I am trying to use Python 3.4.2 to control ImageJ
what I want to do is from python code , I want to sent orders to imageJ to analayse some images, detecting edges, contrast, noise etc
there is a similar question here
How to connect ImageJ to python?
but there is no answer, like "install this, and control the Find Edges button with this command"
I wonder how can I do that, can somebody help me
I have found this link, and this link, and they say that it is possible by using "import ij" but there is no ij library that I can use or install.
also ImageJ website states in "How can I call ImageJ from my software?" that "If your software is written in another language such as C or Python, there are many ways to integrate Java functionality. You must choose which one is best for your particular requirements." but there are no specifics
this Google webpage says that with "py4ij" I can control imagej with python "Py4IJ - Python for ImageJ - plugin and IDE that allows Python and Jython access to the ImageJ"
but I am not sure how to run it, Help
as an alternative to Imagej is Fiji but I am not sure if python can control it or I have to use Fiji, and Fiji tutorial
my last alternative is Using OpenCV for image processing but I actually need to use ImageJ or Fiji, so OpenCV is not a valid answer
thanks
EDIT
according to the first answer, it suggest to write a CellProfiler's RunImageJ module, but my question is should I have to install CellProfiler? from here, following the examples here and here and running the module
or should I follow the native Python idea from this link
in any case the first answer link talks about Jython, but I can not use Jython, the latest version of it is based on python2.7 and I am using 3.4, and there is no development for jython 3.x
help
Integration of Python with ImageJ was recently discussed on the new ImageJ forum; see the Python scripting thread.
While it focuses on calling native-code-wrapped Python modules such as NumPy from ImageJ, the reverse direction (calling ImageJ from Python) is also addressed by some of the solutions, particularly CellProfiler's RunImageJ module. As discussed there, a dedicated programmer could start there and champion a more general solution for the benefit of the community.
In general, this issue is discussed on the ImageJ wiki on the Python page, particularly the section on limitations.
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'd like to use OpenCV functions, like Hough Transform and Corner Detection, in Sikuli.
I tried the OpenCV installation instructions for CPython on Sikuli and it's a no go.
I understand that Sikuli is Jython and this might be the hard way to do things. What are the easier alternatives?
I'd still like to use Sikuli & Python because the code I write just works; but maybe I'm hitting the limits of Sikuli.
You could use Automa as an alternative to Sikuli. It is a pure Python library (so you can use any other Python library with it) and its image search algorithms are fully compatible with Sikuli. In fact, it uses OpenCV's Python bindings itself, and thus ships with them.
Disclaimer: I'm one of Automa's developers.
Generally spoken: Python modules containing C-based code (which is the case for Python OpenCV) cannot be used in the Sikuli Script (Jython).
The integration of some OpenCV features in Sikuli is realized using the Java-To-C interface (JNI) and the usage of OpenCV features itself is coded in C++.
If you want to use OpenCV features not supported by Sikuli, then you either have to use the above mentioned JNI approach or use the Java implementation of OpenCV (javacv) (Java stuff can be used seamlessly from Jython scripts).
Another option of course is to implement the additional things in plain Python scripts using the Python/OpenCV and call these scripts via the C-Python interpreter in a subprocess.
I'm trying to write some code using OpenCV. My sensor is from Point Grey Systems, and it uses the FlyCapture API to grab images. I'd like to grab those images and do some stuff in OpenCV to them, using Python. FlyCapture is all C/C++, so I'm firing up SWIG to create the bindings. Am I reinventing the wheel? Do python bindings for FlyCapture already exist somewhere that I don't know about?
As of FlyCapture 2.11 there are official Point Grey / FLIR python wrappers. I've used the python 2.7 so far.
the pyflycapture2 is still available as well...
just started using this wrapper last week pyflycapture2
working well so far with my FireFly MV USB
Here's a new Cython wrapper I started for the FlyCapture V1 API:
https://github.com/kbrafford/pyfly1
It also has some wx.Python demos showing it working and allowing you to assess performance.
If the Python language is your only restriction, you may use the wrappers for FlyCapture from the JavaCPP Presets by calling the appropriate functions via Jython.
I am trying to use VTK from python. I tried to find and could not realy find anything on the web which can be used for documentation. I tried looking at the c++ documentation but the methods are very different.
Thanks a lot
You could see the python examples at VTK's wiki. There is another resource by going to the official nightly documentation and looking for a particular class; in the section examples for many (not all) classes you can find implementations in python (also in c++ and tcl). A third option is to go to the source folder of your last downloaded release of VTK; look for the folder "Examples", there you will also find different VTK implementations in python (besides C++ and tcl)
I recommend you use Mayavi and TVTK from Enthought, the API is much pythonic:
http://code.enthought.com/projects/mayavi/
On the VTK website you can find the VTK User's Guide. It is pretty thorough.
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I'm looking to set up my development environment at home for writing Windows applications in Python.
For my first piece, I'm writing a simple, forms-based application that stores data input as XML (and can read that information back.) I do want to set up the tools I'd use professionally, though, having already done a round of didactic programming.
