def plot_greens(self, shear_normal='shear', greens_ary=None, fnum=0, do_sort=True, y_scale='log', x_scale='linear'):
'''
# default prams: (self, shear_normal='shear', greens_ary=None, fnum=0, do_sort=True, y_scale='log', x_scale='linear')
#
# note that this can memory-explode for large greens files. it might be better to use plot_green_hist with (cumulative=True) parameter
# and bins= or n_bins={something reasonable} .
'''
#
if greens_ary == None:
shear_normal = shear_normal_aliases(shear_normal)
if shear_normal=='greens_shear': g_data = self.get_shear()
if shear_normal=='greens_normal': g_data = self.get_normal()
#
sh_0 = g_data.shape
g_data.shape = (1, g_data.size)
#
plt.figure(fnum)
plt.ion()
plt.clf()
ax = plt.gca()
ax.set_xscale(x_scale)
ax.set_yscale(y_scale)
if not do_sort:
ax.plot(xrange(g_data.size), g_data[0], '.')
#plt.vlines(xrange(g_data.size), g_data[0], numpy.zeros(len(g_data[0])))
#
else:
# and a distribution:
# (but note, as stated above, for large arrays, this can be a problem; consider using plot_greens_hist() ).
#
#print "lens: ", len(X), " ", len(Y)
ax.plot([x+1 for x in xrange(len(g_data[0]))], sorted(g_data[0]), '.-')
#
del(g_data)
def main():
pylab.ion();
ind = [0,];
ldft = [0,];
lfft = [0,];
lpfft = [0,]
# plot a graph Dft vs Fft, lists just support size until 2**9
for i in range(1, 9, 1):
t_before = time.clock();
dsprocessing.dspDft(rand(2**i).tolist());
dt = time.clock() - t_before;
ldft.append(dt);
print ("dft ", 2**i, dt);
#pylab.plot([2**i,], [time.clock()-t_before,]);
t_before = time.clock();
dsprocessing.dspFft(rand(2**i).tolist());
dt = time.clock() - t_before;
print ("fft ", 2**i, dt);
lfft.append(dt);
#pylab.plot([2**i,], [time.clock()-t_before,]);
ind.append(2**i);
# python fft just to compare
t_before = time.clock();
pylab.fft(rand(2**i).tolist());
dt = time.clock() - t_before;
lpfft.append(dt);
pylab.plot(ind, ldft);
pylab.plot(ind, lfft);
pylab.plot(ind, lpfft);
pylab.show();
return [ind, ldft, lfft, lpfft];
def InitializePlot(self, goal_config):
self.fig = pl.figure()
lower_limits, upper_limits = self.boundary_limits
pl.xlim([lower_limits[0], upper_limits[0]])
pl.ylim([lower_limits[1], upper_limits[1]])
pl.plot(goal_config[0], goal_config[1], 'gx')
# Show all obstacles in environment
for b in self.robot.GetEnv().GetBodies():
if b.GetName() == self.robot.GetName():
continue
bb = b.ComputeAABB()
pl.plot([bb.pos()[0] - bb.extents()[0],
bb.pos()[0] + bb.extents()[0],
bb.pos()[0] + bb.extents()[0],
bb.pos()[0] - bb.extents()[0],
bb.pos()[0] - bb.extents()[0]],
[bb.pos()[1] - bb.extents()[1],
bb.pos()[1] - bb.extents()[1],
bb.pos()[1] + bb.extents()[1],
bb.pos()[1] + bb.extents()[1],
bb.pos()[1] - bb.extents()[1]], 'r')
pl.ion()
pl.show()
def hinton(W, maxWeight=None):
"""
Draws a Hinton diagram for visualizing a weight matrix.
Temporarily disables matplotlib interactive mode if it is on,
otherwise this takes forever.
"""
reenable = False
if P.isinteractive():
P.ioff()
P.clf()
height, width = W.shape
if not maxWeight:
maxWeight = 2**N.ceil(N.log(N.max(N.abs(W)))/N.log(2))
P.fill(N.array([0,width,width,0]),N.array([0,0,height,height]),'gray')
P.axis('off')
P.axis('equal')
for x in xrange(width):
for y in xrange(height):
_x = x+1
_y = y+1
w = W[y,x]
if w > 0:
_blob(_x - 0.5, height - _y + 0.5, min(1,w/maxWeight),'white')
elif w < 0:
_blob(_x - 0.5, height - _y + 0.5, min(1,-w/maxWeight),'black')
if reenable:
P.ion()
P.show()
def cmap_plot(cmdLine):
pylab.figure(figsize=[5,10])
a=outer(ones(10),arange(0,1,0.01))
subplots_adjust(top=0.99,bottom=0.00,left=0.01,right=0.8)
maps=[m for m in cm.datad if not m.endswith("_r")]
maps.sort()
l=len(maps)+1
for i, m in enumerate(maps):
print m
subplot(l,1,i+1)
pylab.setp(pylab.gca(),xticklabels=[],xticks=[],yticklabels=[],yticks=[])
imshow(a,aspect='auto',cmap=get_cmap(m),origin="lower")
pylab.text(100.85,0.5,m,fontsize=10)
# render plot
if cmdLine:
pylab.show(block=True)
else:
pylab.ion()
pylab.plot([])
pylab.ioff()
status = 1
return status
def show_results(path, S, costs, animated=0, target_speed=.1, save_output=None):
P.ion()
fig1 = P.figure(0); fig1.clear()
ax = fig1.add_subplot(1,1,1)
ax.axis('scaled')
ax.axis([-1,1,-1,1])
if path:
draw_path(ax, path)
if animated:
animate_car(ax, S, remove_car=True, sleep=animated, save_output=save_output)
else:
animate_car(ax, S, remove_car=False, sleep=0, save_output=save_output,
alphas=linspace(0.1,.5,len(S))**2)
if costs is not None:
# show summary statistics
fig2 = P.figure(1); fig2.clear()
ax2 = fig2.add_subplot(2,1,1)
ax3 = fig2.add_subplot(2,1,2)
ax2.plot(costs, label='state cost');
ax2.set_ylabel('Controller score')
ax3.plot([speed for _,_,_,speed,_ in S], label='actual')
ax3.plot([0, len(S)], [target_speed, target_speed], 'k--',
label='target')
ax3.legend(loc='best')
ax3.set_ylabel('speed')
def test_path(): "generate and draw a random path" path = genpath() P.ion() P.clf() draw_path(P.gca(), path) P.draw()
def makeimg(wav):
global callpath
global imgpath
fs, frames = wavfile.read(os.path.join(callpath, wav))
pylab.ion()
# generate specgram
pylab.figure(1)
# generate specgram
pylab.specgram(
frames,
NFFT=256,
Fs=22050,
detrend=pylab.detrend_none,
window=numpy.hamming(256),
noverlap=192,
cmap=pylab.get_cmap('Greys'))
x_width = len(frames)/fs
pylab.ylim([0,11025])
pylab.xlim([0,round(x_width,3)-0.006])
img_path = os.path.join(imgpath, wav.replace(".wav",".png"))
pylab.savefig(img_path)
return img_path
def __init__(self, window_size, easting_offset, northing_offset):
self.rad_to_deg = 180.0/pi
# Get parameters
self.plot_pose = plot_pose
self.plot_gnss = plot_gnss
self.plot_odometry = plot_odometry
self.plot_yaw = plot_yaw
self.trkpt_threshold = 0.1 # [m]
# Initialize map
self.offset_e = easting_offset
self.offset_n = northing_offset
self.window_size = window_size
self.map_title = map_title
self.odo = []
self.gnss = []
self.pose_pos = []
self.odo_yaw = []
self.gnss_yaw = []
self.ahrs_yaw = []
self.pose_yaw = []
self.wpt_mode = 0
self.wpt_destination = False
self.wpt_target = False
self.pose_image_save = True # save an image for time-lapse video generation
self.pose_image_count = 0
ion() # turn interaction mode on
def InitializePlot(self, goal_config): # default
self.fig = pl.figure()
pl.xlim([self.lower_limits[0], self.upper_limits[0]])
pl.ylim([self.lower_limits[1], self.upper_limits[1]])
pl.plot(goal_config[0], goal_config[1], "gx")
# Show all obstacles in environment
for b in self.robot.GetEnv().GetBodies():
if b.GetName() == self.robot.GetName():
continue
bb = b.ComputeAABB()
pl.plot(
[
bb.pos()[0] - bb.extents()[0],
bb.pos()[0] + bb.extents()[0],
bb.pos()[0] + bb.extents()[0],
bb.pos()[0] - bb.extents()[0],
bb.pos()[0] - bb.extents()[0],
],
[
bb.pos()[1] - bb.extents()[1],
bb.pos()[1] - bb.extents()[1],
bb.pos()[1] + bb.extents()[1],
bb.pos()[1] + bb.extents()[1],
bb.pos()[1] - bb.extents()[1],
],
"r",
)
pl.ion()
pl.show()
def __init__(self, ca, cmap=None):
"""
CAPlotter() constructor keeps a reference to the CA model, and
optionally a colormap to be used with plots.
Parameters
----------
ca : LandlabCellularAutomaton object
Reference to a CA model
cmap : Matplotlib colormap (optional)
Colormap to be used in plotting
"""
import matplotlib
# Set the colormap; default to matplotlib's "jet" colormap
if cmap is None:
self._cmap = matplotlib.cm.jet
else:
self._cmap = cmap
# Keep a reference to the CA model
self.ca = ca
# Initialize the plot and remember the grid type
plt.ion()
plt.figure(1)
if type(ca.grid) is landlab.grid.hex.HexModelGrid:
self.gridtype = 'hex'
else:
self.gridtype = 'rast'
def qqplotfromq(qnull,qemp):
'''
Given uniform quartile values, and emprirical ones, make a qq plot
'''
pl.ion()
pl.plot(qnull, qemp, '.',markersize = 2)
addqqplotinfo(qnull,qnull.flatten().shape[0])
def drawModel(self):
PL.ion() # bug fix by Alex Hill in 2013
if self.modelFigure == None or self.modelFigure.canvas.manager.window == None:
self.modelFigure = PL.figure()
self.modelDrawFunc()
self.modelFigure.canvas.manager.window.update()
PL.show() # bug fix by Hiroki Sayama in 2016
def bistability_analysis():
f2_range = linspace(0, 0.4, 41)
t = linspace(0, 50000, 1000)
ion()
ss_aBax_vals_up = []
ss_aBax_vals_down = []
for f2 in f2_range:
model.parameters['Bid_0'].value = f2 * 1e-1
bax_total = 2e-1
# Do "up" portion of hysteresis plot
model.parameters['aBax_0'].value = 0
model.parameters['cBax_0'].value = bax_total
x = odesolve(model, t)
figure('up')
plot(t, x['aBax_']/bax_total)
ss_aBax_vals_up.append(x['aBax_'][-1]/bax_total)
# Do "down" portion of hysteresis plot
model.parameters['aBax_0'].value = bax_total
model.parameters['cBax_0'].value = 0
x = odesolve(model, t)
figure('down')
plot(t, x['aBax_']/bax_total)
ss_aBax_vals_down.append(x['aBax_'][-1]/bax_total)
figure()
plot(f2_range, ss_aBax_vals_up, 'r')
plot(f2_range, ss_aBax_vals_down, 'g')
def qqplotp(pv,fileout = None, pnames=pnames(), rownames=rownames(),alphalevel = 0.05,legend=None,xlim=None,ylim=None,ycoord=10,plotsize="652x526",title=None,dohist=True):
'''
Read in p-values from filein and make a qqplot adn histogram.
If fileout is provided, saves the qqplot only at present.
Searches through p until one is found. '''
import pylab as pl
pl.ion()
fs=8
h1=qqplot(pv, fileout, alphalevel,legend,xlim,ylim,addlambda=True)
#lambda_gc=estimate_lambda(pv)
#pl.legend(["gc="+ '%1.3f' % lambda_gc],loc=2)
pl.title(title,fontsize=fs)
#wm=pl.get_current_fig_manager()
#e.g. "652x526+100+10
xcoord=100
#wm.window.wm_geometry(plotsize + "+" + str(xcoord) + "+" + str(ycoord))
if dohist:
h2=pvalhist(pv)
pl.title(title,fontsize=fs)
#wm=pl.get_current_fig_manager()
width_height=plotsize.split("x")
buffer=10
xcoord=int(xcoord + float(width_height[0])+buffer)
#wm.window.wm_geometry(plotsize + "+" + str(xcoord) + "+" + str(ycoord))
else: h2=None
return h1,h2
def hinton(W, maxWeight=None):
"""
Source: http://wiki.scipy.org/Cookbook/Matplotlib/HintonDiagrams
Draws a Hinton diagram for visualizing a weight matrix.
Temporarily disables matplotlib interactive mode if it is on,
otherwise this takes forever.
"""
reenable = False
if pl.isinteractive():
pl.ioff()
pl.clf()
height, width = W.shape
if not maxWeight:
maxWeight = 2**np.ceil(np.log(np.max(np.abs(W)))/np.log(2))
pl.fill(np.array([0,width,width,0]),np.array([0,0,height,height]),'gray')
pl.axis('off')
pl.axis('equal')
for x in xrange(width):
for y in xrange(height):
_x = x+1
_y = y+1
w = W[y,x]
if w > 0:
_blob(_x - 0.5, height - _y + 0.5, min(1,w/maxWeight),'white')
elif w < 0:
_blob(_x - 0.5, height - _y + 0.5, min(1,-w/maxWeight),'black')
if reenable:
pl.ion()
pl.show()
def plotDirections(aabb=(),mask=0,bins=20,numHist=True,noShow=False,sphSph=False):
"""Plot 3 histograms for distribution of interaction directions, in yz,xz and xy planes and
(optional but default) histogram of number of interactions per body. If sphSph only sphere-sphere interactions are considered for the 3 directions histograms.
:returns: If *noShow* is ``False``, displays the figure and returns nothing. If *noShow*, the figure object is returned without being displayed (works the same way as :yref:`yade.plot.plot`).
"""
import pylab,math
from yade import utils
for axis in [0,1,2]:
d=utils.interactionAnglesHistogram(axis,mask=mask,bins=bins,aabb=aabb,sphSph=sphSph)
fc=[0,0,0]; fc[axis]=1.
subp=pylab.subplot(220+axis+1,polar=True);
# 1.1 makes small gaps between values (but the column is a bit decentered)
pylab.bar(d[0],d[1],width=math.pi/(1.1*bins),fc=fc,alpha=.7,label=['yz','xz','xy'][axis])
#pylab.title(['yz','xz','xy'][axis]+' plane')
pylab.text(.5,.25,['yz','xz','xy'][axis],horizontalalignment='center',verticalalignment='center',transform=subp.transAxes,fontsize='xx-large')
if numHist:
pylab.subplot(224,polar=False)
nums,counts=utils.bodyNumInteractionsHistogram(aabb if len(aabb)>0 else utils.aabbExtrema())
avg=sum([nums[i]*counts[i] for i in range(len(nums))])/(1.*sum(counts))
pylab.bar(nums,counts,fc=[1,1,0],alpha=.7,align='center')
pylab.xlabel('Interactions per body (avg. %g)'%avg)
pylab.axvline(x=avg,linewidth=3,color='r')
pylab.ylabel('Body count')
if noShow: return pylab.gcf()
else:
pylab.ion()
pylab.show()
def plotSpectrum(spectrum,filename=""): pylab.ion() pylab.figure(0) pylab.clf() pylab.plot(spectrum) pylab.draw() pylab.savefig(filename)
def plotSpectrum6(spectrum1On,spectrum2On,spectrum3On,spectrum4On,spectrum1Off,spectrum2Off,spectrum3Off,spectrum4Off,thetaL,thetaR,filename=""):
pylab.ion()
pylab.figure(0)
pylab.clf()
pylab.grid()
pylab.subplot(321)
pylab.plot(spectrum1On,'r')
pylab.plot(spectrum1Off)
pylab.title('Channel1')
pylab.subplot(322)
pylab.title('Channel2')
pylab.plot(spectrum2On,'r')
pylab.plot(spectrum2Off)
pylab.subplot(323)
pylab.title('Channel3')
pylab.plot(spectrum3On,'r')
pylab.plot(spectrum3Off)
pylab.subplot(324)
pylab.title('Channel4')
pylab.plot(spectrum4On,'r')
pylab.plot(spectrum4Off)
pylab.subplot(325)
pylab.title('ThetaL')
pylab.plot(thetaL,'r')
pylab.subplot(326)
pylab.title('ThetaR')
pylab.plot(thetaR,'r')
pylab.draw()
pylab.savefig(filename)
def save_plot(self, filename):
plt.ion()
targarr = np.array(self.targvalue)
self.posi[0].set_xdata(self.wt_positions[:,0])
self.posi[0].set_ydata(self.wt_positions[:,1])
while len(self.plotel)>0:
self.plotel.pop(0).remove()
self.plotel = self.shape_plot.plot(np.array([self.wt_positions[[i,j],0] for i, j in self.elnet_layout.keys()]).T,
np.array([self.wt_positions[[i,j],1] for i, j in self.elnet_layout.keys()]).T, 'y-', linewidth=1)
for i in range(len(self.posb)):
self.posb[i][0].set_xdata(self.iterations)
self.posb[i][0].set_ydata(targarr[:,i])
self.legend.texts[i].set_text('%s = %8.2f'%(self.targname[i], targarr[-1,i]))
self.objf_plot.set_xlim([0, self.iterations[-1]])
self.objf_plot.set_ylim([0.5, 1.2])
if not self.title == '':
plt.title('%s = %8.2f'%(self.title, getattr(self, self.title)))
plt.draw()
