def CompareProcedure():
with HDF5Reader('2Dlake_light.h5') as f:
# TODO nothing is done with these metadata
metadata = f.readMetadata()
# reading the data attributes for determining the format
dataAttributes = f.readDataAttributes()
data = f.readData()
print dataAttributes['intervals']
print dataAttributes[METADATA.resultformat_name]
bargridoh = BarGridKernel.initFromHDF5(metadata, dataAttributes, data)
hm = HDF5Manager([BarGridKernel])
bargrid = hm.readKernel('2Dlake_light.h5')
bargrid2 = BarGridKernel.readPatrickSaintPierrebis('../samples/2D_light.txt')
distancegriddimensions = [31,31] #[301,301]
distancegridintervals = map(lambda e: e-1, distancegriddimensions)
resizebargrid = bargrid.toBarGridKernel(bargrid.originCoords, bargrid.oppositeCoords, distancegridintervals)
resizebargrid2 = bargrid2.toBarGridKernel(bargrid2.originCoords, bargrid2.oppositeCoords, distancegridintervals)
print(bargrid.bars[0])
print(bargrid2.bars[0])
print(bargrid.bars[10000])
print(bargrid2.bars[10000])
for i in range(len(bargrid.bars)):
if bargrid.bars[i][2]!=bargrid2.bars[i][2]:
print bargrid.bars[i]
print bargrid2.bars[i]
print "merde"
print(bargrid.originCoords)
print(bargridoh.originCoords)
print(bargrid.oppositeCoords)
print(bargridoh.oppositeCoords)
print(bargrid.intervalNumberperaxis)
print(bargridoh.intervalNumberperaxis)
print(bargrid.permutation)
print(bargridoh.permutation)
print(resizebargrid.bars[0])
print(resizebargrid2.bars[0])
print(resizebargrid.bars[30])
print(resizebargrid2.bars[30])
for i in range(len(resizebargrid.bars)):
if resizebargrid.bars[i][2]!=resizebargrid2.bars[i][2]:
print resizebargrid.bars[i]
print resizebargrid2.bars[i]
print "merde"
print "youpi"
def writeViablesPointsHDF5(filename, dt, p0, l0, dp, dl, np, nl):
with open(filename+".txt", 'w') as f:
f.write("Pas de temps : {:f}\n".format(dt))
firstCol,tabp = computeTrajectoryP(dt, p0, l0, dp, dl, np, nl, umax, nmax, pmax, lmax, b, r, q, m)
iLmin=ceil((lmin-l0)/dl)
iLmax=floor((lmax-l0)/dl)
iPmax=floor(pmax/dp)
# preparing regulargridkernel
grid=numpy.array([
i>=iLmin and i<=iLmax and j<=iPmax and
(i<firstCol or (i<firstCol+len(tabp) and p0+j*dp<=tabp[i-firstCol]))
for i in numpy.arange(nl) for j in numpy.arange(np)
]).reshape(np,nl)
rgk = RegularGridKernel([p0,l0],[dp,dl])
rgk.setGrid(grid)
# preparing gridbarkernel
bars = []
for i in range(int(iLmin),int(iLmax+1)):
viablesPoints=numpy.argwhere(grid[i])
if len(viablesPoints)>0:
bars.append([i,viablesPoints[0][0],viablesPoints[-1][0]])
bgk = BarGridKernel([p0,l0],None, None, data=bars)
# writing raw points
for i in range(nl):
for j in range(np):
if grid[i,j]:
f.write("{:f} {:f}\n".format(l0+i*dl,p0+j*dp))
HDF5Manager.writeKernel(rgk, filename+".h5", compression="gzip", compression_opts=9)
writeHDF5_coords(rgk, filename+"_coords.h5", compression="gzip", compression_opts=9)
def testRead():
dataway = '../samples/2D.txt'
metadataway = '../samples/2D_metadata.txt'
h5way = '2D.h5'
hm = HDF5Manager([BarGridKernel])
grid = BarGridKernel.readPatrickSaintPierrebis(dataway)
myre = re.compile('^#(.*):(.*)$')
with open(metadataway) as f:
for line in f:
if line.startswith('#'):
k,v = myre.match(line).groups()
grid.metadata[k.strip()]=v.strip()
grid.metadata[METADATA.statedimension] = int(grid.metadata[METADATA.statedimension])
grid.metadata['results.submissiondate'] = time.strftime('%Y-%m-%d %H:%M',time.localtime())
print grid.permutation
print grid.originCoords
hm.writeKernel(grid, h5way)
grid = []
# grid2 = hm.readKernel(h5way)
# print(grid2.metadata)
# print(metadata.category)
# print(grid2.metadata[METADATA.category])
# print(grid2.metadata[METADATA.results_submissiondate])
# print(grid2.metadata[METADATA.results_formatparametervalues])
# print grid2.permutation
# print grid2.originCoords
# print(grid2.kernelMinPoint)
# print(grid2.kernelMaxPoint)
return grid
def CompareProcedure():
with HDF5Reader('2Dlake_light.h5') as f:
# TODO nothing is done with these metadata
metadata = f.readMetadata()
# reading the data attributes for determining the format
dataAttributes = f.readDataAttributes()
data = f.readData()
print dataAttributes['intervals']
print dataAttributes[METADATA.resultformat_title]
bargridoh = BarGridKernel.initFromHDF5(metadata, dataAttributes, data)
hm = HDF5Manager([BarGridKernel])
bargrid = hm.readKernel('2Dlake_light.h5')
bargrid2 = FileFormatLoader.PspModifiedLoader().read(
'../samples/2D_light.txt')
distancegriddimensions = [31, 31] #[301,301]
distancegridintervals = map(lambda e: e - 1, distancegriddimensions)
resizebargrid = bargrid.toBarGridKernel(bargrid.originCoords,
bargrid.oppositeCoords,
distancegridintervals)
resizebargrid2 = bargrid2.toBarGridKernel(bargrid2.originCoords,
bargrid2.oppositeCoords,
distancegridintervals)
print(bargrid.bars[0])
print(bargrid2.bars[0])
print(bargrid.bars[10000])
print(bargrid2.bars[10000])
for i in range(len(bargrid.bars)):
if bargrid.bars[i][2] != bargrid2.bars[i][2]:
print bargrid.bars[i]
print bargrid2.bars[i]
print "merde"
print(bargrid.originCoords)
print(bargridoh.originCoords)
print(bargrid.oppositeCoords)
print(bargridoh.oppositeCoords)
print(bargrid.intervalNumberperaxis)
print(bargridoh.intervalNumberperaxis)
print(bargrid.permutation)
print(bargridoh.permutation)
print(resizebargrid.bars[0])
print(resizebargrid2.bars[0])
print(resizebargrid.bars[30])
print(resizebargrid2.bars[30])
for i in range(len(resizebargrid.bars)):
if resizebargrid.bars[i][2] != resizebargrid2.bars[i][2]:
print resizebargrid.bars[i]
print resizebargrid2.bars[i]
print "merde"
print "youpi"
def readFile(self, f):
'''
Returns an object of class BarGridKernel loaded from an output file from the software of Patrick Saint-Pierre.
'''
bgk = None
origin = list(map(float, re.findall('-?\d+\.?\d*', f.readline())))
dimension = len(origin)
if dimension == 0 :
raise FileFormatException("Dimensions must be > 0")
opposite = list(map(float, re.findall('-?\d+\.?\d*', f.readline())))
intervalNumber = list(map(int, re.findall('[0-9]+', f.readline())))
if dimension !=len(opposite) or dimension!=len(intervalNumber):
raise FileFormatException("Dimensions of metadata mismatch")
pointSize = list(map(int, re.findall('[0-9]+', f.readline())))
intervalNumber = [e//pointSize[0] for e in intervalNumber]
# reading columns headers and deducing permutation of variables
line = f.readline()
columnNumbertoIgnore = len(re.findall('empty', line))
permutVector = list(map(int, re.findall('[0-9]+', line)))
permutation = np.zeros(dimension * dimension,int).reshape(dimension,dimension)
for i in range(dimension):
permutation[i][permutVector[i]-1]=1
# Ok, creating the container object
bgk = BarGridKernel(origin, opposite, intervalNumber,permutation)
# ignoring lines until 'Initxx'
stop=False
while not stop:
line = f.readline()
if 'Initxx' in line:
stop = True
# reading bars
stop = False
while not stop:
# using a while loop, because the for loop seems buggy with django InMemoryUploadedFile reading
line = f.readline()
if not line:
stop = True
else:
coords = list(map(int, re.findall('[0-9]+', line)))
coords = [e // pointSize[0] for e in coords]
bgk.addBar(coords[columnNumbertoIgnore:-2], coords[-2], coords[-1])
# TODO what is done with modelMetadata and nbDim
return bgk
def readFile(self, f):
'''
Returns an object of class BarGridKernel loaded from an output file from the software of Patrick Saint-Pierre.
'''
bgk = None
origin = list(map(float, re.findall('-?\d+\.?\d*', f.readline())))
dimension = len(origin)
if dimension == 0 :
raise FileFormatException("Dimensions must be > 0")
opposite = list(map(float, re.findall('-?\d+\.?\d*', f.readline())))
intervalNumber = list(map(int, re.findall('[0-9]+', f.readline())))
if dimension !=len(opposite) or dimension!=len(intervalNumber):
raise FileFormatException("Dimensions of metadata mismatch")
pointSize = list(map(int, re.findall('[0-9]+', f.readline())))
intervalNumber = [e//pointSize[0] for e in intervalNumber]
# reading columns headers and deducing permutation of variables
line = f.readline()
columnNumbertoIgnore = len(re.findall('empty', line))
permutVector = list(map(int, re.findall('[0-9]+', line)))
permutation = np.zeros(dimension * dimension,int).reshape(dimension,dimension)
for i in range(dimension):
permutation[i][permutVector[i]-1]=1
# Ok, creating the container object
bgk = BarGridKernel(origin, opposite, intervalNumber,permutation)
# ignoring lines until 'Initxx'
stop=False
while not stop:
line = f.readline()
if 'Initxx' in line:
stop = True
# reading bars
stop = False
while not stop:
# using a while loop, because the for loop seems buggy with django InMemoryUploadedFile reading
line = f.readline()
if not line:
stop = True
else:
coords = list(map(int, re.findall('[0-9]+', line)))
coords = [e // pointSize[0] for e in coords]
bgk.addBar(coords[columnNumbertoIgnore:-2], coords[-2], coords[-1])
# TODO what is done with modelMetadata and nbDim
return bgk
def toBarGridKernel(self, newOriginCoords, newOppositeCoords, intervalNumberperaxis):
'''
Convert to a BarGridKernel with another underlying grid, with a given number of intervals per axis.
If no origin or opposite is given, it will be deduced from the lower or upper cell.
Returns an instance of BarGridKernel.
'''
minBoundsCoordinates = self.getMinBoundsCoordinates()
intervalsSizes = (np.array([max([c[i+1] for c in self.cells]) for i in minBoundsCoordinates], float)-np.array([min([c[i] for c in self.cells]) for i in minBoundsCoordinates], float))/(np.array(intervalNumberperaxis)+np.array([1]*len(intervalNumberperaxis)))
if not newOriginCoords:
newOriginCoords = np.array([min([c[i] for c in self.cells]) for i in minBoundsCoordinates], float) + intervalsSizes / 2
else:
newOriginCoords = np.array(newOriginCoords, float)
if not newOppositeCoords:
newOppositeCoords = np.array([max([c[i+1] for c in self.cells]) for i in minBoundsCoordinates], float) - intervalsSizes / 2
else:
newOppositeCoords = np.array(newOppositeCoords, float)
# newIntervalNumberperaxis = (newOppositeCoords - newOriginCoords) / intervalsSizes
bgk = BarGridKernel(newOriginCoords, newOppositeCoords, intervalNumberperaxis)
# print list(newOppositeCoords)
# print list(intervalsSizes)
for cell in self.cells:
cell_start = [cell[i] for i in minBoundsCoordinates]
cell_end = [cell[i+1] for i in minBoundsCoordinates]
start_int = np.floor(np.array(intervalNumberperaxis) * (np.array(cell_start, float) + intervalsSizes / 2 - newOriginCoords)/(newOppositeCoords - newOriginCoords))
start_int = np.array([max(start_int[i],0) for i in range(len(start_int))],int)
end_int = np.ceil(np.array(intervalNumberperaxis) * (np.array(cell_end, float) - intervalsSizes / 2 - newOriginCoords)/(newOppositeCoords - newOriginCoords))
end_int = np.array([min(end_int[i],intervalNumberperaxis[i]) for i in range(len(end_int))],int)
# now adding all the points on the grid of the BGK between start and end of the Kd cell
next_point = list(start_int[:-1])
bgk.addBar(next_point, start_int[-1], end_int[-1])
while any(next_point!=end_int[:-1]):
for i,coord in reversed(list(enumerate(next_point))):
if next_point[i] < end_int[i]:
next_point[i] += 1
break
else:
next_point[i] = start_int[i]
bgk.addBar(next_point, start_int[-1], end_int[-1])
return bgk
def toBarGridKernel(self, newOriginCoords, newOppositeCoords, intervalNumberperaxis):
'''
Convert to a BarGridKernel with another underlying grid, with a given number of intervals per axis.
If no origin or opposite is given, it will be deduced from the lower or upper cell.
Returns an instance of BarGridKernel.
'''
minBoundsCoordinates = self.getMinBoundsCoordinates()
intervalsSizes = (np.array([max([c[i+1] for c in self.cells]) for i in minBoundsCoordinates], float)-np.array([min([c[i] for c in self.cells]) for i in minBoundsCoordinates], float))/(np.array(intervalNumberperaxis)+np.array([1]*len(intervalNumberperaxis)))
if not newOriginCoords:
newOriginCoords = np.array([min([c[i] for c in self.cells]) for i in minBoundsCoordinates], float) + intervalsSizes / 2
else:
newOriginCoords = np.array(newOriginCoords, float)
if not newOppositeCoords:
newOppositeCoords = np.array([max([c[i+1] for c in self.cells]) for i in minBoundsCoordinates], float) - intervalsSizes / 2
else:
newOppositeCoords = np.array(newOppositeCoords, float)
# newIntervalNumberperaxis = (newOppositeCoords - newOriginCoords) / intervalsSizes
bgk = BarGridKernel(newOriginCoords, newOppositeCoords, intervalNumberperaxis)
# print list(newOppositeCoords)
# print list(intervalsSizes)
for cell in self.cells:
cell_start = [cell[i] for i in minBoundsCoordinates]
cell_end = [cell[i+1] for i in minBoundsCoordinates]
start_int = np.floor(np.array(intervalNumberperaxis) * (np.array(cell_start, float) + intervalsSizes / 2 - newOriginCoords)/(newOppositeCoords - newOriginCoords))
start_int = np.array([max(start_int[i],0) for i in range(len(start_int))],int)
end_int = np.ceil(np.array(intervalNumberperaxis) * (np.array(cell_end, float) - intervalsSizes / 2 - newOriginCoords)/(newOppositeCoords - newOriginCoords))
end_int = np.array([min(end_int[i],intervalNumberperaxis[i]) for i in range(len(end_int))],int)
# now adding all the points on the grid of the BGK between start and end of the Kd cell
next_point = list(start_int[:-1])
bgk.addBar(next_point, start_int[-1], end_int[-1])
while any(next_point!=end_int[:-1]):
for i,coord in reversed(list(enumerate(next_point))):
if next_point[i] < end_int[i]:
next_point[i] += 1
break
else:
next_point[i] = start_int[i]
bgk.addBar(next_point, start_int[-1], end_int[-1])
return bgk
def readFile(self, f):
metadata={}
bgk = None
f.readline()
nbDim = re.match('\s*([0-9]*)\s.*',f.readline()).group(1)
metadata[METADATA.dynamicsdescription] = f.readline()
metadata[METADATA.stateconstraintdescription] = f.readline()
metadata[METADATA.targetdescription] = f.readline()
for i in range(4): f.readline()
dimensionsSteps = list(map(int, re.findall('[0-9]+', f.readline())))
for i in range(2): f.readline()
origin = list(map(int, re.findall('[0-9]+', f.readline())))
maxPoint = list(map(int, re.findall('[0-9]+', f.readline())))
for i in range(5): f.readline()
# ND Why? Why not opposite = maxPoint
opposite = origin
bgk = BarGridKernel(origin, opposite, dimensionsSteps, metadata=metadata)
# reading until some lines with 'Initxx'
stop=False
initxx=False
# ND Why restrict min/max point to integer position
bgk.kernelMinPoint = [e//1 for e in origin]
bgk.kernelMaxPoint = [e//1 for e in maxPoint]
while not stop:
line = f.readline()
if 'Initxx' in line:
initxx = True
elif initxx and 'Initxx' not in line:
stop = True
# reading bars
for line in f:
coords = list(map(int, re.findall('[0-9]+', line)))
# ND Why convert point to integer position
coords = [e//1 for e in coords]
bgk.addBar(coords[2:-2], coords[-2], coords[-1])
# TODO what is done with modelMetadata and nbDim
return bgk
else :
histodict['0'] = self.totalpointNumber()
occurnumber[0] = self.totalpointNumber()
return histodict
if __name__ == "__main__":
import time
norm = EucNorm()
# bargrid = BarGridKernel([0,0], [10,10], [10,10])
# bargrid.addBar([1],3,7)
# bargrid.addBar([2],5,5)
# bargrid.addBar([3],0,10)
bargrid = BarGridKernel.readPatrickSaintPierrebis('../samples/2D_light.txt')
distancegriddimensions = [31,31]#[2001,2001]
distancegridintervals = map(lambda e: e-1, distancegriddimensions)
print "of"
print distancegridintervals
print bargrid.kernelMinPoint
print bargrid.kernelMaxPoint
startTime = time.time()
resizebargrid = bargrid.toBarGridKernel(bargrid.originCoords, bargrid.oppositeCoords, distancegridintervals)
readTime = time.time() - startTime
print('resize in {:.2f}s'.format(readTime))
resizebargrid2 = bargrid.toBarGridKernel(bargrid.originCoords, bargrid.oppositeCoords, distancegridintervals)
for bar in resizebargrid2.bars:
