package org.autoplot.netCDF; import java.awt.Window; import java.io.File; import java.io.IOException; import java.util.ArrayList; import java.util.LinkedHashMap; import java.util.List; import java.util.Map; import java.util.Map.Entry; import java.util.logging.Level; import java.util.logging.Logger; import javax.swing.DefaultComboBoxModel; import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JTree; import javax.swing.tree.DefaultMutableTreeNode; import javax.swing.tree.DefaultTreeModel; import javax.swing.tree.TreePath; import org.das2.util.DasExceptionHandler; import org.das2.util.LoggerManager; import org.das2.util.filesystem.FileSystem; import org.das2.util.monitor.NullProgressMonitor; import org.das2.util.monitor.ProgressMonitor; import org.autoplot.datasource.DataSetURI; import org.autoplot.datasource.DataSourceEditorPanel; import org.autoplot.datasource.URISplit; import static org.autoplot.netCDF.NetCDFDataSourceFactory.checkMatlab; import ucar.ma2.DataType; import ucar.nc2.Attribute; import ucar.nc2.Dimension; import ucar.nc2.NetcdfFile; import ucar.nc2.Structure; import ucar.nc2.Variable; import ucar.nc2.dataset.NetcdfDataset; /** * Editor panel for HDF5 files. * @author faden@cottagesystems.com */ public class HDF5DataSourceEditorPanel extends javax.swing.JPanel implements DataSourceEditorPanel { private String vapScheme; Map allParameterInfo; /** * Creates new form HDF5DataSourceEditorPanel */ public HDF5DataSourceEditorPanel() { initComponents(); } /** * This method is called from within the constructor to initialize the form. * WARNING: Do NOT modify this code. The content of this method is always * regenerated by the Form Editor. */ @SuppressWarnings("unchecked") // //GEN-BEGIN:initComponents private void initComponents() { bindingGroup = new org.jdesktop.beansbinding.BindingGroup(); jSplitPane2 = new javax.swing.JSplitPane(); jSplitPane1 = new javax.swing.JSplitPane(); advancedPanel = new javax.swing.JPanel(); jLabel5 = new javax.swing.JLabel(); subsetComboBox = new javax.swing.JComboBox(); whereCB = new javax.swing.JCheckBox(); whereParamList = new javax.swing.JComboBox(); whereOp = new javax.swing.JComboBox(); whereTF = new javax.swing.JTextField(); jTabbedPane1 = new javax.swing.JTabbedPane(); jScrollPane1 = new javax.swing.JScrollPane(); parameterTree = new javax.swing.JTree(); jPanel1 = new javax.swing.JPanel(); jScrollPane3 = new javax.swing.JScrollPane(); xParameterTree = new javax.swing.JTree(); xCheckBox = new javax.swing.JCheckBox(); jPanel3 = new javax.swing.JPanel(); jScrollPane4 = new javax.swing.JScrollPane(); yParameterTree = new javax.swing.JTree(); yCheckBox = new javax.swing.JCheckBox(); parameterInfoLabel = new javax.swing.JLabel(); jSplitPane2.setOrientation(javax.swing.JSplitPane.VERTICAL_SPLIT); jSplitPane2.setResizeWeight(0.5); advancedPanel.setBorder(javax.swing.BorderFactory.createTitledBorder("Advanced")); advancedPanel.setMaximumSize(new java.awt.Dimension(285, 32767)); jLabel5.setText("Load subset of the data:"); jLabel5.setToolTipText("Load a subset of the data records, for example:
[0:100] first 100 records
[-100:] last 100 records
[::10] every tenth record
"); subsetComboBox.setEditable(true); subsetComboBox.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "", "::10", "0:100", "-100:", "0:10000:5" })); subsetComboBox.setToolTipText("Load a subset of the data records, for example:
[0:100] first 100 records
[-100:] last 100 records
[::10] every tenth record
"); whereCB.setText("Only load data where:"); whereCB.setToolTipText("return only the records where the condition is true"); whereParamList.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "Item 1", "Item 2", "Item 3", "Item 4" })); org.jdesktop.beansbinding.Binding binding = org.jdesktop.beansbinding.Bindings.createAutoBinding(org.jdesktop.beansbinding.AutoBinding.UpdateStrategy.READ_WRITE, whereCB, org.jdesktop.beansbinding.ELProperty.create("${selected}"), whereParamList, org.jdesktop.beansbinding.BeanProperty.create("enabled")); bindingGroup.addBinding(binding); whereOp.setModel(new javax.swing.DefaultComboBoxModel(new String[] { ".eq", ".gt", ".lt", ".ne", ".within" })); binding = org.jdesktop.beansbinding.Bindings.createAutoBinding(org.jdesktop.beansbinding.AutoBinding.UpdateStrategy.READ_WRITE, whereCB, org.jdesktop.beansbinding.ELProperty.create("${selected}"), whereOp, org.jdesktop.beansbinding.BeanProperty.create("enabled")); bindingGroup.addBinding(binding); whereTF.setText("0"); whereTF.setToolTipText("enter the value, or \"mode\" for the most frequently occuring value."); binding = org.jdesktop.beansbinding.Bindings.createAutoBinding(org.jdesktop.beansbinding.AutoBinding.UpdateStrategy.READ_WRITE, whereCB, org.jdesktop.beansbinding.ELProperty.create("${selected}"), whereTF, org.jdesktop.beansbinding.BeanProperty.create("enabled")); bindingGroup.addBinding(binding); javax.swing.GroupLayout advancedPanelLayout = new javax.swing.GroupLayout(advancedPanel); advancedPanel.setLayout(advancedPanelLayout); advancedPanelLayout.setHorizontalGroup( advancedPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING) .addGroup(advancedPanelLayout.createSequentialGroup() .addContainerGap() .addComponent(whereParamList, 0, 161, Short.MAX_VALUE) .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED) .addComponent(whereOp, javax.swing.GroupLayout.PREFERRED_SIZE, 84, javax.swing.GroupLayout.PREFERRED_SIZE) .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED) .addComponent(whereTF, javax.swing.GroupLayout.PREFERRED_SIZE, 53, javax.swing.GroupLayout.PREFERRED_SIZE)) .addGroup(advancedPanelLayout.createSequentialGroup() .addGroup(advancedPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING) .addComponent(jLabel5) .addComponent(whereCB) .addGroup(advancedPanelLayout.createSequentialGroup() .addContainerGap() .addComponent(subsetComboBox, javax.swing.GroupLayout.PREFERRED_SIZE, 175, javax.swing.GroupLayout.PREFERRED_SIZE))) .addGap(0, 135, Short.MAX_VALUE)) ); advancedPanelLayout.setVerticalGroup( advancedPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING) .addGroup(advancedPanelLayout.createSequentialGroup() .addComponent(jLabel5) .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED) .addComponent(subsetComboBox, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE) .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED) .addComponent(whereCB) .addGap(8, 8, 8) .addGroup(advancedPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE) .addComponent(whereParamList, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE) .addComponent(whereOp, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE) .addComponent(whereTF, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)) .addContainerGap(245, Short.MAX_VALUE)) ); jSplitPane1.setRightComponent(advancedPanel); jTabbedPane1.setToolTipText("\"plot\" selects the dependent parameter for plotting. \"x\" allows specification of an independent parameter upon which the \"plot\" parameter depends."); parameterTree.setRootVisible(false); parameterTree.addTreeSelectionListener(new javax.swing.event.TreeSelectionListener() { public void valueChanged(javax.swing.event.TreeSelectionEvent evt) { parameterTreeValueChanged(evt); } }); jScrollPane1.setViewportView(parameterTree); jTabbedPane1.addTab("select variable", jScrollPane1); xParameterTree.setRootVisible(false); xParameterTree.addTreeSelectionListener(new javax.swing.event.TreeSelectionListener() { public void valueChanged(javax.swing.event.TreeSelectionEvent evt) { xParameterTreeValueChanged(evt); } }); jScrollPane3.setViewportView(xParameterTree); xCheckBox.setText("Set Variable for X"); xCheckBox.setToolTipText("Specify the parameter to use for the X tags, overriding any settings found in the file.\n"); javax.swing.GroupLayout jPanel1Layout = new javax.swing.GroupLayout(jPanel1); jPanel1.setLayout(jPanel1Layout); jPanel1Layout.setHorizontalGroup( jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING) .addComponent(jScrollPane3) .addGroup(javax.swing.GroupLayout.Alignment.TRAILING, jPanel1Layout.createSequentialGroup() .addContainerGap() .addComponent(xCheckBox) .addContainerGap(196, Short.MAX_VALUE)) ); jPanel1Layout.setVerticalGroup( jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING) .addGroup(jPanel1Layout.createSequentialGroup() .addComponent(xCheckBox) .