def getParamCovMat(prefix,dlogpower = 2, theoconstmult = 1.,dlogfilenames = ['dlogpnldloga.dat'],volume=256.**3,startki = 0, endki = 0, veff = [0.]):
"""
Calculates parameter covariance matrix from the power spectrum covariance matrix and derivative term
in the prefix directory
"""
nparams = len(dlogfilenames)
kpnl = M.load(prefix+'pnl.dat')
k = kpnl[startki:,0]
nk = len(k)
if (endki == 0):
endki = nk
pnl = M.array(kpnl[startki:,1],M.Float64)
covarwhole = M.load(prefix+'covar.dat')
covar = covarwhole[startki:,startki:]
if len(veff) > 1:
sqrt_veff = M.sqrt(veff[startki:])
else:
sqrt_veff = M.sqrt(volume*M.ones(nk))
dlogs = M.reshape(M.ones(nparams*nk,M.Float64),(nparams,nk))
paramFishMat = M.reshape(M.zeros(nparams*nparams*(endki-startki),M.Float64),(nparams,nparams,endki-startki))
paramCovMat = paramFishMat * 0.
# Covariance matrices of dlog's
for param in range(nparams):
if len(dlogfilenames[param]) > 0:
dlogs[param,:] = M.load(prefix+dlogfilenames[param])[startki:,1]
normcovar = M.zeros(M.shape(covar),M.Float64)
for i in range(nk):
normcovar[i,:] = covar[i,:]/(pnl*pnl[i])
M.save(prefix+'normcovar.dat',normcovar)
f = k[1]/k[0]
if (volume == -1.):
volume = (M.pi/k[0])**3
#theoconst = volume * k[1]**3 * f**(-1.5)/(12.*M.pi**2) #1 not 0 since we're starting at 1
for ki in range(1,endki-startki):
for p1 in range(nparams):
for p2 in range(nparams):
paramFishMat[p1,p2,ki] = M.sum(M.sum(\
M.inverse(normcovar[:ki+1,:ki+1]) *
M.outerproduct(dlogs[p1,:ki+1]*sqrt_veff[:ki+1],\
dlogs[p2,:ki+1]*sqrt_veff[:ki+1])))
paramCovMat[:,:,ki] = M.inverse(paramFishMat[:,:,ki])
return k[1:],paramCovMat[:,:,1:]
def ListColorMaps(self):
"""Utility function to display matplotlib color maps as an image"""
p.rc('text', usetex=False)
a=p.outerproduct(numpy.arange(0,1,0.01),numpy.ones(10))
p.figure(figsize=(10,5))
p.subplots_adjust(top=0.8,bottom=0.05,left=0.01,right=0.99)
maps=[m for m in p.cm.datad.keys() if not m.endswith("_r")]
maps.sort()
l=len(maps)+1
i=1
for m in maps:
p.subplot(1,l,i)
p.axis("off")
p.imshow(a,aspect='auto',cmap=p.get_cmap(m),origin="lower")
p.title(m,rotation=90,fontsize=10)
i=i+1
#savefig("colormaps.png",dpi=100,facecolor='gray')
p.show()
def ListColorMaps(self):
"""Utility function to display matplotlib color maps as an image"""
p.rc('text', usetex=False)
a = p.outerproduct(numpy.arange(0, 1, 0.01), numpy.ones(10))
p.figure(figsize=(10, 5))
p.subplots_adjust(top=0.8, bottom=0.05, left=0.01, right=0.99)
maps = [m for m in p.cm.datad.keys() if not m.endswith("_r")]
maps.sort()
l = len(maps) + 1
i = 1
for m in maps:
p.subplot(1, l, i)
p.axis("off")
p.imshow(a, aspect='auto', cmap=p.get_cmap(m), origin="lower")
p.title(m, rotation=90, fontsize=10)
i = i + 1
#savefig("colormaps.png",dpi=100,facecolor='gray')
p.show()
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv is None:
argv = sys.argv
parser = E.OptionParser(
version="%prog version: $Id$",
usage=globals()["__doc__"])
parser.add_option(
"-c", "--components-tsv-file", dest="filename_components", type="string",
help="filename with component information.")
