Differences

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--- usage:batch_processing [2019/12/20 18:37] – [Editing the Double FAST script] pseudomoaner
+++ usage:batch_processing [2020/06/26 11:48] (current) – [Installing Double FAST] pseudomoaner
@@ Line 11: / Line 11: @@
 The .m files required to run Double FAST are included in the main distribution of FAST, available from the [[setup:installation|download page]]. Please ensure that you download option 1, the Matlab-based version of FAST.
-Double FAST requires both these files and the main FAST files have been added to your Matlab path.
+To run, double FAST requires that both these files and the main FAST files have been added to your Matlab path.
-===== Editing the Double FAST script =====
+===== Using Double FAST script =====
 To run Double FAST, you will need to perform two tasks:
   - Run FAST once on a single dataset, using the standard GUI. This generates files containing the settings used for each stage of the analysis.
-  - Directly edit the DoubleFAST.m script.
+  - Set up the DoubleFAST.m script.
-If you are not used to editing code directly, don't panic! All you need to do is tell the software where your datasets are, and what stages in the analysis you would like to perform. By leaving these stages in your hands, DoubleFAST allows you to flexibly adapt your analysis to many different dataset structures and analytical requirements.
+If you are not used to editing code directly, don't panic! All you need to do is tell the software where your datasets are, and what stages in the analysis you would like to perform. By leaving these stages in your hands, Double FAST allows you to flexibly adapt your analysis to many different dataset structures and analytical requirements.
 Once you have run FAST on your initial dataset, open the DoubleFAST.m script, available within the DoubleFast directory of your FAST installation. At the top of this script are the key variables that you need to define.
@@ Line 34: / Line 34: @@
 By default, this is set up assuming a root-branch structure as shown below:
-<diagram>
+{{ :usage:batchprocessfiles.png?nolink&200 |}}
-| RRR | | | | | | | | | |RRR{background-color:#ccffff}=Root
-| |!| | | | | | | | | |
-| |)|-|-| EE1 | | | | |EE1{background-color:#ccffcc}=Branch 1
-| |!| | | |!| | | | | |
-| |!| | | |`|-|-| IM1 |IM1{background-color:#ffcccc}=Dataset 1.czi
-| |!| | | | | | | | | |
-| |)|-|-| EE2 | | | | | |EE2{background-color:#ccffcc}=Branch 2
-| |!| | | | | | | | | |
-| |`|-|-| EE3 | | | | | |EE3{background-color:#ccffcc}=Branch 3
-</diagram>
 However, this can be flexibly adjusted according to your requirements. The only requirement is that **batchRoots** is defined as a cell array containing the paths to all of your datasets.
@@ Line 96: / Line 86: @@
 Once you have finished setting up Double FAST, you can run it simply by pressing the 'run' button at the top of the editor, or by pressing F5. Double FAST will now run through each of your datasets one by one, performing the specified operations on each one.
-===== Video demonstration =====