Added a generic ASCII trajectory converter

Many bug fixes related to ud

MDANSE/App/GUI/Framework/Plugins/AtomSelectionPlugin.py

@@ -36,9 +36,10 @@ import os
 import wx
 import wx.aui as wxaui
 
-from MDANSE import LOGGER, REGISTRY, UD_STORE
+from MDANSE import LOGGER, REGISTRY
 from MDANSE.Core.Error import Error
 from MDANSE.Externals.pubsub import pub
+from MDANSE.Framework.UserDefinitionsStore import UD_STORE
 from MDANSE.Framework.AtomSelectionParser import AtomSelectionParser, AtomSelectionParserError
 from MDANSE.MolecularDynamics.Trajectory import sorted_atoms
 

MDANSE/App/GUI/Framework/Plugins/AtomTransmutationPlugin.py

@@ -33,8 +33,9 @@ import os
 
 import wx
 
-from MDANSE import ELEMENTS, LOGGER, REGISTRY, UD_STORE
+from MDANSE import ELEMENTS, LOGGER, REGISTRY
 from MDANSE.Externals.pubsub import pub as Publisher
+from MDANSE.Framework.UserDefinitionsStore import UD_STORE
 
 from MDANSE.App.GUI.Framework.Plugins.AtomSelectionPlugin import AtomSelectionPlugin
 

MDANSE/App/GUI/Framework/Plugins/AxisSelectionPlugin.py

@@ -35,8 +35,10 @@ import os
 import wx
 import wx.aui as wxaui
 
-from MDANSE import LOGGER, REGISTRY, UD_STORE
+from MDANSE import LOGGER, REGISTRY
 from MDANSE.Externals.pubsub import pub
+from MDANSE.Framework.UserDefinitionsStore import UD_STORE
+
 from MDANSE.App.GUI.Framework.Plugins.ComponentPlugin import ComponentPlugin
 from MDANSE.App.GUI.ComboWidgets.UserDefinitionsPanel import UserDefinitionsPanel
 from MDANSE.MolecularDynamics.Trajectory import find_atoms_in_molecule, get_chemical_objects_dict

MDANSE/App/GUI/Framework/Plugins/BasisSelectionPlugin.py

@@ -35,8 +35,10 @@ import os
 import wx
 import wx.aui as wxaui
 
-from MDANSE import LOGGER, REGISTRY, UD_STORE
+from MDANSE import LOGGER, REGISTRY
 from MDANSE.Externals.pubsub import pub
+from MDANSE.Framework.UserDefinitionsStore import UD_STORE
+
 from MDANSE.App.GUI.Framework.Plugins.ComponentPlugin import ComponentPlugin
 from MDANSE.App.GUI.ComboWidgets.UserDefinitionsPanel import UserDefinitionsPanel
 from MDANSE.MolecularDynamics.Trajectory import find_atoms_in_molecule, get_chemical_objects_dict
@@ -124,7 +126,7 @@ class BasisSelectionPlugin(ComponentPlugin):
                 
         self._moleculeNames.SetItems(sorted(self._molecularContents.keys()))        
         
-    def on_close(self, event):
+    def on_close(self, event=None):
         
         self.parent.clear_selection()
         self.parent.mgr.ClosePane(self.parent.mgr.GetPane(self))
@@ -138,7 +140,6 @@ class BasisSelectionPlugin(ComponentPlugin):
         if (not origin) or (not xAxis) or (not yAxis):
             LOGGER("One of the atom selection is empty. Please select some values.", "error", ["dialog"])
             return
-
         
         if (origin == xAxis) or (origin == yAxis) or (xAxis == yAxis):
             LOGGER("A basis can not be set from identical atom selections.", "error", ["dialog"])

MDANSE/App/GUI/Framework/Plugins/JobPlugin.py

@@ -33,7 +33,6 @@ Created on Apr 14, 2015
 import os
 import subprocess               
 import sys
-import tempfile
 import time
 
 import wx

MDANSE/App/GUI/Framework/Plugins/QVectorsPlugin.py

@@ -37,9 +37,11 @@ import wx.aui as wxaui
 import wx.grid as wxgrid
 from wx.lib.delayedresult import startWorker
 
