-                      r235f514
+                      r98e3f24
     Simulation canvas for real-space simulation of SAS scattering intensity.
     The user can create an arrangement of basic shapes and estimate I(q) and
     I(q_x, q_y). Error estimates on the simulation are also available.
+    I(q_x, q_y). Error estimates on the simulation are also available.
     Example:
     import sas.sascalc.realspace.VolumeCanvas as VolumeCanvas
     canvas = VolumeCanvas.VolumeCanvas()
     canvas.setParam('lores_density', 0.01)
     sphere = SphereDescriptor()
     handle = canvas.addObject(sphere)
 …
     output, error = canvas.getIqError(q=0.1)
     output, error = canvas.getIq2DError(0.1, 0.1)
     or alternatively:
     iq = canvas.run(0.1)
     i2_2D = canvas.run([0.1, 1.57])
 """
 from sas.models.BaseComponent import BaseComponent
+from sas.sascalc.calculator.BaseComponent import BaseComponent
 from sas.sascalc.simulation.pointsmodelpy import pointsmodelpy
 from sas.sascalc.simulation.geoshapespy import geoshapespy
 …
 import os.path, math
 class ShapeDescriptor:
+class ShapeDescriptor(object):
     """
         Class to hold the information about a shape
         The descriptor holds a dictionary of parameters.
         Note: if shape parameters are accessed directly
         from outside VolumeCanvas. The getPr method
         should be called before evaluating I(q).
     """
     def __init__(self):
 …
         self.params['is_lores'] = True
         self.params['order'] = 0
     def create(self):
         """
 …
         z0 = self.params["center"][2]
         geoshapespy.set_center(self.shapeObject, x0, y0, z0)
         # Set orientation
         x0 = self.params["orientation"][0]
 …
         z0 = self.params["orientation"][2]
         geoshapespy.set_orientation(self.shapeObject, x0, y0, z0)
 class SphereDescriptor(ShapeDescriptor):
     """
         Descriptor for a sphere
         The parameters are:
             - radius [Angstroem] [default = 20 A]
             - Contrast [A-2] [default = 1 A-2]
     """
     def __init__(self):
         """
             Initialization
         """
+        """
         ShapeDescriptor.__init__(self)
         # Default parameters
         self.params["type"]   = "sphere"
+        self.params["type"] = "sphere"
         # Radius of the sphere
         self.params["radius"] = 20.0
 …
         self.shapeObject = geoshapespy.new_sphere(\
             self.params["radius"])
         ShapeDescriptor.create(self)
+        ShapeDescriptor.create(self)
         return self.shapeObject
 class CylinderDescriptor(ShapeDescriptor):
     """
         Descriptor for a cylinder
         Orientation: Default cylinder is along Y
         Parameters:
             - Length [default = 40 A]
 …
         """
             Initialization
         """
+        """
         ShapeDescriptor.__init__(self)
         # Default parameters
         self.params["type"]   = "cylinder"
+        self.params["type"] = "cylinder"
         # Length of the cylinder
         self.params["length"] = 40.0
 …
         # Constrast parameter
         self.params["contrast"] = 1.0
     def create(self):
         """
 …
         ShapeDescriptor.create(self)
         return self.shapeObject
 class EllipsoidDescriptor(ShapeDescriptor):
     """
         Descriptor for an ellipsoid
         Parameters:
             - Radius_x along the x-axis [default = 30 A]
 …
         """
             Initialization
         """
+        """
         ShapeDescriptor.__init__(self)
         # Default parameters
         self.params["type"]   = "ellipsoid"
+        self.params["type"] = "ellipsoid"
         self.params["radius_x"] = 30.0
         self.params["radius_y"] = 20.0
         self.params["radius_z"] = 10.0
         self.params["contrast"] = 1.0
     def create(self):
         """
 …
         """
         self.shapeObject = geoshapespy.new_ellipsoid(\
             self.params["radius_x"], self.params["radius_y"],
+            self.params["radius_x"], self.params["radius_y"],
             self.params["radius_z"])
         ShapeDescriptor.create(self)
+        ShapeDescriptor.create(self)
         return self.shapeObject
 class HelixDescriptor(ShapeDescriptor):
     """
         Descriptor for an helix
         Parameters:
             -radius_helix: the radius of the helix [default = 10 A]
 …
         """
             Initialization
         """
+        """
         ShapeDescriptor.__init__(self)
         # Default parameters
         self.params["type"]   = "singlehelix"
+        self.params["type"] = "singlehelix"
         self.params["radius_helix"] = 10.0
         self.params["radius_tube"] = 3.0
 …
         """
         self.shapeObject = geoshapespy.new_singlehelix(\
             self.params["radius_helix"], self.params["radius_tube"],
+            self.params["radius_helix"], self.params["radius_tube"],
             self.params["pitch"], self.params["turns"])
         ShapeDescriptor.create(self)
+        ShapeDescriptor.create(self)
         return self.shapeObject
 class PDBDescriptor(ShapeDescriptor):
     """
         Descriptor for a PDB set of points
         Parameter:
             - file = name of the PDB file
 …
             Initialization
             @param filename: name of the PDB file to load
         """
+        """
         ShapeDescriptor.__init__(self)
         # Default parameters
         self.params["type"]   = "pdb"
+        self.params["type"] = "pdb"
         self.params["file"] = filename
         self.params['is_lores'] = False
 …
         """
         self.shapeObject = pointsmodelpy.new_pdbmodel()
         pointsmodelpy.pdbmodel_add(self.shapeObject, self.params['file'])
         #ShapeDescriptor.create(self)
+        pointsmodelpy.pdbmodel_add(self.shapeObject, self.params['file'])
+        #ShapeDescriptor.create(self)
         return self.shapeObject
 # Define a dictionary for the shape until we find
 # a better way to create them
 …
               'ellipsoid':EllipsoidDescriptor,
               'singlehelix':HelixDescriptor}
 class VolumeCanvas(BaseComponent):
     """
         Class representing an empty space volume to add
+        Class representing an empty space volume to add
         geometrical object to.
         For 1D I(q) simulation, getPr() is called internally for the
         first call to getIq().
     """
+    """
     def __init__(self):
         """
 …
         """
         BaseComponent.__init__(self)
         ## Maximum value of q reachable
         self.params['q_max'] = 0.1
 …
         self.params['scale'] = 1.0
         self.params['background'] = 0.0
         self.lores_model = pointsmodelpy.new_loresmodel(self.params['lores_density'])
         self.complex_model = pointsmodelpy.new_complexmodel()
         self.shapes = {}
         self.shapecount = 0
+        self.shapecount = 0
         self.points = None
         self.npts = 0
         self.hasPr = False
+        self.hasPr = False
     def _model_changed(self):
         """
             Reset internal data members to reflect the fact that the
+            Reset internal data members to reflect the fact that the
             real-space model has changed
         """
         self.hasPr  = False
+        self.hasPr = False
         self.points = None
     def addObject(self, shapeDesc, id = None):
+    def addObject(self, shapeDesc, id=None):
         """
             Adds a real-space object to the canvas.
             @param shapeDesc: object to add to the canvas [ShapeDescriptor]
             @param id: string handle for the object [string] [optional]
 …
         if id is None:
             id = shapeDesc.params["type"]+str(self.shapecount)
         # Self the order number
         shapeDesc.params['order'] = self.shapecount
 …
         return id
     def add(self, shape, id = None):
+    def add(self, shape, id=None):
         """
             The intend of this method is to eventually be able to use it
 …
             analytical solutions. For instance, if one adds a cylinder and
             it is the only shape on the canvas, the analytical solution
             could be called. If multiple shapes are involved, then
+            could be called. If multiple shapes are involved, then
             simulation has to be performed.
             This function is deprecated, use addObject().
