def prepare_kernel(s):
mod = SourceModule("""
__global__ void update_src(int idx, int tstep, float *f) {
f[idx] += sin(0.1*tstep);
}
__global__ void update(int nx, int ny, float *c, float *f, float *g) {
int tx = threadIdx.x;
int idx = blockIdx.x*blockDim.x + tx;
extern __shared__ float gs[];
gs[tx+1] = g[idx];
int i = idx/ny, j = idx%ny;
if(j>0 && j<ny-1) {
if(tx==0) gs[tx]=g[idx-1];
if(tx==blockDim.x-1) gs[tx+2]=g[idx+1];
}
__syncthreads();
if(i>0 && j>0 && i<nx-1 && j<ny-1) {
f[idx] = c[idx]*(g[idx+ny]+g[idx-ny]+gs[tx+2]+gs[tx]-4*gs[tx+1])+2*gs[tx+1]-f[idx];
}
}
""")
s.update_src = mod.get_function("update_src")
s.update = mod.get_function("update")
Db, s.Dg = (256,1,1), (s.nx*s.ny/256+1, 1)
s.nnx, s.nny = sc.int32(s.nx), sc.int32(s.ny)
s.update_src.prepare("iiP", block=(1,1,1))
s.update.prepare("iiPPP", block=Db, shared=(256+2)*4)
def __init__( s, Nx, Ny, Nz, dx ): FdtdSpace.__init__( s, Nx, Ny, Nz, dx ) s.bytes_f = sc.zeros(1,'f').nbytes s.kNx = sc.int32(s.Nx) s.kNy = sc.int32(s.Ny) s.kNz = sc.int32(s.Nz)
def initMainArrays( Ntot, devFx, devFy, devFz, initArray ): TPB = 512 if ( Ntot%TPB == 0 ): BPG = Ntot/TPB else: BPG = Ntot/TPB + 1 print 'init main arrays: Ntot=%d, TPB=%d, BPG=%d' % (Ntot, TPB, BPG) initArray( sc.int32(Ntot), devFx, block=(TPB,1,1), grid=(BPG,1) ) initArray( sc.int32(Ntot), devFy, block=(TPB,1,1), grid=(BPG,1) ) initArray( sc.int32(Ntot), devFz, block=(TPB,1,1), grid=(BPG,1) )
def initMainArrays(Ntot, devFx, devFy, devFz, initArray):
TPB = 512
if (Ntot % TPB == 0):
BPG = Ntot / TPB
else:
BPG = Ntot / TPB + 1
print 'init main arrays: Ntot=%d, TPB=%d, BPG=%d' % (Ntot, TPB, BPG)
initArray(sc.int32(Ntot), devFx, block=(TPB, 1, 1), grid=(BPG, 1))
initArray(sc.int32(Ntot), devFy, block=(TPB, 1, 1), grid=(BPG, 1))
initArray(sc.int32(Ntot), devFz, block=(TPB, 1, 1), grid=(BPG, 1))
def _extract_features_std(self, wav, text):
wav_pre = audio.preemphasis(wav)
linear_target = audio.spectrogram(wav_pre).astype(sp.float32)
mel_target = audio.melspectrogram(wav_pre).astype(sp.float32)
input_data = sp.asarray(text_to_sequence(str(text, encoding='utf8'),
self._cleaner_names),
dtype=sp.int32)
input_length = sp.int32(len(input_data))
return input_data, [input_length], mel_target.T, linear_target.T, [
sp.int32(len(linear_target.T))
]
def differentiate( self ): Ntot = (self.Nx - 1)*(self.Ny - 1) tpb = 512 if ( Ntot%tpb == 0 ): bpg = Ntot/tpb else: bpg = Ntot/tpb + 1 Db = ( tpb, 1, 1 ) Dg = ( bpg, 1 ) self.diff( sc.int32(self.Nx), sc.int32(self.Ny), sc.float32(self.dx), self.dev_A, self.dev_dA, block=Db, grid=Dg )
def initmem_in_dev( self ): Ntot = self.Nx*self.Ny tpb = 512 if ( Ntot%tpb == 0 ): bpg = Ntot/tpb else: bpg = Ntot/tpb + 1 Db = ( tpb, 1, 1 ) Dg = ( bpg, 1 ) self.initmem( sc.int32(Ntot), self.dev_A, block=Db, grid=Dg ) self.initmem( sc.int32(Ntot), self.dev_dA, block=Db, grid=Dg )
def splitTimeSeries(x, y, spliceTimes, nPtsPerPiece=1):
"""
Syntax:
xPieces,yPieces=splitTimeSeries(x,y,spliceTimes, nPtsPerPiece=1)
"""
nPieces = len(spliceTimes)
xPieces = list()
yPieces = list()
for n in sc.arange(nPieces - 1):
a = sc.int32(sc.where(x >= spliceTimes[n])[0].min())
b = sc.int32(a + nPtsPerPiece)
xPieces.append(x[a:b])
yPieces.append(y[a:b])
return sc.array(xPieces), sc.array(yPieces)
def read_pst(pst_path):
""" read tillvision based .pst files as uint16.
note: this func was flagged deprecated ("use the version in gioIO" instead,
but that one never existed ... ")
problematic: does not work on all .pst on my machine """
inf_path = os.path.splitext(pst_path)[0] + '.inf'
# reading stack size from inf
meta = {}
with open(inf_path,'r') as fh:
# fh.next()
for line in fh.readlines():
try:
k,v = line.strip().split('=')
meta[k] = v
except:
pass
shape = sp.int32((meta['Width'],meta['Height'],meta['Frames']))
raw = sp.fromfile(pst_path,dtype='int16')
data = sp.reshape(raw,shape,order='F')
return data.astype('uint16')
def read_pst(pst_path):
""" read tillvision based .pst files as uint16.
note: this func was flagged deprecated ("use the version in gioIO" instead,
but that one never existed ... ")
problematic: does not work on all .pst on my machine """
inf_path = os.path.splitext(pst_path)[0] + '.inf'
# reading stack size from inf
meta = {}
with open(inf_path,'r') as fh:
# fh.next()
for line in fh.readlines():
try:
k,v = line.strip().split('=')
meta[k] = v
except:
pass
shape = sp.int32((meta['Width'],meta['Height'],meta['Frames']))
raw = sp.fromfile(pst_path,dtype='int16')
data = sp.reshape(raw,shape,order='F')
return data.astype('uint16')
def DiscreteRand(alphabet):
""" Returns a symbol from alphabet with a uniform probability distribution over alphabet
alphabet - is a n x 1 numpy vector containing symbols of the alphabet [1:n] """
n = len(alphabet)
U = sp.rand()
X = sp.int32(n*U) + 1
return alphabet[X-1]
def Hacker(Stats, cards):
hearts = [
'Aheart', '2heart', '3heart', '4heart', '5heart', '6heart', '7heart',
'8heart', '9heart', '10heart', 'Jheart', 'Qheart', 'Kheart'
]
spades = [
'Aspade', '2spade', '3spade', '4spade', '5spade', '6spade', '7spade',
'8spade', '9spade', '10spade', 'Jspade', 'Qspade', 'Kspade'
]
clubs = [
'Aclub', '2club', '3club', '4club', '5club', '6club', '7club', '8club',
'9club', '10club', 'Jclub', 'Qclub', 'Kclub'
]
diamonds = [
'Adiamond', '2diamond', '3diamond', '4diamond', '5diamond', '6diamond',
'7diamond', '8diamond', '9diamond', '10diamond', 'Jdiamond',
'Qdiamond', 'Kdiamond'
]
Deck = hearts + diamonds + clubs + spades
DeckArray = sp.array(Deck)
data = Counter(np.where(Stats[:, 0:3] == (convert(cards)))[0].tolist())
x = 0
while data.most_common(10)[x][1] == 3:
index = data.most_common(10)[x][0]
print index
print DeckArray[sp.int32(Stats[index, :])]
print
x = x + 1
def getParameters(self, key="name", parse=True):
"""return the parameters of an xml model structure(key: key of the attributes, parse: True/False if true attributes are parsed, i.e. eval evaluated etc."""
params = self.getElementsByTagName('param', 1)
rv = {}
for param in params:
value = param.getAttribute('value')
if parse:
ptype = param.getAttribute('type')
if (param.getAttribute('eval')):
value = eval(value)
elif (ptype == 'matrix'):
value = self.parseMatrixParameter(value)
elif (ptype == 'double'):
value = S.double(value)
elif (ptype == 'int'):
value = S.int32(value)
elif (ptype == 'str'):
#no action for string
pass
else:
raise Exception(
"Invalid Attribute exception attribute %s has no type or eval!"
