Merge branch 'hotfix-1.0.3.d'

CHANGELOG

 version 1.0.3.c:
 ----------------
+* redirected the sys.stdout and sys.stderr to the LOGGER
+* implemented a write method so as ConsoleHandler behaves as a file-like object
+* the job short name appears now explicitely in the saved job files
+* small refactoring of MDANSE __init__
+* small refactoring of ClassRegistry
+* removed the explicit imports of the framework classes
+* the plotter show the last loaded data now
+* bug fix in rmsd job: the PBC were not applied to the calculation
+* bug fix in AtomSelectionConfigurator::get_indexes
 * bug fix when saving user definitions
 * bug fix with the initial size of the user definitions plugins
 * updated the job template writing

MDANSE/Core/ClassRegistry.py

@@ -106,10 +106,6 @@ class ClassRegistry(object):
      
             moduleName, _ = os.path.splitext(moduleFile)
             
-            if moduleDir not in sys.path:        
-                sys.path.insert(0,moduleDir)
-
-
             # Any error that may occur here has to be caught. In such case the module is skipped.    
             try:
                 filehandler,path,description = imp.find_module(moduleName, [moduleDir])

MDANSE/Framework/Configurators/AtomSelectionConfigurator.py

@@ -135,7 +135,7 @@ class AtomSelectionConfigurator(IConfigurator):
             if indexesPerElement.has_key(v):
                 indexesPerElement[v].extend(self['indexes'][i])
             else:
-                indexesPerElement[v] = self['indexes'][i]
+                indexesPerElement[v] = self['indexes'][i][:]
                 
         return indexesPerElement
             

MDANSE/Framework/Configurators/__init__.py

-__all__ = ['AtomSelectionConfigurator', 
-           'AtomTransmutationConfigurator', 
-           'AtomsListConfigurator', 
-           'AxisSelectionConfigurator', 
-           'BasisSelectionConfigurator', 
-           'BooleanConfigurator', 
-           'ComplexNumberConfigurator', 
-           'FloatConfigurator', 
-           'FramesConfigurator', 
-           'GroupingLevelConfigurator', 
-           'InputDirectoryConfigurator', 
-           'InputFileConfigurator', 
-           'InstrumentResolutionConfigurator', 
-           'IntegerConfigurator', 
-           'InterpolationOrderConfigurator', 
-           'MMTKTrajectoryConfigurator', 
-           'McStasInstrumentConfigurator', 
-           'McStasOptionsConfigurator', 
-           'McStasParametersConfigurator', 
-           'MultipleChoicesConfigurator', 
-           'NetCDFInputFileConfigurator', 
-           'OutputDirectoryConfigurator', 
-           'OutputFilesConfigurator', 
-           'PartialChargeConfigurator', 
-           'ProjectionConfigurator', 
-           'PythonObjectConfigurator', 
-           'PythonScriptConfigurator', 
-           'QVectorsConfigurator', 
-           'RangeConfigurator', 
-           'RunningModeConfigurator', 
-           'SingleChoiceConfigurator', 
-           'StringConfigurator', 
-           'TrajectoryVariableConfigurator', 
-           'VectorConfigurator', 
-           'WeightsConfigurator']

MDANSE/Framework/Formats/__init__.py

-__all__ = ['ASCIIFormat', 'NetCDFFormat', 'SVGFormat']
\ No newline at end of file

MDANSE/Framework/Handlers/IHandler.py

@@ -35,4 +35,4 @@ class IHandler(object):
     Base class for the handlers of MDANSE logger.
     '''
     
-    _registry = "handler"                
\ No newline at end of file
+    _registry = "handler"
\ No newline at end of file

MDANSE/Framework/Handlers/__init__.py

-__all__ = ['ColorizingStreamHandler', 'LogfileHandler']
\ No newline at end of file

MDANSE/Framework/InputData/__init__.py

-__all__ = ['EmptyData', 'InputFileData', 'MMTKTrajectoryInputData', 'MVITraceInputData', 'NetCDFInputData', 'PeriodicTableInputData']
\ No newline at end of file