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED) .addComponent(jScrollPane3, javax.swing.GroupLayout.DEFAULT_SIZE, 338, Short.MAX_VALUE)) ); jTabbedPane1.addTab("X", jPanel1); jPanel3.setAlignmentX(0.0F); yParameterTree.setRootVisible(false); yParameterTree.addTreeSelectionListener(new javax.swing.event.TreeSelectionListener() { public void valueChanged(javax.swing.event.TreeSelectionEvent evt) { yParameterTreeValueChanged(evt); } }); jScrollPane4.setViewportView(yParameterTree); yCheckBox.setText("Set Variable for Y"); yCheckBox.setToolTipText("Specify the parameter to use for the X tags, overriding any settings found in the file. "); javax.swing.GroupLayout jPanel3Layout = new javax.swing.GroupLayout(jPanel3); jPanel3.setLayout(jPanel3Layout); jPanel3Layout.setHorizontalGroup( jPanel3Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING) .addComponent(jScrollPane4) .addGroup(jPanel3Layout.createSequentialGroup() .addContainerGap() .addComponent(yCheckBox) .addGap(0, 196, Short.MAX_VALUE)) ); jPanel3Layout.setVerticalGroup( jPanel3Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING) .addGroup(jPanel3Layout.createSequentialGroup() .addComponent(yCheckBox) .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED) .addComponent(jScrollPane4, javax.swing.GroupLayout.DEFAULT_SIZE, 338, Short.MAX_VALUE)) ); jTabbedPane1.addTab("Y", jPanel3); jSplitPane1.setLeftComponent(jTabbedPane1); jSplitPane2.setTopComponent(jSplitPane1); parameterInfoLabel.setText("jLabel1"); parameterInfoLabel.setVerticalAlignment(javax.swing.SwingConstants.TOP); parameterInfoLabel.setMinimumSize(new java.awt.Dimension(49, 100)); jSplitPane2.setRightComponent(parameterInfoLabel); javax.swing.GroupLayout layout = new javax.swing.GroupLayout(this); this.setLayout(layout); layout.setHorizontalGroup( layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING) .addComponent(jSplitPane2) ); layout.setVerticalGroup( layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING) .addComponent(jSplitPane2, javax.swing.GroupLayout.Alignment.TRAILING, javax.swing.GroupLayout.DEFAULT_SIZE, 505, Short.MAX_VALUE) ); bindingGroup.bind(); }// //GEN-END:initComponents private void parameterTreeValueChanged(javax.swing.event.TreeSelectionEvent evt) {//GEN-FIRST:event_parameterTreeValueChanged TreePath tp= evt.getPath(); parameter= String.valueOf(tp.getPathComponent(1)); // String longName= parameters.get(parameter); String longName= ""+ parameters.get(parameter) + "
" + allParameterInfo.get(parameter) + ""; parameterInfoLabel.setText( longName ); String dims= longName.substring(parameter.length()); List varnames= new ArrayList<>(); for ( Entry ps : parameters.entrySet() ) { String v= ps.getValue(); int i= v.indexOf("["); if ( dims.startsWith( v.substring(i,v.length()-1) ) ) { varnames.add(ps.getKey()); } } whereParamList.setModel( new DefaultComboBoxModel( varnames.toArray() ) ); }//GEN-LAST:event_parameterTreeValueChanged private void xParameterTreeValueChanged(javax.swing.event.TreeSelectionEvent evt) {//GEN-FIRST:event_xParameterTreeValueChanged xCheckBox.setSelected(true); }//GEN-LAST:event_xParameterTreeValueChanged private void yParameterTreeValueChanged(javax.swing.event.TreeSelectionEvent evt) {//GEN-FIRST:event_yParameterTreeValueChanged yCheckBox.setSelected(true); }//GEN-LAST:event_yParameterTreeValueChanged // Variables declaration - do not modify//GEN-BEGIN:variables private javax.swing.JPanel advancedPanel; private javax.swing.JLabel jLabel5; private javax.swing.JPanel jPanel1; private javax.swing.JPanel jPanel3; private javax.swing.JScrollPane jScrollPane1; private javax.swing.JScrollPane jScrollPane3; private javax.swing.JScrollPane jScrollPane4; private javax.swing.JSplitPane jSplitPane1; private javax.swing.JSplitPane jSplitPane2; private javax.swing.JTabbedPane jTabbedPane1; private javax.swing.JLabel parameterInfoLabel; private javax.swing.JTree parameterTree; private javax.swing.JComboBox subsetComboBox; private javax.swing.JCheckBox whereCB; private javax.swing.JComboBox whereOp; private javax.swing.JComboBox whereParamList; private javax.swing.JTextField whereTF; private javax.swing.JCheckBox xCheckBox; private javax.swing.JTree xParameterTree; private javax.swing.JCheckBox yCheckBox; private javax.swing.JTree yParameterTree; private org.jdesktop.beansbinding.BindingGroup bindingGroup; // End of variables declaration//GEN-END:variables private static final Logger logger= LoggerManager.getLogger("apdss.hdf5"); URISplit split; /** * URI parameters, like arg_0. */ Map params; /** * parameter name to short descriptions of the parameter. */ Map parameters= new LinkedHashMap(); /** * the parameter within the HDF5 file to be plotted. */ String parameter; /** * the variables in the HDF5 file. */ List vars; @Override public boolean reject(String uri) throws Exception { split = URISplit.parse(uri); if ( split.resourceUri==null ) { return true; } FileSystem fs = FileSystem.create( DataSetURI.toUri(split.path) ); return fs.isDirectory( split.file.substring(split.path.length()) ); } @Override public boolean prepare(String uri, Window parent, ProgressMonitor mon) throws Exception { split= URISplit.parse(uri); File cdfFile= DataSetURI.getFile( split.resourceUri, mon ); DataSetURI.checkLength(cdfFile); return true; } private void fillTree( JTree parameterTree, Map mm, String param ) { DefaultMutableTreeNode root= new DefaultMutableTreeNode(""); List expand=new ArrayList(mm.size()); TreePath selection=null; for ( Map.Entry e: mm.entrySet() ) { try { DefaultMutableTreeNode node= new DefaultMutableTreeNode( e.getKey() ); root.add( node ); if ( e.getKey().equals(param) ) { selection= new TreePath( new Object[] { root, node } ); } } catch ( Exception t ) { logger.log(Level.WARNING,t.getMessage(),t); } } DefaultTreeModel tm= new DefaultTreeModel( root ); parameterTree.setModel(tm); if ( selection!=null ) { parameterTree.setSelectionPath(selection); parameterTree.scrollPathToVisible(selection); } for ( TreePath tp: expand ) { parameterTree.expandPath(tp); } } @Override public void setURI(String uri) { split= URISplit.parse(uri); vapScheme= split.vapScheme; params= URISplit.parseParams(split.params); try { File cdfFile = DataSetURI.getFile( split.resourceUri, new NullProgressMonitor() ); String fileName= cdfFile.toString(); logger.log(Level.FINE, "opening cdf file {0}", fileName); String resource= fileName; checkMatlab( resource ); NetcdfFile f= NetcdfFile.open( resource ); NetcdfDataset dataset= new NetcdfDataset( f ); vars= (List)dataset.getVariables(); dataset.close(); allParameterInfo= new LinkedHashMap<>(vars.size()); for (Variable v : vars) { if ( v.getDimensions().isEmpty() ) continue; if ( v instanceof Structure ) { for ( Variable v2: ((Structure) v).getVariables() ) { if ( !v2.getDataType().isNumeric() ) continue; StringBuilder description= new StringBuilder( v2.getName()+"[" ); for ( int k=0; k0 ) description.append(","); try { String n= d.getName(); if ( n!=null && !n.equals(v2.getName()) ) { description.append(d.getName()).append("="); } description.append(d.getLength()); } catch ( NullPointerException ex ) { throw ex; } } description.append("]"); parameters.put( v2.getName(), description.toString() ); } } else { boolean isFormattedTime= v.getDataType()==DataType.CHAR && v.getRank()==2 && v.getShape(1)>=14; if ( isFormattedTime ) { logger.log(Level.FINE, "detected formatted time: {0}", v.getName()); } if ( !isFormattedTime && !v.getDataType().isNumeric() ) continue; StringBuilder description= new StringBuilder( v.getName()+"[" ); for ( int k=0; k0 ) description.append(","); try { String n= d.getName(); if ( n!=null && !n.equals(v.getName()) ) { description.append(d.getName()).append("="); } description.append(d.getLength()); } catch ( NullPointerException ex ) { throw ex; } } description.append("]"); // begin small kludge for CDAWeb. List as= v.getAttributes(); for ( Attribute a: as ) { if ( a.getName().equals("CATDESC") ) { description.append("
").append(a.getStringValue()); } } // end small kludge for CDAWeb. parameters.put( v.getName(), description.toString() ); } StringBuilder info= new StringBuilder(); info.append(v.getDescription()); allParameterInfo.put( v.getName(), info.toString() ); } //String label= "Select Parameter (%d parameters):"; int numData= parameters.size(); //this.selectVariableLabel.setText( String.format( label, numData ) ); this.jTabbedPane1.setTitleAt(0,"Select Variable (of "+numData+")"); String param= params.get("arg_0"); String subset= null; if ( param!=null ) { int i= param.indexOf("["); if ( i!=-1 ) { subset= param.substring(i); param= param.substring(0,i); } } fillTree( this.parameterTree, parameters, param ); xParameterTree.setModel( this.parameterTree.getModel() ); String sx= params.get( "x" ); if ( sx!=null ) { fillTree( this.xParameterTree, parameters, sx ); //TODO: tree is filled twice. } yParameterTree.setModel( this.parameterTree.getModel() ); String sy= params.get( "y" ); if ( sy!=null ) { fillTree( this.yParameterTree, parameters, sy ); //TODO: tree is filled twice. } logger.finest("close hdf"); DefaultComboBoxModel cbmodel= new DefaultComboBoxModel(); for ( String p: params.keySet() ) { cbmodel.addElement(p); } if ( param==null ) { if ( !params.isEmpty() ) { parameter= params.entrySet().iterator().next().getKey(); param= parameter; parameterInfoLabel.setText(""); } else { parameterInfoLabel.setText("(no plottable parameters)"); } } if ( param!=null ) { if ( subset!=null ) { if ( subset.startsWith("[") ) subset= subset.substring(1); // note I think they always will. if ( subset.endsWith("]") ) subset= subset.substring(0,subset.length()-1); subsetComboBox.setSelectedItem( subset ); } else { subsetComboBox.setSelectedItem(""); } } if ( parameter!=null ) { parameter= parameter.replaceAll("%3D", "="); } List varnames= new ArrayList<>(); for ( Entry p: parameters.entrySet() ) { varnames.add(p.getKey()); } whereParamList.setModel( new DefaultComboBoxModel( varnames.toArray() ) ); String where= params.get("where"); if ( where!=null && where.length()>0 ) { whereCB.setSelected(true); int i= where.indexOf("."); if ( i>-1 ) { whereParamList.setSelectedItem(where.substring(0,i)); int i0= where.indexOf("("); int i1= where.indexOf(")",i0); whereOp.setSelectedItem(where.substring(i,i0)); whereTF.setText( where.substring(i0+1,i1).replaceAll("\\+"," ")); } } else { whereCB.setSelected(false); } } catch (IOException | IllegalArgumentException | NullPointerException ex) { DasExceptionHandler.handle( ex ); logger.log(Level.SEVERE, ex.getMessage(), ex); } } @Override public void markProblems(List problems) { logger.log(Level.FINE, "markProblems: {0}", problems.toString()); } @Override public JPanel getPanel() { return this; } @Override public String getURI() { String subset= subsetComboBox.getSelectedItem().toString().trim(); if ( subset.length()>0 && subset.charAt(0)!='[' ) { subset= "["+subset+"]"; } String p= parameter; if ( subset.length()>0 ) { p= p+subset; } params.put( "arg_0", p ); if ( xCheckBox.isSelected() ) { TreePath xtp= xParameterTree.getSelectionPath(); if ( xtp!=null ) { Object odep0= xtp.getLastPathComponent() ; params.put( "x", odep0.toString() ); // TODO weak code assumes toString works. } } else { params.remove("x"); } if ( yCheckBox.isSelected() ) { TreePath ytp= yParameterTree.getSelectionPath(); if ( ytp!=null ) { Object oy= ytp.getLastPathComponent() ; params.put( "y", oy.toString() ); // TODO weak code assumes toString works. } } else { params.remove("y"); } if ( whereCB.isSelected() ) { if ( whereParamList.getSelectedItem()!=null ) { params.put( "where", String.format( "%s%s(%s)", whereParamList.getSelectedItem(), whereOp.getSelectedItem(), whereTF.getText().replaceAll(" ","+") ) ); } else { params.remove("where"); } } else { params.remove("where"); } split.vapScheme= vapScheme; split.params= URISplit.formatParams(params); if ( split.params!=null && split.params.length()==0 ) split.params= null; //https://sourceforge.net/p/autoplot/bugs/1913/ return URISplit.format(split); } public static void main( String[] args ) throws Exception { //String uri= "/home/jbf/ct/autoplot/data/hdf/20020908_CRRES_FluxAssimOut.h5"; String uri= "/home/jbf/ct/autoplot/data/hdf/brian/FU1_ZEP_Counts_v1-5681_20110301_v1.0.0.h5"; DataSourceEditorPanel ep= new HDF5DataSourceEditorPanel(); if ( !ep.reject(uri) ) { ep.prepare( uri, null, new NullProgressMonitor() ); ep.setURI( uri ); if ( JOptionPane.showConfirmDialog( null, ep )==JOptionPane.OK_OPTION ) { System.err.println( ep.getURI() ); } } } }