I am working on flow cytometry.
I want to parse the .fcs files using python. I have researched on internet that there is a module fcm but that is for linux os and I am working on windows.
I want to know that how can I parse .fcs files in windows using python?
If anyone knows how can I use fcm in windows kindly let me know too.
Pyfcm does work on Windows. A tutorial for loading fcs files is at http://packages.python.org/fcm/basic.html. Installers are at http://www.lfd.uci.edu/~gohlke/pythonlibs/#py-fcm
Check out FlowPy. The pre-requirements listed on its download page all link to Windows binaries. Seems to be a nice FCS GUI (and even non-GUI) project.
Yet another python project for analysing flow cytometry data is FlowCytometryTools: http://gorelab.bitbucket.org/flowcytometrytools/
After python is set up with the required dependencies (matplotlib, pandas, etc.), this should work on any operating system.
I am the maintainer of the FCM codebase, inherited after the original author graduated. FCM was developed to support an hierarchical Dirichlet process (HDP) clustering algorithm. I eventually decided to separate the functionality into 3 different libraries:
FlowIO: for those that simply need to read FCS data or create new FCS files
FlowUtils: for performing basic flow functions (compensation & transforms)
FlowStats: for those looking to use the specific HDP clustering algorithm
In addition to these, we've recently started development on FlowKit, which promises to be a more high-level and (hopefully) more intuitive Python framework for flow cytometry analysis and visualization, including GatingML support.
Note that both FlowIO and FlowUtils are on PyPI and available to install via pip, and both should be more compatible with all platforms including Windows, Mac, and Linux due to the reduced number of dependencies and recent bug fixes.
Related
I'm building a rendering engine in Python for fun. I need to load 3D scenes. Any standard modern format like DAE, 3DS, or MAX would work: I can convert my files easily between standard formats.
OpenSceneGraph seems to be the most comprehensive and well-maintained solution. It would be ideal to be able to use it in Python without much hassle. Are there working Python bindings for OSG that are easy to install, work on Mac OS X (I'm on 10.8), and are compatible with the latest versions of OSG?
I searched around and came across osgswig (http://code.google.com/p/osgswig/) and PyOSG (http://sourceforge.net/projects/pyosg/), but they don't seem to be actively maintained. I don't see any recent activity related to these packages, and it seems that people had trouble running osgswig on OSX. Ideally, I'd like to find something that "just works", without major compilation hassles. I'd like to just install a package and be able to import a module that will let me load COLLADA or 3DS files.
I also came across pycollada (https://github.com/pycollada/pycollada). It seems active, but fairly early-stage. Ideally, I'd like a reasonably comprehensive package that supports specular maps, normal maps, and other reasonably advanced features. Animation would be nice as well.
In summary, I need to load 3D scenes in Python. Bindings for OSG would probably be ideal, because OSG is so comprehensive. But I need something that works on OSX. I would also prefer something that can be installed reasonably easily. Does something like this exist?
Thanks!
Take a look at Open Asset Import Library (short name: Assimp). It is a portable Open Source library to import various well-known 3D model formats in a uniform manner. http://www.assimp.org/
You should loot at panda3D (http://www.panda3d.org/), it's a game engine with extensive python bindings. It has the features you want : http://www.panda3d.org/manual/index.php/Features
I used it for a few years and it was a solid tool.
I made my own fork of a mirror of a clone of the osgswig project for a similar purpose. I have it working with OpenSceneGraph version 3.2.1 on Windows and Mac; and it's likely I will eventually polish it for linux too. I'm already delivering one product to customers based on my version of osgswig, and I'm considering making others. Find my fork here:
https://github.com/cmbruns/osgswig
If others show enough interest, I might be coaxed into creating binary installers for my version of the osgswig module, to make installation easier.
If you just want the easiest OpenSceneGraph bindings for OSG 3.2.1, you can stop reading this answer here. Read on for more of my thoughts for the future.
Though I am maintaining a fork of osgswig (as stated above), I sort of hate SWIG, and I would prefer to use bindings based on Boost.Python, rather than on SWIG. For large, complex C++ APIs, like OpenSceneGraph, Boost.Python can be much more elegant than SWIG, both for the API consumer, and for the binding maintainer (me, and me). I found one project using Boost.Python to wrap OSG, at https://code.google.com/p/osgboostpython/, but the developer is lovingly wrapping each part of the interface by hand, and has thus only completed a tiny fraction of the large OpenSceneGraph API.
Taking that Boost.Python based project as inspiration, I created yet another OpenSceneGraph Python binding project, at https://github.com/JaneliaSciComp/osgpyplusplus. Eventually, I want to use this osgpyplusplus project for all my python osg needs. And I would appreciate help in making it ready. Right now, osgpyplusplus suffers from the following weaknesses, compared to osgswig:
osgpyplusplus is not yet used in any working product
The build environment is tricky to set up, requiring both Boost.Python and Pyplusplus
I haven't paid much attention to osgpyplusplus recently, so it might rust away if I continue to ignore it.