parser.add_option("-o", "--component", dest="component", type="string",
help="restrict output to component.")
parser.add_option("-s", "--filename-node-colours", dest="filename_node_colours", type="string",
help="filename with node colours.")
parser.add_option("-l", "--filename-node-labels", dest="filename_node_labels", type="string",
help="filename with node labels.")
parser.add_option("-w", "--weights-tsv-file", dest="weights", action="store_true",
help="use weights.")
parser.add_option("--edge-colour", dest="edge_colour", type="choice",
choices=("heat", "jet", ),
help="colour edges.")
parser.add_option("--format-node", dest="filename_node_format", type="string",
help="filename with node formats.")
parser.add_option("--format-edge", dest="filename_edge_format", type="string",
help="filename with edge formats.")
parser.add_option("--format-graph", dest="filename_graph_format", type="string",
help="filename with graph format.")
parser.add_option("--no-titles", dest="titles", action="store_false",
help="do not output titles.")
parser.add_option("--weight-range", dest="weight_range", type="string",
help="weight range. Comma separated values or 'auto'")
parser.add_option("--add-edge-labels", dest="add_edge_labels", action="store_true",
help="add edge labels to edges.")
parser.set_defaults(
min_weight=0.0,
max_weight=1.0,
num_colours=100,
min_colour=16,
filename_components=None,
component=None,
filename_subset=None,
colours=None,
filename_labels=None,
weights=False,
edge_colour=None,
default_edge_colour="18",
filename_format_graph=None,
filename_format_edge=None,
filename_format_node=None,
filename_format_bipartite=None,
titles=True,
edge_labels=True,
column_edge_weight=3,
column_edge_colour=3,
weight_range="auto",
add_edge_labels=False,
)
(options, args) = E.Start(parser)
options.column_edge_weight -= 1
options.column_edge_colour -= 1
components = None
# read components
if options.filename_components:
lines = open(options.filename_components, "r").readlines()
components = {}
for line in lines:
id, cid = string.split(line[:-1], "\t")
components[id] = cid
if options.filename_subset:
lines = open(options.filename_subset, "r").readlines()
subset = {}
for line in lines:
id = string.split(line[:-1], "\t")[0]
subset[id] = 1
colours = {}
if options.filename_node_colours:
infile = open(options.filename_node_colours, "r")
while 1:
line = infile.readline()
if not line:
break
if line[0] == "#":
continue
id, colour = string.split(line[:-1], "\t")[:2]
colours[id] = colour
infile.close()
labels = {}
if options.filename_labels:
infile = open(options.filename_labels, "r")
while 1:
line = infile.readline()
if not line:
break
if line[0] == "#":
continue
id, label = string.split(line[:-1], "\t")[:2]
if id in labels:
labels[id] += "," + label
else:
labels[id] = label
infile.close()
if options.weight_range == "auto":
lines = sys.stdin.readlines()
mi, ma = None, None
for line in lines:
if line[0] == "#":
continue
try:
v = float(line[:-1].split("\t")[2])
except ValueError:
continue
except IndexError:
continue
if mi is None:
mi = v
else:
mi = min(v, mi)
if ma is None:
ma = v
else:
ma = max(v, ma)
options.min_weight = mi
options.max_weight = ma
if options.loglevel >= 1:
options.stdlog.write("# using automatic weight range from %f to %f\n" % (
options.min_weight, options.max_weight))
else:
lines = sys.stdin
options.min_weight, options.max_weight = map(
float, options.weight_range.split(","))
options.stdout.write("graph: {\n")
if options.filename_format_graph:
options.stdout.write(
string.join(open(options.filename_format_graph, "r").readlines()))
else:
options.stdout.write(FORMAT_GRAPH)
if options.add_edge_labels:
options.stdout.write("display_edge_labels: yes\n")
left_nodes = {}
right_nodes = {}
touched = {} # remove repeats (several links between the same nids)
if options.edge_colour:
import matplotlib
import pylab
colour_map = pylab.get_cmap(options.edge_colour)
if options.edge_colour == "jet":
