def GetMaxPart():
print("Scanning trajectory for parameters...")
with cd.TrajHandle(trajPath) as th:
n = len(th.ReadFrame(th.maxFrames))
print("Done!")
print("System contains {0} particles".format(n * 180))
return n * 180
def __init__(self, fPath):
self.filePath = fPath
self.th = celldiv.TrajHandle(fPath)
Visualizer.ind += 1
self.ind = Visualizer.ind
self.pF = None
bpy.data.worlds["World"].horizon_color=[0.051, 0.051, 0.051]
bpy.data.scenes["Scene"].render.alpha_mode='SKY'
self.firstfaces = []
with open("/home/pranav/dev/celldiv/C180_pentahexa.csv", newline='') as g:
readerfaces = csv.reader(g, delimiter=",")
for row in readerfaces:
self.firstfaces.append([int(v) for v in row])
def flatten(trajPath, storePath, inc, name=None, f=False):
if name == None:
storePath += "/flattened.xvg"
else:
storePath += "/" + name + ".xvg"
print("writing to %s" % storePath)
if os.path.isfile(storePath):
print("overwriting {0}".format(storePath))
CMx = 0
CMy = 0
CMz = 0
with open(storePath, "w") as outFileHandle:
t = celldiv.TrajHandle(trajPath)
try:
c = 0
while c < t.maxFrames:
frame = t.ReadFrame(inc)
c += 1
nCells = len(frame)
t.nCellsLastFrame
print("frame ", t.currFrameNum, nCells, " cells")
CM = np.vstack([np.mean(c, axis=1) for c in frame])
outFileHandle.write("%s\n" %
" ".join([str(a) for a in CM[:, 0]]))
outFileHandle.write("%s\n" %
" ".join([str(a) for a in CM[:, 1]]))
if f:
outFileHandle.write("%s\n" %
" ".join([str(a) for a in CM[:, 2]]))
except celldiv.IncompleteTrajectoryError as e:
print("broken", e)
return n * 180
def WriteFrame(frame, n):
nP = len(frame) * 180
outHandle.write("%d\n" % n)
outHandle.write("%d, t = %d\n" % (nP, th.currFrameNum))
CoM = np.mean(np.vstack(frame), axis=0)
for c in frame:
c = c[:-12] - CoM
for p in c.tolist():
outHandle.write("C ")
outHandle.write(" ".join([str(a) for a in p]))
outHandle.write("\n")
if nP < n:
for _ in range(n - nP):
outHandle.write(filler)
n = GetMaxPart()
filler = "C 0.0 0.0 0.0\n"
with cd.TrajHandle(trajPath) as th, open(args.out, "w") as outHandle:
if args.frame != -1:
frame = th.ReadFrame(frameNum=args.frame)
WriteFrame(frame, len(frame) * 180)
else:
for i in tqdm(range(min(args.max, int(th.maxFrames / args.skip)))):
frame = th.ReadFrame(inc=args.skip)
WriteFrame(frame, n)
def measurePacking(filePath, storePath, name=None):
fileName = os.path.splitext(os.path.split(filePath)[1])[0]
print("Processing %s" % filePath)
if name == None:
storePath += '/' + fileName + '/' + '3DPacking/'
else:
storePath += '/' + fileName + '/' + name + '/'
try:
os.makedirs(storePath)
except:
pass
dataPath = storePath + "data_best.dat"
# Now read trajectory file and get the centre of masses of
# all cells at every time step
if os.path.isfile(dataPath):
if os.path.getmtime(dataPath) > os.path.getmtime(filePath):
print("{0} already processed.".format(filePath))
print("Skipping")
return dataPath
print("Generating cell CoMs...")
with celldiv.TrajHandle(filePath) as s,\
open(storePath + "data.dat", 'w') as f:
while True:
try:
frame = s.ReadFrame(inc=aRate)
except:
break
step = s.step
if s.fatalError:
break
nCells = len(frame)
frame = [cell[:180] for cell in frame]
if nCells > 3:
CoMs = np.array([np.mean(cell, axis=0) for cell in frame])
sysCoM = np.mean(CoMs, axis=0)
CoMs -= sysCoM
if args.flat == True:
CoMs = CoMs[:, 0:2]
print("Doing Del of", CoMs.shape[0], "cells at step", step)
try:
d = Delaunay(CoMs)
indices, indptr = d.vertex_neighbor_vertices
count = []
for p in range(nCells):
n = len(indptr[indices[p]:indices[p + 1]])
if n > len(count):
for i in range(len(count), n):
count.append(0)
count[n - 1] += 1 / nCells
f.write(", ".join([str(c) for c in count]))
f.write("\n")
except QhullError:
print("delaunay failed, skipping")
pass
return dataPath
cellNeighs = [list(set(n)) for n in cellNeighs]
return cellNeighs
neighCells = GenCellNeighs()
neighs = [0 for _ in range(nCells)]
#print("Doing neighbour search of {} particles in {} cells\n".format(nCells*180, nCells))
for i in range(nCells):
iCell = frame[i]
for j in neighCells[i]:
jCell = frame[j]
dr = iCell - jCell[:, np.newaxis]
r = np.linalg.norm(dr, axis=2)
if ((r < 0.3)).sum() > 0:
neighs[i] += 1
return neighs
def WriteNeighs(f, step, neighs):
f.write("{}\n".format(step))
f.write(",".join([str(n) for n in neighs]) + "\n")
with cd.TrajHandle(trajFile) as tj, open(outputFile, "w") as f:
if args.frame_num > 0:
WriteNeighs(f, tj.currFrameNum,
GetNeighs(tj.ReadFrame(args.frame_num)))
else:
for i in tqdm(range(tj.maxFrames)):
WriteNeighs(f, tj.currFrameNum, GetNeighs(tj.ReadFrame()))
outName = os.path.splitext(args.out)
fig, ax = plt.subplots()
fig.set_size_inches(10, 10)
ax.set_xlabel("$X$")
ax.set_ylabel("$Y$")
frames = []
maxes = []
mins = []
if args.set_limits:
with cd.TrajHandle(trajPath) as th:
print("Getting movie limits...")
if args.last_frame > 0 and args.last_frame > th.maxFrames:
print("Trajectory only has {0} frames".format(th.maxFrames))
args.last_frame = -1
if args.frame > 0 and args.frame > th.maxFrames:
print("Trajectory only has {0} frames".format(th.maxFrames))
args.frame = th.maxFrames
if args.frame > 0:
frame = np.vstack(th.ReadFrame(args.frame))
elif args.last_frame > 0:
frame = np.vstack(th.ReadFrame(args.last_frame))
else:
if not noClear and os.path.exists(sPath):
for f in os.listdir(sPath):
os.remove(sPath + f)
cellInds = []
minInd = args.min_cells - 1
if len(args.inds) > 0:
minInd = max(minInd, min(args.inds))
stopAt = args.num_frames
# Set material color
bpy.data.materials['Material'].diffuse_color = [(1 / 255.0) * c
for c in args.cell_color]
bpy.data.materials['Material'].specular_intensity = args.specular_intensity
with celldiv.TrajHandle(filename) as th:
frameCount = 1
try:
for i in range(int(th.maxFrames / nSkip)):
frameCount += 1
if frameCount > args.num_frames:
break
f = th.ReadFrame(inc=nSkip)
if len(f) < minInd + 1:
print("Only ", len(f), "cells in frame ", th.currFrameNum,
" skipping...")
continue
