Merge pull request #20 from ankushaggarwal/name-change

Changed UniformAxisymmetricTubeInflationExtension to TubeInflation

Examples/examples.py

@@ -72,7 +72,7 @@ def validate_tube():
     material = MatModel('goh','nh')
     mm = material.models
     mm[0].fiber_dirs = [np.array([0,cos(0.1),sin(0.1)]),np.array([0,cos(-0.1),sin(-0.1)])]
-    sample = UniformAxisymmetricTubeInflationExtension(material,force_measure='pressure')
+    sample = TubeInflation(material,force_measure='pressure')
     force_sol = sample.force_controlled(np.array([-0.29167718]),sample.parameters)
     print(force_sol)
 
@@ -106,7 +106,7 @@ def von_mises(sigma_list):
     mm = material.models
     mm[0].fiber_dirs = [np.array([0,cos(0.1),sin(0.1)]),np.array([0,cos(-0.1),sin(-0.1)])]
 
-    sample = UniformAxisymmetricTubeInflationExtension(material,force_measure='pressure')
+    sample = TubeInflation(material,force_measure='pressure')
     params = sample.parameters
     params['k1_0']=5.
     params['k2_0']=15.
@@ -124,8 +124,8 @@ def von_mises(sigma_list):
     plt.ylabel('von-Mises stress')
     plt.show()
 
-    intima = UniformAxisymmetricTubeInflationExtension(material)
-    media = UniformAxisymmetricTubeInflationExtension(material)
+    intima = TubeInflation(material)
+    media = TubeInflation(material)
     artery = LayeredTube(intima,media)
     combined_parameters = artery.parameters
     combined_parameters[0]['Ri']=1.0

Examples/test2.py

@@ -38,7 +38,7 @@ def DOEobs(npoints,theta):
 
 
 mm[0].fiber_dirs = [np.array([0,cos(0.1),sin(0.1)]),np.array([0,cos(-0.1),sin(-0.1)])]
-sample = UniformAxisymmetricTubeInflationExtension(material,force_measure='pressure')
+sample = TubeInflation(material,force_measure='pressure')
 print(sample.disp_controlled([1.1],sample.parameters))
 print(sample.force_controlled(np.array([-0.29167718]),sample.parameters))
 
@@ -61,5 +61,5 @@ def DOEobs(npoints,theta):
 print((result(l2)-result(l))*parameters['mu_1'])
 
 #material = MatModel('nh')
-sample = UniformAxisymmetricTubeInflationExtension(material,force_measure='pressure')
+sample = TubeInflation(material,force_measure='pressure')
 print(sample.disp_controlled([1.1],parameters))

Examples/tube-model-prob.py

@@ -42,7 +42,7 @@ def cal_output(params):
 material = MatModel('yeoh')
 mm = material.models
 
-sample = UniformAxisymmetricTubeInflationExtension(material,force_measure='pressure')
+sample = TubeInflation(material,force_measure='pressure')
 #params = sample.parameters
 Theta = RandomParameters(*sample.parameters_wbounds())
 #Theta.add('phi',0.1,0,pi/2.,'uniform')

Tests/test_examples.py

@@ -2,7 +2,7 @@
 import pytest
 
 mat_model_list = ['nh','yeoh','ls','mn','expI1','goh','Holzapfel','hgo','hy','volPenalty','polyI4','ArrudaBoyce','Gent','splineI1I4','StructModel']
-samples_list = [UniaxialExtension,PlanarBiaxialExtension,UniformAxisymmetricTubeInflationExtension, LinearSpring]
+samples_list = [UniaxialExtension,PlanarBiaxialExtension,TubeInflation, LinearSpring]
 
 def test_mat_creation():
     #Test creating all individual material models
@@ -89,7 +89,7 @@ def test_layered_samples():
     assert sample.disp_controlled(sample._samples[0]._x0, sample.parameters) == pytest.approx(0.0)
     assert sample.force_controlled(np.zeros_like(sample._samples[0]._x0), sample.parameters) == pytest.approx(sample._samples[0]._x0, 1e-3)
 
-    sample = LayeredTube(UniformAxisymmetricTubeInflationExtension(material),UniformAxisymmetricTubeInflationExtension(material))
+    sample = LayeredTube(TubeInflation(material),TubeInflation(material))
     assert isinstance(sample, LayeredSamples)
     assert len(sample._samples) == 2
     assert sample._samples[0]._mat_model == material
@@ -160,4 +160,4 @@ def test_validate_tube():
     # assert artery0Dmodel() == None
 
 def test_randomex():
-    assert randomex() == None
+    assert randomex() == None

docs/source/theory_tube.rst

@@ -1,5 +1,5 @@
 =========================================================
-UniformAxisymmetricTubeInflationExtension and LayeredTube
+TubeInflation and LayeredTube
 =========================================================
 
 
@@ -62,10 +62,10 @@ where :math:`\bar{\sigma}_{rr}(R)` is the Cauchy normal stress in the
 (first) radial direction without the Lagrange multiplier term. Once
 :math:`{p}(R)` is known, all components of stresse tensors at any radius 
 can be calculated using the usual definition of Cauchy stress via 
-:py:meth:`SampleExperiment.UniformAxisymmetricTubeInflationExtension.cauchy_stress` 
+:py:meth:`SampleExperiment.TubeInflation.cauchy_stress` 
 function.
 
-:py:class:`UniformAxisymmetricTubeInflationExtension` samples can be “layered” via
+:py:class:`TubeInflation` samples can be “layered” via
 :py:class:`LayeredTube`. Such a setup can be used for representing, for example,
 tissues that have multiple layers with different material models and
 possibly even incompatible reference radius. The result would be that

pymecht/SampleExperiment.py

@@ -476,7 +476,10 @@ def _observe(self,stress):
             return np.array([s1,s2])*self._thick
         return np.array([s1,s2])
 
-class UniformAxisymmetricTubeInflationExtension(SampleExperiment):
+def UniformAxisymmetricTubeInflationExtension(*margs, **args):
+    raise ValueError("The name has changed from UniformAxisymmetricTubeInflationExtension to TubeInflation. Please use TubeInflation instead")
+
+class TubeInflation(SampleExperiment):
     '''
     For simulating uniform axisymmetric inflation of a tube
 
@@ -528,10 +531,10 @@ def __init__(self,mat_model,disp_measure='radius',force_measure='force'):
                 warnings.warn("Even number of fiber families are expected. The results may be spurious")
             for f in F:
                 if f[0]!=0:
-                    warnings.warn("The UniformAxisymmetricTubeInflationExtension assumes that fibers are aligned in a helical direction. This is not satisfied and the results may be spurious.")
+                    warnings.warn("The TubeInflation assumes that fibers are aligned in a helical direction. This is not satisfied and the results may be spurious.")
             for f1, f2 in zip(*[iter(F)]*2):
                 if (f1+f2)[1] != 0. and (f1+f2)[2] != 0.:
-                    warnings.warn("The UniformAxisymmetricTubeInflationExtension assumes that fibers are symmetric. This is not satisfied and the results may be spurious.")
+                    warnings.warn("The TubeInflation assumes that fibers are symmetric. This is not satisfied and the results may be spurious.")
                     print(f1,f2)
         self._compute = partial(self._mat_model.stress,stresstype='cauchy',incomp=False,Fdiag=True)
         if self._inp == 'stretch':
@@ -936,21 +939,21 @@ class LayeredTube(LayeredSamples):
 
     Parameters
     ----------
-    *samplesList: list of UniformAxisymmetricTubeInflationExtension
-        Any number of UniformAxisymmetricTubeInflationExtension objects constituting the layers
+    *samplesList: list of TubeInflation
+        Any number of TubeInflation objects constituting the layers
 