#print self.iterations[-1] , ': ' + ', '.join(['%s=%6.2f'%(self.targname[i], targarr[-1,i]) for i in range(len(self.targname))])
with open(self.result_file+'.results','a') as f:
f.write( '%d:'%(self.inc) + ', '.join(['%s=%6.2f'%(self.targname[i], targarr[-1,i]) for i in range(len(self.targname))]) +
'\n')
#plt.show()
#plt.savefig(filename)
display(plt.gcf())
#plt.show()
clear_output(wait=True)
def image_loop(self, decay):
import pylab
fig = pylab.figure()
pylab.ion()
img = pylab.imshow(self.image, vmax=1, vmin=-1,
interpolation='none', cmap='binary')
if self.track_periods is not None:
colors = ([(0,0,1), (0,1,0), (1,0,0), (1,1,0), (1,0,1)] * 10)[:len(self.p_y)]
scatter = pylab.scatter(self.p_y, self.p_x, s=50, c=colors)
else:
scatter = None
while True:
#fig.clear()
#print self.track_periods
#pylab.plot(self.delta)
#pylab.hist(self.delta, 50, range=(0000, 15000))
img.set_data(self.image)
if scatter is not None:
scatter.set_offsets(np.array([self.p_y, self.p_x]).T)
c = [(r,g,b,min(self.track_certainty[i],1)) for i,(r,g,b) in enumerate(colors)]
scatter.set_color(c)
if display_mode == 'quick':
# this is much faster, but doesn't work on all systems
fig.canvas.draw()
fig.canvas.flush_events()
else:
# this works on all systems, but is kinda slow
pylab.pause(0.001)
self.image *= decay
def run():
colors = [
'b', 'g', 'r', 'c', 'm', 'y', 'k',
'b--', 'g--', 'r--', 'c--', 'm--', 'y--', 'k--',
'bo', 'go', 'ro', 'co', 'mo', 'yo', 'ko',
'b+', 'g+', 'r+', 'c+', 'm+', 'y+', 'k+',
'b*', 'g*', 'r*', 'c*', 'm*', 'y*', 'k*',
'b|', 'g|', 'r|', 'c|', 'm|', 'y|', 'k|',
]
plots = defaultdict(list)
heap_size = []
order = ['Heap change']
manager = pylab.get_current_fig_manager()
manager.resize(1400, 1350)
pylab.ion()
for entry in read_data():
heap_size.append(entry["after"]["size_bytes"])
pylab.subplot(2, 1, 1)
pylab.plot(heap_size, 'r', label='Heap size')
pylab.legend(["Heap size"], loc=2)
pylab.subplot(2, 1, 2)
plots["Heap change"].append(entry["change"]["size_bytes"])
for thing in entry["change"]["details"]:
if thing["what"] not in order:
order.append(thing["what"])
plots[thing["what"]].append(thing["size_bytes"])
for what, color in zip(order, colors):
pylab.plot(plots[what], color, label=what)
pylab.legend(order, loc=3)
pylab.draw()
def run(self):
plts = {}
graphs = {}
pos = 0
plt.ion()
plt.style.use('ggplot')
for name in sorted(self.names.values()):
p = plt.subplot(math.ceil(len(self.names) / 2), 2, pos+1)
p.set_ylim([0, 100])
p.set_title(self.machine_classes[name] + " " + name)
p.get_xaxis().set_visible(False)
X = range(0, NUM_ENTRIES, 1)
Y = NUM_ENTRIES * [0]
graphs[name] = p.plot(X, Y)[0]
plts[name] = p
pos += 1
plt.tight_layout()
while True:
for name, p in plts.items():
graphs[name].set_ydata(self.loads[name])
plt.draw()
plt.pause(0.05)
def sintest(self, AMP=0.5, FREQ=1, TIME=5, mode='velocity'):
# freq in hertz
# amp in radians
self.tstart = time.time()
t = time.time()-self.tstart
self.setpos(0)
pylab.ion()
print('**Running Sin Test**')
while t<TIME:
t = time.time()-self.tstart
ctrl = AMP*np.sin(FREQ*2.0*np.pi*t)
if mode == 'velocity':
self.setvel(ctrl)
output = self.getvel()
if mode == 'pos':
self.setpos(ctrl)
output = self.getpos()
pylab.plot([t],[output],color='blue', marker='*')
pylab.plot([t],[ctrl],color='red')
pylab.draw()
self.stop()
def __init__(self, net, task, valueNetwork=None, **args):
self.net = net
self.task = task
self.setArgs(**args)
if self.valueLearningRate == None:
self.valueLearningRate = self.learningRate
if self.valueMomentum == None:
self.valueMomentum = self.momentum
if self.supervisedPlotting:
from pylab import ion
ion()
# adaptive temperature:
self.tau = 1.
# prepare the datasets to be used
self.weightedDs = ImportanceDataSet(self.task.outdim, self.task.indim)
self.rawDs = ReinforcementDataSet(self.task.outdim, self.task.indim)
self.valueDs = SequentialDataSet(self.task.outdim, 1)
# prepare the supervised trainers
self.bp = BackpropTrainer(self.net, self.weightedDs, self.learningRate,
self.momentum, verbose=False,
batchlearning=True)
# CHECKME: outsource
self.vnet = valueNetwork
if valueNetwork != None:
self.vbp = BackpropTrainer(self.vnet, self.valueDs, self.valueLearningRate,
self.valueMomentum, verbose=self.verbose)
# keep information:
self.totalSteps = 0
self.totalEpisodes = 0
def plotInit(Plotting, Elements): if (Plotting == 2): loc = [i.xy for i in Elements] x = [i.real for i in loc] y = [i.imag for i in loc] x = list(sorted(set(x))) x.remove(-10) y = list(sorted(set(y))) X, Y = pylab.meshgrid(x, y) U = pylab.ones(shape(X)) V = pylab.ones(shape(Y)) pylab.ion() fig, ax = pylab.subplots(1,1) graph = ax.quiver(X, Y, U, V) pylab.draw() else: pylab.ion() graph, = pylab.plot(1, 'ro', markersize = 2) x = 2 pylab.axis([-x,x,x,-x]) graph.set_xdata(0) graph.set_ydata(0) pylab.draw() return graph
def histoCase( self ):
print "Building Histogram"
header = self.histoAxis.get()
if ( self.filterNum.get() == "None" ):
data = self.dataInstance.getNumericAxis( self.histoAxis.get() )
else:
labels = []
data = []
for set in self.main.histoCols:
labels.append( set[0] )
data.append( set[1] )
pylab.ion()
if ( self.filterNum.get() == "None" ):
pylab.hist( data, bins=self.bins.get(), label=header )
else:
pylab.hist( data, bins=self.bins.get(), label=labels )
pylab.legend()
pylab.xlabel( header )
pylab.ylabel("Frequency")
pylab.title("Histogram" )
pylab.show()
def animate_1D(time, var, x, ylab=' '):
"""Animate a 2d array with a sequence of 1d plots
Input: time = one-dimensional time vector;
var = array with first dimension = len(time) ;
x = (optional) vector width dimension equal to var.shape[1];
ylab = ylabel for plot
"""
import pylab
import numpy
pylab.close()
pylab.ion()
# Initial plot
vmin=var.min()
vmax=var.max()
line, = pylab.plot( (x.min(), x.max()), (vmin, vmax), 'o')
# Lots of plots
for i in range(len(time)):
line.set_xdata(x)
line.set_ydata(var[i,:])
pylab.draw()
pylab.xlabel('x')
pylab.ylabel(ylab)
pylab.title('time = ' + str(time[i]))
return
def __init__(self,file):
# Task parameters
self.running = True
# Class variables
self.origin = Vector(0,0)
self.position = Vector(0,0)
self.position_list = []
# init plot
self.fig = pyplot.figure(num=None, figsize=(8, 8), dpi=80, facecolor='w', edgecolor='k')
self.area = 2
ion()
# Init transform
self.tf = tf.TransformListener()
self.br = tf.TransformBroadcaster()
self.quaternion = np.empty((4, ), dtype=np.float64)
# Init node
self.rate = rospy.Rate(10)
# Init subscriber
self.imu_sub = rospy.Subscriber('/fmInformation/imu', Imu, self.onImu )
# Init stat
self.file = file
self.deviations = []
def saveHintonDiagram(W, directory):
maxWeight = None
#print "Weight: ", W
"""
Draws a Hinton diagram for visualizing a weight matrix.
Temporarily disables matplotlib interactive mode if it is on,
otherwise this takes forever.
