 plot foo bar grid plot foo bar psym 1 plot foo bar x OR scatter foo bar plot foo bar psym 1 symsize 3 plot foo bar x ms 5 or spell out markersize 5 plot foo bar xran 2 10 yran 2 10 plot foo bar xlim 2 10 ylim 2 10 err indgen 20 10 err arange 20 10 plot foo bar psym 2 errplot foo bar err bart err errorbar foo bar err fmt o0 errorbar foo bar err 2 err 29 error bars in x and y Overplotting with default behaviour changed Not recommended or used in any other examples plot foo bar oplot foo bar2 plot foo bar plot foo bar2 hold True Text titles and legends xyouts 2 25 hello text 2 25 hello 28 plot foo bar title Demo xtitle foo ytitle bar plot foo bar title Demo xla
9. Using Python for Interactive Data Analysis Perry Greenfield Robert Jedrzejewski Vicki Laidler Space Telescope Science Institute 18th April 2005 1 Tutorial 2 Reading and plotting spectral data In this tutorial I will cover some simple plotting commands using Matplotlib a Python plotting package developed by John Hunter of the University of Chicago I will also talk about reading FITS tables delve a little deeper into some of Python s data structures and use a few more of Python s features that make coding in Python so straightforward To emphasize the platform independence all of this will be done on a laptop running Windows 2000 1 1 Example session to read spectrum and plot it The sequence of commands below represent reading a spectrum from a FITS table and using matplotlib to plot it Each step will be explained in more detail in following subsections gt gt gt import pyfits gt gt gt from pylab import import plotting module gt gt gt pyfits info fuse fits gt gt gt tab pyfits getdata fuse fits gt gt gt tab names gt gt gt tab formats gt gt gt flux tab field flux gt gt gt wave tab field wave gt gt gt flux shape show shape of flux column array gt gt gt plot wave flux plot flux vs wavelength add xlabel using symbols for lambda angstrom gt gt gt xlabel r lambda angstrom size 13 gt gt gt ylabel Flux Overplot smooth
10. area with axes and data points ticks title and labels is called an axes object There may be many of these in a figure Underneath matplotlib has a very object oriented framework It s possible to do quite a bit without knowing the details of it but the most intricate or elaborate plots most likely will require some direct manipulation of these objects For the most part this tutorial will avoid these but a few examples will be shown of this usage While there may be many figures and many axes on a figure the matplotlib functional interface i e pylab has the concept of current figures axes and images It is to these that commands that operate on figures axes or images apply to Typically most plots generate each in turn and so it usually isn t necessary to change the current figure axes or image except by the usual method of creating a new one There are ways to change the current figure axes or image to a previous one These will be covered in a later tutorial Matplotlib works with many backends which is another term for windowing systems or plotting formats We recommend for now anyway using the standard if not quite as snazzy Tkinter windows These are compatible with PyRAF graphics so that matplotlib can be used in the same session as PyRAF if you use the TkAgg backend Matplotlib has a very large number of configuration options Some of these deal with backend defaults some with display conventions and default plottin
11. bel foo ylabel bar plot foo bar 2 psym 1 oplot foo bar psym 2 plot foo bar 2 x label double plot foo bar o label single legend twicebar bar psym 1 2 upper right legend loc upper right k klegend will default to upper right if no location is specified Note the space in the location specification string plot foo bar title systime import time plot foo bar label time asctime Window Manipulation erase clf OR cla window 2 figure 2 wset 1 figure 1 wdelete 2 close 2 wshow no equivalent Log plotting plot_oo foo bar loglog foo 1 bar 1 plot_io foo bar semilogy foo bar plot_oi foo bar semilogx foo bar Warning numbers that are invalid for logarithms lt will not be plotted but will silently fail no warning message is generated Warning you can t alternate between linear plots containing zero or negative points and log plots of valid data without clearing the figure first it will generate an exception Postscript output set_plot ps device file myplot ps land plot foo bar device close plot foo bar savefig myplot ps orientation landscape 29 Viewing image data im mrdfits myfile fits 1 tv im loadct 5 loadct 0 contour im xloa
