def get_h0_extrap(ref,d,hexp=1):
nomatch=get_numeric_nomatch_keys()
nomatch.append('ngrid')
d1 = get_matching(ref,d,nomatch)
h_min = []
max_eval=[]
for d2 in d1:
try:
h_min.append(min(d2.grid[1:]-d2.grid[0:-1])**hexp)
except:
h_min.append(1./(d2.data['ngrid']-1)**hexp)
max_eval.append(max(d2.evals.imag))
uh = list(sets.Set(h_min))
min_uh = min(uh)
uuh = []
for uh1 in uh:
if len(Numeric.nonzero(Numeric.absolute(Numeric.array(uuh)-uh1)<1e-8))==0:
uuh.append(uh1)
min_eval=[]
#print Numeric.sort(uuh)
for hm in uuh:
inds = Numeric.nonzero(Numeric.absolute(Numeric.array(h_min)-hm)<1e-8)
min_eval.append(min(Numeric.take(max_eval,inds)))
inds = Numeric.argsort(uuh)
h_min = list(Numeric.take(uuh,inds))
min_eval = list(Numeric.take(min_eval,inds))
if len(min_eval)>1:
m=(min_eval[1]-min_eval[0])/(h_min[1]-h_min[0])
else:
m=0
return min_eval[0]-m*h_min[0]
def renumberAtoms(self, indices): conf = self.configuration() for a in self.atomList(): a.index = indices[a.index] indices = Numeric.argsort(indices) conf.array[:] = Numeric.take(conf.array, indices) self._changed(1)
def draw(self, graphics):
"""Draws the graphics object |graphics|, which can be
a PolyLine3D or a VisualizationGraphics object."""
self.last_draw = (graphics, )
self.configure(cursor='watch')
self.update_idletasks()
graphics.project(self.axis, self.plane)
p1, p2 = graphics.boundingBoxPlane()
center = 0.5*(p1+p2)
scale = self.plotbox_size / (p2-p1)
sign = scale/Numeric.fabs(scale)
if self.scale is None:
minscale = Numeric.minimum.reduce(Numeric.fabs(scale))
self.scale = 0.9*minscale
scale = sign*self.scale
box_center = self.plotbox_origin + 0.5*self.plotbox_size
shift = -center*scale + box_center + self.translate
graphics.scaleAndShift(scale, shift)
items, depths = graphics.lines()
sort = Numeric.argsort(depths)
for index in sort:
x1, y1, x2, y2, color, width = items[index]
Line(self.canvas, x1, y1, x2, y2, fill=color, width=width)
self.configure(cursor='top_left_arrow')
self.update_idletasks()
def set_source( self, source, titledict=None, hidden=None ):
"""Set the data source
shapes - a GvShapes instance
titledict - dictionary of titles for properties (optional)
hidden - properties to hide
reset all the internal parameters
"""
self.clear()
#trap setting to None or an invalid shapes object
if source == None or source._o == None or len(source) == 0:
return
self.source = source
self.source_changed_id = self.source.connect( 'changed', self.source_changed_cb )
self.subset = []
schema = source.get_schema()
self.n_cols = len(schema)
self.n_rows = len(source)
# no shapes initially selected.
# Shapes are selected by source index.
self.selected_shapes=Numeric.zeros([len(source),1])
# Sorted position of shape- initially in order of location in source.
# Used to map nRow->source index and vice versa.
self.indices=Numeric.array(range(len(source)))+1
self.inv_indices=Numeric.argsort(self.indices)
self.sort_reverse=0
self.subindices=None
self.inv_subindices=None
self.sort_property=None
self.titledict={}
if titledict is None:
titledict={}
self._hidden_titles=[]
if hidden is not None:
for item in hidden:
self._hidden_titles.append(item)
for i in range(len(schema)):
title = schema[i][0]
if title not in self._hidden_titles:
if titledict.has_key(title):
self.titles.append(titledict[title])
self.titledict[titledict[title]]=title
else:
self.titles.append(title)
self.titledict[title]=title
#update the scrollbars
self.bCalcAdjustments = gtk.TRUE
self.expose()
def load_balancing(self):
"""Function balancing load between nodes"""
self.t1 = time.time()
w_numbers = self.pypar.gather(Numeric.array([len(self.w_block)]),
self.master_rank)
tmp_w_numbers = copy.deepcopy(w_numbers)
w_numbers = self.pypar.broadcast(tmp_w_numbers, self.master_rank)
self.no_of_walkers = Numeric.sum(w_numbers)
self.__find_opt_w_p_node()
#self.__set_w_p_node()
self.first_balance = False
balanced = Numeric.array(self.loc_walkers)
difference = w_numbers - balanced
diff_sort = Numeric.argsort(difference)
prev_i_min = diff_sort[0]
while sum(abs(difference)) != 0:
diff_sort = Numeric.argsort(difference)
i_max = diff_sort[-1]
i_min = diff_sort[0]