"""
reenable = False
if pylab.isinteractive():
pylab.ioff()
pylab.clf()
height, width = W.shape
if not maxWeight:
maxWeight = 2**numpy.ceil(numpy.log(numpy.max(numpy.abs(W)))/numpy.log(2))
pylab.fill(numpy.array([0,width,width,0]),numpy.array([0,0,height,height]),'gray')
pylab.axis('off')
pylab.axis('equal')
for x in xrange(width):
for y in xrange(height):
_x = x+1
_y = y+1
w = W[y,x]
if w > 0:
_blob(_x - 0.5, height - _y + 0.5, min(1,w/maxWeight),'white')
elif w < 0:
_blob(_x - 0.5, height - _y + 0.5, min(1,-w/maxWeight),'black')
if reenable:
pylab.ion()
#pylab.show()
pylab.savefig(directory)
def evolve(nx, kappa, tau, tmax, dovis=0, returnInit=0):
"""
the main evolution loop. Evolve
phi_t = kappa phi_{xx} + (1/tau) R(phi)
from t = 0 to tmax
"""
# create the grid
gr = grid(nx, ng=1, xmin=0.0, xmax=100.0,
vars=["phi", "phi1", "phi2"])
# pointers to the data at various stages
phi = gr.data["phi"]
phi1 = gr.data["phi1"]
phi2 = gr.data["phi2"]
# initialize
gr.initialize(20, 1)
phiInit = phi.copy()
# runtime plotting
if dovis == 1:
pylab.ion()
t = 0.0
while (t < tmax):
dt = estDt(gr, kappa, tau)
if (t + dt > tmax):
dt = tmax - t
# react for dt/2
phi1[:] = react(gr, phi, tau, dt / 2)
gr.fillBC("phi1")
# diffuse for dt
phi2[:] = diffuse(gr, phi1, kappa, dt)
gr.fillBC("phi2")
# react for dt/2 -- this is the updated solution
phi[:] = react(gr, phi2, tau, dt / 2)
gr.fillBC("phi")
t += dt
if dovis == 1:
pylab.clf()
pylab.plot(gr.x, phi)
pylab.xlim(gr.xmin, gr.xmax)
pylab.ylim(0.0, 1.0)
pylab.draw()
print(t)
if returnInit == 1:
return phi, gr.x, phiInit
else:
return phi, gr.x
import numpy as np import pylab as py import pickle as pk import covariance_utils as cu import fisher.forecast.fisher_util as ut py.ion() theory_file = 'camb_spectra2/params_LCDM_planckbestfit_r_0.01_lensedtotCls.dat' tell, tTT, tEE, tBB, tTE = ut.read_spectra(theory_file, raw=False) nsims = 10 sim_runs = 1 #simlength = 100 simlength = len(tell) delta_bin = 50 fft_scale = 16 map_scale = 4. window_scale = 32. noise_scale = 0.00001 #ratio of signal_scale signal_scale = 1.0 order = 3 apply_window = True noise_off = False ################################################################################# x = np.arange(simlength + 1, dtype=float) / (simlength) * 10. * np.pi #Truncate input spectra to be in multiples of delta_bin extra = np.mod(len(tTT), delta_bin)
get_ipython().magic('load_ext autoreload')
get_ipython().magic('autoreload 2')
except NameError:
print('Not IPYTHON')
pass
import sys
import numpy as np
import psutil
import glob
import os
import scipy
from ipyparallel import Client
# mpl.use('Qt5Agg')
import pylab as pl
pl.ion()
#%%
import caiman as cm
from caiman.source_extraction.cnmf import cnmf as cnmf
from caiman.components_evaluation import evaluate_components
from caiman.utils.visualization import plot_contours, view_patches_bar
from caiman.base.rois import extract_binary_masks_blob
#%%
c, dview, n_processes = cm.cluster.setup_cluster(backend='local',
n_processes=None,
single_thread=False)
#%%
is_patches = True
is_dendrites = False #
# You should have received a copy of the GNU General Public License
# along with NEST. If not, see <http://www.gnu.org/licenses/>.
'''
NEST Topology Module Example
Create layer of 4x3 iaf_psc_alpha neurons, visualize
BCCN Tutorial @ CNS*09
Hans Ekkehard Plesser, UMB
'''
import nest
import pylab
import nest.topology as topo
pylab.ion()
nest.ResetKernel()
l1 = topo.CreateLayer({
'columns': 4,
'rows': 3,
'extent': [2.0, 1.5],
'elements': 'iaf_psc_alpha'
})
nest.PrintNetwork()
nest.PrintNetwork(2)
nest.PrintNetwork(2, l1)
topo.PlotLayer(l1, nodesize=50)
z = z * z + c
if (z.real * z.real + z.imag * z.imag) >= 4:
return i
return 255
@autojit
def create_fractal(min_x, max_x, min_y, max_y, image, iters):
height = image.shape[0]
width = image.shape[1]
pixel_size_x = (max_x - min_x) / width
pixel_size_y = (max_y - min_y) / height
for x in range(width):
real = min_x + x * pixel_size_x
for y in range(height):
imag = min_y + y * pixel_size_y
color = mandel(real, imag, iters)
image[y, x] = color
return image
image = np.zeros((1024, 1024), dtype=np.uint8)
#image = np.zeros((500, 750), dtype=np.uint8)
imshow(create_fractal(-2.0, 1.0, -1.0, 1.0, image, 20))
jet()
ion()
show()
def orthview(
map=None,
fig=None,
rot=None,
coord=None,
unit="",
xsize=800,
half_sky=False,
title="Orthographic view",
nest=False,
min=None,
max=None,
flip="astro",
remove_dip=False,
remove_mono=False,
gal_cut=0,
format="%g",
format2="%g",
cbar=True,
cmap=None,
notext=False,
norm=None,
hold=False,
margins=None,
sub=None,
return_projected_map=False,
):
"""Plot a healpix map (given as an array) in Orthographic projection.
Parameters
----------
map : float, array-like or None
An array containing the map.
If None, will display a blank map, useful for overplotting.
fig : int or None, optional
The figure number to use. Default: create a new figure
rot : scalar or sequence, optional
Describe the rotation to apply.
In the form (lon, lat, psi) (unit: degrees) : the point at
longitude *lon* and latitude *lat* will be at the center. An additional rotation
of angle *psi* around this direction is applied.
coord : sequence of character, optional
Either one of 'G', 'E' or 'C' to describe the coordinate
system of the map, or a sequence of 2 of these to rotate
the map from the first to the second coordinate system.
half_sky : bool, optional
Plot only one side of the sphere. Default: False
unit : str, optional
A text describing the unit of the data. Default: ''
xsize : int, optional
The size of the image. Default: 800
title : str, optional
The title of the plot. Default: 'Orthographic view'
nest : bool, optional
If True, ordering scheme is NESTED. Default: False (RING)
min : float, optional
The minimum range value
max : float, optional
The maximum range value
flip : {'astro', 'geo'}, optional
Defines the convention of projection : 'astro' (default, east towards left, west towards right)
or 'geo' (east towards roght, west towards left)
remove_dip : bool, optional
If :const:`True`, remove the dipole+monopole
remove_mono : bool, optional
If :const:`True`, remove the monopole
gal_cut : float, scalar, optional
Symmetric galactic cut for the dipole/monopole fit.
Removes points in latitude range [-gal_cut, +gal_cut]
format : str, optional
The format of the scale label. Default: '%g'
format2 : str, optional
Format of the pixel value under mouse. Default: '%g'
cbar : bool, optional
Display the colorbar. Default: True
notext : bool, optional
If True, no text is printed around the map
norm : {'hist', 'log', None}
Color normalization, hist= histogram equalized color mapping,
log= logarithmic color mapping, default: None (linear color mapping)
hold : bool, optional
If True, replace the current Axes by an OrthographicAxes.
use this if you want to have multiple maps on the same
figure. Default: False
sub : int, scalar or sequence, optional
Use only a zone of the current figure (same syntax as subplot).
Default: None
margins : None or sequence, optional
Either None, or a sequence (left,bottom,right,top)
giving the margins on left,bottom,right and top
of the axes. Values are relative to figure (0-1).
Default: None
return_projected_map : bool
if True returns the projected map in a 2d numpy array
See Also
--------
mollview, gnomview, cartview, azeqview
"""
# Create the figure
import pylab
if not (hold or sub):
f = pylab.figure(fig, figsize=(8.5, 5.4))
extent = (0.02, 0.05, 0.96, 0.9)
elif hold:
f = pylab.gcf()
left, bottom, right, top = np.array(f.gca().get_position()).ravel()
extent = (left, bottom, right - left, top - bottom)
f.delaxes(f.gca())
else: # using subplot syntax
f = pylab.gcf()
if hasattr(sub, "__len__"):
nrows, ncols, idx = sub
else:
nrows, ncols, idx = sub // 100, (sub % 100) // 10, (sub % 10)
if idx < 1 or idx > ncols * nrows:
raise ValueError("Wrong values for sub: %d, %d, %d" % (nrows, ncols, idx))
c, r = (idx - 1) % ncols, (idx - 1) // ncols
if not margins:
margins = (0.01, 0.0, 0.0, 0.02)
extent = (
c * 1. / ncols + margins[0],
1. - (r + 1) * 1. / nrows + margins[1],
1. / ncols - margins[2] - margins[0],
1. / nrows - margins[3] - margins[1],
)
extent = (
extent[0] + margins[0],
extent[1] + margins[1],
extent[2] - margins[2] - margins[0],
extent[3] - margins[3] - margins[1],
)
# extent = (c*1./ncols, 1.-(r+1)*1./nrows,1./ncols,1./nrows)
# f=pylab.figure(fig,figsize=(8.5,5.4))
# Starting to draw : turn interactive off
wasinteractive = pylab.isinteractive()
pylab.ioff()
try:
if map is None:
map = np.zeros(12) + np.inf
cbar = False
ax = PA.HpxOrthographicAxes(
f, extent, coord=coord, rot=rot, format=format2, flipconv=flip
)
f.add_axes(ax)
if remove_dip:
map = pixelfunc.remove_dipole(
map, gal_cut=gal_cut, nest=nest, copy=True, verbose=True
)
elif remove_mono:
map = pixelfunc.remove_monopole(
map, gal_cut=gal_cut, nest=nest, copy=True, verbose=True
)
img = ax.projmap(
map,
nest=nest,
xsize=xsize,
half_sky=half_sky,
coord=coord,
vmin=min,
vmax=max,
cmap=cmap,
norm=norm,
)
if cbar:
im = ax.get_images()[0]
b = im.norm.inverse(np.linspace(0, 1, im.cmap.N + 1))
v = np.linspace(im.norm.vmin, im.norm.vmax, im.cmap.N)
if matplotlib.__version__ >= "0.91.0":
cb = f.colorbar(
im,
ax=ax,
orientation="horizontal",
shrink=0.5,
aspect=25,
ticks=PA.BoundaryLocator(),
pad=0.05,
fraction=0.1,
boundaries=b,
values=v,
format=format,
)
else:
# for older matplotlib versions, no ax kwarg
cb = f.colorbar(
im,
orientation="horizontal",
shrink=0.5,
aspect=25,
ticks=PA.BoundaryLocator(),
pad=0.05,
fraction=0.1,
boundaries=b,
values=v,
format=format,
)
cb.solids.set_rasterized(True)
ax.set_title(title)
if not notext:
ax.text(
0.86,
0.05,
ax.proj.coordsysstr,
fontsize=14,
fontweight="bold",
transform=ax.transAxes,
)
if cbar:
cb.ax.text(
0.5,
-1.0,
unit,
fontsize=14,
transform=cb.ax.transAxes,
ha="center",
va="center",
)
f.sca(ax)
finally:
pylab.draw()
if wasinteractive:
pylab.ion()
# pylab.show()
if return_projected_map:
return img
def gnomview(
map=None,
fig=None,
rot=None,
coord=None,
unit="",
xsize=200,
ysize=None,
reso=1.5,
title="Gnomonic view",
nest=False,
remove_dip=False,
remove_mono=False,
gal_cut=0,
min=None,
max=None,
flip="astro",
format="%.3g",
cbar=True,
cmap=None,
norm=None,
hold=False,
sub=None,
margins=None,
notext=False,
return_projected_map=False,
):
"""Plot a healpix map (given as an array) in Gnomonic projection.
