corrections to manifest

Add pure-python integrator to verlet chain example

MANIFEST.in

@@ -1,6 +1,6 @@
 recursive-include pyqtgraph *.py *.ui *.m README *.txt
 recursive-include tests *.py *.ui
-recursive-include examples *.py *.ui
+recursive-include examples *.py *.ui *.gz *.cfg
 recursive-include doc *.rst *.py *.svg *.png *.jpg
 recursive-include doc/build/html *
 recursive-include tools *

examples/verlet_chain/chain.py

@@ -1,7 +1,7 @@
 import pyqtgraph as pg
 import numpy as np
 import time
-from .relax import relax
+from . import relax
 
 
 class ChainSim(pg.QtCore.QObject):
@@ -52,7 +52,7 @@ class ChainSim(pg.QtCore.QObject):
         self.mrel1[self.fixed[l2]] = 0
         self.mrel2 = 1.0 - self.mrel1
 
-        for i in range(100):
+        for i in range(10):
             self.relax(n=10)
         
         self.initialized = True
@@ -75,6 +75,10 @@ class ChainSim(pg.QtCore.QObject):
         else:
             dt = now - self.lasttime
         self.lasttime = now
+        
+        # limit amount of work to be done between frames
+        if not relax.COMPILED:
+            dt = self.maxTimeStep
 
         if self.lastpos is None:
             self.lastpos = self.pos
@@ -103,8 +107,9 @@ class ChainSim(pg.QtCore.QObject):
         
         
     def relax(self, n=50):
-        # speed up with C magic
-        relax(self.pos, self.links, self.mrel1, self.mrel2, self.lengths, self.push, self.pull, n)
+        # speed up with C magic if possible
+        relax.relax(self.pos, self.links, self.mrel1, self.mrel2, self.lengths, self.push, self.pull, n)
         self.relaxed.emit()
         
+        
 

examples/verlet_chain/relax.py

@@ -2,22 +2,69 @@ import ctypes
 import os
 
 so = os.path.join(os.path.dirname(__file__), 'maths.so')
-lib = ctypes.CDLL(so)
+try:
+    lib = ctypes.CDLL(so)
+    COMPILED = True
+except OSError:
+    COMPILED = False
 
-lib.relax.argtypes = [
-    ctypes.c_void_p,
-    ctypes.c_void_p,
-    ctypes.c_void_p,
-    ctypes.c_void_p,
-    ctypes.c_void_p,
-    ctypes.c_void_p,
-    ctypes.c_void_p,
-    ctypes.c_int,
-    ctypes.c_int,
-    ]
 
-def relax(pos, links, mrel1, mrel2, lengths, push, pull, iters):
-    nlinks = links.shape[0]
-    lib.relax(pos.ctypes, links.ctypes, mrel1.ctypes, mrel2.ctypes, lengths.ctypes, push.ctypes, pull.ctypes, nlinks, iters)
-    
+if COMPILED:
+    lib.relax.argtypes = [
+        ctypes.c_void_p,
+        ctypes.c_void_p,
+        ctypes.c_void_p,
+        ctypes.c_void_p,
+        ctypes.c_void_p,
+        ctypes.c_void_p,
+        ctypes.c_void_p,
+        ctypes.c_int,
+        ctypes.c_int,
+        ]
 
