Examples with Dataset net.imagej.Dataset used on opensource projects

Example 11 with Dataset

use of net.imagej.Dataset in project vcell by virtualcell.

the class ProjectService method saveDataset.

private void saveDataset(Dataset dataset, Path path) throws IOException {
    Dataset datasetToSave = dataset.duplicate();
    // SCIFIO cannot save 1-bit images so we must convert to 8-bit
    if (datasetToSave.firstElement() instanceof BitType) {
        @SuppressWarnings("unchecked") Img<BitType> img = (Img<BitType>) dataset.getImgPlus().getImg();
        Img<UnsignedByteType> converted = opService.convert().uint8(img);
        ImgPlus<UnsignedByteType> convertedImgPlus = new ImgPlus<>(converted, dataset.getName());
        datasetToSave.setImgPlus(convertedImgPlus);
    }
    String name = dataset.getName();
    if (FilenameUtils.getExtension(name).isEmpty()) {
        // Default save extension
        name += ".tif";
    }
    Path filePath = Paths.get(path.toString(), name);
    datasetIOService.save(datasetToSave, filePath.toString());
}

Example 12 with Dataset

use of net.imagej.Dataset in project vcell by virtualcell.

the class CompareController method compareMap.

private void compareMap(int comparisonType, RandomAccessibleInterval<BitType> mask) {
    List<Dataset> datasets = view.getDatasets();
    if (datasets.size() != 2) {
        System.err.println("Cannot construct comparison map with number of images not equal to 2");
        return;
    }
    if (comparisonType == CompareMap.PERCENT_DIFFERENCE || comparisonType == CompareMap.RATIO) {
        Dataset secondDataset = datasets.get(1);
        if ((boolean) opService.run("intervalContains", secondDataset, 0, mask)) {
            showContainsZeroDialog();
            return;
        }
    }
    opService.run("compareMap", datasets.get(0), datasets.get(1), comparisonType, mask);
}

Example 13 with Dataset

use of net.imagej.Dataset in project vcell by virtualcell.

the class MainController method getDatasetFromFile.

private Dataset getDatasetFromFile(File file) {
    DatasetIOService datasetIOService = context.getService(DatasetIOService.class);
    Dataset dataset = null;
    try {
        dataset = datasetIOService.open(file.getAbsolutePath());
    } catch (IOException e) {
        e.printStackTrace();
    }
    return dataset;
}

Example 14 with Dataset

use of net.imagej.Dataset in project vcell by virtualcell.

the class MainController method addActionListenersToView.

