working with new vispy

Pavel Govyadinov
1 parent 25fa0bfe
Showing 7 changed files with 162 additions and 84 deletions Show diff stats
GraphCanvas.py
GraphWidget.py
GuiVisPy_tube.py
TubeCanvas.py
TubeWidget.py
graph_shaders.py
subgraph_shaders.py
@@ -13,6 +13,7 @@ from vispy.gloo import set_viewport, set_state, clear, set_blend_color, context
 from vispy.util.transforms import perspective, translate, rotate, scale
 import vispy.gloo.gl as glcore
 from vispy import app
+import copy
 import numpy as np
 import math
@@ -91,7 +92,6 @@ class GraphCanvas(scene.SceneCanvas):
         self.moving = False
         self.moving_cluster = False
         self.selection = False
-
         n = 10
         ne = 10
         #Init dummy structures
@@ -209,6 +209,9 @@ class GraphCanvas(scene.SceneCanvas):
         self.timer = app.Timer('auto', connect=self.on_timer, start=False)
+        #self.constant = app.Timer('auto', connect=self.update, start=True)
+        self.num=0
+        print(self.context.config)
     def on_timer(self, event):
         #get the temporary positions of the vertices (and edges)
@@ -285,7 +288,7 @@ class GraphCanvas(scene.SceneCanvas):
         self.program_s.bind(self.vbo_s)
         self.program_e_s.bind(self.vbo_cluster_lines)
-        self.update()
+        self.refresh()
     """
         Function that recolors vertices based on the selected statistic
@@ -306,7 +309,7 @@ class GraphCanvas(scene.SceneCanvas):
         self.vbo = gloo.VertexBuffer(self.data)
         self.program.bind(self.vbo)
         #self.program_e.bind(self.vbo)
-        self.update()
+        self.refresh()
     def update_color_buffers(self):
         color = self.G.vertex_properties["RGBA"].get_2d_array(range(4)).T
@@ -352,7 +355,7 @@ class GraphCanvas(scene.SceneCanvas):
         self.vbo = gloo.VertexBuffer(self.data)
         self.program.bind(self.vbo)
         #self.program_e.bind(self.vbo)
-        self.update()
+        self.refresh()
     """
@@ -461,7 +464,7 @@ class GraphCanvas(scene.SceneCanvas):
         self.vbo_line = gloo.VertexBuffer(self.line_data)
         self.program.bind(self.vbo)
         self.program_e.bind(self.vbo_line)
-        self.update()
+        self.refresh()
     """
         Sets the edge color based on the the cluster the vertices belongs to
@@ -480,10 +483,10 @@ class GraphCanvas(scene.SceneCanvas):
         Test function that only binds the buffer
     """
     def gen_vertex_vbo_minimalist(self):
-        self.update()
+        self.refresh()
         self.vbo.set_data(self.data)
         self.program.bind(self.vbo)
-        self.update()
+        self.refresh()
     """
         Helper function that generates the framebuffer object that stores the vertices
@@ -540,7 +543,7 @@ class GraphCanvas(scene.SceneCanvas):
             self.program_s.bind(self.vbo_s)
         if DEBUG:
             print(self.view)
-        self.update()
+        self.refresh()
     """
         Helper function that creates colored "block" lines based on the edges
@@ -898,7 +901,7 @@ class GraphCanvas(scene.SceneCanvas):
 #            self.program_s.bind(self.vbo_s)
 #        if DEBUG:
 #            print(self.view)
-#        self.update()
+#        self.refresh()
     """
@@ -928,12 +931,59 @@ class GraphCanvas(scene.SceneCanvas):
         #Generate the clusters
         self.labels = nwt.Network.spectral_clustering(G,'length', n_clusters = n_c)
+        bb = nwt.AABB(G)
+        #print("FLJKKHDFLKJFDLKJFDLKJ ", m)
+        pts = []
+        x, y, z = bb.project_grid(3)
+        for i in range(3):
+            for j in range(3):
+                for k in range(3):
+                    pts.append(np.array([x[i], y[j], z[k]]))
+        
         #self.labels = nwt.Network.spectral_clustering(G,'length')
         #Add clusters as a vertex property
         G.vertex_properties["clusters"] = G.new_vertex_property("int", vals=self.labels)
         num_clusters = len(np.unique(self.labels))
         self.n_c = n_c
+        new_indices = []
+        pos = G.vertex_properties["p"].get_2d_array(range(3)).T
+        
+        #for each cluster find the average vertex position and match to closest point
+        #in the unique grid.
+        for i in range(n_c):
+            point = np.sum(pos[np.argwhere(self.labels == i)], axis=0)/len(np.argwhere(self.labels == i))
+            d = 100000000.0
+            idx = -1
+            for j in range(len(pts)):
+                dist = np.sqrt(np.power(pts[j][0]-point[0,0],2) + np.power(pts[j][1]-point[0,1],2) + np.power(pts[j][2]-point[0,2],2))
+                if dist < d:
+                    d = dist
+                    idx = j
+            new_indices.append(idx)
+            pts[idx] = np.array([100000000.0, 1000000000.0, 100000000.0])
+        #since there are more points than clusters, we need to make the indices range from
+        #[0, n_c)
+        j=0
+        unique_indices = np.array(new_indices)
+        for i in range(n_c):
+            idx = np.argmin(new_indices)
+            unique_indices[idx] = j
+            j += 1
+            new_indices[idx] = 100
+            
+        lbl = np.zeros(self.labels.shape)
+        for i in range(n_c):
+            idxs = np.argwhere(self.labels == i)
+            new_idx = np.argwhere(unique_indices == i)
+            lbl[idxs] = unique_indices[i]
+            
+        self.labels = lbl
+        G.vertex_properties["clusters"] = G.new_vertex_property("int", vals=self.labels)  
+        
+            
+            
+            
         #add colormap
         G.vertex_properties["RGBA"] = nwt.Network.map_property_to_color(G, G.vertex_properties["clusters"])
@@ -1072,7 +1122,7 @@ class GraphCanvas(scene.SceneCanvas):
             self.program_s.bind(self.vbo_s)
         if DEBUG:
             print(self.view)
-        self.update()
+        self.refresh()
     """
         Loads the data G and generates all the buffers necessary as well as performs
@@ -1143,7 +1193,7 @@ class GraphCanvas(scene.SceneCanvas):
             self.program_s.bind(self.vbo_s)
         if DEBUG:
             print(self.view)
-        self.update()
+        self.refresh()
     """
         Function that changes and redraws the buffer during a resize event.
@@ -1165,7 +1215,20 @@ class GraphCanvas(scene.SceneCanvas):
         if(self.subgraphs):
             self.program_e_s.draw('triangles', indices=self.index_clusters_s)
             self.program_s.draw('triangles', indices=self.index_s)
+        print("updated  ", self.num)
+        self.num += 1
+        #self._u
+        #self._update_pending = True
+        #app.Canvas.update(self)
+        #super(scene.SceneCanvas, self).update()    #This forces redrawd
+    """
+        refreshes the canvas and forces the redraw. A workaround for issue in
+        vispy 0.6.3
+    """
+    def refresh(self):
+        self.update()
+        app.Canvas.update(self)
 #    """
 #        A function to animate from one layout to another layout given a new G.
@@ -1259,7 +1322,7 @@ class GraphCanvas(scene.SceneCanvas):
         #    print(self.color_dict[tuple(color)])
         #reset the original buffer
-        self.update()
+        self.refresh()
         #Return the element under the click.
         if clusters == False:
@@ -1343,7 +1406,7 @@ class GraphCanvas(scene.SceneCanvas):
         def update_vbo(self):
             self.vbo = gloo.VertexBuffer(self.data)
             self.program.bind(self.vbo)
-            self.update()
+            self.refresh()
         def update_vertex_alpha(self, vertex, alpha):
             temp = self.G.vertex_properties["RGBA"][vertex]
@@ -1605,7 +1668,7 @@ class GraphCanvas(scene.SceneCanvas):
                     self.program_e.bind(self.vbo_line)
                     #self.program.draw('points')
                     self.location = event.pos
-                    self.update()
+                    self.refresh()
             elif(self.moving == True and self.moving_cluster == True):
                 if(len(self.c_id) < 2):
                     #Project into GLSpace and get before and after move coordinates
@@ -1640,7 +1703,7 @@ class GraphCanvas(scene.SceneCanvas):
                         self.vbo_s = gloo.VertexBuffer(self.clusters)
                         self.program_s.bind(self.vbo_s)
                     self.update_cluster_line_vbo()
-                    self.update()
+                    self.refresh()
             else:
@@ -1660,7 +1723,7 @@ class GraphCanvas(scene.SceneCanvas):
                 self.program_s['u_view'] = self.view
                 self.program_e_s['u_view'] = self.view
                 self.location = event.pos
-                self.update()
+                self.refresh()
     """
         Handles the mouse wheel zoom event.
@@ -1687,4 +1750,4 @@ class GraphCanvas(scene.SceneCanvas):
         self.program_s['u_view'] = self.view
         self.program_e_s['u_view'] = self.view
         #print(event.delta[1])
-        self.update()
+        self.refresh()
@@ -7,7 +7,7 @@ Created on Mon Aug  5 15:42:19 2019
 """
 from GraphCanvas import GraphCanvas
-from pyqtgraph.Qt import QtCore, QtGui, QtWidgets
+from PyQt5 import QtCore, QtGui, QtWidgets
 import network_dep as nwt
 import numpy as np
@@ -19,14 +19,16 @@ Initializes the entire QTlayout and sets the mouse press events.
 These are connected to the slots such that each is processes by this class
 and the class it wraps.
 """    
-class GraphWidget(QtGui.QWidget):
+#class GraphWidget(QtGui.QWidget):
+class GraphWidget(QtWidgets.QWidget):
     select = QtCore.pyqtSignal(list)
     def __init__(self):
         super(GraphWidget, self).__init__()
-        box = QtGui.QVBoxLayout(self)
+        box = QtWidgets.QVBoxLayout(self)
         self.resize(500,500)
         self.setLayout(box)
         self.canvas = GraphCanvas()
+        self.setUpdatesEnabled(True)
         #self.canvas.create_native()
         box.addWidget(self.canvas.native)
         self.color = True
@@ -37,8 +39,9 @@ class GraphWidget(QtGui.QWidget):
         self.canvas.events.mouse_release.connect(self.on_mouse_release)
         self.canvas.events.mouse_move.connect(self.on_mouse_move)
         self.canvas.events.mouse_double_click.connect(self.on_mouse_double_click)
-
+        #self.canvas.events.
         #self.show()
+        #self.repaint()
     """
     Handles the right click mouse event at the QWidget level.
@@ -49,11 +52,16 @@ class GraphWidget(QtGui.QWidget):
     The context menu level actions are also coded in this section of the code.
     """
     def on_mouse_press(self, event):
+        self.canvas.set_current(event)
         if event.button == 2:
             if self.canvas.view[0][0] >= 0.0010:
+                self.canvas.update()
                 c_id = self.canvas.get_clicked_id(event)
+                self.canvas.update()
             else:
+                self.canvas.update()
                 c_id = self.canvas.get_clicked_id(event, clusters=True)
+                self.canvas.update()
             #right click
             if(c_id == None):
                 menu = QtWidgets.QMenu(self)
@@ -178,15 +186,16 @@ class GraphWidget(QtGui.QWidget):
         Handles the mouse double click event.
         Pass-through function.
     """
+    
     def on_mouse_double_click(self, event):
         self.canvas.update_path(event)
         self.select.emit(self.canvas.get_path())
-        old_pos = self.canvas.G.vertex_properties["pos"].get_2d_array(range(3)).T
-        nG = nwt.Network.gen_new_fd_layout(self.canvas.G)
+#        old_pos = self.canvas.G.vertex_properties["pos"].get_2d_array(range(3)).T
+#        nG = nwt.Network.gen_new_fd_layout(self.canvas.G)
         #    def animate(self, new_G):
 #            
-        new_pos = nG.vertex_properties["pos"].get_2d_array(range(3)).T
-        self.canvas.animate(old_pos, new_pos)
+#        new_pos = nG.vertex_properties["pos"].get_2d_array(range(3)).T
+#        self.canvas.animate(old_pos, new_pos)
     """
         Handles the mouse release event.
@@ -7,35 +7,39 @@ Created on Thu Jan 31 15:29:40 2019
 `"""
 from vispy import app
-
+import vispy
 import network_dep as nwt
-from pyqtgraph.Qt import QtCore, QtGui, QtWidgets
-import pyqtgraph as pg
+#from pyqtgraph.Qt import QtCore, QtGui, QtWidgets
+from PyQt5 import QtCore, QtGui, QtWidgets
+#import pyqtgraph as pg
 import numpy as np
 import math
 from mpl_toolkits.mplot3d import Axes3D
-import matplotlib
-import matplotlib.pyplot as plt
-matplotlib.use('Qt5Agg')
+#import matplotlib
+#import matplotlib.pyplot as plt
+#matplotlib.use('Qt5Agg')
 from GraphWidget import GraphWidget
 from TubeWidget import TubeWidget
+#vispy.use(app='egl')
 DEBUG = False
-
 #set the backend. for different versions of PyQt
 app.use_app(backend_name='PyQt5')
+app.set_interactive(True)
+
 #Define a top level application
-appMain = QtGui.QApplication([])
+appMain = QtWidgets.QApplication([])
+#QtWidgets.QApplication.setAttribute(QtCore.Qt.AA_ShareOpenGLContexts, True)
 ##Define a toplevel Widget
-top = QtGui.QWidget()
+top = QtWidgets.QWidget()
 top.resize(900, 900)
@@ -46,7 +50,7 @@ fibers.canvas.create_native()
 #plt = hist.addPlot()
-layout = QtGui.QGridLayout()
+layout = QtWidgets.QGridLayout()
 graph = GraphWidget()
 graph.canvas.create_native()
@@ -54,14 +58,15 @@ graph.connect(fibers)
 fibers.connect(graph)
 #initialize the layout
-layout.addWidget(graph, 0, 0, 2, 3)
-layout.addWidget(fibers, 0, 2, 2, 3)
+layout.addWidget(graph.canvas.native, 0, 0, 2, 3)
+layout.addWidget(fibers.canvas.native, 0, 2, 2, 3)
 layout.setColumnStretch(0, 2)
 layout.setRowStretch(0, 2)
 layout.setColumnStretch(2, 1)
 layout.setRowStretch(0, 1)
 top.setLayout(layout)
+
 top.show()
@@ -95,8 +100,8 @@ G, bbl, bbu = load_nwt(&quot;/home/pavel/Documents/Python/GraphGuiQt/network_4.nwt&quot;)
 #G, bbl, bbu = load_nwt("/home/pavel/Documents/Python/GraphGuiQt/net`````````work_test_251_1kx3_short_NEW.nwt")
 #ret = nwt.Network.get_affinity_matrix(G, "length")
-node_image = QtGui.QImage("/home/pavel/Documents/Python/GraphGuiQt/node_tex.jpg")
-node_tex = QtGui.QBitmap.fromImage(node_image)
+#node_image = QtGui.QImage("/home/pavel/Documents/Python/GraphGuiQt/node_tex.jpg")
+#node_tex = QtGui.QBitmap.fromImage(node_image)
 if DEBUG:
     print(node_tex.depth())
@@ -109,10 +114,12 @@ graph.canvas.set_data(G, bbl, bbu)
 fibers.canvas.set_data(G, bbl, bbu, 16)
 #fibers.draw_all(G, center, fibers, graph, node_tex)
 graph.set_g_view(fibers)
+
 ## Start Qt event loop unless running in interactive mode.
 if __name__ == '__main__':
-    import sys
-    if (sys.flags.interactive != 1) or not hasattr(QtCore, 'PYQT_VERSION'):
-        QtGui.QApplication.instance().exec_()
-
+    #import sys
+    #if (sys.flags.interactive != 1) or not hasattr(QtCore, 'PYQT_VERSION'):
+        #QtGui.QApplication.instance().exec_()
+    app.set_interactive(enabled=True)
+    app.run()
@@ -10,7 +10,7 @@ Created on Mon Aug  5 15:56:47 2019
     Class that extends the vispy SceneCanvas to draw 3D tubes
 """
-from vispy import gloo, scene
+from vispy import gloo, scene, app
 from vispy.gloo import set_viewport, set_state, clear, set_blend_color, context
 from vispy.gloo import gl
 from vispy.util.transforms import perspective, translate, rotate, scale
@@ -47,6 +47,7 @@ class TubeDraw(scene.SceneCanvas):
         self.cylinder_data = np.zeros(5*5, dtype=[('a_position', np.float32, 3),
                                   ('a_normal', np.float32, 3),
                                   ('a_fg_color', np.float32, 4),
+                                  ('a_selection', np.float32, 1),
                                   #('a_linewidth', np.float32, 1),
                                   ])
         self.triangle_data = np.random.randint(size=(5, 3), low=0,
@@ -82,6 +83,8 @@ class TubeDraw(scene.SceneCanvas):
         self.program['u_eye'] = self.camera
         self.program['u_up'] = self.up
         self.program['u_target'] = np.asarray([0., 0., 0.], dtype=np.float32)
+#        self.bb = np.ones((26, 3), dtype=np.float32)
+#        self.program['u_bb'] = self.bb
@@ -170,6 +173,10 @@ class TubeDraw(scene.SceneCanvas):
         self.projection = perspective(90.0, self.physical_size[0]/self.physical_size[1], 1.0, 1000.0)
         self.program['u_projection'] = self.projection
+
+    def refresh(self):
+        self.update()
+        app.Canvas.update(self)
     #Creates a cylinder around ever segment in the microvascular network.
     def gen_cylinder_vbo(self, G, num_sides = 32):
         i = 0
@@ -417,7 +424,8 @@ class TubeDraw(scene.SceneCanvas):
             #gloo.set_depth_func('lequal')
             #clear(color='white', depth=True)
             #print(gloo.wrappers.get_gl_configuration())
-        self.update()
+        self.refresh()
+
                 #print(self.canvas.edge_dict[(e[1], e[0])])
     #Handles the mouse wheel event, i.e., zoom
     def on_mouse_wheel(self, event):
@@ -456,7 +464,8 @@ class TubeDraw(scene.SceneCanvas):
         self.program['u_eye'] = self.camera
         #print(self.view)
         #print(event.delta[1])
-        self.update()
+        self.refresh()
+
@@ -534,7 +543,7 @@ class TubeDraw(scene.SceneCanvas):
             self.program['u_eye'] = self.camera
             self.program['u_up'] = self.up
             #self.program['u_LightPos'] = [self.camera[0], self.camera[1], self.camera[2]]
-            self.update()
+            self.refresh()
     #reverts the mouse state during release.
     def on_mouse_release(self, event):
@@ -11,19 +11,20 @@ Created on Mon Aug  5 15:53:16 2019
     methods necessary to use the QT signals and slots API.
 """
-from pyqtgraph.Qt import QtCore, QtGui, QtWidgets
+#from pyqtgraph.Qt import QtCore, QtGui, QtWidgets
+from PyQt5 import QtCore, QtGui, QtWidgets
 from TubeCanvas import TubeDraw
 import numpy as np
 #import trimesh as tm
 DEBUG = False
-class TubeWidget(QtGui.QWidget):
+class TubeWidget(QtWidgets.QWidget):
     sigUpdate = QtCore.pyqtSignal(float, float, float)
     #Initializes the QT wrapper class.
     def __init__(self):
         super(TubeWidget, self).__init__()
-        box = QtGui.QVBoxLayout(self)
+        box = QtWidgets.QVBoxLayout(self)
         self.resize(500,500)
         self.setLayout(box)
         self.canvas = TubeDraw()
@@ -11,7 +11,7 @@ from vispy import gloo, app, scene
 #shaders for drawing nodes
 vert = """
-#version 120
+
 // Uniforms
 // ------------------------------------
 uniform float u_size;
@@ -58,7 +58,7 @@ void main (void) {
 """
 frag = """
-#version 120
+
 // Constants
 // ------------------------------------
 uniform mat4 u_model;
@@ -90,8 +90,9 @@ void main()
  {
     float size = v_size + 2*(v_linewidth + 1.5*v_antialias);
     float t = v_linewidth/2.0-v_antialias;
-    // The marker function needs to be linked with this shader
-    float r = marker(gl_PointCoord, size);
+    vec2 p = (gl_PointCoord.xy - vec2(0.5,0.5))*size;
+    float r = length(p);
+    r -= v_size/2;
     float d = abs(r) - t;
     if( r > (v_linewidth/3.0+v_antialias))
     {
@@ -103,7 +104,7 @@ void main()
        {
            float alpha = d/v_antialias;
            alpha = new_alpha(v_zoom_level);
-            gl_FragColor = mix(vec4(1,1,1,0.9), v_bg_color, max(1.0-alpha, 0.3));
+           gl_FragColor = mix(vec4(1,1,1,0.9), v_bg_color, max(1.0-alpha, 0.3));
        }
        else
        {
@@ -132,7 +133,14 @@ void main()
                 else
                     gl_FragColor = vec4(gl_Color.rgb, max(1.0-alpha, 0.1));
             else
-                gl_FragColor = mix(v_bg_color, v_fg_color, alpha);
+                {
+                        //gl_FragColor = mix(v_bg_color, v_fg_color, alpha);            vec3 color = vec3(1.0, 0.0, 0.0);
+                        vec3 normal = normalize(vec3(p.xy, d));
+                        vec3 direction = normalize(vec3(1.0, 1.0, 5.0));
+                        float diffuse = max(0.0, dot(direction, normal));
+                        float specular = pow(diffuse, 24.0);
+                        gl_FragColor = mix(vec4(max(diffuse*v_bg_color.rgb, specular*vec3(0.7)), 1.0), v_fg_color, alpha);
+                }
     }
@@ -177,7 +185,7 @@ float new_alpha(float zoom_level)
 vs = """
-#version 120
+
 // Uniforms
 // ------------------------------------
@@ -215,7 +223,7 @@ void main() {
 """
 fs = """
-#version 120
+
 // Varying
 // ------------------------------------
 varying vec4 v_fg_color;
@@ -8,7 +8,6 @@ Created on Mon Aug  5 15:35:04 2019
 #shaders for drawing supernodes
 vert_s = """
-#version 120
 // Uniforms
 // ------------------------------------
 uniform mat4 u_model;
@@ -50,7 +49,6 @@ void main (void) {
 """
 frag_s = """
-#version 120
 const float pi = 3.1415926535897932384626433832795;
 // Varyings
 // ------------------------------------
@@ -99,6 +97,12 @@ void main()
          if(dist < 0.25)
          {
               //gl_FragColor = v_cluster_color;
+//              vec2 p = (gl_FragCoord.xy - v_value);
+//              vec3 normal = normalize(vec3(p.xy, dist));
+//              vec3 direction = normalize(vec3(1.0, 1.0, 5.0));
+//              float diffuse = max(0.0, dot(direction, normal));
+//              float specular = pow(diffuse, 24.0);
+//              gl_FragColor = vec4(max(diffuse*v_cluster_color.rgb, specular*vec3(1.0)), 1.0);
               gl_FragColor = vec4(v_cluster_color.rgb, n_alpha);
          }
          if(dist > 0.3 && 0.55 > dist)
@@ -139,28 +143,6 @@ void main()
                       gl_FragColor = vec4(0.93, 0.949, 0.329, n_alpha);
                       //gl_FragColor = vec4(1.0, 1.0, 0.0, n_alpha);
               }
-              //else
-              //{
-              //        discard;
-              //}
-
-//              if(angle > -pi && angle < -pi/4.0)
-//              {
-//                    //gl_FragColor = vec4(0.32, 0.61, 0.93, n_alpha);
-//                      gl_FragColor = vec4(1.0, 0.0, 0.0, n_alpha);
-//              }
-//              else if(angle > -pi/4.0 && angle < 0.0)
-//              {
-//                  gl_FragColor = vec4(0.0, 1.0, 0.0, n_alpha);
-//              }
-//              else if(angle > 0.0 && angle < pi/2.0)
-//              {
-//                  gl_FragColor = vec4(0.0, 0.0, 1.0, n_alpha);
-//              }
-//              else if(angle > pi/2.0 && angle < pi)
-//              {
-//                  gl_FragColor = vec4(1.0, 1.0, 0.0, n_alpha);
-//              }
          }
     }
     else
@@ -200,7 +182,6 @@ float new_alpha(float zoom_level)
 """
 vs_s = """
-#version 120
 // Uniforms
 // ------------------------------------
@@ -237,7 +218,7 @@ void main() {
 """
 fs_s = """
-#version 120
+
 // Varying
 // ------------------------------------
 varying vec4 v_fg_color;