# for some reason I had problems with aisee colour indices > 128. Thus,
# I suggest staying below 128.
step_size = (options.max_weight - options.min_weight) / \
float(options.num_colours + 1)
increment = 1.0 / float(options.num_colours + 1)
v, vv = options.min_weight, 0.0
for x in range(options.min_colour, options.min_colour + options.num_colours + 1):
rgba = colour_map(vv)
r, g, b = map(lambda x: int(x * 255.0), rgba[:3])
options.stdout.write(" colorentry %i: %03i %03i %03i // weight = %f\n" %
(x, r, g, b, v))
v += step_size
vv += increment
colour_scale = options.num_colours / \
(options.max_weight - options.min_weight)
def calc_colour_index(x):
v = min(options.max_weight, float(x))
v = max(options.min_weight, v) - options.min_weight
v = min(options.num_colours - 1, int(v * colour_scale)) + \
options.min_colour
return str(v)
colour_conversion = calc_colour_index
# save legend
a = pylab.outerproduct(
pylab.arange(options.min_weight, options.max_weight, step_size), 1)
pylab.figure(figsize=(10, 5))
pylab.imshow(a, cmap=colour_map, origin="lower")
pylab.colorbar()
pylab.savefig("legend.png", dpi=100, facecolor='gray')
else:
raise "unknown colour scheme", options.colour_scheme
if options.filename_format_edge:
options.stdout.write(
string.join(open(options.filename_format_edge, "r").readlines()))
else:
options.stdout.write(FORMAT_EDGE)
first = True
for line in lines:
if line[0] == "#":
continue
if first:
first = False
if options.titles:
continue
try:
weight = 1.0
colour = options.default_edge_colour
x = string.split(line[:-1], "\t")
id1, id2 = x[:2]
if options.edge_colour:
colour = colour_conversion(x[options.column_edge_colour])
if options.edge_labels:
weight = x[options.column_edge_weight]
except ValueError:
continue
# patch for PFAM domains
# id1, id2 = map(string.atoi, string.split(line[:-1], "\t")[:2])
if id1 == id2:
continue
if options.filename_subset:
if id1 not in subset or id2 not in subset:
continue
if options.component is not None:
if id1 not in components:
continue
if id2 not in components:
continue
if components[id1] != options.component or components[id2] != options.component:
continue
if options.filename_format_bipartite:
left_nodes[id1] = 1
right_nodes[id2] = 1
else:
left_nodes[id1] = 1
left_nodes[id2] = 1
if id1 < id2:
key = "%s-%s" % (id1, id2)
else:
key = "%s-%s" % (id2, id1)
if key in touched:
continue
touched[key] = 1
edge_attributes = ['color: %s' % colour]
if options.add_edge_labels:
edge_attributes.append('label: "%s"' % weight)
options.stdout.write('\tedge: { thickness: 3 sourcename: "%s" targetname: "%s" %s}\n' % (
id1, id2, " ".join(edge_attributes)))
# sort nodes according to key
if options.filename_format_node:
options.stdout.write(
"".join(open(options.filename_format_node, "r").readlines()))
else:
options.stdout.write(FORMAT_NODE)
PrintNodes(left_nodes, labels, colours)
if options.filename_format_bipartite:
if options.format_bipartite == "default":
options.stdout.write(FORMAT_BIPARTITE)
else:
options.stdout.write(
"".join(open(options.filename_format_bipartite, "r").readlines()))
PrintNodes(right_nodes, labels, colours)
options.stdout.write("}\n")
E.Stop()
def main( argv = None ):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv == None: argv = sys.argv
#--------------------------------------------------------
# command line parsing options
parser = E.OptionParser( version = "%prog version: $Id: graph_links2gdl.py 2782 2009-09-10 11:40:29Z andreas $", usage = globals()["__doc__"])
parser.add_option("-c", "--filename-components", dest="filename_components", type="string",
help="filename with component information." )
parser.add_option("-o", "--component", dest="component", type="string",
help="restrict output to component." )
parser.add_option("-s", "--filename-node-colours", dest="filename_node_colours", type="string",
