Use Workflows to Automate Tasks

You can use the workflow features in OMNIC Paradigm software to automate important procedures and frequent tasks. A workflow is a series of software operations that can be initiated with the click of a button. The software operations are represented by tiles, which you drag and drop onto the workflow canvas in OMNIC Paradigm software. You can specify settings for data collection, provide instructions for operators, and define data processing, reporting, and archiving in advance. Once a workflow has been created, operators can use it repeatedly to complete the steps the same way every time.

This article provides an overview of these basic workflow features and tools:

• Workflow pane
• Run Workflow window
• Workflow editor

Workflow Pane

The workflow pane is always available at the bottom of the OMNIC Paradigm dashboard. Use this space to preview and play workflows you’ve created, and to open the workflow editor to edit or create a new workflow.

Figure 1. Workflow Pane on the OMNIC Paradigm Dashboard

Table 1. Work with existing workflows from the workflow pane

Run Workflow Window

Use the Run Workflow window to test or run a workflow. To open the Run Workflow window, right-click a workflow and select Run.

Figure 2. Right-click a Workflow and select Run

1. Selected workflow (double-click to open and run this workflow)

From the Play Workflow window, use the arrow button to move to the next task in the workflow. The workflow will play exactly as it has been designed, with tasks and operator messages displayed as indicated by the workflow.

Figure 3. Run Workflow Window

1. Toolbar

To stop the workflow and return to the dashboard, click the Stop button in the Play Workflow window. (If the workflow doesn’t have a Stop button, click the Dashboard button on the toolbar to stop the workflow.)

The workflow editor contains all the tools for creating workflows, including the workflow menu, toolbar, tile selection bar, and canvas. To open the workflow editor, right-click a workflow name on the dashboard and choose Edit from the shortcut menu.

You can also open the workflow editor from the OMNIC Paradigm main window by choosing:
File (menu) > Workflows > Create Workflow

The workflow canvas is where you select and set up the tasks you want the workflow to perform and join tasks together to create the workflow. The workflow editor opens with the mandatory “Workflow Start” and “Workflow End” tiles displayed on the canvas. Available settings for each tile in the current workflow are in the expandable sections below the canvas. Tools for scrolling, zooming and resetting the canvas view are at the right. A handy toolbar is above the canvas.

Figure 4. Workflow Editor

Each task is represented by a colorful tile in the tile selection bar. Here are some commonly used examples:

Tools for creating, opening, and exporting workflows are located in the Workflow submenu (available from the OMNIC Paradigm File menu). Example workflows, available here, are a good place to start, or you can create a workflow from a spectrum’s history. See “Create and Run Your First Workflow” for details.

Tiles can be added, moved, copied and deleted to create the desired workflow. For more information, see the article titled “Edit a Workflow.”

This article explains a simple way to create workflows in OMNIC Paradigm software. For basic information about workflows and brief descriptions of the workflow features and editing tools, see the article titled “About Workflows” in the OMNIC Paradigm online help.

There are several ways to create workflows. Some approaches may work better than the others, depending on the steps you are trying to automate and how you want to start. For example, you can create a new workflow by:

• building a workflow from scratch
• editing a workflow that someone gave you
• duplicating an example workflow provided with the software
• performing the measurement tasks you want to automate and letting the software create the workflow from the spectrum’s history information

This article shows how the software can create a workflow automatically based on the history of an acquired spectrum. It also demonstrates how to:

• run a workflow from the workflow editor or dashboard
• identify workflow generated spectra
• edit a workflow by adding tiles, and
• fix a common workflow error

The last section provides useful tips for creating and editing workflows.

Create a Workflow

To create a new workflow from an acquired spectrum

1. From the OMNIC Paradigm dashboard, acquire a spectrum of a sample material. It doesn’t matter what kind of material or sampling technique you use. If the software requires a new background measurement, go ahead and do that first. When the sample measurement is completed, the sample spectrum is displayed in the spectral view.

