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src/l/i/libNeuroML-HEAD/neuroml/loaders.py   libNeuroML(Download)
 
        #This needs to become an "Optimized Morphology" of some kind
        return arraymorph.ArrayMorphology(vertices=vertices, 
                       connectivity=connection_indices, 
                       name=name )
    def __extract_morphology(cls, node):
            loaded_morphology = arraymorph.ArrayMorphology()
            loaded_morphology.physical_mask = node.physical_mask[:]
            loaded_morphology.vertices = node.vertices[:]
            loaded_morphology.connectivity = node.connectivity[:]

src/l/i/libNeuroML-HEAD/neuroml/examples/arraymorph_generation.py   libNeuroML(Download)
    axon_segments.append(axon_segment)
 
test_morphology = am.ArrayMorphology()
test_morphology.segments.append(soma)
test_morphology.segments += axon_segments

src/l/i/libNeuroML-HEAD/neuroml/examples/arraymorph.py   libNeuroML(Download)
    axon_segments.append(axon_segment)
 
test_morphology = am.ArrayMorphology()
test_morphology.segments.append(soma)
test_morphology.segments += axon_segments

src/l/i/libNeuroML-HEAD/neuroml/benchmarks/arraymorph_benchmarks.py   libNeuroML(Download)
        connectivity = range(-1,num_segments)
 
        big_arraymorph = am.ArrayMorphology(vertices = vertices,
                                            connectivity = connectivity)
 

src/l/i/libNeuroML-0.1.9.1/neuroml/test/test_arraymorph.py   libNeuroML(Download)
            axon_segments.append(axon_segment)
 
        test_morphology = am.ArrayMorphology()
        test_morphology.segments.append(soma)
        test_morphology.segments += axon_segments
        physical_mask[20] = 1
 
        self.complex_morphology = am.ArrayMorphology(vertices=vertices,
                                                     connectivity=connectivity,
                                                     physical_mask=physical_mask,
        self.valid_connectivity = [-1,0,1,2]
 
        self.optimized_morphology = am.ArrayMorphology(vertices=self.valid_vertices,
                                                       connectivity=self.valid_connectivity,
                                                       id = 'test_arraymorph')
        soma = neuroml.Segment(proximal = proximal_point,
                               distal = distal_point,)
        self.small_morphology = am.ArrayMorphology()
        self.small_morphology.segments.append(soma)
 
    def test_to_root(self):
        new_morphology = am.ArrayMorphology(self.optimized_morphology.vertices,
                                       self.optimized_morphology.connectivity)
 
        new_morphology.to_root(2)

src/l/i/libNeuroML-HEAD/neuroml/test/test_arraymorph.py   libNeuroML(Download)
            axon_segments.append(axon_segment)
 
        test_morphology = am.ArrayMorphology()
        test_morphology.segments.append(soma)
        test_morphology.segments += axon_segments
        physical_mask[20] = 1
 
        self.complex_morphology = am.ArrayMorphology(vertices=vertices,
                                                     connectivity=connectivity,
                                                     physical_mask=physical_mask,
        self.valid_connectivity = [-1,0,1,2]
 
        self.optimized_morphology = am.ArrayMorphology(vertices=self.valid_vertices,
                                                       connectivity=self.valid_connectivity,
                                                       id = 'test_arraymorph')
        soma = neuroml.Segment(proximal = proximal_point,
                               distal = distal_point,)
        self.small_morphology = am.ArrayMorphology()
        self.small_morphology.segments.append(soma)
 
    def test_to_root(self):
        new_morphology = am.ArrayMorphology(self.optimized_morphology.vertices,
                                       self.optimized_morphology.connectivity)
 
        new_morphology.to_root(2)

src/l/i/libNeuroML-0.1.9.1/neuroml/test/test_integration.py   libNeuroML(Download)
        connectivity = [-1,0,1,2]
 
        self.optimized_morphology = am.ArrayMorphology(vertices=vertices,
                                                       connectivity=connectivity,
                                                       id="arraymorph_test")

src/l/i/libNeuroML-HEAD/neuroml/test/test_integration.py   libNeuroML(Download)
        connectivity = [-1,0,1,2]
 
        self.optimized_morphology = am.ArrayMorphology(vertices=vertices,
                                                       connectivity=connectivity,
                                                       id="arraymorph_test")

src/l/i/libNeuroML-0.1.9.1/neuroml/test/test_writers.py   libNeuroML(Download)
        connectivity = range(-1,num_segments)
 
        big_arraymorph = am.ArrayMorphology(vertices = vertices,
                                            connectivity = connectivity)
        transposed_x = x+10
        transposed_vertices = np.array([transposed_x,y,z,d]).T
 
        transposed_arraymorph = am.ArrayMorphology(vertices = transposed_vertices,
        fatter_vertices = np.array([x,y,z,bigger_d]).T
 
        fatter_arraymorph = am.ArrayMorphology(vertices = fatter_vertices,
                                               connectivity = connectivity)
 
        connectivity = range(-1,num_segments)
 
        big_arraymorph = am.ArrayMorphology(vertices = vertices,
                                            connectivity = connectivity)
        transposed_x = x+10
        transposed_vertices = np.array([transposed_x,y,z,d]).T
 
        transposed_arraymorph = am.ArrayMorphology(vertices = transposed_vertices,

src/l/i/libNeuroML-HEAD/neuroml/test/test_writers.py   libNeuroML(Download)
        connectivity = range(-1,num_segments)
 
        big_arraymorph = am.ArrayMorphology(vertices = vertices,
                                            connectivity = connectivity)
        transposed_x = x+10
        transposed_vertices = np.array([transposed_x,y,z,d]).T
 
        transposed_arraymorph = am.ArrayMorphology(vertices = transposed_vertices,
        fatter_vertices = np.array([x,y,z,bigger_d]).T
 
        fatter_arraymorph = am.ArrayMorphology(vertices = fatter_vertices,
                                               connectivity = connectivity)
 
        connectivity = range(-1,num_segments)
 
        big_arraymorph = am.ArrayMorphology(vertices = vertices,
                                            connectivity = connectivity)
        transposed_x = x+10
        transposed_vertices = np.array([transposed_x,y,z,d]).T
 
        transposed_arraymorph = am.ArrayMorphology(vertices = transposed_vertices,

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