plugins/ScreenPanel.java

@@ -16,12 +16,11 @@ import ch.psi.utils.swing.TextEditor;
 import ch.psi.pshell.bs.PipelineServer;
 import ch.psi.pshell.bs.StreamValue;
 import ch.psi.pshell.core.JsonSerializer;
-import ch.psi.pshell.device.DescStatsDouble;
+import ch.psi.pshell.data.DataManager;
 import ch.psi.pshell.device.Device;
 import ch.psi.pshell.epics.ChannelInteger;
 import ch.psi.pshell.epics.DiscretePositioner;
 import ch.psi.pshell.epics.Epics;
-import ch.psi.pshell.imaging.Calibration;
 import ch.psi.pshell.imaging.Colormap;
 import ch.psi.pshell.imaging.ColormapSource;
 import ch.psi.pshell.imaging.ColormapSource.ColormapSourceConfig;
@@ -66,7 +65,6 @@ import java.awt.event.WindowEvent;
 import java.awt.image.BufferedImage;
 import java.io.FileInputStream;
 import java.lang.reflect.Array;
-import java.lang.reflect.Field;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.ArrayList;
@@ -147,8 +145,7 @@ public class ScreenPanel extends Panel {
 
         ImageData() {
             if (server != null) {
-                StreamValue cache = server.getStream().take();
-
+                cache = server.getStream().take();
                 String prefix = goodRegion ? "gr_" : "";
                 x_fit_mean = getServerDouble(prefix + "x_fit_mean", cache);
                 y_fit_mean = getServerDouble(prefix + "y_fit_mean", cache);
@@ -206,7 +203,8 @@ public class ScreenPanel extends Panel {
         public double[] x_fit_gauss_function;
         public double[] y_profile;
         public double[] y_fit_gauss_function;
-        PointDouble[] sliceCenters;
+        public PointDouble[] sliceCenters;
+        public StreamValue cache;
     }
 
     class Frame extends ImageData {
@@ -752,54 +750,54 @@ public class ScreenPanel extends Panel {
         onChangeColormap(null);
         checkBackground.setEnabled(true);
         if (changed) {
-            comboScreen.setModel(new DefaultComboBoxModel());
-            comboFilter.setModel(new DefaultComboBoxModel());
+            comboScreen.setModel(new DefaultComboBoxModel()); comboScreen.setEnabled(false);
+            comboFilter.setModel(new DefaultComboBoxModel()); comboFilter.setEnabled(false);
+            if (getCameraType(cameraName).equals("ELECTRONS")){
+                //Parallelizing initialization
+                devicesInitTask = new Thread(() -> {
+                    try {
+                        if (cameraName.contains("DSRM")) {
+                            screen = new DiscretePositioner("CurrentScreen", cameraName + ":POSITION_SP", cameraName + ":POSITION");
+                        } else {
+                            screen = new DiscretePositioner("CurrentScreen", cameraName + ":SET_SCREEN1_POS", cameraName + ":GET_SCREEN1_POS");
+                        }
+                        screen.setMonitored(true);
+                        screen.initialize();
+                        DefaultComboBoxModel model = new DefaultComboBoxModel();
+                        for (String pos : screen.getPositions()) {
+                            model.addElement(pos);
+                        }
+                        comboScreen.setModel(model);
+                        comboScreen.setSelectedItem(screen.read());
 
-            //Parallelizing initialization
-            devicesInitTask = new Thread(() -> {
-                try {
-                    if (cameraName.contains("DSRM")) {
-                        screen = new DiscretePositioner("CurrentScreen", cameraName + ":POSITION_SP", cameraName + ":POSITION");
-                    } else {
-                        screen = new DiscretePositioner("CurrentScreen", cameraName + ":SET_SCREEN1_POS", cameraName + ":GET_SCREEN1_POS");
+                    } catch (Exception ex) {
+                        comboScreen.setModel(new DefaultComboBoxModel());
+                        System.err.println(ex.getMessage());
+                        screen = null;
                     }
-                    screen.setMonitored(true);
-                    screen.initialize();
-                    DefaultComboBoxModel model = new DefaultComboBoxModel();
-                    for (String pos : screen.getPositions()) {
-                        model.addElement(pos);
-                    }
-                    comboScreen.setModel(model);
-                    comboScreen.setSelectedItem(screen.read());
+                    comboScreen.setEnabled(screen != null);
+                    valueScreen.setDevice(screen);
 
-                } catch (Exception ex) {
-                    comboScreen.setModel(new DefaultComboBoxModel());
-                    System.err.println(ex.getMessage());
-                    screen = null;
-                }
-                comboScreen.setEnabled(screen != null);
-                valueScreen.setDevice(screen);
-
-                try {
-                    filter = new DiscretePositioner("CurrentFilter", cameraName + ":SET_FILTER", cameraName + ":GET_FILTER");
-                    filter.setMonitored(true);
-                    filter.initialize();
-                    DefaultComboBoxModel model = new DefaultComboBoxModel();
-                    for (String pos : filter.getPositions()) {
-                        model.addElement(pos);
+                    try {
+                        filter = new DiscretePositioner("CurrentFilter", cameraName + ":SET_FILTER", cameraName + ":GET_FILTER");
+                        filter.setMonitored(true);
+                        filter.initialize();
+                        DefaultComboBoxModel model = new DefaultComboBoxModel();
+                        for (String pos : filter.getPositions()) {
+                            model.addElement(pos);
+                        }
+                        comboFilter.setModel(model);
+                        comboFilter.setSelectedItem(filter.read());
+                    } catch (Exception ex) {
+                        System.err.println(ex.getMessage());
+                        filter = null;
                     }
-                    comboFilter.setModel(model);
-                    comboFilter.setSelectedItem(filter.read());
-                } catch (Exception ex) {
-                    System.err.println(ex.getMessage());
-                    filter = null;
-                }
-                comboFilter.setEnabled(filter != null);
-                valueFilter.setDevice(filter);
-            });
-            devicesInitTask.start();
+                    comboFilter.setEnabled(filter != null);
+                    valueFilter.setDevice(filter);
+                });
+                devicesInitTask.start();
+            }
         }
-
     }
 
     volatile Dimension imageSize;
@@ -1622,123 +1620,178 @@ public class ScreenPanel extends Panel {
         }
     }
 
-    void writeFrameMetadata(String path, Frame frame) throws Exception {
-        getContext().getDataManager().setAttribute("/", "Camera", String.valueOf(cameraName));
-        getContext().getDataManager().setAttribute("/", "Screen", String.valueOf(valueScreen.getLabel().getText()));
-        getContext().getDataManager().setAttribute("/", "Filter", String.valueOf(valueFilter.getLabel().getText()));
-        Calibration cal = renderer.getCalibration();
-        getContext().getDataManager().setAttribute("/", "Calibration", cal == null ? new double[]{1, 1, 0, 0}
-                : new double[]{cal.getScaleX(), cal.getScaleY(), cal.getOffsetX(), cal.getOffsetY()});
-        getContext().getDataManager().setAttribute(path, "Timestamp", Chrono.getTimeStr(frame.data.getTimestamp(), "HH:mm:ss.SSS"));
-        if (server != null) {
-            try {
-                getContext().getDataManager().setAttribute("/", "ROI", server.getRoi());
-            } catch (Exception ex) {
-                getContext().getDataManager().setAttribute("/", "ROI", new int[]{0, 0, -1, -1});
-            }
-            if (frame != null) {
-                for (Field f : ImageData.class.getFields()) {
-                    Object value = f.get(frame);
-                    getContext().getDataManager().setAttribute(path, f.getName(), (value == null) ? Double.NaN : value);
-                }
-            }
-            getContext().getDataManager().setAttribute("/", "GoodRegion", goodRegion);
-            getContext().getDataManager().setAttribute("/", "Slicing", slicing);
-            for (String name : new String[]{"x_axis", "y_axis", "gr_x_axis", "gr_y_axis"}) {
-                double[] val = getServerDoubleArray(name);
-                if (val != null) {
-                    getContext().getDataManager().setAttribute("/", name, val);
-                }
-            }
-        }
-    }
-
     void saveSnapshot() throws Exception {
-        getContext().setExecutionPars("snapshot");
-        String path = "/data";
-        String snapshotFile = null;
-        synchronized (imageBuffer) {
-            Frame id = getCurrentFrame();
-            if (id == null) {
-                throw new Exception("No current image");
-            }
-            Object data = id.data.getMatrix();
-            getContext().getDataManager().setDataset(path, data, id.data.isUnsigned());
-            writeFrameMetadata(path, id);
-            getContext().getDataManager().closeOutput();
-            //Enforce the same timestamp to data & image files.
-            //snapshotFile = getContext().getSetup().expandPath("{images}/{date}_{time}_snapshot.png", getContext().getExecutionPars().getStart());        
-            snapshotFile = getContext().getExecutionPars().getPath() + ".png";
-            //renderer.saveSnapshot(snapshotFile, "png", true);            
-            ImageBuffer.saveImage(SwingUtils.createImage(renderer), snapshotFile, "png");
-
-        }
-
-        JPanel panel = new JPanel();
-        GridBagLayout layout = new GridBagLayout();
-        layout.columnWidths = new int[]{0, 180};   //Minimum width
-        layout.rowHeights = new int[]{30, 30, 30};   //Minimum height
-        panel.setLayout(layout);
-        JComboBox comboLogbook = new JComboBox(new String[]{"SwissFEL commissioning data", "SwissFEL commissioning"});
-        JTextField textComment = new JTextField();
-        GridBagConstraints c = new GridBagConstraints();
-        c.gridx = 0;
-        c.gridy = 0;
-        panel.add(new JLabel("Data file:"), c);
-        c.gridy = 1;
-        panel.add(new JLabel("Logbook:"), c);
-        c.gridy = 2;
-        panel.add(new JLabel("Comment:"), c);
-        c.fill = GridBagConstraints.HORIZONTAL;
-        c.gridx = 1;
-        panel.add(textComment, c);
-        c.gridy = 1;
-        panel.add(comboLogbook, c);
-        c.gridy = 0;
-        panel.add(new JLabel(getContext().getExecutionPars().getPath()), c);
-
-        if (SwingUtils.showOption(getTopLevel(), "Success", panel, OptionType.OkCancel) == OptionResult.Yes) {
-            StringBuilder message = new StringBuilder();
-            message.append("Camera: ").append(cameraName).append(" (").
-                    append((server != null) ? "server" : "direct").append(")").append("\n");
-            message.append("Screen: ").append(String.valueOf(valueScreen.getLabel().getText())).append("\n");
-            message.append("Filter: ").append(String.valueOf(valueFilter.getLabel().getText())).append("\n");
-            message.append("Data file: ").append(getContext().getExecutionPars().getPath()).append("\n");
-            message.append("Comment: ").append(textComment.getText()).append("\n");
-            if ((fitOv != null) /*&& (fitOv.length > 5)*/) {
-                for (int i=0; i<fitOv.length; i++ ){
-                    if (fitOv[i] instanceof Overlays.Text){
-                        Overlays.Text text = (Overlays.Text) fitOv[i];
-                        message.append(text.getText()).append("\n");
-                    }
+            String snapshotFile = null;
+            synchronized (imageBuffer) {
+                Frame frame = getCurrentFrame();
+                if (frame == null) {
+                    throw new Exception("No current image");
                 }
+                ArrayList<Frame> frames = new ArrayList<>();
+                frames.add(frame);
+                this.saveFrames("camera_snapshot", frames);
+
+                //Enforce the same timestamp to data & image files.
+                snapshotFile = getContext().getExecutionPars().getPath() + ".png";
+                ImageBuffer.saveImage(SwingUtils.createImage(renderer), snapshotFile, "png");
+            }
+            
+            JPanel panel = new JPanel();
+            GridBagLayout layout = new GridBagLayout();
+            layout.columnWidths = new int[]{0, 180};   //Minimum width
+            layout.rowHeights = new int[]{30, 30, 30};   //Minimum height
+            panel.setLayout(layout);
+            JComboBox comboLogbook = new JComboBox(new String[]{"SwissFEL commissioning data", "SwissFEL commissioning"});
+            JTextField textComment = new JTextField();
+            GridBagConstraints c = new GridBagConstraints();
+            c.gridx = 0;
+            c.gridy = 0;
+            panel.add(new JLabel("Data file:"), c);
+            c.gridy = 1;
+            panel.add(new JLabel("Logbook:"), c);
+            c.gridy = 2;
+            panel.add(new JLabel("Comment:"), c);
+            c.fill = GridBagConstraints.HORIZONTAL;
+            c.gridx = 1;
+            panel.add(textComment, c);
+            c.gridy = 1;
+            panel.add(comboLogbook, c);
+            c.gridy = 0;
+            panel.add(new JLabel(getContext().getExecutionPars().getPath()), c);
+
+            if (SwingUtils.showOption(getTopLevel(), "Success", panel, OptionType.OkCancel) == OptionResult.Yes) {
+                StringBuilder message = new StringBuilder();
+                message.append("Camera: ").append(cameraName).append(" (").
+                        append((server != null) ? "server" : "direct").append(")").append("\n");
+                message.append("Screen: ").append(String.valueOf(valueScreen.getLabel().getText())).append("\n");
+                message.append("Filter: ").append(String.valueOf(valueFilter.getLabel().getText())).append("\n");
+                message.append("Data file: ").append(getContext().getExecutionPars().getPath()).append("\n");
+                message.append("Comment: ").append(textComment.getText()).append("\n");
+                if ((fitOv != null) && (fitOv.length > 5)) {
+                    Overlays.Text text = (Overlays.Text) fitOv[5];
+                    message.append(text.getText()).append("\n");
+                }
+                elog((String) comboLogbook.getSelectedItem(), "ScreenPanel Snapshot", message.toString(), new String[]{snapshotFile});
             }
-            elog((String) comboLogbook.getSelectedItem(), "ScreenPanel Snapshot", message.toString(), new String[]{snapshotFile});
-        }
-        //SwingUtils.showMessage(getTopLevel(), "Success", "Generated data file:\n" + getContext().getExecutionPars().getPath(), 5000);
-        //elog("SwissFEL commissioning data", "ScreenPanel Snapshot", message.toString(), new String[]{snapshotFile});                
     }
 