Here is our example spectrum (plastic bag measured with an Attenuated Total Reflectance, or ATR, accessory) displayed in the spectral view:

2. Make sure the spectrum is selected in the spectral pane and then perform any processing or analysis steps you like (for example, subtraction, baseline correction, correlation search, etc.).

Here is our example spectrum after applying Advanced ATR Correction and Automatic Baseline Correction and then performing a Correlation Search.

3. Give your spectrum a descriptive name (the software will use this name for the created workflow as the default, or you can give the workflow a new name).

• Right click the image of the original spectrum in the results panel and choose Rename Spectrum.
• Replace the default name with a descriptive name for your workflow and choose OK.
  Here is our renamed example spectrum.

   

4. Once you have completed your processing and analysis steps, click the History button in the results panel.

The history panel shows all the tasks performed on the selected spectrum in the order in which they were performed. Here is the history information for our example spectrum.

5. At the bottom of the history panel, click Create Workflow.

The software creates a workflow that includes all of the steps you just performed. The workflow is displayed in the workflow editor. Each performed task is represented by a colorful tile. Depending on which steps you performed, your workflow may look different from our example below:

6. To save your new workflow, click the Save button on the toolbar.

7. To run the workflow, click the Run button on the toolbar.

The workflow performs the same tasks you completed manually in exactly the same sequence. In our case, we measured a spectrum, performed an Advanced ATR Correction, corrected the spectral baseline, and performed a correlation search.

When the workflow is done, the software returns to the Workflow Editor.

8. Click the Dashboard button on the toolbar to see your newly created workflow in the Workflows list.

The workflow is named automatically based on the name of the spectrum used to create it. Here is our newly created example workflow in the Workflows list and a preview of the workflow in the preview box.

9. The workflow-generated spectra appear in the Measurements list.

Our example workflow created four spectra, the measured background spectrum, the measured sample spectrum, the ATR corrected sample spectrum, and the ATR and baseline corrected sample spectrum with the search results. The workflow-generated spectra are named with the Tile Name properties of their associated workflow tiles.

Add Tiles to a Workflow

This section demonstrates how to use the workflow editing tools to add tiles to your auto-generated workflows.

1. From the dashboard, right-click the workflow name and choose Edit.

The workflow opens in the workflow editor.

2. Add a Tag Spectrum tile to the workflow.
Workflow-generated spectra are saved in the OMNIC Paradigm database along with any data acquired manually. Let’s tag the workflow spectra to associate them with our workflow. This makes it easy to open and view them later.

• In the workflow editor, drag the Tag Measurement tile from the selection bar to the canvas so that your mouse cursor hovers over the grey arrow between the Measurement and ATR Correction tiles.
  The grey arrow changes to a plus sign.

b. Release the mouse button.
The tile is added to that location in the workflow and its settings box is opened below the canvas.

c. In the Tag Settings enter a base name for your workflow-generated spectra, such as “ATR Search Spectra”, make sure Select Spectrum is set to your measured spectrum (“Measurement - Sample”), and choose OK.

The Tag Measurement tile will automatically add the “ATR Search Spectra” tag to each spectrum generated by the workflow. We’ll explain how to search for those spectra later.

Now let’s explore what happens when we add a tile that flags an error.

3. Add a Report Template tile to the workflow.

• In the workflow editor, use the mouse to hover over the grey arrow between the Search and End tiles (arrow changes to a plus (+) sign) and then click the mouse button. The software opens the Add Tile box. (This is another easy way to add tiles.)

b. In the Add Tile box, select the Template Report and choose OK.

The tile is added to that location in the workflow and its settings box is opened below the canvas.

Notice that the Report Template tile has a red border, which indicates the workflow won’t run successfully right now. If we view the Report Template settings, the boxes are all blank.

To fix the problem, we need to specify a template for the report and which results to include.

c. Set Template Type to your preferred report style (we are using the Search Results template), set Search Results To Display to your workflow’s output (“Search Result” in our example) and choose OK.

Notice that the red border is no longer there.

4. To save the updated workflow, click the Save button on the toolbar.

5.To run the workflow, click the Run button on the toolbar.
The workflow runs through all the steps and then displays the final report.

Click the arrow button to end the workflow.

6. Click the Dashboard button on the toolbar to return to the dashboard.

7. If you select the workflow in the Workflows list, the preview has been updated.

8. If you enter your tag in the Search box, the software shows you the workflow-generated spectra in the Measurements list.

To view the spectra in the spectral pane, use Shift + Click to select all four in the Measurements list, then right-click and choose “Open Selected Measurements.”

9. To see the workflow-generated report, click this arrow button and select “Reports.”

Tips on Creating Workflows

Before you head off to create more workflows, read through these answers to common questions about workflows and tips for solving any problems that may occur.

• Is the order in which the tiles appear in the workflow important? Yes, the order of the tiles is important. Each workflow tile builds on the previous tiles, and all the tiles are interconnected by their input requirements and their output results. For example, if you add a Measure tile, it creates an output result (a spectrum), which can only be accessed by tiles positioned after the Measure tile in the workflow. If you want to correct the baseline of an acquired spectrum, you would need to add a Baseline tile after the Measure tile, and then set the Baseline input to the Measurement output (i.e., the spectrum). Otherwise, the Baseline tile will have a red border, indicating it contains options that must be set before the workflow will run. If you see a tile that has a red border, use the mouse to hover over that tile for help finding the source of the problem.
• Do I need to add a background measurement to my workflow? Not unless you want the workflow to perform an operation only on the background spectrum. If you only need a background spectrum in order to process your measured sample data, then you just need to add a Measure tile to the workflow and use the Measure tile settings to define the background measurement.
• Can I change the titles of the workflow tiles? Each workflow tile has a setting that specifies the tile name. (Double-click the tile in the workflow editor to open its associated settings.) The Tile Name setting can be used to add detail to your workflow. This can help the workflow developer keep things organized, especially when creating workflows that contain multiple paths or loops, or multiple tiles of the same type (several Measure tiles, for example, in the same workflow).
  The tile names may also be used to name output files when the workflow is run. Here are some examples:
  • – Measure tile. This tile acquires background and sample spectra. When the workflow is run, the sample spectrum is saved with the tile name of its associated Measure tile.
  • – ATR Correction Tile, Process Tile, etc.. Tiles that operate on acquired spectra generate output spectra that are saved along with the final sample spectrum when the workflow is run. Each interim “processed” spectrum is saved with the tile name of the workflow tile that generated it.
  • – Report tile. This tile creates a sample report. When the workflow is run, the report is saved with the tile name of its associated Report tile.
• Should every workflow have an Export tile? The answer to this question is “no.” Any spectra and reports generated from a workflow are saved automatically in the OMNIC Paradigm database, along with all the other spectra and reports that are created manually with the spectrometer (that is, not from a workflow). If you want to save your workflow-generated spectra and reports as files that can be archived or opened elsewhere (from your OMNIC Paradigm workstation software, for example), use an Export tile to create those files automatically.
• Why doesn’t my workflow run? Before you run a newly created workflow, ensure there are no tiles with a red border. Here is an example:

The workflow will not run to completion if it contains a tile with a red border.
If your workflow has a red bordered tile, use the mouse to hover over the tile for tips on how to solve the problem. Typically, the red border indicates the tile contains required options that have not been set. However, it can also mean the tile is “illegal.” For example, if you place a Processing tile before a Measure tile in a workflow, the Processing tile will have a red border and the workflow will contain an unresolvable error because there is no output spectrum to baseline correct.

Workflow tiles are icons that represent the tasks a workflow can perform. Each tile has settings that define what the tile does when the workflow runs. To see a tile’s settings, add the tile to your workflow on the workflow canvas, then double-click the tile.

This reference of workflow tiles is organized alphabetically. Each tile description includes a description of available settings.

Archive

Send data and reports to a user specified location. This location can be on your local system or on a network or flash drive for alternate storage.

ATR Correction

Corrects ATR spectra for the effects of variation in the depth of penetration and the shifting infrared absorption bands that occur with the ATR technique.

Decision

With a Decision tile, you can control the flow of the workflow based on criteria that you specify. For example, you can provide two separate paths based on whether or not a correlation search result had a match value above a specified threshold.

Delay

Pauses the workflow for the indicated amount of time before proceeding.

Embedded Workflow

Use the Embedded Workflow tile to include one workflow in another.

Using the Embedded Workflow tile, you can create one workflow for a subset of common tiles or processes and then reuse that workflow in many other workflows. If you want to change a setting or update a tile in the embedded workflow, you can make the change once rather than having to manually edit the settings in every workflow.

You can update any embedded workflows in the Workflow Editor. Open the workflow that includes the Embedded Workflow tile, right-click an empty space on the canvas and click Update Embedded Workflow(s). Then select any embedded workflows that you want to update.

It is recommended that you always keep embedded workflows up to date to ensure the workflows behave as expected.

End

Every workflow has at least one End tile. If your workflow includes Decision or Selection tiles, there may be more than one possible ending.

Equation

The Equation tile is an advanced tile for evaluating complex equations. You can include variables from other tiles in the equation and use built-in functions for common problems, such as calculating an average or rounding a value. You can also use functions to find peak height or peak location or to perform other operations on a spectrum.

The tables below list valid operators and functions.

Arithmetic Operations

Comparison Operations

Logical Operations

Functions 

Export

Send data and reports to a user specified location. This location can be on your local system or on a network or flash drive for alternate storage.

Instruction

Use the Instruction tile to provide additional instructions to the workflow operator. The Instruction tile can also include entry fields for the operator to enter text or numeric data. These entries can later be used in the workflow. For instance, text entered by the operator can be added to a custom report.

Load Spectrum

Load a SPA file to use during the workflow. You can browse to a file location on the instrument computer or on a flash drive or network location.

This can be useful for importing a saved spectrum to use as a reference. For instance, you may want to import a reference spectrum to use in a subtraction operation.

Measure

Use the measure tile to measure the background and a sample and to set the measurement settings. Spectra and reports created during the workflow are saved to the database and can be archived with the Archive tile.

Peak Analysis

Find peak locations or analyze the Peak Height or the Peak Ratio of a spectrum.

Processing

The Processing tile includes several tools for processing spectral data, including subtraction, normalization, correlation, basic spectral math, and baseline correction.

Repeat

Loop a portion of the workflow to repeat steps.

Report

Create a custom report that can be stored, archived, or printed. Reports generated in the workflow are available in the Reports section of the dashboard.

Run Program

Use the Run Program tile to have your workflow run an executable file. For example, use this tile to create a step in your workflow that runs a third-party automated sampling accessory.

Combine this tile with the Variable tile or other tiles to create powerful workflows. For example, use the count variable from the Repeat tile to automatically increment an argument passed to the executable.

The Run Program tile can run only executable files that do not require any user interaction and that do not have a user interface.

Save Results

Exports collected data to a CSV file.

Search

Perform a correlation or a multi-component search.

Selection

With a Selection tile, the operator chooses which path the workflow should follow.

Start

This is the first tile in every workflow. The Start tile is added to the workflow canvas automatically each time a new workflow is created.

Tag Spectrum

Apply a tag to spectra created during the workflow.

Template Report

Generate a report from a template. Reports generated in the workflow are available in the Reports section of the dashboard. Most of the settings for a template report depend on the template type that is selected.

TQ Analyst

Quantify the components of the sample using a specified quantification method.

Variable

Use the Variable tile to assign a new value to an existing variable or to create a new, custom variable. Variables created or edited with the variable tile can be used in other tiles.

Workflow Table

Import a CSV file to use as a template for your workflow.

With the Workflow Table tile, you can import a table of options to use throughout the workflow. For example, with this tile, you can select one option when you begin the workflow and then automatically load specific variables, methods, and images throughout the workflow that correspond to that option.