use of qupath.lib.plugins.workflow.WorkflowStep in project qupath by qupath.
the class Commands method resetClassifications.
/**
* Select objects that are instances of a specified class, logging an appropriate method in the workflow.
*
* @param imageData
* @param cls
*/
public static void resetClassifications(final ImageData<?> imageData, final Class<? extends PathObject> cls) {
if (imageData == null) {
logger.warn("No classifications to reset!");
return;
}
// Do the reset
QP.resetClassifications(imageData.getHierarchy(), cls);
// Log the appropriate command
Map<String, String> params = Collections.singletonMap("Type", PathObjectTools.getSuitableName(cls, false));
String method;
if (cls == PathDetectionObject.class)
method = "resetDetectionClassifications();";
else
// TODO: Get a suitable name to disguise Java classes
method = "resetClassifications(" + cls.getName() + ");";
WorkflowStep newStep = new DefaultScriptableWorkflowStep("Reset classifications", params, method);
WorkflowStep lastStep = imageData.getHistoryWorkflow().getLastStep();
if (newStep.equals(lastStep))
imageData.getHistoryWorkflow().replaceLastStep(newStep);
else
imageData.getHistoryWorkflow().addStep(newStep);
}
use of qupath.lib.plugins.workflow.WorkflowStep in project qupath by qupath.
the class TMACommands method promptToExportTMAData.
/**
* Prompt to export summary TMA data for a specific image to a directory.
* @param qupath
* @param imageData
*/
public static void promptToExportTMAData(QuPathGUI qupath, ImageData<BufferedImage> imageData) {
String title = "Export TMA data";
if (imageData == null) {
Dialogs.showNoImageError(title);
return;
}
PathObjectHierarchy hierarchy = imageData == null ? null : imageData.getHierarchy();
if (hierarchy == null || hierarchy.isEmpty() || hierarchy.getTMAGrid() == null || hierarchy.getTMAGrid().nCores() == 0) {
Dialogs.showErrorMessage(title, "No TMA data available!");
return;
}
var overlayOptions = qupath.getViewers().stream().filter(v -> v.getImageData() == imageData).map(v -> v.getOverlayOptions()).findFirst().orElse(qupath.getOverlayOptions());
String defaultName = ServerTools.getDisplayableImageName(imageData.getServer());
File file = Dialogs.promptToSaveFile(null, null, defaultName, "TMA data", ".qptma");
if (file != null) {
if (!file.getName().endsWith(".qptma"))
file = new File(file.getParentFile(), file.getName() + ".qptma");
double downsample = PathPrefs.tmaExportDownsampleProperty().get();
TMADataIO.writeTMAData(file, imageData, overlayOptions, downsample);
WorkflowStep step = new DefaultScriptableWorkflowStep("Export TMA data", "exportTMAData(\"" + GeneralTools.escapeFilePath(file.getParentFile().getAbsolutePath()) + "\", " + downsample + ")");
imageData.getHistoryWorkflow().addStep(step);
// PathAwtIO.writeTMAData(file, imageData, viewer.getOverlayOptions(), Double.NaN);
}
}
use of qupath.lib.plugins.workflow.WorkflowStep in project qupath by qupath.
the class Commands method resetSelection.
/**
* Reset the selection for an image.
* @param imageData
*/
public static void resetSelection(final ImageData<?> imageData) {
if (imageData == null) {
logger.warn("No image available!");
return;
}
// Do the action reset
imageData.getHierarchy().getSelectionModel().clearSelection();
// Log the appropriate command
String method = "resetSelection();";
WorkflowStep newStep = new DefaultScriptableWorkflowStep("Reset selection", method);
WorkflowStep lastStep = imageData.getHistoryWorkflow().getLastStep();
if (newStep.equals(lastStep))
imageData.getHistoryWorkflow().replaceLastStep(newStep);
else
imageData.getHistoryWorkflow().addStep(newStep);
}
use of qupath.lib.plugins.workflow.WorkflowStep in project qupath by qupath.
the class MeasurementManager method promptToRemoveAllMeasurements.
private boolean promptToRemoveAllMeasurements() {
var selectedClass = comboBox.getSelectionModel().getSelectedItem();
var selectedItems = new ArrayList<>(measurementList);
if (selectedClass == null || selectedItems.isEmpty()) {
Dialogs.showErrorMessage("Remove measurements", "No measurements selected!");
return false;
}
String number = selectedItems.size() == 1 ? String.format("'%s'", selectedItems.iterator().next()) : selectedItems.size() + " measurements";
if (!Dialogs.showConfirmDialog("Remove measurements", "Are you sure you want to permanently remove " + number + "?"))