What tools are professional python developers using these days? In order to have a working python environment, what version of the compiler should I be using? What editor is common for professionals? What libraries are considered a must-have for every serious python developer?
Specifically, which Windowing and XML libraries are de rigeur for working in Windows?
I like Eclipse + PyDev (with extensions).
It is available on Windows, and it works very well well. However, there are many other IDEs, with strengths and weakness.
As for the interpreter (Python is interpreted, not compiled!), you have three main choices: CPython, IronPython and Jython.
When people say "Python" they usually refer to "CPython" that is the reference implementation, but the other two (based, respectively, on .Net and Java) are full pythons as well :-)
In your case, I would maybe go on IronPython, because it will allow you to leverage your knowledge of .Net to build the GUI and treating the XML, while leaving the implementation of business logic to Python.
Finally, should you decide to use CPython, finally, there are several choices for working with xml:
minidom; included in the standard library
lxml, faster and with a better API; it means an additional installation on top of Python.
Lots of questions, most hard to answer correctly. First of all, most of python development happens on unix-like platforms. You will hit many walls during development on Windows box.
Python is not a compiled lanugage, current preferred version for production is 2.5. For environement setup you should take a look at virtualenv. Editor is a personal choice, many Python developers use Vim, you can customize it pretty well to suite your needs.
About libraries, Python is very strong around this area and it's really hard to say what is a must to know. If you want to handle XML, I would preffer lxml.
If you go for CPython, make sure you get the win32 extensions by Mark Hammond, either as a separate download which you install on top of the vanilla Python installation, or as part of ActiveState's ActivePython. It includes an integrated editor and debugger.
Jython has recently reached 2.5 compliancy, but we quickly ran into recursion limit issues.
The standard distribution includes IDLE, a graphical editor and debugger.
I like shells, so I'm using IPython for interactive work, and pydb as debugger (unfortunately, I had problems getting pydb to work under Windows).
"What tools are professional python developers using these days?"
Lots
"In order to have a working python environment, what version of the compiler should I be using?"
["compiler" is meaningless. I'll assume you mean "Python"]
We use 2.5.4. We'll be upgrading to 2.6 as soon as we've done the testing.
"What editor is common for professionals?"
We use Komodo Edit.
"What libraries are considered a must-have for every serious python developer?"
We use Django, XLRD, PIL, and a few others. We don't plan this kind of thing in advance. As our requirements arrive, we start looking for libraries. We don't "pre-load" a bunch of "must-have" libraries. The very idea is silly. We load what we need to solve the problems we have.
There are no set standards in these matters, and for good reasons:
there is a fair amount of good choice
different people are productive with different tools
different tools and libraries are suited for solving different problems
That said, I think it's a valid question exactly because there is a fair amount of good choice. When there is too much choice people often do not chose at all and move on. You still need to do your own research to decide what is best for you but you may find here some good starting points.
Here is what I use professionally on windows:
python 2.5.4
latest wxPython
XRC Resource Editor from the wxPython docs & demos for the grunt of the tedious GUI design
lxml or gnosis utils for xml
WingIDE Professional
Taking the headline question literally, the answer has to be IronPython. The 2.0 releases are equivalent to CPython 2.5, and the 2.6 release (currently at beta2) is intended to match CPython 2.6 (full 2.6 release some time in the next couple of months). With either you can use the state of the art in Windows GUI frameworks, i.e. WPF; and you get the whole .net XML support libraries (excepting Linq to XML, which relies on clever bits of C# that IronPython cannot yet emulate).
I've used NetBeans Python plug-in happily as an IDE for IronPython using WPF.
The answer would depend on what you want to do with Python. If you want to do web programming, Python is blessed with many web frameworks. The most popular ones are: Django, Pylons, and Turbogears. There's also Google App Engine, where you can deploy your Python webapp (based on GAE framework) to Google's infrastructure. If you want to do Desktop programming then there is PyQT and TkInter, or you can even try using Java Swing with Jython. And if you want to do Mobile app programming then there is Python for S60 which is backed by Nokia.
Python is interpreted language, so there is no compiler (although the interpreter also compiles your python module into bytecode). I would recommend using Python 2.6 as it has some syntax and libraries that is different compared to 2.5. You can also start learning Python 3.0 too.
There is several IDE that is good for Python. You don't have to get yourself attached into one editor/IDE because most of them are good ones. For the commercial ones there is WingIDE which is really focus on making IDE for Python and I would really recommend IntelliJ IDEA with Python plugin which is really nice if you often look at the libraries in your Python environment. For the free ones (as others have said) there is Komodo Edit or you can also try Netbeans with Python plugin.
As for the must-have libraries, this is depending on what you want to do. What kind of application you want to develop with Python. But I think every Python developer should consider PIL for imaging library. I also use simplejson quite often, because I prefer using JSON rather than XML. If you are using XML though, you can use lxml as it is really fast in parsing XML.