Batch Manager¶
Batch process computationally intensive tasks.
See also
Video Tutorial¶
This tutorial shows how to create a New Project, open images in the Viewer, use the Stimulus Mapping module and perform Caiman motion correction
This is currently used for Caiman Motion Correction, CNMF, CNMF 3D and CNMFE.
The Batch Manager can be accessed in the viewer through Modules -> Batch Manager. If you don’t have a batch open you will be prompted with a dialog to open a batch or to select a location for a new batch.
Warning
The full path to the batch directory must not contain spaces or special characters, only a-z, A-Z, 0-9 and underscores.
The Batch Manager processes the batch items in external processes, allowing you to add batch items when that batch is being processed.
Layout¶
Window title: Name of batch directory
Top: Parent directory of batch directory
Top left: list of batch items and some controls.
Colors
Description
Green
Finished without exceptions
Red
Did not finish, click on the item to see the exceptions in the bottom right information area
Yellow
Currently being processed
Orange
Item aborted by user
Blue
Output data for this item are being moved from the work dir to the batch dir.
Button
Description
Start
Process the batch from the first item.
Start at selection
Process the batch starting from the item that is currently selected in the list.
Delete selection
Delete the item that is currently being selected along with the associated data in the batch dir.
Export shell scripts
Export bash scripts so that the batch items can be run on a computing cluster
Abort current item
Abort the current batch item and move on to the next item
Abort batch
Abort the current item and stop processing the batch
New batch
Create a new batch
Open batch
Open a batch
View Input
Open the input work environment, in the viewer, for the currently selected item
Use work dir: Check this box to use the work dir that has been set in the System Configuration. This feature is only available on Linux & Mac OSX.
Top right: Standard out from the external processes that are processing the batch items.
Bottom left: Parameters for the selected batch item. The first line is the UUID of the batch item.
Bottom right: Output information area for the currently selected item.
Scheduling¶
You can schedule a batch to run at a later time using the following bash script. Doesn’t work for a snap installation yet.
Usage:
Usage: mesmerize-scheduler -b <batch> -i <start item> -t <start time>
-b full batch path in quotes, no spaces
-i uuid of the batch item to start from, no quotes
-t time at which to start the batch, no quotes
examples of how to specify time:
23:00 7:30Feb30
use 24hr time and no spaces
Full usage example:
mesmerize-scheduler -b "/share/data/temp/kushal/pc2_batch" -i a80d1923-e490-4eb3-ba4f-7e651d4cf938 -t 2:00