private void addActionListenersToView() {
    view.addNewListener(event -> {
        model.setProject(new Project("New project"));
    });
    view.addOpenListener(event -> {
        JFileChooser fileChooser = new JFileChooser();
        fileChooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
        int returnVal = fileChooser.showOpenDialog(view);
        if (returnVal == JFileChooser.APPROVE_OPTION) {
            Task<Project, String> loadTask = projectService.load(fileChooser.getSelectedFile());
            loadTask.addPropertyChangeListener(propertyChangeEvent -> {
                if (propertyChangeEvent.getPropertyName().equals(Task.STATE) && loadTask.getState() == SwingWorker.StateValue.DONE) {
                    try {
                        model.setProject(loadTask.get());
                    } catch (InterruptedException | ExecutionException e) {
                        e.printStackTrace();
                    }
                }
            });
            try {
                executeTaskWithProgressDialog(loadTask, view, "Loading...", false);
            } catch (InterruptedException | ExecutionException e) {
                e.printStackTrace();
            }
        }
    });
    view.addSaveListener(event -> {
        Task<Void, String> saveTask = projectService.save(model.getProject());
        try {
            executeTaskWithProgressDialog(saveTask, view, "Saving...", false);
        } catch (InterruptedException | ExecutionException e) {
            e.printStackTrace();
        }
    });
    view.addSaveAsListener(event -> {
        JFileChooser fileChooser = new JFileChooser();
        int returnVal = fileChooser.showSaveDialog(view);
        if (returnVal == JFileChooser.APPROVE_OPTION) {
            File file = fileChooser.getSelectedFile();
            model.setProjectTitle(file.getName());
            Task<Void, String> saveAsTask = projectService.saveAs(model.getProject(), file);
            try {
                executeTaskWithProgressDialog(saveAsTask, view, "Saving...", false);
            } catch (InterruptedException | ExecutionException e) {
                e.printStackTrace();
            }
        }
    });
    view.addImportDataListener(event -> {
        JFileChooser fileChooser = new JFileChooser();
        fileChooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
        if (presentOpenFileChooser(fileChooser)) {
            Dataset dataset = getDatasetFromFile(fileChooser.getSelectedFile());
            model.addData(dataset);
        }
    });
    view.addImportGeometryListener(event -> {
        JFileChooser fileChooser = new JFileChooser();
        fileChooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
        if (presentOpenFileChooser(fileChooser)) {
            Dataset dataset = getDatasetFromFile(fileChooser.getSelectedFile());
            model.addGeometry(dataset);
        }
    });
    view.addImportResultsSingleListener(event -> {
        JFileChooser fileChooser = new JFileChooser();
        fileChooser.setFileSelectionMode(JFileChooser.FILES_ONLY);
        if (presentOpenFileChooser(fileChooser)) {
            Dataset dataset = getDatasetFromFile(fileChooser.getSelectedFile());
            model.addResult(dataset);
        }
    });
    view.addImportResultsTimeSeriesListener(event -> {
        JFileChooser fileChooser = new JFileChooser();
        fileChooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
        if (presentOpenFileChooser(fileChooser)) {
            try {
                Dataset dataset = vCellResultService.importCsv(fileChooser.getSelectedFile());
                model.addResult(dataset);
            } catch (FileNotFoundException e) {
                e.printStackTrace();
            }
        }
    });
    view.addExportListener(event -> {
        Dataset dataset = view.getSelectedDataset();
        if (dataset == null) {
            JOptionPane.showMessageDialog(view, "Please select a dataset to export.", "No dataset selected", JOptionPane.PLAIN_MESSAGE);
            return;
        }
        JFileChooser fileChooser = new JFileChooser();
        fileChooser.setSelectedFile(new File(dataset.getName()));
        int returnVal = fileChooser.showSaveDialog(view);
        if (returnVal == JFileChooser.APPROVE_OPTION) {
            try {
                datasetIOService.save(dataset.duplicate(), fileChooser.getSelectedFile().getPath());
            } catch (IOException e) {
                e.printStackTrace();
            }
        }
    });
    view.addChangeAxesListener(event -> {
        Dataset dataset = view.getSelectedDataset();
        if (dataset == null) {
            JOptionPane.showMessageDialog(view, "Please select a dataset to edit.", "No dataset selected", JOptionPane.PLAIN_MESSAGE);
            return;
        }