     Examples
     --------
         >>> import pymecht as pmt
         >>> mat_model = pmt.MatModel('nh')
-        >>> s1 = pmt.UniformAxisymmetricTubeInflationExtension(mat_model)
-        >>> s2 = pmt.UniformAxisymmetricTubeInflationExtension(mat_model)
-        >>> s3 = pmt.UniformAxisymmetricTubeInflationExtension(mat_model)
+        >>> s1 = pmt.TubeInflation(mat_model)
+        >>> s2 = pmt.TubeInflation(mat_model)
+        >>> s3 = pmt.TubeInflation(mat_model)
         >>> layered_sample = pmt.LayeredPlanarBiaxial(s1,s2,s3)
     '''
     def __init__(self,*samplesList):
         super().__init__(*samplesList)
-        if not all([isinstance(s,UniformAxisymmetricTubeInflationExtension) or isinstance(s,LinearSpring) for s in self._samples]):
+        if not all([isinstance(s,TubeInflation) or isinstance(s,LinearSpring) for s in self._samples]):
             raise ValueError("The class only accepts objects of type SampleExperiment")
         for i,s in enumerate(samplesList):
             if i==0:
@@ -1064,7 +1067,7 @@ def specify_single_fiber(sample,angle=0, degrees=True, verbose=True):
         for UniaxialExtension or PlanarBiaxialExtension
             with respect to the x-axis and in the xy plane
 
-        for UniformAxisymmetricTubeInflationExtension
+        for TubeInflation
             with respect to the theta-axis and in the theta-z plane
 
     degrees: bool
@@ -1077,12 +1080,12 @@ def specify_single_fiber(sample,angle=0, degrees=True, verbose=True):
     if degrees:
         angle_rad = np.deg2rad(angle)
     models = sample._mat_model.models
-    if isinstance(sample,UniformAxisymmetricTubeInflationExtension):
+    if isinstance(sample,TubeInflation):
         vec = np.array([0,np.cos(angle_rad), np.sin(angle_rad)])
     elif isinstance(sample,PlanarBiaxialExtension) or isinstance(sample,UniaxialExtension):
         vec = np.array([np.cos(angle_rad), np.sin(angle_rad),0])
     else:
-        raise ValueError("The helper function is only implemented for UniaxialExtension, PlanarBiaxialExtension, and UniformAxisymmetricTubeInflationExtension")
+        raise ValueError("The helper function is only implemented for UniaxialExtension, PlanarBiaxialExtension, and TubeInflation")
     for m in models:
         m.fiber_dirs = vec
     if verbose:
@@ -1104,7 +1107,7 @@ def specify_two_fibers(sample,angle, degrees = True, verbose=True):
         for UniaxialExtension or PlanarBiaxialExtension
             with respect to the x-axis and in the xy plane
         
-        for UniformAxisymmetricTubeInflationExtension
+        for TubeInflation
             with respect to the theta-axis and in the theta-z plane
 
     degrees: bool
@@ -1117,12 +1120,12 @@ def specify_two_fibers(sample,angle, degrees = True, verbose=True):
     if degrees:
         angle_rad = np.deg2rad(angle)
     models = sample._mat_model.models
-    if isinstance(sample,UniformAxisymmetricTubeInflationExtension):
+    if isinstance(sample,TubeInflation):
         vec = [np.array([0,np.cos(angle_rad), np.sin(angle_rad)]), np.array([0,np.cos(-angle_rad), np.sin(-angle_rad)])]
     elif isinstance(sample,PlanarBiaxialExtension) or isinstance(sample,UniaxialExtension):
         vec = [np.array([np.cos(angle_rad), np.sin(angle_rad),0]), np.array([np.cos(-angle_rad), np.sin(-angle_rad),0])]
     else:
-        raise ValueError("The helper function is only implemented for UniaxialExtension, PlanarBiaxialExtension, and UniformAxisymmetricTubeInflationExtension")
+        raise ValueError("The helper function is only implemented for UniaxialExtension, PlanarBiaxialExtension, and TubeInflation")
     for m in models:
         m.fiber_dirs = vec
     if verbose: