Instructions to run SeedWater Segmenter:

1: Install (and then test) python and necessary modules
------------------------------------
Windows:
    Download Enthought Python Distribution:
        http://www.enthought.com/products/edudownload.php
            (No need to enter personal info...)
    Install EPD
        If on XP, choose install for all users
        If on Windows 7 or Vista, choose install for just me
    Test:
        Open a DOS window (can invoke it by running the command "cmd")
        Type and run "C:\Python26\python.exe"
        Type and run "import numpy"
            (It works if it pops up with the ">>>" below and does not genetate a large error message)
Ubuntu (or Debian):
    Install the necessary packages with this command:
        sudo apt-get install python-setuptools python-wxtools python-numpy python-scipy python-matplotlib python-imaging python-xlrd python-xlwt
        ( Make sure you have the "Community" source available )
    Test:
        In a terminal, run "python"
        Type and run "import numpy"
            (It works if it pops up with the ">>>" below and does not genetate a large error message)
Mac OS X:
    Download Enthought Python Distribution:
        http://www.enthought.com/products/edudownload.php
            (No need to enter personal info...)
    Install EPD
    Test:
        In Terminal, run "python"
        Type and run "import numpy"
            (It works if it pops up with the ">>>" below and does not genetate a large error message)
Other:
    Ask me...

2: Install Python Dependencies and SeedWaterSegmenter:
---------------------------------------
The watershed algorithm that used to come from a modified version of PyMorph by Luis Pedro
now comes from the package "mahotas" by Luis Pedro (new implementation of the same algorithm).
It is much faster!

SeedWater also depends on a number of other packages by David Mashburn that used to be included in SWS but are now separate packages:
    cmpGen
    EllipseFitter
    FilenameSort
    GifTiffLoader
    ImageContour

To install all of these, open a shell (cmd on Windows (use "Run as Administrator"), Terminal on Mac and Linux)
Type and run the command:
    easy_install mahotas cmpGen EllipseFitter FilenameSort GifTiffLoader ImageContour SeedWaterSegmenter
Give it permission if needed


3: Test SeedWater
--------------------
Double-click "SeedWaterSegmenter.py" and run it.
    Wait a long time.
    If it crashes, try this:
        Open "SeedWaterSegmenter.py", find the value USE_COMPILE.  Change it to False
        Try SeedWater again...
        If it still crashes, try Double-clicking CompileNTest_SeedWaterImports_pyx.py and run it.
        Then try SeedWater again...
(If it still won't run, let me know and I'll try to help!)
Hooray it works!

To get started using it, select a tiff stack in the window it opens and then hit Ctrl-G to run gaussian...
After that, move to Figure 2. This is where you can now view and edit the seed points.




BTW, if you plan on doing any significant work with python yourself, I DEFINITELY recommend getting these coding tools:

* Geany for editing and running scripts (Windows/Linux only ... on Mac, you might try Editra or SciTE or Stani's Python Editor instead)
  http://www.geany.org/

* PySlices for interactive use.  PySlices is a modified version of PyCrust that I made to support multi-line command blocks... look at these for more info:
  http://code.google.com/p/wxpysuite/
