| 1 | #!/usr/bin/env python |
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| 2 | """ Volume Canvas |
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| 3 | Simulation canvas |
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| 4 | """ |
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| 5 | |
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| 6 | from sans.models.BaseComponent import BaseComponent |
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| 7 | from sansModeling.pointsmodelpy import pointsmodelpy |
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| 8 | from sansModeling.geoshapespy import geoshapespy |
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| 9 | |
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| 10 | import os.path |
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| 11 | |
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| 12 | class ShapeDescriptor: |
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| 13 | """ |
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| 14 | Class to hold the information about a shape |
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| 15 | """ |
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| 16 | def __init__(self): |
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| 17 | """ |
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| 18 | Initialization |
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| 19 | """ |
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| 20 | ## Real space object |
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| 21 | self.shapeObject = None |
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| 22 | ## Parameters of the object |
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| 23 | self.params = {} |
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| 24 | self.params["center"] = [0, 0, 0] |
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| 25 | self.params["orientation"] = [0, 0, 0] |
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| 26 | # Default to lores shape |
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| 27 | self.params['is_lores'] = True |
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| 28 | self.params['order'] = 0 |
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| 29 | |
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| 30 | def create(self): |
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| 31 | """ |
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| 32 | Create an instance of the shape |
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| 33 | """ |
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| 34 | # Set center |
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| 35 | x0 = self.params["center"][0] |
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| 36 | y0 = self.params["center"][1] |
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| 37 | z0 = self.params["center"][2] |
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| 38 | geoshapespy.set_center(self.shapeObject, x0, y0, z0) |
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| 39 | |
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| 40 | # Set orientation |
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| 41 | x0 = self.params["orientation"][0] |
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| 42 | y0 = self.params["orientation"][1] |
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| 43 | z0 = self.params["orientation"][2] |
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| 44 | geoshapespy.set_orientation(self.shapeObject, x0, y0, z0) |
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| 45 | |
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| 46 | class SphereDescriptor(ShapeDescriptor): |
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| 47 | """ |
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| 48 | Descriptor for a sphere |
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| 49 | """ |
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| 50 | def __init__(self): |
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| 51 | """ |
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| 52 | Initialization |
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| 53 | """ |
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| 54 | ShapeDescriptor.__init__(self) |
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| 55 | # Default parameters |
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| 56 | self.params["type"] = "sphere" |
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| 57 | self.params["radius"] = 20.0 |
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| 58 | self.params["contrast"] = 1.0 |
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| 59 | |
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| 60 | def create(self): |
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| 61 | """ |
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| 62 | Create an instance of the shape |
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| 63 | @return: instance of the shape |
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| 64 | """ |
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| 65 | self.shapeObject = geoshapespy.new_sphere(\ |
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| 66 | self.params["radius"]) |
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| 67 | |
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| 68 | ShapeDescriptor.create(self) |
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| 69 | return self.shapeObject |
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| 70 | |
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| 71 | class CylinderDescriptor(ShapeDescriptor): |
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| 72 | """ |
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| 73 | Descriptor for a cylinder |
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| 74 | """ |
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| 75 | def __init__(self): |
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| 76 | """ |
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| 77 | Initialization |
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| 78 | """ |
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| 79 | ShapeDescriptor.__init__(self) |
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| 80 | # Default parameters |
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| 81 | self.params["type"] = "cylinder" |
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| 82 | self.params["length"] = 40.0 |
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| 83 | self.params["radius"] = 10.0 |
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| 84 | self.params["contrast"] = 1.0 |
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| 85 | |
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| 86 | def create(self): |
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| 87 | """ |
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| 88 | Create an instance of the shape |
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| 89 | @return: instance of the shape |
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| 90 | """ |
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| 91 | self.shapeObject = geoshapespy.new_cylinder(\ |
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| 92 | self.params["radius"], self.params["length"]) |
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| 93 | |
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| 94 | ShapeDescriptor.create(self) |
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| 95 | return self.shapeObject |
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| 96 | |
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| 97 | |
