Examples with FitParams flimlib.flimj.FitParams used on opensource projects

Example 1 with FitParams

use of flimlib.flimj.FitParams in project flimj-ui by flimlib.

the class SettingsCtrl method initialize.

@Override
public void initialize() {
    paramLabels = new ArrayList<>();
    paramValues = new ArrayList<>();
    paramFixed = new ArrayList<>();
    paramIndices = new ArrayList<>();
    presentDatasets = new HashMap<>();
    // keep only the table header (remove the preview parameters)
    paramPane.getChildren().removeIf(child -> GridPane.getRowIndex(child) > 0);
    // numerical fields
    iThreshSpinner.setMin(0.0);
    iThreshSpinner.setStepSize(1.0);
    iThreshSpinner.getNumberProperty().addListener((obs, oldVal, newVal) -> {
        FitParams<FloatType> params = getParams();
        params.iThresh = newVal.floatValue();
        ObjectProperty<Double> binSizeProperty = binSizeSpinner.getNumberProperty();
        if (binSizeProperty.get() == 0.0) {
            threshBinZero = newVal.floatValue();
        }
        // recalculate global trans for pixels above threshold
        fp.invalidateGlobalTrans();
        // turn off estimate based on percentage
        // otherwise user's setting iThresh = 0 triggers that
        params.iThreshPercent = params.iThresh >= 0 ? -1 : 5;
        requestUpdate();
    });
    HashMap<String, Double> kwMap = new HashMap<>();
    kwMap.put("FULL", -1.0);
    binSizeSpinner.setKwMap(kwMap);
    binSizeSpinner.setIntOnly(true);
    binSizeSpinner.setMin(0.0);
    binSizeSpinner.setMax(255.0);
    binSizeSpinner.setStepSize(1.0);
    binSizeSpinner.getNumberProperty().addListener((obs, oldVal, newVal) -> {
        MainCtrl mainCtrl = (MainCtrl) parentCtrl;
        // display pending state
        mainCtrl.setProgress(-1.0);
        // binning will freeze the JFX thread and not allow the +/- event to be consumed
        // which causes indefinite +/- and resulting calls to setBinning()
        fp.submitRunnable(() -> {
            fp.setBinning(newVal.intValue());
            // update of UI components should be run from JFX thread
            Platform.runLater(() -> {
                binSizeSpinner.setDisable(fullBinningCheckBox.isSelected());
                // restore from pending state
                mainCtrl.setProgress(null);
                requestUpdate();
            });
        });
    });
    fullBinningCheckBox.selectedProperty().addListener(new ChangeListener<Boolean>() {

        private double lastSize;

        @Override
        public void changed(ObservableValue<? extends Boolean> observable, Boolean oldValue, Boolean newValue) {
            ObjectProperty<Double> binSizeProperty = binSizeSpinner.getNumberProperty();
            ObjectProperty<Double> iThreshProperty = iThreshSpinner.getNumberProperty();
            if (newValue) {
                lastSize = binSizeProperty.get();
                binSizeProperty.set(-1.0);
                iThreshProperty.set(threshBinZero);
                iThreshSpinner.setDisable(true);
            } else {
                binSizeSpinner.setDisable(false);
                binSizeProperty.set(lastSize);
                iThreshSpinner.setDisable(false);
                iThreshProperty.set(threshBinZero);
            }
        }
    });
    // CB's
    noiseChoiceBox.setConverter(new StringConverter<NoiseType>() {

        @Override
        public String toString(NoiseType noiseType) {
            switch(noiseType) {
                case NOISE_GAUSSIAN_FIT:
                    return "Gaussian (Fit)";
                case NOISE_POISSON_FIT:
                    return "Poisson (Fit)";
                case NOISE_POISSON_DATA:
                    return "Poisson (Data)";
                case NOISE_MLE:
                    return "MLE";
                default:
                    return "";
            }
        }