return false;
logger.info("Removing all measurements for ", PathObjectTools.getSuitableName(selectedClass, true));
Class<? extends PathObject> cls = comboBox.getSelectionModel().getSelectedItem();
String script;
var hierarchy = imageData.getHierarchy();
if (cls == PathAnnotationObject.class) {
script = "clearAnnotationMeasurements()";
QP.clearAnnotationMeasurements(hierarchy);
} else if (cls == PathCellObject.class) {
script = "clearCellMeasurements()";
QP.clearCellMeasurements(hierarchy);
} else if (cls == PathTileObject.class) {
script = "clearTileMeasurements()";
QP.clearTileMeasurements(hierarchy);
} else if (cls == PathRootObject.class) {
script = "clearRootMeasurements()";
QP.clearRootMeasurements(hierarchy);
} else if (cls == TMACoreObject.class) {
script = "clearTMACoreMeasurements()";
QP.clearTMACoreMeasurements(hierarchy);
} else {
script = "clearMeasurements(" + cls.getName() + ")";
QP.clearMeasurements(hierarchy, cls);
}
// Keep for scripting
WorkflowStep step = new DefaultScriptableWorkflowStep("Clear all measurements", script);
imageData.getHistoryWorkflow().addStep(step);
// Update
refreshMeasurements();
updateCurrentList();
filterText.set("");
return true;
}
use of qupath.lib.plugins.workflow.WorkflowStep in project qupath by qupath.
the class SummaryMeasurementTableCommand method showTable.
/**
* Show a measurement table for the specified image data.
* @param imageData the image data
* @param type the object type to show
*/
public void showTable(ImageData<BufferedImage> imageData, Class<? extends PathObject> type) {
if (imageData == null) {
Dialogs.showNoImageError("Show measurement table");
return;
}
final PathObjectHierarchy hierarchy = imageData.getHierarchy();
ObservableMeasurementTableData model = new ObservableMeasurementTableData();
model.setImageData(imageData, imageData == null ? Collections.emptyList() : imageData.getHierarchy().getObjects(null, type));
SplitPane splitPane = new SplitPane();
HistogramDisplay histogramDisplay = new HistogramDisplay(model, true);
// table.setTableMenuButtonVisible(true);
TableView<PathObject> table = new TableView<>();
table.getSelectionModel().setSelectionMode(SelectionMode.MULTIPLE);
table.getSelectionModel().getSelectedItems().addListener(new ListChangeListener<PathObject>() {
@Override
public void onChanged(ListChangeListener.Change<? extends PathObject> c) {
synchronizeSelectionModelToTable(hierarchy, c, table);
}
});
StringProperty displayedName = new SimpleStringProperty(ServerTools.getDisplayableImageName(imageData.getServer()));
var title = Bindings.createStringBinding(() -> {
if (type == null)
return "Results " + displayedName.get();
else
return PathObjectTools.getSuitableName(type, false) + " results - " + displayedName.get();
}, displayedName);
// Handle double-click as a way to center on a ROI
// var enter = new KeyCodeCombination(KeyCode.ENTER);
table.setRowFactory(params -> {
var row = new TableRow<PathObject>();
row.setOnMouseClicked(e -> {
if (e.getClickCount() == 2) {
maybeCenterROI(row.getItem());
}
});
// });
return row;
});
// Create columns according to the table model
// for (int i = 0; i < model.getColumnCount(); i++) {
// // Add string column
// if (model.getColumnClass(i).equals(String.class)) {
// TableColumn<PathObject, String> col = null;
// col = new TableColumn<>(model.getColumnName(i));
// col.setCellValueFactory(new Callback<CellDataFeatures<PathObject, String>, ObservableValue<String>>() {
// public ObservableValue<String> call(CellDataFeatures<PathObject, String> val) {
// return new SimpleStringProperty(val.getValue().getDisplayedName());
// }
// });
// col.setCellFactory(column -> new BasicTableCell<String>());
// table.getColumns().add(col);
// }
// }
boolean tmaCoreList = TMACoreObject.class.isAssignableFrom(type);
// Add TMA core columns, if suitable
if (tmaCoreList) {
TableColumn<PathObject, ROI> col = new TableColumn<>("Image");