12. cial data structure That they share much with the other two and arrays will be come clearer soon First we ll note here that there are several ways to define literal strings One can define them in the ordinary sense using either single quotes or double quotes Furthermore one can define multiline strings using triple single or double quotes to start and end the string For example gt gt gt s gt This is an example of a multi line string that goes on and on and on gt gt gt s This is an example nof a string that ngoes on and on nand on gt gt gt print s This is an example of a string that goes on and on and on As with C one uses the backslash character in combination with others to denote special characters The most common is n for new line which means one uses to indicate a single is desired See the Python documentation for the full set For certain cases like regular expressions or MS Windows path names it is more desirable to avoid special intepretation of backslashes This is accomplished by prefacing the string with an r for raw mode gt gt gt print two lines n in this example two lines in this example gt gt gt print r but not n this one but not n this one Strings are full fledged Python objects with many useful methods for manipulating them The following is a brief list of all those available with a few examples illustrating their
13. ctangle that will be the new view region for the plot The left and right arrow buttons can be used to restore different views of the plot a history is kept of every zoom and pan The button with a house will return it the the original view The button with a diskette allows one to save the plot to a png or postscript file You can resize the window and the plot will re adjust to the new window size Also note that this and many of the other pylab commands result in a cryptic printout That s because these function calls return a value In Python when you are in an interactive mode the act of entering a value at the command line whether it is a literal value evaluated expression or return value of a function Python attempts to print out some information on it Sometimes that shows you the value of the object if it is simple enough like for numeric values or strings or sometimes it just shows the type of the object which is what is being shown here The functions return a value so that you can assign it to a variable to manipulate the plot later it s not necessary to do that though We are likely to change the behavior of the object so that nothing is printed even though it is still returned so your session screen will not be cluttered with these messages It is possible to customize plots in many ways This section will just illustrate a few possibilities gt gt gt xlabel r lambda angstrom size 13 lt matplotlib text T
14. dct f pyfits open myfile fits im f 1 data imshow im jetQ gray contour im no equivalent Histograms mu 100 amp sigma 15 amp x fltarr 10000 seed 123132 for i 0 9999 do x i mu sigma randomn seed plothist x mu sigma 10 15 x mu sigma randn 10000 n bins patches hist x 50 Note that histograms are specified a bit differently and also look a bit different instead of skyline style bar chart Multiple plots ona page p multi 4 2 2 plot foo bar plot bar foo plot foo 20 foo plot foo bar foo subplot 221 plot foo bar subplot 222 plot bar foo subplot 223 plot foo 20 f 00 subplot 224 plot foo bar foo Erasing and redrawing a subplot no equivalent subplot 222 cla scatter bar foo plotting x y color and size no obvious equivalent scatter foo bar c footbar s 10 foo Adding a colorbar no obvious equivalent colorbar Some comparisons Some additional functionality modify axes without replotting add labels generate hardcopy without replotting colored lines and points many more point styles smarter legends TeX style math symbols supported interactive pan zoom Some functionality that is not yet conveniently wrapped These are items that are available through the 00 machinery but are not yet wrapped into conve
15. ed spectrum as dashed line gt gt gt from numarray convolve import boxcar gt gt gt sflux boxcar flux flat 100 smooth flux array gt gt gt plot wave sflux r hold True overplot red dashed line gt gt gt subwave wave flat 100 sample every 100 wavelengths gt gt gt subflux flix flat 100 read table names of columns formats of columns reference flux column gt gt gt plot subwave subflat og overplot points as green circles gt gt gt errorbar subwave subflux yerr 0 05 subflux fmt k gt gt gt legend unsmoothed smoothed every 100 gt gt gt text 1007 0 5 Hi There save to png and postscript files gt gt gt savefig fuse png gt gt gt savefig fuse ps 1 2 Using Python tools on Windows Most of the basic tools we are developing and using for data analysis will work perfectly well on a Windows machine The exception is PyRAF since it is an interface to IRAF and IRAF only works on Unix like platforms There is no port of IRAF to Windows nor is there likely to be in the near future But numarray PyFITS Matplotlib and of course Python all work on Windows and are relatively straightforward to install 1 3 Reading FITS table data and other asides As well as reading regular FITS images PyFITS also reads tables as arrays of records recarrays in numarray parlance These record arrays may be indexed just li
