Merging Develop (#4)

* feat: added openep_env folder

* initial commit

* feat: Trisurf plot with colorbar

* fix: matlab indexing in Triangular matrix, subtract 1

* feat: plt grid off

* fix: colorbar positioned to left of the 3-d figure

* feat: replacing the Nan values in voltage with 0, normalising the colorbar with min and max value of voltage

* Initial commit

* initial commit

* initial commit

* feat: coloring the shell with the voltage value

* fix: deleted libraries which are not currently required

* feat:color scale according to threshold voltage

* fix: commenting and cleaning up code

* fix: minor

* feat: drawing edges - identifying unique and unshared edge points

* feat: find unique_edges, unshared_edges, unique_unshared_edges & single instance of the edges

* Initial commit

* Initial commit

* Initial commit

* Openep Visualisation Examples

* feat: test01

* fix: minor

Co-authored-by: jayrajan <[email protected]>

Author: ericspod

.gitignore

@@ -109,6 +109,7 @@ venv/
 ENV/
 env.bak/
 venv.bak/
+openep_env
 
 # Spyder project settings
 .spyderproject

README.md

@@ -0,0 +1,3 @@
+# OpenEP Platform
+
+The open source solution for electrophysiology data analysis

docs/requirements.txt

@@ -0,0 +1,3 @@
+scipy==1.5.4
+matplotlib==3.3.4
+numpy==1.19.5

examples/openep_visualisation.ipynb

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+# Code written by Jerin Rajan on 18th Mar 2021
+# Functions to support OpenEp visualisation
+
+import scipy.io as sio
+from scipy.spatial import ConvexHull, Delaunay
+from scipy import ndimage as ndi
+import numpy as np
+import matplotlib.pyplot as plt
+import matplotlib as mp
+from matplotlib import cm
+from matplotlib.colors import ListedColormap, LinearSegmentedColormap
+from skimage import feature
+import trimesh as tm
+# from matplotlib.tri import Triangulation
+
+
+# Declarations
+file_path = '../openep/openep-examples-main/openep_dataset_1.mat'
+data_tri_X_lst = []
+data_tri_T_lst = []
+x_values = []
+y_values = list()
+z_values = list()
+# voltage threshold to split the colorbar by solid and JET
+volt_threshold = 2
+
+
+
+# Load the file
+# Main MAT File - userdata
+main_file = sio.loadmat(file_path)
+
+# Parsing TriRep Anatomy Data
+# .X & .Triangulation
+
+# Vertices/Points = .X
+data_tri_X = main_file['userdata']['surface_triRep_X'][0][0]
+x = data_tri_X[:,0]
+y = data_tri_X[:,1]
+z = data_tri_X[:,2]
+
+# Triangulation/faces - .T
+data_tri_T = main_file['userdata']['surface_triRep_Triangulation'][0][0]
+# Resolving indexing issue - matlab to python
+t = data_tri_T-1
+
+data_act_bip = main_file['userdata']['surface'][0][0]['act_bip'][0][0]
+voltage_data = data_act_bip[:,1]
+
+# Checking for NaN values and replacing with 0 in voltage data
+voltage_new = np.asarray(list(map(lambda x:0 if np.isnan(x) else x, voltage_data)))
+
+
+
+# ColorShell
+# coloring the shell by the voltage value rather than z-axis height
+min_volt = min(voltage_new)
+max_volt = max(voltage_new)
+
+# normalisation - normalising the voltage - values
+norm = mp.colors.Normalize(vmin=min_volt, vmax=max_volt)
+
+# Plot the Mesh
+# Create a new fig window
+fig = plt.figure()
+# get the current 3d axis on the current fig
+ax1 = fig.gca(projection='3d')
+
+
+# defining a custom color scalar field
+# if only nodal values are known, then the signal need to be averaged by the triangles
+color = np.mean(voltage_new[t], axis=1)
+
+# Voltage Threshold - to split the colorbar axis
+# determining the size of the voltage values
+diff_volt = max_volt - min_volt
+
+dist_below_threshold = volt_threshold - min_volt
+dist_above_threshold = max_volt - volt_threshold
+
+# splitting the colorbar
+# color below threshold - size
+size_below_threshold = round((dist_below_threshold/diff_volt)*256)
+# color above threshold - size
+size_above_threshold = 256 - size_below_threshold
+
+# Define Colormap - Reverse JET
+cm_jet = plt.cm.get_cmap('jet_r',size_below_threshold)
+newcolors = cm_jet(np.linspace(0,1,256))
+# Magenta - RGBA array
+magenta = np.array([255/255, 0/255, 255/255, 1])
+# Gray - RGBA array
+gray = np.array([128/255, 128/255, 128/255, 1])
+
+# Creating new colormap columns
+# Col 1 - Jet
+col1 = cm_jet(np.linspace(0,1,42))
+# Col2 - Magenta
+col2 = np.zeros((214,4)) + magenta
+# Combining Col1 + Col2
+final_col = np.concatenate((col1,col2))
+# NewColormap
+newcmp = ListedColormap(final_col)
+
+# Points - vertices
+points = data_tri_X
+print('x-y-z points\n',points.shape)
+
+
+# Trimesh object
+mesh = tm.Trimesh(vertices=points,faces=t)
+
+# All edges
+print('total number of edges:\n',mesh.edges.shape)
+
+
+
+# Unique edges
+unique_edges = mesh.edges_unique
+print('unique edges of the mesh\n',unique_edges.shape)
+
+# Identify the unshared edges
+unshared_edges = mesh.face_adjacency_unshared
+print('unshared\n',unshared_edges.shape)
+
+unique_edges_in_unshared = []
+for item in unshared_edges:
+    if item in unique_edges:
+        unique_edges_in_unshared.append(item)
+    else:
+        pass
+unique_edges_in_unshared = np.array(unique_edges_in_unshared)
+print('unique edges in unshared:\n',unique_edges_in_unshared)
+
+# Identify the unique unshared edges
+uniques = {}
+count = 0
+for a,b in unique_edges_in_unshared:
+    if (a,b) not in uniques and (b,a) not in uniques:
+        uniques[(a,b)]=(a,b)
+    else:
+        if (a,b) in uniques:
+            del uniques[(a,b)]
+        else:
+            del uniques[(b,a)]
+# print('uniques\n',uniques)
+
+unique_unshared_edges = np.array(list(uniques.values()))
+print('unique_unshared_edges:\n',unique_unshared_edges.shape)
+
+# Get the vertex points for unique unshared edges
+
+
+# extract the ponts/vertices of the unique unshared edges
+for item in unique_unshared_edges:
+    for i in item:
+        x_values.append(points[i][0])
+        y_values.append(points[i][1])
+        z_values.append(points[i][2])
+        # print('unshared_edge_coordinates(x);\n',x_values.append(points[i][0]))
+        # print('unshared_edge_coordinates(y);\n',y_values.append(points[i][1]))
+        # print('unshared_edge_coordinates(z);\n',z_values.append(points[i][2]))
+
+# Get the unique edge points
+x_values_array = np.array(x_values).reshape(len(x_values),1)
+y_values_array = np.array(y_values).reshape(len(y_values),1)
+z_values_array = np.array(z_values).reshape(len(z_values),1)
+
+
+xx = np.array(x_values).reshape(1,len(x_values))
+yy = np.array(y_values).reshape(1,len(y_values))
+zz = np.array(z_values).reshape(1,len(z_values))
+print('xx-values\n',xx)
+print('yy-values\n',yy.shape)
+print('zz-values\n',zz.shape)
+
+
+print('x_values\n',x_values_array.shape)
+print('y_values\n',y_values_array.shape)
+print('z_values\n',z_values_array.shape)
+
+print('x-values\n',x)
+print('y-values\n',y.shape)
+print('z-values\n',z.shape)
+
+# # Join the unique edges together
+unique_unshared_edge_points = np.concatenate((x_values_array,
+                                              y_values_array,
+                                              z_values_array),
+                                              axis=1)
+print('border_points:\n',unique_unshared_edge_points.shape)
+
+# tri = Triangulation(x_values_array,y_values_array,z_values_array)
+
+surf = ax1.plot_trisurf(xx[0],
+                       yy[0],
+                       zz[0],
+                       linewidth=0.1)
+
+# mesh1 = tm.Trimesh(vertices=unique_unshared_edge_points,faces=t)
+# #
+# mesh1.show()
+
+# Plotting the border to the axis
+# ax1.plot_trisurf(xx[0],
+#                  yy[0],
+#                  zz[0],
+#                  triangles=t,
+#                  linewidth=0.5)
+
+surf1 = ax1.plot_trisurf(x,
+                         y,
+                         z,
+                         triangles=t,
+                         linewidth=0.5,
+                         antialiased=True,
+                         cmap=newcmp)
+
+
+# print('dir:\n',dir(surf1))
+# print('typeofsurf',type(surf1))
+# surf1.set_edgecolor([0,0,0,1])
+surf1.set_array(color)
+# surf1.set_markeredgecolor([0,0,0,1])
+# surf1.set_fc([0.0,1,0])
+ax1.set_title('OpenEP TriRep Anatomy Data')
+plt.axis('off')
+
+# Colour Pallette, Position Left
+cb = plt.colorbar(mp.cm.ScalarMappable(norm=norm, cmap=newcmp),
+                  ax=[ax1],
+                  location='left',
+                  label='Voltage (mV)')
+
+# Show plot
+plt.show()
+
+
+
+# DRAWMAP plots an OpenEP map
+# userdata is a Carto data structure
+def draw_map(
+        userdata, *arg):
+    pass

main.py

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+'''
+Library for importing, exporting and doing visualisation on the triangular meshes
+'''

openep-app/visualisation/visualisation.py

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+import unittest
+
+class TestVisualisation(unittest.TestCase):
+    def test_01(self):
+        pass
+
+if __name__ == '__main__':
+    unittest.main()