Examples with SimplePluginWorkflowStep qupath.lib.plugins.workflow.SimplePluginWorkflowStep used on opensource projects

Example 1 with SimplePluginWorkflowStep

use of qupath.lib.plugins.workflow.SimplePluginWorkflowStep in project qupath by qupath.

the class WorkflowCommandLogView method runWorkflowStepInteractively.

/**
 * Launch a plugin dialog for a specified WorkflowStep.
 *
 * TODO: Run any scriptable step
 *
 * @param qupath
 * @param step
 */
@SuppressWarnings({ "unchecked", "rawtypes" })
private static void runWorkflowStepInteractively(final QuPathGUI qupath, final WorkflowStep step) {
    ImageData<BufferedImage> imageData = qupath.getImageData();
    if (imageData == null) {
        Dialogs.showNoImageError("Run workflow step");
        return;
    }
    if (step instanceof SimplePluginWorkflowStep) {
        if (step instanceof SimplePluginWorkflowStep) {
            SimplePluginWorkflowStep pluginStep = (SimplePluginWorkflowStep) step;
            String pluginClassName = pluginStep.getPluginClass();
            PathPlugin<BufferedImage> plugin = null;
            try {
                Class<? extends PathPlugin> cls = (Class<? extends PathPlugin>) Class.forName(pluginClassName);
                plugin = qupath.createPlugin(cls);
                Map<String, ?> parameterMap = pluginStep.getParameterMap();
                String arg = null;
                if (parameterMap != null && !parameterMap.isEmpty()) {
                    arg = ParameterList.getParameterListJSON(parameterMap, " ");
                }
                qupath.runPlugin(plugin, arg, true);
            } catch (ClassNotFoundException e1) {
                Dialogs.showErrorNotification("Plugin class not found", "No plugin class found with name " + pluginClassName);
            } catch (Exception e1) {
                Dialogs.showErrorNotification("Plugin error", "Error running plugin " + plugin.getName() + " - see log for details");
                logger.error(e1.getLocalizedMessage(), e1);
            }
        }
    } else if (step instanceof ScriptableWorkflowStep) {
    // TODO: Run command script
    }
}

Example 2 with SimplePluginWorkflowStep

use of qupath.lib.plugins.workflow.SimplePluginWorkflowStep in project qupath by qupath.

the class TMADearrayerPluginIJ method addWorkflowStep.

@Override
protected void addWorkflowStep(final ImageData<BufferedImage> imageData, final String arg) {
    WorkflowStep step = new SimplePluginWorkflowStep(getName(), (Class<? extends PathPlugin<?>>) getClass(), arg, "if (!isTMADearrayed()) {\n\t", "\n\treturn;\n}");
    imageData.getHistoryWorkflow().addStep(step);
    logger.info("{}", step);
}

Example 3 with SimplePluginWorkflowStep

use of qupath.lib.plugins.workflow.SimplePluginWorkflowStep in project qupath by qupath.

the class AbstractPlugin method addWorkflowStep.

/**
 * Add a workflow step to the ImageData indicating the argument that this plugin was run with.
 *
 * Subclasses may override this if a better workflow step should be logged.
 *
 * A subclass may also override this to avoid adding a workflow step at all.
 *
 * @param imageData
 * @param arg
 */
protected void addWorkflowStep(final ImageData<T> imageData, final String arg) {
    @SuppressWarnings("unchecked") WorkflowStep step = new SimplePluginWorkflowStep(getName(), (Class<? extends PathPlugin<T>>) getClass(), arg);
    imageData.getHistoryWorkflow().addStep(step);
    logger.debug("Adding workflow step: {}", step);
}