col.setCellValueFactory(val -> new SimpleObjectProperty<>(val.getValue().getROI()));
double maxWidth = maxDimForTMACore;
double padding = 10;
col.setCellFactory(column -> new TMACoreTableCell(table, imageData.getServer(), maxWidth, padding));
col.widthProperty().addListener((v, o, n) -> table.refresh());
col.setMaxWidth(maxWidth + padding * 2);
table.getColumns().add(col);
// While here, make sure we have fewer bins - don't usually have all that many cores
histogramDisplay.setNumBins(10);
}
// Create numeric columns
for (String columnName : model.getAllNames()) {
// Add column
if (model.isStringMeasurement(columnName)) {
TableColumn<PathObject, String> col = new TableColumn<>(columnName);
col.setCellValueFactory(column -> model.createStringMeasurement(column.getValue(), column.getTableColumn().getText()));
col.setCellFactory(column -> new BasicTableCell<>());
table.getColumns().add(col);
} else {
TableColumn<PathObject, Number> col = new TableColumn<>(columnName);
col.setCellValueFactory(column -> model.createNumericMeasurement(column.getValue(), column.getTableColumn().getText()));
col.setCellFactory(column -> new NumericTableCell<PathObject>(histogramDisplay));
table.getColumns().add(col);
}
}
// Set the PathObjects - need to deal with sorting, since a FilteredList won't handle it directly
SortedList<PathObject> items = new SortedList<>(model.getItems());
items.comparatorProperty().bind(table.comparatorProperty());
table.setItems(items);
List<ButtonBase> buttons = new ArrayList<>();
ToggleButton btnHistogram = new ToggleButton("Show histograms");
btnHistogram.selectedProperty().addListener((v, o, n) -> {
if (n) {
Pane paneHistograms = histogramDisplay.getPane();
splitPane.getItems().add(paneHistograms);
} else if (histogramDisplay != null)
splitPane.getItems().remove(histogramDisplay.getPane());
});
buttons.add(btnHistogram);
// Button btnScatterplot = new Button("Show scatterplots");
// btnScatterplot.setOnAction(e -> {
// SwingUtilities.invokeLater(() -> {
// JDialog dialog = new ScatterplotDisplay(null, "Scatterplots: " + displayedName, model).getDialog();
// dialog.setLocationRelativeTo(null);
// dialog.setVisible(true);
// });
// });
// buttons.add(btnScatterplot);
Button btnCopy = new Button("Copy to clipboard");
btnCopy.setOnAction(e -> {
// TODO: Deal with repetition immediately below...
Set<String> excludeColumns = new HashSet<>();
for (TableColumn<?, ?> col : table.getColumns()) {
if (!col.isVisible())
excludeColumns.add(col.getText());
}
copyTableContentsToClipboard(model, excludeColumns);
});
buttons.add(btnCopy);
Button btnSave = new Button("Save");
btnSave.setOnAction(e -> {
Set<String> excludeColumns = new HashSet<>();
for (TableColumn<?, ?> col : table.getColumns()) {
if (!col.isVisible())
excludeColumns.add(col.getText());
}
File fileOutput = promptForOutputFile();
if (fileOutput == null)
return;
if (saveTableModel(model, fileOutput, excludeColumns)) {
WorkflowStep step;
String includeColumns;
if (excludeColumns.isEmpty())
includeColumns = "";
else {
List<String> includeColumnList = new ArrayList<>(model.getAllNames());
includeColumnList.removeAll(excludeColumns);
includeColumns = ", " + includeColumnList.stream().map(s -> "'" + s + "'").collect(Collectors.joining(", "));
}
String path = qupath.getProject() == null ? fileOutput.toURI().getPath() : fileOutput.getParentFile().toURI().getPath();
if (type == TMACoreObject.class) {
step = new DefaultScriptableWorkflowStep("Save TMA measurements", String.format("saveTMAMeasurements('%s'%s)", path, includeColumns));
} else if (type == PathAnnotationObject.class) {
step = new DefaultScriptableWorkflowStep("Save annotation measurements", String.format("saveAnnotationMeasurements('%s\'%s)", path, includeColumns));
} else if (type == PathDetectionObject.class) {
step = new DefaultScriptableWorkflowStep("Save detection measurements", String.format("saveDetectionMeasurements('%s'%s)", path, includeColumns));
} else {
