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Commit 0d5930cd authored by eric pellegrini's avatar eric pellegrini
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docstringed new configurator classes

parent 33aab3bb
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MDANSE/Framework/Configurators/AtomSelectionConfigurator.py
View file @ 0d5930cd
......@@ -176,16 +176,19 @@ class AtomSelectionConfigurator(IConfigurator):
def get_information(self):
'''
Returns some informations about this configurator.
Returns some informations the atom selection.
:return: the information about this configurator
:return: the information about the atom selection.
:rtype: str
'''
if not self.has_key("n_selected_atoms"):
return "No configured yet"
info = []
info.append("Number of selected atoms:%d\n" % self["n_selected_atoms"])
info.append("Level of selection:%s\n" % self["level"])
info.append("Number of selected groups:%d\n" % self["n_groups"])
info.append("Selected elements:%s\n" % self["contents"].keys())
info.append("Number of selected atoms:%d" % self["n_selected_atoms"])
info.append("Level of selection:%s" % self["level"])
info.append("Number of selected groups:%d" % self["n_groups"])
info.append("Selected elements:%s" % self["contents"].keys())
return "".join(info)
\ No newline at end of file
return "\n".join(info)
\ No newline at end of file
MDANSE/Framework/Configurators/AtomTransmutationConfigurator.py
View file @ 0d5930cd
......@@ -52,7 +52,7 @@ class AtomTransmutationConfigurator(IConfigurator):
* Drag a molecular viewer on it,
* Drag into the Molecular Viewer the Atom transmutation plugin
:note: this configurator depends on 'trajectory' and 'atom_selection' configurators to be properly configured
:note: this configurator depends on 'trajectory' and 'atom_selection' configurators to be configured
"""
type = 'atom_transmutation'
......@@ -138,11 +138,14 @@ class AtomTransmutationConfigurator(IConfigurator):
def get_information(self):
'''
Returns some informations about this configurator.
Returns some informations the atoms selected for being transmutated.
:return: the information about this configurator
:return: the information about the atoms selected for being transmutated.
:rtype: str
'''
if not self.has_key("value"):
return "Not configured yet"
if self["value"] is None:
return "No atoms selected for deuteration"
......
MDANSE/Framework/Configurators/ComplexNumberConfigurator.py
View file @ 0d5930cd
......@@ -48,9 +48,9 @@ class ComplexNumberConfigurator(IConfigurator):
:param name: the name of the configurator as it will be appear in the configuration
:type name: str
:param mini: the minimum modulus of the input value. If None, no restriction in the modulus minimum.
:param mini: the minimum modulus allowed for the input value. If None, no restriction for the minimum.
:type mini: float or None
:param maxi: the maximum modulus of the input value. If None, no restriction in the modulus maximum.
:param maxi: the maximum modulus allowed for the input value. If None, no restriction for the maximum.
:type maxi: float or None
:param choices: the list of complex numbers allowed for the input value. If None, any value will be allowed.
:type choices: list of complex or None
......@@ -69,9 +69,9 @@ class ComplexNumberConfigurator(IConfigurator):
'''
Configure an input value.
:param configuration: the current configuration
:param configuration: the current configuration.
:type configuration: a MDANSE.Framework.Configurable.Configurable object
:param value: the input value
:param value: the input complex number.
:type value: complex
'''
......@@ -94,9 +94,9 @@ class ComplexNumberConfigurator(IConfigurator):
@property
def mini(self):
'''
Returns the minimum value allowed for an input value of this configurator.
Returns the minimum value allowed for an input complex number.
:return: the minimum value allowed for an input value of this configurator
:return: the minimum value allowed for the modulus of an input complex number.
:rtype: float or None
'''
......@@ -105,9 +105,9 @@ class ComplexNumberConfigurator(IConfigurator):
@property
def maxi(self):
'''
Returns the maximum value allowed for an input value of this configurator.
Returns the maximum value allowed for the modulus of an input complex number.
:return: the maximum value allowed for an input value of this configurator
:return: the maximum value allowed for an input complex number.
:rtype: float or None
'''
......@@ -116,9 +116,9 @@ class ComplexNumberConfigurator(IConfigurator):
@property
def choices(self):
'''
Returns the list of floats allowed for an input value of this configurator.
Returns the list of floats allowed for an input complex number.