if i_min == prev_i_min and i_max != diff_sort[1]:
i_min = diff_sort[1]
if self.myrank == i_max:
self.pypar.send(self.w_block[balanced[i_max]:], i_min)
args = [
balanced[i_max], self.particles, self.dimensions,
self.w_block[0:balanced[i_max]]
]
self.w_block = WalkerArray.WalkerArray(*args)
elif self.myrank == i_min:
recv_buff = self.pypar.receive(i_max)
args = [
len(self.w_block) + difference[i_max], self.particles,
self.dimensions,
Numeric.concatenate((self.w_block[:], recv_buff))
]
self.w_block = WalkerArray.WalkerArray(*args)
difference[i_min] += difference[i_max]
difference[i_max] = 0
prev_i_min = i_min
def load_balancing(self):
"""Function balancing load between nodes"""
self.t1 = time.time()
w_numbers = self.pypar.gather(Numeric.array([len(self.w_block)]),
self.master_rank)
tmp_w_numbers = copy.deepcopy(w_numbers)
w_numbers = self.pypar.broadcast(tmp_w_numbers,self.master_rank)
self.no_of_walkers = Numeric.sum(w_numbers)
self.__find_opt_w_p_node()
#self.__set_w_p_node()
self.first_balance = False
balanced = Numeric.array(self.loc_walkers)
difference = w_numbers-balanced
diff_sort = Numeric.argsort(difference)
prev_i_min = diff_sort[0]
while sum(abs(difference))!=0:
diff_sort = Numeric.argsort(difference)
i_max = diff_sort[-1]
i_min = diff_sort[0]
if i_min == prev_i_min and i_max!=diff_sort[1]:
i_min = diff_sort[1]
if self.myrank==i_max:
self.pypar.send(self.w_block[balanced[i_max]:],i_min)
args = [balanced[i_max],
self.particles,
self.dimensions,
self.w_block[0:balanced[i_max]]]
self.w_block = WalkerArray.WalkerArray(*args)
elif self.myrank==i_min:
recv_buff = self.pypar.receive(i_max)
args = [len(self.w_block)+difference[i_max],
self.particles,
self.dimensions,
Numeric.concatenate((self.w_block[:],recv_buff))]
self.w_block = WalkerArray.WalkerArray(*args)
difference[i_min]+=difference[i_max]
difference[i_max]=0
prev_i_min = i_min
def testSort (self):
"Test sort, argsort, argmax, argmin, searchsorted"
s = (3,2,5,1,4,0)
sm = [s, Numeric.array(s)[::-1]]
se = Numeric.array(s)[0:0]
assert_eq(Numeric.sort(s), self.a)
assert len(Numeric.sort(se)) == 0
assert_eq(Numeric.argsort(s), [5,3,1,0,4,2])
assert len(Numeric.argsort(se)) == 0
assert_eq(Numeric.sort(sm, axis = -1), [[0,1,2,3,4,5],[0,1,2,3,4,5]])
assert_eq(Numeric.sort(sm, axis = 0), [[0,2,1,1,2,0],[3,4,5,5,4,3]])
assert_eq(Numeric.searchsorted(Numeric.arange(10), (5,2)), [5,2])
assert Numeric.argmax(s) == 2
assert Numeric.argmin(s) == 5
assert_eq(Numeric.argmax(sm, axis=-1), [2,3])
assert_eq(Numeric.argmax(sm, axis=1), [2,3])
assert_eq(Numeric.argmax(sm, axis=0), [0,1,0,1,0,1])
assert_eq(Numeric.argmin(sm, axis=-1), [5,0])
assert_eq(Numeric.argmin(sm, axis=1), [5,0])
def getnearestgen(self,ra1,dec1,ra2,dec2,j):#measure distances from ra1, dec1 to members in catalog ra2, dec2
sig5=N.zeros(len(ra1),'f')
sig10=N.zeros(len(ra1),'f')
for i in range(len(ra1)):
angdist=my.DA(c.z[j],h100)#kpc/arcsec
dspec=N.sqrt((ra1[i]-ra2)**2+(dec1[i]-dec2)**2)#sorted array of distances in degrees
dspecsort=N.take(dspec,N.argsort(dspec))
sig5[i]=5./(N.pi)/(dspecsort[5]*3600.*angdist/1000.)**2#convert from deg to arcsec, multiply by DA (kpc/arcsec), divide by 1000 to convert to Mpc, index 5 element b/c 0 is itself
sig10[i]=10./(N.pi)/(dspecsort[10]*3600.*angdist/1000.)**2#convert from deg to arcsec, multiply by DA (kpc/arcsec), divide by 1000 to convert to Mpc, index 5 element b/c 0 is itself
return sig5, sig10
def get_unstable_evals(self):
unst = []
inds = []
for i in range(len(self.evals)):
if abs(self.evals[i].imag) > 0:
inds.append(i)
unst.append(self.evals[i])
sort_inds = list(Numeric.argsort(Numeric.array(unst).imag))
sort_inds.reverse()
self.unst_inds = Numeric.take(inds,sort_inds)
self.unst = Numeric.take(unst,sort_inds)
return Numeric.array(self.unst)
def __init__(self, universe=None, temperature = 300):
if universe == None:
return
Features.checkFeatures(self, universe)
self.universe = universe
self.temperature = temperature
self.sqrt_mass = Numeric.sqrt(self.universe.masses().array)
self.sqrt_mass = self.sqrt_mass[:, Numeric.NewAxis]
self._forceConstantMatrix()
ev = self._diagonalize()
self.imaginary = Numeric.less(ev, 0.)