MDANSE/Framework/InstrumentResolutions/__init__.py

-__all__ = ['GaussianResolution', 
-           'IdealResolution', 
-           'LorentzianResolution', 
-           'PseudoVoigtResolution', 
-           'SquareResolution', 
-           'TriangularResolution']
\ No newline at end of file

MDANSE/Framework/Jobs/IJob.py

@@ -292,8 +292,8 @@ class IJob(Configurable):
         f.write('################################################################\n')
         f.write('\n')
     
-        f.write('job = REGISTRY[%r][%r]()\n' % ('job',cls._type))
-        f.write('job.run(parameters,status=True)')
+        f.write('%s = REGISTRY[%r][%r]()\n' % (cls._type,'job',cls._type))
+        f.write('%s.run(parameters,status=True)' % (cls._type))
          
         f.close()
         

MDANSE/Framework/Jobs/RootMeanSquareDeviation.py

@@ -37,7 +37,7 @@ import numpy
 from MDANSE import REGISTRY
 from MDANSE.Framework.Jobs.IJob import IJob
 from MDANSE.Mathematics.Arithmetic import weight
-from MDANSE.MolecularDynamics.Analysis import mean_square_deviation
+from MDANSE.MolecularDynamics.Trajectory import read_atoms_trajectory
 
 class RootMeanSquareDeviation(IJob):
     """
@@ -67,16 +67,12 @@ class RootMeanSquareDeviation(IJob):
     
     def initialize(self):
 
-        self.numberOfSteps = self.configuration['frames']['number']
+        self.numberOfSteps = self.configuration['atom_selection']['selection_length']
         
-        self.referenceFrame = self.configuration['reference_frame']['value'] % self.configuration['trajectory']['length']
+        self._referenceIndex = self.configuration['reference_frame']['value']
         
         # Will store the time.
         self._outputData.add("time","line", self.configuration['frames']['time'], units='ps')
-
-        self._indexes = self.configuration['atom_selection'].get_indexes()
-
-        self._masses = numpy.array([m for masses in self._configuration['atom_selection']['masses'] for m in masses],dtype=numpy.float64)
                                     
         # Will store the mean square deviation
         for element in self.configuration['atom_selection']['unique_names']:
@@ -90,19 +86,20 @@ class RootMeanSquareDeviation(IJob):
         @type index: int.              
         """
         
-        # get the Frame index
-        frameIndex = self.configuration['frames']['value'][index] 
-        
-        self.configuration['trajectory']['instance'].universe.setFromTrajectory(self.configuration['trajectory']['instance'], frameIndex)
-        
-        conf1 = self.configuration['trajectory']['instance'].configuration[self.referenceFrame]
-        conf2 = self.configuration['trajectory']['instance'].universe.configuration()
+        indexes = self.configuration['atom_selection']["indexes"][index]
+        masses = self.configuration['atom_selection']["masses"][index]
         
-        rmsd = {}
-        for k,v in self._indexes.items():
-            rmsd[k] = mean_square_deviation(conf1.array[v,:],conf2.array[v,:],masses=None,root=False)
+        series = read_atoms_trajectory(self.configuration["trajectory"]["instance"],
+                                       indexes,
+                                       first=self.configuration['frames']['first'],
+                                       last=self.configuration['frames']['last']+1,
+                                       step=self.configuration['frames']['step'],
+                                       weights=masses)
+
+        # Compute the squared sum of the difference between all the coordinate of atoms i and the reference ones 
+        squaredDiff = numpy.sum((series-series[self._referenceIndex,:])**2,axis=1)
                 
-        return index, rmsd
+        return index, squaredDiff
                         
     def combine(self, index, x):
         """
@@ -112,22 +109,28 @@ class RootMeanSquareDeviation(IJob):
             #. x (any): The returned result(s) of run_step
         """     
                 
-        # The symbol of the atom.
-        for element in x.keys():
-            self._outputData["rmsd_%s" % element][index] = x[element]                                
+        element = self.configuration['atom_selection']["names"][index]
+        
+        self._outputData["rmsd_%s" % element] += x
         
     def finalize(self):
         """
         Finalize the job.
         """
-            
-        weights = self.configuration["weights"].get_weights()
-        nAtomsPerElement = self.configuration['atom_selection'].get_natoms()
                 
+        # The RMSDs per element are averaged.
+        nAtomsPerElement = self.configuration['atom_selection'].get_natoms()
+        for element, number in nAtomsPerElement.items():
+            self._outputData["rmsd_%s" % element] /= number
+
+        weights = self.configuration["weights"].get_weights()
         rmsdTotal = weight(weights,self._outputData,nAtomsPerElement,1,"rmsd_%s")
-                
+        rmsdTotal = numpy.sqrt(rmsdTotal)
         self._outputData.add("rmsd_total","line", rmsdTotal, axis="time", units="nm") 
-        
+            
+        for element, number in nAtomsPerElement.items():
+            self._outputData["rmsd_%s" % element]  = numpy.sqrt(self._outputData["rmsd_%s" % element])
+      
         # Write the output variables.
          
         self._outputData.write(self.configuration['output_files']['root'], self.configuration['output_files']['formats'], self._info)

MDANSE/Framework/Jobs/__init__.py

-__all__ = ['CHARMM', 
-           'Castep', 
-           'DFTB', 
-           'DL_POLY', 
-           'DMol', 
-           'Discover', 
-           'Forcite', 
-           'Generic', 
-           'LAMMPS', 
-           'NAMD', 
-           'PDB', 
-           'VASP', 
-           'XPLOR',
-           'AngularCorrelation', 
-           'AreaPerMolecule', 
-           'BoxTranslatedTrajectory', 
-           'CenterOfMassesTrajectory', 
-           'CoordinationNumber', 
-           'CroppedTrajectory', 
-           'CurrentCorrelationFunction', 
-           'Density', 
-           'DensityOfStates', 
-           'DensityProfile', 
-           'DipoleAutoCorrelationFunction', 
-           'DynamicCoherentStructureFactor', 
-           'DynamicIncoherentStructureFactor', 
-           'Eccentricity', 
-           'ElasticIncoherentStructureFactor', 
-           'GaussianDynamicIncoherentStructureFactor', 
-           'GeneralAutoCorrelationFunction', 
-           'GlobalMotionFilteredTrajectory', 
-           'McStasVirtualInstrument', 
-           'MeanSquareDisplacement', 
-           'MolecularTrace', 
-           'OrderParameter', 
-           'PairDistributionFunction', 
-           'PositionAutoCorrelationFunction', 
-           'RadiusOfGyration', 
-           'RefoldedMembraneTrajectory', 
-           'RigidBodyTrajectory', 
-           'RootMeanSquareDeviation', 
-           'RootMeanSquareFluctuation', 
-           'SolventAccessibleSurface', 
-           'SpatialDensity', 
-           'StaticStructureFactor', 
-           'StructureFactorFromScatteringFunction', 
-           'Temperature', 
-           'UnfoldedTrajectory', 
-           'VelocityAutoCorrelationFunction', 
-           'Voronoi', 
-           'XRayStaticStructureFactor']
\ No newline at end of file

MDANSE/Framework/OutputVariables/__init__.py

-__all__ = ['LineOutputVariable', 'SurfaceOutputVariable', 'VolumeOutputVariable']
\ No newline at end of file

MDANSE/Framework/Projectors/__init__.py

-__all__ = ['AxialProjector','NullProjector', 'PlanarProjector']
\ No newline at end of file

MDANSE/Framework/QVectors/__init__.py

-__all__ = ['ApproximateDispersionLatticeQVectors', 
-           'CircularLatticeQVectors', 
-           'CircularQVectors', 
-           'DispersionLatticeQVectors', 
-           'GridQVectors', 
-           'LatticeQvectors', 
-           'LinearLatticeQVectors', 
-           'LinearQVectors', 
-           'MillerIndicesQVectors', 
-           'SphericalLatticeQVectors', 
-           'SphericalQVectors']
\ No newline at end of file

MDANSE/Framework/Selectors/__init__.py

-__all__ = ['All', 
-           'Amine', 
-           'AtomFullName', 
-           'AtomIndex', 
-           'AtomName', 
-           'AtomPicked', 
-           'AtomSymbol', 
-           'AtomType', 
-           'Backbone', 
-           'CarboHydrogen', 
-           'CarbonAlpha', 
-           'ChainName', 
-           'Expression', 
-           'HeteroHydrogen', 
-           'Hydroxyl', 
-           'Macromolecule', 
-           'Methyl', 
-           'MoleculeIndex', 
-           'MoleculeName', 
-           'NitroHydrogen', 
-           'NucleotideBase', 
-           'NucleotideName', 
-           'NucleotideType', 
-           'OxyHydrogen', 
-           'PDBFile', 
-           'Phosphate', 
-           'PythonScript', 
-           'ResidueClass', 
-           'ResidueName', 
-           'ResidueType', 
-           'SideChain', 
-           'Sulphate', 
-           'SulphurHydrogen', 
-           'Thiol', 
-           'Within']
\ No newline at end of file

MDANSE/Framework/__init__.py

-from MDANSE.Framework.Configurators import *
-from MDANSE.Framework.Formats import *
-from MDANSE.Framework.Handlers import *
-from MDANSE.Framework.InputData import *
-from MDANSE.Framework.InstrumentResolutions import *
-from MDANSE.Framework.Jobs import *
-from MDANSE.Framework.OutputVariables import *
-from MDANSE.Framework.Projectors import *
-from MDANSE.Framework.QVectors import *
-from MDANSE.Framework.Selectors import *
+import os
+
+from MDANSE import PLATFORM, REGISTRY
+
+REGISTRY.update(os.path.join(os.path.dirname(__file__),"*"))
+
+macrosDirectories = sorted([x[0] for x in os.walk(PLATFORM.macros_directory())][0:])
+for d in macrosDirectories:
+    REGISTRY.update(d)

MDANSE/GUI/Handlers/ConsoleHandler.py

@@ -82,6 +82,10 @@ class ConsoleHandler(IHandler, logging.Handler):
         @type record: logging.LogRecord        
         """
         
+        record.msg = record.msg.strip()
+        if not record.msg:
+            return
+        
         self.style.SetTextColour(ConsoleHandler.COLORS.get(record.levelname,wx.BLACK))
                                     
         # Set the the created text attribute as the default style for the text ctrl.                            
@@ -91,5 +95,11 @@ class ConsoleHandler(IHandler, logging.Handler):
         self._window.AppendText(self.format(record))
 
         self._window.AppendText("\n")
-
+        
+    def write(self,message):
+        
+        record = logging.LogRecord("console",logging.INFO,None,None,message,None,None,None)
+        
+        self.emit(record)
+        
 REGISTRY["console"] = ConsoleHandler
\ No newline at end of file

MDANSE/GUI/Handlers/__init__.py

-__all__ = ['ConsoleHandler', 'DialogHandler']
\ No newline at end of file

MDANSE/GUI/MainFrame.py

@@ -91,12 +91,17 @@ class MainFrame(wx.Frame):
         self.build_dialog()
         
         # Add some handlers to the loggers
-        LOGGER.add_handler("console", REGISTRY['handler']['console'](self._panels["controller"].pages["logger"]), level="info")
+        consoleHandler = REGISTRY['handler']['console'](self._panels["controller"].pages["logger"])
+        LOGGER.add_handler("console", consoleHandler, level="info")
         LOGGER.add_handler("dialog", REGISTRY['handler']['dialog'](), level="error")
         LOGGER.start()
         
+        # Redirect all output to the console logger
+        sys.stdout = consoleHandler
+        sys.stderr = consoleHandler
+                
         sys.excepthook = excepthook
-         
+                 
     def build_dialog(self):
         
         self.build_menu()
@@ -349,7 +354,7 @@ or directly to the MDANSE mailing list:
         item = self.GetMenuBar().FindItemById(event.GetId())
         converter = item.GetText()
                         
-        f = JobFrame(self,self._converters[converter],"Trajectory converter")
+        f = JobFrame(self,self._converters[converter],os.path.join(PLATFORM.home_directory(),"trajectory_conversion.nc"))
         f.Show()
 
     def on_open_periodic_table(self, event):