Recent changes to Filtering images

WikiPage Filtering images modified by Gert Wollny

Gert Wollny — Fri, 22 Feb 2013 16:26:32 -0000

--- v4
+++ v5
@@ -53,4 +53,4 @@
 1. Each file is filtered individually by using [mia-2dimagefilterstack](http://mia.sourceforge.net/userref/Secmia2dimagefilterstack.html) or [mia-3dimagefilterstack](http://mia.sourceforge.net/userref/Secmia3dimagefilterstack.html) respectively.
 2. A series of ND images is interpreted as a (N+1)D image. This is currently only implemented for series of 2D images with the program [mia-2dstackfilter](http://mia.sourceforge.net/userref/Secmia2dstackfilter.html).

-In both cases the image files must be numbered consecutively.
+In both cases the image files must be numbered consecutively (see [Interpreting file series]).

WikiPage Filtering images modified by Gert Wollny

Gert Wollny — Fri, 22 Feb 2013 16:07:03 -0000

--- v3
+++ v4
@@ -1,7 +1,13 @@
+[TOC]
+
+#Intro
+
 MIA supports the filtering of 2D images, 3D images, and series of 2D images interpreted as 3D images. 
 The syntax for filtering a single 2D or 3D images is, essentially, the same, only the program that needs to be called it either [mia-2dimagefilter](http://mia.sourceforge.net/userref/Secmia2dimagefilter.html) or [mia-3dimagefilter](http://mia.sourceforge.net/userref/Secmia3dimagefilter.html). The set of supported filters is different, you may consult the availabe [2D filters](http://mia.sourceforge.net/userref/SecPlugintype2dimagefilter.html) and [3d filters](http://mia.sourceforge.net/userref/SecPlugintype3dimagefilter.html).

 To understand the syntax of the filter specifications, you might first consult the [Guide to plugin specification]. 
+
+

 # Single image filter

WikiPage Filtering images modified by Gert Wollny

Gert Wollny — Fri, 22 Feb 2013 16:05:50 -0000

--- v2
+++ v3
@@ -33,12 +33,13 @@
     mia-2dimagefilter -i input.png -o output.png median:w=1 tee:file=temp.@ \
        binarize:min=100,max=200 close mask:input=temp.@

-Here, the input image is filtered by using a median filter, then the result is stored in the internal storage (this is indicated by the suffix **.@**), and after running a binarization and morphological closing, the so obtained mask is applied to the median filtered image loaded from the internal storage. Note however, if a plug.in loads a file (like the mask filter above), and this file has to be read from the disk, then it will be read immediately. a construct like 
+Here, the input image is filtered by using a median filter, then the result is stored in the internal storage (this is indicated by the suffix **.@**), and after running a binarization and morphological closing, the so obtained mask is applied to the median filtered image loaded from the internal storage. 
+
+Note however, it is **not** possible to save the file to disk and then load it in the same call to mia-2dimagefilter, i.e. in the following command, the mask filter will try to load *temp.png* right away, before the *tee* filter will store it.  

     :::bash 
     mia-2dimagefilter -i input.png -o output.png tee:file=temp.png mask:input=temp.png

-is **not** possible. 

 # Running filters on multiple files

@@ -47,6 +48,3 @@
 2. A series of ND images is interpreted as a (N+1)D image. This is currently only implemented for series of 2D images with the program [mia-2dstackfilter](http://mia.sourceforge.net/userref/Secmia2dstackfilter.html). 

 In both cases the image files must be numbered consecutively.
-
-   
-

WikiPage Filtering images modified by Gert Wollny

Gert Wollny — Fri, 22 Feb 2013 16:03:07 -0000

--- v1
+++ v2
@@ -3,7 +3,11 @@

 To understand the syntax of the filter specifications, you might first consult the [Guide to plugin specification]. 

+# Single image filter 
+
 In the following the examples for filtering a single images are given for 2D images. 
+
+## Running one filter 

 The simplest case, running only one filter, is done like: 

@@ -14,7 +18,35 @@

 Note, the output file format must support the pixel type of the filter output. Currently, this will only be checked when the file is actually saved (see also [tickets:#5]). 

+## Specifying a filter chain 

+Filters can be chained on the command line, e.g to run a median filter followed by a binarization run: 

+    :::bash 
+    mia-2dimagefilter -i input.png -o output.png median:w=1 binarize:min=100,max=200

+## Re-using output of earlier filters later in the pipeline

+It is also possible to store the result within the filter chain and reload it later, e.g.  
+
+    :::bash 
+    mia-2dimagefilter -i input.png -o output.png median:w=1 tee:file=temp.@ \
+       binarize:min=100,max=200 close mask:input=temp.@ 
+
+Here, the input image is filtered by using a median filter, then the result is stored in the internal storage (this is indicated by the suffix **.@**), and after running a binarization and morphological closing, the so obtained mask is applied to the median filtered image loaded from the internal storage. Note however, if a plug.in loads a file (like the mask filter above), and this file has to be read from the disk, then it will be read immediately. a construct like 
+
+    :::bash 
+    mia-2dimagefilter -i input.png -o output.png tee:file=temp.png mask:input=temp.png
+
+is **not** possible. 
+
+# Running filters on multiple files
+
+Two options are available to run filters on multiple files: 
+1. Each file is filtered individually by using [mia-2dimagefilterstack](http://mia.sourceforge.net/userref/Secmia2dimagefilterstack.html) or [mia-3dimagefilterstack](http://mia.sourceforge.net/userref/Secmia3dimagefilterstack.html) respectively.
+2. A series of ND images is interpreted as a (N+1)D image. This is currently only implemented for series of 2D images with the program [mia-2dstackfilter](http://mia.sourceforge.net/userref/Secmia2dstackfilter.html). 
+
+In both cases the image files must be numbered consecutively.
+
+   
+

WikiPage Filtering images modified by Gert Wollny

Gert Wollny — Fri, 22 Feb 2013 13:52:03 -0000

MIA supports the filtering of 2D images, 3D images, and series of 2D images interpreted as 3D images.
The syntax for filtering a single 2D or 3D images is, essentially, the same, only the program that needs to be called it either mia-2dimagefilter or mia-3dimagefilter. The set of supported filters is different, you may consult the availabe 2D filters and 3d filters.

To understand the syntax of the filter specifications, you might first consult the [Guide to plugin specification].

In the following the examples for filtering a single images are given for 2D images.

The simplest case, running only one filter, is done like:

mia-2dimagefilter -i input.png -o output.v convert:map=linear,repn=float,a=1.5,b=-20

Here, the input image is a PNG image, with 8 or 16 bit unsigned pixel values, and each pixel x is converted to a floating point valued pixel by applying a linear mapping according to 1.5 x - 20.

Note, the output file format must support the pixel type of the filter output. Currently, this will only be checked when the file is actually saved (see also [tickets:#5]).