===== Overview of modular functions in EMAN2 =====

EMAN2's modular function interface is one of its most powerful features, permitting a wide range of different algorithms
to be selected through a single common interface. It also means new algorithms can be added to the system without making
any changes to the end-user programs. For example, if you have an idea for a new alignment algorithm, (and you know a little
C++), you can easily inset the algorithm in EMAN2's core library, and it will immediately become available as an option
in any program that uses alignment algorithms, including the graphical interface !

==== From the command-line ====

Many of the command-line programs accept modular functions as options. For example, you will find '--process' in many different
programs, including //e2proc2d.py// and //e2proc3d.py//. Similarly, '--align' and '--cmp' or '--aligncmp' are found many places.
'--process' requires the name of a 'processor' and its parameters. '--align' takes the name of an 'aligner' and its parameters, etc.

To find documentation for all currently available modular classes:
<code>
$ e2help.py
Help is available on the following topics:
processors, cmps, aligners, averagers, projectors, reconstructors, analyzers, symmetries, orientgens
</code> 
These are the available categories of functions.

To get a list of all of the functions in a category, for example:
<code>
$ e2help.py cmps

Available comparitors:
ccc         :  mask(EMDATA)   negative(INT)   
ccc.tomo    :  ccf(EMDATA)   norm(BOOL)   normalize(EMDATA)   searchx(INT)   searchy(INT)   searchz(INT)   
dot         :  mask(EMDATA)   negative(INT)   normalize(INT)   
frc         :  ampweight(INT)   maxres(FLOAT)   minres(FLOAT)   nweight(INT)   snrweight(INT)   sweight(INT)   zeromask(INT)   
lod         :  mask(EMDATA)   negative(INT)   normalize(INT)   
optvariance :  debug(INT)   invert(INT)   keepzero(INT)   matchamp(INT)   matchfilt(INT)   radweight(INT)   
phase       :  ampweight(INT)   maxres(FLOAT)   minres(FLOAT)   snrfn(INT)   snrweight(INT)   zeromask(INT)   
quadmindot  :  negative(INT)   normalize(INT)   
sqeuclidean :  mask(EMDATA)   normto(INT)   zeromask(INT)   
</code>
Which lists the name, parameters, and the type of each parameter for each function.

For even more details:
<code>
$ e2help.py processors -v 2
</code>

There can be quite a few functions in each category, so you can optionally add a word to act as a filter:
<code>
$ e2help.py processors filter
</code>

Using modular functions from the command-line is very simple. The basic specification is:
<code>
--process=<processor_name>:<parm>=<value>:<parm>=<value>...

for example

--process=filter.lowpass.gauss:cutoff_abs=.1
--cmp=ccc
--aligncmp=frc:ampweight=1:snrweight=1
</code>

==== In the GUI ====

That said, there are a LOT of algorithms, particularly in the 'processor' category. For that reason, we also provide a graphical
tool called [[EMAN2:Programs/e2filtertool|e2filtertool.py]]. That program will allow you to construct chains of processors through a graphical interface then
see the command-line that would be required to produce that exact effect.

The workflow interface also provides graphical mechanisms for specifying the required modular functions. Generally this is done via a pop-up menu for the
function name, followed by a text box where parameters in the <parm>=<value>:<parm>=<value> can be specified.

==== From Python ====
For python users, the modular functions are used very similarly to the command-line. The function name is passed as a string, and the parameters are passed
as a dictionary. For example:

<code>
image=test_image()
image2=test_image()

image.process("filter.lowpass.gauss",{"cutoff_abs":.1})

sim=image.cmp("ccc",image2)
sim=image.cmp("phase",image2,{"maxres":10,"apix":2})
</code>