-from MDANSE import LOGGER, REGISTRY, UD_STORE
+from MDANSE import LOGGER, REGISTRY
 from MDANSE.Externals.pubsub import pub
 
+from MDANSE.Framework.UserDefinitionsStore import UD_STORE
+
 from MDANSE.App.GUI.ComboWidgets.ConfigurationPanel import ConfigurationPanel
 from MDANSE.App.GUI.ComboWidgets.ProgressBar import ProgressBar
 from MDANSE.App.GUI.Framework.Plugins.ComponentPlugin import ComponentPlugin

MDANSE/App/GUI/Framework/Widgets/UserDefinitionWidget.py

@@ -34,7 +34,7 @@ import os
 
 import wx.combo
 
-from MDANSE.Framework.UserDefinitions.IUserDefinition import UD_STORE
+from MDANSE.Framework.UserDefinitionsStore import UD_STORE
 
 from MDANSE.App.GUI.Framework.Widgets.IWidget import IWidget
 from MDANSE.App.GUI.ComboWidgets.ComboCheckbox import ComboCheckbox

MDANSE/App/GUI/Main.py

@@ -13,7 +13,6 @@ class MainApplication(wx.App):
         f.Show()
         self.SetTopWindow(f)
         return True
-        
 
 class PeriodicTableApplication(wx.App):
     
@@ -24,7 +23,6 @@ class PeriodicTableApplication(wx.App):
         self.SetTopWindow(f)
         return True
 
-        
 class PlotterApplication(wx.App):
     
     def OnInit(self):
@@ -42,4 +40,9 @@ class UserDefinitionViewerApplication(wx.App):
         f.Show()
         self.SetTopWindow(f)
         return True
+    
+if __name__ == "__main__":
+    
+    app = MainApplication()
+    app.MainLoop()
     
\ No newline at end of file

MDANSE/App/GUI/MainFrame.py

@@ -57,7 +57,7 @@ class MainFrame(wx.Frame):
         
         # Add some handlers to the loggers
         LOGGER.add_handler("console", REGISTRY['handler']['console'](self._panels["controller"].pages["logger"]), level="info")
-        LOGGER.add_handler("dialog", REGISTRY['handler']['dialog'], level="error")
+        LOGGER.add_handler("dialog", REGISTRY['handler']['dialog'](), level="error")
         LOGGER.start()
                                 
     def build_dialog(self):

MDANSE/Framework/Configurators/AtomSelectionConfigurator.py

@@ -35,7 +35,7 @@ import operator
 
 import numpy
 
-from MDANSE.Framework.UserDefinitions.IUserDefinition import UD_STORE, UserDefinitionError
+from MDANSE.Framework.UserDefinitionsStore import UD_STORE, UserDefinitionsStoreError
 from MDANSE.Framework.Configurators.IConfigurator import IConfigurator, ConfiguratorError
 from MDANSE.Framework.AtomSelectionParser import AtomSelectionParser
 
@@ -91,7 +91,7 @@ class AtomSelectionConfigurator(IConfigurator):
         try:
             ud = UD_STORE[trajConfig["basename"],"atom_selection",value]        
         # The input value is an atom selection string: parse it and update the configuration
-        except UserDefinitionError:
+        except UserDefinitionsStoreError:
             parser = AtomSelectionParser(trajConfig["instance"].universe)
             self["indexes"] = parser.parse(value)
             self["expression"] = value

MDANSE/Framework/Configurators/AtomTransmutationConfigurator.py

@@ -31,7 +31,7 @@ Created on Mar 30, 2015
 '''
 
 from MDANSE import ELEMENTS
-from MDANSE.Framework.UserDefinitions.IUserDefinition import UD_STORE
+from MDANSE.Framework.UserDefinitionsStore import UD_STORE
 from MDANSE.Framework.Configurators.IConfigurator import IConfigurator, ConfiguratorError
 from MDANSE.Framework.AtomSelectionParser import AtomSelectionParser
         

