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stacker:docs:howtouseit [2014/03/03 22:06]
rjlittlefield [Saving Work In A “Project”]
stacker:docs:howtouseit [2020/04/06 22:19]
rjlittlefield [Batch Processing] Revise for new dialog layout
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 In the following example, the user has defined one batch, consisting of 7 folders of source images. ​ A new project will be constructed for each folder of source images, PMax and DMap will be run within each project, the projects will be saved in a designated location, and output images will be both retained within the projects and written to external files.  ​ In the following example, the user has defined one batch, consisting of 7 folders of source images. ​ A new project will be constructed for each folder of source images, PMax and DMap will be run within each project, the projects will be saved in a designated location, and output images will be both retained within the projects and written to external files.  ​
  
-{{:​stacker:​docs:​howtouseit:​image010.jpg}}+{{:​stacker:​docs:​howtouseit:​image010v2.jpg}}
  
-For batch usage, ​the appropriate contrast threshold for DMap is best determined by running a typical stack interactively. ​ Then you can set Options > Preferences ​to apply that same threshold unattended to all folders in the batch.+Pressing ​the "Save Batch to Queue" button causes ​the bottom panel of the Batch Queue dialog to update so that it looks like this:
  
-{{:​stacker:​docs:​howtouseit:​image011.jpg}}+{{:​stacker:​docs:​howtouseit:​image010p5v2.jpg}} 
 + 
 +At this point, pressing the "Run All Batches"​ button will cause the indicated tasks to be run against the indicated folders or projects. ​ (Note the ordering, "​tasks:​ folders"​ .) 
 + 
 +In the Batch Queue dialog, the “Add Current Project” button has two different uses, as follows:  
 + 
 +  - If the currently open project has been saved at some point and thus has a well-defined name, then that name is simply recorded. ​ This allows a sequence of batch operations to be constructed incrementally,​ by opening a project and specifying tasks to be done with it, then opening a different project, specifying tasks for that project, and so on.  In this case, the batch queue entries will look something like this: \\ {{:​stacker:​docs:​howtouseit:​image012v2.jpg}} \\ \\  
 +  - If the currently open project is new and has never been saved, then pressing Add Current Project records the target as “%CurrentProject%”. Batch operations defined in this way can be executed on multiple different projects at various times. ​ This feature is particularly useful in combination with Save Batch Script and Load Batch Script. ​ In this case, the batch queue entries will look like this: \\ {{:​stacker:​docs:​howtouseit:​image013v2.jpg}}
  
 Note that each task may have different options (preferences) set for it.  The task records whatever Options > Preferences are in effect at the time the Add button is pressed.  ​ Note that each task may have different options (preferences) set for it.  The task records whatever Options > Preferences are in effect at the time the Add button is pressed.  ​
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 The options for a task can be confirmed and/or changed by highlighting the task and pressing Change Options. ​ Options can also be displayed in a textual form by highlighting a task and pressing Details. The options for a task can be confirmed and/or changed by highlighting the task and pressing Change Options. ​ Options can also be displayed in a textual form by highlighting a task and pressing Details.
  
-In the Batch Queue dialog, the “Add Current Project” button has two different uses, as follows: ​+For batch usage, the appropriate contrast threshold for DMap is best determined by running a typical stack interactively. ​ Then you can set Options > Preferences to apply that same threshold unattended to all folders in the batch.
  
-  - If the currently open project has been saved at some point and thus has a well-defined name, then that name is simply recorded. ​ This allows a sequence of batch operations to be constructed incrementally,​ by opening a project and specifying tasks to be done with it, then opening a different project, specifying tasks for that project, and so on.  In this case, the batch queue entries will look something like this: \\ {{:​stacker:​docs:​howtouseit:​image012.jpg}} ​\\ \\  +{{:​stacker:​docs:​howtouseit:​image011v2.jpg}}
-  - If the currently open project is new and has never been saved, then pressing Add Current Project records the target as “%CurrentProject%”. Batch operations defined in this way can be executed on multiple different projects at various times. ​ This feature is particularly useful in combination with Save Batch Script and Load Batch Script. ​ In this case, the batch queue entries will look like this: \\ {{:​stacker:​docs:​howtouseit:​image013.jpg}} +
-  +
-Similarly, the setting for disposition of output images to “Save in source folder” does different things depending on the target of the batch operation, as follows:+
  
-  * If the target is a folder of source images, then output images will go into that folder.  ​ 
-  * If the target is a new project and “New projects are temporary (do not save)”, then output images will go in the folder of the first source image. ​ 
-  * If the target is a project that has already been saved or will be saved as a result of “Disposition of new projects”,​ then output images will go in the root of the project folder. ​ 
  
 The batch capability can also be used to provide an API (Application Programming Interface) that allows Zerene Stacker to be controlled by another application such as [[http://​rsbweb.nih.gov/​ij/​|ImageJ]] or a command script. ​ For details, see, **[[:​stacker:​docs:​batchapi|Batch API: Running Zerene Stacker From Another Application]]**. The batch capability can also be used to provide an API (Application Programming Interface) that allows Zerene Stacker to be controlled by another application such as [[http://​rsbweb.nih.gov/​ij/​|ImageJ]] or a command script. ​ For details, see, **[[:​stacker:​docs:​batchapi|Batch API: Running Zerene Stacker From Another Application]]**.
stacker/docs/howtouseit.txt · Last modified: 2023/12/10 05:10 by rjlittlefield
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