self.frequencies = Numeric.sqrt(Numeric.fabs(ev)) / (2.*Units.pi)
self.sort_index = Numeric.argsort(self.frequencies)
self._scale(temperature)
del self.sqrt_mass
def plot_Re_w_maxG(ref,var_key,var_key2,d=None,r0=.84,minn=1,maxn=3300,g=None,neg=None,tt=['a'],rind=0,uv2=None,notitle=False):
[g,matching,d]=plot_Re_w_varG(ref,var_key,var_key2,d=d,r0=r0,minn=minn,maxn=maxn,g=g,neg=neg,tt=tt,rind=rind,uv2=uv2,notitle=notitle,varG=-1)
g.ylabel('{/Symbol w}_{{/Symbol G}_{max}}')
nums = [matching[i].num for i in range(len(matching))]
print nums
inds = Numeric.argsort(nums)
for i in range(len(nums)):
if matching[inds[i]].data['Vz0']!=0:
uniq_num = nums[inds[i]]
break
if type(r0)==type([]):
fnb = 'plots/%d_var_%s_%s_Re_maxG_r0_multi'%(uniq_num,var_key,var_key2)
else:
fnb = 'plots/%d_var_%s_%s_Re_maxG_r0_%g'%(uniq_num,var_key,var_key2,r0)
print fnb
g('set key out')
g.hardcopy(fnb+'.eps',eps=True)
g.hardcopy(fnb+'.ps',size=(7,5),fontsize=24,eps=False)
g.refresh()
return [g,matching,d]
def plot_Re_w_varG(ref,var_key,var_key2,d=None,r0=.84,minn=1,maxn=3300,g=None,neg=None,tt=['a'],rind=0,uv2=None,notitle=False,varG=-1):
if d==None:
d = get_all_list(minn=minn,maxn=maxn)
if type(ref)!=type(1):
print 'ref must be of type int'
if type(var_key)!=type(''):
print 'var_key must be of type string'
if type(var_key2)!=type(''):
print 'var_key2 must be of type string'
if type(rind)!=type(1):
print 'rind must be of type int'
matching = get_matching(ref,d=d,nomatch_keys=get_numeric_nomatch_keys()+[var_key,var_key2])
if g==None:
g = Gnuplot.Gnuplot(persist=1)
g('set key left top Left reverse')
g.xlabel(var_key)
g.ylabel('{/Symbol w}_{min{/Symbol G}}')
xfac = 1
if var_key=='Vz0':
wA = abs(matching[0].get_wA())
xfac = 1./(wA/matching[0].data['k'])
g.xlabel('V_z(r=0)/v_A')
g.itemlist = []
for i in range(len(matching)):
if matching[i].data['num']==ref:
ref_ind = i
break
ttl = ''
for tt1 in tt:
ttl=ttl+'%s=%g, '%(tt1,matching[ref_ind].data[tt1])
ttl = ttl[:-2]
if notitle==False:
g.title(ttl)#'V_z(r=a)=%g'%matching[0].Vz([matching[0].data['a']]))
else:
g('unset title')
var_list = []
var2_list = []
min_eval = []
nums = []
matching2 = []
for i in range(len(matching)):
evals = matching[i].evals
if neg!=None:
inds = Numeric.nonzero(evals.real<1e-5)
evals = Numeric.take(evals,inds)
ind = Numeric.argsort(evals.imag)
if evals[ind[varG]].imag==0:
continue
min_eval.append(evals[ind[varG]].real)
var_list.append(matching[i].data[var_key])
var2_list.append(matching[i].data[var_key2])
nums.append(matching[i].num)
matching2.append(matching[i])
matching = matching2
if len(var2_list)==0:
return
if uv2==None:
uv2 = Numeric.sort(list(sets.Set(var2_list)))
else:
uv2 = Numeric.sort(uv2)
i = 1
for u2 in uv2:
inds = Numeric.nonzero(Numeric.array(var2_list)==u2)
if len(inds)<=1:
i = i+1
continue
v1 = Numeric.take(var_list,inds)*xfac
ev1 = Numeric.take(min_eval,inds)
d1 = matching[inds[rind]]
#print u2
#print v1,ev1
g.itemlist.append(Gnuplot.Data(v1,ev1,title='%s=%g'%(var_key2,d1.data[var_key2]),with='points %d'%i))
def permutation(n):
"permutation(n) = a permutation of indices range(n)"
return Numeric.argsort(random(n))
if '1P' in sys.argv:#One plot overlayed
g = Gnuplot.Gnuplot()
g.itemlist = []
for i in range(len(d)):
g.itemlist.append(d[i][1])
for i in range(len(g.itemlist)):
g.itemlist[i].set_option(with='lines',title=ylabels[i])
# g.refresh()
g('set key right bottom Left reverse')
g.xlabel('r')
g.ylabel('Arb. units')
g.hardcopy(fn,eps=True,fontsize=18,solid=False)
elif 'animate' in sys.argv:
g = Gnuplot.Gnuplot()
items = []
inds = list(Numeric.argsort(h_min))
inds.reverse()
for i in range(len(d)):
items.append(d[inds[i]][1])
items[i].set_option(with='lines',title=ylabels[inds[i]])
if i > 0:
items[i].set_option(with='lines ls 3')
g.itemlist = [items[i]]
if i>0:
g.itemlist.insert(0,items[0])
g('set key right bottom Left reverse')
g('set yrange [-50:50]')
g.hardcopy(fn[:-4]+'animate-%d'%i+'.eps',solid=True,size=(4,3),linewidth=3,dashlength=50,eps=True,fontsize=24)
else:
multiplot.multiplot(d,ylabels,fn)
#os.system('gv %s &'%fn)
def sort_one(self,snap,id):
atoms = snap.atoms
ids = atoms[:,id]
ordering = Numeric.argsort(ids)
for i in xrange(len(atoms[0])):
atoms[:,i] = Numeric.take(atoms[:,i],ordering)
#! /usr/pppl/python/2.3.5x/bin/python
import Numeric, Gnuplot, sys, sets
from get_EV import *
ref = int(sys.argv[1])
d = get_EV(ref,output_folder='output_vcyl')
len_branch = len(d.evals)/6-1
xs = 1.5
ys = 2.5*math.log(len_branch)
dy = ys/len_branch
dx = xs/3.
inds = list(Numeric.argsort(d.evals.real))
inds.reverse()
x = Numeric.arange(0,d.data['a'],1./(d.data['ngrid']*10))
#print inds
#print Numeric.take(d.evals.real,inds)
fns = ['fast', 'alfven', 'slow']
for i in range(3):
g = Gnuplot.Gnuplot()
g('set output "plots/%d_all_%s.eps"'%(ref,fns[i]))
g('set term postscript enhanced eps solid 8')
g('set size %g,%g'%(xs,ys))
g('set multiplot')
g('set size %g,%g'%(dx,dy))
if len_branch>50:
g('unset xtics')
#g('unset ytics')
#g('set yrange [0:1]')
g('set xrange [0:%g]'%d.data['a'])
for j in range(len_branch-1,-1,-1):
flog.write('%d\n'%nv)
totn = totn*nv
for i in range(nv):
val[j].append(raw_input('Enter value %d of %s. '%(i+1,var[j])))
flog.write('%s\n'%val[j][i])
print val
flog.close()
#sys.exit()
fin = start+totn-1
print fin
indlen = []
for j in range(len(var)):
indlen.append(len(val[j]))
print indlen
inds = list(Numeric.argsort(indlen))
print inds
var_sort = []
val_sort = []
indlen = list(Numeric.take(indlen,inds))
for ind in inds:
var_sort.append(var[ind])
val_sort.append(val[ind])
indlen
val = val_sort
var = var_sort
print var
print val
indarray = list(Numeric.indices(indlen))
for j in range(len(indarray)):
indarray[j] = Numeric.ravel(indarray[j])
def source_sort( self, sort_property=None,reverse=None ):
# Need to call expose event after sorting to display
# inv_indices/inv_subindices map (nRow-1)->source/subset
# index; indices/subindices map source/subset index->nRow
if ((self.source is None) or (len(self.source) < 1)):
return
# clear editing cell selections
self.current_row = 0
self.current_row_src = -1
if sort_property is None:
# default to last one if sort property not specified
sort_property=self.sort_property
if reverse is None:
reverse=self.sort_reverse
if (len(self.subset) == 0):
self.subindices=None
self.inv_subindices=None
if sort_property is None:
self.sort_property=sort_property
self.sort_reverse=reverse
if self.sort_reverse == 0:
self.inv_indices=Numeric.array(range(len(self.source)))
else:
self.inv_indices=Numeric.array(range(len(self.source)-1,-1,-1))
# Grid rows are from 1...N (titles are 0)
self.indices=Numeric.argsort(self.inv_indices)+1
return
else:
# If a subset is defined, the main set shouldn't be
# used at all in expose. Don't bother sorting it.
self.indices=None
self.inv_indices=None
if sort_property is None:
self.sort_property=sort_property
self.sort_reverse=reverse
if self.sort_reverse == 0:
self.inv_subindices=Numeric.array(range(len(self.subset)))
else:
self.inv_subindices=Numeric.array(range(len(self.subset)-1,-1,-1))
self.subindices=Numeric.argsort(self.inv_subindices)+1
return
# Check that requested sort property exists
have_prop=0
prop_type='string'
for cprop in self.source.get_schema():
if cprop[0] == sort_property:
have_prop=1
prop_type=cprop[1]
if have_prop == 1:
self.sort_property=sort_property
self.sort_reverse=reverse
if (len(self.subset) == 0):
ind_list=[]
count=0
if ((prop_type == 'float') or (prop_type == 'integer')):
for cshape in self.source:
# convert to float so sorting is numeric
ind_list.append((float(cshape.get_property(sort_property)),count))
count=count+1
else:
# sort as a string
for cshape in self.source:
ind_list.append((cshape.get_property(sort_property),count))
count=count+1
ind_list.sort()
if self.sort_reverse == 1:
ind_list.reverse()
self.inv_indices=Numeric.zeros((count,))
for c_ind in range(count):
self.inv_indices[c_ind]=ind_list[c_ind][1]
self.indices=Numeric.argsort(self.inv_indices)+1
else:
ind_list=[]
if ((prop_type == 'float') or (prop_type == 'integer')):
count = 0
for cindex in self.subset:
ind_list.append((float(self.source[cindex].get_property(sort_property)),count))
count=count+1
else:
count=0
for cindex in self.subset:
ind_list.append((self.source[cindex].get_property(sort_property),count))
count=count+1
ind_list.sort()
if self.sort_reverse == 1:
ind_list.reverse()
self.inv_subindices=Numeric.zeros((len(self.subset),))
for c_ind in range(len(self.subset)):
self.inv_subindices[c_ind]=ind_list[c_ind][1]
self.subindices=Numeric.argsort(self.inv_subindices)+1
else:
print 'Invalid sort property.'