Though osgpyplusplus probably wraps most of the OpenSceneGraph API, there are probably some important missing pieces that won't be identified until someone tries to develop a significant project with it.
It would be a lot of work for me to create a binary module installer for osgpyplusplus at this point, so please don't ask me to.
I'm testing different languages to developp a desktop application for Mac&Windows.
I thought that Python+Wx worth a try so I wrote a simple hello world.
Then, I tried the py2app to package my application as a Mac application.
What a surprise to find that my hellworld.app weight as much as 75 MB !! (then I have an error at runtime but that's not the question)
Here is my question : is there a way to distribute a standalone wxPython application that weight less than a few MB ? (for instance, an adress book app).
(a Swing HelloWorld is around 3KB, plus around 20MB for the JRE)
Thank you
I would highly remmoend you using PyINstaller, which can be found here: link
it works like a chamr for me so far and it support most of the major libraries:
wxpython pyqt and even django (although i dont really understand the whole django support thing ;-) )
PyInstaller is a program that converts (packages) Python programs into stand-alone executables, under Windows, Linux, and Mac OS X. Its main advantages over similar tools are that PyInstaller works with any version of Python since 2.2, it builds smaller executables thanks to transparent compression, it is fully multi-platform, and use the OS support to load the dynamic libraries, thus ensuring full compatibility.
The main goal of PyInstaller is to be compatible with 3rd-party packages out-of-the-box. This means that, with PyInstaller, all the required tricks to make external packages work are already integrated within PyInstaller itself so that there is no user intervention required. You'll never be required to look for tricks in wikis and apply custom modification to your files or your setup scripts. As an example, libraries like PyQt, Django or matplotlib are fully supported, without having to handle plugins or external data files manually. Check our compatibility list of SupportedPackages.
i hope this helps, good luck and tell if you need anymore help
For quite some time now, I've been fighting in vain to get a software I'm working on to work under Windows. It's written in Python (the 2.x series), and although all Linux users can benefit from its GUI when they use the source package, it seems that many people who download it go for the Windows package, for which I've only been able to provide command-line binaries.
The GUI was built using Glade/GTK, and uses poppler to embed a PDF viewer. I've found various howto's in the past (I don't have them at hand right now, sorry), which I've tried to follow religiously, but I never got things to work at all.
So, is there a reliable tutorial explaining exactly how to install the needed libraries (GTK and Poppler), so that I can build the corresponding binaries for my users?
There is a window installer here: http://download.gnome.org/binaries/win32/pygtk/2.22/
Is it somehow possible to extract .cab files in python?
Not strictly answering what you asked, but if you are running on a windows platform you could spawn a process to do it for you.
Taken from Wikipedia:
Microsoft Windows provides two
command-line tools for creation and
extraction of CAB files. They are
MAKECAB.EXE (included within Windows
packages such as 'ie501sp2.exe' and
'orktools.msi'; also available from
the SDK, see below) and EXTRACT.EXE
(included on the installation CD),
respectively. Windows XP also provides
the EXPAND.EXE command.
I had the same problem last week so I implemented this in python. Comments, additions and especially pull requests welcome: https://github.com/hughsie/python-cabarchive
Oddly, the msilib can only create or append to .CAB files, but not extract them. :(
However, the hachoir parser module can apparently read & edit Cabinets. (I have not used it, though, so I couldn't tell you how fitting it is or not!)
I wrote a Python program. I would like to add to it an installation script that will set up everything necessary - like desktop icon, entry in the menu, home directory file, etc.
I'm working on Linux (ubuntu). When a Python program is installed, what needs to happen in general? I know that it probably depends on the nature of the program.
Can you give me some general ideas? Or, point me in the right direction? I have no idea how to look for this on Google.
Thanks
If it's a Python program you're trying to package, you should consider using its 'standard' distribution framework distutils. I can't replicate the entire document here but I'd recommend that you read it. Once you're done with that, check out the Hitchhikers guide to packaging which contains details on distribute - the extensions to distutils that allow you to package and distribute more effectively.
You could create an rpm easily using checkinstall. Search for checkinstall in google and download it. It will allow you to create an rpm and set the options.
For Ubuntu if you want it to be easily distributable to other Ubuntu users it'll have to be packaged properly, which is no simple task. You might want to consult their Packaging Guide for more information.
Otherwise, generally speaking there are a few standard packaging options for Python. Setuptools is popular, but becoming reviled lately. Read James Bennett's blog post "On Packaging" for a decent in-depth look into the ups and downs of the Python packaging world.
How a program is launched and placed in the menu is determined by a .desktop file (you can read the specification or just look at some examples from /usr/share/applications). Properly installing a program (placing all files in the right directories and so on) requires either making a package like a deb or rpm, or you could use something like distutils or setuptools.
It may also help to just look at some (open source) examples of Python programs for Linux.