Examples with Module org.scijava.module.Module used on opensource projects

Example 1 with Module

use of org.scijava.module.Module in project imagej-omero by imagej.

the class ModuleAdapter method launch.

/**
 * Executes the associated ImageJ module as an OMERO script.
 *
 * @throws IOException
 * @throws ServerError
 * @throws ExecutionException
 * @throws CannotCreateSessionException
 * @throws PermissionDeniedException
 * @throws DSAccessException
 * @throws DSOutOfServiceException
 */
public void launch() throws ServerError, IOException, ExecutionException, PermissionDeniedException, CannotCreateSessionException, DSOutOfServiceException, DSAccessException {
    // populate inputs
    log.debug(info.getTitle() + ": populating inputs");
    final HashMap<String, Object> inputMap = new HashMap<>();
    for (final String name : client.getInputKeys()) {
        final ModuleItem<?> input = getInput(name);
        final Class<?> type = input.getType();
        final Object value = omeroService.toImageJ(client, client.getInput(name), type);
        inputMap.put(input.getName(), value);
    }
    // execute ImageJ module
    log.debug(info.getTitle() + ": executing module");
    final Future<Module> future = moduleService.run(info, true, inputMap);
    final Module module = moduleService.waitFor(future);
    final HashMap<String, TableData> tables = new HashMap<>();
    // populate outputs, except tables
    log.debug(info.getTitle() + ": populating outputs");
    for (final ModuleItem<?> item : module.getInfo().outputs()) {
        final Object value = omeroService.toOMERO(client, item.getValue(module));
        final String name = getOutputName(item);
        if (value == null) {
            log.warn(info.getTitle() + ": output '" + name + "' is null");
        }
        if (value instanceof omero.RType)
            client.setOutput(name, (omero.RType) value);
        if (value instanceof TableData)
            tables.put(name, (TableData) value);
    }
    createOutputLinks(inputMap, tables);
    gateway.disconnect();
    log.debug(info.getTitle() + ": completed execution");
}

Example 2 with Module

use of org.scijava.module.Module in project imagej-ops by imagej.

the class DefaultOpMatchingService method moduleConforms.

/**
 * Verifies that the given candidate's module conforms.
 * <p>
 * Helper method of {@link #filterMatches(List)}.
 * </p>
 */
private boolean moduleConforms(final OpCandidate candidate) {
    // create module and assign the inputs
    final Module module = createModule(candidate, candidate.getArgs());
    candidate.setModule(module);
    // make sure the op itself is happy with these arguments
    final Object op = module.getDelegateObject();
    if (op instanceof Contingent) {
        final Contingent c = (Contingent) op;
        if (!c.conforms()) {
            candidate.setStatus(StatusCode.DOES_NOT_CONFORM);
            return false;
        }
    }
    // found a match!
    return true;
}

Example 3 with Module

use of org.scijava.module.Module in project imagej-omero by imagej.

the class ModuleAdapter method getJobInfo.

/**
 * Converts ImageJ module metadata to OMERO job metadata.
 */
public omero.RType getJobInfo() {
    // populate module metadata
    final omero.grid.JobParams params = new omero.grid.JobParams();
    // info.getName();
    params.name = "[ImageJ] " + info.getTitle();
    params.version = getVersion();
    params.description = info.getDescription();
    params.stdoutFormat = "text/plain";
    params.stderrFormat = "text/plain";
    // Instantiate and preprocess the module
    final Module m = moduleService.createModule(info);
    final List<PreprocessorPlugin> pre = pluginService.createInstancesOfType(PreprocessorPlugin.class);
    final ModuleRunner mr = new ModuleRunner(getContext(), m, pre, null);
    mr.preProcess();
    // count module inputs and outputs
    final int inputCount = m.getInputs().size();
    final int outputCount = m.getOutputs().size();
    final int inputDigits = String.valueOf(inputCount).length();
    final int outputDigits = String.valueOf(outputCount).length();
    // convert metadata for each module input
    params.inputs = new HashMap<>();
    int inputIndex = 0;
    for (final ModuleItem<?> item : info.inputs()) {
        if (item.getVisibility() == ItemVisibility.MESSAGE)
            continue;
        if (m.isInputResolved(item.getName()))
            continue;
        final omero.grid.Param param = omeroService.getJobParam(item);
        if (param != null) {
            param.grouping = pad(inputIndex++, inputDigits);
            params.inputs.put(getInputName(item), param);
        }
    }
    // convert metadata for each module output
    params.outputs = new HashMap<>();
    int outputIndex = 0;
    for (final ModuleItem<?> item : info.outputs()) {
        final omero.grid.Param param = omeroService.getJobParam(item);
        if (param != null) {
            param.grouping = pad(outputIndex++, outputDigits);
            params.outputs.put(getOutputName(item), param);
        }
    }
    return omero.rtypes.rinternal(params);
}

Example 4 with Module

use of org.scijava.module.Module in project imagej-ops by imagej.

the class DefaultOpMatchingService method createModule.

/**
 * Helper method of {@link #match(OpCandidate, Object[])}.
 */
private Module createModule(final OpCandidate candidate, final Object... args) {
    // create the module
    final Module module = moduleService.createModule(candidate.cInfo());
    // unwrap the created op
    final Op op = OpUtils.unwrap(module, candidate.getRef());
    // inject the op execution environment
    op.setEnvironment(candidate.ops());
    // populate the inputs and return the module
    return assignInputs(module, args);
}

Example 5 with Module

use of org.scijava.module.Module in project imagej-ops by imagej.

the class DefaultOpMatchingService method match.

/**
 * Helper method of {@link #match(OpCandidate)}.
 */
private Module match(final OpCandidate candidate, final Object[] args) {
    // check that each parameter is compatible with its argument
    final int badIndex = typesMatch(candidate, args);
    if (badIndex >= 0) {
        final String message = typeClashMessage(candidate, args, badIndex);
        candidate.setStatus(StatusCode.ARG_TYPES_DO_NOT_MATCH, message);
        return null;
    }
    // create module and assign the inputs
    final Module module = createModule(candidate, args);
    candidate.setModule(module);
    // make sure the op itself is happy with these arguments
    final Object op = module.getDelegateObject();
    if (op instanceof Contingent) {
        final Contingent c = (Contingent) op;
        if (!c.conforms()) {
            candidate.setStatus(StatusCode.DOES_NOT_CONFORM);
            return null;
        }
    }
    // found a match!
    return module;
}