16. efault behavior for image display to avoid interpolating and set the image so that pixel 0 0 appears in the lower left of the window image interpolation nearest see help imshow for options image origin lower lower upper I also wanted to change the default colors and symbols lines marker None like psym 0 plots are line plots by default lines color gt k black lines markerfacecolor k black lines markeredgecolor k black 26 text color k black Symbols will be solid colored not hollow unless you change markerfacecolor to match the color of the background About overplotting behavior The default behavior for matplotlib is that every plot is a smart overplot stretching the axes if necessary and one must explicitly clear the axes or clear the figure to start a new plot It s possible to change this behavior in the setup file to get new plots by default axes hold False whether to clear the axes by default on and override it by specifying the hold keyword in the plotting call However I DO NOT recommend this it takes a bit of getting used to but I found it easier to completely change paradigms to build up the plot piece by piece than it is to remember which commands will decorate an existing plot and which won t Some philosophical differences Matplotlib tends towards atomic commands to control each plot element independently rather than keywords on a plot command This take
17. es family font family eg sans serif cursive fantasy fontangle the font slant normal italic oblique horizontalalignment left right center verticalalignment top bottom center multialignment left right center only for multiline strings name font name eg Sans Courier Helvetica position X y position variant font variant eg normal small caps rotation angle in degrees for text orientation size size in points style normal italic or oblique text the text string itself weight e g normal bold heavy light These two sets of properties are the most ubiquitous Others tend to be specialized to a specific task or function The following illustrates with some examples plots are not shown starting with the ways of specifying red for a plotline gt gt gt x arange 100 gt gt gt y x 100 2 gt gt gt plot x y r gt gt gt plot x y c red gt gt gt plot x y color ff0000 gt gt gt lines plot x y lines is a list of objects each has set methods for each property gt gt gt set lines color 1 0 0 or gt gt gt lines 0 set_color red draw object manipulation example gt gt gt plot y 10 g gt markersize 20 every 10 points with large green triangles and dotted line And more examples spec
18. ext instance at 0x029A9F30 gt gt gt gt ylabel Flux lt matplotlib text Text instance at 0x02A07BCO gt 6e 12 5e 12 4e 12 x 3e 12 L 2e 12 le 12 Q 980 1000 1020 1040 1060 1080 1100 One can add standard axis labels This example shows that it is possible to use special symbols using T X notation Overplots are possible First we make a smoothed spectrum to overplot gt gt gt from numarray convolve import boxcar yet another way to import functions gt gt gt sflux boxcar flux flat 100 smooth flux array using size 100 box gt gt gt plot wave sflux r hold True overplot red dashed line lt matplotlib lines Line2D instance at 0x0461FC60 gt This example shows that one can use the hold keyword to overplot and how to use different colors and linestyles This case uses a terse representation for dashed and r for red to set the values but there are more verbose ways to set these attibutes As an aside the function that matplotlib uses are closely patterned after matlab Next we subsample the array to overplot circles and error bars for just those points gt gt gt subwave wave flat 100 sample every 100 wavelengths gt gt gt subflux flux flat 100 gt gt gt plot subwave subflat og hold True overplot points as green circles lt matplotlib lines Line2D instance at O0x046EBE40 gt gt gt gt error tab field error gt gt gt
