def __init__(self,**kwargs):
Geom.__init__(self,**kwargs)
self.name = "forceLayout"
self._id = 'forceLayout'
self._build_js()
self._build_css()
self.styles = dict([(k[0].replace('_','-'), k[1]) for k in kwargs.items()])
def __init__(self,x,y,**kwargs):
Geom.__init__(self,**kwargs)
self.x = x
self.y = y
self.params = [x,y]
self.debug = True
self.name = "line"
self._build_js()
self._build_css()
def __init__(self, x, y, **kwargs):
Geom.__init__(self, **kwargs)
self.x = x
self.y = y
self.params = [x, y]
self.debug = True
self.name = "line"
self._build_js()
self._build_css()
def __init__(self,x,y,c=None,**kwargs):
Geom.__init__(self, **kwargs)
self.x = x
self.y = y
self.c = c
self._id = 'point_%s_%s_%s'%(self.x,self.y,self.c)
self.params = [x,y,c]
self.name = "point"
self.build_css()
self.build_js()
def __init__(self,x,yupper,ylower,**kwargs):
Geom.__init__(self,**kwargs)
self.x = x
self.yupper = yupper
self.ylower = ylower
self.params = [x, yupper, ylower]
self.debug = True
self.name = "area"
self._build_js()
self._build_css()
def __init__(self, x, yupper, ylower, **kwargs):
Geom.__init__(self, **kwargs)
self.x = x
self.yupper = yupper
self.ylower = ylower
self.params = [x, yupper, ylower]
self.debug = True
self.name = "area"
self._build_js()
self._build_css()
def __init__(self,x, **kwargs):
"""
x : string
name of the column you want to use to define the x-axis
"""
Geom.__init__(self, **kwargs)
self.x = x
self.params = [x]
self._id = 'xaxis'
self.name = 'xaxis'
self.build_css()
self.build_js()
def init_geom(self):
bravais = self.bravais.GetValue()
alat, unit = self.alat.GetValue()
sc = self.sc.GetValue()
dist = self.dist.GetValue()
if len(self.types) == 0:
comp = dict(zip([il.GetValue() for il in self.type_label], [ifs.GetValue() for ifs in self.typefs]))
else:
comp = dict(zip(self.types, [ifs.GetValue() for ifs in self.typefs]))
g = Geom()
g.initialize(bravais, comp, sc, alat, unit, dist_level=dist)
g.geom2opts()
return g.opts["AtomicCoordinatesAndAtomicSpecies"]
def __init__(self, var, orient=None, **kwargs):
"""
var : string
name of the column you want to use to define the axis
"""
Geom.__init__(self, **kwargs)
self.var = var
self.orient = orient
self.params = [var]
self._id = '%s_axis'%var
self.name = '%s_axis'%var
self.build_css()
self.build_js()
def __init__(self, var, orient=None, **kwargs):
"""
var : string
name of the column you want to use to define the axis
"""
Geom.__init__(self, **kwargs)
self.var = var
self.orient = orient
self.params = [var]
self._id = '%s_axis' % var
self.name = '%s_axis' % var
self.build_css()
self.build_js()
def __init__(self, x, label=None, **kwargs):
"""
x : string
name of the column you want to use to define the x-axis
"""
Geom.__init__(self, **kwargs)
self.x = x
self.label = label if label else x
self.params = [x]
self._id = 'xaxis'
self.name = 'xaxis'
self._build_css()
self._build_js()
def __init__(self,y, label=None, **kwargs):
"""
y : string
name of the column you want to use to define the y-axis
"""
Geom.__init__(self, **kwargs)
self.y = y
self.label = label if label else y
self.params = [y]
self._id = 'yaxis'
self.name = 'yaxis'
self._build_css()
self._build_js()
def __init__(self,x,y,**kwargs):
"""
This is a vertical bar chart - the height of each bar represents the
magnitude of each class
x : string
name of the column that contains the class labels
y : string
name of the column that contains the magnitude of each class
"""
Geom.__init__(self,**kwargs)
self.x = x
self.y = y
self.name = "bar"
self._id = 'bar_%s_%s'%(self.x,self.y)
self.build_js()
self.build_css()
self.params = [x,y]
self.styles = dict([(k[0].replace('_','-'), k[1]) for k in kwargs.items()])
def __init__(self, x, y, **kwargs):
"""
This is a vertical bar chart - the height of each bar represents the
magnitude of each class
x : string
name of the column that contains the class labels
y : string
name of the column that contains the magnitude of each class
"""
Geom.__init__(self, **kwargs)
self.x = x
self.y = y
self.name = "bar"
self._id = 'bar_%s_%s' % (self.x, self.y)
self.build_js()
self.build_css()
self.params = [x, y]
self.styles = dict([(k[0].replace('_', '-'), k[1])
for k in kwargs.items()])
def parse_stream(streamfile):
append = 0
crystal = 0
count_shots = 0
count_crystals = 0
frame_stream = []
frames = []
head_check = 0
header = ''
geom = Geom()
stream = open(streamfile)
all_reflections = []
REFLECTIONS = 0
PEAKS = 0
GEOM_FLAG = 0
geom = ''
filenames = []
indexed = []
for index, line in enumerate(stream):
### GEt header
while (head_check == 0):
header += line
if '----- Begin geometry file -----' in line: GEOM_FLAG = 1
if GEOM_FLAG: geom += line
#if GEOM_FLAG:
# if line.startswith('clen'):
# #print line.split('=')
# geom.distance = float(line.split('=')[1].split(';')[0].strip())
# if 'corner_x' in line:
# geom.bx = -1 * float(line.split('=')[1].split(';')[0].strip())
# if 'corner_y' in line:
# geom.by = -1 * float(line.split('=')[1].split(';')[0].strip())
# if 'res' in line:
# geom.ps = 1 / float(line.split('=')[1].split(';')[0].strip())
# if 'photon_energy' in line:
# geom.energy = float(line.split('=')[1].split(';')[0].strip())
# geom.wl = 12398.425 / geom.energy
# if 'max_fs' in line:
# geom.max_fs = float(line.split('=')[1].split(';')[0].strip())
# if 'max_ss' in line:
# geom.max_ss = float(line.split('=')[1].split(';')[0].strip())
if '----- End geometry file -----' in line: GEOM_FLAG = 0
break
### Get beginning of an image
if 'Begin chunk' in line:
count_shots += 1
append = 1
head_check = 1
# frame_stream.append(l)
### If
elif 'Image filename' in line:
frame = Frame()
frame.filename = line.split()[2].strip()
filenames.append(frame.filename)
# The division by 10 is to convert from nm-1 to Angstrom-1
elif 'indexed_by' in line:
if 'none' not in line:
count_crystals += 1
crystal = 1
frame.indexing = line.split()[2].strip()
indexed.append(frame.filename)
else:
frame.indexing = 'none'
#SACLA specific - not needed
# try:
# f = os.path.split(filename)[1]
# tag = os.path.splitext(f)[0].split('tag_')[1]
# frame.timeline = tag
#except:
# pass
elif 'diffraction_resolution_limit' in line:
res = float(line.split()[5])
frame.res = res
elif 'Cell parameters' in line:
a0, b0, c0 = line.split()[2:5]
frame.a = float(a0)
frame.b = float(b0)
frame.c = float(c0)
elif 'astar' in line:
x, y, z = line.split()[2:5]
frame.astar[0] = float(x) / 10
frame.astar[1] = float(y) / 10
frame.astar[2] = float(z) / 10
elif 'bstar' in line:
x, y, z = line.split()[2:5]
frame.bstar[0] = float(x) / 10
frame.bstar[1] = float(y) / 10
frame.bstar[2] = float(z) / 10
elif 'cstar' in line:
x, y, z = line.split()[2:5]
frame.cstar[0] = float(x) / 10
frame.cstar[1] = float(y) / 10
frame.cstar[2] = float(z) / 10
elif 'End of reflections' in line:
REFLECTIONS = 0
elif 'End of peak list' in line:
PEAKS = 0
elif "End chunk" in line:
if crystal == 1:
#frame_stream.append(line)
#frame.all = frame_stream
frames.append(frame)
append = 0
frame_stream = []
crystal = 0
if REFLECTIONS:
h, k, l, I, SIG, P, BKG, X, Y = line.split()[0:9]
# bkg, x, y = line.split()[6:9]
# SNR = float(line.split()[3]) / float(line.split()[4])
frame.reflections.append([
int(h),
int(k),
int(l),
float(I),
float(SIG),
float(BKG),
float(X),
float(Y)
]) # geom.get_resolution(float(x), float(y)) ])
#frame.hkl_stream.append(line)
#if append == 1: frame_stream.append(line)
if PEAKS:
X, Y, RES, I, panel = line.split()
frame.peaks.append(
[float(X),
float(Y),
float(RES),
float(I),
str(panel)])
if ' h k l I sigma(I)' in line:
REFLECTIONS = 1
#append = 0
if ' fs/px ss/px (1/d)/nm^-1 Intensity' in line:
PEAKS = 1
#if count_shots % 1000 == 0: print '%7i frames parsed, %7i crystals found\r' % (count_shots, count_crystals),
sys.stdout.flush()
#print '%7i frames parsed, %7i crystals found\r' % (count_shots, count_crystals),
#sys.stdout.flush()
#print
return header, frames, geom, all_reflections
def parse_stream(self):
crystal = 0
count_shots = 0
count_crystals = 0
self.frames = []
self.header = ''
geom = Geom()
stream = open(self.streamfile)
all_reflections = []
head_check = 0
REFLECTIONS = 0
PEAKS = 0
GEOM_FLAG = 0
self.geom = ''
self.filenames = []
self.indexed = []
emit = 0
for index, line in enumerate(stream):
prt = 0
### GEt header
while (head_check == 0):
self.header += line
if '----- Begin geometry file -----' in line: GEOM_FLAG = 1
if GEOM_FLAG: self.geom += line
# if GEOM_FLAG:
# if line.startswith('clen'):
# #print line.split('=')
# geom.distance = float(line.split('=')[1].split(';')[0].strip())
# if 'corner_x' in line:
# geom.bx = -1 * float(line.split('=')[1].split(';')[0].strip())
# if 'corner_y' in line:
# geom.by = -1 * float(line.split('=')[1].split(';')[0].strip())
# if 'res' in line:
# geom.ps = 1 / float(line.split('=')[1].split(';')[0].strip())
# if 'photon_energy' in line:
# geom.energy = float(line.split('=')[1].split(';')[0].strip())
# geom.wl = 12398.425 / geom.energy
# if 'max_fs' in line:
# geom.max_fs = float(line.split('=')[1].split(';')[0].strip())
# if 'max_ss' in line:
# geom.max_ss = float(line.split('=')[1].split(';')[0].strip())
if '----- End geometry file -----' in line:
GEOM_FLAG = 0
self.sendGEOM.emit(self.geom)
break
### Get beginning of an image
if 'Begin chunk' in line:
count_shots += 1
append = 1
head_check = 1
# frame_stream.append(l)
### If
elif 'Image filename' in line:
frame = Frame()
frame.filename = line.split()[2].strip()
self.filenames.append(frame.filename)
# The division by 10 is to convert from nm-1 to Angstrom-1
elif 'indexed_by' in line:
if 'none' not in line:
count_crystals += 1
crystal = 1
frame.indexing = line.split()[2].strip()
self.indexed.append(frame.filename)
else:
frame.indexing = 'none'
elif 'diffraction_resolution_limit' in line:
res = float(line.split()[5])
frame.res = res
elif 'Cell parameters' in line:
a0, b0, c0 = line.split()[2:5]
frame.a = float(a0)
frame.b = float(b0)
frame.c = float(c0)
elif 'astar' in line:
x, y, z = line.split()[2:5]
frame.astar[0] = float(x) / 10
frame.astar[1] = float(y) / 10
frame.astar[2] = float(z) / 10
elif 'bstar' in line:
x, y, z = line.split()[2:5]
frame.bstar[0] = float(x) / 10
frame.bstar[1] = float(y) / 10
frame.bstar[2] = float(z) / 10
elif 'cstar' in line:
x, y, z = line.split()[2:5]
frame.cstar[0] = float(x) / 10
frame.cstar[1] = float(y) / 10
frame.cstar[2] = float(z) / 10
elif 'End of reflections' in line:
REFLECTIONS = 0
elif 'End of peak list' in line:
PEAKS = 0
elif "End chunk" in line:
prt = 1
if crystal == 1:
# frame_stream.append(line)
# frame.all = frame_stream
self.frames.append(frame)
crystal = 0
if REFLECTIONS:
h, k, l, I, SIG, P, BKG, X, Y, panel = line.split()[0:10]
frame.reflections.append([
int(h),
int(k),
int(l),
float(I),
float(SIG),
float(BKG),
float(X),
float(Y),
str(panel)
]) # geom.get_resolution(float(x), float(y)) ])
# frame.hkl_stream.append(line)
# if append == 1: frame_stream.append(line)
if PEAKS:
X, Y, RES, I, panel = line.split()
frame.peaks.append(
[float(X),
float(Y),
float(RES),
float(I),
str(panel)])
if ' h k l I sigma(I)' in line:
REFLECTIONS = 1
# append = 0
if ' fs/px ss/px (1/d)/nm^-1 Intensity' in line:
PEAKS = 1
if count_shots % 500 == 0 and count_shots > 500 and prt == 1:
prt = 0
print('%7i frames parsed, %7i crystals found' %
(count_shots, count_crystals))
if emit == 0:
self.update.emit([self.filenames, self.indexed])
emit += 1
if emit % 4 == 0:
self.info.emit((count_shots, count_crystals))
sys.stdout.flush()
print('%7i frames parsed, %7i crystals found\r' %
(count_shots, count_crystals))
#sys.stdout.flush()
self.info.emit((count_shots, count_crystals))
self.moveToThread(self.mainThread)
self.finished.emit()
self.update.emit([self.filenames, self.indexed])
def __init__(self, streamfile, mainThread=None):
super(CrystFELStreamLight, self).__init__()
self.streamfile = streamfile
self.mainThread = mainThread
self.geometry = Geom()
def grad_Y(self, u, Y):
NYs = self.iYobs.size
NY = Y.size
cols = self.iYobs
rows = np.arange(NYs)
vals = np.full(NYs, 1.0)
Hy = sps.coo_matrix((vals, (rows, cols)), shape=(NYs, NY))
return sps.vstack([-Hy, np.sqrt(self.gamma) * self.L])
if __name__ == '__main__':
L = np.array([1.0, 1.0])
N = np.array([32, 32])
g = Geom(L, N)
g.calculate()
ul = 2.0
ur = 1.0
bc = BC(g)
bc.dirichlet(g, "left", ul)
bc.dirichlet(g, "right", ur)
# Hydraulic conductivity
npr.seed(0)
se = SEKernel(std_dev=1.0, cor_len=0.15, std_dev_noise=0.0)
CY = se.covar(g.cells.centroids.T, g.cells.centroids.T)
Nc = np.prod(N)
Y = se.sample(CY, npr.randn(Nc))
K = np.exp(Y)