             @param shape: name of the object to add to the canvas [string]
             @param id: string handle for the object [string] [optional]
 …
         if id is None:
             id = "shape"+str(self.shapecount)
         # shapeDesc = ShapeDescriptor(shape.lower())
         if shape.lower() in shape_dict:
 …
         else:
             raise ValueError("VolumeCanvas.add: Unknown shape %s" % shape)
         return self.addObject(shapeDesc, id)
 …
     def setParam(self, name, value):
         """
             Function to set the value of a parameter.
+    def setParam(self, name, value):
+        """
+            Function to set the value of a parameter.
             Both VolumeCanvas parameters and shape parameters
             are accessible.
+            are accessible.
             Note: if shape parameters are accessed directly
             from outside VolumeCanvas. The getPr method
             should be called before evaluating I(q).
             TODO: implemented a check method to protect
             against that.
             @param name: name of the parameter to change
             @param value: value to give the parameter
         """
         # Lowercase for case insensitivity
         name = name.lower()
         # Look for shape access
         toks = name.split('.')
         # If a shape identifier was given, look the shape up
         # in the dictionary
 …
             else:
                 raise ValueError("Could not find shape %s" % toks[0])
         else:
             # If we are not accessing the parameters of a
+            # If we are not accessing the parameters of a
             # shape, see if the parameter is part of this object
             BaseComponent.setParam(self, name, value)
             self._model_changed()
     def getParam(self, name):
+    def getParam(self, name):
         """
             @param name: name of the parameter to change
         """
         #TODO: clean this up
         # Lowercase for case insensitivity
         name = name.lower()
         # Look for sub-model access
         toks = name.split('.')
 …
         else:
             raise ValueError("VolumeCanvas.getParam: Could not find %s" % name)
     def getParamList(self, shapeid=None):
         """
                return a full list of all available parameters from
+               return a full list of all available parameters from
            self.params.keys(). If a key in self.params is a instance
            of ShapeDescriptor, extend the return list to:
+           of ShapeDescriptor, extend the return list to:
            [param1,param2,shapeid.param1,shapeid.param2.......]
 …
                 header = key2 + '.'
                 for key3 in value2.params:
                     fullname = header + key3
+                    fullname = header + key3
                     param_list.append(fullname)
         else:
             if not shapeid in self.shapes:
 …
     def getShapeList(self):
         """
             Return a list of the shapes
+            Return a list of the shapes
         """
         return self.shapes.keys()
 …
         # Create the object model
         shapeDesc.create()
         if shapeDesc.params['is_lores']:
             # Add the shape to the lores_model
+            pointsmodelpy.lores_add(self.lores_model,
+                shapeDesc.shapeObject, shapeDesc.params['contrast'])
+            pointsmodelpy.lores_add(self.lores_model,
+                                    shapeDesc.shapeObject,
+                                    shapeDesc.params['contrast'])
     def _createVolumeFromList(self):
 …
             Whenever we change a parameter of a shape, we have to re-create
             the whole thing.
             Items with higher 'order' number take precedence for regions
             of space that are shared with other objects. Points in the
+            of space that are shared with other objects. Points in the
             overlapping region belonging to objects with lower 'order'
             will be ignored.
             Items are added in decreasing 'order' number.
             The item with the highest 'order' will be added *first*.
             [That conventions is prescribed by the realSpaceModeling module]
         """
         # Create empty model
         self.lores_model = \
 …
         # Create empty complex model
         self.complex_model = pointsmodelpy.new_complexmodel()
         # Order the object first
         obj_list = []
         for shape in self.shapes:
             order = self.shapes[shape].params['order']
             # find where to place it in the list
             stored = False
             for i in range(len(obj_list)):
                 if obj_list[i][0] > order:
 …
                     stored = True
                     break
             if not stored:
                 obj_list.append([order, shape])
         # Add each shape
         len_list = len(obj_list)
 …
             self._addSingleShape(shapedesc)
         return 0
+        return 0
     def getPr(self):
         """
 …
             This method should always be called after the shapes
             on the VolumeCanvas have changed.