19. g styles linewidth color background etc The configuration file matplotlibrc is a simple ascii file and for the most part most of the settings are obvious in how they are to be set Note that usage for interactive plotting requires a few changes to the standard matplotlibrc file as downloaded we have changed the defaults for our standard installation at STScI A copy of this modified file may be obtained from http stsdas stsci edu python matplotlibrc Matplotlib looks for this file in a number of locations including the current directory There is an environmental variable that may be set to indicate where the file may be found if yours is not in a standard location Some of the complexity of matplotlib reflects the many kinds of usages it can be applied to Plots generated in script mode generally have interactive mode disabled to prevent needless regenerations of plots In such usage one must explicitly ask for a plot to be rendered with the show command In interactive mode one must avoid the show command otherwise it starts up a GUI window that will prevent input from being typed at the interactive command line Using the standard Python interpreter the only backend that supports interactive mode is TkAgg This is due to the fact most windowing systems require an event loop to be running that conflicts with the Python interpreter input loop Tkinter is special in that the Python interpreter makes special provisions for checking Tk event
20. g them by an integer is equivalent to adding them that many times All these operations result in new strings lists and tuples gt gt gt hello world hello world gt gt gt 1 2 3 4 5 1 2 3 4 5 gt gt gt 5 hello hello hello hello hello hello 1 5 5 Dictionaries Lists strings and tuples are probably somewhat familiar to most of you They look a bit like arrays in that they have a certain number of elements in a sequence and you can refer to each element of the sequence by using its index Lists and tuples behave very much like arrays of pointers where the pointers can point to integers floating point values strings lists etc The methods allow one to do the kinds of things you need to do to arrays insert delete elements replace elements of one type with another count them iterate over them access them sequentially or directly etc 12 Dictionaries are different Dictionaries define a mapping between a key and a value The key can be either a string an integer a floating point number or a tuple technically it must be immutable or unchangable but not a list dictionary array or other user created object while the value has no limitations So here s a dictionary gt gt gt thisdict a 26 7 1 random string 66 4 6 3 As dictionaries go this one is pretty useless There s a key whose name is the string a with the floating point value
21. he shape of these column arrays is the combination of the number of rows and the size of the columns Since in this case the colums contain arrays the result will be two dimensional albeit with one of the dimensions only having length one gt gt gt wave tab field wave gt gt gt flux tab field flux gt gt gt flux shape 1 10001 The arrays obtained by the field method are not copies of the table data but instead are views into the record array If one modifies the contents of the array then the table itself has changed Likewise if a record i e row of the record array is modified the corresponding column array will change This is best shown with a different table gt gt gt tab2 getdata table2 fits gt gt gt tab2 shape how many rows 3 gt gt gt tab2 array M51 13 5 2 NGC4151 5 7999999999999998 5 Crab Nebula 11 119999999999999 3 formats 1a13 1Float64 1Int16 shape 3 names targname flux nobs gt gt gt col3 tab2 field nobs gt gt gt col3 array 2 5 3 type Int16 gt gt gt col1 2 99 gt gt gt tab2 array M51 13 5 2 NGC4151 5 7999999999999998 5 Crab Nebula 11 119999999999999 99 formats 1a13 1Float64 1Int16 shape 3 names targname flux nobs Numeric column arrays may be treated just l
22. ified that list remains unchanged if the list contains mutable things like lists it is possible to change the contents of mutable things within a tuple but you can t remove that mutable item from the tuple Tuples have no standard methods 1 5 4 Standard operations on sequences Sequences may be indexed and sliced just like arrays gt gt gt s 0 h gt gt gt mylist2 mylist 1 gt gt gt mylist2 thello 2 3 11 Note that unlike arrays slices produce a new copy Likewise index and slice asignment are permitted for lists but not for tuples or strings which are also im mutable gt gt gt mylist 0 99 gt gt gt mylist 99 thello 2 3 gt gt gt mylist2 1 hello 2 3 note change doesn t appear on copy gt gt gt mylist 1 2 2 3 4 gt gt gt mylist 1 2 3 4 2 3 Note that unlike arrays slices may be assigned a different sized element The list is suitably resized There are many built in functions that work with sequences An important one is len which returns the length of the sequence E g gt gt gt len s 11 This function works on arrays as well arrays are also sequences but it will only return the length of the next dimension not the total size gt gt gt x array 1 2 3 4 gt gt gt print x 1 2 3 4 gt gt gt len x 2 For strings lists and tuples adding them concatenates them multiplyin
