restored load_from function

gen/generate.py

@@ -12,7 +12,7 @@ def main():
     nthreads = int(sys.argv[1])
     
     print("Using %d thread(s)" % nthreads)
-    basenet = netflow.load_network_from('../netflow/network/network.h5', isBaseNet=True)
+    basenet = netflow.load_network_from('../netflow/network/network.h5')
     print("Network statistics:")
     pore_throat_counts = [len(pore.throats) for pore in basenet.pores]
     print("Max. number of throats per pore: %d" % max(pore_throat_counts))

netflow/netgen.py

@@ -56,14 +56,9 @@ class Network:
     
     Lmax must be smaller than the smallest side length of the network ub-lb.
     """
-    throatIdx = 0
-    # Globals: Lengths and radii of all throats present in base network.
-    # Only used for the generate_dendrogram generator
-    throatL = []
-    throatR = []
     def __init__(self, lb: List[float] = [], ub: List[float] = [], \
         pores: List[Pore] = None, throats: List[Throat] = None, \
-        Lmax: float = 0.0, label: str = None, isBaseNet: bool = False):
+        Lmax: float = 0.0, label: str = None):
         # lower/upper bounds for network volume
         self.lb = lb.copy(); self.ub = ub.copy()
         # sets with pores and throats
@@ -78,9 +73,6 @@ class Network:
             self.label = datetime.today().isoformat(sep=' ',timespec='seconds')
         else:
             self.label = label
-        self.isBaseNet = isBaseNet
-        # Lengths of network domain
-        self.L = [ub-lb for lb,ub in zip(self.lb,self.ub)]
     def __repr__(self):
         # count in/out resp. labelled pores
         k = sum([int(pore.label != LABELS[0]) for pore in self.pores])
@@ -109,17 +101,6 @@ class Network:
         self.throats.add(throat)
         pore1.throats.add(throat); pore2.throats.add(throat)
         return throat
-    def connect_pores_generator(self, pore1: Pore, pore2: Pore, r: float, \
-        throat_id: int = -1, label: str = LABELS[0]) -> Throat:
-        """Establish a throat connection between two pores."""
-        throat = Throat(pore1, pore2, r, label, throat_id)
-        lt = distance(*throat_ends(throat, self.L))
-        Network.throatL.append(lt)
-        Network.throatR.append(r)
-        pore1.throats.add(Network.throatIdx)
-        pore2.throats.add(Network.throatIdx)
-        Network.throatIdx += 1
-        return throat
 
 class CellList:
     """CellList class dividing physical domain into equally-sized cells
@@ -127,7 +108,8 @@ class CellList:
     find_candidates() assumes pore is located in interior of domain (non-periodic)
     """
     def __init__(self, pores: List[Pore], domainSize: List[float], cellSize: float, \
-                        basenet: Network, nInterior: int):
+                        basenet: Network, throatL: List[float], throatR: List[float], \
+                        nInterior: int):
         from math import ceil
         self.dim = len(domainSize)
         self.Lmax = basenet.Lmax
@@ -143,6 +125,10 @@ class CellList:
         self.poresSorted = [set() for _ in range(self.totalCells)]
         # For each pore keep track of nbor pores connected to it
         self.connPores = [set() for _ in range(nInterior)]
+        # List of (target) throat lengths from base network
+        self.throatL = throatL
+        # List of throat radii from base network
+        self.throatR = throatR
         
         throatTotal = 0
         for i, pore in enumerate(pores):
@@ -183,7 +169,7 @@ class CellList:
             candidates = self.find_candidates(pore)
             # Find best candidate for each throat of pore
             for idx, throatIdx in enumerate(pore.throats):
-                lt = Network.throatL[throatIdx]
+                lt = self.throatL[throatIdx]
                 