     void saveStack() throws Exception {
-        getContext().setExecutionPars("snapshot");
-        ArrayList<Double> x = new ArrayList<>();
-        ArrayList<Double> y = new ArrayList<>();
-        synchronized (imageBuffer) {
-            for (int i = 0; i < imageBuffer.size(); i++) {
-                Frame frame = imageBuffer.get(i);
-                String path = "/data_" + i;
-                getContext().getDataManager().setDataset(path, frame.data.getMatrix(), frame.data.isUnsigned());
-                writeFrameMetadata(path, frame);
-                x.add(frame.x_fit_mean);
-                y.add(frame.y_fit_mean);
+            synchronized (imageBuffer) {
+                saveFrames("camera_stack", imageBuffer);
             }
+            SwingUtils.showMessage(getTopLevel(), "Success", "Generated data file:\n" + getContext().getExecutionPars().getPath(), 5000);
+        }
+    
+    
+        public static String getCameraType(String name){
+            for (String s : new String[]{"LCAM"}){
+                if (name.contains(s)){
+                    return "LCAM";
+                }
+            }
+            for (String s : new String[]{"DSCR", "DSRM", "DLAC"}){
+                if (name.contains(s)){
+                    return "ELECTRONS";
+                }
+            }
+            for (String s : new String[]{"PROF", "PPRM", "PSSS", "PSCR", "PSRD"}){
+                if (name.contains(s)){
+                    return "PHOTONICS";
+                }
+            }
+            return "UNKNOWN";      
         }
-        DescStatsDouble xs = new DescStatsDouble(x.toArray(new Double[0]), -1);
-        DescStatsDouble ys = new DescStatsDouble(y.toArray(new Double[0]), -1);
 
-        getContext().getDataManager().closeOutput();
-        SwingUtils.showMessage(getTopLevel(), "Success", "Generated data file:\n" + getContext().getExecutionPars().getPath(), 5000);
-    }
+        public Map<String, Object> getProcessingParameters(StreamValue value) throws IOException {
+            return (Map) JsonSerializer.decode(value.getValue("processing_parameters").toString(), Map.class);
+        }
+    
+        void saveFrames(String name, ArrayList<Frame> frames) throws IOException{
+            ArrayList<StreamValue> values = new ArrayList<>();
+            for (Frame frame : frames){
+                values.add(frame.cache);
+            }
+            saveImages(name, values);
+        }
+
+        void saveImages(String name, ArrayList<StreamValue> images) throws IOException{
+            int depth = images.size();
+            if (depth == 0){
+                return;
+            }
+            StreamValue first = images.get(0);
+            String pathRoot = "/camera1/";
+            String pathImage = pathRoot + "image";
+            String pathPid = pathRoot + "pulse_id";
+            String pathTimestampStr = pathRoot + "timestamp_str";
+            Map<String, Object> processingPars = getProcessingParameters(first);
+            String camera = (String) processingPars.get("camera_name");
+            String type = getCameraType(camera);
+            
+            int width = ((Number)first.getValue("width")).intValue();
+            int height = ((Number)first.getValue("height")).intValue();
+            Class dataType = first.getValue("image").getClass().getComponentType();
+            
+            getContext().setExecutionPars(name);
+            DataManager dm = getContext().getDataManager();                        
+            
+            //Create tables            
+            dm.createDataset(pathImage, dataType, new int[]{depth, height, width});
+            dm.createDataset(pathPid, Long.class, new int[]{depth});
+            dm.createDataset(pathTimestampStr, String.class, new int[]{depth});
+            for (String id : first.getIdentifiers()){
+                Object val = first.getValue(id);
+                if (id.equals("image")){
+                } else if (id.equals("processing_parameters")){
+                    Map<String, Object> pars = getProcessingParameters(first);
+                    for (String key : pars.keySet()){
+                        if ((pars.get(key) != null) && (pars.get(key) instanceof Map)){    
+                            for (Object k : ((Map)pars.get(key)).keySet()){
+                                Object v = ((Map)pars.get(key)).get(k);
+                                dm.setAttribute(pathImage, key + " " + k, (v == null)? "" : v);
+                            }
+                        } else {
+                            dm.setAttribute(pathImage, key, (pars.get(key) == null)? "" : pars.get(key));
+                        }
+                    }
+                } else if (val.getClass().isArray()) {
+                     dm.createDataset(pathRoot + id, Double.class, new int[]{depth, Array.getLength(val)});                        
+                } else {
+                     dm.createDataset(pathRoot + id, val.getClass(), new int[]{depth});          
+                }
+            }           
+            
+            //Add metadata
+            dm.setAttribute(pathRoot,"Camera", camera);
+            dm.setAttribute(pathRoot,"Images", depth);
+            dm.setAttribute(pathRoot,"Interval", -1);
+            dm.setAttribute(pathRoot,"Type", type);
+            if (type.equals("ELECTRONS")){
+                dm.setAttribute(pathRoot,"Screen", String.valueOf(valueScreen.getLabel().getText()));
+                dm.setAttribute(pathRoot,"Filter", String.valueOf(valueFilter.getLabel().getText()));
+            }
+            
+            //Save data
+            for (int index=0; index<depth; index++){
+                StreamValue streamValue = images.get(index);
+                dm.setItem(pathImage, streamValue.getValue("image"),  new long[]{index,0,0}, new int[]{1, height, width});
+                dm.setItem(pathPid, streamValue.getPulseId(), index);
+                dm.setItem(pathTimestampStr, Chrono.getTimeStr(streamValue.getTimestamp(), "YYYY-MM-dd HH:mm:ss.SSS") , index);
+                
+                for (String id : streamValue.getIdentifiers()){
+                    Object val = streamValue.getValue(id);
+                    if (id.equals("image")){
+                    } else if (id.equals("processing_parameters")){
+                    } else if (val.getClass().isArray()) {
+                         dm.setItem(pathRoot + id, val, index);                        
+                    } else {
+                         dm.setItem(pathRoot + id, val, index);                        
+                    }
+                }                           
+            }
+            getContext().getDataManager().closeOutput();            
+        }
+    
 
     StandardDialog calibrationDialolg;