23. ifying text gt gt gt textobj xlabel hello color red ha right gt gt gt set textobj color wheat change color gt gt gt set textobj size 5 change size 1 7 2 implot example You can duplicate simple use of the IRAF task implot like this gt gt gt pixdata pyfits getdata pix fits gt gt gt plot pixdata 100 hold False plots row 101 gt gt gt plot pixdatal 200 hold True overplots col 201 19 500 400 300 200 100 0 100 200 300 400 500 600 1 7 3 imshow example Images can be displayed both using numdisplay which was introduced in the last tutorial and works perfectly well on Windows with DS9 and the matplotlib imshow command gt gt gt import numdisplay gt gt gt numdisplay open gt gt gt numdisplay display pixdata z1 0 z2 1000 gt gt gt clf clears the current figure gt gt gt imshow pixdata vmin 0 vmax 1000 gt gt gt grayQ loads a greyscale color table 20 500 400 300 200 100 0 100 200 300 400 500 The default type of display in Matplotlib out of the box has the Y coordinate increasing from top to bottom This behavior can be overriden by changing a line in the matplotlibrc file image origin lower The matplotlibrc that is the default on STScI unix systems Solaris Linux and Mac has this already set up If you are using Windows you will need to
24. ike any other numarray array Columns that contain character fields are returned as character arrays with their own methods described in the PyFITS User Manual Updated or modified tables can be written to FITS files using the same functions as for image or array data 1 4 Quick introduction to plotting The package matplotlib is used to plot arrays and display image data This section gives a few examples of how to make quick plots More examples will appear later in the tutorial these plots assume that the matplotlibrce file has been properly configured the default version at STScI has been set up that way There will be more information about the matplotlibrc file later in the tutorial First we must import the functional interface to matplotlib gt gt gt from pylab import To plot flux vs wavelength gt gt gt plot wave flux lt matplotlib lines Line2D instance at 0x02A07440 gt lid M 0 O ja Zoom to rect mode x 1006 Note that the resulting plot is interactive The toolbar at the bottom is used for a number of actions The button with arrows arranged in a cross pattern is used for panning or zooming the plot In this mode the zooming is accomplished by using the middle mouse button dragging it in the x direction affects the zoom in that direction and likewise for the y direction The button with a magnifying glass and rectangle is used for the familiar zoom to rectangle use the left mouse button to drag define a re
25. k function with the required event This is getting a little bit ahead of ourselves here since we weren t going to explain functions until the next lesson but it s impossible to explain event handling without it This is best explained using an example Say you want to print the X and Y coordinates when you click the mouse in an image Start by displaying the image in an imshow window gt gt gt imshow pixdata vmin 0 vmax 200 Then set up a handler to print out the X and Y coordinates This will be run every time the mouse button is clicked until the listener function is killed gt gt gt def clicker event if event inaxes print event xdata event ydata gt gt gt This is a very simple handler it just checks whether the cursor is inside the figure if event inaxes and if it it it prints out the X and Y coordinates in data coordinates i e in the coordinates as specified by the axes If the cursor is outside the figure nothing is done Now we set up a listener by connecting the event we are looking for button_press_event with the function we will call clicker gt gt gt cid connect button_press_event clicker The connect function returns a connect id which we will use when we want to kill the listener Now when we press the mouse button when we are in the figure we get the coordinates printed out on our screen This works even if we zoom the image since we have reques
26. ke numeric arrays though numeric operations cannot be performed on the record arrays themselves All the columns in a table may be accessed as arrays as well gt gt gt import pyfits When you import a module how does Python know where to look for it When you start up Python there is a search path defined that you can access using the path attribute of the sys module So gt gt gt import sys gt gt gt sys path P C WINNT system32 python23 zip C Documents and Settings rij SSB demo C Python23 DLLs C Python23 lib C Python23 lib plat win C Python23 lib lib tk C Python23 C Python23 lib site packages C Python23 lib site packages Numeric C Python23 lib site package s gtk 2 0 C Python23 lib site packages win32 C Python23 lib site packages win32 lib C Python23 lib site packages Pythonwin This is a list of the directories that Python will search when you import a module If you want to find out where Python actually found your imported module the __file__ attribute shows the location gt gt gt pyfits __file__ C Python23 lib site packages pyfits pyc Note the double characters in the file specifications Python uses as its escape character which means that the following character is interpreted in a special way For example n means newline t means tab and a means
27. mage display unresampled image in figure figlegend display legend for figure figtext add text to figure e object creation modification mode info functions axes create axes object on current figure cla clear current axes clf clear current figure close close a figure window delaxes delete axes object from the current figure draw force a redraw of the current figure gca get the current axes object gcf get the current figure gci get the current image hold set the hold state overdraw or clear ioff set interactive mode off ion set interactive mode on isinteractive test for interactive mode ishold test for hold mode re control the default parameters subplot create an axes within a grid of axes e color table functions autumn bone cool copper flag gray hot hsv pink prism spring summer winter 16 1 7 Plotting mini Cookbook 1 7 1 customizing standard plots The two tables below list the properties of data and text properties and information about what values they can take The variants shown in parentheses indicate acceptable abbreviations when used as keywords 17 Data properties Property Value alpha Alpha transparency between 0 and 1 inclusive antialiased aa Use antialiased rendering True or False color c Style 1 b gt blue g gt breen y gt red c gt cyan m gt magenta y gt yellow
28. nient functions for the interactive user We welcome feedback on which of these would be most important 30 or useful subtitles loadct to dynamically modify or flick through colortables tvrdc x y to read the xy position of the cursor histogram specification by bin interval rather than number of bins Some still missing functionality These are items for which the machinery has not yet been developed surface plots save to save everything in an environment journal to capture commands amp responses ipython can capture commands Symbols line styles and colors psym equivalences 0 line 1 plus 2 asterisk unsupported overplotting with x is close 3 dot 4 diamond d 5 triangle 6 square s 7 cross x 10 histogram ls steps linestyle equivalences 1 solid 2 dotted 3 dashed 4 dash dot The E line styles are supported solid line dashed line dash dot line dotted line points gt pixels o circle symbols triangle up symbols v triangle down symbols lt triangle left symbols gt triangle right symbols s square symbols plus symbols cross symbols diamond symbols thin diamond symbols a JK 31 tripod down symbols tripod up symbols tripod left symbols tripod right symbols hexagon symbols rotated hexagon symbols pentagon symbols vertical line symbols horizontal line symbols steps use gnu
29. of 26 7 The second key is the integer 1 and its value is the list containing a string and a floating point value The third key is the floating point number 6 3 with the empty string as its value Dictionaries are examples of a mapping data type or associative array The order of the key value pairs in the dictionary is not related to the order in which the entries were accumulated the only thing that matters is the association between the key and the value So dictionaries are great for for example holding IRAF parameter value sets associating numbers with filter names and passing keyword value pairs to functions Like lists they have a decent set of built in methods so for a dictionary D D copy Returns a shallow copy of the dictionary D has_key k Returns True if key k is in D otherwise False D items Returns a list of all the key value pairs D keys Returns a list of all the keys D values Returns a list of all the values D iteritems Returns an iterator on all items D iterkeys Returns an iterator an all keys D itervalues Returns an iterator on all keys D get k x Returns D k if k is in D otherwise x D clear Removes all items D update D2 For each k in D2 sets D k D2 k D setdefault k x Returns D k if k is in D otherwise sets D k x and returns x D popitem Removes and returns an arbitrary item So for example we could store the ACS photometric zeropoints in a dictionary whe
30. plot style steps kwarg only The following color strings are supported h E pee WN a b blue g green T red Cc cyan m magenta y yellow k black w white Matplotlib also accepts rgb and colorname specifications eg hex rgb or white Approximate color table equivalences loadct 0 gray O loadct 1 almost bone loadct 3 almost copper loadct 13 almost jet Color tables for images autumn bone cool copper flag gray hot hsv jet pink prism spring summer winter The generic matplotlib tutorial http matplotlib sourceforge net tutorial html 32
31. re the key is the name of the filter gt gt gt zeropoints F435W 25 779 F475W 26 168 F502N 22 352 F550M 24 867 F555W 25 724 F606W 26 398 F625W 25 731 F658N 22 365 F660N 21 389 F775W 25 256 F814W 25 501 F850LP 24 326 F892N 21 865 gt gt gt filter hdr filteri gt gt gt if filter find CLEAR 1 filter hdr filter2 gt gt gt zp zeropoints filter Sweet huh You will be seeing a lot more dictionaries over the next weeks so you should learn to love them The power afforded by dictionaries lists tuples and strings and their built in methods is one of the great strengths of Python 1 5 6 A section about nothing Python uses a special value to represent a null value called None Functions that don t return a value actually return None At the interactive prompt a None value is not printed but a print None will show its presence 13 1 6 More on plotting It is impossible in a short tutorial to cover all the aspects of plotting The following will attempt to give a broad brush outline of matplotlib terminology what functionality is available and show a few examples 1 6 1 matplotlib lingo configuration and modes of usage The whole area that matplotlib uses for plotting is called a figure Matplotlib supports multiple figures at the same time Interactively a figure corresponds to a window A plot a box
32. ring the terminal bell So if you really _want_ a backslash you have to escape it with another backslash Also note that the extension of the pyfits module is pyc instead of py the pyc file is the bytecode compiled version of the py file that is automatically generated whenever a new version of the module is executed I have a FITS table of FUSE data in my current directory with the imaginative name of fuse fits gt gt gt pyfits info fuse fits Filename fuse fits No Name Type Cards Dimensions Format 0 PRIMARY PrimaryHDU 365 0 Int16 1 SPECTRUM BinTableHDU 35 1R x 7C 10001E 10001E 10001E 10001J 10001E 10001E 100011 gt gt gt tab pyfits getdata fuse fits returns table as record array PyFITS record arrays have a names attribute that contains the names of the different columns of the array there is also a format attribute that describes the type and contents of each column gt gt gt tab names L WAVE FLUX ERROR COUNTS WEIGHTS BKGD QUALITY gt gt gt tab formats 10001Float32 10001Float32 10001Float32 10001Float32 10001Float32 10001Float32 10001Int16 The latter indicates that each column element contains a 10001 element array of the types indicated gt gt gt tab shape 1 The table only has one row Each of the columns may be accessed as it own array by using the field method Note that t
33. s available within pylab for quick perusal followed by several examples e basic plot types with associated modifying functions bar bar charts barh horizontal bar charts boxplot box and whisker plots contour contourf filled contours errorbar errorbar plot hist histogram plot implot display image within axes boundaries resamples image loglog log log plot plot x y plots pie polar quiver vector field plot scatter semilogx log x linear y x y plot semilogy linear x log y x y plot stem spy plot sparsity pattern using markers spy2 plot sparsity pattern using image e plot decorators and modifiers axhline plot horizontal line across axes axvline plot vetical line across axes axhspan plot horizontal bar across axes axvspan plot vertical bar across axes clabel label contour lines clim adjust color limits of current image grid set whether grids are visible 15 legend add legend to current axes rgrids customize the radial grids and labels for polar plots table add table to axes text add text to axes thetagrids for polar plots title add title to axes xlabel add x axes label ylabel add y axes label xlim set get x axes limits ylim set get y axes limits xticks set get x ticks yticks set get y ticsk o figure functions colorbar add colorbar to current figure figi
34. s getting used to but adds versatility Thus it may take more commands to accomplish something in matplotlib than it does in IDL but the advantage is that these commands can be done in any order or repeatedly tweaked until it s just right This is particularly apparent when making hardcopy plots the mode of operation is to tweak the plot until it looks the way you want then press a button to save it to disk Since the pylab interface is essentially a set of convenience functions layered on top of the 00 machinery sometimes by different developers there is occasionally a little bit of inconsistency in how things work between different functions For instance the errorbar function violates the principle in the previous paragraph it s not an atomic function that can be added to an existing plot and the scatter function is more restrictive in its argument set than the plot function but offers a couple of different keywords that add power Some syntactic differences You can NOT abbreviate a keyword argument in matplotlib Some keywords have had some shorthand versions programmed in as alternates for instance lw 2 instead of linewidth 2 but you need to know the shorthand Python uses indentation for loop control leading spaces will cause an error if you are at the interactive command line To issue 2 commands on the same line use a semicolon instead of an ampersand 27 The Rosetta Stone IDL Matplotlib
35. s thus no event loop must be run IPython has been developed to support running all the backends while accepting commands Do not expect to be able to use a matplotlib backend while using a different windowing system within Python Generally speaking different windowing frameworks cannot coexist within the same process Since matplotlib takes its heritage from matlab it tends toward using more functions to build a plot rather than many keyword arguments Nevertheless there are many plot parameters that may be set through keyword arguments The axes command allows arbitrary placement of plots within a figure even allowing plots to be inset within others For cases where one has a regular grid of plots say 2x2 the subplot command is used to place these within the figure in a convenient way See one of the examples later for its use Generally matplotlib doesn t try to be too clever about layout It has general rules for how much spaces is needed for tick labels and other plot titles and labels If you have text that requires more space than that It s up 14 to you to replot with suitable adjustments to the parameters Because of the way that matplotlib renders interactive graphics by drawing to internal memory and then moving to a display window it is slow to display over networks impossible over dial ups slow over broadband gigabit networks are quite usable however 1 6 2 matplot functions The following lists most of the function
36. ted the coordinates in data space so Matplotlib takes care of determining the X and Y coordinates correctly for us When we re done we can just do the following gt gt gt disconnect cid and we are no longer listening for button presses There are more details in the Matplotlib manual 1 8 Exercises 1 Using only Python tools open the fits file fuse fits extract the flux and error columns from the table and plot these against each other using plot Scale the flux and error by 1 0e12 before plotting 2 Smooth pix fits with a 31x31 boxcar filter see first tutorial and make a contour plot at 90 70 50 and 30 and 10 of the peak value of the smoothed image Repeat 2 except before generating a contour plot display the unsmoothed image underneath Change the colortable to gray and label your favorite feature with a mathematical expression Save the result as a jpeg file and view it in your favorite jpeg viewer P ESE US ON Extra credit parroting the readcursor example write a short callback function to display a cross cut plot of a displayed image on a left mouse button click and a vertical cut plot on a right button click overplotting the image 25 Appendix D IDL plotting compared with matplotlib MATPLOTLIB for IDL Users March 2005 Vicki Laidler About this document This is not a complete discussion of the power of matplotlib the 00 machinery or pylab the functional interface This document only provides a
37. ty lists are permitted 10 append x adds x to the end of the list extend x concatenate the list x to the list count x return number of elements equal to x index x i j return location of first item equal to x insert i x insert x at ith position pop i return last item or ith item and remove it from the list remove x remove first occurence of x from list reverse reverse elements in place sort cmp key reverse sort the list in place how sorts on disparate types are handled are described in the documentation 1 5 3 Tuples One can view tuples as just like lists in some respects They are created from lists of items within a pair of parentheses For example gt gt gt mytuple 1 hello 2 3 Because parentheses are also used in expressions there is the odd case of creating a tuple with only one element gt gt gt mytuple 2 not a tuple doesn t work since 2 is evaluated as the integer 2 instead of a tuple For single element tuples it is necessary to follow the element with a comma gt gt gt mytuple 2 this is a tuple Likewise empty tuples are permitted gt gt gt mytuple If tuples are a lot like lists why are they needed They differ in one important characteristic why this is needed won t be explained here just take our word for it They cannot be changed once created they are called immutable Once that list of items is ident
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