                 if (len(candidates) == 0):
                     self.set_throat(pore.index, -1, idx)
@@ -682,10 +668,23 @@ def generate_dendrogram(basenet: Network, targetsize: List[int], \
     # check valid number of threads
     if (nthreads < 1):
         raise ValueError('Number of threads must be >= 1!')
-    # check network provided was initialized properly
-    if (not basenet.isBaseNet):
-        raise ValueError('Provided network was not initialized as base network!')
+    
+    # Initialize throat lengths and radii of base network to be used
+    # later
+    throatIdxMap = {}  # {int (throat id): int (throat index)}
+    throatBaseIdx = 0
+    throatL = []
+    throatR = []
+    baseL = [ub-lb for lb,ub in zip(basenet.lb,basenet.ub)]
+    for pore in basenet.pores:
+        for throat in pore.throats:
+            lt = distance(*throat_ends(throat, baseL))
+            throatL.append(lt)
+            throatR.append(throat.r)
+            throatIdxMap[throat] = throatBaseIdx
+            throatBaseIdx += 1
         
+    del baseL  # no longer needed
     # pores, distributed based on dendrogram of basenet
     if (not mute): print("distributing pores...")
     # make indexable and discard in-/outflow pores
@@ -701,8 +700,9 @@ def generate_dendrogram(basenet: Network, targetsize: List[int], \
         for s in product(*[range(k) for k in targetsize]):
             for k, pore in enumerate(basepores):
                 pos = [random()*l for l in L]
+                poreThroatIdx = set(throatIdxMap[throat] for throat in pore.throats)
                 pores.append(Pore(pos=pos, r=pore.r, label=LABELS[0], 
-                    throats=pore.throats.copy(), index=runningIndex))
+                    throats=poreThroatIdx, index=runningIndex))
                 runningIndex += 1
     else: # dendrogram-based
         # extract cluster hierarchy from basenet
@@ -737,12 +737,18 @@ def generate_dendrogram(basenet: Network, targetsize: List[int], \
                         [ctr[j] - w1*dist/(w1+w2)*vec[j] for j in range(d)]
                     touched[p1] = touched[p2] = True
             # add section pores in random order to pores of new network
+            baseThroatIdx = 0
             for k, pore in enumerate(basepores):
+                [throat in pore.throats]
                 pos = [c-lb + si*(ub-lb) \
                     for c,si,lb,ub in zip(centroids[k],s,basenet.lb,basenet.ub)]
+                poreThroatIdx = set(throatIdxMap[throat] for throat in pore.throats)
                 pores.insert(randint(0,len(pores)), Pore(pos=pos,
-                    r=pore.r, label=LABELS[0], throats=pore.throats.copy()))
-                
+                    r=pore.r, label=LABELS[0], throats=poreThroatIdx))
+        
+        # Throat index map no longer needed
+        del throatIdxMap
+        
         print("left {0:d} of {1:d} clusters (incl. {2:d} pores) untouched".\
             format(sum([int(not j) for j in touched]), len(touched), len(basepores)))
         # flip pores outside back into domain and set respective index of all pores
@@ -762,7 +768,8 @@ def generate_dendrogram(basenet: Network, targetsize: List[int], \
     # Domain size including periodic buffer layers on all sides
     trueDomainSize = [L[i] + 2 * basenet.Lmax for i in range(d)]
     # Initialize cell-list; Place each pore in respective cell-set
-    cellList = CellList(pores, trueDomainSize, basenet.Lmax, basenet, n)
+    cellList = CellList(pores, trueDomainSize, basenet.Lmax, basenet, \
+                          throatL, throatR, n)
     
     # Divide by two (since we are counting every throat twice)
     totalThroats = len(cellList.poreMatchTable) // 2
@@ -804,7 +811,6 @@ def generate_dendrogram(basenet: Network, targetsize: List[int], \
             print("Throats left: %d Throats Unrealized: %d (%.2f%%)" % \
                  (throatsLeft, throatsUnrealized, throatsUnrealized / totalThroats * 100.))
         
-        
         nRemain = len(poresRemain)
         if (nRemain > serialThresh):
             # Compute loads and displacements for all threads
@@ -840,7 +846,6 @@ def generate_dendrogram(basenet: Network, targetsize: List[int], \
             if (len(poreTtbr) == 0): continue  # Nothing left to do
             # Set of indices of connected pores
             pConn = cellList.connPores[pore.index]
-            
             matches = cellList.fetch_matches(pore)
             
             for throatIdx, match in zip(pore.throats, matches):
@@ -853,7 +858,6 @@ def generate_dendrogram(basenet: Network, targetsize: List[int], \
                     break
                     
                 nbor = pores[match]
-                
                 nborc = nbor # memorize potential periodic copy
                 # find original of buffer layer pore
                 if (nbor.label != LABELS[0]):
@@ -872,15 +876,15 @@ def generate_dendrogram(basenet: Network, targetsize: List[int], \
                 # Update sets of connected pores
                 cellList.update_connection(pore.index, nbor.index)
                 
-                r = Network.throatR[throatIdx]
-                targetLen = Network.throatL[throatIdx]
+                r = throatR[throatIdx]
+                targetLen = throatL[throatIdx]
                 # Compute actual throat length between pores
                 lt = distance(pore.pos, nborc.pos)
                 
                 # connect pore to nbor
                 throats.append([pore, nbor, lbl, r])
                 # remove most similar throat of nbor
-                ranking = [(nborThroatIdx, abs(Network.throatL[nborThroatIdx] - lt)) \
+                ranking = [(nborThroatIdx, abs(throatL[nborThroatIdx] - lt)) \
                             for nborThroatIdx in nborTtbr]
                 nborThroatIdx, _ = min(ranking, key=lambda il: il[1])
                 
@@ -1232,14 +1236,14 @@ def save_network_to(filename: str, network: Network):
             data=wrk)
 
 
-def load_network_from(filename: str, isBaseNet: bool) -> Network:
+def load_network_from(filename: str) -> Network:
     """Load pore network from hdf5 file."""
     import h5py
     import numpy as np
     f = h5py.File(filename, 'r')
     # global network properties
     network = Network(label=f['network_label'][0].decode('utf-8'),
-        lb=list(f['lb']), ub=list(f['ub']), Lmax=f['Lmax'][0], isBaseNet=isBaseNet)
+        lb=list(f['lb']), ub=list(f['ub']), Lmax=f['Lmax'][0])
 
     # pores
     pid = np.array(f['pores/id'])
@@ -1258,11 +1262,6 @@ def load_network_from(filename: str, isBaseNet: bool) -> Network:
     if 'label' in f['pores']: # are there any labels != ''?
         for id, strg in zip(f['pores/label/id'],f['pores/label/strg']):
             pores[id].label = strg.decode('utf-8')
-
-    # pick appropriate connector method if generation algorithm is used
-    connector_method = network.connect_pores
-    if isBaseNet:
-        connector_method = network.connect_pores_generator
         
     # throats
     tid = np.array(f['throats/id'])
@@ -1271,7 +1270,7 @@ def load_network_from(filename: str, isBaseNet: bool) -> Network:
         [pores[id] for id in np.array(f['throats/pore1'])],
         [pores[id] for id in np.array(f['throats/pore2'])],
         np.array(f['throats/r'])):
-        throats[id] = connector_method(pore1, pore2, r, id)
+        throats[id] = network.connect_pores(pore1, pore2, r, id)
 
     # labels
     if 'label' in f['throats']: # are there any labels != ''?

petsc-solve/solve_flow.py

@@ -22,7 +22,7 @@ def main():
     if (rank == root):
         netPath = sys.argv[1]
         try:
-            net = netflow.load_network_from(netPath, isBaseNet=False)
+            net = netflow.load_network_from(netPath)
         except Exception as e:
             print("Error: {}".format(e))
             comm.Abort(1)

visualize/visualize.py

@@ -13,7 +13,7 @@ def coord_transform(pos: List[float], lb: float, ub: float):
     return np.array(list(map(transform, pos)))
     
 def main():
-    dendro = netflow.load_network_from("network/dendro.h5")
+    dendro = netflow.load_network_from("../gen/networks/dendro_1_1_1.h5")
     
     # Setup GUI
     vis = o3d.visualization.VisualizerWithKeyCallback()