        ChangeAxesPanel panel = new ChangeAxesPanel(dataset);
        int returnVal = JOptionPane.showConfirmDialog(view, panel, "Change Axes", JOptionPane.OK_CANCEL_OPTION, JOptionPane.PLAIN_MESSAGE);
        if (returnVal == JOptionPane.OK_OPTION) {
            model.changeAxes(dataset, panel.getSelectedAxisTypes());
        }
    });
    view.addDeleteListener(event -> {
        Dataset dataset = view.getSelectedDataset();
        if (dataset == null) {
            JOptionPane.showMessageDialog(view, "Please select a dataset to delete.", "No dataset selected", JOptionPane.PLAIN_MESSAGE);
            return;
        }
        int result = JOptionPane.showConfirmDialog(view, "Are you sure you want to delete \"" + dataset.getName() + "\"?", "Delete", JOptionPane.OK_CANCEL_OPTION);
        if (result == JOptionPane.OK_OPTION) {
            model.delete(dataset);
        }
    });
    view.addCompareDatasetsListener(event -> {
        List<Dataset> datasetList = model.getProject().getData();
        datasetList.addAll(model.getProject().getGeometry());
        datasetList.addAll(model.getProject().getResults());
        Dataset[] datasetArray = datasetList.toArray(new Dataset[datasetList.size()]);
        DatasetSelectionPanel panel = new DatasetSelectionPanel();
        String descriptionA = "Dataset A:";
        String descriptionB = "Dataset B:";
        panel.addComboBox(datasetArray, descriptionA);
        panel.addComboBox(datasetArray, descriptionB);
        int returnVal = JOptionPane.showConfirmDialog(view, panel, "Select datasets to compare", JOptionPane.OK_CANCEL_OPTION, JOptionPane.PLAIN_MESSAGE);
        if (returnVal == JOptionPane.OK_OPTION) {
            ArrayList<Dataset> datasets = new ArrayList<>();
            datasets.add(panel.getSelectedDatasetForDescription(descriptionA));
            datasets.add(panel.getSelectedDatasetForDescription(descriptionB));
            if (!Datasets.areSameSize(datasets.toArray(new Dataset[datasets.size()]), 0, 1)) {
                JOptionPane.showMessageDialog(view, "The selected datasets are not the same size.", "Incompatible datasets", JOptionPane.ERROR_MESSAGE);
                return;
            }
            CompareView compareView = new CompareView(datasets);
            new CompareController(compareView, model, context);
            compareView.setVisible(true);
            for (Dataset dataset : datasets) {
                inFrameDisplayService.displayDataset(dataset, compareView);
            }
        }
    });
    view.addConstructTIRFGeometryListener(event -> {
        List<Dataset> dataList = model.getProject().getData();
        Dataset[] dataArray = dataList.toArray(new Dataset[dataList.size()]);
        ConstructTIRFGeometryInputPanel panel = new ConstructTIRFGeometryInputPanel(dataArray);
        int returnVal = JOptionPane.showConfirmDialog(view, panel, "Construct TIRF Geometry", JOptionPane.OK_CANCEL_OPTION, JOptionPane.PLAIN_MESSAGE);
        if (returnVal == JOptionPane.OK_OPTION) {
            Dataset dataset = panel.getData();
            int sliceIndex = panel.getSliceIndex();
            double wavelength = panel.getWavelength();
            double angle = panel.getAngle();
            double zSpacing = panel.getZSpacing();
            Dataset geometry = (Dataset) opService.run("constructTIRFGeometry", dataset, sliceIndex, wavelength, angle, zSpacing);
            String baseName = FilenameUtils.getBaseName(dataset.getName());
            String extension = FilenameUtils.getExtension(dataset.getName());
            geometry.setName(baseName + "_geometry." + extension);
            model.addGeometry(geometry);
        }
    });
    view.addConstructTIRFImageListener(event -> {
        List<Dataset> geometry = model.getProject().getGeometry();
        List<Dataset> results = model.getProject().getResults();
        Dataset[] geometryArray = geometry.toArray(new Dataset[geometry.size()]);
        Dataset[] resultsArray = results.toArray(new Dataset[results.size()]);
        ConstructTIRFImageInputPanel panel = new ConstructTIRFImageInputPanel(geometryArray, resultsArray);
        int returnVal = JOptionPane.showConfirmDialog(view, panel, "Construct TIRF Image", JOptionPane.OK_CANCEL_OPTION, JOptionPane.PLAIN_MESSAGE);
        if (returnVal == JOptionPane.OK_OPTION) {
            Dataset selectedGeometry = panel.getGeometry();
            Dataset selectedMembraneResults = panel.getMembraneResults();
            Dataset selectedVolumeResults = panel.getVolumeResults();
            double wavelength = panel.getWavelength();
            double angle = panel.getAngle();
            double zSpacing = panel.getZSpacing();
            double xySpacing = panel.getXSpacing() * panel.getYSpacing();
            Dataset result = (Dataset) opService.run("constructTIRFImage", selectedGeometry, selectedMembraneResults, selectedVolumeResults, wavelength, angle, zSpacing, xySpacing);
            String baseName = FilenameUtils.getBaseName(selectedGeometry.getName());
            if (baseName.endsWith("_geometry")) {
                baseName = baseName.substring(0, baseName.length() - "_geometry".length());
            }
            String extension = FilenameUtils.getExtension(selectedGeometry.getName());
            result.setName(baseName + "_constructed_TIRF." + extension);
            model.addResult(result);
        }
    });
    view.addNewModelListener(event -> {
        Task<List<VCellModel>, String> loadTask = vCellModelService.getModels(vCellService);
        try {
            List<VCellModel> models = executeTaskWithProgressDialog(loadTask, view, "Loading models...", false);
            VCellModelSelectionDialog dialog = new VCellModelSelectionDialog(view, vCellModelService);
            dialog.setModels(models);
            int resultVal = dialog.display();
            if (resultVal == JOptionPane.OK_OPTION) {
                VCellModel selectedModel = dialog.getSelectedModel();
                if (selectedModel != null) {
                    model.addModel(selectedModel);
                }
            }
        } catch (InterruptedException | ExecutionException e) {
            e.printStackTrace();
        }
    });
    view.addSimulateModelListener(event -> {
        VCellModel vCellModel = view.getSelectedModel();
        if (vCellModel == null) {
            JOptionPane.showMessageDialog(view, "Please select a model to simulate.", "No model selected", JOptionPane.PLAIN_MESSAGE);
            return;
        } else if (vCellModel.getSimulationState() == SimulationState.running) {
            JOptionPane.showMessageDialog(view, "This simulation is currently in progress", "Simulation in progress", JOptionPane.PLAIN_MESSAGE);
            return;
        }
        SimulateModelPanel panel = new SimulateModelPanel(vCellModel);
        int returnVal = JOptionPane.showConfirmDialog(view, panel, "Simulate model", JOptionPane.OK_CANCEL_OPTION, JOptionPane.PLAIN_MESSAGE);
        if (returnVal == JOptionPane.OK_OPTION) {
            // Update parameters of model from user input
            HashMap<Parameter, ASTNode> parameterMathMap = panel.getParameterMathMap();
            Model sbmlModel = vCellModel.getSbmlDocument().getModel();
            for (Parameter parameter : parameterMathMap.keySet()) {
                sbmlModel.getParameter(parameter.getId()).setValue(parameter.getValue());
                ASTNode math = parameterMathMap.get(parameter);
                if (math != null) {
                    ExplicitRule rule = sbmlModel.getRuleByVariable(parameter.getId());
                    if (rule != null) {
                        rule.setMath(math);
                    }
                }
            }
            SimulationSpec simSpec = new SimulationSpec();
            simSpec.setOutputTimeStep(panel.getTimeStep());
            simSpec.setTotalTime(panel.getTotalTime());
            Task<List<Dataset>, SimulationState> task = vCellService.runSimulation(vCellModel, simSpec, panel.getSelectedSpecies(), panel.getShouldCreateIndividualDatasets());
            task.addPropertyChangeListener(propertyChangeEvent -> {
                if (propertyChangeEvent.getPropertyName().equals(Task.SUBTASK)) {
                    model.setSimulationStateForVCellModel(task.getSubtask(), vCellModel);
                }
            });
            task.addDoneListener(propertyChangeEvent -> {
                try {
                    List<Dataset> results = task.get();
                    for (Dataset result : results) {
                        model.addResult(result);
                    }
                    System.out.println(results.toString());
                } catch (InterruptedException | ExecutionException e) {
                    e.printStackTrace();
                }
            });
            task.execute();
        }
    });
    view.addTabbedPaneChangeListener(event -> {
        view.clearListSelection();
    });
    view.addListSelectionListener(event -> {
        if (!event.getValueIsAdjusting()) {
            Object selected = ((JList<?>) event.getSource()).getSelectedValue();
            if (Dataset.class.isInstance(selected)) {
                view.displayDataset((Dataset) selected);
            } else if (VCellModel.class.isInstance(selected)) {
                view.displayModel((VCellModel) selected);
            }
        }
    });
}

Example 15 with Dataset

use of net.imagej.Dataset in project vcell by virtualcell.

the class MainView method displaySelectedDataset.

public void displaySelectedDataset() {
    Dataset dataset = getSelectedDataset();
    if (dataset == null)
        return;
    displayDataset(dataset);
}