Recent changes to MIA and Python

MIA and Python modified by Gert Wollny

Gert Wollny — Fri, 09 Jan 2015 17:39:40 -0000

--- v4
+++ v5
@@ -3,9 +3,11 @@
 * [Installing the mia-python module] 
 * [Using mia from Python]

+In addition, as of version >= 2.2.3 experimental support for [NiPyPe](http://nipy.sourceforge.net/nipype/) is provided, i.e. for all MIA command line tools the according interfaces are provided.
+
+* [MIA and NiPyPe]

-

MIA and Python modified by Gert Wollny

Gert Wollny — Thu, 12 Dec 2013 15:08:47 -0000

--- v3
+++ v4
@@ -1,7 +1,7 @@
 Support from Python for certain MIA functionallity be achieved by installing the pymia Python wrapper.  Currently, the wrapper provides an interface for image filtering and image registration.

-## [Installing the mia-python module] 
-## [Using mia from Python] 
+* [Installing the mia-python module] 
+* [Using mia from Python]

MIA and Python modified by Gert Wollny

Gert Wollny — Thu, 12 Dec 2013 12:35:31 -0000

--- v2
+++ v3
@@ -1,48 +1,7 @@
 Support from Python for certain MIA functionallity be achieved by installing the pymia Python wrapper.  Currently, the wrapper provides an interface for image filtering and image registration.

 ## [Installing the mia-python module] 
-
-## Using mia from Python 
-
-The name of the module is simply *mia*, hence the is is loaded as 
-
-    :::python 
-    import mia
-
-The functionality currently exposed to Python  is limited to loading images, running 2D and 3D filters on gray scale image, and running image registration. Within Python the images are represented as numpy arrays, in fact no MIA objects are exposed directly to Python. 
-
-### Loading images
-
-MIA provides two functions for loading images, one for 2D images and one for 3D images. To load a 2D image from *filename*, run 
-
-    :::python 
-    image = mia.load_image2d(filename)
-
-Note, that all meta data is lost, only the raw pixel data is returned. Likewise for 3D data. To preserve metadat you might want to have a look into [nibabel](http://nipy.org/nibabel/).  
-
-
-### Filtering 
-
-The *mia.filter* function transparently distinguishes between 2D and 3D images. Filters are specified as strings like they are given on the [mia-2dimagefilter](http://mia.sourceforge.net/userref/Secmia2dimagefilter.html) and [mia-3dimagefilter](http://mia.sourceforge.net/userref/Secmia3dimagefilter.html) command line.
-
-Filters can be run one at a time, or as a pipeline. To run a single filter, e.g. a *median* filter of *half filter width* 3 on an image *input* run 
-
-    :::python 
-    filtered = mia.filter(input, "median:w=3")
-
-To run a filter chain, e.g. the above median, followed by a *mean-least-variance* filter with a filter width parameter 5, provide the filters as a list: 
-
-    :::python 
-    filtered = mia.filter(input, ["median:w=3", "mlv:w=5"])
-
-Note that the filters function converts the *input* to the internal MIA image format, creates and runs the filters, and then converts the images back to *numpy* arrays. Therefore, for performance reasons, it is best to run the filter chains instead of one filter at a time. 
-
-In order to avoid re-creating filters one can enable the filter cache by calling 
-
-    :::python 
-    mia.set_filter_plugin_cache(True)
-
-Then, filters with the same description are re-used  in subsequent calls to the *mia.filter* function. The filters in MIA normally work like functions, i.e. no state changes when it is called. *However, in some rare cases, when external data is loaded by means of a filter parameter, this may actually not work like expected (cf. [tickets:#134]).*
+## [Using mia from Python]

MIA and Python modified by Gert Wollny

Gert Wollny — Wed, 11 Dec 2013 12:50:43 -0000

--- v1
+++ v2
@@ -1,5 +1,52 @@
 Support from Python for certain MIA functionallity be achieved by installing the pymia Python wrapper.  Currently, the wrapper provides an interface for image filtering and image registration.

-[Installing the mia-python module] 
+## [Installing the mia-python module] 
+
+## Using mia from Python 
+
+The name of the module is simply *mia*, hence the is is loaded as 
+
+    :::python 
+    import mia
+
+The functionality currently exposed to Python  is limited to loading images, running 2D and 3D filters on gray scale image, and running image registration. Within Python the images are represented as numpy arrays, in fact no MIA objects are exposed directly to Python. 
+
+### Loading images
+
+MIA provides two functions for loading images, one for 2D images and one for 3D images. To load a 2D image from *filename*, run 
+
+    :::python 
+    image = mia.load_image2d(filename)
+
+Note, that all meta data is lost, only the raw pixel data is returned. Likewise for 3D data. To preserve metadat you might want to have a look into [nibabel](http://nipy.org/nibabel/).  

+### Filtering 
+
+The *mia.filter* function transparently distinguishes between 2D and 3D images. Filters are specified as strings like they are given on the [mia-2dimagefilter](http://mia.sourceforge.net/userref/Secmia2dimagefilter.html) and [mia-3dimagefilter](http://mia.sourceforge.net/userref/Secmia3dimagefilter.html) command line.
+
+Filters can be run one at a time, or as a pipeline. To run a single filter, e.g. a *median* filter of *half filter width* 3 on an image *input* run 
+
+    :::python 
+    filtered = mia.filter(input, "median:w=3")
+
+To run a filter chain, e.g. the above median, followed by a *mean-least-variance* filter with a filter width parameter 5, provide the filters as a list: 
+
+    :::python 
+    filtered = mia.filter(input, ["median:w=3", "mlv:w=5"])
+
+Note that the filters function converts the *input* to the internal MIA image format, creates and runs the filters, and then converts the images back to *numpy* arrays. Therefore, for performance reasons, it is best to run the filter chains instead of one filter at a time. 
+
+In order to avoid re-creating filters one can enable the filter cache by calling 
+
+    :::python 
+    mia.set_filter_plugin_cache(True)
+
+Then, filters with the same description are re-used  in subsequent calls to the *mia.filter* function. The filters in MIA normally work like functions, i.e. no state changes when it is called. *However, in some rare cases, when external data is loaded by means of a filter parameter, this may actually not work like expected (cf. [tickets:#134]).*
+
+
+
+
+
+
+

MIA and Python modified by Gert Wollny

Gert Wollny — Wed, 11 Dec 2013 12:13:33 -0000

Support from Python for certain MIA functionallity be achieved by installing the pymia Python wrapper. Currently, the wrapper provides an interface for image filtering and image registration.

[Installing the mia-python module]