        @Override
        public NoiseType fromString(String string) {
            switch(string) {
                case "Gaussian (Fit)":
                    return NoiseType.NOISE_GAUSSIAN_FIT;
                case "Poisson (Fit)":
                    return NoiseType.NOISE_POISSON_FIT;
                case "Poisson (Data)":
                    return NoiseType.NOISE_POISSON_DATA;
                case "MLE":
                    return NoiseType.NOISE_MLE;
                default:
                    return null;
            }
        }
    });
    // kept separate from numerical fields because they don't have onChange
    ChangeListener<Object> paramPaneUpdateHandler = (obs, oldVal, newVal) -> {
        final Integer nComp = nCompChoiceBox.getValue();
        final FitType algo = algoChoiceBox.getValue();
        FitParams<FloatType> params = getParams();
        params.nComp = nComp;
        fp.setAlgo(algo);
        setupParams(algo, nComp);
        // https://github.com/flimlib/flimj-ui/issues/9
        if (algo == FitType.Bayes) {
            nCompChoiceBox.setValue(1);
            nCompChoiceBox.setDisable(true);
            noiseChoiceBox.setDisable(true);
        } else {
            nCompChoiceBox.setDisable(false);
            noiseChoiceBox.setDisable(false);
        }
        // resize and initialize the two arrays
        int nParam = fp.getNParam();
        int fillStart = params.paramFree.length;
        params.param = Arrays.copyOf(params.param, nParam);
        params.paramMap = ArrayImgs.floats(params.param, FitProcessor.swapInLtAxis(new long[] { 1, 1, nParam }, params.ltAxis));
        params.paramFree = Arrays.copyOf(params.paramFree, nParam);
        for (int i = fillStart; i < params.paramFree.length; i++) params.paramFree[i] = true;
        requestUpdate();
    };
    algoChoiceBox.valueProperty().addListener(paramPaneUpdateHandler);
    nCompChoiceBox.valueProperty().addListener(paramPaneUpdateHandler);
    noiseChoiceBox.valueProperty().addListener((obs, oldVal, newVal) -> {
        getParams().noise = noiseChoiceBox.getValue();
        requestUpdate();
    });
    irfChoiceBox.getItems().add("From file");
    irfChoiceBox.valueProperty().addListener((obs, oldVal, newVal) -> {
        // if no item is now selected, select the previously selected item
        if (newVal == null) {
            irfChoiceBox.setValue(oldVal);
            return;
        }
        // this happens when we recover from the above situation
        if (oldVal == null) {
            return;
        }
        FitParams<FloatType> chosenIRF;
        if ("From file".equals(newVal)) {
            // the name of selected dataset
            String currentSelection = oldVal;
            // choose from file
            File irfFile = getUIs().chooseFile("Choose IRF transient file", null, FileWidget.OPEN_STYLE);
            if (irfFile != null) {
                // not cancelled
                String irfPath = irfFile.getPath();
                if (irfPath.endsWith("asc") || getDss().canOpen(irfPath)) {
                    try {
                        chosenIRF = IRFDatasetFromFile(irfPath);
                        // throw away if canceled by user
                        if (chosenIRF != null) {
                            // use file name as irf name
                            currentSelection = irfPath.substring(irfPath.lastIndexOf(File.separator) + 1);
                            // add to options if not present ([0] = "None")
                            if (!presentDatasets.containsKey(currentSelection)) {
                                irfChoiceBox.getItems().add(1, currentSelection);
                            }
                            // remember/update IRF
                            presentDatasets.put(currentSelection, chosenIRF);
                        }
                    } catch (Exception e) {
                        getUIs().showDialog(String.format("Error occurred during opening %s\nSee Console log.", irfPath), "FLIMJ", MessageType.ERROR_MESSAGE, OptionType.OK_CANCEL_OPTION);
                        getLogs().error(e.getMessage());
                    }
                } else
                    getUIs().showDialog(String.format("%s cannot be opened as a Dataset or an ASCII number list.", irfPath), "FLIMJ", MessageType.ERROR_MESSAGE, OptionType.OK_CANCEL_OPTION);
            }
            // either set to the new, valid dataset or stick to the old one
            irfChoiceBox.setValue(currentSelection);
            return;
        } else if (!"None".equals(newVal)) {
            // locate the chosen dataset
            chosenIRF = presentDatasets.get(newVal);
        } else
            chosenIRF = null;
        // update IRF information and notify fp
        fp.setIRF(chosenIRF);
        requestUpdate();
    });
    fitButton.setOnAction(event -> {
        MainCtrl mainCtrl = (MainCtrl) parentCtrl;
        // check fit status every 0.1s untill stopped
        Timeline fittingBusyAnimTL = new Timeline(new KeyFrame(Duration.seconds(0.1), e -> mainCtrl.setProgress(fp.getFitProgress())));
        fittingBusyAnimTL.setCycleCount(Timeline.INDEFINITE);
        // do heavy lifting on a separate thread
        fp.submitRunnable(() -> {
            fittingBusyAnimTL.play();
            fp.fitDataset();
            // update UI when done
            Platform.runLater(() -> {
                // show "Done" for a brief moment
                fittingBusyAnimTL.stop();
                fittingBusyAnimTL.getKeyFrames().setAll(new KeyFrame(Duration.seconds(0.1), e -> mainCtrl.setProgress(null)));
                fittingBusyAnimTL.setCycleCount(1);
                fittingBusyAnimTL.play();
                // set new options
                List<String> previewOptions = new ArrayList<>();
                for (Text label : paramLabels) previewOptions.add(label.getText());
                previewOptions.add("τₘ");
                fp.setPreviewOptions(previewOptions);
                requestUpdate();
            });
        });
    });
}