for i in range(len(var2_list2)):
var2_list2[i] = float(var2_list2[i])
var2_list2.sort()
uniq_var2 = var2_list2
b_opt = []
opt_b_local = []
v_opt = []
for v2 in uniq_var2:
max_eval = []
var_list1 = []
for i in range(len(matching_files)):
if var2_list[i]==v2:
max_eval.append(max_imag[i])
var_list1.append(var_list[i])
ind = Numeric.argsort(max_eval)
inds = list(Numeric.argsort(var_list1))
inds.reverse()
for i in range(len(inds)-1):
if var_key=='nu':
if max_eval[inds[i]]*2>max_eval[inds[i+1]]:
continue
else:
h_min = 1./v2
b_opt.append((var_list1[inds[i]]*1./h_min**hexp))
v_opt.append((h_min))
break
else:
if max_eval[inds[i]]>max_eval[inds[i+1]]:
continue
else:
for uh1 in ux:
if len(Numeric.nonzero(Numeric.absolute(Numeric.array(uux)-uh1)<1e-8))==0:
uux.append(uh1)
for x1 in uux:
x2.append(x1)
inds = Numeric.nonzero(Numeric.absolute(Numeric.array(var_list)-x1)<1e-8)
z2.append(min(Numeric.take(ev_list,inds)))
inds = Numeric.nonzero(Numeric.array(ev_list)==z2[-1])
min_files.append(Numeric.take(matching_files,inds)[0])
y2a = Numeric.take(ev1_list,inds)
y2.append(y2a[0])
var_list = x2
ev_list = z2
ev1_list = y2
#print 1./Numeric.array(var_list)
inds = Numeric.argsort(var_list)
var_list = list(Numeric.take(var_list,inds))
ev_list = list(Numeric.take(ev_list,inds))
ev1_list = list(Numeric.take(ev1_list,inds))
min_files = list(Numeric.take(min_files,inds))
for i in range(len(x2)):
print var_list[i],':',min_files[i],' ',
print ''
#print var_list[0:2],ev_list[0:2]
tt = ''
for i in range(len(print_keys)):
if print_keys[i] != var_key:
tt = tt+'%s=%g, '%(print_keys[i],d1[print_keys[i]])
#g.title(tt[:-2])
#g1.title(tt[:-2])
g('set xrange [0:%g]'%(max(var_list)*1.1))
x[0] = x[1]/10000.0
y = Numeric.zeros(len(x),typecode=Numeric.Float)
ygrid = Numeric.zeros(len(xgrid),typecode=Numeric.Float)
dk = data
A = dk['a']**2
s2 = dk['s2']
evals = d.evals.real**2
if data['fe_type'] == 'linconst':
xgrid = xgrid+xgrid[1]/2.
for gamma_ind in range(6):#min(nphi,len(gamma)-1)):#nphi,2):
for i in range(len(x)):
y[i] = sf.bessel_J1(x[i]*gamma[gamma_ind])[0]
for i in range(len(xgrid)):
ygrid[i] = sf.bessel_J1(xgrid[i]*gamma[gamma_ind])[0]
omega1 = dk['Bz0']**2/(2*dk['rho0']*s2/(5./3.)*dk['Bz0']**2*A)*(A*dk['k']**2+gamma[gamma_ind]**2)*(1+s2)*(1-(1-4*s2*A*dk['k']**2/((1+s2)**2*(A*dk['k']**2+gamma[gamma_ind]**2)))**(1./2.))
min_ind = Numeric.argsort(Numeric.absolute(evals-omega1))[0]
print 'min_ind=',min_ind
error = evals[min_ind]-omega1
#EV =get_evec_3(data,3,min_ind)
EV = d.get_evec1('3',min_ind,x).real
fac =((EV[-2]+EV[-2])/2./ygrid[-2])
fac = EV[-1]/y[-1]
if data['fe_type'] == 'linconst':
fac = EV[0]/(ygrid[0]+ygrid[1])*4
g = Gnuplot.Gnuplot(persist=1)
#print 'x=',x,'y=',y,'EV=',EV,'fac=',fac
g.plot(Gnuplot.Data(x,y,with='lines',title='Exact'),Gnuplot.Data(x,EV/fac,title='Computed'),title='{/Symbol w}^2=%g; Analytic=%g'%(evals[min_ind],omega1))
#if gamma_ind < 10:
#g.hardcopy('plots/%s.evecz_slow_%d.eps'%(sys.argv[1],min_ind),eps=True)
sys.exit()
def source_sort(self, sort_property=None, reverse=None):
# Need to call expose event after sorting to display
# inv_indices/inv_subindices map (nRow-1)->source/subset
# index; indices/subindices map source/subset index->nRow
if ((self.source is None) or (len(self.source) < 1)):
return
# clear editing cell selections
self.current_row = 0
self.current_row_src = -1
if sort_property is None:
# default to last one if sort property not specified
sort_property = self.sort_property
if reverse is None:
reverse = self.sort_reverse
if (len(self.subset) == 0):
self.subindices = None
self.inv_subindices = None
if sort_property is None:
self.sort_property = sort_property
self.sort_reverse = reverse
if self.sort_reverse == 0:
self.inv_indices = Numeric.array(range(len(self.source)))
else:
self.inv_indices = Numeric.array(
range(len(self.source) - 1, -1, -1))
# Grid rows are from 1...N (titles are 0)
self.indices = Numeric.argsort(self.inv_indices) + 1
return
else:
# If a subset is defined, the main set shouldn't be
# used at all in expose. Don't bother sorting it.
self.indices = None
self.inv_indices = None
if sort_property is None:
self.sort_property = sort_property
self.sort_reverse = reverse
if self.sort_reverse == 0:
self.inv_subindices = Numeric.array(range(len(
self.subset)))
else:
self.inv_subindices = Numeric.array(
range(len(self.subset) - 1, -1, -1))
self.subindices = Numeric.argsort(self.inv_subindices) + 1
return
# Check that requested sort property exists
have_prop = 0
prop_type = 'string'
for cprop in self.source.get_schema():
if cprop[0] == sort_property:
have_prop = 1
prop_type = cprop[1]
if have_prop == 1:
self.sort_property = sort_property
self.sort_reverse = reverse
if (len(self.subset) == 0):
ind_list = []
count = 0
if ((prop_type == 'float') or (prop_type == 'integer')):
for cshape in self.source:
# convert to float so sorting is numeric
ind_list.append(
(float(cshape.get_property(sort_property)), count))
count = count + 1
else:
# sort as a string
for cshape in self.source:
ind_list.append(
(cshape.get_property(sort_property), count))
count = count + 1
ind_list.sort()
if self.sort_reverse == 1:
ind_list.reverse()
self.inv_indices = Numeric.zeros((count, ))
for c_ind in range(count):
self.inv_indices[c_ind] = ind_list[c_ind][1]
self.indices = Numeric.argsort(self.inv_indices) + 1
else:
ind_list = []
if ((prop_type == 'float') or (prop_type == 'integer')):
count = 0
for cindex in self.subset:
ind_list.append((float(
self.source[cindex].get_property(sort_property)),
count))
count = count + 1
else:
count = 0
for cindex in self.subset:
ind_list.append(
(self.source[cindex].get_property(sort_property),
count))
count = count + 1
ind_list.sort()
if self.sort_reverse == 1:
ind_list.reverse()
self.inv_subindices = Numeric.zeros((len(self.subset), ))
for c_ind in range(len(self.subset)):
self.inv_subindices[c_ind] = ind_list[c_ind][1]
self.subindices = Numeric.argsort(self.inv_subindices) + 1
else:
print 'Invalid sort property.'
def set_source(self, source, titledict=None, hidden=None):
"""Set the data source
shapes - a GvShapes instance
titledict - dictionary of titles for properties (optional)
hidden - properties to hide
reset all the internal parameters
"""
self.clear()
#trap setting to None or an invalid shapes object
if source == None or source._o == None or len(source) == 0:
return
self.source = source
self.source_changed_id = self.source.connect('changed',
self.source_changed_cb)
self.subset = []
schema = source.get_schema()
self.n_cols = len(schema)
self.n_rows = len(source)
# no shapes initially selected.
# Shapes are selected by source index.
self.selected_shapes = Numeric.zeros([len(source), 1])
# Sorted position of shape- initially in order of location in source.
# Used to map nRow->source index and vice versa.
self.indices = Numeric.array(range(len(source))) + 1
self.inv_indices = Numeric.argsort(self.indices)
self.sort_reverse = 0
self.subindices = None
self.inv_subindices = None
self.sort_property = None
self.titledict = {}
if titledict is None:
titledict = {}
self._hidden_titles = []
if hidden is not None:
for item in hidden:
self._hidden_titles.append(item)
for i in range(len(schema)):
title = schema[i][0]
if title not in self._hidden_titles:
if titledict.has_key(title):
self.titles.append(titledict[title])
self.titledict[titledict[title]] = title
else:
self.titles.append(title)
self.titledict[title] = title
#update the scrollbars
self.bCalcAdjustments = gtk.TRUE
self.expose()
def GetTree(
dbhandle,
nid,
lsequence,
table_name_links,
resolution,
min_length,
min_neighbours=None,
combine_repeats=None,
max_evalue=None,
residue_level=None,
parser=None,
):
## retrieve blast matrix
## make sure, add_self is 1, so that there are no empty columns
blast_matrix = NeighbourTools.BuildBLASTMatrix(
dbhandle,
nid,
resolution,
table_name_links,
combine_repeats,
max_evalue=max_evalue,
residue_level=residue_level,
parser=parser,
add_self=1,
)
if param_loglevel >= 3:
print "# ------> blast matrix for %i:" % (nid), blast_matrix.shape
sys.stdout.flush()
MatlabTools.WriteMatrix(blast_matrix, outfile=open("blast_%i.matrix" % nid, "w"))
nneighbours, lmatrix = blast_matrix.shape
if param_loglevel >= 2:
print "# rows in blast matrix for %i: " % (nid), nneighbours
sys.stdout.flush()
if nneighbours < min_neighbours:
return tree
## calculate dot product of the matrix
dot_matrix = Numeric.matrixmultiply(Numeric.transpose(blast_matrix), blast_matrix)
## perform some matrix magic
if param_multiply:
for x in range(0, param_multiply):
dot_matrix = Numeric.matrixmultiply(dot_matrix, dot_matrix)
if param_loglevel >= 3:
MatlabTools.WriteMatrix(dot_matrix, outfile=open("correlation_%i_%i.matrix" % (nid, x), "w"))
if param_matrix_loop_fill:
MatrixLoopFill(dot_matrix)
if param_matrix_add_local_bias:
MatrixAddLocalBias(dot_matrix)
if param_normalize:
MatrixNormalize(dot_matrix, Numeric.sum(blast_matrix))
if param_loglevel >= 3:
print "# correlation matrix for %i:" % (nid), dot_matrix.shape
MatlabTools.WriteMatrix(dot_matrix, outfile=open("correlation_%i.matrix" % nid, "w"))
## rearrange matrix if necessary
map_row_new2old = range(0, lmatrix)
if param_permute:
row_indices, col_indices = CorrespondenceAnalysis.GetIndices(dot_matrix)
if not row_indices:
print "# error for %i: correspondence analysis did not converge" % nid
else:
map_row_new2old = Numeric.argsort(row_indices)
dot_matrix = CorrespondenceAnalysis.GetPermutatedMatrix(dot_matrix, map_row_new2old, map_row_new2old)
if param_loglevel >= 3:
print "# permuted correlation matrix for %i:" % (nid), dot_matrix.shape
MatlabTools.WriteMatrix(dot_matrix, outfile=open("permuted_%i.matrix" % nid, "w"))
full_range = dot_matrix.shape
xtree = SplitMatrix(
nid, dot_matrix, (0, lmatrix), 0, int(min_length / resolution), param_min_distance_border, map_row_new2old
)
if param_loglevel >= 3:
print "# xtree=", xtree
sys.stdout.flush()
tree = [(0, 0, 0, [(1, lsequence)])]
ConvertTreeToList(tree, 0, xtree, lsequence)
if param_loglevel >= 3:
print "# tree="
for t in tree:
print "#", string.join(map(str, t), "\t")
return tree
g.ylabel('{/Symbol G t}_w')
for v2 in uv2:
inds = Numeric.nonzero(Numeric.array(var_list2)==v2)
evi = []
evn = []
v1list = []
for v1 in uv1:
try:
ind = list(Numeric.take(var_list1,inds)).index(v1)
except:
continue
evi.append(get_h0_extrap(Numeric.take(match_num,inds)[ind],matching_files,hexp=hexp))
ind = b.index(v1)
evn.append(evi[-1]/ev[ind])
v1list.append(v1)
inds = Numeric.argsort(v1list)
v1list = Numeric.take(v1list,inds)
evi = Numeric.take(evi,inds)*tw
evn = Numeric.take(evn,inds)*tw
if 'norm' in sys.argv:
evi = evn
if 'ASH' in sys.argv: #This is the arcsinh scaling
for j in range(len(evi)):
evi[j] = cmath.asinh(sfi*evi[j]).real
if len(v1list)>0:
ttl1 = '%s=%g'%(var_key2,v2)
if var_key2=='tw':
ttl = '{/Symbol t}_w'
if v2==-1:
ttl1 = "%s={/Symbol \245}"%(ttl)
elif v2==0:
import ranlib
print ">>> Symmetry number: %d\n" % sym
cell = map(float, cell.split())
refl_file = opReadCl(refl_file_name)
hkletc = read_xds_hkl(refl_file, ncol)
nrefl = hkletc.shape[0]
print ">>> Total number of reflections: ", nrefl
S = calc_reso(hkletc[:, :3], cell)
# Add a resolution column in the table
S.shape = (nrefl, 1)
hkletc = Numeric.concatenate((hkletc[:, :5], S), 1)
# Sort the table by order of the last column= resolution
hkletc = Numeric.take(hkletc, Numeric.argsort(hkletc[:, -1]))
if not highest_res:
highest_res = hkletc[0, -1]
elif highest_res < hkletc[0, -1]:
highest_res = hkletc[0, -1]
reso_bins = res_bin(highest_res, nbin)
reso_bins.insert(0, 999.99)
s_bins = 1 / (2 * Numeric.array(reso_bins))
print "\n Resol.\n limit S N <I> <SIGMA> <I/SIGMA>\n"
for n in range(nbin):
lowr, highr = reso_bins[n], reso_bins[n + 1]
select = (lowr > hkletc[:, -1]) * (hkletc[:, -1] >= highr)
nselect = Numeric.sum(select)
Imean = Numeric.sum(hkletc[:, 3] * select) / nselect
maxx = EV.data['a']
if 'xr' in sys.argv:
ind = sys.argv.index('xr')
minx = max(0,float(sys.argv[ind+1]))
maxx = min(EV.data['a'],float(sys.argv[ind+2]))
x = Numeric.arange(minx,maxx,EV.data['a']/(EV.data['ngrid']*N_fac))
coords = ['1','2','3','r']
nc = len(coords)
ne = len(evec_nums)
xs = 1.
dx = xs/nc
ys = 1.
dy = ys/ne
g = Gnuplot.Gnuplot()
fn = 'plots/%s.evecs'%num
inds = Numeric.argsort(evec_nums)
for evec_num in Numeric.take(evec_nums,inds):
fn = fn+'_%d'%(evec_num)
fn = fn+'.eps'
print 'Output to %s'%fn
g('set output "%s"'%fn)
g('set term postscript eps enhanced dl 2 ')
g('set multiplot')
g('set size %g,%g'%(dx,dy))
g('set xtics ( 0, "" 0.5,"1" 1)')
g('set xrange [0:1]')
for j in range(ne):
evec_num = evec_nums[j]
for i in range(nc):
coord = coords[i]
if j==ne-1:
for line in infile:
if line.find('#') > -1:
continue
t=line.split()
if float(t[0]) < lmin:
continue
if float(t[0]) > lmax:
break
wavea.append(float(t[0]))#wavelength in um
fluxa.append(float(t[1]))
infile.close()
wavea=py.array(wavea,'f')
fluxa=py.array(fluxa,'f')
fluxa=N.take(fluxa,N.argsort(wavea))#sort y according to x rankings
wavea=N.take(wavea,N.argsort(wavea))
waveoh=[]
fluxoh=[]
infile=open('nearIR_skybg_2.dat','r')
for line in infile:
if line.find('#') > -1:
continue
t=line.split()
if float(t[0])/1000. < lmin:
continue
if float(t[0])/1000. > lmax:
break
def permutation(n):
"permutation(n) = a permutation of indices range(n)"
return Numeric.argsort(random(n))
print ">>> Symmetry number: %d\n" % sym
cell = map(float, cell.split())
refl_file = opReadCl(refl_file_name)
hkletc = read_xds_hkl(refl_file, ncol)
nrefl = hkletc.shape[0]
print ">>> Total number of reflections: ", nrefl
S = calc_reso(hkletc[:,:3], cell)
# Add a resolution column in the table
S.shape = (nrefl,1)
hkletc = Numeric.concatenate((hkletc[:,:5],S),1)
# Sort the table by order of the last column= resolution
hkletc = Numeric.take(hkletc, Numeric.argsort(hkletc[:,-1]))
if not highest_res:
highest_res = hkletc[0,-1]
elif highest_res < hkletc[0,-1]:
highest_res = hkletc[0,-1]
reso_bins = res_bin(highest_res,nbin)
reso_bins.insert(0, 999.99)
s_bins = 1/(2*Numeric.array(reso_bins))
print "\n Resol.\n limit S N <I> <SIGMA> <I/SIGMA>\n"
for n in range(nbin):
lowr, highr = reso_bins[n], reso_bins[n+1]
select = (lowr > hkletc[:,-1]) * (hkletc[:,-1] >= highr)
nselect = Numeric.sum(select)
Imean = Numeric.sum(hkletc[:,3]*select)/nselect
nfacy = 1
if 'tw-1' in sys.argv and var_key=='tw':
nfacy = d2.data['tw']
evals = d2.evals
if 'wr' in sys.argv: #This is for the range in Re(w)
ind = sys.argv.index('wr')
wr1 = float(sys.argv[ind+1])
wr2 = float(sys.argv[ind+2])
inds = Numeric.nonzero((evals.real>wr1)*(evals.real<wr2))
evals = Numeric.take(evals,inds)
maxunstable.append(max(evals.imag)*nfacy)
maxvarlist.append(var_list[i])
if len(maxvarlist)==0:
print 'Warning!!! The value of %s=%g is not valid'%(var_key2,v2)
continue
inds = Numeric.argsort(maxvarlist)
maxvarlist = Numeric.take(maxvarlist,inds)
maxunstable = Numeric.take(maxunstable,inds)
ttl1 = '%s=%g'%(ttl,v2)
if var_key2=='tw':
if v2==-1:
ttl1 = "%s={/Symbol \245}"%(ttl)
elif v2==0:
ttl1 = "%s=0"%(ttl)
else:
ttl1 = '%s=10^%d'%(ttl,int((cmath.log10(v2)).real))
elif var_key2=='Vz0':
if v2==0:
ttl1 = 'V_{z0}=0'
else:
wA = abs(d2.get_wA())