Parameters
----------
map : array-like
The map to project, supports masked maps, see the `ma` function.
If None, use a blank map, useful for
overplotting.
fig : None or int, optional
A figure number. Default: None= create a new figure
rot : scalar or sequence, optional
Describe the rotation to apply.
In the form (lon, lat, psi) (unit: degrees) : the point at
longitude *lon* and latitude *lat* will be at the center. An additional rotation
of angle *psi* around this direction is applied.
coord : sequence of character, optional
Either one of 'G', 'E' or 'C' to describe the coordinate
system of the map, or a sequence of 2 of these to rotate
the map from the first to the second coordinate system.
unit : str, optional
A text describing the unit of the data. Default: ''
xsize : int, optional
The size of the image. Default: 200
ysize : None or int, optional
The size of the image. Default: None= xsize
reso : float, optional
Resolution (in arcmin). Default: 1.5 arcmin
title : str, optional
The title of the plot. Default: 'Gnomonic view'
nest : bool, optional
If True, ordering scheme is NESTED. Default: False (RING)
min : float, scalar, optional
The minimum range value
max : float, scalar, optional
The maximum range value
flip : {'astro', 'geo'}, optional
Defines the convention of projection : 'astro' (default, east towards left, west towards right)
or 'geo' (east towards roght, west towards left)
remove_dip : bool, optional
If :const:`True`, remove the dipole+monopole
remove_mono : bool, optional
If :const:`True`, remove the monopole
gal_cut : float, scalar, optional
Symmetric galactic cut for the dipole/monopole fit.
Removes points in latitude range [-gal_cut, +gal_cut]
format : str, optional
The format of the scale label. Default: '%g'
hold : bool, optional
If True, replace the current Axes by a MollweideAxes.
use this if you want to have multiple maps on the same
figure. Default: False
sub : int or sequence, optional
Use only a zone of the current figure (same syntax as subplot).
Default: None
margins : None or sequence, optional
Either None, or a sequence (left,bottom,right,top)
giving the margins on left,bottom,right and top
of the axes. Values are relative to figure (0-1).
Default: None
notext: bool, optional
If True: do not add resolution info text. Default=False
return_projected_map : bool
if True returns the projected map in a 2d numpy array
See Also
--------
mollview, cartview, orthview, azeqview
"""
import pylab
if not (hold or sub):
f = pylab.figure(fig, figsize=(5.8, 6.4))
if not margins:
margins = (0.075, 0.05, 0.075, 0.05)
extent = (0.0, 0.0, 1.0, 1.0)
elif hold:
f = pylab.gcf()
left, bottom, right, top = np.array(pylab.gca().get_position()).ravel()
if not margins:
margins = (0.0, 0.0, 0.0, 0.0)
extent = (left, bottom, right - left, top - bottom)
f.delaxes(pylab.gca())
else: # using subplot syntax
f = pylab.gcf()
if hasattr(sub, "__len__"):
nrows, ncols, idx = sub
else:
nrows, ncols, idx = sub // 100, (sub % 100) // 10, (sub % 10)
if idx < 1 or idx > ncols * nrows:
raise ValueError("Wrong values for sub: %d, %d, %d" % (nrows, ncols, idx))
c, r = (idx - 1) % ncols, (idx - 1) // ncols
if not margins:
margins = (0.01, 0.0, 0.0, 0.02)
extent = (
c * 1. / ncols + margins[0],
1. - (r + 1) * 1. / nrows + margins[1],
1. / ncols - margins[2] - margins[0],
1. / nrows - margins[3] - margins[1],
)
extent = (
extent[0] + margins[0],
extent[1] + margins[1],
extent[2] - margins[2] - margins[0],
extent[3] - margins[3] - margins[1],
)
# f=pylab.figure(fig,figsize=(5.5,6))
# Starting to draw : turn interactive off
wasinteractive = pylab.isinteractive()
pylab.ioff()
try:
if map is None:
map = np.zeros(12) + np.inf
cbar = False
map = pixelfunc.ma_to_array(map)
ax = PA.HpxGnomonicAxes(
f, extent, coord=coord, rot=rot, format=format, flipconv=flip
)
f.add_axes(ax)
if remove_dip:
map = pixelfunc.remove_dipole(map, gal_cut=gal_cut, nest=nest, copy=True)
elif remove_mono:
map = pixelfunc.remove_monopole(map, gal_cut=gal_cut, nest=nest, copy=True)
img = ax.projmap(
map,
nest=nest,
coord=coord,
vmin=min,
vmax=max,
xsize=xsize,
ysize=ysize,
reso=reso,
cmap=cmap,
norm=norm,
)
if cbar:
im = ax.get_images()[0]
b = im.norm.inverse(np.linspace(0, 1, im.cmap.N + 1))
v = np.linspace(im.norm.vmin, im.norm.vmax, im.cmap.N)
if matplotlib.__version__ >= "0.91.0":
cb = f.colorbar(
im,
ax=ax,
orientation="horizontal",
shrink=0.5,
aspect=25,
ticks=PA.BoundaryLocator(),
pad=0.08,
fraction=0.1,
boundaries=b,
values=v,
format=format,
)
else:
cb = f.colorbar(
im,
orientation="horizontal",
shrink=0.5,
aspect=25,
ticks=PA.BoundaryLocator(),
pad=0.08,
fraction=0.1,
boundaries=b,
values=v,
format=format,
)
cb.solids.set_rasterized(True)
ax.set_title(title)
if not notext:
ax.text(
-0.07,
0.02,
"%g '/pix, %dx%d pix"
% (
ax.proj.arrayinfo["reso"],
ax.proj.arrayinfo["xsize"],
ax.proj.arrayinfo["ysize"],
),
fontsize=12,
verticalalignment="bottom",
transform=ax.transAxes,
rotation=90,
)
ax.text(
-0.07,
0.6,
ax.proj.coordsysstr,
fontsize=14,
fontweight="bold",
rotation=90,
transform=ax.transAxes,
)
lon, lat = np.around(ax.proj.get_center(lonlat=True), ax._coordprec)
ax.text(
0.5,
-0.03,
"(%g,%g)" % (lon, lat),
verticalalignment="center",
horizontalalignment="center",
transform=ax.transAxes,
)
if cbar:
cb.ax.text(
1.05,
0.30,
unit,
fontsize=14,
fontweight="bold",
transform=cb.ax.transAxes,
ha="left",
va="center",
)
f.sca(ax)
finally:
pylab.draw()
if wasinteractive:
pylab.ion()
# pylab.show()
if return_projected_map:
return img
def sofispec1Dredu(files,
_interactive,
_ext_trace,
_dispersionline,
_automaticex,
_verbose=False):
# print "LOGX:: Entering `sofispec1Dredu` method/function in %(__file__)s"
# % globals()
import re
import string
import sys
import os
os.environ["PYRAF_BETA_STATUS"] = "1"
import ntt
try:
import pyfits
except:
from astropy.io import fits as pyfits
import numpy as np
import datetime
import pylab as pl
from pyraf import iraf
dv = ntt.dvex()
now = datetime.datetime.now()
datenow = now.strftime('20%y%m%d%H%M')
MJDtoday = 55927 + (datetime.date.today() -
datetime.date(2012, 01, 01)).days
scal = np.pi / 180.
hdr0 = ntt.util.readhdr(re.sub('\n', '', files[0]))
_gain = ntt.util.readkey3(hdr0, 'gain')
_rdnoise = ntt.util.readkey3(hdr0, 'ron')
std_sun, rastd_sun, decstd_sun, magstd_sun = ntt.util.readstandard(
'standard_sofi_sun.txt')
std_vega, rastd_vega, decstd_vega, magstd_vega = ntt.util.readstandard(
'standard_sofi_vega.txt')
std_phot, rastd_phot, decstd_phot, magstd_phot = ntt.util.readstandard(
'standard_sofi_phot.txt')
outputfile = []
objectlist, RA, DEC = {}, {}, {}
for img in files:
img = re.sub('\n', '', img)
hdr = ntt.util.readhdr(img)
_ra = ntt.util.readkey3(hdr, 'RA')
_dec = ntt.util.readkey3(hdr, 'DEC')
_grism = ntt.util.readkey3(hdr, 'grism')
_filter = ntt.util.readkey3(hdr, 'filter')
_slit = ntt.util.readkey3(hdr, 'slit')
cc_sun = np.arccos(
np.sin(_dec * scal) * np.sin(decstd_sun * scal) +
np.cos(_dec * scal) * np.cos(decstd_sun * scal) * np.cos(
(_ra - rastd_sun) * scal)) * ((180 / np.pi) * 3600)
cc_vega = np.arccos(
np.sin(_dec * scal) * np.sin(decstd_vega * scal) +
np.cos(_dec * scal) * np.cos(decstd_vega * scal) * np.cos(
(_ra - rastd_vega) * scal)) * ((180 / np.pi) * 3600)
cc_phot = np.arccos(
np.sin(_dec * scal) * np.sin(decstd_phot * scal) +
np.cos(_dec * scal) * np.cos(decstd_phot * scal) * np.cos(
(_ra - rastd_phot) * scal)) * ((180 / np.pi) * 3600)
if min(cc_sun) < 100:
_type = 'sun'
elif min(cc_phot) < 100:
_type = 'stdp'
elif min(cc_vega) < 100:
_type = 'vega'
else:
_type = 'obj'
if min(cc_phot) < 100:
if _verbose:
print img, 'phot', str(min(cc_phot)), str(
std_phot[np.argmin(cc_phot)])
ntt.util.updateheader(
img, 0, {
'stdname': [std_phot[np.argmin(cc_phot)], ''],
'magstd': [float(magstd_phot[np.argmin(cc_phot)]), '']
})
# ntt.util.updateheader(img,0,{'magstd':[float(magstd_phot[argmin(cc_phot)]),'']})
elif min(cc_sun) < 100:
if _verbose:
print img, 'sun', str(min(cc_sun)), str(
std_sun[np.argmin(cc_sun)])
ntt.util.updateheader(
img, 0, {
'stdname': [std_sun[np.argmin(cc_sun)], ''],
'magstd': [float(magstd_sun[np.argmin(cc_sun)]), '']
})
# ntt.util.updateheader(img,0,{'magstd':[float(magstd_sun[argmin(cc_sun)]),'']})
elif min(cc_vega) < 100:
if _verbose:
print img, 'vega', str(min(cc_vega)), str(
std_vega[np.argmin(cc_vega)])
ntt.util.updateheader(
img, 0, {
'stdname': [std_vega[np.argmin(cc_vega)], ''],
'magstd': [float(magstd_vega[np.argmin(cc_vega)]), '']
})
# ntt.util.updateheader(img,0,{'magstd':[float(magstd_vega[argmin(cc_vega)]),'']})
else:
if _verbose:
print img, 'object'
_OBID = (ntt.util.readkey3(hdr, 'esoid'))
if _type not in objectlist:
objectlist[_type] = {}
if _grism not in objectlist[_type]:
objectlist[_type][_grism] = {}
if _OBID not in objectlist[_type][_grism]:
objectlist[_type][_grism][_OBID] = []
objectlist[_type][_grism][_OBID].append(img)
if 'stdp' not in objectlist:
print '### warning: not photometric standard'
else:
print '### photometric standard in the list of object'
if 'sun' not in objectlist:
print '### warning: not telluric G standard (sun type)'
else:
print '### telluric G standard (sun type) in the list of object'
if 'vega' not in objectlist:
print '### warning: not telluric A standard (vega type)'
else:
print '### telluric A standard (vega type) in the list of object'
iraf.noao(_doprint=0, Stdout=0)
iraf.imred(_doprint=0, Stdout=0)
iraf.specred(_doprint=0, Stdout=0)
iraf.immatch(_doprint=0, Stdout=0)
iraf.imutil(_doprint=0, Stdout=0)
toforget = ['specred.apall', 'specred.transform']
for t in toforget:
iraf.unlearn(t)
iraf.specred.apall.readnoi = _rdnoise
iraf.specred.apall.gain = _gain
iraf.specred.dispaxi = 2
for _type in objectlist:
for setup in objectlist[_type]:
for _ID in objectlist[_type][setup]:
listmerge = objectlist[_type][setup][_ID]
listmerge = ntt.sortbyJD(listmerge)
_object = ntt.util.readkey3(ntt.util.readhdr(listmerge[0]),
'object')
if string.count(_object, '/') or string.count(
_object, '.') or string.count(_object, ' '):
nameobj = string.split(_object, '/')[0]
nameobj = string.split(nameobj, ' ')[0]
nameobj = string.split(nameobj, '.')[0]
else:
nameobj = _object
_date = ntt.util.readkey3(ntt.util.readhdr(listmerge[0]),
'date-night')
outputimage = nameobj + '_' + _date + \
'_' + setup + '_merge_' + str(MJDtoday)
outputimage = ntt.util.name_duplicate(listmerge[0],
outputimage, '')
print '### setup= ', setup, ' name field= ', nameobj, ' merge image= ', outputimage, '\n'
#################
# added to avoid crashing with a single frame
# header will not be updated with all info
#################
if len(listmerge) == 1:
ntt.util.delete(outputimage)
iraf.imutil.imcopy(listmerge[0],
output=outputimage,
verbose='no')
answ = 'n'
else:
if os.path.isfile(outputimage) and _interactive:
answ = raw_input(
'combine frame of dithered spectra already created. Do you want to make it again [[y]/n] ? '
)
if not answ:
answ = 'y'
else:
answ = 'y'
#################
if answ in ['Yes', 'y', 'Y', 'yes']:
if _interactive:
automaticmerge = raw_input(
'\n### Do you want to try to find the dither bethween frames automatically [[y]/n]'
)
if not automaticmerge:
automaticmerge = 'yes'
elif automaticmerge.lower() in ['y', 'yes']:
automaticmerge = 'yes'
else:
automaticmerge = 'no'
else:
automaticmerge = 'yes'
if automaticmerge == 'yes':
offset = 0
offsetvec = []
_center0 = ntt.sofispec1Ddef.findaperture(
listmerge[0], False)
_offset0 = ntt.util.readkey3(
ntt.util.readhdr(listmerge[0]), 'xcum')
print '\n### Try to merge spectra considering their offset along x axes .......'
f = open('_offset', 'w')
for img in listmerge:
_center = ntt.sofispec1Ddef.findaperture(
img, False)
_center2 = (
float(_center) +
(float(_offset0) - float(_center0))) * (-1)
_offset = (-1) * \
ntt.util.readkey3(
ntt.util.readhdr(img), 'xcum')
if abs(_center2 - _offset) >= 20:
automaticmerge = 'no'
break
else:
offset3 = _center2
offsetvec.append(offset3)
line = str(offset3) + ' 0\n'
f.write(line)
f.close()
if automaticmerge == 'yes':
print '### automatic merge .......... done'
else:
print '\n### warning: try identification of spectra position in interactive way '
offset = 0
offsetvec = []
_z1, _z2, goon = ntt.util.display_image(
listmerge[0], 1, '', '', False)
print '\n### find aperture on first frame and use it as reference position of ' \
'the spectra (mark with ' + '"' + 'm' + '"' + ')'
_center0 = ntt.sofispec1Ddef.findaperture(
listmerge[0], True)
_offset0 = ntt.util.readkey3(
ntt.util.readhdr(listmerge[0]), 'xcum')
print '\n### find the aperture on all the spectra frames (mark with ' + '"' + 'm' + '"' + ')'
f = open('_offset', 'w')
for img in listmerge:
print '\n### ', img
_z1, _z2, goon = ntt.util.display_image(
img, 1, '', '', False)
_center = ntt.sofispec1Ddef.findaperture(img, True)
_center2 = (
float(_center) +
(float(_offset0) - float(_center0))) * (-1)
_offset = (-1) * \
ntt.util.readkey3(
ntt.util.readhdr(img), 'xcum')
print '\n### position from dither header: ' + str(
_offset)
print '### position identified interactively: ' + str(
_center2)
offset3 = raw_input(
'\n### which is the right position [' +
str(_center2) + '] ?')
