Appion

h1. How to add an AppionLoop GUI page

See feature #2634 for more information on the code that supports these directions.

# *Add a wiki page to the [[Appion_Processing|Appion User Guide]] describing how to use this feature*

# *Add a publication reference for the package you are using*

 

## Edit /myami/myamiweb/processing/inc/publicationList.inc to include an entry for any references you need to add to your launch page.

 

# *Create a new form class for your feature*

 

** Create a new file in myami/myamiweb/processing/inc/forms. Call it coolFeatureForm.inc.

** Create a class in this file that extends the BasicLoopForm class like this:

<pre>

require_once "basicLoopForm.inc";

class AutoMaskForm extends BasicLoopForm

{

...

</pre>

** Examples are available in autoMaskForm.inc and makeDDstackForm.inc

 

# *Set parameters needed by the BasicLoopForm class in the constructor*

 

<pre>

//------ Set Parameters for the parent class, BasicLoopForm (general Appion params) -----//

// Set the publications to be references on the web pages

$pubList = array('appion'); // The publication reference key that you added to publicationList.inc

$this->setPublications( $pubList );

// Job Type should be unique to Appion. Used in the database to determine the type of job being run.

$this->setJobType( 'maskmaker' ); 

// The name of the folder that all runs of this job type will be stored in.

$this->setOutputDirectory( 'mask' );  

// A portion of the run name that will be common (by default) to all runs of this job type. A unique number is appended to individual run names.

$this->setBaseRunName( 'maskrun' ); 

// The title on the web page for this feature.

$this->setTitle( 'Auto Masking Launcher' ); 

// The Heading on the web page for this feature.

$this->setHeading( 'Automated Masking with EM Hole Finder' ); 

// The name of the python executable file that this GUI corresponds to. It should be based on the AppionLoop class and located in the myami/appion/bin folder.

$this->setExeFile( 'automasker.py' );

// A URL corresponding to a wiki page in the Appion User Guide with information on running this feature.  

$this->setGuideURL( "http://emg.nysbc.org/projects/appion/wiki/Appion_Processing" );

// True to activate "test single image" field of Appion Loop parameters.

$this->setTestable( True ); 

// The output directory will be created in the Appion run directory rather than Leginon.

$this->setUseLegOutDir( False );

// Flag to hide the description field of the run parameters. True enables the description field.

$this->setShowDesc( False ); 

</pre>

 

# *Take an inventory of the parameters that are specific to your new feature and are passed into your python executable file*

** Make a list of all the parameters that your GUI needs to expose to the user. For each parameter decide on:

### *id* I might also call it a parameter key or name. This should match the name of the parameter as it appears on the command line. So a flag in a command that looks like "--mycoolflag" should be named "mycoolflag" in this class.

### *default value*

### *label* This is the text that is actually shown to the user in the GUI next to the GUI element associated with it (check box, selection, text, etc)

### *help text* A longer description of the parameter and tips for what a user should set it to.

### *validations* Decide what should be considered valid values for this parameter. Is it required? Does it have to be a number or greater than zero? 

 

# *Add your parameters help text to myami/myamiweb/processing/js/help.js*

 

** Open myami/myamiweb/processing/js/help.js

** Add a new namespace for your form, you can copy the 'simple' section. Don't forget any commas.

** add a help string for each of the parameter keys in your form

 

# *Add your parameters to your form class*

 

** Back in the class that you created to extend BasicLoopForm, add your parameters.

** First set the help section using the namespace that you just added to help.js.

<pre>

// Get an instance of the form parameters associated with this class

$params = $this->getFormParams();

// The help section corresponds to the array key for these parameters found in help.js for popup help.

$params->setHelpSection( "em_hole_finder" );

</pre>

** Add a line for each of the parameters in your form

<pre>

$params->addParam( "downsample", $downsample, "Downsample" );

$params->addParam( "compsizethresh", $compsizethresh, "Component size thresholding" );

</pre>