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| 98 | class EllipsoidDescriptor(ShapeDescriptor): |
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| 99 | """ |
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| 100 | Descriptor for an ellipsoid |
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| 101 | """ |
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| 102 | def __init__(self): |
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| 103 | """ |
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| 104 | Initialization |
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| 105 | """ |
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| 106 | ShapeDescriptor.__init__(self) |
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| 107 | # Default parameters |
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| 108 | self.params["type"] = "ellipsoid" |
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| 109 | self.params["radius_x"] = 30.0 |
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| 110 | self.params["radius_y"] = 20.0 |
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| 111 | self.params["radius_z"] = 10.0 |
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| 112 | self.params["contrast"] = 1.0 |
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| 113 | |
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| 114 | def create(self): |
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| 115 | """ |
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| 116 | Create an instance of the shape |
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| 117 | @return: instance of the shape |
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| 118 | """ |
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| 119 | self.shapeObject = geoshapespy.new_ellipsoid(\ |
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| 120 | self.params["radius_x"], self.params["radius_y"], |
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| 121 | self.params["radius_z"]) |
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| 122 | |
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| 123 | ShapeDescriptor.create(self) |
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| 124 | return self.shapeObject |
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| 125 | |
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| 126 | class HelixDescriptor(ShapeDescriptor): |
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| 127 | """ |
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| 128 | Descriptor for an helix |
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| 129 | """ |
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| 130 | def __init__(self): |
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| 131 | """ |
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| 132 | Initialization |
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| 133 | """ |
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| 134 | ShapeDescriptor.__init__(self) |
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| 135 | # Default parameters |
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| 136 | self.params["type"] = "singlehelix" |
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| 137 | self.params["radius_helix"] = 10.0 |
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| 138 | self.params["radius_tube"] = 3.0 |
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| 139 | self.params["pitch"] = 34.0 |
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| 140 | self.params["turns"] = 3.0 |
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| 141 | self.params["contrast"] = 1.0 |
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| 142 | |
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| 143 | def create(self): |
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| 144 | """ |
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| 145 | Create an instance of the shape |
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| 146 | @return: instance of the shape |
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| 147 | """ |
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| 148 | self.shapeObject = geoshapespy.new_singlehelix(\ |
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| 149 | self.params["radius_helix"], self.params["radius_tube"], |
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| 150 | self.params["pitch"], self.params["turns"]) |
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| 151 | |
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| 152 | ShapeDescriptor.create(self) |
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| 153 | return self.shapeObject |
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| 154 | |
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| 155 | class PDBDescriptor(ShapeDescriptor): |
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| 156 | """ |
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| 157 | Descriptor for a PDB set of points |
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| 158 | """ |
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| 159 | def __init__(self, filename): |
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| 160 | """ |
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| 161 | Initialization |
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| 162 | @param filename: name of the PDB file to load |
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| 163 | """ |
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| 164 | ShapeDescriptor.__init__(self) |
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| 165 | # Default parameters |
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| 166 | self.params["type"] = "pdb" |
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| 167 | self.params["file"] = filename |
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| 168 | self.params['is_lores'] = False |
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| 169 | |
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| 170 | def create(self): |
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| 171 | """ |
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| 172 | Create an instance of the shape |
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| 173 | @return: instance of the shape |
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| 174 | """ |
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| 175 | self.shapeObject = pointsmodelpy.new_pdbmodel() |
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| 176 | pointsmodelpy.pdbmodel_add(self.shapeObject, self.params['file']) |
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| 177 | |
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| 178 | #ShapeDescriptor.create(self) |
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| 179 | return self.shapeObject |
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| 180 | |
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| 181 | # Define a dictionary for the shape until we find |
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| 182 | # a better way to create them |
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| 183 | shape_dict = {'sphere':SphereDescriptor, |
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| 184 | 'cylinder':CylinderDescriptor, |
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| 185 | 'ellipsoid':EllipsoidDescriptor, |
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| 186 | 'singlehelix':HelixDescriptor} |
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| 187 | |
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| 188 | class VolumeCanvas(BaseComponent): |
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| 189 | """ |
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| 190 | Class representing an empty space volume to add |
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| 191 | geometrical object to. |