if not offset3:
offset3 = _center2
offsetvec.append(offset3)
line = str(offset3) + ' 0\n'
f.write(line)
f.close()
print offsetvec
start = int(max(offsetvec) - min(offsetvec))
print start
f = open('_goodlist', 'w')
print listmerge
for img in listmerge:
f.write(img + '\n')
f.close()
ntt.util.delete(outputimage)
ntt.util.delete('_output.fits')
yy1 = pyfits.open(listmerge[0])[0].data[:, 10]
iraf.immatch.imcombine('@_goodlist',
'_output',
combine='sum',
reject='none',
offset='_offset',
masktyp='',
rdnoise=_rdnoise,
gain=_gain,
zero='mode',
Stdout=1)
_head = pyfits.open('_output.fits')[0].header
if _head['NAXIS1'] < 1024:
stop = str(_head['NAXIS1'])
else:
stop = '1024'
iraf.imutil.imcopy('_output[' + str(start) + ':' + stop +
',*]',
output=outputimage,
verbose='no')
print outputimage
print len(listmerge)
hdr1 = ntt.util.readhdr(outputimage)
ntt.util.updateheader(
outputimage, 0, {
'SINGLEXP':
[False, 'TRUE if resulting from single exposure'],
'M_EPOCH':
[False, 'TRUE if resulting from multiple epochs'],
'EXPTIME': [
ntt.util.readkey3(hdr1, 'EXPTIME') *
len(listmerge),
'Total integration time per pixel (s)'
],
'TEXPTIME': [
float(ntt.util.readkey3(hdr1, 'TEXPTIME')) *
len(listmerge),
'Total integration time of all exposures (s)'
],
'APERTURE': [
2.778e-4 * float(
re.sub('long_slit_', '',
ntt.util.readkey3(hdr1, 'slit'))),
'[deg] Aperture diameter'
],
'NOFFSETS': [2, 'Number of offset positions'],
'NUSTEP': [0, 'Number of microstep positions'],
'NJITTER': [
int(ntt.util.readkey3(hdr1, 'NCOMBINE') / 2),
'Number of jitter positions'
]
})
hdr = ntt.util.readhdr(outputimage)
matching = [s for s in hdr.keys() if "IMCMB" in s]
for imcmb in matching:
aaa = iraf.hedit(outputimage,
imcmb,
delete='yes',
update='yes',
verify='no',
Stdout=1)
if 'SKYSUB' in hdr.keys():
aaa = iraf.hedit(outputimage,
'SKYSUB',
delete='yes',
update='yes',
verify='no',
Stdout=1)
mjdend = []
mjdstart = []
num = 0
for img in listmerge:
num = num + 1
hdrm = ntt.util.readhdr(img)
ntt.util.updateheader(
outputimage, 0, {
'PROV' + str(num): [
ntt.util.readkey3(hdrm, 'ARCFILE'),
'Originating file'
],
'TRACE' + str(num): [img, 'Originating file']
})
mjdend.append(ntt.util.readkey3(hdrm, 'MJD-END'))
mjdstart.append(ntt.util.readkey3(hdrm, 'MJD-OBS'))
_dateobs = ntt.util.readkey3(
ntt.util.readhdr(listmerge[np.argmin(mjdstart)]),
'DATE-OBS')
_telapse = (max(mjdend) - min(mjdstart)) * \
60. * 60 * 24. # *86400
_tmid = (max(mjdend) + min(mjdstart)) / 2
_title = str(_tmid)[0:9] + ' ' + str(ntt.util.readkey3(hdr, 'object')) + ' ' + str(
ntt.util.readkey3(hdr, 'grism')) + ' ' + \
str(ntt.util.readkey3(hdr, 'filter')) + \
' ' + str(ntt.util.readkey3(hdr, 'slit'))
ntt.util.updateheader(
outputimage, 0, {
'MJD-OBS': [min(mjdstart), 'MJD start'],
'MJD-END': [max(mjdend), 'MJD end'],
'TELAPSE': [_telapse, 'Total elapsed time [days]'],
'TMID': [_tmid, '[d] MJD mid exposure'],
'TITLE': [_title, 'Dataset title'],
'DATE-OBS': [_dateobs, 'Date of observation']
})
# missing: merge airmass
else:
print '\n### skip making again combined spectrum'
objectlist[_type][setup][_ID] = [outputimage]
print '\n### setup= ', setup, ' name field= ', nameobj, ' merge image= ', outputimage, '\n'
if outputimage not in outputfile:
outputfile.append(outputimage)
ntt.util.updateheader(
outputimage, 0,
{'FILETYPE': [42116, 'combine 2D spectra frame']})
if _verbose:
if 'obj' in objectlist:
print objectlist['obj']
if 'stdp' in objectlist:
print objectlist['stdp']
if 'sun' in objectlist:
print objectlist['sun']
if 'vega' in objectlist:
print objectlist['vega']
if 'obj' not in objectlist.keys():
sys.exit('\n### error: no objects in the list')
sens = {}
print '\n############################################\n### extract the spectra '
# print objectlist
for setup in objectlist['obj']:
reduced = []
for _ID in objectlist['obj'][setup]:
for img in objectlist['obj'][setup][_ID]:
hdr = ntt.util.readhdr(img)
print '\n### next object\n ', img, ntt.util.readkey3(
hdr, 'object')
_grism = ntt.util.readkey3(hdr, 'grism')
_exptimeimg = ntt.util.readkey3(hdr, 'exptime')
_JDimg = ntt.util.readkey3(hdr, 'JD')
imgex = ntt.util.extractspectrum(img,
dv,
_ext_trace,
_dispersionline,
_interactive,
'obj',
automaticex=_automaticex)
if imgex not in outputfile:
outputfile.append(imgex)
ntt.util.updateheader(
imgex, 0, {
'FILETYPE': [42107, 'extracted 1D wave calib'],
'PRODCATG': [
'SCIENCE.' +
ntt.util.readkey3(hdr, 'tech').upper(),
'Data product category'
]
})
hdr = ntt.util.readhdr(imgex)
matching = [s for s in hdr.keys() if "TRACE" in s]
for imcmb in matching:
aaa = iraf.hedit(imgex,
imcmb,
delete='yes',
update='yes',
verify='no',
Stdout=1)
ntt.util.updateheader(imgex, 0,
{'TRACE1': [img, 'Originating file']})
if os.path.isfile('database/ap' +
re.sub('_ex.fits', '', imgex)):
if 'database/ap' + re.sub('_ex.fits', '',
imgex) not in outputfile:
outputfile.append('database/ap' +
re.sub('_ex.fits', '', imgex))
########################### telluric standard #############
if 'sun' in objectlist and setup in objectlist['sun']:
_type = 'sun'
elif 'vega' in objectlist and setup in objectlist['vega']:
_type = 'vega'
else:
_type = 'none'
if _type in ['sun', 'vega']:
stdref = ntt.__path__[0] + '/standard/fits/' + str(
_type) + '.fits'
stdvec, airmassvec, JDvec = [], [], []
for _ID in objectlist[_type][setup]:
for std in objectlist[_type][setup][_ID]:
_airmassstd = ntt.util.readkey3(
ntt.util.readhdr(std), 'airmass')
_JDstd = ntt.util.readkey3(ntt.util.readhdr(std),
'JD')
JDvec.append(abs(_JDstd - _JDimg))
stdvec.append(std)
airmassvec.append(_airmassstd)
stdtelluric = stdvec[np.argmin(JDvec)]
_exptimestd = ntt.util.readkey3(
ntt.util.readhdr(stdtelluric), 'exptime')
_magstd = ntt.util.readkey3(ntt.util.readhdr(stdtelluric),
'magstd')
print '\n\n ##### closer standard for telluric corrections #### \n\n'
print stdtelluric, airmassvec[np.argmin(JDvec)]
stdtelluric_ex = ntt.util.extractspectrum(
stdtelluric,
dv,
False,
False,
_interactive,
'std',
automaticex=_automaticex)
if stdtelluric_ex not in outputfile:
outputfile.append(stdtelluric_ex)
ntt.util.updateheader(
stdtelluric_ex, 0,
{'FILETYPE': [42107, 'extracted 1D wave calib ']})
ntt.util.updateheader(
stdtelluric_ex, 0, {
'PRODCATG': [
'SCIENCE.' + ntt.util.readkey3(
ntt.util.readhdr(stdtelluric_ex),
'tech').upper(), 'Data product category'
]
})
hdr = ntt.util.readhdr(stdtelluric_ex)
matching = [s for s in hdr.keys() if "TRACE" in s]
for imcmb in matching:
aaa = iraf.hedit(stdtelluric_ex,
imcmb,
delete='yes',
update='yes',
verify='no',
Stdout=1)
ntt.util.updateheader(
stdtelluric_ex, 0,
{'TRACE1': [stdtelluric, 'Originating file']})
###########################################################
# SN tellurich calibration
imgf = re.sub('_ex.fits', '_f.fits', imgex)
imgf, senstelluric = ntt.sofispec1Ddef.calibrationsofi(
imgex, stdtelluric_ex, stdref, imgf, _interactive)
if imgf not in outputfile:
outputfile.append(imgf)
if senstelluric not in outputfile:
outputfile.append(senstelluric)
ntt.util.updateheader(
imgf,
0,
{
'FILETYPE': [42208, '1D wave calib, tell cor.'],
# 'SNR': [ntt.util.StoN(imgf, 50),
'SNR': [
ntt.util.StoN2(imgf, False),
'Average signal to noise ratio per pixel'
],
'TRACE1': [imgex, 'Originating file'],
'ASSON1': [
re.sub('_f.fits', '_2df.fits', imgf),
'Name of associated file'
],
'ASSOC1': [
'ANCILLARY.2DSPECTRUM',
'Category of associated file'
]
})
###########################################################