help="filename with node colours." )
parser.add_option("-l", "--filename-node-labels", dest="filename_node_labels", type="string",
help="filename with node labels." )
parser.add_option("-w", "--weights", dest="weights", action="store_true",
help="use weights." )
parser.add_option( "--edge-colour", dest="edge_colour", type="choice",
choices=("heat", "jet", ),
help="colour edges." )
parser.add_option( "--format-node", dest="filename_node_format", type="string",
help="filename with node formats." )
parser.add_option( "--format-edge", dest="filename_edge_format", type="string",
help="filename with edge formats." )
parser.add_option( "--format-graph", dest="filename_graph_format", type="string",
help="filename with graph format." )
parser.add_option( "--no-titles", dest="titles", action="store_false",
help="do not output titles." )
parser.add_option( "--weight-range", dest="weight_range", type="string",
help="weight range. Comma separated values or 'auto'")
parser.add_option( "--add-edge-labels", dest="add_edge_labels", action="store_true",
help="add edge labels to edges." )
parser.set_defaults(
min_weight = 0.0,
max_weight = 1.0,
num_colours = 100,
min_colour = 16,
filename_components = None,
component = None,
filename_subset = None,
colours = None,
filename_labels = None,
weights = False,
edge_colour = None,
default_edge_colour = "18",
filename_format_graph = None,
filename_format_edge = None,
filename_format_node = None,
filename_format_bipartite = None,
titles = True,
edge_labels = True,
column_edge_weight = 3,
column_edge_colour = 3,
weight_range = "auto",
add_edge_labels = False,
)
(options, args) = E.Start( parser )
options.column_edge_weight -= 1
options.column_edge_colour -= 1
components = None
## read components
if options.filename_components:
lines = open(options.filename_components,"r").readlines()
components = {}
for line in lines:
id, cid = string.split(line[:-1], "\t")
components[id] = cid
if options.filename_subset:
lines = open(options.filename_subset,"r").readlines()
subset= {}
for line in lines:
id = string.split(line[:-1], "\t")[0]
subset[id] = 1
colours = {}
if options.filename_node_colours:
infile = open(options.filename_node_colours, "r")
while 1:
line = infile.readline()
if not line: break
if line[0] == "#": continue
id, colour = string.split(line[:-1], "\t")[:2]
colours[id] = colour
infile.close()
labels = {}
if options.filename_labels:
infile = open(options.filename_labels, "r")
while 1:
line = infile.readline()
if not line: break
if line[0] == "#": continue
id, label = string.split(line[:-1], "\t")[:2]
if labels.has_key(id):
labels[id] += "," + label
else:
labels[id] = label
infile.close()
if options.weight_range == "auto":
lines = sys.stdin.readlines()
mi, ma = None, None
for line in lines:
if line[0] == "#": continue
try:
v = float(line[:-1].split("\t")[2])
except ValueError:
continue
except IndexError:
continue
if mi == None:
mi = v
else:
mi = min(v, mi)
if ma == None:
ma = v
else:
ma = max(v, ma)
options.min_weight = mi
options.max_weight = ma
if options.loglevel >= 1:
options.stdlog.write("# using automatic weight range from %f to %f\n" % (options.min_weight, options.max_weight) )
else:
lines = sys.stdin
options.min_weight, options.max_weight = map(float, options.weight_range.split(","))
options.stdout.write( "graph: {\n" )
if options.filename_format_graph:
options.stdout.write( string.join(open(options.filename_format_graph, "r").readlines() ) )
else:
options.stdout.write( FORMAT_GRAPH )
if options.add_edge_labels:
options.stdout.write( "display_edge_labels: yes\n" )
left_nodes = {}
right_nodes = {}
touched = {} # remove repeats (several links between the same nids)
if options.edge_colour :
import matplotlib
import pylab
colour_map = pylab.get_cmap( options.edge_colour )
if options.edge_colour == "jet":
