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Batch Processing

435 bytes added, 07:13, 25 June 2018
Start work on documenting SciJava batch processor - more updates and new screenshots to follow
= Overview =
A fundamental benefit to creating [[Scripting|scripts and macros]] in [[ImageJ]] is the ability to **reuse ** their functionality **on more than one image**. Although this can be done manually, there are multiple ways to easily automate this batch processing.
= General workflow =
# Create a basic macro /script which operates on the active imageor on a single file.
#* The [[Introduction into Macro Programming#The_recorder|macro recorder]] is an excellent way to generate macro code.
#* The [[Introduction into Macro Programming]] explains the principles of macro writing.
#* See below for details.
= Easy option Option 1 - {{bc | Process | Batch | Macro...}} =
The fastest way to start batch conversion is via the [http://imagej.net/docs/guide/146-29.html#toc-Subsubsection-29.12.3 {{bc | Process | Batch | Macro...}}] command. This will open a dialog (below) that will allow you to specify an input and output directory. You can select an output file format, and then use the <code>Add Macro Code</code> drop-down to generate a macro with the desired functionality.
[[Image:BatchProcess.png|center]]
= Flexible option Option 2 - Script Template =
Open the [[Using_the_Script_Editor|script editor]], select {{bc | Templates | ImageJ 1.x | Batch | Process Folder (IJ1 Macro)}}. This will generate the following boilerplate:
Lines 26 and 27 can now be edited, replaced with the functional macro code you would like to apply to all images of a given type in a folder. Furthermore you can now modify the batch processing logic itself, for example if you need to customize what (if any) output information is saved.
 
= Option 3 - Batch Processing with Script Parameters =
 
{{Notice|This section is currently being expanded to document the current state of the [https://github.com/scijava/batch-processor/ SciJava Batch Processor]. The Batch Processor is a new addition to the SciJava/ImageJ framework. If you encounter any issues, please report/ask on the [[forum]].}}
 
= See also =
Bureaucrat, emailconfirmed, incoming, administrator, uploaders
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