MDANSE/Framework/Configurators/AxisSelectionConfigurator.py

@@ -30,7 +30,7 @@ Created on Mar 30, 2015
 @author: Eric C. Pellegrini and Bachir Aoun
 '''
 
-from MDANSE.Framework.UserDefinitions.IUserDefinition import UD_STORE
+from MDANSE.Framework.UserDefinitionsStore import UD_STORE, UserDefinitionsStoreError
 from MDANSE.Framework.Configurators.IConfigurator import IConfigurator
 from MDANSE.MolecularDynamics.Trajectory import find_atoms_in_molecule
         
@@ -73,11 +73,12 @@ class AxisSelection(IConfigurator):
         
         trajConfig = configuration[self._dependencies['trajectory']]
                 
-        ud = UD_STORE[trajConfig["basename"],"axis_selection",value]        
-        if ud is not None:
-            self.update(ud)
-        else:
+        try: 
+            ud = UD_STORE[trajConfig["basename"],"axis_selection",value]
+        except UserDefinitionsStoreError:
             self.update(value)
+        else:
+            self.update(ud)
 
         e1 = find_atoms_in_molecule(trajConfig['instance'].universe,self['molecule'], self['endpoint1'], True)
         e2 = find_atoms_in_molecule(trajConfig['instance'].universe,self['molecule'], self['endpoint2'], True)

MDANSE/Framework/Configurators/BasisSelectionConfigurator.py

@@ -30,7 +30,7 @@ Created on Mar 30, 2015
 @author: Eric C. Pellegrini and Bachir Aoun
 '''
 
-from MDANSE.Framework.UserDefinitions.IUserDefinition import UD_STORE
+from MDANSE.Framework.UserDefinitionsStore import UD_STORE, UserDefinitionsStoreError
 from MDANSE.Framework.Configurators.IConfigurator import IConfigurator
 from MDANSE.MolecularDynamics.Trajectory import find_atoms_in_molecule
 
@@ -74,12 +74,14 @@ class BasisSelection(IConfigurator):
         '''
 
         trajConfig = configuration[self._dependencies['trajectory']]
-
-        ud = UD_STORE[trajConfig["basename"],"basis_selection",value]        
-        if ud is not None:
-            self.update(ud)
-        else:
+            
+        try: 
+            ud = UD_STORE[trajConfig["basename"],"basis_selection",value]
+        except UserDefinitionsStoreError:
             self.update(value)
+        else:
+            self.update(ud)
+            
                 
         e1 = find_atoms_in_molecule(trajConfig['instance'].universe,self['molecule'], self['origin'], True)
         e2 = find_atoms_in_molecule(trajConfig['instance'].universe,self['molecule'], self['x_axis'], True)

MDANSE/Framework/Configurators/QVectorsConfigurator.py

@@ -31,7 +31,7 @@ Created on May 22, 2015
 '''
 
 from MDANSE import REGISTRY
-from MDANSE.Framework.UserDefinitions.IUserDefinition import UD_STORE
+from MDANSE.Framework.UserDefinitionsStore import UD_STORE, UserDefinitionsStoreError
 from MDANSE.Framework.Configurators.IConfigurator import IConfigurator, ConfiguratorError
 
 class QVectorsConfigurator(IConfigurator):
@@ -70,15 +70,11 @@ class QVectorsConfigurator(IConfigurator):
 
         trajConfig = configuration[self._dependencies['trajectory']]
 
-        ud = UD_STORE[trajConfig["basename"],"q_vectors",value]        
-        if ud is not None:
+        try:        
+            ud = UD_STORE[trajConfig["basename"],"q_vectors",value]
             
