package org.autoplot.jythonsupport; import java.awt.Color; import java.io.File; import java.io.IOException; import java.net.URISyntaxException; import java.text.ParseException; import java.util.LinkedHashMap; import java.util.Map; import java.util.logging.Logger; import org.autoplot.datasource.FileSystemUtil; import org.das2.datum.Datum; import org.das2.datum.DatumRange; import org.das2.datum.Units; import org.python.core.Py; import org.python.core.PyArray; import org.python.core.PyDictionary; import org.das2.qds.QubeDataSetIterator; import org.python.core.PyFloat; import org.python.core.PyFunction; import org.python.core.PyInteger; import org.python.core.PyJavaInstance; import org.python.core.PyList; import org.python.core.PyLong; import org.python.core.PyNone; import org.python.core.PyObject; import org.python.core.PyString; import org.python.core.PyTuple; import org.das2.qds.DDataSet; import org.das2.qds.DataSetUtil; import org.das2.qds.MutablePropertyDataSet; import org.das2.qds.QDataSet; import org.autoplot.datasource.URISplit; import org.das2.qds.ops.Ops; import org.das2.util.filesystem.FileSystem; import org.das2.util.monitor.ProgressMonitor; /** * Contains operations that are only available to Jython code, and is dependent * on the jython libraries. * * @author jbf */ public class JythonOps { private static final Logger logger= Logger.getLogger("jython"); public static QDataSet applyLambda(QDataSet ds, PyFunction f ) { QubeDataSetIterator it = new QubeDataSetIterator(ds); DDataSet result = DDataSet.create(DataSetUtil.qubeDims(ds)); while (it.hasNext()) { it.next(); double d = it.getValue(ds); PyFloat r = (PyFloat) f.__call__(new PyFloat(d)); it.putValue( result, r.getValue() ); } return result; } public static QDataSet applyLambda( QDataSet ds1, QDataSet ds2, PyFunction f ) { QubeDataSetIterator it = new QubeDataSetIterator(ds1); DDataSet result = DDataSet.create(DataSetUtil.qubeDims(ds1)); while (it.hasNext()) { it.next(); double d1 = it.getValue(ds1); double d2 = it.getValue(ds2); PyFloat r = (PyFloat) f.__call__( new PyFloat(d1), new PyFloat(d2) ); it.putValue( result, r.getValue() ); } return result; } public static QDataSet applyLambda( QDataSet ds1, QDataSet ds2, QDataSet ds3, PyFunction f ) { QubeDataSetIterator it = new QubeDataSetIterator(ds1); DDataSet result = DDataSet.create(DataSetUtil.qubeDims(ds1)); while (it.hasNext()) { it.next(); double d1 = it.getValue(ds1); double d2 = it.getValue(ds2); double d3 = it.getValue(ds3); PyFloat r = (PyFloat) f.__call__( new PyFloat(d1), new PyFloat(d2), new PyFloat(d3) ); it.putValue( result, r.getValue() ); } return result; } // public static QDataSet coerce( PyObject arg0 ) { // System.err.println("======================================================"); // System.err.println("coerce( PyObject ) command that makes a QDataSet is deprecated--use coerceToDs( PyObject ) instead."); // System.err.println("native python coerce command will be available soon. Contact faden @ cottagesystems.com if you need assistance."); // System.err.println(" sleeping for 3 seconds."); // System.err.println("======================================================"); // try { // Thread.sleep(3000); // } catch (InterruptedException ex) { // Logger.getLogger(Util.class.getName()).log(Level.SEVERE, null, ex); // } // return coerceToDs( arg0 ); // } /** * @deprecated use dataset command. * @param arg0 * @return */ public static QDataSet coerceToDs( PyObject arg0 ) { return dataset( arg0 ); } /** * coerce a python array or list into a QDataSet. * @param arg0 Python object or Datum * @return QDataSet * @see org.das2.qds.ops.Ops#dataset(java.lang.Object) */ public static QDataSet dataset( PyObject arg0 ) { if ( arg0 instanceof PyQDataSet ) { return ((PyQDataSet)arg0).rods; } else if ( arg0 instanceof PyDatum ) { return DataSetUtil.asDataSet( ((PyDatum)arg0).datum ); } else if ( arg0 instanceof PyList ) { return PyQDataSetAdapter.adaptList( (PyList)arg0 ) ; } else if ( arg0 instanceof PyArray ) { return PyQDataSetAdapter.adaptArray( (PyArray) arg0 ); } else if ( arg0 instanceof PyTuple ) { return PyQDataSetAdapter.adaptTuple( (PyTuple) arg0 ); } else if ( arg0 instanceof PyInteger ) { return DataSetUtil.asDataSet( ((Double)arg0.__tojava__( Double.class )).doubleValue() ); } else if ( arg0 instanceof PyLong ) { return DataSetUtil.asDataSet( ((Double)arg0.__tojava__( Double.class )).doubleValue() ); } else if ( arg0 instanceof PyFloat ) { return DataSetUtil.asDataSet( ((Double)arg0.__tojava__( Double.class )).doubleValue() ); } else if ( arg0 instanceof PyJavaInstance && ( ((PyJavaInstance)arg0).__tojava__(Datum.class) instanceof Datum ) ) { return DataSetUtil.asDataSet( (Datum)((PyJavaInstance)arg0).__tojava__(org.das2.datum.Datum.class) ); } else if ( arg0 instanceof PyJavaInstance && ( ((PyJavaInstance)arg0).__tojava__(DatumRange.class) instanceof DatumRange ) ) { return DataSetUtil.asDataSet( (DatumRange)((PyJavaInstance)arg0).__tojava__(org.das2.datum.DatumRange.class) ); } else if ( arg0 instanceof PyJavaInstance && ( ((PyJavaInstance)arg0).__tojava__(QDataSet.class) instanceof QDataSet ) ) { return DataSetUtil.asDataSet( ((PyJavaInstance)arg0).__tojava__(QDataSet.class) ); } else if ( arg0 instanceof PyString ) { try { return Ops.dataset(arg0.toString()); } catch (IllegalArgumentException ex) { throw Py.SyntaxError( "unable to parse string: "+arg0 ); } } else if ( arg0 instanceof PyNone ) { // In python code, support test like "ds!=None" return null; } else { throw Py.TypeError("JythonOps is unable to coerce "+arg0+" to QDataSet"); } } /** * coerce Python objects like arrays Lists and Arrays into a QDataSet. * @param arg0 * @param u unit context, which may be ignored for Datums, etc. * @return * @see Ops#dataset(java.lang.Object, org.das2.datum.Units) */ public static QDataSet dataset( PyObject arg0, Units u ) { if ( arg0 instanceof PyQDataSet ) { return ((PyQDataSet)arg0).rods; } else if ( arg0 instanceof PyList ) { return Ops.putProperty( PyQDataSetAdapter.adaptList( (PyList)arg0 ), QDataSet.UNITS, u ); } else if ( arg0 instanceof PyArray ) { return Ops.putProperty( PyQDataSetAdapter.adaptArray( (PyArray) arg0 ), QDataSet.UNITS, u ); } else if ( arg0 instanceof PyInteger ) { return DataSetUtil.asDataSet( ((Double)arg0.__tojava__( Double.class )).doubleValue(), u ); } else if ( arg0 instanceof PyLong ) { return DataSetUtil.asDataSet( ((Double)arg0.__tojava__( Double.class )).doubleValue(), u ); } else if ( arg0 instanceof PyFloat ) { return DataSetUtil.asDataSet( ((Double)arg0.__tojava__( Double.class )).doubleValue(), u ); } else if ( arg0 instanceof PyJavaInstance && ( ((PyJavaInstance)arg0).__tojava__(Datum.class) instanceof Datum ) ) { return DataSetUtil.asDataSet( (Datum)((PyJavaInstance)arg0).__tojava__(org.das2.datum.Datum.class) ); } else if ( arg0 instanceof PyJavaInstance && ( ((PyJavaInstance)arg0).__tojava__(DatumRange.class) instanceof DatumRange ) ) { return DataSetUtil.asDataSet( (DatumRange)((PyJavaInstance)arg0).__tojava__(org.das2.datum.DatumRange.class) ); } else if ( arg0 instanceof PyString ) { try { return DataSetUtil.asDataSet( u.parse(arg0.toString()) ); } catch ( ParseException ex ) { throw Py.SyntaxError( "unable to parse string: "+arg0 ); } catch (IllegalArgumentException ex) { throw Py.SyntaxError( "unable to parse string: "+arg0 ); } } else if ( arg0 instanceof PyNone ) { // In python code, support test like "ds!=None" return null; } else { throw Py.TypeError("JythonOps is unable to coerce "+arg0+" to QDataSet"); } } /** * coerce python objects to Datum * @param arg0 Python object, one of rank 0 dataset, int, float, or String. * @return Datum * @see org.das2.qds.ops.Ops#datum(java.lang.Object) */ public static Datum datum( PyObject arg0 ) { if ( arg0 instanceof PyQDataSet ) { QDataSet ds= ((PyQDataSet)arg0).rods; if ( ds.rank()>0 ) { throw new IllegalArgumentException("QDataSet is not rank zero and cannot be converted to datum: "+ds); } else { return DataSetUtil.asDatum(ds); } } else if ( arg0 instanceof PyDatum ) { return ((PyDatum)arg0).datum; } else if ( arg0 instanceof PyInteger ) { return Units.dimensionless.createDatum(((PyInteger)arg0).getValue()); } else if ( arg0 instanceof PyFloat ) { return Units.dimensionless.createDatum(((PyFloat)arg0).getValue()); } else if ( arg0 instanceof PyJavaInstance ) { return Ops.datum( ((PyJavaInstance)arg0).__tojava__(java.lang.Object.class) ); } else if ( arg0 instanceof PyString ) { return Ops.datum(arg0.toString()); } else { throw Py.TypeError("unable to coerce "+arg0+" to Datum"); } } /** * coerce python objects to DatumRange * See http://jfaden.net:8080/hudson/job/autoplot-test029/ * This supports: * @param arg0 PyQDataSet, String, array or List. * @throws IllegalArgumentException if the argument cannot be parsed or converted. * @return DatumRange */ public static DatumRange datumRange( PyObject arg0 ) { if ( arg0 instanceof PyQDataSet ) { QDataSet ds= ((PyQDataSet)arg0).rods; if ( ds.rank()>1 ) { throw new IllegalArgumentException("QDataSet is not rank one and cannot be converted to datumRange: "+ds); } else { return DataSetUtil.asDatumRange(ds); } } else if ( arg0 instanceof PyList ) { PyObject p1= ((PyList)arg0).__getitem__(0); PyObject p2= ((PyList)arg0).__getitem__(1); return new DatumRange( datum( p1 ), datum( p2 ) ); } else if ( arg0 instanceof PyArray ) { PyObject p1= ((PyArray)arg0).__getitem__(0); PyObject p2= ((PyArray)arg0).__getitem__(1); return new DatumRange( datum( p1 ), datum( p2 ) ); } else if ( arg0 instanceof PyJavaInstance ) { return Ops.datumRange( ((PyJavaInstance)arg0).__tojava__(java.lang.Object.class) ); } else if ( arg0 instanceof PyString ) { return Ops.datumRange(arg0.toString()); } else { throw Py.TypeError("unable to coerce "+arg0+" to DatumRange"); } } /** * coerce python objects to DatumRange, when the units are known. * * @param arg0 PyQDataSet, String, array or List. * @param context the units. * @return range with the same magnitude, but context units. */ public static DatumRange datumRange( PyObject arg0, Units context ) { DatumRange newRange= JythonOps.datumRange(arg0); if ( ! context.isConvertibleTo(newRange.getUnits()) ) { newRange= DatumRange.newDatumRange( newRange.min().value(), newRange.max().value(), context ); } else if ( context!=newRange.getUnits() ) { newRange= new DatumRange( newRange.min().convertTo(context), newRange.max().convertTo(context) ); } return newRange; } /** * get the color from the python object, for example: * * @param val the value * @return java.awt.Color */ public static Color color( PyObject val ) { Color c=null; if (val==Py.None) { c= new Color( 0, 0, 0, 0 ); } else if (val.__tojava__(Color.class) != Py.NoConversion) { c = (Color) val.__tojava__(Color.class); } else if (val instanceof PyFloat) { c = new Color((int) ((PyFloat) val).getValue()); } else if (val instanceof PyInteger) { c = new Color(((PyInteger) val).getValue()); } else if (val instanceof PyQDataSet) { c = new Color((int) ((PyQDataSet) val).getQDataSet().value()); } else if (val instanceof PyTuple) { String sval= val.toString(); sval= sval.substring(1,sval.length()-1); if (sval != null) { c = Ops.colorFromString(sval); } else { throw new IllegalArgumentException("can't identify color"); } } else { String sval = (String) val.__str__().__tojava__(String.class); if (sval != null) { c = Ops.colorFromString(sval); } else { throw new IllegalArgumentException("can't identify color"); } } return c; } /** * download the resource, unpack it, and add it to the search path. Note * such scripts will not work with Webstart releases! * * Here is an example use: * 
{@code
     *import sys
     *addToSearchPath( sys.path, 'http://www-us.apache.org/dist//commons/math/binaries/commons-math3-3.6.1-bin.zip/commons-math3-3.6.1/commons-math3-3.6.1.jar', monitor )
     *from org.apache.commons.math3.distribution import BetaDistribution
     *beta= BetaDistribution(2,5)
     *
     *xx= linspace(0,1.0,100)
     *yy= zeros(100)
     *for i in indgen(100):
     *    yy[i]= beta.density(xx[i].value())
     *#yy= map( xx, beta.density )
     *plot( xx, yy )
     *}
* @param syspath the list of folders to search, should be sys.path. * @param path the path to add, which should be a jar file, possibly contained within a zip on an http site. * @param mon monitor for the download. * @return the name of the folder or jar file added. * @see https://sourceforge.net/p/autoplot/feature-requests/584/, which shows * @throws IOException * @throws URISyntaxException */ public static String addToSearchPath( PyList syspath, String path, ProgressMonitor mon ) throws IOException, URISyntaxException { if ( System.getProperty("javawebstart.version")!=null ) { logger.warning("Jython addToSearchPath will probably fail because this is not supported with Webstart."); } if ( path.endsWith(".jar") ) { File jarFile= FileSystemUtil.doDownload( path, mon ); File destDir= FileSystem.settings().getLocalCacheDir(); destDir= new File( destDir, "jar" ); String ss= path.replace("://", "/"); destDir= new File( destDir, ss ); org.das2.util.filesystem.FileSystemUtil.unzipFile( jarFile, destDir); syspath.append( new PyString(destDir.toString()) ); return destDir.toString(); } else { throw new IllegalArgumentException("only jar files can be added."); } } /** * convenience method for creating URIs. * @param vapScheme null or the data source scheme, such as "vap+das2server" or "vap+cdaweb" * @param resourceUri null or the resource uri, such as "http://www-pw.physics.uiowa.edu/das/das2Server" * @param args null or a map/dictionary of arguments, including "arg_0" for a positional argument. * @return the URI. If vapScheme is null, then the URI will be implicit. */ public static String formUri( String vapScheme, String resourceUri, Object args ) { Map jargs= new LinkedHashMap(); if ( args!=null ) { if ( args instanceof PyDictionary ) { PyDictionary pd= (PyDictionary)args; for ( Object k: pd.keys() ) { jargs.put( String.valueOf(k), String.valueOf( pd.get( new PyString( String.valueOf(k) ) ) ) ); // TODO: surely there's an easier way } } else if ( args instanceof Map ) { Map m= (Map)args; for ( Object k: ((Map)args).keySet() ) { jargs.put( String.valueOf(k), m.get( k ) ); } } else { throw new IllegalArgumentException("args cannot be converted to Map"); } } return URISplit.format( vapScheme, resourceUri, jargs ); } /** * converts types often seen in Jython codes to the correct type. For * example, ds= putProperty( ds, 'UNITS', 'seconds since 2012-01-01'). * * @param ds * @param name * @param value * @return the dataset, possibly converted to a mutable dataset. */ public static MutablePropertyDataSet putProperty( QDataSet ds, String name, Object value ) { return Ops.putProperty( ds, name, value ); } /** * run the function on a different thread * @param func a jython callable. */ public static void invokeSometime( final PyObject func ) { Runnable run= new Runnable() { public void run() { func.__call__(); } }; new Thread(run).start(); } /** * run the function on a different thread * @param func a jython callable. * @param arg an object to pass to the callable as an argument */ public static void invokeSometime( final PyObject func, final PyObject arg ) { Runnable run= new Runnable() { public void run() { func.__call__(arg); } }; new Thread(run).start(); } }