             @return: calculation output flag
+            @return: calculation output flag
         """
         # To find a complete example of the correct call order:
         # In LORES2, in actionclass.py, method CalculateAction._get_iq()
         # If there are not shapes, do nothing
         if len(self.shapes) == 0:
             self._model_changed()
             return 0
         # generate space filling points from shape list
         self._createVolumeFromList()
 …
         self.points = pointsmodelpy.new_point3dvec()
         pointsmodelpy.complexmodel_add(self.complex_model,
                                         self.lores_model, "LORES")
+        pointsmodelpy.complexmodel_add(self.complex_model,
+                                       self.lores_model, "LORES")
         for shape in self.shapes:
             if self.shapes[shape].params['is_lores'] == False:
                 pointsmodelpy.complexmodel_add(self.complex_model,
+            if not self.shapes[shape].params['is_lores']:
+                pointsmodelpy.complexmodel_add(self.complex_model,
                     self.shapes[shape].shapeObject, "PDB")
         #pointsmodelpy.get_lorespoints(self.lores_model, self.points)
         self.npts = pointsmodelpy.get_complexpoints(self.complex_model, self.points)
         # expecting the rmax is a positive float or 0. The maximum distance.
         #rmax = pointsmodelpy.get_lores_pr(self.lores_model, self.points)
         rmax = pointsmodelpy.get_complex_pr(self.complex_model, self.points)
         self.hasPr = True
+        #rmax = pointsmodelpy.get_lores_pr(self.lores_model, self.points)
+        rmax = pointsmodelpy.get_complex_pr(self.complex_model, self.points)
+        self.hasPr = True
         return rmax
     def run(self, q = 0):
+    def run(self, q=0):
         """
             Returns the value of I(q) for a given q-value
 …
         else:
             raise ValueError("run(q): bad type for q")
     def runXY(self, q = 0):
+    def runXY(self, q=0):
         """
             Standard run command for the canvas.
             Redirects to the correct method
+            Redirects to the correct method
             according to the input type.
             @param q: q-value [float] or [list] [A-1]
 …
         else:
             raise ValueError("runXY(q): bad type for q")
     def _create_modelObject(self):
         """
             Create the simulation model obejct from the list
             of shapes.
             This method needs to be called each time a parameter
             changes because of the way the underlying library
             was (badly) written. It is impossible to change a
             parameter, or remove a shape without having to
+            was (badly) written. It is impossible to change a
+            parameter, or remove a shape without having to
             refill the space points.
             TODO: improve that.
         """
         # To find a complete example of the correct call order:
         # In LORES2, in actionclass.py, method CalculateAction._get_iq()
         # If there are not shapes, do nothing
         if len(self.shapes) == 0:
             self._model_changed()
             return 0
         # generate space filling points from shape list
         self._createVolumeFromList()
 …
         self.points = pointsmodelpy.new_point3dvec()
         pointsmodelpy.complexmodel_add(self.complex_model,
                                         self.lores_model, "LORES")
+        pointsmodelpy.complexmodel_add(self.complex_model,
+                                       self.lores_model, "LORES")
         for shape in self.shapes:
             if self.shapes[shape].params['is_lores'] == False:
                 pointsmodelpy.complexmodel_add(self.complex_model,
+            if not self.shapes[shape].params['is_lores']:
+                pointsmodelpy.complexmodel_add(self.complex_model,
                     self.shapes[shape].shapeObject, "PDB")
         #pointsmodelpy.get_lorespoints(self.lores_model, self.points)
         self.npts = pointsmodelpy.get_complexpoints(self.complex_model, self.points)
     def getIq2D(self, qx, qy):
         """
 …
             @return: I(q) [cm-1]
         """
         # If this is the first simulation call, we need to generate the
         # space points
         if self.points is None:
             self._create_modelObject()
             # Protect against empty model
             if self.points is None:
                 return 0
         # Evalute I(q)
         norm =  1.0e8/self.params['lores_density']*self.params['scale']
+        # Evalute I(q)
+        norm = 1.0e8/self.params['lores_density']*self.params['scale']
         return norm*pointsmodelpy.get_complex_iq_2D(self.complex_model, self.points, qx, qy)\
             + self.params['background']
     def write_pr(self, filename):
         """
             Write P(r) to an output file
             @param filename: file name for P(r) output
         """
         if self.hasPr == False:
+        """
+        if not self.hasPr:
             self.getPr()
         pointsmodelpy.outputPR(self.complex_model, filename)
     def getPrData(self):
         """
             Write P(r) to an output file
             @param filename: file name for P(r) output
         """
         if self.hasPr == False:
+        """
+        if not self.hasPr:
             self.getPr()
         return pointsmodelpy.get_pr(self.complex_model)
     def getIq(self, q):
         """
             Returns the value of I(q) for a given q-value
             This method should remain internal to the class
             and the run() method should be used instead.