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| 192 | """ |
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| 193 | |
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| 194 | def __init__(self): |
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| 195 | """ |
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| 196 | Initialization |
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| 197 | """ |
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| 198 | BaseComponent.__init__(self) |
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| 199 | |
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| 200 | ## Maximum value of q reachable |
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| 201 | self.params['q_max'] = 0.1 |
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| 202 | self.params['lores_density'] = 0.1 |
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| 203 | self.params['scale'] = 1.0 |
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| 204 | self.params['background'] = 0.0 |
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| 205 | |
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| 206 | self.lores_model = pointsmodelpy.new_loresmodel(self.params['lores_density']) |
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| 207 | self.complex_model = pointsmodelpy.new_complexmodel() |
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| 208 | self.shapes = {} |
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| 209 | self.shapecount = 0 |
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| 210 | self.points = None |
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| 211 | self.npts = 0 |
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| 212 | self.hasPr = False |
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| 213 | |
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| 214 | def add(self, shape, id = None): |
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| 215 | """ |
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| 216 | @param shape: name of the object to add to the canvas [string] |
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| 217 | @param id: string handle for the object [string] [optional] |
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| 218 | @return: string handle for the object |
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| 219 | """ |
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| 220 | # If the handle is not provided, create one |
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| 221 | if id == None: |
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| 222 | id = "shape"+str(self.shapecount) |
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| 223 | |
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| 224 | #shapeDesc = ShapeDescriptor(shape.lower()) |
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| 225 | if shape.lower() in shape_dict: |
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| 226 | shapeDesc = shape_dict[shape.lower()]() |
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| 227 | elif os.path.isfile(shape): |
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| 228 | # A valid filename was supplier, create a PDB object |
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| 229 | shapeDesc = PDBDescriptor(shape) |
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| 230 | else: |
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| 231 | raise ValueError, "VolumeCanvas.add: Unknown shape %s" % shape |
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| 232 | |
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| 233 | # Self the order number |
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| 234 | shapeDesc.params['order'] = self.shapecount |
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| 235 | # Store the shape in a dictionary entry associated |
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| 236 | # with the handle |
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| 237 | self.shapes[id] = shapeDesc |
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| 238 | self.shapecount += 1 |
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| 239 | |
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| 240 | #model changed, need to recalculate P(r) |
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| 241 | self.hasPr = False |
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| 242 | |
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| 243 | return id |
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| 244 | |
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| 245 | def delete(self, id): |
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| 246 | """ |
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| 247 | Delete a shape. The ID for the shape is required. |
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| 248 | @param id: string handle for the object [string] [optional] |
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| 249 | """ |
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| 250 | |
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| 251 | if self.shapes.has_key(id): |
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| 252 | del self.shapes[id] |
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| 253 | else: |
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| 254 | raise KeyError, "VolumeCanvas.delete: could not find shape ID" |
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| 255 | |
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| 256 | #model changed, need to recalculate P(r) |
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| 257 | self.hasPr = False |
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| 258 | |
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| 259 | |
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| 260 | def setParam(self, name, value): |
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| 261 | """ |
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| 262 | @param name: name of the parameter to change |
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| 263 | @param value: value to give the parameter |
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| 264 | """ |
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| 265 | |
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| 266 | # Lowercase for case insensitivity |
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| 267 | name = name.lower() |
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| 268 | |
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| 269 | # Look for shape access |
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| 270 | toks = name.split('.') |
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| 271 | |
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| 272 | # If a shape identifier was given, look the shape up |
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| 273 | # in the dictionary |
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| 274 | if len(toks)>1: |
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| 275 | if toks[0] in self.shapes.keys(): |
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| 276 | # The shape was found, now look for the parameter |
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| 277 | if toks[1] in self.shapes[toks[0]].params: |
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| 278 | # The parameter was found, now change it |
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| 279 | self.shapes[toks[0]].params[toks[1]] = value |
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| 280 | self.hasPr = False |
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| 281 | else: |
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| 282 | raise ValueError, "Could not find parameter %s" % name |
