Module: CreateBatchFiles

Create Batch Files produces files that allow individual batches of images to be processed separately on a cluster of computers

This module creates files that can be submitted in parallel to a cluster for faster processing. It should be placed at the end of an image processing pipeline.

If your computer mounts the file system differently than the cluster computers, CreateBatchFiles can replace the necessary parts of the paths to the image and output files. For instance, a Windows machine might access files images by mounting the file system using a drive letter, like this:

Z:\imaging_analysis

and the cluster computers access the same file system like this:

/imaging/analysis

In this case, the local root path is Z:\imaging_analysis and the cluster root path is /imaging/analysis.

Settings:

Store batch files in default output folder?

Do you want to store the batch files in the default output folder? Check this box to store batch files in the Default Output folder. Uncheck the box to enter the path to the folder that will be used to store these files.

Output folder path

What is the path to the output folder?

Are the cluster computers running Windows?

Check this box if the cluster computers are running one of the Microsoft Windows operating systems. If you check this box, CreateBatchFiles will modify all paths to use the Windows file separator (backslash \). If you leave the box unchecked, CreateBatchFiles will modify all paths to use the Unix or Macintosh file separator (slash,/).

Local root path

What is the path to files on this computer? This is the root path on the local machine (i.e., the computer setting up the batch files). If CreateBatchFiles finds any pathname that matches the local root path at the begining, it will replace the start with the cluster root path.

For example, if you have mapped the remote cluster machine like this:

Z:\your_data\images (on a Windows machine, for instance)

and the cluster machine sees the same folder like this:

/server_name/your_name/your_data/images

you would enter Z: here and /server_name/your_name/ for the cluster path in the next setting.

Cluster root path

What is the path to files on the cluster? This is the cluster root path, i.e., how the cluster machine sees the top-most folder where your input/output files are stored.

For example, if you have mapped the remote cluster machine like this:

Z:\your_data\images (on a Windows machine, for instance)

and the cluster machine sees the same folder like this:

/server_name/your_name/your_data/images

you would enter Z: in the previous setting for the local machine path and /server_name/your_name/ here.