+    def relax(pos, links, mrel1, mrel2, lengths, push, pull, iters):
+        nlinks = links.shape[0]
+        lib.relax(pos.ctypes, links.ctypes, mrel1.ctypes, mrel2.ctypes, lengths.ctypes, push.ctypes, pull.ctypes, nlinks, iters)
+        
+else:
+    def relax(pos, links, mrel1, mrel2, lengths, push, pull, iters):
+        lengths2 = lengths**2
+        for i in range(iters):
+            #p1 = links[:, 0]
+            #p2 = links[:, 1]
+            #x1 = pos[p1]
+            #x2 = pos[p2]
+            
+            #dx = x2 - x1
+            
+            #dist = (dx**2).sum(axis=1)**0.5
+            
+            #mask = (npush & (dist < lengths)) | (npull & (dist > lengths))
+            ##dist[mask] = lengths[mask]
+            #change = (lengths-dist) / dist
+            #change[mask] = 0
+            
+            #dx *= change[:, np.newaxis]
+            #print dx
+            
+            ##pos[p1] -= mrel2 * dx
+            ##pos[p2] += mrel1 * dx
+            #for j in range(links.shape[0]):
+                #pos[links[j,0]] -= mrel2[j] * dx[j]
+                #pos[links[j,1]] += mrel1[j] * dx[j]
+                
+            
+            for l in range(links.shape[0]):
+                p1, p2 = links[l];
+                x1 = pos[p1]
+                x2 = pos[p2]
+                
+                dx = x2 - x1
+                dist2 = (dx**2).sum()
+               
+                if (push[l] and dist2 < lengths2[l]) or (pull[l] and dist2 > lengths2[l]):
+                    dist = dist2 ** 0.5
+                    change = (lengths[l]-dist) / dist
+                    dx *= change
+                    pos[p1] -= mrel2[l] * dx
+                    pos[p2] += mrel1[l] * dx

examples/verlet_chain_demo.py

@@ -1,26 +1,38 @@
 """
 Mechanical simulation of a chain using verlet integration.
 
+Use the mouse to interact with one of the chains.
 
+By default, this uses a slow, pure-python integrator to solve the chain link
+positions. Unix users may compile a small math library to speed this up by 
+running the `examples/verlet_chain/make` script.
 
 """
+
 import initExample ## Add path to library (just for examples; you do not need this)
 
 import pyqtgraph as pg
 from pyqtgraph.Qt import QtCore, QtGui
 import numpy as np
 
-from verlet_chain import ChainSim
+import verlet_chain
 
-sim = ChainSim()
+sim = verlet_chain.ChainSim()
 
-
-chlen1 = 80
-chlen2 = 60
+if verlet_chain.relax.COMPILED:
+    # Use more complex chain if compiled mad library is available.
+    chlen1 = 80
+    chlen2 = 60
+    linklen = 1
+else:
+    chlen1 = 10
+    chlen2 = 8
+    linklen = 8
+    
 npts = chlen1 + chlen2
 
 sim.mass = np.ones(npts)
-sim.mass[chlen1-15] = 100
+sim.mass[int(chlen1 * 0.8)] = 100
 sim.mass[chlen1-1] = 500
 sim.mass[npts-1] = 200
 
@@ -31,8 +43,10 @@ sim.fixed[chlen1] = True
 sim.pos = np.empty((npts, 2))
 sim.pos[:chlen1, 0] = 0
 sim.pos[chlen1:, 0] = 10
-sim.pos[:chlen1, 1] = np.arange(chlen1)
-sim.pos[chlen1:, 1] = np.arange(chlen2)
+sim.pos[:chlen1, 1] = np.arange(chlen1) * linklen
+sim.pos[chlen1:, 1] = np.arange(chlen2) * linklen
+# to prevent miraculous balancing acts:
+sim.pos += np.random.normal(size=sim.pos.shape, scale=1e-3)
 
 links1 = [(j, i+j+1) for i in range(chlen1) for j in range(chlen1-i-1)]
 links2 = [(j, i+j+1) for i in range(chlen2) for j in range(chlen2-i-1)]
@@ -55,7 +69,8 @@ sim.push = np.concatenate([push1, push2, np.array([True], dtype=bool)])
 sim.pull = np.ones(sim.links.shape[0], dtype=bool)
 sim.pull[-1] = False
 
-mousepos = sim.pos[0]
+# move chain initially just to generate some motion if the mouse is not over the window
+mousepos = np.array([30, 20])
 
 
 def display():