:return: the choices allowed for an input value of this configurator
:return: the choices allowed for an input complex number.
:rtype: list of floats or None
'''
......
MDANSE/Framework/Configurators/FloatConfigurator.py
View file @ 0d5930cd
......@@ -45,13 +45,13 @@ class FloatConfigurator(IConfigurator):
'''
Initializes the configurator.
:param name: the name of the configurator as it will be appear in the configuration
:param name: the name of the configurator as it will be appear in the configuration.
:type name: str
:param mini: the minimum value of the input value. If None, no restriction in the modulus minimum.
:param mini: the minimum value allowed for the input value. If None, no restriction for the minimum.
:type mini: float or None
:param maxi: the maximum value of the input value. If None, no restriction in the modulus maximum.
:param maxi: the maximum value allowed for the input value. If None, no restriction for the maximum.
:type maxi: float or None
:param choices: the list of complex numbers allowed for the input value. If None, any value will be allowed.
:param choices: the list of floats allowed for the input value. If None, any value will be allowed.
:type choices: list of float or None
'''
......@@ -96,9 +96,9 @@ class FloatConfigurator(IConfigurator):
@property
def mini(self):
'''
Returns the minimum value allowed for an input value of this configurator.
Returns the minimum value allowed for an input float.
:return: the minimum value allowed for an input value of this configurator
:return: the minimum value allowed for an input float.
:rtype: float or None
'''
......@@ -107,9 +107,9 @@ class FloatConfigurator(IConfigurator):
@property
def maxi(self):
'''
Returns the maximum value allowed for an input value of this configurator.
Returns the maximum value allowed for an input float.
:return: the maximum value allowed for an input value of this configurator
:return: the maximum value allowed for an input float.
:rtype: float or None
'''
......@@ -118,9 +118,9 @@ class FloatConfigurator(IConfigurator):
@property
def choices(self):
'''
Returns the list of floats allowed for an input value of this configurator.
Returns the list of floats allowed for an input float.
:return: the choices allowed for an input value of this configurator
:return: the choices allowed for an input float.
:rtype: list of floats or None
'''
......
MDANSE/Framework/Configurators/InputDirectoryConfigurator.py
View file @ 0d5930cd
......@@ -27,17 +27,19 @@
'''
Created on Mar 30, 2015
@author: pellegrini
@author: Eric C. Pellegrini
'''
import os
from MDANSE import PLATFORM
from MDANSE.Framework.Configurators.IConfigurator import IConfigurator, ConfiguratorError
from MDANSE.Framework.Configurators.IConfigurator import IConfigurator
class InputDirectoryConfigurator(IConfigurator):
"""
This Configurator allows to set as input an (existing) directory.
This Configurator allows to set an input directory.
The directory will be created at configuration time if it does not exist.
"""
type = "input_directory"
......@@ -45,14 +47,27 @@ class InputDirectoryConfigurator(IConfigurator):
_default = os.getcwd()
def configure(self, configuration, value):
'''
Configure an input directory.
:param configuration: the current configuration.
:type configuration: a MDANSE.Framework.Configurable.Configurable object
:param value: the input directory.
:type value: str
'''
value = PLATFORM.get_path(value)
if not os.path.exists(value):
raise ConfiguratorError('invalid type for input value', self)
PLATFORM.create_directory(value)
self['value'] = value
def get_information(self):
'''
Returns some informations about this configurator.
:return: the information about this configurator
:rtype: str
'''
return "Input directory: %r" % self['value']
\ No newline at end of file
MDANSE/Framework/Configurators/InputFileConfigurator.py
View file @ 0d5930cd
......@@ -27,7 +27,7 @@
'''
Created on Mar 30, 2015
@author: pellegrini
@author: Eric C. Pellegrini
'''
import os
......@@ -37,42 +37,64 @@ from MDANSE.Framework.Configurators.IConfigurator import IConfigurator, Configur
class InputFileConfigurator(IConfigurator):
"""
This Configurator allows to set as input any existing file.
This Configurator allows to set an input file.
"""
type = 'input_file'
_default = ""
def __init__(self, name, checkExistence=True, wildcard="All files|*.*", **kwargs):
def __init__(self, name, wildcard="All files|*.*",**kwargs):
'''
Initializes the configurator object.
:param name: the name of the configurator as it will be appear in the configuration.
:type name: str
:param wildcard: the wildcard used to filter the file. This will be used in MDANSE GUI when
browsing for the input file.
:type wildcard: str
'''
# The base class constructor.
IConfigurator.__init__(self, name, **kwargs)
self._checkExistence = checkExistence
self._wildcard = wildcard
def configure(self, configuration, value):
if self.checkExistence:
value = PLATFORM.get_path(value)
if not os.path.exists(value):
raise ConfiguratorError("the input file %r does not exist." % value, self)
'''
Configure an input file.
:param configuration: the current configuration.
:type configuration: a MDANSE.Framework.Configurable.Configurable object
:param value: the input file.
:type value: str
'''
value = PLATFORM.get_path(value)
if not os.path.exists(value):
raise ConfiguratorError("the input file %r does not exist." % value, self)
self["value"] = value
self["filename"] = value
@property
def checkExistence(self):
return self._checkExistence
@property
def wildcard(self):
'''
Returns the wildcard used to filter the input file.
:return: the wildcard used to filter the input file.
:rtype: str
'''
return self._wildcard
def get_information(self):
'''
Returns some informations about this configurator.
:return: the information about this configurator
:rtype: str
'''
return "Input file: %r" % self["value"]
\ No newline at end of file
MDANSE/Framework/Configurators/InstrumentResolutionConfigurator.py
View file @ 0d5930cd
......@@ -27,7 +27,7 @@
'''
Created on Mar 30, 2015
@author: pellegrini
@author: Eric C. Pellegrini
'''
import numpy
......@@ -37,17 +37,45 @@ from MDANSE.Framework.Configurators.IConfigurator import IConfigurator, Configur
class InstrumentResolutionConfigurator(IConfigurator):
"""
This configurator allow to set a simulated instrument resolution.
Clicking on the SET button open a widget allowing to select one function into
a set of basics, and to parameterized it, then the resulting kernel will be
automatically sampled and convoluted with the signal.
This configurator allows to set an instrument resolution.
The instrument resolution will be used in frequency-dependant analysis (e.g. the vibrational density
of states) when performing the fourier transform of its time-dependant counterpart. This allow to
convolute of the signal with a resolution function to have a better match with experimental spectrum.
In MDANSE, the instrument resolution are defined in frequency (energy) space and are internally
inverse-fourier-transformed to get a time-dependant version. This time-dependant resolution function will then
be multiplied by the time-dependant signal to get the resolution effect according to the Fourier Transform theorem:
.. math:: TF(f(t) * r(t)) = F(\omega) \conv R(\omega) = G(\omega)
where f(t) and r(t) are respectively the time-dependant signal and instrument resolution and
F(\omega) and R(\omega) are their corresponding spectrum. Hence, G(\omega) represents the signal
convoluted by the instrument resolution and, as such, represents the quantity to be compared directly with
experimental results.
An instrument resolution is represented in MDANSE by a kernel function and a sets of parameters for this function.
MDANSE currently supports the aussian, lorentzian, square, triangular and pseudo-voigt kernels.
:note: this configurator depends on the 'frame' configurator to be configured
"""
type = "instrument_resolution"
_default = ('gaussian', {'mu': 0.0, 'sigma': 0.0001})
def configure(self, configuration, value):
'''
Configure the instrument resolution.
:param configuration: the current configuration
:type configuration: a MDANSE.Framework.Configurable.Configurable object
:param value: the instrument resolution. It must be input as a 2-tuple where the 1st element is the instrument resolution
kernel and the 2nd element is a dictionary that stores the parameters for this kernel.
is a string representing one of the supported instrument resolution
:type value: 2-tuple
'''
framesCfg = configuration[self._dependencies['frames']]
......@@ -87,6 +115,26 @@ You should change your resolution function settings to make it sharper.''',self)
self["time_window"] = resolution.timeWindow
self["kernel"] = kernel
self["parameters"] = parameters
def get_information(self):
'''
Returns some informations the instrument resolution.
return "None yet"
\ No newline at end of file
:return: the information the instrument resolution.