step = new DefaultScriptableWorkflowStep("Save measurements", String.format("saveMeasurements('%s', %s%s)", path, type == null ? null : type.getName(), includeColumns));
}
imageData.getHistoryWorkflow().addStep(step);
}
});
buttons.add(btnSave);
Stage frame = new Stage();
frame.initOwner(qupath.getStage());
frame.titleProperty().bind(title);
BorderPane paneTable = new BorderPane();
paneTable.setCenter(table);
// Add text field to filter visible columns
TextField tfColumnFilter = new TextField();
GridPane paneFilter = new GridPane();
paneFilter.add(new Label("Column filter"), 0, 0);
paneFilter.add(tfColumnFilter, 1, 0);
GridPane.setHgrow(tfColumnFilter, Priority.ALWAYS);
paneFilter.setHgap(5);
if (tmaCoreList) {
CheckBox cbHideMissing = new CheckBox("Hide missing cores");
paneFilter.add(cbHideMissing, 2, 0);
cbHideMissing.selectedProperty().addListener((v, o, n) -> {
if (n) {
model.setPredicate(p -> (!(p instanceof TMACoreObject)) || !((TMACoreObject) p).isMissing());
} else
model.setPredicate(null);
});
cbHideMissing.setSelected(true);
}
paneFilter.setPadding(new Insets(2, 5, 2, 5));
paneTable.setBottom(paneFilter);
StringProperty columnFilter = tfColumnFilter.textProperty();
columnFilter.addListener((v, o, n) -> {
String val = n.toLowerCase().trim();
if (val.isEmpty()) {
for (TableColumn<?, ?> col : table.getColumns()) {
if (!col.isVisible())
col.setVisible(true);
}
return;
}
for (TableColumn<?, ?> col : table.getColumns()) {
col.setVisible(col.getText().toLowerCase().contains(val));
}
});
BorderPane pane = new BorderPane();
// pane.setCenter(table);
splitPane.getItems().add(paneTable);
pane.setCenter(splitPane);
GridPane panelButtons = PaneTools.createColumnGridControls(buttons.toArray(new ButtonBase[0]));
pane.setBottom(panelButtons);
PathObjectHierarchyListener listener = new PathObjectHierarchyListener() {
@Override
public void hierarchyChanged(PathObjectHierarchyEvent event) {
if (event.isChanging())
return;
if (!Platform.isFxApplicationThread()) {
Platform.runLater(() -> hierarchyChanged(event));
return;
}
if (imageData != null)
displayedName.set(ServerTools.getDisplayableImageName(imageData.getServer()));
model.refreshEntries();
table.refresh();
if (histogramDisplay != null)
histogramDisplay.refreshHistogram();
}
};
QuPathViewer viewer = qupath.getViewer();
TableViewerListener tableViewerListener = new TableViewerListener(viewer, table);
frame.setOnShowing(e -> {
hierarchy.addPathObjectListener(listener);
viewer.addViewerListener(tableViewerListener);
});
frame.setOnHiding(e -> {
hierarchy.removePathObjectListener(listener);
viewer.removeViewerListener(tableViewerListener);
});
Scene scene = new Scene(pane, 600, 500);
frame.setScene(scene);
frame.show();
// Add ability to remove entries from table
ContextMenu menu = new ContextMenu();
Menu menuLimitClasses = new Menu("Show classes");
menu.setOnShowing(e -> {
Set<PathClass> representedClasses = model.getBackingListEntries().stream().map(p -> p.getPathClass() == null ? null : p.getPathClass().getBaseClass()).collect(Collectors.toCollection(() -> new HashSet<>()));
representedClasses.remove(null);
if (representedClasses.isEmpty()) {
menuLimitClasses.setVisible(false);
} else {
menuLimitClasses.setVisible(true);
}
menuLimitClasses.getItems().clear();
List<PathClass> sortedClasses = new ArrayList<>(representedClasses);
Collections.sort(sortedClasses);
MenuItem miClass = new MenuItem("All");
miClass.setOnAction(e2 -> {
model.setPredicate(null);
histogramDisplay.refreshHistogram();
});
menuLimitClasses.getItems().add(miClass);
for (PathClass pathClass : sortedClasses) {
miClass = new MenuItem(pathClass.getName());
miClass.setOnAction(e2 -> {
model.setPredicate(p -> pathClass.isAncestorOf(p.getPathClass()));
histogramDisplay.refreshHistogram();
});
menuLimitClasses.getItems().add(miClass);
}
});
if (type != TMACoreObject.class) {
menu.getItems().add(menuLimitClasses);
table.setContextMenu(menu);
}
}
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