% param)
rv[str(param.getAttribute(key))] = value
return rv
def getFileList(dataDir, prefix, suffix, showNames=0):
"""
Example:
files=getFileList(dataDir, prefix, suffix)
"""
files=list()
for f in os.listdir(dataDir):
a= sc.int32(os.path.isfile(os.path.join(dataDir,f)))
b= sc.int32(str.find(f,prefix)>-1)
c= sc.int32(str.find(f,suffix)>0)
#print(a,b,c)
if (a*b*c):
files.append(f)
nFiles = len(files)
if showNames:
print("Found %d files with the indicated string"%nFiles)
print(files)
return files
def createBurstingTrain(maxTime, burstRate=10.0, interBurstRate=30.0, nonBurstProp=0.1):
nSpikes= sc.int32(maxTime/burstRate)
nBursts = (1-nonBurstProp) * nSpikes
b, ibis, ibrs= createNGammaTrains(nPulses=nSpikes, nTrains=1, meanRate=burstRate,graph=0.0)
for n in sc.arange(nBursts):
tr, isi, ifr= createNGammaTrains(nPulses=nSpikes, nTrains=1, meanRate=burstRate,graph=0.0)
return train
def alphaFunction(x, A=1.0, tau=1.0, downAccel=1.0):
"""
alphaFunction creates an alpha function with amplitude A, time constant tau,
and downward acceleration downAccel.
Example:
alphaFunction(x, A=1.0, tau=1.0, downAccel=1.0)
"""
aa = sc.int32(x > 0)
xovertau = x / tau
return A * aa * xovertau * sc.exp(downAccel * (1 - xovertau))
def importWave(self):
"""Wave file to ndarray"""
wf = wave.open(self.filename, 'rb')
waveframes = wf.readframes(wf.getnframes())
self.framerate = wf.getframerate()
data = sp.fromstring(waveframes, sp.int16)
self.duration = float(wf.getnframes()) / self.framerate
if(wf.getnchannels() == 2):
left = sp.array([data[i] for i in range(0, data.size, 2)])
right = sp.array([data[i] for i in range(1, data.size, 2)])
left = sp.int32(left); right = sp.int32(right)
data = sp.int16(left+right) / 2
if(self.fs == None):
self.fs = self.framerate
else:
#data = self.resample(data, data.size*(self.fs/self.framerate))
data = ssig.decimate(data, int(self.framerate/self.fs))
self.duration_list = sp.arange(0, self.duration, 1./self.fs)
data = ssig.detrend(data)
return data
def glmnetSet(opts = None):
import scipy
# default options
options = {
"weights" : scipy.empty([0]),
"offset" : scipy.empty([0]),
"alpha" : scipy.float64(1.0),
"nlambda" : scipy.int32(100),
"lambda_min" : scipy.empty([0]),
"lambdau" : scipy.empty([0]),
"standardize" : True,
"intr" : True,
"thresh" : scipy.float64(1e-7),
"dfmax" : scipy.empty([0]),
"pmax" : scipy.empty([0]),
"exclude" : scipy.empty([0], dtype = scipy.integer),
"penalty_factor" : scipy.empty([0]),
"cl" : scipy.array([[scipy.float64(-scipy.inf)], [scipy.float64(scipy.inf)]]),
"maxit" : scipy.int32(1e5),
"gtype" : [],
"ltype" : 'Newton',
"standardize_resp" : False,
"mtype" : 'ungrouped'
}
# quick return if no user opts
if opts == None:
print('pdco default options:')
print(options)
return options
# if options are passed in by user, update options with values from opts
optsInOptions = set(opts.keys()) - set(options.keys());
if len(optsInOptions) > 0: # assert 'opts' keys are subsets of 'options' keys
print(optsInOptions, ' : unknown option for glmnetSet')
raise ValueError('attempting to set glmnet options that are not known to glmnetSet')
else:
options.update(opts) # update values
return options
def getFileList(dataDir, prefix, suffix, includeDataDir=1):
"""
getFileList look for files with specific prefix and suffix within the directory dataDir
Example:
files=getFileList(dataDir, prefix, suffix)
"""
files = list()
for f in os.listdir(dataDir):
a = sc.int32(os.path.isfile(os.path.join(dataDir, f)))
b = sc.int32(str.find(f, prefix) > -1)
c = sc.int32(str.find(f, suffix) > 0)
#print(a,b,c)
if (a * b * c):
if includeDataDir:
files.append(dataDir + f)
else:
files.append(f)
nFiles = len(files)
print("Found %d files with the indicated string" % nFiles)
print(files)
return files
def extractDebleachedData(filePath):
allData = igor.load(filePath)
bbb = allData.children[0].userstr[b"S_waveNames"]
aaa = bbb.decode("UTF-8")
dataNames = aaa.split(";")[:-1]
waves = list()
for m in sc.arange(len(dataNames)):
waveNum = sc.int32(dataNames[m][1 + str.rfind(dataNames[0], "e"):])
str1 = "waves.append(allData." + dataNames[m] + "_%d.data)" % (
waveNum - 1)
#print(dataNames[m],str1)
exec(str1)
return sc.array(waves)
def initmem_psi_in_dev( s ): initmem = s.get_kernel_initmem() N = sc.int32( s.size_x ) Db = ( s.tpb_x, 1, 1 ) Dg = ( s.bpg_x, 1 ) initmem( N, s.psixEyf, block=Db, grid=Dg ) initmem( N, s.psixEyb, block=Db, grid=Dg ) initmem( N, s.psixEzf, block=Db, grid=Dg ) initmem( N, s.psixEzb, block=Db, grid=Dg ) initmem( N, s.psixHyf, block=Db, grid=Dg ) initmem( N, s.psixHyb, block=Db, grid=Dg ) initmem( N, s.psixHzf, block=Db, grid=Dg ) initmem( N, s.psixHzb, block=Db, grid=Dg ) N = sc.int32( s.size_y ) Db = ( s.tpb_y, 1, 1 ) Dg = ( s.bpg_y, 1 ) initmem( N, s.psiyEzf, block=Db, grid=Dg ) initmem( N, s.psiyEzb, block=Db, grid=Dg ) initmem( N, s.psiyExf, block=Db, grid=Dg ) initmem( N, s.psiyExb, block=Db, grid=Dg ) initmem( N, s.psiyHzf, block=Db, grid=Dg ) initmem( N, s.psiyHzb, block=Db, grid=Dg ) initmem( N, s.psiyHxf, block=Db, grid=Dg ) initmem( N, s.psiyHxb, block=Db, grid=Dg ) N = sc.int32( s.size_z ) Db = ( s.tpb_z, 1, 1 ) Dg = ( s.bpg_z, 1 ) initmem( N, s.psizExf, block=Db, grid=Dg ) initmem( N, s.psizExb, block=Db, grid=Dg ) initmem( N, s.psizEyf, block=Db, grid=Dg ) initmem( N, s.psizEyb, block=Db, grid=Dg ) initmem( N, s.psizHxf, block=Db, grid=Dg ) initmem( N, s.psizHxb, block=Db, grid=Dg ) initmem( N, s.psizHyf, block=Db, grid=Dg ) initmem( N, s.psizHyb, block=Db, grid=Dg )
def compute_sample(ysample, xsample, binindex):
upper_index = sp.int32(sp.ceil(binindex))
lower_index = sp.int32(sp.floor(binindex))
ppy_upper = interpolate.interp1d(
bimodal_partial_cdf[:, upper_index], self.y_eval_space)
ppy_lower = interpolate.interp1d(
bimodal_partial_cdf[:, lower_index], self.y_eval_space)
a = bimodal_partial_cdf[:, upper_index]
b = bimodal_partial_cdf[:, lower_index]
samples_upper = ppy_upper(ysample * (max(a) - min(a)) * 0.9999 +
min(a) * 1.001)
samples_lower = ppy_lower(ysample * (max(b) - min(b)) * 0.9999 +
min(b) * 1.001)
#Lerp over the lower and upper
a = self.x_eval_space[upper_index]
b = self.x_eval_space[lower_index]
return samples_lower + (samples_upper -
samples_lower) / (a - b) * (xsample - b)
def Hacker(Stats,cards):
hearts=['Aheart','2heart','3heart','4heart','5heart','6heart','7heart','8heart','9heart','10heart','Jheart','Qheart','Kheart']
spades=['Aspade','2spade','3spade','4spade','5spade','6spade','7spade','8spade','9spade','10spade','Jspade','Qspade','Kspade']
clubs=['Aclub','2club','3club','4club','5club','6club','7club','8club','9club','10club','Jclub','Qclub','Kclub']
diamonds=['Adiamond','2diamond','3diamond','4diamond','5diamond','6diamond','7diamond','8diamond','9diamond','10diamond','Jdiamond','Qdiamond','Kdiamond']
Deck=hearts+diamonds+clubs+spades
DeckArray = sp.array(Deck)
data = Counter(np.where(Stats[:,0:3]==(convert(cards)))[0].tolist())
x=0
while data.most_common(10)[x][1]==3:
index=data.most_common(10)[x][0]
print index
print DeckArray[sp.int32(Stats[index,:])]
print
x=x+1
def load_lst(self):
""" reads metadata from a .lst file. Needed to generate output in the
.gloDatamix format """
lst_path = self.OpenFileDialog(title='load lst',default_dir=self.Main.Options.general['cwd'],extension='*.lst')[0]
# read
self.Main.Data.Metadata.LSTdata = gio.read_lst(lst_path)
self.Main.Options.flags['LST_was_read'] = True
# update labels
ind_map = self.map_lst_inds_to_path_inds()
#concentration
concs = [str(self.Main.Data.Metadata.LSTdata.loc[ind_map[n]]['OConc']) for n in range(self.Main.Data.nTrials)]
new_concs = []
for conc in concs:
if sp.int32(conc) > 0: # info is in dilutions
new_conc = str(-1 * sp.around(sp.log10(sp.int32(conc))))
new_concs.append(new_conc)
else:
new_concs.append(conc)
# label
labels = [self.Main.Data.Metadata.LSTdata.loc[ind_map[n]]['Odour'] for n in range(self.Main.Data.nTrials)]
# combine
new_labels = [labels[i]+new_concs[i] for i in range(len(labels))]
self.Main.Data.Metadata.trial_labels = new_labels
self.Main.MainWindow.Front_Control_Panel.Data_Selector.set_current_labels(self.Main.Data.Metadata.trial_labels)
# set stimulus timing
# cycle time
pass
def SetProjMatPETSC(cpCorArray,ProjMat,DA,vg):
m = DA.getSizes()[0]
dx = 4./m
AO = DA.getAO()
psnx = sp.int32(sp.floor_divide(cpCorArray[:,0]+2.,dx))
psny = sp.int32(sp.floor_divide(cpCorArray[:,1]+2.,dx))
idxbl = psnx+psny*m
idxbr = psnx+1+psny*m
idxul = psnx+(psny+1)*m
idxur = psnx+1+(psny+1)*m
idxbl = AO.app2petsc(idxbl)
idxbr = AO.app2petsc(idxbr)
idxul = AO.app2petsc(idxul)
idxur = AO.app2petsc(idxur)
start,end = vg.getOwnershipRange()
modx = sp.mod(cpCorArray[:,0]+2.,dx)
mody = sp.mod(cpCorArray[:,1]+2.,dx)
dx2 = dx**2
for i in sp.arange(end-start):
ProjMat[i+start,idxbl[i]] = (dx-modx[i])*(dx-mody[i])/dx2
ProjMat[i+start,idxbr[i]] = modx[i]*(dx-mody[i])/dx2
ProjMat[i+start,idxul[i]] = (dx-modx[i])*mody[i]/dx2
ProjMat[i+start,idxur[i]] = modx[i]*mody[i]/dx2
return
def get_spike_inds(SpikeTrain):
"""
get the indices of spike times relative to an AnalogSignal with equal
sampling rate.
Args:
SpikeTrain (neo.core.SpikeTrain): the SpikeTrain
Returns:
list: a list of indices
"""
SpikeTrain = copy.deepcopy(SpikeTrain)
SpikeTrain -= SpikeTrain.t_start
SpikeTrain.t_start = 0 * pq.s
inds = sp.int32((SpikeTrain * SpikeTrain.sampling_rate).simplified)
return inds
def initmem_main_in_dev( s ):
initmem = s.get_kernel_initmem()
tpb = 512
bpg = s.calc_bpg( s.size2, tpb )
N = sc.int32( s.size2 )
Db = (tpb,1,1)
Dg = (bpg,1)
initmem( N, s.devEx, block=Db, grid=Dg )
initmem( N, s.devEy, block=Db, grid=Dg )
initmem( N, s.devEz, block=Db, grid=Dg )
initmem( N, s.devHx, block=Db, grid=Dg )
initmem( N, s.devHy, block=Db, grid=Dg )
initmem( N, s.devHz, block=Db, grid=Dg )
def reorder_labels(labels):
nClusters = sp.int32(sp.amax(labels.flatten()) + 1)
labels0_vec = sp.zeros((labels.shape[0], nClusters), 'bool')
labelsi_vec = labels0_vec.copy()
for i in range(nClusters):
labels0_vec[:, i] = (labels[:, 0] == i)
for i in range(labels.shape[1]):
for j in range(nClusters):
labelsi_vec[:, j] = (labels[:, i] == j)
D = pairwise_distances(labelsi_vec.T, labels0_vec.T, metric='dice')
D[~sp.isfinite(D)] = 1
ind1 = linear_assignment(D)
labels[:, i] = ind1[sp.int16(labels[:, i]), 1]
return labels
def draw_matches(img1, img2, sel_matches, k1, k2):
h1, w1 = img1.shape[:2]
h2, w2 = img2.shape[:2]
view = sp.zeros((max(h1, h2), w1 + w2, 3), sp.uint8)
view[:h1, :w1, 0] = img1
view[:h2, w1:, 0] = img2
view[:, :, 1] = view[:, :, 0]
view[:, :, 2] = view[:, :, 0]
position = None
if (sel_matches is not None) and (k2 is not None):
#don't use in final production
for m in sel_matches:
# draw the keypoints matches
color = tuple([sp.random.randint(0, 255) for _ in iter(range(3))])
cv2.line(
view, (int(k1[m.queryIdx].pt[0]), int(k1[m.queryIdx].pt[1])),
(int(k2[m.trainIdx].pt[0] + w1), int(k2[m.trainIdx].pt[1])),
color)
kp2 = [k2[m.trainIdx] for m in sel_matches]
kp1 = [k1[m.queryIdx] for m in sel_matches]
p1 = cv2.KeyPoint_convert(kp1)
p2 = cv2.KeyPoint_convert(kp2)
if sum(1 for _ in sel_matches) >= 4:
H, status = cv2.findHomography(p1, p2, cv2.RANSAC, 5.0)
else:
H, status = None, None
if H is not None:
corners = sp.float32([[0, 0], [w1, 0], [w1, h1], [0, h1]])
position = cv2.perspectiveTransform(corners.reshape(1, -1, 2),
H).reshape(-1, 2)
area = computeArea(position)
print("Area : " + str(area))
if area > (w2 * h2 / 150) and area < (w2 * h2 / 1.4):
corners = sp.int32(position + (w1, 0))
cv2.polylines(view, [corners], True, (255, 255, 255))
else:
position = None
cv2.imshow("view", view)
return position
def read_pst(pst_path):
""" read tillvision based .pst files as uint16 """
inf_path = os.path.splitext(pst_path)[0] + '.inf'
# reading stack size from inf
meta = {}
with open(inf_path,'r') as fh:
# fh.next()
for line in fh.readlines():
try:
k,v = line.strip().split('=')
meta[k] = v
except:
pass
shape = sp.int32((meta['Width'],meta['Height'],meta['Frames']))
raw = sp.fromfile(pst_path,dtype='int16')
data = sp.reshape(raw,shape,order='F')
return data.astype('uint16')
def getParameters(self,key="name",parse=True):
"""return the parameters of an xml model structure(key: key of the attributes, parse: True/False if true attributes are parsed, i.e. eval evaluated etc."""
params = self.getElementsByTagName('param',1)
rv = {}
for param in params:
value = param.getAttribute('value')
if parse:
ptype = param.getAttribute('type')
if(param.getAttribute('eval')):
value = eval(value)
elif(ptype=='matrix'):
value = self.parseMatrixParameter(value)
elif(ptype=='double'):
value = S.double(value)
elif(ptype=='int'):
value = S.int32(value)
elif(ptype=='str'):
#no action for string
pass
else:
raise Exception("Invalid Attribute exception attribute %s has no type or eval!" % param)
rv[str(param.getAttribute(key))]=value
return rv
def extractDebleachedFminData(filePath):
"""
extractDebleachedFminData takes a path to a pxp data file as only argument and extracts all the wave data found there,
provided the data has the suffix F_min
Example:
dataDir="./microcircuitsNetworks/"
fileName= "cort76dp1c.pxp"
waveData, timeStamps=extractDebleachedFminData(dataDir+fileName)
"""
allData = igor.load(filePath)
#dataNames= st.digits.split(allData.children[0].userstr["S_waveNames"], ";")[:-1]
bbb = allData.children[0].userstr[b"S_waveNames"]
aaa = bbb.decode("UTF-8")
dataNames = aaa.split(";")[:-1]
waves = list()
for m in sc.arange(len(dataNames)):
waveNum = sc.int32(dataNames[m][1 + str.rfind(dataNames[0], "e"):])
str1 = "waves.append(allData." + dataNames[m] + "_%dF_min.data)" % (
waveNum - 1)
#print(dataNames[m],str1)
exec(str1)
return sc.array(waves), sc.array(allData.sec.data)
def extractPXPData(fName):
"""
extractPXPData
Example:
allData=extractPXPData("microcircuitsNetworks/cort76dp1c.pxp")
"""
allData = igor.load(fName)
# Dictionary containing the names of recorded variables during the experiment
bbb = allData.children[0].userstr[b"S_waveNames"]
aaa = bbb.decode("UTF-8")
dataNames = aaa.split(";")[:-1]
extractedData1 = list()
extractedData2 = list()
for nam in dataNames:
if len(nam) > 3:
myInd = sc.int32(nam[4:]) - 1
str2 = "w2=allData." + nam + ".data" % (myInd)
exec(str2)
extractedData2.append(w2)
else:
print("Found empty string")
rawData = sc.array(extractedData2)
return rawData
def updateE( s, tstep, F ): s.update_src.prepared_call( (s.bpg,1), s.kNx, s.kNy, s.kNz, sc.int32(tstep), F )
def _calculate_length(self, data):
"""Calculates the length of the next entry in a dbus.ByteArray."""
return scipy.int32(len(data)).newbyteorder('B').tostring()
def alphaFunction(x, A=1.0, tau=1.0, downAccel=1.0):
aa= sc.int32(x>0)
xovertau = x/tau
return A* xovertau * sc.exp( downAccel*(1 - xovertau))
def glmnet(*, x, y, family='gaussian', **options):
# check inputs: make sure x and y are scipy, float64 arrays
# fortran order is not checked as we force a convert later
if not (isinstance(x, scipy.sparse.csc.csc_matrix)):
if not (isinstance(x, scipy.ndarray) and x.dtype == 'float64'):
raise ValueError('x input must be a scipy float64 ndarray')
else:
if not (x.dtype == 'float64'):
raise ValueError('x input must be a float64 array')
if not (isinstance(y, scipy.ndarray) and y.dtype == 'float64'):
raise ValueError('y input must be a scipy float64 ndarray')
# create options
if options is None:
options = glmnetSet()
## match the family, abbreviation allowed
fambase = [
'gaussian', 'binomial', 'poisson', 'multinomial', 'cox', 'mgaussian'
]
# find index of family in fambase
indxtf = [x.startswith(family.lower())
for x in fambase] # find index of family in fambase
famind = [i for i in range(len(indxtf)) if indxtf[i] == True]
if len(famind) == 0:
raise ValueError('Family should be one of '
'gaussian'
', '
'binomial'
', '
'poisson'
', '
'multinomial'
', '
'cox'
', '
'mgaussian'
'')
elif len(famind) > 1:
raise ValueError(
'Family could not be uniquely determined : Use a longer description of the family string.'
)
else:
family = fambase[famind[0]]
## prepare options
options = glmnetSet(options)
#print('glmnet.py options:')
#print(options)
## error check options parameters
alpha = scipy.float64(options['alpha'])
if alpha > 1.0:
print('Warning: alpha > 1.0; setting to 1.0')
options['alpha'] = scipy.float64(1.0)
if alpha < 0.0:
print('Warning: alpha < 0.0; setting to 0.0')
options['alpha'] = scipy.float64(0.0)
parm = scipy.float64(options['alpha'])
nlam = scipy.int32(options['nlambda'])
nobs, nvars = x.shape
# check weights length
weights = options['weights']
if len(weights) == 0:
weights = scipy.ones([nobs, 1], dtype=scipy.float64)
elif len(weights) != nobs:
raise ValueError('Error: Number of elements in '
'weights'
' not equal to number of rows of '
'x'
'')
# check if weights are scipy nd array
if not (isinstance(weights, scipy.ndarray) and weights.dtype == 'float64'):
raise ValueError('weights input must be a scipy float64 ndarray')
# check y length
nrowy = y.shape[0]
if nrowy != nobs:
raise ValueError('Error: Number of elements in '
'y'
' not equal to number of rows of '
'x'
'')
# check ne
ne = options['dfmax']
if len(ne) == 0:
ne = nvars + 1
# check nx
nx = options['pmax']
if len(nx) == 0:
nx = min(ne * 2 + 20, nvars)
# check jd
exclude = options['exclude']
# TBD: test this
if not (len(exclude) == 0):
exclude = scipy.unique(exclude)
if scipy.any(exclude < 0) or scipy.any(exclude >= nvars):
raise ValueError('Error: Some excluded variables are out of range')
else:
jd = scipy.append(len(exclude),
exclude + 1) # indices are 1-based in fortran
else:
jd = scipy.zeros([1, 1], dtype=scipy.integer)
# check vp
vp = options['penalty_factor']
if len(vp) == 0:
vp = scipy.ones([1, nvars])
# inparms
inparms = glmnetControl()
# cl
cl = options['cl']
if any(cl[0, :] > 0):
raise ValueError('Error: The lower bound on cl must be non-positive')
if any(cl[1, :] < 0):
raise ValueError('Error: The lower bound on cl must be non-negative')
cl[0, cl[0, :] == scipy.float64('-inf')] = -1.0 * inparms['big']
cl[1, cl[1, :] == scipy.float64('inf')] = 1.0 * inparms['big']
if cl.shape[1] < nvars:
if cl.shape[1] == 1:
cl = cl * scipy.ones([1, nvars])
else:
raise ValueError(
'Error: Require length 1 or nvars lower and upper limits')
else:
cl = cl[:, 0:nvars]
exit_rec = 0
if scipy.any(cl == 0.0):
fdev = inparms['fdev']
if fdev != 0:
optset = dict()
optset['fdev'] = 0
glmnetControl(optset)
exit_rec = 1
isd = scipy.int32(options['standardize'])
intr = scipy.int32(options['intr'])
if (intr == True) and (family == 'cox'):
print('Warning: Cox model has no intercept!')
jsd = scipy.int32(options['standardize_resp'])
thresh = options['thresh']
lambdau = options['lambdau']
lambda_min = options['lambda_min']
if len(lambda_min) == 0:
if nobs < nvars:
lambda_min = 0.01
else:
lambda_min = 1e-4
lempty = (len(lambdau) == 0)
if lempty:
if (lambda_min >= 1):
raise ValueError('ERROR: lambda_min should be less than 1')
flmin = lambda_min
ulam = scipy.zeros([1, 1], dtype=scipy.float64)
else:
flmin = 1.0
if any(lambdau < 0):
raise ValueError('ERROR: lambdas should be non-negative')
ulam = -scipy.sort(-lambdau) # reverse sort
nlam = lambdau.size
maxit = scipy.int32(options['maxit'])
gtype = options['gtype']
if len(gtype) == 0:
if (nvars < 500):
gtype = 'covariance'
else:
gtype = 'naive'
# ltype
ltype = options['ltype']
ltypelist = ['newton', 'modified.newton']
indxtf = [x.startswith(ltype.lower()) for x in ltypelist]
indl = [i for i in range(len(indxtf)) if indxtf[i] == True]
if len(indl) != 1:
raise ValueError('ERROR: ltype should be one of '
'Newton'
' or '
'modified.Newton'
'')
else:
kopt = indl[0]
if family == 'multinomial':
mtype = options['mtype']
mtypelist = ['ungrouped', 'grouped']
indxtf = [x.startswith(mtype.lower()) for x in mtypelist]
indm = [i for i in range(len(indxtf)) if indxtf[i] == True]
if len(indm) == 0:
raise ValueError('Error: mtype should be one of '
'ungrouped'
' or '
'grouped'
'')
elif (indm == 2):
kopt = 2
#
offset = options['offset']
# sparse (if is_sparse, convert to compressed sparse row format)
is_sparse = False
if scipy.sparse.issparse(x):
is_sparse = True
tx = scipy.sparse.csc_matrix(x, dtype=scipy.float64)
x = tx.data
x = x.reshape([len(x), 1])
irs = tx.indices + 1
pcs = tx.indptr + 1
irs = scipy.reshape(irs, [
len(irs),
])
pcs = scipy.reshape(pcs, [
len(pcs),
])
else:
irs = scipy.empty([0])
pcs = scipy.empty([0])
if scipy.sparse.issparse(y):
y = y.todense()
## finally call the appropriate fit code
if family == 'gaussian':
# call elnet
fit = elnet(x, is_sparse, irs, pcs, y, weights, offset, gtype, parm,
lempty, nvars, jd, vp, cl, ne, nx, nlam, flmin, ulam,
thresh, isd, intr, maxit, family)
elif (family == 'binomial') or (family == 'multinomial'):
# call lognet
fit = lognet(x, is_sparse, irs, pcs, y, weights, offset, parm, nobs,
nvars, jd, vp, cl, ne, nx, nlam, flmin, ulam, thresh, isd,
intr, maxit, kopt, family)
elif family == 'cox':
# call coxnet
fit = coxnet(x, is_sparse, irs, pcs, y, weights, offset, parm, nobs,
nvars, jd, vp, cl, ne, nx, nlam, flmin, ulam, thresh, isd,
maxit, family)
elif family == 'mgaussian':
# call mrelnet
fit = mrelnet(x, is_sparse, irs, pcs, y, weights, offset, parm, nobs,
nvars, jd, vp, cl, ne, nx, nlam, flmin, ulam, thresh,
isd, jsd, intr, maxit, family)
elif family == 'poisson':
# call fishnet
fit = fishnet(x, is_sparse, irs, pcs, y, weights, offset, parm, nobs,
nvars, jd, vp, cl, ne, nx, nlam, flmin, ulam, thresh,
isd, intr, maxit, family)
else:
raise ValueError(
'calling a family of fits that has not been implemented yet')
if exit_rec == 1:
optset['fdev'] = fdev
#TODO: Call glmnetControl(optset) to set persistent parameters
# return fit
return fit
synth.setnchannels(1)
synth.setsampwidth(2)
synth.setframerate(samplingrate)
remain = sound.getnframes()
while remain > 0:
s = min(chunk, remain)
# read frames
data_sound = sound.readframes(s)
data_noise = noise.readframes(s)
# convert
ary_sound = sp.fromstring(data_sound, sp.int16)
ary_noise = sp.fromstring(data_noise, sp.int16)
int32_ary_sound = sp.int32(ary_sound)
int32_ary_noise = sp.int32(ary_noise)
ary2 = sp.int16(int32_ary_sound + int32_ary_noise)
data2 = ary2.tostring()
synth.writeframes(data2)
remain = remain - s
sound.close()
noise.close()
synth.close()
infile = 'tools/sound/noisy.wav'
signal, params = read_signal(infile, WINSIZE)
nf = len(signal) / (WINSIZE / 2) - 1
sig_out = sp.zeros(len(signal), sp.float32)
window = sp.hanning(WINSIZE)
def parse(self):
self.mshfid = open(self.mshfilename, 'r')
#Advance to nodes
line = self.mshfid.readline()
while(line.find("$Nodes") < 0):
line = self.mshfid.readline()
pass
line = self.mshfid.readline() #This line should contain number of nodes
#Check that number of nodes in file is still the number of nodes in memory
if(not sp.int32(line) == self.Nnodes):
self.__error__("Something wrong. Aborting.")
exit(-1)
self.__inform__("Parsing nodes")
if len(self.nodes_rules) == 0:
self.__inform__("No rules for nodes... skipping nodes.")
for i in range(self.Nnodes):
self.mshfid.readline()
else:
#Read all nodes and do stuff
for i in range(self.Nnodes):
#Parse the line
sl = self.mshfid.readline().split()
tag = sp.int32(sl[0])
x = sp.double(sl[1])
y = sp.double(sl[2])
z = sp.double(sl[3])
#Figure out the groups to which this node belongs
physgroups = []
for grp in self.physical_groups:
if self.nodes_in_physical_groups[grp][tag] == 1:
physgroups.append(grp)
for condition, action in self.nodes_rules:
if condition(tag,x,y,z,physgroups):
action(tag,x,y,z)
pass
#Read another 2 lines after nodes are done. This should be $Elements
line = self.mshfid.readline()
line = self.mshfid.readline()
if(line.find("$Elements") == 0):
self.__inform__("Parsing elements")
else:
self.__error__("Something wrong reading elements. ")
exit(-1)
line = self.mshfid.readline() #This line should contain number of elements
#Check that number of elements in file is still the number of elements in memory
if(not sp.int32(line) == self.Nelem):
self.__error__("Something wrong. Aborting.")
exit(-1)
if len(self.elements_rules) == 0:
self.__inform__("No rules for elements... skipping elements.")
for i in range(self.Nelem):
self.mshfid.readline()
else:
#Read all elements and do stuff
nodes = []
for i in range(self.Nelem):
sl = self.mshfid.readline().split()
#Parse the line
eletag = sp.int32(sl[0])
eletype = sp.int32(sl[1])
ntags = sp.int32(sl[2])
physgrp = sp.int32(sl[3])
partition = sp.int32(sl[4])
if ntags >= 2:
physgrp = sp.int32(sl[3])
nodes = sp.array(sl[(3 + ntags)::], dtype=sp.int32)
for condition, action in self.elements_rules:
if condition(eletag,eletype,physgrp,nodes):
action(eletag,eletype,physgrp,nodes)
pass
else:
self.__error__(".msh file has < 2 tags element with tag " + str(eletag))
pass
def generate_gloDatamix_Meta(self):
""" generates a pd.Dataframe with the Metadata ordered in such a way that
it fits the .gloDatamix definition. """
# preparations
gloMeta = []
inds_map = self.map_lst_inds_to_path_inds()
for n, path in enumerate(self.Main.Data.Metadata.paths):
for i in range(len(self.Main.ROIs.ROI_list)):
lst_values = self.Main.Data.Metadata.LSTdata.loc[inds_map[n]]
# roi centroid
pos = self.Main.ROIs.ROI_list[i].get_center()
# stim
if self.Main.Options.preprocessing['stimuli'].shape[0] == 2:
stim2on, stim2off = self.Main.Options.preprocessing[
'stimuli'][1, :]
else:
stim2on, stim2off = ['-1', '-1']
# age
if lst_values['Age'] != -1:
try:
NAge, NAgeMax = lst_values['Age'].split('-')
except:
NAge = '-1'
NAgeMax = '-1'
else:
NAge = '-1'
NAgeMax = '-1'
row = OrderedDict()
row['NGloTag'] = str(self.Main.ROIs.ROI_list[i].label)
row['NOdorNr'] = '-999'
row['NOConc'] = str(lst_values['OConc'])
row['NStim_ON'] = str(
self.Main.Options.preprocessing['stimuli'][0, 0])
row['NStim_Off'] = str(
self.Main.Options.preprocessing['stimuli'][0, 1])
row['NNoFrames'] = str(self.Main.Data.nFrames)
row['NFrameTime'] = str(
sp.int32(self.Main.Options.preprocessing['dt'] * 1000))
row['NRealTime'] = str(lst_values['MTime'])
row['NPhConc'] = str(lst_values['PhConc'])
row['NshiftX'] = str(lst_values['ShiftX'])
row['NshiftY'] = str(lst_values['ShiftY'])
row['NcontMeasu'] = '0'
row['NNumMeasu'] = '0'
row['Nstim_ISI'] = '0'
row['NodorN'] = '1'
row['Nstim2ON'] = str(stim2on)
row['Nstim2OFF'] = str(stim2off)
row['NAge'] = str(NAge)
row['NAgeMax'] = str(NAgeMax)
row['TGloInfo'] = 'Coor' + str(
int(sp.around(pos[0], decimals=0))) + ':' + str(
int(sp.around(pos[1], decimals=0)))
row['TOdour'] = str(lst_values['Odour'])
row['T_dbb1'] = str(lst_values['DBB1'])
row['Tcomment'] = str(lst_values['Comment'])
row['TPharma'] = str(lst_values['Pharma'])
row['TPhtime'] = str(lst_values['PhTime'])
row['Tos9time'] = str(lst_values['PhTime'])
row['TLabel'] = lst_values['Label']
row['Tanimal'] = lst_values['DBB1'].strip().split('\\')[0]
row['T_dbb2'] = 'noDBB2'
gloMeta.append(row)
# make a pd.DataFrame out of it:
gloMetaDF = pd.DataFrame(columns=list(gloMeta[0].keys()))
for i in range(len(gloMeta)):
gloMetaDF = gloMetaDF.append(pd.Series(gloMeta[i]),
ignore_index=True)
return gloMetaDF
def propagate(s, tn): s.update_src.prepared_call((1,1),s.src_pt,sc.int32(tn),s.g_gpu) s.update.prepared_call(S.Dg,s.nx,s.ny,s.c_gpu,s.f_gpu,s.g_gpu) s.update.prepared_call(S.Dg,s.nx,s.ny,s.c_gpu,s.g_gpu,s.f_gpu)
# Get the kernel from the modules
initArray = mod_common.get_function("initArray")
updateE = mod_dielectric.get_function("updateE")
updateH = mod_dielectric.get_function("updateH")
updateSrc = mod_source.get_function("updateSrc")
'''
updateCPMLxE = mod_cpml.get_function("updateCPMLxE")
updateCPMLxH = mod_cpml.get_function("updateCPMLxH")
updateCPMLyE = mod_cpml.get_function("updateCPMLyE")
updateCPMLyH = mod_cpml.get_function("updateCPMLyH")
updateCPMLzE = mod_cpml.get_function("updateCPMLzE")
updateCPMLzH = mod_cpml.get_function("updateCPMLzH")
'''
# Initialize the device arrays
kNtot_devF = sc.int32(Ntot_devF)
initMainArrays( kNtot_devF, devEx, devEy, devEz, initArray )
initMainArrays( kNtot_devF, devHx, devHy, devHz, initArray )
'''
kNtotpmlx = sc.int32(Ntotpmlx)
kNtotpmly = sc.int32(Ntotpmly)
kNtotpmlz = sc.int32(Ntotpmlz)
initPsiArrays( kNtotpmlx, TPBpmlx, BPGpmlx, psixEyf, psixEyb, psixEzf, psixEzb, initArray )
initPsiArrays( kNtotpmlx, TPBpmlx, BPGpmlx, psixHyf, psixHyb, psixHzf, psixHzb, initArray )
initPsiArrays( kNtotpmly, TPBpmly, BPGpmly, psiyEzf, psiyEzb, psiyExf, psiyExb, initArray )
initPsiArrays( kNtotpmly, TPBpmly, BPGpmly, psiyHzf, psiyHzb, psiyHxf, psiyHxb, initArray )
initPsiArrays( kNtotpmlz, TPBpmlz, BPGpmlz, psizExf, psizExb, psizEyf, psizEyb, initArray )
initPsiArrays( kNtotpmlz, TPBpmlz, BPGpmlz, psizHxf, psizHxb, psizHyf, psizHyb, initArray )
'''
""" ion() from matplotlib.patches import Rectangle rect1 = Rectangle((100,0),20,150,facecolor='0.4') rect2 = Rectangle((100,180),20,140,facecolor='0.4') rect3 = Rectangle((100,350),20,150,facecolor='0.4') gca().add_patch(rect1) gca().add_patch(rect2) gca().add_patch(rect3) imsh = imshow(sc.ones((500,500),'f').T, cmap=cm.hot, origin='lower', vmin=0, vmax=0.1) #imsh = imshow(c.T, cmap=cm.hot, origin='lower', vmin=0, vmax=0.1) colorbar() """ Db, Dg = (256,1,1), (nx*ny/256+1,1) nx, ny = sc.int32(nx), sc.int32(ny) src_pt = sc.int32((nx/3)*nx+ny/2) initzero(nx*ny,f_gpu,g_gpu,block=Db,grid=Dg) for tstep in xrange(1001): update_src(src_pt,sc.int32(tstep),g_gpu,block=(1,1,1),grid=(1,1)) update(nx,ny,c_gpu,f_gpu,g_gpu,block=Db,grid=Dg,shared=258*4) update(nx,ny,c_gpu,g_gpu,f_gpu,block=Db,grid=Dg,shared=258*4) """ if tstep>1000: #if tstep%10 == 0: print tstep cuda.memcpy_dtoh(f,f_gpu) imsh.set_array( sc.sqrt(f[nx/3*2-100:nx/3*2+400,ny/2-250:ny/2+250].T**2) ) #imsh.set_array( sc.sqrt(f.T**2) )
#This script checks the number of patches in patch_load.txt.
#It prints the difference between the total number of patch and the theoretical number of patch.
import scipy
import matplotlib.pyplot as plt
# USer defined parameters
nmpi = 400
npatchx = 256
npatchy = 128
npatchz = 128
###########################
filename = "patch_load.txt"
file = open(filename)
data = file.readlines()
noutput = len(data)/(nmpi+1)
for iout in range(noutput):
data_first =data[(nmpi+1)*iout+1:(nmpi+1)*iout+nmpi+1]
for j in range(nmpi):
data_first[j]= scipy.int32(data_first[j].split()[-1])
arrfirst = scipy.array(data_first)
print arrfirst.sum()-(npatchx*npatchy*npatchz)
class gmshTranslator:
"""
gmshTranslator
Class that takes an input gmsh file (.msh) and provides functionality to parse and transform
the .msh to other formats.
"""
####################################################################################################
####################################################################################################
def __init__(self, mshfilename):
self.mshfilename = mshfilename
self.mshfid = open(mshfilename,"r")
#Initially, parse elements to know what nodes are in which physical groups.
reading_physnames = 0
reading_nodes = 0
reading_elements = 0
self.__inform__("Initializing...")
self.Nphys = 0
self.Nnodes = 0
self.Nelem = 0
self.physical_groups = []
self.nodes_in_physical_groups = {}
self.physical_group_dims = {}
self.physical_group_names = {}
linenumber = 1
for line in self.mshfid:
#################################################
# Identify begining of nodes and elements sections
if line.find("$PhysicalNames") >= 0:
reading_physnames = 1
continue
if line.find("$Nodes") >= 0:
reading_nodes = 1
continue
if line.find("$Elements") >= 0:
reading_elements = 1
continue
#################################################
#################################################
#Identify end of nodes and element sections
if line.find("$EndPhysicalNames") >= 0:
reading_physnames = 0
continue
if line.find("$EndElements") >= 0:
reading_elements = 0
continue
if line.find("$EndNodes") >= 0:
reading_nodes = 0
continue
#################################################
#If this is the first line of nodes, read the number of nodes.
if reading_physnames == 1:
self.Nphys = sp.int32(line)
self.__inform__("Mesh has " + str(self.Nphys) + " physical groups.")
reading_physnames = 2
continue
if reading_nodes == 1:
self.Nnodes = sp.int32(line)
self.__inform__("Mesh has " + str(self.Nnodes) + " nodes.")
reading_nodes = 2
continue
#If this is the first line of elements, read the number of elements
if reading_elements == 1:
self.Nelem = sp.int32(line)
self.__inform__("Mesh has " + str(self.Nelem) + " elements.")
reading_elements = 2
continue
if reading_physnames == 2:
sl = line.split()
grpdim = sp.int32(sl[0]) # spatial dimension of the physical group (0 = point, 1 = line, 2 = surface, 3 = volume)
physgrp = sp.int32(sl[1]) # group number
grpname = ( " ".join(sl[2:]) )[1:-1] # strip quotation marks
self.physical_group_dims[physgrp] = grpdim
self.physical_group_names[physgrp] = grpname
#Now parse elements and populate the list of nodes in groups
if reading_elements == 2:
sl = sp.array( line.split(), dtype = sp.int32)
eletag = sl[0]
eletype = sl[1]
ntags = sl[2]
physgrp = 0
partition = 0
if ntags >= 2:
physgrp = sl[3]
nodelist = sl[(3 + ntags)::]
# sys.stdout.write(str(nodelist.size) + " ")
if physgrp in self.physical_groups:
self.nodes_in_physical_groups[physgrp][nodelist] = 1
else:
self.nodes_in_physical_groups[physgrp] = -sp.ones(self.Nnodes+1, dtype=sp.int16)
self.nodes_in_physical_groups[physgrp][nodelist] = 1
self.physical_groups.append(physgrp)
pass
else:
self.__error__(".msh file has < 2 tags at line " + str(linenumber))
linenumber += 1
#end for line
self.__inform__("Processed " + str(linenumber) +" lines.")
self.__inform__("There are " + str(len(self.physical_groups)) + " physical groups available: ")
for g in self.physical_groups:
self.__inform__(" > %s: \"%s\" (dimension %d)" % (str(g), self.physical_group_names[g], self.physical_group_dims[g]))
# create inverse mapping from names -> IDs so that the user can refer to physical groups by name
#
self.physical_groups_by_name = {}
for k,v in self.physical_group_names.items():
self.physical_groups_by_name[v] = k
self.nodes_rules = []
self.elements_rules = []
#end def __init__
self.mshfid.close()
####################################################################################################
####################################################################################################
def __del__(self):
self.mshfid.close()
self.__inform__("Ending")
####################################################################################################
####################################################################################################
def add_elements_rule(self, condition, action):
self.elements_rules.append((condition, action))
pass
####################################################################################################
####################################################################################################
def add_nodes_rule(self, condition, action):
self.nodes_rules.append((condition, action))
pass
####################################################################################################
####################################################################################################
def clear_rules(self):
self.nodes_rules = []
self.elements_rules = []
pass
####################################################################################################
####################################################################################################
def parse(self):
self.mshfid = open(self.mshfilename, 'r')
#Advance to nodes
line = self.mshfid.readline()
while(line.find("$Nodes") < 0):
line = self.mshfid.readline()
pass
line = self.mshfid.readline() #This line should contain number of nodes
#Check that number of nodes in file is still the number of nodes in memory
if(not sp.int32(line) == self.Nnodes):
self.__error__("Something wrong. Aborting.")
exit(-1)
self.__inform__("Parsing nodes")
if len(self.nodes_rules) == 0:
self.__inform__("No rules for nodes... skipping nodes.")
for i in range(self.Nnodes):
self.mshfid.readline()
else:
#Read all nodes and do stuff
for i in range(self.Nnodes):
#Parse the line
sl = self.mshfid.readline().split()
tag = sp.int32(sl[0])
x = sp.double(sl[1])
y = sp.double(sl[2])
z = sp.double(sl[3])
#Figure out the groups to which this node belongs
physgroups = []
for grp in self.physical_groups:
if self.nodes_in_physical_groups[grp][tag] == 1:
physgroups.append(grp)
for condition, action in self.nodes_rules:
if condition(tag,x,y,z,physgroups):
action(tag,x,y,z)
pass
#Read another 2 lines after nodes are done. This should be $Elements
line = self.mshfid.readline()
line = self.mshfid.readline()
if(line.find("$Elements") == 0):
self.__inform__("Parsing elements")
else:
self.__error__("Something wrong reading elements. ")
exit(-1)
line = self.mshfid.readline() #This line should contain number of elements
#Check that number of elements in file is still the number of elements in memory
if(not sp.int32(line) == self.Nelem):
self.__error__("Something wrong. Aborting.")
exit(-1)
if len(self.elements_rules) == 0:
self.__inform__("No rules for elements... skipping elements.")
for i in range(self.Nelem):
self.mshfid.readline()
else:
#Read all elements and do stuff
nodes = []
for i in range(self.Nelem):
sl = self.mshfid.readline().split()
#Parse the line
eletag = sp.int32(sl[0])
eletype = sp.int32(sl[1])
ntags = sp.int32(sl[2])
physgrp = sp.int32(sl[3])
partition = sp.int32(sl[4])
if ntags >= 2:
physgrp = sp.int32(sl[3])
nodes = sp.array(sl[(3 + ntags)::], dtype=sp.int32)
for condition, action in self.elements_rules:
if condition(eletag,eletype,physgrp,nodes):
action(eletag,eletype,physgrp,nodes)
pass
else:
self.__error__(".msh file has < 2 tags element with tag " + str(eletag))
pass
#Helper functions to do typical tasks, such as checking if node or element is in a group
def is_element_in(self, this_physgrp):
def is_element_in_physgrp(eletag,eletype,physgrp,nodes):
if this_physgrp == "!any":
return True
return self.physical_groups_by_name[this_physgrp] == physgrp
return is_element_in_physgrp
def is_node_in(self, this_physgrp):
def is_node_in_physgrp(tag,x,y,z,physgroups):
if this_physgrp == "!any":
return True
return self.physical_groups_by_name[this_physgrp] in physgroups
return is_node_in_physgrp
####################################################################################################
####################################################################################################
def __inform__(self, msg):
print ("gmshTranslator: " + msg)
####################################################################################################
####################################################################################################
def __error__(self, msg):
sys.stderr.write("gmshTranslator: ERROR! -> " + msg + "\n")
#GMSH element definitions
line_2_node = sp.int32(1) # 2-node line.
triangle_3_node = sp.int32(2) # 3-node triangle.
quadrangle_4_node = sp.int32(3) # 4-node quadrangle.
tetrahedron_4_node = sp.int32(4) # 4-node tetrahedron.
hexahedron_8_node = sp.int32(5) # 8-node hexahedron.
prism_6_node = sp.int32(6) # 6-node prism.
pyramid_5_node = sp.int32(7) # 5-node pyramid.
line_3_node = sp.int32(8) # 3-node second order line (2 nodes associated with the vertices and 1 with the edge).
triangle_6_node = sp.int32(9) # 6-node second order triangle (3 nodes associated with the vertices and 3 with the edges).
quadrangle_9_node = sp.int32(10) # 9-node second order quadrangle (4 nodes associated with the vertices, 4 with the edges and 1 with the face).
tetrahedron_10_node = sp.int32(11) # 10-node second order tetrahedron (4 nodes associated with the vertices and 6 with the edges).
hexahedron_27_node = sp.int32(12) # 27-node second order hexahedron (8 nodes associated with the vertices, 12 with the edges, 6 with the faces and 1 with the volume).
prism_18_node = sp.int32(13) # 18-node second order prism (6 nodes associated with the vertices, 9 with the edges and 3 with the quadrangular faces).
pyramid_14_node = sp.int32(14) # 14-node second order pyramid (5 nodes associated with the vertices, 8 with the edges and 1 with the quadrangular face).
point_1_node = sp.int32(15) # 1-node point.
quadrangle_8_node = sp.int32(16) # 8-node second order quadrangle (4 nodes associated with the vertices and 4 with the edges).
hexahedron_20_node = sp.int32(17) # 20-node second order hexahedron (8 nodes associated with the vertices and 12 with the edges).
prism_15_node = sp.int32(18) # 15-node second order prism (6 nodes associated with the vertices and 9 with the edges).
pyramid_13_node = sp.int32(19) # 13-node second order pyramid (5 nodes associated with the vertices and 8 with the edges).
triangle_9_node_incomplete = sp.int32(20) # 9-node third order incomplete triangle (3 nodes associated with the vertices, 6 with the edges)
triangle_10_node = sp.int32(21) # 10-node third order triangle (3 nodes associated with the vertices, 6 with the edges, 1 with the face)
triangle_12_node_incomplete = sp.int32(22) # 12-node fourth order incomplete triangle (3 nodes associated with the vertices, 9 with the edges)
triangle_15_node = sp.int32(23) # 15-node fourth order triangle (3 nodes associated with the vertices, 9 with the edges, 3 with the face)
triangle_15_node_incomplete = sp.int32(24) # 15-node fifth order incomplete triangle (3 nodes associated with the vertices, 12 with the edges)
triangle_21_node = sp.int32(25) # 21-node fifth order complete triangle (3 nodes associated with the vertices, 12 with the edges, 6 with the face)
edge_4_node = sp.int32(26) # 4-node third order edge (2 nodes associated with the vertices, 2 internal to the edge)
edge_5_node = sp.int32(27) # 5-node fourth order edge (2 nodes associated with the vertices, 3 internal to the edge)
edge_6_node = sp.int32(28) # 6-node fifth order edge (2 nodes associated with the vertices, 4 internal to the edge)
tetrahedron_20_node = sp.int32(29) # 20-node third order tetrahedron (4 nodes associated with the vertices, 12 with the edges, 4 with the faces)
tetrahedron_35_node = sp.int32(30) # 35-node fourth order tetrahedron (4 nodes associated with the vertices, 18 with the edges, 12 with the faces, 1 in the volume)
tetrahedron_56_node = sp.int32(31) # 56-node fifth order tetrahedron (4 nodes associated with the vertices, 24 with the edges, 24 with the faces, 4 in the volume)
hexahedron_64_node = sp.int32(92) # 64-node third order hexahedron (8 nodes associated with the vertices, 24 with the edges, 24 with the faces, 8 in the volume)
hexahedron_125_node = sp.int32(93) # 125-node fourth order hexahedron (8 nodes associated with the vertices, 36 with the edges, 54 with the faces, 27 in the volume)
theta0 = 10.0
Ntest = 100
# --------------------------------------------
# Load all database
# --------------------------------------------
ttt = time.clock()
if not os.path.exists('qm7.pkl'): os.system('wget http://www.quantum-machine.org/data/qm7.pkl')
dataset = pickle.load(open('qm7.pkl','r'))
# --------------------------------------------
# Extract training data and test set
# --------------------------------------------
allP = dataset['P'][range(0,split)+range(split+1,5)].flatten()
print "TIMER load_data", time.clock() - ttt
nteach = sp.int32(sp.exp(sp.linspace(sp.log(2*Ntest), sp.log(allP.size), 25)))
# --------------------------------------------
# Loop over different training set sizes
# --------------------------------------------
alpha = []
alpha_std = []
mae_error = []
errors = []
for Nteach in nteach:
# --------------------------------------------
# First time include the test set to calculate their alpha
# --------------------------------------------
print "\n", "-"*60, "\n"
print "N teach = %d" % Nteach
synth.setnchannels(1)
synth.setsampwidth(2)
synth.setframerate(samplingrate)
remain = sound.getnframes()
while remain > 0:
s = min(chunk, remain)
#read frames
data_sound = sound.readframes(s)
data_noise = noise.readframes(s)
#convert
ary_sound = sp.fromstring(data_sound, sp.int16)
ary_noise = sp.fromstring(data_noise, sp.int16)
int32_ary_sound = sp.int32(ary_sound)
int32_ary_noise = sp.int32(ary_noise)
ary2 = sp.int16(int32_ary_sound + int32_ary_noise)
data2 = ary2.tostring()
synth.writeframes(data2)
remain = remain - s
sound.close()
noise.close()
synth.close()
infile = 'tools/sound/noisy.wav'
signal, params = read_signal(infile, WINSIZE)
nf = len(signal) / (WINSIZE / 2) - 1
sig_out = sp.zeros(len(signal), sp.float32)
window = sp.hanning(WINSIZE)
ion() from matplotlib.patches import Rectangle rect1 = Rectangle((100,0),20,150,facecolor='0.4') rect2 = Rectangle((100,180),20,140,facecolor='0.4') rect3 = Rectangle((100,350),20,150,facecolor='0.4') gca().add_patch(rect1) gca().add_patch(rect2) gca().add_patch(rect3) #imsh = imshow(sc.ones((500,500),'f').T, cmap=cm.hot, origin='lower', vmin=0, vmax=0.1) imsh = imshow(output.T, cmap=cm.hot, origin='lower', vmin=0, vmax=0.1) colorbar() # main loop for tn in xrange(3000): if mpi.rank == 1: src_pt = sc.int32(100*ny + 1501) S.update_src.prepared_call((1,1), src_pt, sc.int32(tn), S.f_gpu) S.update.prepared_call(S.Dg, sc.int32(S.nx), sc.int32(ny), S.c_gpu, S.f_gpu, S.g_gpu) S.exchange(S.f_gpu) S.update.prepared_call(S.Dg, sc.int32(S.nx), sc.int32(ny), S.c_gpu, S.g_gpu, S.f_gpu) S.exchange(S.g_gpu) if tn>100 and tn%100 == 0: if mpi.rank == 0: cuda.memcpy_dtoh(S.f,S.f_gpu) output[:1000,:] = S.f[1:-1,1:-1] output[1000:2000,:] = mpi.world.recv(1,10) output[2000:3000,:] = mpi.world.recv(2,10) #imsh.set_array( sc.sqrt(output[1900:2400,1250:1750].T**2) )
y_start=p_coordinate[1]*(shape[1]-1)
y_end=y_start+shape[1]
k=0 #Counts the components
for group in list_group:
Fields_local[k,x_start:x_end,y_start:y_end]=group._f_getChild(namecycle).read()[:,:,0]
k=k+1
h5proc_file.close()
#End of read_proc loop
#Reassemble data from each processors on procs 0,1 and 2 ####
for k in range(K):
if (rankproc > 0 ):
buffer=Fields_local[k,1:,:].astype("float32") #Account for overlapping
else:
buffer=Fields_local[k,:,:].astype("float32")
vec_count=scipy.arange(numproc,dtype='int32') #Initialize for all procs
matsize=scipy.int32(buffer.size)
gridcomm.Allgather([matsize,1,MPI.INT],[vec_count,1,MPI.INT])
vec_stride = [vec_count[:j].sum() for j in range(numproc)]
gridcomm.Gatherv([buffer,buffer.size,MPI.FLOAT],[Fields_global,vec_count,vec_stride,MPI.FLOAT],root=k)
#End of the field gathering loop ############
#################################################################
# Plot single frames by procs 0,1 and 2 #######################
if rankproc < K :
if rankproc==0 and K==3:
indice='x'
elif rankproc==1 and K==3:
indice='y'
elif rankproc ==2 and K==3:
indice='z'
#if field == 'B' and grid == 0:
pa = {
'Flux_Ca': 0.0,
'tau_Ca': 20.0,
'ss_Ca': 0.01,
'alpha_p': 1.0,
'beta_p': 10.0,
'ss_x': 1.0,
'tau_x': 50.0,
'le_x': 1.0
}
pa['beta/alpha_p'] = pa['beta_p'] / pa['alpha_p']
pinfty = U0[0] / (U0[0] + pa['beta/alpha_p'])
print('p_infty = %g' % pinfty)
timeStep = 1 / 40.0
timeMax = 550.
nSteps = sc.int32(timeMax / timeStep)
timeSamples = sc.arange(0, timeMax, timeStep)
stimInterval = 50.0
stimTimes = stimInterval * sc.arange(1, 11)
stimIdx = sc.int32(stimTimes / timeStep)
print(stimIdx)
ff = sc.zeros(len(timeSamples))
ff[stimIdx] = 200.0 * timeStep
pa['ic'] = U0
pa['stepSize'] = timeStep
pa['timeMax'] = timeMax
pa['nSteps'] = nSteps
c, p, x, f3d = stsp3d_profile(pa)
# Runs on 2D
U0 = sc.array([0.05, 0.5])
def __init__(self, mshfilename):
self.mshfilename = mshfilename
self.mshfid = open(mshfilename,"r")
#Initially, parse elements to know what nodes are in which physical groups.
reading_physnames = 0
reading_nodes = 0
reading_elements = 0
self.__inform__("Initializing...")
self.Nphys = 0
self.Nnodes = 0
self.Nelem = 0
self.physical_groups = []
self.nodes_in_physical_groups = {}
self.physical_group_dims = {}
self.physical_group_names = {}
linenumber = 1
for line in self.mshfid:
#################################################
# Identify begining of nodes and elements sections
if line.find("$PhysicalNames") >= 0:
reading_physnames = 1
continue
if line.find("$Nodes") >= 0:
reading_nodes = 1
continue
if line.find("$Elements") >= 0:
reading_elements = 1
continue
#################################################
#################################################
#Identify end of nodes and element sections
if line.find("$EndPhysicalNames") >= 0:
reading_physnames = 0
continue
if line.find("$EndElements") >= 0:
reading_elements = 0
continue
if line.find("$EndNodes") >= 0:
reading_nodes = 0
continue
#################################################
#If this is the first line of nodes, read the number of nodes.
if reading_physnames == 1:
self.Nphys = sp.int32(line)
self.__inform__("Mesh has " + str(self.Nphys) + " physical groups.")
reading_physnames = 2
continue
if reading_nodes == 1:
self.Nnodes = sp.int32(line)
self.__inform__("Mesh has " + str(self.Nnodes) + " nodes.")
reading_nodes = 2
continue
#If this is the first line of elements, read the number of elements
if reading_elements == 1:
self.Nelem = sp.int32(line)
self.__inform__("Mesh has " + str(self.Nelem) + " elements.")
reading_elements = 2
continue
if reading_physnames == 2:
sl = line.split()
grpdim = sp.int32(sl[0]) # spatial dimension of the physical group (0 = point, 1 = line, 2 = surface, 3 = volume)
physgrp = sp.int32(sl[1]) # group number
grpname = ( " ".join(sl[2:]) )[1:-1] # strip quotation marks
self.physical_group_dims[physgrp] = grpdim
self.physical_group_names[physgrp] = grpname
#Now parse elements and populate the list of nodes in groups
if reading_elements == 2:
sl = sp.array( line.split(), dtype = sp.int32)
eletag = sl[0]
eletype = sl[1]
ntags = sl[2]
physgrp = 0
partition = 0
if ntags >= 2:
physgrp = sl[3]
nodelist = sl[(3 + ntags)::]
# sys.stdout.write(str(nodelist.size) + " ")
if physgrp in self.physical_groups:
self.nodes_in_physical_groups[physgrp][nodelist] = 1
else:
self.nodes_in_physical_groups[physgrp] = -sp.ones(self.Nnodes+1, dtype=sp.int16)
self.nodes_in_physical_groups[physgrp][nodelist] = 1
self.physical_groups.append(physgrp)
pass
else:
self.__error__(".msh file has < 2 tags at line " + str(linenumber))
linenumber += 1
#end for line
self.__inform__("Processed " + str(linenumber) +" lines.")
self.__inform__("There are " + str(len(self.physical_groups)) + " physical groups available: ")
for g in self.physical_groups:
self.__inform__(" > %s: \"%s\" (dimension %d)" % (str(g), self.physical_group_names[g], self.physical_group_dims[g]))
# create inverse mapping from names -> IDs so that the user can refer to physical groups by name
#
self.physical_groups_by_name = {}
for k,v in self.physical_group_names.items():
self.physical_groups_by_name[v] = k
self.nodes_rules = []
self.elements_rules = []
#end def __init__
self.mshfid.close()
def generate_gloDatamix_Meta(self):
""" generates a pd.Dataframe with the Metadata ordered in such a way that
it fits the .gloDatamix definition. """
# preparations
gloMeta = []
inds_map = self.map_lst_inds_to_path_inds()
for n,path in enumerate(self.Main.Data.Metadata.paths):
for i in range(len(self.Main.ROIs.ROI_list)):
lst_values = self.Main.Data.Metadata.LSTdata.loc[inds_map[n]]
# roi centroid
pos = self.Main.ROIs.ROI_list[i].get_center()
# stim
if self.Main.Options.preprocessing['stimuli'].shape[0] == 2:
stim2on,stim2off = self.Main.Options.preprocessing['stimuli'][1,:]
else:
stim2on,stim2off = ['-1','-1']
# age
if lst_values['Age'] != -1:
try:
NAge,NAgeMax = lst_values['Age'].split('-')
except:
NAge = '-1'
NAgeMax = '-1'
else:
NAge = '-1'
NAgeMax = '-1'
row = OrderedDict()
row['NGloTag'] = str(self.Main.ROIs.ROI_list[i].label)
row['NOdorNr'] = '-999'
row['NOConc'] = str(lst_values['OConc'])
row['NStim_ON'] = str(self.Main.Options.preprocessing['stimuli'][0,0])
row['NStim_Off'] = str(self.Main.Options.preprocessing['stimuli'][0,1])
row['NNoFrames'] = str(self.Main.Data.nFrames)
row['NFrameTime'] = str(sp.int32(self.Main.Options.preprocessing['dt'] * 1000))
row['NRealTime'] = str(lst_values['MTime'])
row['NPhConc'] = str(lst_values['PhConc'])
row['NshiftX'] = str(lst_values['ShiftX'])
row['NshiftY'] = str(lst_values['ShiftY'])
row['NcontMeasu'] = '0'
row['NNumMeasu'] = '0'
row['Nstim_ISI'] = '0'
row['NodorN'] = '1'
row['Nstim2ON'] = str(stim2on)
row['Nstim2OFF'] = str(stim2off)
row['NAge'] = str(NAge)
row['NAgeMax'] = str(NAgeMax)
row['TGloInfo'] = 'Coor' + str(int(sp.around(pos[0],decimals=0))) + ':' + str(int(sp.around(pos[1],decimals=0)))
row['TOdour'] = str(lst_values['Odour'])
row['T_dbb1'] = str(lst_values['DBB1'])
row['Tcomment'] = str(lst_values['Comment'])
row['TPharma'] = str(lst_values['Pharma'])
row['TPhtime'] = str(lst_values['PhTime'])
row['Tos9time'] = str(lst_values['PhTime'])
row['TLabel'] = lst_values['Label']
row['Tanimal'] = lst_values['DBB1'].strip().split('\\')[0]
row['T_dbb2'] = 'noDBB2'
gloMeta.append(row)
# make a pd.DataFrame out of it:
gloMetaDF = pd.DataFrame(columns=gloMeta[0].keys())
for i in range(len(gloMeta)):
gloMetaDF = gloMetaDF.append(pd.Series(gloMeta[i]),ignore_index=True)
return gloMetaDF
# Load all database
# --------------------------------------------
ttt = time.clock()
if not os.path.exists('qm7.pkl'): os.system('wget http://www.quantum-machine.org/data/qm7.pkl')
dataset = pickle.load(open('qm7.pkl','r'))
# --------------------------------------------
# Extract training data and test set
# --------------------------------------------
split = 1
N_models = 1
theta0 = 10.0
Nfixed = 100
allP = dataset['P'][range(0,split)+range(split+1,5)].flatten()
nteachs = sp.int32(sp.exp(sp.linspace(sp.log(Nfixed+0.0), sp.log(allP.size), 30)))
Ptest = dataset['P'][split]
Xtest = dataset['X'][Ptest]
Ttest = dataset['T'][Ptest]
print "TIMER load_data", time.clock() - ttt
alpha = []
covmat = []
alpha_std = []
for Nteach in nteachs:
print "\n", "-"*60, "\n"
print "N teach = %d" % Nteach
# Select training data
P = allP[:Nteach]