Example 2 with FitParams

use of flimlib.flimj.FitParams in project flimj-ui by flimlib.

the class FLIMJCommand method initFX.

/**
 * Initializes the GUI frame.
 *
 * @param fxPanel the embeded channel
 * @throws IOException if the fxml is not found
 * @return <code>true</code> - if the operation is successful
 * @see <a href=
 *      "https://docs.oracle.com/javase/8/javafx/interoperability-tutorial/swing-fx-interoperability.htm">oracle
 *      doc</a>
 */
private boolean initFX(final JFXPanel fxPanel) throws IOException {
    // load scene
    final FXMLLoader loader = AbstractCtrl.getFXMLLoader("plugin-layout");
    final Scene scene = loader.<Scene>load();
    fxPanel.setScene(scene);
    // init fitting worker
    final FitParams<FloatType> params = new FitParams<>();
    if (!FitParamsPrompter.populate(params, datasetView.getData(), datasetView))
        return false;
    fp = new FitProcessor(datasetView.context(), params);
    // init controllers
    final MainCtrl mainCtrl = loader.<MainCtrl>getController();
    mainCtrl.setFitProcessor(fp);
    fp.refreshControllers();
    fp.updateFit();
    return true;
}

Example 3 with FitParams

use of flimlib.flimj.FitParams in project flimj-ui by flimlib.

the class SettingsCtrl method IRFDatasetFromFile.

private FitParams<FloatType> IRFDatasetFromFile(String irfPath) throws IOException {
    FitParams<FloatType> irfParams = new FitParams<>();
    if (irfPath.endsWith(".asc")) {
        // read whitespace separated data
        ArrayList<Float> irfTrans = new ArrayList<>();
        Scanner sc = new Scanner(new File(irfPath));
        while (sc.hasNextBigDecimal()) irfTrans.add(sc.nextBigDecimal().floatValue());
        sc.close();
        // get origTrans' size and ltAxis
        int ltAxis = fp.getParams().ltAxis;
        long[] transDim = new long[3];
        fp.getOrigTrans().dimensions(transDim);
        float[] irfTransArr = new float[(int) transDim[ltAxis]];
        // place the data at the end so that the leading 0's can be used for shifting
        for (int i = Math.max(irfTransArr.length - irfTrans.size(), 0), j = 0; i < irfTransArr.length; i++, j++) irfTransArr[i] = irfTrans.get(j);
        // create a fake image out of a single array along the ltAxis
        irfParams.transMap = Views.interval(Views.extendBorder(ArrayImgs.floats(irfTransArr, new long[] { 1, 1, irfTransArr.length })), new long[] { 0, 0, 0 }, new long[] { transDim[0] - 1, transDim[1] - 1, transDim[2] - 1 });
        irfParams.ltAxis = ltAxis;
    } else if (getDss().canOpen(irfPath)) {
        final Dataset dataset = getDss().open(irfPath);
        final Localizable pos = new Point(Intervals.minAsLongArray(dataset));
        if (!FitParamsPrompter.populate(irfParams, dataset, pos))
            irfParams = null;
    }
    return irfParams;
}