Resolved documentation errors up to registration.py

AmpScan/fe.py

@@ -9,8 +9,16 @@ import numpy as np
 from numpy.linalg import solve
 
 class feMixin(object):
+    """
+    Finite element docstring.
+
+    """
     
     def addFE(self, files):
+        """
+        Numpy style docstring
+
+        """
         if len(files) == 1:
             data = np.load(files[0], encoding='bytes').item()
             for k in list(data.keys()):
@@ -26,6 +34,10 @@ class feMixin(object):
         
         
     def getSurf(self):
+        """
+        Numpy style docstring
+
+        """
         # Find verts with a pressure value for external surface
         valInd = self.values[:, 0].astype(int)
         # Find faces in array 
@@ -46,16 +58,22 @@ class feMixin(object):
     def calcPPI(self):
         """
         Function to calculate the peak pressure indicies
+
         """
         self.values
     
     def calcGradients(self):
         """
         Function to calculate the gradients in values along z and theta
+
         """
         np.gradient(self.values)
     
     def addSurrogate(self, dat, theta=True):
+        """
+        Numpy style docstring
+
+        """
         if isinstance(dat, str):
             self.surrogate = np.load(dat).item()
         else:
@@ -65,6 +83,10 @@ class feMixin(object):
             self.surrogate['sm_theta'] = 10 ** self.surrogate['sm_theta']
 
     def surrPred(self, x, norm = True):
+        """
+        Numpy style docstring
+
+        """
         surr = self.surrogate
         sh = surr['sm_U'].shape
         one = np.ones(sh[0])
@@ -85,4 +107,8 @@ class feMixin(object):
     
     @staticmethod
     def comp(a, b):
+        """
+        Numpy style docstring
+
+        """
         return solve(np.dot(a.T, a), np.dot(a.T, b))
\ No newline at end of file

AmpScan/pressSens.py

@@ -12,16 +12,33 @@ from vtk.qt.QVTKRenderWindowInteractor import QVTKRenderWindowInteractor
 
 
 class pressSense(object):
+    """
+    Numpy style docstring
+
+    """
 
     def __init__(self):
         self.actors = {}
         self.antS = {}
         
     def importVert(self, fname, pos='ant'):
+        """
+        Numpy style docstring
+        
+        Parameters
+        ----------
+        fname : file
+            self-explanatory
+
+        """
         self.antS['vert'] = np.loadtxt(fname, delimiter=',')
         self.antS['vert'][:, 1] += -1.0
     
     def importPress(self, fname):
+        """
+        Numpy style docstring
+
+        """
         sF = self.antS['sF']
         val = np.loadtxt(fname, delimiter=',').flatten()
         self.antS['values']  = np.zeros(len(self.antS['faces']))
@@ -40,7 +57,8 @@ class pressSense(object):
             socket 
         sensePos: str
             Aspect of socket the sensor was positioned
-        limbSide: 
+        limbSide: str
+            Either L or R
         """
         vert = mesh['vert']
         faces = mesh['faces']
@@ -81,6 +99,7 @@ class pressSense(object):
         Function to compute face array for pressure sensor 
         
         FIX SO USE QUAD FACES
+
         """
         # define no of rows and columns in sensors
         rows, cols = [15*d, 3*d]
@@ -111,6 +130,7 @@ class pressSense(object):
         Function to compute face array for pressure sensor 
         
         FIX SO USE QUAD FACES
+
         """
         # define no of rows and columns in sensors
         rows, cols = [15*d, 3*d]
@@ -138,6 +158,7 @@ class pressSense(object):
     def intersectLineMesh(line, v, f):
         """
         Function to calculate intersection between line and mesh
+
         """
         
     def addActor(self, pos ='antS', CMap=None, connect=3):
@@ -155,6 +176,7 @@ class pressSense(object):
         from numpy arrays 
         
         Add functions to add vert, add faces, cmap and make LUT
+
         """
 
         def __init__(self, data, CMap=None, bands=None, connect=3):
@@ -206,6 +228,10 @@ class pressSense(object):
 
 
 def func1():
+    """
+    Docstring for method outside of Classes
+
+    """
     path = r'J:\Shared Resources\AmpScan IfLS Team\101 ImpAmp\Upgrade'
     sockets = ['B_PTB.stl', 'B_TSB.stl', 'B_KBM.stl']
     pressure = ['161108_Sub02_T001', '161108_Sub02_T002', '161108_Sub02_T006']

AmpScan/registration.py

@@ -9,51 +9,51 @@ import pandas as pd
 import copy
 from scipy import spatial
 from .core import AmpObject
-"""
-import os
-path = ('J:\\Shared Resources\\AmpScan IfLS Team\\'
-        '100 PYTHON\\STLReader')
-filename = '01_PhantomShell_ICEM_3mm.stl'
-filename2 = '01_PhantomShell_ICEM_3mm_write.stl'
-baseline = 'B_PTB.stl'
-target = 'B_NormalLiner.stl'
-os.chdir(path)
-ampObj = AmpObject(filename)
-regObj = regObject(ampObj)
-ampObj.vert.loc[0,:]
-regObj.vert.loc[0,:]
-ampObj.icp()
-regObj.icp()
-regObj.registration()
-ampObj.registration()
-
-Data = AmpObject(target)
-Data.getBaseline(baseline)
-Reg = regObject(Data)
-Reg.reg_fast()
 
+#"""
+#import os
+#path = ('J:\\Shared Resources\\AmpScan IfLS Team\\'
+#        '100 PYTHON\\STLReader')
+#filename = '01_PhantomShell_ICEM_3mm.stl'
+#filename2 = '01_PhantomShell_ICEM_3mm_write.stl'
+#baseline = 'B_PTB.stl'
+#target = 'B_NormalLiner.stl'
+#os.chdir(path)
+#ampObj = AmpObject(filename)
+#regObj = regObject(ampObj)
+#ampObj.vert.loc[0,:]
+#regObj.vert.loc[0,:]
+#ampObj.icp()
+#regObj.icp()
+#regObj.registration()
+#ampObj.registration()
 
-Use mesh object as parent class with standard function
-and then inherit for all other classes ie socket, residuum, registered
-Either create from filename, object or fv
-
-Standard functions:
-    Rotation 
-    Translation 
-    Read 
-    Write 
-    Normals
-    Slice analyse
-Child classes:
-    Residuum
-    Socket
-    Registration (Target)
-    Soft tissue mesh (Bones, Liner)
-    FE mesh 
-"""
+#Data = AmpObject(target)
+#Data.getBaseline(baseline)
+#Reg = regObject(Data)
+#Reg.reg_fast()
+#
+#
+#Use mesh object as parent class with standard function
+#and then inherit for all other classes ie socket, residuum, registered
+#Either create from filename, object or fv
+#
+#Standard functions:
+#    Rotation 
+#    Translation 
+#    Read 
+#    Write 
+#    Normals
+#    Slice analyse
+#Child classes:
+#    Residuum
+#    Socket
+#    Registration (Target)
+#    Soft tissue mesh (Bones, Liner)
+#    FE mesh 
+#"""
 
 def registration(baseline, target, method='default', steps=5, direct=True):
-    
     """
     Function to register the regObject to the baseline mesh
     
@@ -88,6 +88,10 @@ def registration(baseline, target, method='default', steps=5, direct=True):
     regObj = AmpObject(bData, stype='reg')
     
     def calcError(baseline, regObj, direct=True):
+        """
+        A function within a function will not be documented
+
+        """
         if direct is True:
             values = np.linalg.norm(regObj.vert - baseline.vert, axis=1)
             # Calculate the unit vector normal between corresponding vertices

Internship_Diary/main.tex

@@ -230,4 +230,16 @@ Solution:
 
 Napoleon (sphinx support for numpy or google docstrings) only recognises a specific subset of headings of which "Bug" is not one. Allowed headings are outlined here; \url{http://www.sphinx-doc.org/en/stable/ext/napoleon.html}. I changed the offending section to "Note" which rendered fine.
 
+Traceback 6:
+
+\begin{lstlisting}[language=Python]
+WARNING: autodoc: failed to import module 'AmpScan.cython_ext'; the following exception was raised:
+No module named 'AmpScan.cython_ext'
+\end{lstlisting}
+
+Solution:
+
+This warning occured despite cython\_ext not being included. This occurred due to human error - I removed the 'x' from the '.pyx' when calling the exclude path in apidocs. Adding this solved the issue.
+
 \end{document}
+