Commit 36f7b144 authored by eric pellegrini's avatar eric pellegrini

Docstringed MDANSE.Core.Preferences module

Reintroduced and refactored several analysis
parent c33398f0
......@@ -5,7 +5,7 @@ import wx.aui as wxaui
import wx.py as wxpy
from MDANSE.App.GUI.JobControllerPanel import JobControllerPanel
from MDANSE.App.GUI.Icons import ICONS, scaled_bitmap
from MDANSE.App.GUI.Icons import ICONS
class ControllerPanel(wx.Panel):
......@@ -33,9 +33,9 @@ class ControllerPanel(wx.Panel):
#wxpython 2.9 compatibility
if wx.VERSION[:2] > (2,8):
il = wx.ImageList(16, 16)
il.Add(scaled_bitmap(ICONS["log"], 16,16))
il.Add(scaled_bitmap(ICONS["shell"], 16,16))
il.Add(scaled_bitmap(ICONS["hourglass"], 16,16))
il.Add(ICONS["log",16,16])
il.Add(ICONS["shell",16,16])
il.Add(ICONS["hourglass",16,16])
self._notebook.AssignImageList(il)
self._notebook.AddPage(self._pages["logger"], 'Logger')
......@@ -47,9 +47,9 @@ class ControllerPanel(wx.Panel):
self._notebook.SetPageImage(2, 2)
else:
self._notebook.AddPage(self._pages["logger"], 'Logger', bitmap=scaled_bitmap(ICONS["log"], 16,16))
self._notebook.AddPage(self._pages["console"], 'Console', bitmap=scaled_bitmap(ICONS["shell"], 16,16))
self._notebook.AddPage(self._pages["jobs"], 'Jobs', bitmap=scaled_bitmap(ICONS["hourglass"], 16,16))
self._notebook.AddPage(self._pages["logger"], 'Logger', bitmap=ICONS["log",16,16])
self._notebook.AddPage(self._pages["console"], 'Console', bitmap=ICONS["shell",16,16])
self._notebook.AddPage(self._pages["jobs"], 'Jobs', bitmap=ICONS["hourglass",16,16])
def build_layout(self):
......
......@@ -48,7 +48,7 @@ from MDANSE.Framework.Jobs.JobStatus import JobState
from MDANSE.Externals.pubsub import pub
from MDANSE.Logging.Logger import LOGGER
from MDANSE.App.GUI.Icons import ICONS, scaled_bitmap
from MDANSE.App.GUI.Icons import ICONS
from MDANSE.App.GUI.Events.JobControllerEvent import EVT_JOB_CONTROLLER, JobControllerEvent
class JobController(threading.Thread):
......@@ -196,7 +196,7 @@ class JobControllerPanel(wx.ScrolledWindow):
state = wx.TextCtrl(self, wx.ID_ANY, style=wx.TE_READONLY|wx.ALIGN_CENTER_HORIZONTAL)
progress = wx.Gauge(self, wx.ID_ANY,range=100)
eta = wx.TextCtrl(self, wx.ID_ANY, style=wx.TE_READONLY|wx.ALIGN_CENTER_HORIZONTAL)
kill = wx.BitmapButton(self, wx.ID_ANY, scaled_bitmap(ICONS["stop"], 24, 24))
kill = wx.BitmapButton(self, wx.ID_ANY, ICONS["stop",24,24])
self._gbSizer.Add(name ,pos=(r,0),flag=wx.EXPAND|wx.ALIGN_CENTER_HORIZONTAL)
self._gbSizer.Add(pid ,pos=(r,1),flag=wx.EXPAND|wx.ALIGN_CENTER_HORIZONTAL)
......
......@@ -9,7 +9,7 @@ from MDANSE import LOGGER, REGISTRY
from MDANSE.App.GUI import DATA_CONTROLLER
from MDANSE.App.GUI.ControllerPanel import ControllerPanel
from MDANSE.App.GUI.DataTreePanel import DataTreePanel
from MDANSE.App.GUI.Icons import ICONS, scaled_bitmap
from MDANSE.App.GUI.Icons import ICONS
from MDANSE.App.GUI.PluginsTreePanel import PluginsTreePanel
from MDANSE.App.GUI.WorkingPanel import WorkingPanel
......@@ -34,7 +34,7 @@ class MainFrame(wx.Frame):
self.build_toolbar()
icon = wx.EmptyIcon()
icon.CopyFromBitmap(scaled_bitmap(ICONS["nmoldyn"], 32, 32))
icon.CopyFromBitmap(ICONS["nmoldyn",32,32])
self.SetIcon(icon)
# The main aui manager.
......@@ -98,18 +98,18 @@ class MainFrame(wx.Frame):
self._toolbar = self.CreateToolBar()
loadDataButton = self._toolbar.AddSimpleTool(wx.ID_ANY, scaled_bitmap(ICONS["load"], 32, 32), 'Load a trajectory')
emptyDataButton = self._toolbar.AddSimpleTool(wx.ID_ANY, scaled_bitmap(ICONS["empty_data"], 32, 32), 'Open an empty data (converters ...)')
databaseButton = self._toolbar.AddSimpleTool(wx.ID_ANY, scaled_bitmap(ICONS["periodic_table"], 32, 32), 'Edit the nMolDyn elements database')
plotButton = self._toolbar.AddSimpleTool(wx.ID_ANY,scaled_bitmap(ICONS["plot"], 32, 32), 'Open nMolDyn plotter')
userButton = self._toolbar.AddSimpleTool(wx.ID_ANY,scaled_bitmap(ICONS["user"], 32, 32), 'Edit the user definitions')
preferencesButton = self._toolbar.AddSimpleTool(wx.ID_ANY, scaled_bitmap(ICONS["preferences"], 32, 32), 'Edit the preferences')
logfileButton = self._toolbar.AddSimpleTool(wx.ID_ANY, scaled_bitmap(ICONS["logfile"], 32, 32), 'Display nMOLDYN log file')
helpButton = self._toolbar.AddSimpleTool(wx.ID_ANY, scaled_bitmap(ICONS["help"], 32, 32), 'Help')
websiteButton = self._toolbar.AddSimpleTool(wx.ID_ANY, scaled_bitmap(ICONS["web"], 32, 32), 'Open nMoldyn website')
aboutButton = self._toolbar.AddSimpleTool(wx.ID_ANY, scaled_bitmap(ICONS["about"], 32, 32), 'About nMolDyn')
bugButton = self._toolbar.AddSimpleTool(wx.ID_ANY, scaled_bitmap(ICONS["bug"], 32, 32), 'Bug report')
quitButton = self._toolbar.AddSimpleTool(wx.ID_ANY, scaled_bitmap(ICONS["quit"], 32, 32), 'Quit nMoldyn')
loadDataButton = self._toolbar.AddSimpleTool(wx.ID_ANY, ICONS["load",32,32], 'Load a trajectory')
emptyDataButton = self._toolbar.AddSimpleTool(wx.ID_ANY, ICONS["empty_data",32,32], 'Open an empty data (converters ...)')
databaseButton = self._toolbar.AddSimpleTool(wx.ID_ANY, ICONS["periodic_table",32,32], 'Edit the MDANSE elements database')
plotButton = self._toolbar.AddSimpleTool(wx.ID_ANY,ICONS["plot",32,32], 'Open MDANSE plotter')
userButton = self._toolbar.AddSimpleTool(wx.ID_ANY,ICONS["user",32,32], 'Edit the user definitions')
preferencesButton = self._toolbar.AddSimpleTool(wx.ID_ANY, ICONS["preferences",32,32], 'Edit the preferences')
logfileButton = self._toolbar.AddSimpleTool(wx.ID_ANY, ICONS["logfile",32,32], 'Display nMOLDYN log file')
helpButton = self._toolbar.AddSimpleTool(wx.ID_ANY, ICONS["help",32,32], 'Help')
websiteButton = self._toolbar.AddSimpleTool(wx.ID_ANY, ICONS["web",32,32], 'Open MDANSE website')
aboutButton = self._toolbar.AddSimpleTool(wx.ID_ANY, ICONS["about",32,32], 'About MDANSE')
bugButton = self._toolbar.AddSimpleTool(wx.ID_ANY, ICONS["bug",32,32], 'Bug report')
quitButton = self._toolbar.AddSimpleTool(wx.ID_ANY, ICONS["quit",32,32], 'Quit MDANSE')
self._toolbar.Realize()
......
......@@ -7,27 +7,9 @@ if platform.dist()[0].lower() == "ubuntu":
from MDANSE.App.GUI.DataController import DATA_CONTROLLER
import glob
import sys
from MDANSE import REGISTRY
directories = sorted([x[0] for x in os.walk(os.path.dirname(__file__))][1:])
for d in directories:
for module in glob.glob(os.path.join(d,'*.py')):
moduleDir, moduleFile = os.path.split(module)
if moduleFile == '__init__.py':
continue
moduleName, moduleExt = os.path.splitext(moduleFile)
if moduleDir not in sys.path:
sys.path.append(moduleDir)
# Any error that may occur here has to be caught. In such case the module is skipped.
try:
__import__(moduleName, locals(), globals())
except:
continue
\ No newline at end of file
REGISTRY.update_registry(d)
......@@ -31,8 +31,10 @@ Created on Mar 30, 2015
'''
import abc
import glob
import inspect
import os
import sys
class _Meta(type):
'''
......@@ -98,13 +100,46 @@ class ClassRegistry(abc.ABCMeta):
if issubclass(self, interface):
ClassRegistry._registry[interface.type][typ] = self
break
@classmethod
def update_registry(cls,packageDir):
'''
Update the classes registry by importing all the modules contained in a given package.
Only the classes that are metaclassed by ClassRegistry will be registered.
:param cls: the ClassRegistry instance
:type: ClassRegistry
:param packageDir: the package for which all modules should be imported
:type packageDir: str
'''
for module in glob.glob(os.path.join(packageDir,'*.py')):
moduleDir, moduleFile = os.path.split(module)
if moduleFile == '__init__.py':
continue
moduleName, moduleExt = os.path.splitext(moduleFile)
print moduleName
if moduleDir not in sys.path:
sys.path.append(moduleDir)
# Any error that may occur here has to be caught. In such case the module is skipped.
try:
__import__(moduleName, locals(), globals())
except:
continue
@classmethod
def info(cls, interface):
'''
Returns informations about the subclasses of a given base class stored in the registry.
:param cls: the ClassRegsitry instance
:param cls: the ClassRegistry instance
:type cls: ClassRegistry
:param interface: the name of base class of whom information about its subclasses is requested
:type interface: str
......
#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 Mar 30, 2015
@author: pellegrini
'''
import abc
import collections
import ConfigParser
import os
from MDANSE.Core.Platform import PLATFORM, PlatformError
from MDANSE.Core.Error import Error
from MDANSE.Core.Singleton import Singleton
class PreferencesError(Error):
'''
This class handles the errors that occurs in Preferences.
'''
pass
class PreferencesItem(object):
'''
This is the base class for defining a preferences item.
A preferences item implements is a light object used to check preferences before setting them
but also classify preferences according to their section for a further use in MDANSE GUI.
'''
__metaclass__ = abc.ABCMeta
def __init__(self, name, section, default, *args, **kwargs):
'''
Constructor a new prferences item.
:param name: the name of the preference item
:type name: str
:param section: the section of the preferences item
:type section: str
:param default: the default value for the preferences item
:type default: str
'''
self._name = name
self._section = section
self._default = default
self._value = self._default
@property
def default(self):
'''
Returns the default value of the preferences item.
:return: the default value of the preferences item
:rtype: str
'''
return self._default
def get_default(self):
'''
Returns the default value of the preferences item.
:return: the default value of the preferences item
:rtype: str
'''
return self._default
@property
def name(self):
'''
Returns the name of the preferences item.
:return: the name of the preferences item
:rtype: str
'''
return self._name
def get_name(self):
'''
Returns the name of the preferences item.
:return: the name of the preferences item
:rtype: str
'''
return self._name
@property
def section(self):
'''
Returns the section of the preferences item.