:rtype: str
'''
if not self.has_key("kernel"):
return "No configured yet"
info = ["Instrument resolution kernel:" % self["kernel"]]
if self["parameters"]:
info.append("Parameters:")
for k,v in self["parameters"]:
info.append("%s = %s" % (k,v))
info = "\n".join(info)
return info
\ No newline at end of file
MDANSE/Framework/Configurators/IntegerConfigurator.py
View file @ 0d5930cd
......@@ -34,7 +34,7 @@ from MDANSE.Framework.Configurators.IConfigurator import IConfigurator, Configur
class IntegerConfigurator(IConfigurator):
"""
This Configurator allow to input an Integer Value.
This Configurator allows to input an integer.
"""
type = 'integer'
......@@ -42,6 +42,18 @@ class IntegerConfigurator(IConfigurator):
_default = 0
def __init__(self, name, mini=None, maxi=None, choices=None, **kwargs):
'''
Initializes the configurator.
:param name: the name of the configurator as it will be appear in the configuration.
:type name: str
:param mini: the minimum value allowed for the input value. If None, no restriction for the minimum.
:type mini: int or None
:param maxi: the maximum value allowed for the input value. If None, no restriction for the maximum.
:type maxi: int or None
:param choices: the list of integers allowed for the input value. If None, any value will be allowed.
:type choices: int-list or None
'''
# The base class constructor.
IConfigurator.__init__(self, name, **kwargs)
......@@ -53,6 +65,14 @@ class IntegerConfigurator(IConfigurator):
self._choices = choices if choices is not None else []
def configure(self, configuration, value):
'''
Configure an integer value.
:param configuration: the current configuration.
:type configuration: a MDANSE.Framework.Configurable.Configurable object
:param value: the integer to be configured.
:type value: int
'''
try:
value = int(value)
......@@ -75,19 +95,43 @@ class IntegerConfigurator(IConfigurator):
@property
def mini(self):
'''
Returns the minimum value allowed for an input integer.
:return: the minimum value allowed for an input value integer.
:rtype: int or None
'''
return self._mini
@property
def maxi(self):
'''
Returns the maximum value allowed for an input integer.
:return: the maximum value allowed for an input value integer.
:rtype: int or None
'''
return self._maxi
@property
def choices(self):
'''
Returns the list of integers allowed for an input float.
:return: the choices allowed for an input float.
:rtype: int-list or None
'''
return self._choices
def get_information(self):
'''
Returns some informations about this configurator.
:return: the information about this configurator
:rtype: str
'''
return "Value: %r" % self["value"]
\ No newline at end of file
MDANSE/Framework/Configurators/NetCDFInputFileConfigurator.py
View file @ 0d5930cd
......@@ -55,18 +55,17 @@ class NetCDFInputFileConfigurator(InputFileConfigurator):
InputFileConfigurator.configure(self, configuration, value)
if self.checkExistence:
try:
self['instance'] = NetCDFFile(self['value'], 'r')
except IOError:
raise ConfiguratorError("can not open %r NetCDF file for reading" % self['value'])
try:
self['instance'] = NetCDFFile(self['value'], 'r')
except IOError:
raise ConfiguratorError("can not open %r NetCDF file for reading" % self['value'])
for v in self._variables:
try:
self[v] = self['instance'].variables[v]
except KeyError:
raise ConfiguratorError("the variable %r was not found in %r NetCDF file" % (v,self["value"]))
for v in self._variables:
try:
self[v] = self['instance'].variables[v]
except KeyError:
raise ConfiguratorError("the variable %r was not found in %r NetCDF file" % (v,self["value"]))
@property
def variables(self):
......
MDANSE/Framework/Jobs/McStasVirtualInstrument.py
View file @ 0d5930cd
......@@ -94,11 +94,9 @@ class McStasVirtualInstrument(IJob):
settings['frames'] = ('frames', {"dependencies":{'trajectory':'trajectory'}})
settings['sample_coh'] = ('netcdf_input_file', {"widget":'input_file',
"label":'nMoldyn Coherent Structure Factor',
"checkExistence":True,
"variables":['q','frequency','s(q,f)_total']})
settings['sample_inc'] = ('netcdf_input_file', {"widget":'input_file',
"label":'nMoldyn Incoherent Structure Factor',
"checkExistence":True,
"variables" :['q','frequency','s(q,f)_total']})
settings['temperature'] = ('float', {"default":298.0})
settings['instrument'] = ('mcstas_instrument',{"label":'mcstas instrument'})
......
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