# for some reason I had problems with aisee colour indices > 128. Thus,
# I suggest staying below 128.
step_size = (options.max_weight - options.min_weight) / float(options.num_colours+1)
increment = 1.0 / float(options.num_colours+1)
v, vv = options.min_weight, 0.0
for x in range( options.min_colour, options.min_colour + options.num_colours + 1):
rgba = colour_map( vv )
r, g, b = map( lambda x: int(x * 255.0), rgba[:3] )
options.stdout.write( " colorentry %i: %03i %03i %03i // weight = %f\n" %\
(x,r,g,b,v ) )
v += step_size
vv += increment
colour_scale = options.num_colours / (options.max_weight - options.min_weight )
def calc_colour_index( x ):
v = min( options.max_weight, float(x))
v = max( options.min_weight, v ) - options.min_weight
v = min( options.num_colours - 1, int( v * colour_scale )) + options.min_colour
return str( v )
colour_conversion = calc_colour_index
# save legend
a=pylab.outerproduct(pylab.arange(options.min_weight,options.max_weight,step_size),1)
pylab.figure(figsize=(10,5))
pylab.imshow(a,cmap=colour_map,origin="lower")
pylab.colorbar()
pylab.savefig("legend.png",dpi=100,facecolor='gray')
else:
raise "unknown colour scheme", options.colour_scheme
if options.filename_format_edge:
options.stdout.write( string.join(open(options.filename_format_edge, "r").readlines()) )
else:
options.stdout.write( FORMAT_EDGE )
first = True
for line in lines:
if line[0] == "#": continue
if first:
first = False
if options.titles: continue
try:
weight = 1.0
colour = options.default_edge_colour
x = string.split(line[:-1], "\t")
id1, id2 = x[:2]
if options.edge_colour:
colour = colour_conversion(x[options.column_edge_colour])
if options.edge_labels:
weight = x[options.column_edge_weight]
except ValueError:
continue
## patch for PFAM domains
## id1, id2 = map(string.atoi, string.split(line[:-1], "\t")[:2])
if id1 == id2: continue
if options.filename_subset:
if not subset.has_key(id1) or not subset.has_key(id2):
continue
if options.component != None:
if not components.has_key(id1):
continue
if not components.has_key(id2):
continue
if components[id1] != options.component or components[id2] != options.component:
continue
if options.filename_format_bipartite:
left_nodes[id1] = 1
right_nodes[id2] = 1
else:
left_nodes[id1] = 1
left_nodes[id2] = 1
if id1 < id2:
key = "%s-%s" % (id1,id2)
else:
key = "%s-%s" % (id2,id1)
if touched.has_key(key):
continue
touched[key] = 1
edge_attributes = [ 'color: %s' % colour ]
if options.add_edge_labels:
edge_attributes.append( 'label: "%s"' % weight )
options.stdout.write('\tedge: { thickness: 3 sourcename: "%s" targetname: "%s" %s}\n' % (id1, id2, " ".join(edge_attributes)) )
# sort nodes according to key
if options.filename_format_node:
options.stdout.write( "".join(open(options.filename_format_node, "r").readlines()))
else:
options.stdout.write( FORMAT_NODE )
PrintNodes( left_nodes, labels, colours)
if options.filename_format_bipartite:
if options.format_bipartite == "default":
options.stdout.write( FORMAT_BIPARTITE )
else:
options.stdout.write( "".join(open(options.filename_format_bipartite, "r").readlines()))
PrintNodes( right_nodes, labels, colours)
options.stdout.write ("}\n" )
E.Stop()
options.stdout.write( " colorentry %i: %03i %03i %03i // weight = %f\n" %\
(x,r,g,b,v ) )
v += step_size
vv += increment
colour_scale = options.num_colours / (options.max_weight - options.min_weight )
def calc_colour_index( x ):
v = min( options.max_weight, float(x))
v = max( options.min_weight, v ) - options.min_weight
v = min( options.num_colours - 1, int( v * colour_scale )) + options.min_colour
return str( v )
colour_conversion = calc_colour_index
# save legend
a=pylab.outerproduct(pylab.arange(options.min_weight,options.max_weight,step_size),1)
pylab.figure(figsize=(10,5))
pylab.imshow(a,cmap=colour_map,origin="lower")
pylab.colorbar()
pylab.savefig("legend.png",dpi=100,facecolor='gray')
else:
raise "unknown colour scheme", options.colour_scheme
if options.filename_format_edge:
options.stdout.write( string.join(open(options.filename_format_edge, "r").readlines()) )
else:
options.stdout.write( FORMAT_EDGE )
first = True
for line in lines:
