PyGS 0.4.0

README

PyGS (Python Galaxy Survey) is designed to be an interactive class to deal with large-scale redshift surveys.

Its ideal is to make the run-of-the-mill operations as simple as possible, but to provide enough flexibility in the background to be of real usefulness. While intended as an interactive class, for use with the python shell or IPython, it can of course also be scripted.

Many of the more intensive routines are written in Fortran and made available through F2PY.

Instantiating the class requires a filename, or folder, which contains the survey information (redshifts, angles, magnitudes etc.). Once the import of the data has been successful, a directory structure will be created which is intended to allow speed-of-access and computation, and ease-of-reuse for future calculations. See the documentation for __init__() for detailed explanations.

Most calculations have default options which will be used in the absence of user-specified options, and these are deemed to be the most common usages of the method. However, there is always the opportunity to tweak these as needed. Generally there are ‘convenience’ functions for performing a series of calculations, where it is common to do these together.

-++++++++++++++++++++++++++++++++++++++++++++++++++++ -+ + -+ GUIDE TO INSTALLING AND USING PyGS + -+ + -++++++++++++++++++++++++++++++++++++++++++++++++++++ - - -1. GETTING THE ENVIRONMENT SET UP - a.) Getting a proper environment depends heavily on the OS - that you are using. If using Ubuntu, most installation can - be done via synaptic, if using mac or windows it is a little - more difficult. - b.) First make sure you have a working fortran 90 compiler. - I used gfortran for development. Ubuntu already has - gfortran, mac doesn’t so you will need to install it. I - don’t even know for Windows. - c.) Get python. Ubuntu and mac are shipped with a version of - python. Don’t use it. Install the latest 2.x version (NOT 3.x!) - using your favourite method. HOWEVER, one nice option - to consider at this point is EPD - Enthought Python - Distribution. It comes shipped with basically every module - you’ll need for PyGS and is very easy to install. - d.) If going the way of EPD, install the 64-bit version I think. - Perhaps in the future we may need to use 32-bit. But - try the 64-bit for now. - e.) Once EPD is installed, in terminal, type “which python”. - You should see the python.exe in the EPD folder, not - the standard one shipped with your OS. If it is not the - correct python, you probably have to modify your - .bashrc file with a line saying: - “export PATH = “<path to epd installation folder>”:$PATH” - or something very similar. - f.) If NOT going the way of EPD, then point your $PATH variable - to the new python interpreter you installed by adding - something like - “export PATH = “<path to installation folder>”:$PATH” - .bashrc file. - - f.) Once this is correct (either EPD or not), type “easy_install pip”, - which will install the module pip, which is an easy way to - download and install most good modules. - g.) If NOT using EPD, then you will need to install a few modules - with pip. So type in terminal: - > pip install numpy - > pip install scipy - > pip install matplotlib - > pip install cosmolopy - > pip install asciitable - > pip install ipython - > pip install readline - h.) If using EPD, then there are only a couple of things to install: - > pip install cosmolopy - > pip install asciitable - You can also update the others: - > pip update numpy - > pip update scipy - > pip update matplotlib - - i.) Now your python setup is ready for PyGS. - -2. INSTALLING PyGS - a.) There are two ways to go here: If you just want to use PyGS - and not work on it, (or just want to try it out easily before you - start working on it), then download just the tar.gz file under the - dist folder. If you want to work on PyGS, then download - everything under the PyGS folder (that includes setup.py, - README.txt etc). - - - To install the just usable version: - b.) After downloading the tar.gz file, untar it, then in the terminal, - enter the untarred directory and then type: - > python setup.py install - (You may need to type sudo beforehand depending on - where your files are installed). - - c.) As long as everything installs correctly (it may not, I’ve only tested - it with my specific OS and compiler etc.) then you are right to go. - - - What to do with the source code: - d.) If you would like to have the source in the same way that I do on - my computer then you will have downloaded the whole PyGS - directory. The source code itself is under PyGS/PyGS. The - fortran code is under /fort. The only python file is the PyGS.py - file, which contains the class with many methods. You can - quite simply install the modules to your root python installation - by running the install.sh script after you make changes. - -3. USING PyGS IN THE INTERPRETER - a.) Type ipython in the terminal. - - b.) type: - > from PyGS import PyGS - NOTE: what we are doing here is saying - “from the package PyGS,import the module PyGS” - - c.) A few handy things in ipython: typing a variable or class - name followed by a ? brings up information about that - class/method/variable. I have tried to document PyGS - fairly well so doing this can help. For instance type - > PyGS.PyGS? - Also, typing PyGS.PyGS.<tab> will bring up the methods - and variables that PyGS contains (NOTE the dot after - PyGS). Tab acts as an autocomplete. This is also very - helpful. - - d.) Make sure that you have a file containing Survey information. - If the file has a header with the information about each column - then the class may automatically detect which columns - correspond to which variables (redshift, ra, dec etc). - However, this may not be the case, and the program may - ask you what columns correspond to what. So make sure - you know where redshift, ra, dec and mag_r are. - - e.) type: - > x = PyGS.PyGS(“<full path to survey>”) - and follow the prompts if there are any. There are other options - when importing the survey but you can explore them later. - What this will do is import the survey info to the current session - and importantly create a folder where your file is, named after - the file which will house a similar file, formatted for future use - in the program (to make importing it easier next time). - - f.) type: - > x.<tab> - a list of methods will come up that you can perform on the survey. - Just choose one! You can type any one followed by a ? to see what - it does