:return: the section of the preferences item
:rtype: str
'''
return self._section
def get_section(self):
'''
Returns the section of the preferences item.
:return: the section of the preferences item
:rtype: str
'''
return self._section
def reset(self):
'''
Reset the preferences item to its default value
'''
self._value = self._default
@property
def value(self):
'''
Returns the value of the preferences item.
:return: the value of the preferences item
:rtype: str
'''
return self._value
def get_value(self):
'''
Returns the value of the preferences item.
:return: the value of the preferences item
:rtype: str
'''
return self._value
@abc.abstractmethod
def set_value(self,value):
'''
Set the value of the preferences item.
:param value: the value of the preferences item
:type value: str
'''
pass
class InputDirectory(PreferencesItem):
'''
This class implements a preferences item that handles an input directory.
When set to a given input directory, if this one does not exists, it will be be created.
'''
type = "input_directory"
def set_value(self, value):
'''
Set the value of the input directory preferences item.
:param value: the input directory
:type value: str
'''
value = PLATFORM.get_path(value)
try:
PLATFORM.create_directory(value)
except PlatformError:
raise PreferencesError('Error when setting input directory %r' % value)
self._value = value
class Preferences(collections.OrderedDict):
'''
This class implements the MDANSE preferences.
Preferences are defined using the ConfigParser python module that allows to read and write
preferences stored in a formatted INI file (RFC822).
'''
__metaclass__ = Singleton
def __init__(self):
'''
Constructs the preferences
'''
self["working_directory"] = InputDirectory("working_directory", "paths", PLATFORM.home_directory())
self["macros_directory"] = InputDirectory("macros_directory", "paths", os.path.join(PLATFORM.home_directory(), "mdanse_macros"))
self._parser = ConfigParser.ConfigParser()
for s in self._items.values():
try:
self._parser.add_section(s.section)
except ConfigParser.DuplicateSectionError:
pass
# Overwrite the default preferences with the user defined loaded ones.
try:
self.load()
except PreferencesError:
pass
@property
def parser(self):
'''
Returns the configuration parser object used to serialize the preferences.
:return: the configuration parser bound to the preferences
:rtype: ConfigParser.ConfigParser
'''
return self._parser
def __getitem__(self, item):
'''
Get the value of a selected preferences item.
:param item: the preferences item
:type item: str
:return: the values of the preferences item.
:rtype: str
'''
try:
value = self[item].value
except KeyError:
raise PreferencesError("The preferences item %r is not valid" % item)
else:
return value
def __setitem__(self, item, value):
'''
Set the value of a preferences item.
:param item: the preferences item
:type item: str
:param value: the value to set for the preferences item.
:type value: any
'''
if not self._items.has_key(item):
return
try:
self._items[item].value = value
except KeyError:
raise PreferencesError("The preferences item %r is not valid" % item)
def load(self):
'''
Load the preferences from a preferences file.
'''
path = PLATFORM.preferences_file()
if not isinstance(path,basestring):
raise PreferencesError("Invalid type for preferences filename: %s" % path)
if not os.path.exists(path):
raise PreferencesError("The preferences files %s does not exists. nMolDyn will use the default preferences." % path)
try:
# Read the preferences and overwrites the nmoldyn default preferences.
self._parser.read(path)
except ConfigParser.ParsingError as e:
raise PreferencesError(e)
for s in self._parser.sections():
for k, v in self._parser.items(s):
self[k] = v
def save(self):
'''
Save the preferences to a file.
'''
path = PLATFORM.preferences_file()
try:
f = open(path, "w")
except (IOError,TypeError) as e:
raise PreferencesError(e)
for v in self._items.values():
self._parser.set(v.section,v.name,v.value)
# Write the preferences.
self._parser.write(f)
# Closes the preferences file.
f.close()
PREFERENCES = Preferences()
\ No newline at end of file
#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 Apr 10, 2015
@author: pellegrini
'''
import collections
import numpy
from MDANSE.Mathematics.Signal import correlation
from MDANSE.Framework.Jobs.IJob import IJob
from MDANSE.MolecularDynamics.Trajectory import read_atoms_trajectory
class AngularCorrelation(IJob):
'''
Computes the angular correlation for a set of molecules.
Vector defined by user, starting at the origin pointing towards the direction.
Origin and direction can either be an atom or a center definition. In this particular case the origin
is the head group geometric center designated with the sphere and the direction is simply the last atom
of the tail chain. The correlation is calculated for the angle formed between the same vector at
different times
**Calculation:** \n
angle at time T is calculated as the following: \n
.. math:: \\overrightarrow{vector} = \\overrightarrow{direction} - \\overrightarrow{origin}
.. math:: \phi(T = T_{1}-T_{0}) = arcos( \\overrightarrow{vector(T_{1})} . \\overrightarrow{vector(T_{0})} )
**Output:** \n
#. angular_correlation_legendre_1st: :math:`<cos(\phi(T))>`
#. angular_correlation_legendre_2nd: :math:`<\\frac{1}{2}(3cos(\phi(T))^{2}-1)>`
**Usage:** \n
This analysis is used to study molecule's orientation and rotation relaxation.
'''
type = 'ac'
label = "Angular Correlation"
category = ('Dynamics',)
ancestor = "mmtk_trajectory"
configurators = collections.OrderedDict()
configurators['trajectory'] = ('mmtk_trajectory',{})
configurators['frames'] = ('frames', {"dependencies":{'trajectory':'trajectory'}})
configurators['axis_selection'] = ('axis_selection',{"dependencies":{'trajectory':'trajectory'}})
configurators['per_axis'] = ('boolean', {"label":"output contribution per axis", "default":False})
configurators['output_files'] = ('output_files', {"formats":["netcdf","ascii"]})
configurators['running_mode'] = ('running_mode',{})
def initialize(self):
"""
Initialize the input parameters and analysis self variables
"""
self.numberOfSteps = self.configuration['axis_selection']['n_axis']
self._outputData.add("times","line", self.configuration['frames']['time'],units='ps')
self._outputData.add("axis_index","line", numpy.arange(self.configuration['axis_selection']['n_axis']), units='au')
self._outputData.add('ac',"line", (self.configuration['frames']['number'],), axis="times", units="au")
if self.configuration['per_axis']['value']:
self._outputData.add('ac_per_axis',"surface", (self.configuration['axis_selection']['n_axis'],self.configuration['frames']['number'],), axis='axis_index|times', units="au")
def run_step(self, index):
"""
Runs a single step of the job.\n
:Parameters:
#. index (int): The index of the step.
:Returns:
#. index (int): The index of the step.
#. vectors (numpy.array): The calculated vectors
"""
e1, e2 = self.configuration['axis_selection']['endpoints'][index]
e1 = read_atoms_trajectory(self.configuration["trajectory"]["instance"],
e1,
first=self.configuration['frames']['first'],
last=self.configuration['frames']['last']+1,
step=self.configuration['frames']['step'])
e2 = read_atoms_trajectory(self.configuration["trajectory"]["instance"],
e2,
first=self.configuration['frames']['first'],
last=self.configuration['frames']['last']+1,
step=self.configuration['frames']['step'])
diff = e2 - e1
modulus = numpy.sqrt(numpy.sum(diff**2,1))
diff /= modulus[:,numpy.newaxis]
ac = correlation(diff,axis=0,reduce=1)
return index, ac
def combine(self, index, x):
"""
Combines returned results of run_step.\n
:Parameters:
#. index (int): The index of the step.\n
#. x (any): The returned result(s) of run_step
"""
self._outputData['ac'] += x
if self.configuration['per_axis']['value']:
self._outputData['ac_per_axis'][index,:] = x
def finalize(self):
"""
Finalizes the calculations (e.g. averaging the total term, output files creations ...).
"""
self._outputData['ac'] /= self.configuration['axis_selection']['n_axis']
self._outputData.write(self.configuration['output_files']['root'], self.configuration['output_files']['formats'], self.header)
self.configuration['trajectory']['instance'].close()
\ No newline at end of file
#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