Installation for development or instrument control

Warning

These installation instructions are outdated, but retained as they have a little more explanation for some of the choices. Most notably we now recommend python 3.6 or 3.7 for new installs. Use the new instructions as a first stop and read this in conjunction with the updated instructions.

If you want to contribute to PYMEs development, or you want to use PYME in a context (e.g. instrument control) which requires modification to some of the scripts you will want to have the PYME sources somewhere you can easily find, modify and update them.

If you just want to use the data analysis features then you are strongly advised to follow the instructions in Installation of PYME on 64 bit Windows, OSX, or Linux instead.

The easiest (and only supported) way of getting a development build up and running also uses Anaconda. Although PYME will work with other python 2.7 distributions, this will involve considerably more effort to navigate the many dependencies.

STEP 1: Installing Anaconda

Download and install Anaconda from https://store.continuum.io/cshop/anaconda/. Choose the 64 bit version of Python 2.7 for your prefered platform.

Warning

Anaconda is available in both Python 2.7 and Python 3.x flavours. PYME will only work with the Python 2.7 version.

STEP 2: Add the david_baddeley channel and install dependencies

We maintain a conda channel with packaged versions of a number of dependencies which are either not available through the standard conda libraries or for which the required version is newer than the anaconda default. This channel also has a metapackage pyme-depends which lists should install the dependencies 1.

To tell anaconda about our channel, and to install the dependencies we need to open a terminal window 2 and run the following two commands:

conda config --add channels david_baddeley
conda install pyme-depends

This should download and install the required dependencies.

STEP 3: Install git

If you are contemplating a source install you probably don’t need explicit instructions here, and might well already have it, but as a fallback git is conda installable: conda install git.

STEP 4: Install a c/c++ compiler

Building PYME requires a c compiler. On Linux, make sure gcc, g++ and the standard development tools are installed. On OSX, install XCode, and on windows download and install MS Visual C for Python 2.7.

STEP 5: Get the code

The code is stored in a github repository. Get the current copy by doing

git clone https://github.com/python-microscopy/python-microscopy

If you are going to be doing significant development and plan on issuing pull requests, it might be reasonable to create a private fork on github at this point and clone from that (this is reasonably easy to set up later, so if you’re unsure just pull the code from the default repository and go from there).

STEP 6: Install

Change to the directory where you cloned the code and execute the following.

python setup.py develop

Note

If you are on OSX, you might want to do the following instead to avoid problems running GUI scripts:

/PATH/TO/ANACONDA/python.app/Contents/MacOS/python setup.py develop

this will ensure that the correct “shebang” is used to ensure that you don’t run into issues with using a non-framework build.

At this point you should have a functioning install.

Note

Due to some slightly weird interplay between numpy distutils and setuptools python setup.py develop works from the base directory of the repository, but if you want to run python setup.py install instead you’ll need to drop down one directory into the PYME directory first.

Further configuration (mostly optional)

Windows

If not already done by the setup script, create shortcuts somewhere (eg the start menu), to the following scripts:

  • PYTHONDIR\Scripts\PYMEAquire.exe (data acquisition)

  • PYTHONDIR\Scripts\launchWorkers.exe (real time analysis)

  • PYTHONDIR\Scripts\dh5view.exe (raw data viewer)

  • PYTHONDIR\Scripts\LMVis\VisGUI.exe (analysed data viewer)

Where PYTHONDIR is the location of your python installation (typically c:\Python27 or similar) Optionally associate .h5 files with dh5view (will also open .tif, .kdf & .psf if you want) and .h5r files with VisGUI. I typically do this by clicking on one of the files, using the ‘Open With’ option, and telling it to remember. If you’re using the sample database, you can also associate .pmu files with PYTHONDIR\Scripts\pymeUrlOpener.cmd.

Linux (Gnome)

Change to the PYME/gnome directory and run install_gnome.sh. This should (hopefully) set up associations and :) thumbnailing! With any luck, file permissions should be OK out of the repository, but there’s a chance you’re going to have to make a couple of the scripts executable.

OSX

Build the opener stubs (to allow file association) by executing the following:

cd osxLaunchers
xcodebuild -alltargets

Basic Configuration

In addition to the setup detailed above, PYME has a couple of configuration options which are controlled by environment variables. These are:

PYMEDATADIR

Default location where PYMEAcquire saves data. Eg D:\. Also place where other parts of analysis chain look for data.

PYMEMICRPATH

Used with sample database to know where (on the local machine) the microscope computer is mapped.

PYMENASPATH

As for PYMEMICRPATH, but for the NAS

When useing PYME for data acquisition you probably want to set at least PYMEDATADIR, as the default is not particularly useful.

You should now have a setup which works for simulation*, data analysis, & visualisation. Interfacing with hardware obviously requires a little more work - see Configuring PYME Acquire.

* simulation probably won’t work perfectly until you’ve done the EMGain calibration section of Configuring PYME Acquire.

Prerequisites for the adventurous

The prefered way of getting pre-requisites is to use the pyme-depends package as noted above. If using a non-anaconda python distribution, the pre-requisites will need to be sources and installed manually. Below is an outdated and unmaintained list of pre-requisites. A more up to date list can be found by looking at meta.yaml file used to generate the conda package.

PYME requires:

  • Python 2.7

  • a c compiler (on windows I recommend the free Visual C for python, on linux or OSX just use the platform gcc)

  • python-dev (only on Linux - has the Python development header files)

and the following Python packages:

  • Numpy

  • Scipy

  • Matplotlib

  • wxPython (>2.8.11)

  • pytables

  • Pyro (any 3.x version should work - the newer version 4 won’t)

  • PyOpenGL

  • PIL (Python Imaging Library)

  • pywin32 (only req. on windows)

For full functionality, the following are also useful:

  • PySerial [acquisition with real hardware]

  • PyFFTW3

  • MySQL-python [sample DB server]

  • Django (>1.2) [sample DB server]

  • Django-south [sample DB server]

  • Mayavi2

  • traits

  • traits-ui

  • Delny [some very rarely used segmentation code]

  • jinja2

  • cherrypy

  • scikit-image

  • scikit-learn

  • networkx

  • toposort

  • shapely

  • zeroconf

  • requests

  • pandas

  • yaml

There are a couple of (mostly historical) caveats:

  • I have had problems with getting Delny to compile/install on Win/OSX, although this might have been fixed in the interim. It’s only required in PYME for some very rarely used functionality, so can usually be safely ignored.

  • On some (most?) versions of windows, the network stack is broken. Pyro needs to be told about this by setting an environment variable - PYRO_BROKEN_MSGWAITALL=1. I can confirm that this is the case for pretty much every XP system, but can’t comment on Vista/7). Pyro falls back on another (slower) piece of code when this the flag is set, so it should be safe in any case. Can’t remember exactly how to diagnose the problem other than that Pyro falls over with cryptic error messages.

  • All nodes on the network need to have the same version of Pyro

Footnotes

1

This package should track with the current state of the dependencies. At present, however, the dependencies for the python-microscopy package are likely to be updated earlier and more often. If a dependency seems to be missing, check the meta.yaml file in the python-microscopy directory and if necessary use conda install to install the missing package. Please report any missing dependencies so I can fix them.

2

On OSX use spotlight to launch the Terminal app, on Windows, launch the Anaconda Command Prompt from the “Anaconda” group in the start menu.