-            self["parameters"] = ud['parameters']
-            self["type"] = ud['generator']
-            self["is_lattice"] = ud['is_lattice']
-            self["q_vectors"] = ud['q_vectors']
-        
-        else:                        
+        except UserDefinitionsStoreError:
+
             generator, parameters = value
             generator = REGISTRY["q_vectors"][generator](trajConfig["instance"])
             generator.setup(parameters)
@@ -86,6 +82,12 @@ class QVectorsConfigurator(IConfigurator):
                         
             if not data:
                 raise ConfiguratorError("no Q vectors could be generated", self)
+        
+        else:                        
+            self["parameters"] = ud['parameters']
+            self["type"] = ud['generator']
+            self["is_lattice"] = ud['is_lattice']
+            self["q_vectors"] = ud['q_vectors']
 
             self["parameters"] = parameters
             self["type"] = generator.type

MDANSE/Framework/Jobs/Converters/Generic.py

+#MDANSE : Molecular Dynamics Analysis for Neutron Scattering Experiments
+#------------------------------------------------------------------------------------------
+#Copyright (C)
+#2015- Eric C. Pellegrini Institut Laue-Langevin
+#BP 156
+#6, rue Jules Horowitz
+#38042 Grenoble Cedex 9
+#France
+#pellegrini[at]ill.fr
+#goret[at]ill.fr
+#aoun[at]ill.fr
+#
+#This library is free software; you can redistribute it and/or
+#modify it under the terms of the GNU Lesser General Public
+#License as published by the Free Software Foundation; either
+#version 2.1 of the License, or (at your option) any later version.
+#
+#This library is distributed in the hope that it will be useful,
+#but WITHOUT ANY WARRANTY; without even the implied warranty of
+#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+#Lesser General Public License for more details.
+#
+#You should have received a copy of the GNU Lesser General Public
+#License along with this library; if not, write to the Free Software
+#Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+
+''' 
+Created on Jun 08, 2015
+
+@author: Eric C. Pellegrini
+'''
+
+import collections
+
+import numpy
+
+from MMTK import Atom, AtomCluster
+from MMTK.ParticleProperties import Configuration, ParticleVector
+from MMTK.Trajectory import Trajectory, SnapshotGenerator, TrajectoryOutput
+from MMTK.Universe import InfiniteUniverse, ParallelepipedicPeriodicUniverse
+
+from MDANSE import ELEMENTS
+from MDANSE.Core.Error import Error
+from MDANSE.Framework.Jobs.Converters.Converter import Converter
+                 
+class GenericConverterError(Error):
+    pass
+                                                  
+class GenericConverter(Converter):
+    """
+    """
+
+    type = 'generic'
+    
+    label = "Generic"
+
+    category = ('Converters',)
+    
+    ancestor = None
+
+    settings = collections.OrderedDict()   
+    settings['gt_file'] = ('input_file',{'wildcard':"Generic trajectory files|*.gtf|All files|*"})
+    settings['output_file'] = ('output_files', {'formats':["netcdf"]})
+                    
+    def initialize(self):
+        '''
+        Initialize the job.
+        '''
+
+        self._gtFile = open(self.configuration["gt_file"]["filename"], 'rb')
+
+        if self._gtFile.readline().strip() != "MOLECULAR_CONTENTS":
+            raise GenericConverterError("Invalid keyword #1. Must be 'MOLECULAR_CONTENTS'")
+
+        # Read the number of molecular types that define the universe        
+        try:
+            nMolecularTypes=int(self._gtFile.readline())
+        except ValueError:
+            raise GenericConverterError("Invalid type for 'MOLECULAR_CONTENTS' keyword. Must be an integer corresponding to the number of molecular types found in the simulation.")
+
+        # Blank line
+        self._gtFile.readline()
+
+        self._molecularTypes = collections.OrderedDict()
+        
+        for _ in range(nMolecularTypes):
+            molName = self._gtFile.readline().strip()
+            if self._molecularTypes.has_key(molName):
+                raise GenericConverterError("Duplicate molecule name.")
+            self._molecularTypes[molName] = []
+            line = self._gtFile.readline().strip()
+            while line: 
+                atomName, atomType = line.split()
+                if not atomType in ELEMENTS:
+                    raise GenericConverterError("Unknown atom type: %s" % atomType)
+                self._molecularTypes[molName].append((atomName,atomType))                
+                line = self._gtFile.readline().strip()
+
+        if self._gtFile.readline().strip() != "MOLECULES":
+            raise GenericConverterError("Invalid keyword #2. Must be 'MOLECULES'")
+        
+        self._molecules = []
+        line=self._gtFile.readline().strip()
+        while line:
+            molName,nMols=line.strip().split()
+            if not self._molecularTypes.has_key(molName):
+                raise GenericConverterError("Unknown molecule name: %s" % molName)
+            try:
+                nMols = int(nMols)
+            except ValueError:
+                raise GenericConverterError("Invalid type for the number of atoms in molecule %s. Must be an integer." % molName);
+            
+            self._molecules.append((molName,nMols))
+            
+            line=self._gtFile.readline().strip()
+                                 
+        # Read the number of steps
+        if self._gtFile.readline().strip() != "NSTEPS":
+            raise GenericConverterError("Invalid keyword#4: must be 'NSTEPS'")         
+        try:
+            self.numberOfSteps=int(self._gtFile.readline())
+        except ValueError:
+            raise GenericConverterError("Invalid type for 'NSTEPS' keyword. Must be an integer corresponding to the number of steps of the simulation.")
+
+        # Read a blank line
+        self._gtFile.readline()
+
+        # Read the number of steps
+        if self._gtFile.readline().strip() != "TIMESTEP":
+            raise GenericConverterError("Invalid keyword#5: must be 'TIMESTEP'")
+         
+        # Read the time step        
+        try:
+            self._timeStep=float(self._gtFile.readline())
+        except ValueError:
+            raise GenericConverterError("Invalid type for 'TIMESTEP' keyword. Must be a float corresponding to the actual timestep of the simulation.")
+
+        # Read a blank line
+        self._gtFile.readline()
+
+        self._headerBlockSize=self._gtFile.tell()
+        
+        # Read the first frame to define the size of various data block
+
+        # Read the current step number
+        if self._gtFile.readline().strip() != "STEP":
+            raise GenericConverterError("Invalid frame block. Must start with 'STEP' keyword.")
+        try:
+            _=int(self._gtFile.readline())
+        except ValueError:
+            raise GenericConverterError("Invalid type for 'STEP' keyword. Must be a in corresponding to the current step number of the simulation.")
+                    
+        # Read a blank line
+        self._gtFile.readline()
+
+        self._pbc = (self._gtFile.readline().strip() == "CELL")
+                        
+        if self._pbc:
+            self._universe = ParallelepipedicPeriodicUniverse()
+            pos = self._gtFile.tell()
+            self._gtFile.readline()
+            self._gtFile.readline()
+            self._gtFile.readline()
+            self._cellBlockSize=self._gtFile.tell()-pos
+        else:
+            self._universe = InfiniteUniverse()
+
+        for molName,nMols in self._molecules:
+             
+            for _ in range(nMols):
+                molType = self._molecularTypes[molName]
+ 
+                temp = [Atom(atomType,name=atomName) for atomName,atomType in molType]
+                 
+                if len(temp)==1:
+                    self._universe.addObject(temp[0])
+                else:
+                    self._universe.addObject(AtomCluster(temp,name=molName))
+                    
+        # Read a blank line
+        self._gtFile.readline()
+        
+        # Read the current configuration
+        if self._gtFile.readline().strip() != "CONFIGURATION":
+            raise GenericConverterError("Invalid frame block. Must contain 'CONFIGURATION' keyword.")
+        
+        pos = self._gtFile.tell()
+        
+        for _ in range(self._universe.numberOfAtoms()):
+            line=self._gtFile.readline()
+        self._dataBlockSize=self._gtFile.tell()-pos
+        line=line.split(',')
+        n=len(line)
+        if n==3:
+            self._hasVelocities=False
+            self._hasForces=False
+        elif n==6:
+            self._hasVelocities=True
+            self._hasForces=False
+        elif n==9:
+            self._hasVelocities=True
+            self._hasForces=True          
+        else:
+            raise GenericConverterError("Invalid configuration line. Must contain3, 6 0r 9 comma-separated fixed-formatted floats.")
+        
+        # Read a blank line
+        self._gtFile.readline()
+        
+        if (self._hasVelocities or self._hasForces):
+            self._universe.initializeVelocitiesToTemperature(0.0)
+            self._velocities = ParticleVector(self._universe)
+        
+        if self._hasForces:
+            self._forces = ParticleVector(self._universe)
+                                    
+        # A MMTK trajectory is opened for writing.
+        self._trajectory = Trajectory(self._universe, self.configuration['output_file']['files'][0], mode='w')
+ 
+        # A frame generator is created.
+        self._snapshot = SnapshotGenerator(self._universe, actions = [TrajectoryOutput(self._trajectory, ["all"], 0, None, 1)])
+        
+        self._frameBlockSize = self._gtFile.tell() - self._headerBlockSize
+    
+    def run_step(self, index):
+        """Runs a single step of the job.
+        
+        @param index: the index of the step.
+        @type index: int.
+
+        @note: the argument index is the index of the loop note the index of the frame.      
+        """
+        
+        self._gtFile.seek(self._headerBlockSize+index*self._frameBlockSize)
+        
+        # Read a blank line
+        self._gtFile.readline()
+        try:
+            step=int(self._gtFile.readline())
+        except ValueError:
+            raise GenericConverterError('Invalid step number value.')
+
+        if self._pbc:        
+            # Read two junk lines
+            self._gtFile.readline()
+            self._gtFile.readline()
+            
+            cell = numpy.array([v.split(",") for v in self._gtFile.read(self._cellBlockSize).splitlines()],dtype=numpy.float64)
+            
+            if cell.shape != (3,3):
+                raise GenericConverterError('Invalid cell data.')
+            
+            self._universe.setShape(cell)
+            
+        # Read two junk lines
+        self._gtFile.readline()
+        self._gtFile.readline()
+            
+        config = numpy.array([v.split(",") for v in self._gtFile.read(self._dataBlockSize).splitlines()],dtype=numpy.float64)
+        
+        self._universe.setConfiguration(Configuration(self._universe, config[:,0:3]))
+        
+        self._universe.foldCoordinatesIntoBox()
+        
+        data = {"time" : step*self._timeStep}
+        
+        if self._hasVelocities:
+            self._velocities.array = config[:,3:6]
+            self._universe.setVelocities(self._velocities)
+
+        if self._hasForces:
+            self._forces.array = config[:,6:9]
+            data["forces"] = self._forces
+                             
+        # Store a snapshot of the current configuration in the output trajectory.
+        self._snapshot(data=data)
+                                                                        
+        return index, None
+        
+    def combine(self, index, x):
+        """
+        @param index: the index of the step.
+        @type index: int.
+        
+        @param x:
+        @type x: any.
+        """
+        
+        pass
+    
+    def finalize(self):
+        """
+        Finalize the job.
+        """
+        
+        self._gtFile.close()
+
+        # Close the output trajectory.
+        self._trajectory.close()
+                

MDANSE/Framework/Jobs/IJob.py

@@ -74,7 +74,7 @@ class JobError(Error):
         trace.append("\n%s" % self._message)
 
         trace = '\n'.join(trace)
-        
+                
         LOGGER(trace,'error',[job._name])
 
         if job._status is not None:
@@ -128,7 +128,7 @@ class IJob(Configurable):
                         
         return name
         
-    def __init__(self, status=None):
+    def __init__(self, status=False):
         """
         The base class constructor.        
         """
@@ -143,7 +143,7 @@ class IJob(Configurable):
         
         self._info = ""
                                         
-        if status is not None:
+        if status:
             self._status = JobStatus(self)
         else:
             self._status = None
@@ -467,7 +467,10 @@ class IJob(Configurable):
             if getattr(self,'numberOfSteps', 0) <= 0:
                 raise JobError(self,"Invalid number of steps for job %s" % self._name)
     
-            mode = self.configuration['running_mode']['mode']
+            if self.configuration.has_key('running_mode'):
+                mode = self.configuration['running_mode']['mode']