             @param q: q-value [float]
             @return: I(q) [float]
         """
         if self.hasPr == False:
+        if not self.hasPr:
             self.getPr()
         # By dividing by the density instead of the actuall V/N,
         # we have an uncertainty of +-1 on N because the number
+        # By dividing by the density instead of the actuall V/N,
+        # we have an uncertainty of +-1 on N because the number
         # of points chosen for the simulation is int(density*volume).
         # Propagation of error gives:
 …
         # where N is stored in self.npts
         norm =  1.0e8/self.params['lores_density']*self.params['scale']
+        norm = 1.0e8/self.params['lores_density']*self.params['scale']
         #return norm*pointsmodelpy.get_lores_i(self.lores_model, q)
         return norm*pointsmodelpy.get_complex_i(self.complex_model, q)\
             + self.params['background']
     def getError(self, q):
         """
 …
             @return: I(q) [float]
         """
         if self.hasPr == False:
+        if not self.hasPr:
             self.getPr()
         # By dividing by the density instead of the actual V/N,
         # we have an uncertainty of +-1 on N because the number
+        # By dividing by the density instead of the actual V/N,
+        # we have an uncertainty of +-1 on N because the number
         # of points chosen for the simulation is int(density*volume).
         # Propagation of error gives:
 …
         # where N is stored in self.npts
         norm =  1.0e8/self.params['lores_density']*self.params['scale']
+        norm = 1.0e8/self.params['lores_density']*self.params['scale']
         #return norm*pointsmodelpy.get_lores_i(self.lores_model, q)
         return norm*pointsmodelpy.get_complex_i_error(self.complex_model, q)\
             + self.params['background']
     def getIqError(self, q):
         """
             Return the simulated value along with its estimated
             error for a given q-value
             Propagation of errors is used to evaluate the
             uncertainty.
             @param q: q-value [float]
             @return: mean, error [float, float]
 …
             Return the simulated value along with its estimated
             error for a given q-value
             Propagation of errors is used to evaluate the
             uncertainty.
             @param qx: qx-value [float]
             @param qy: qy-value [float]
 …
         """
         self._create_modelObject()
         norm =  1.0e8/self.params['lores_density']*self.params['scale']
+        norm = 1.0e8/self.params['lores_density']*self.params['scale']
         val = norm*pointsmodelpy.get_complex_iq_2D(self.complex_model, self.points, qx, qy)\
             + self.params['background']
         # Simulation error (statistical)
         norm =  1.0e8/self.params['lores_density']*self.params['scale'] \
                 * math.pow(self.npts/self.params['lores_density'], 1.0/3.0)/self.npts
+        norm = 1.0e8/self.params['lores_density']*self.params['scale'] \
+               * math.pow(self.npts/self.params['lores_density'], 1.0/3.0)/self.npts
         err = norm*pointsmodelpy.get_complex_iq_2D_err(self.complex_model, self.points, qx, qy)
         # Error on V/N
         simerr = 2*val/self.npts
         # The error used for the position is over-simplified.
         # The actual error was empirically found to be about
         # an order of magnitude larger.
         return val, 10.0*err+simerr

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SasView

Changeset 98e3f24 in sasview for src/sas/sascalc

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src/sas/sascalc/realspace/VolumeCanvas.py

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