Workflows
Contents
Workflows¶
nextPYP supports the use of pre-defined sequences of blocks, called Workflows.
The program ships with workflows for the Single-particle tutorial, the Tomography tutorial and the Classification tutorial.
1. Import a workflow¶
Go the Dashboard, create a new or open an existing project, then click on Import Workflow
Choose a workflow from the list and click Import
A form will appear asking for any required parameters. This typically includes the location of the raw data (and associated files) and Computing resources to use
Click Save, Run, and Start Run for N blocks (where N is the number of blocks in the workflow)
Inspect the results of the Workflow by navigating into each block
2. Defining custom workflows¶
Workflows are defined using .toml files. Here is an example:
name = "Test workflow"
description = """\
Here goes the workflow description.
"""
# comments here are useful to share info with other workflow authors looking at this file
[blocks.rawdata]
blockId = "sp-rawdata"
name = "Raw Data"
[blocks.rawdata.args]
data_path = { ask = true }
scope_pixel = 0.66
scope_voltage = 300
[blocks.preprocessing]
blockId = "sp-preprocessing"
name = "Pre-processing"
parent = "rawdata"
[blocks.preprocessing.args]
detect_rad = 75
detect_method = "all"
slurm_tasks = 7
slurm_memory = 14
The location of the .toml files must be specified in nextPYP’s configuration file, using the entry workflowDirs:
workflowDirs = ["/path/to/workflows"]