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| 283 | else: |
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| 284 | raise ValueError, "Could not find shape %s" % toks[0] |
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| 285 | |
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| 286 | else: |
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| 287 | # If we are not accessing the parameters of a |
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| 288 | # shape, see if the parameter is part of this object |
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| 289 | BaseComponent.setParam(self, name, value) |
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| 290 | self.hasPr = False |
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| 291 | |
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| 292 | def getParam(self, name): |
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| 293 | """ |
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| 294 | @param name: name of the parameter to change |
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| 295 | """ |
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| 296 | #TODO: clean this up |
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| 297 | |
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| 298 | # Lowercase for case insensitivity |
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| 299 | name = name.lower() |
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| 300 | |
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| 301 | # Look for sub-model access |
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| 302 | toks = name.split('.') |
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| 303 | if len(toks) == 1: |
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| 304 | try: |
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| 305 | self.params.has_key(toks[0]) |
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| 306 | except KeyError: |
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| 307 | raise ValueError, \ |
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| 308 | "VolumeCanvas.getParam: Could not find %s" % name |
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| 309 | |
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| 310 | value = self.params[toks[0]] |
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| 311 | if isinstance(value, ShapeDescriptor): |
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| 312 | raise ValueError, \ |
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| 313 | "VolumeCanvas.getParam: Cannot get parameter value." |
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| 314 | else: |
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| 315 | return value |
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| 316 | |
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| 317 | elif len(toks) == 2: |
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| 318 | try: |
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| 319 | self.shapes.has_key(toks[0]) |
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| 320 | except KeyError: |
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| 321 | raise ValueError, \ |
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| 322 | "VolumeCanvas.getParam: Could not find %s" % name |
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| 323 | |
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| 324 | shapeinstance = self.shapes[toks[0]] |
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| 325 | |
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| 326 | try: |
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| 327 | shapeinstance.params.has_key(toks[1]) |
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| 328 | except KeyError: |
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| 329 | raise ValueError, \ |
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| 330 | "VolumeCanvas.getParam: Could not find %s" % name |
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| 331 | |
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| 332 | return shapeinstance.params[toks[1]] |
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| 333 | |
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| 334 | else: |
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| 335 | raise ValueError, \ |
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| 336 | "VolumeCanvas.getParam: Could not find %s" % name |
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| 337 | |
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| 338 | def getParamList(self, shapeid = None): |
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| 339 | """ |
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| 340 | return a full list of all available parameters from |
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| 341 | self.params.keys(). If a key in self.params is a instance |
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| 342 | of ShapeDescriptor, extend the return list to: |
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| 343 | [param1,param2,shapeid.param1,shapeid.param2.......] |
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| 344 | |
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| 345 | If shapeid is provided, return the list of parameters that |
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| 346 | belongs to that shape id only : [shapeid.param1, shapeid.param2...] |
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| 347 | """ |
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| 348 | |
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| 349 | param_list = [] |
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| 350 | if shapeid == None: |
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| 351 | for key1 in self.params.keys(): |
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| 352 | #value1 = self.params[key1] |
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| 353 | param_list.append(key1) |
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| 354 | for key2 in self.shapes.keys(): |
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| 355 | value2 = self.shapes[key2] |
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| 356 | header = key2 + '.' |
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| 357 | for key3 in value2.params.keys(): |
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| 358 | fullname = header + key3 |
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| 359 | param_list.append(fullname) |
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| 360 | |
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| 361 | else: |
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| 362 | try: |
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| 363 | self.shapes.has_key(shapeid) |
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| 364 | except KeyError: |
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| 365 | raise ValueError, \ |
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| 366 | "VolumeCanvas: getParamList: Could not find %s" % shapeid |
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| 367 | header = shapeid + '.' |
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| 368 | param_list = self.shapes[shapeid].params.keys() |
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| 369 | for i in range(len(param_list)): |
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| 370 | param_list[i] = header + param_list[i] |
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| 371 | |
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| 372 | return param_list |
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| 373 | |
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| 374 | def getShapeList(self): |
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| 375 | """ |
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| 376 | Return a list of the shapes |
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| 377 | """ |
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| 378 | return self.shapes.keys() |
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| 379 | |
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| 380 | def addSingleShape(self, shapeDesc): |
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| 381 | """ |
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| 382 | create shapeobject based on shapeDesc |
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| 383 | @param shapeDesc: shape description |
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| 384 | """ |
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| 385 | #Create the object model |
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| 386 | shapeDesc.create() |
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| 387 | |
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| 388 | if shapeDesc.params['is_lores']: |
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| 389 | # Add the shape to the lores_model |
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| 390 | pointsmodelpy.lores_add(self.lores_model, |
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| 391 | shapeDesc.shapeObject, shapeDesc.params['contrast']) |
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| 392 | |
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| 393 | def createVolumeFromList(self): |
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| 394 | """ |
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| 395 | Create a new lores model with all the shapes in our internal list |
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| 396 | Whenever we change a parameter of a shape, we have to re-create |
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| 397 | the whole thing. |
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| 398 | |
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| 399 | Items with higher 'order' number take precedence for regions |
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| 400 | of space that are shared with other objects. Points in the |
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| 401 | overlapping region belonging to objects with lower 'order' |
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| 402 | will be ignored. |
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| 403 | |
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| 404 | Items are added in decreasing 'order' number. |
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| 405 | The item with the highest 'order' will be added *first*. |
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| 406 | [That conventions is prescribed by the realSpaceModeling module] |
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| 407 | """ |
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| 408 | |
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| 409 | # Create empty model |
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| 410 | self.lores_model = \ |
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| 411 | pointsmodelpy.new_loresmodel(self.params['lores_density']) |
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| 412 | |
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| 413 | # Create empty complex model |
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| 414 | self.complex_model = pointsmodelpy.new_complexmodel() |
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| 415 | |
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| 416 | # Order the object first |
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| 417 | obj_list = [] |
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| 418 | |
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| 419 | for shape in self.shapes: |
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| 420 | order = self.shapes[shape].params['order'] |
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| 421 | # find where to place it in the list |
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| 422 | stored = False |
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| 423 | |
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| 424 | for i in range(len(obj_list)): |
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| 425 | if obj_list[i][0] > order: |
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| 426 | obj_list.insert(i, [order, shape]) |
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| 427 | stored = True |
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| 428 | break |
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| 429 | |
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| 430 | if not stored: |
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| 431 | obj_list.append([order, shape]) |
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| 432 | |
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| 433 | # Add each shape |
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| 434 | len_list = len(obj_list) |
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| 435 | for i in range(len_list-1, -1, -1): |
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| 436 | shapedesc = self.shapes[obj_list[i][1]] |
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| 437 | self.addSingleShape(shapedesc) |
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| 438 | |
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| 439 | return 0 |
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| 440 | |
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| 441 | def getPr(self): |
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| 442 | """ |
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| 443 | Calculate P(r) |
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| 444 | @return: calculation output flag |
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| 445 | """ |
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| 446 | # To find a complete example of the correct call order: |
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| 447 | # In LORES2, in actionclass.py, method CalculateAction._get_iq() |
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| 448 | |
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| 449 | # If there are not shapes, do nothing |
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| 450 | if len(self.shapes) == 0: |
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| 451 | self.hasPr = False |
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| 452 | return 0 |
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| 453 | |
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| 454 | # generate space filling points from shape list |
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| 455 | self.createVolumeFromList() |
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| 456 | |
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| 457 | self.points = pointsmodelpy.new_point3dvec() |
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| 458 | |
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| 459 | pointsmodelpy.complexmodel_add(self.complex_model, |
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| 460 | self.lores_model, "LORES") |
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| 461 | for shape in self.shapes: |
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| 462 | if self.shapes[shape].params['is_lores'] == False: |
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| 463 | pointsmodelpy.complexmodel_add(self.complex_model, |
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| 464 | self.shapes[shape].shapeObject, "PDB") |
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| 465 | |
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| 466 | #pointsmodelpy.get_lorespoints(self.lores_model, self.points) |
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| 467 | self.npts = pointsmodelpy.get_complexpoints(self.complex_model, self.points) |
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| 468 | |
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| 469 | # expecting the rmax is a positive float or 0. The maximum distance. |
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| 470 | #rmax = pointsmodelpy.get_lores_pr(self.lores_model, self.points) |
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| 471 | |
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| 472 | rmax = pointsmodelpy.get_complex_pr(self.complex_model, self.points) |
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| 473 | self.hasPr = True |
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| 474 | |
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| 475 | return rmax |
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| 476 | |
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| 477 | def run(self, q = 0): |
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| 478 | """ |
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| 479 | Returns the value of I(q) for a given q-value |
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| 480 | @param q: q-value [float] |
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| 481 | @return: I(q) [float] |
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| 482 | """ |
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| 483 | #TODO: The right simulation function should be |
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| 484 | # called according to the type of input we get. |
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| 485 | # For now, only a q length is supported. |
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| 486 | return getIq(q) |
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| 487 | |
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| 488 | def getIq(self, q): |
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| 489 | """ |
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| 490 | Returns the value of I(q) for a given q-value |
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| 491 | |
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| 492 | This method should remain internal to the class |
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| 493 | and the run() method should be used instead. |
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| 494 | |
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| 495 | @param q: q-value [float] |
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| 496 | @return: I(q) [float] |
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| 497 | """ |
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| 498 | |
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| 499 | if self.hasPr == False: |
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| 500 | self.getPr() |
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| 501 | |
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| 502 | # By dividing by the density instead of the actuall V/N, |
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| 503 | # we have an uncertainty of +-1 on N because the number |
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| 504 | # of points chosen for the simulation is int(density*volume). |
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| 505 | # Propagation of error gives: |
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| 506 | # delta(1/density^2) = 2*(1/density^2)/N |
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| 507 | # where N is stored in self.npts |
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| 508 | |
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| 509 | norm = 1.0e8/self.params['lores_density']*self.params['scale'] |
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| 510 | #return norm*pointsmodelpy.get_lores_i(self.lores_model, q) |
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| 511 | return norm*pointsmodelpy.get_complex_i(self.complex_model, q)\ |
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| 512 | + self.params['background'] |
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| 513 | |
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| 514 | def getError(self, q): |
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| 515 | """ |
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| 516 | Returns the error of I(q) for a given q-value |
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| 517 | @param q: q-value [float] |
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| 518 | @return: I(q) [float] |
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| 519 | """ |
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| 520 | |
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| 521 | if self.hasPr == False: |
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| 522 | self.getPr() |
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| 523 | |
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| 524 | # By dividing by the density instead of the actuall V/N, |
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| 525 | # we have an uncertainty of +-1 on N because the number |
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| 526 | # of points chosen for the simulation is int(density*volume). |
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| 527 | # Propagation of error gives: |
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| 528 | # delta(1/density^2) = 2*(1/density^2)/N |
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| 529 | # where N is stored in self.npts |
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| 530 | |
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| 531 | norm = 1.0e8/self.params['lores_density']*self.params['scale'] |
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| 532 | #return norm*pointsmodelpy.get_lores_i(self.lores_model, q) |
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| 533 | return norm*pointsmodelpy.get_complex_i_error(self.complex_model, q)\ |
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| 534 | + self.params['background'] |
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| 535 | |
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| 536 | def getIqError(self, q): |
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| 537 | """ |
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| 538 | Return the simulated value along with its estimated |
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| 539 | error for a given q-value |
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| 540 | |
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| 541 | Propagation of errors is used to evaluate the |
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| 542 | uncertainty. |
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| 543 | |
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| 544 | @param q: q-value [float] |
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| 545 | @return: mean, error [float, float] |
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| 546 | """ |
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| 547 | val = self.getIq(q) |
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| 548 | # Simulation error (statistical) |
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| 549 | err = self.getError(q) |
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| 550 | # Error on V/N |
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| 551 | simerr = 2*val/self.npts |
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| 552 | return val, err+simerr |
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| 553 | |
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