imgd = ntt.efoscspec1Ddef.fluxcalib2d(
img, senstelluric) # flux calibration 2d images
ntt.util.updateheader(
imgd, 0, {
'FILETYPE': [
42209,
'2D wavelength and flux calibrated spectrum'
]
})
iraf.hedit(imgd,
'PRODCATG',
delete='yes',
update='yes',
verify='no')
hdrd = ntt.util.readhdr(imgd)
matching = [s for s in hdrd.keys() if "TRACE" in s]
for imcmb in matching:
aaa = iraf.hedit(imgd,
imcmb,
delete='yes',
update='yes',
verify='no',
Stdout=1)
ntt.util.updateheader(
imgd, 0, {'TRACE1': [img, 'Originating file']})
if imgd not in outputfile:
outputfile.append(imgd)
###############################################################
if 'stdp' in objectlist and setup in objectlist['stdp']:
print '\n ##### photometric calibration ######\n '
standardfile = []
for _ID in objectlist['stdp'][setup]:
for stdp in objectlist['stdp'][setup][_ID]:
stdp_ex = ntt.util.extractspectrum(
stdp,
dv,
False,
_dispersionline,
_interactive,
'std',
automaticex=_automaticex)
standardfile.append(stdp_ex)
if stdp_ex not in outputfile:
outputfile.append(stdp_ex)
ntt.util.updateheader(
stdp_ex, 0, {
'FILETYPE':
[42107, 'extracted 1D wave calib'],
'TRACE1': [stdp_ex, 'Originating file'],
'PRODCATG': [
'SCIENCE.' + ntt.util.readkey3(
ntt.util.readhdr(stdp_ex),
'tech').upper(),
'Data product category'
]
})
print '\n### ', standardfile, ' \n'
if len(standardfile) >= 2:
standardfile0 = raw_input(
'which one do you want to use [' +
str(standardfile[0]) + '] ? ')
if not standardfile0:
standardfile0 = standardfile[0]
else:
standardfile0 = standardfile[0]
print standardfile0
stdpf = re.sub('_ex.fits', '_f.fits', standardfile0)
stdpf, senstelluric2 = ntt.sofispec1Ddef.calibrationsofi(
standardfile0, stdtelluric_ex, stdref, stdpf,
_interactive)
if stdpf not in outputfile:
outputfile.append(stdpf)
ntt.util.updateheader(
stdpf, 0, {
'FILETYPE': [42208, '1D wave calib, tell cor'],
'TRACE1': [stdp, 'Originating file']
})
stdname = ntt.util.readkey3(
ntt.util.readhdr(standardfile0), 'stdname')
standardfile = ntt.__path__[0] + '/standard/flux/' + stdname
xx, yy = ntt.util.ReadAscii2(standardfile)
crval1 = pyfits.open(stdpf)[0].header.get('CRVAL1')
cd1 = pyfits.open(stdpf)[0].header.get('CD1_1')
datastdpf, hdrstdpf = pyfits.getdata(stdpf, 0, header=True)
xx1 = np.arange(len(datastdpf[0][0]))
aa1 = crval1 + (xx1) * cd1
yystd = np.interp(aa1, xx, yy)
rcut = np.compress(
((aa1 < 13000) | (aa1 > 15150)) &
((11700 < aa1) | (aa1 < 11000)) & (aa1 > 10000) &
((aa1 < 17800) | (aa1 > 19600)) & (aa1 < 24000),
datastdpf[0][0] / yystd)
aa11 = np.compress(
((aa1 < 13000) | (aa1 > 15150)) &
((11700 < aa1) | (aa1 < 11000)) & (aa1 > 10000) &
((aa1 < 17800) | (aa1 > 19600)) & (aa1 < 24000), aa1)
yy1clean = np.interp(aa1, aa11, rcut)
aa1 = np.array(aa1)
yy1clean = np.array(yy1clean)
A = np.ones((len(rcut), 2), dtype=float)
A[:, 0] = aa11
result = np.linalg.lstsq(A, rcut) # result=[zero,slope]
p = [result[0][1], result[0][0]]
yfit = ntt.util.pval(aa1, p)
pl.clf()
pl.ion()
pl.plot(aa1,
datastdpf[0][0] / yystd,
color='red',
label='std')
pl.plot(aa1, yfit, color='blue', label='fit')
pl.legend(numpoints=1, markerscale=1.5)
# sens function sofi spectra
outputsens = 'sens_' + stdpf
ntt.util.delete(outputsens)
datastdpf[0][0] = yfit
pyfits.writeto(outputsens, np.float32(datastdpf), hdrstdpf)
#################
imgsc = re.sub('_ex.fits', '_sc.fits', imgex)
ntt.util.delete(imgsc)
crval2 = pyfits.open(imgf)[0].header.get('CRVAL1')
cd2 = pyfits.open(imgf)[0].header.get('CD1_1')
dataf, hdrf = pyfits.getdata(imgf, 0, header=True)
xx2 = np.arange(len(dataf[0][0]))
aa2 = crval2 + (xx2) * cd2
yyscale = np.interp(aa2, aa1, yfit)
dataf[0][0] = dataf[0][0] / yyscale
dataf[1][0] = dataf[1][0] / yyscale
dataf[2][0] = dataf[2][0] / yyscale
dataf[3][0] = dataf[3][0] / yyscale
pyfits.writeto(imgsc, np.float32(dataf), hdrf)
ntt.util.updateheader(
imgsc, 0, {
'SENSPHOT': [outputsens, 'sens used to flux cal'],
'FILETYPE':
[42208, '1D wave,flux calib, tell cor'],
'TRACE1': [imgf, 'Originating file']
})
# ntt.util.updateheader(imgsc,0,{'FILETYPE':[42208,'1D wave,flux calib, tell cor']})
# ntt.util.updateheader(imgsc,0,{'TRACE1':[imgf,'']})
print '\n### flux calibrated spectrum= ', imgf, ' with the standard= ', stdpf
if imgsc not in outputfile:
outputfile.append(imgsc)
else:
print '\n### photometric calibrated not performed \n'
print '\n### adding keywords for phase 3 ....... '
reduceddata = ntt.util.rangedata(outputfile)
f = open(
'logfile_spec1d_' + str(reduceddata) + '_' + str(datenow) +
'.raw.list', 'w')
for img in outputfile:
if str(img)[-5:] == '.fits':
hdr = ntt.util.readhdr(img)
# added for DR2
if 'NCOMBINE' in hdr:
_ncomb = ntt.util.readkey3(hdr, 'NCOMBINE')
else:
_ncomb = 1.0
_effron = 12. * \
(1 / np.sqrt(ntt.util.readkey3(hdr, 'ndit') * _ncomb)) * \
np.sqrt(np.pi / 2)
try:
ntt.util.phase3header(img) # phase 3 definitions
ntt.util.updateheader(
img, 0, {
'quality': ['Final', ''],
'EFFRON':
[_effron, 'Effective readout noise per output (e-)']
})
f.write(
ntt.util.readkey3(ntt.util.readhdr(img), 'arcfile') + '\n')
except:
print 'Warning: ' + img + ' is not a fits file'
f.close()
return outputfile, 'logfile_spec1d_' + str(reduceddata) + '_' + str(
datenow) + '.raw.list'
def drawPlots():
global plots, theWorld, time, times, num_households
if plots == None or plots.canvas.manager.window == None:
plots = PL.figure(2)
PL.ion()
PL.figure(2)
PL.hold(True)
PL.subplot(4, 3, 1)
PL.cla()
tot = theWorld.food_shared_totals
food_shared_avg = [tot[i] / (i + 1) for i in range(len(tot))]
PL.plot(food_shared_avg, color='black')
PL.plot(theWorld.food_shared, color='pink')
PL.plot(theWorld.brn_sharing, color='brown')
PL.plot(theWorld.grn_sharing, color='green')
PL.title("Food shared each year (BRN, GRN, tot) and average")
PL.hold(True)
PL.subplot(4, 3, 2)
PL.cla()
interval = 20
step = 0.5
b = [-interval + step * i for i in range(2 * int(interval / step) + 1)]
if theWorld.hh_prestige:
PL.hist(theWorld.hh_prestige, bins=b, color='brown')
PL.title("hh count by prestige")
PL.hold(True)
PL.subplot(4, 3, 3)
PL.cla()
PL.plot(theWorld.populations, color='pink')
PL.plot(theWorld.avg_pop, color='black')
PL.plot(theWorld.avg_pop_100, color='blue')
PL.title("Population, average, and 100-year average")
PL.hold(True)
PL.subplot(4, 3, 4)
PL.cla()
PL.plot(theWorld.avg_ages, color='pink')
PL.plot(theWorld.avg_adult_ages, color='red')
PL.plot(theWorld.avg_hh_age, color='black')
PL.title(
"Average household(black), forager(pink), and adult forager age (red) at end"
)
PL.hold(True)
PL.subplot(4, 3, 5)
PL.cla()
interval = (W.max_founder_kin_span - W.min_founder_kin_span)
step = 0.1
b = [(W.min_founder_kin_span + step * i)
for i in range(int(interval / step) + 1)]
if theWorld.kinship_spans:
PL.hist(theWorld.kinship_spans, bins=b, color='blue')
# PL.axis()
PL.title("population count by kinship span")
PL.hold(True)
PL.subplot(4, 3, 6)
PL.cla()
interval = (W.max_founder_kin_span - W.min_founder_kin_span)
step = 1
b = [(W.min_founder_kin_span + step * i)
for i in range(int(interval / step) + 1)]
if theWorld.kinship_spans:
PL.hist(theWorld.kinship_spans, bins=b, color='blue')
# PL.axis()
PL.title("population count by kinship span")
PL.hold(True)
PL.subplot(4, 3, 7)
PL.cla()
interval = 10
step = 0.05
b = [step * i for i in range(int(interval / step) + 1)]
if theWorld.hh_food_stored:
PL.hist(theWorld.hh_food_stored, bins=b, color='cyan')
# PL.axis()
PL.title("hh counts by food stored")
PL.hold(True)
PL.subplot(4, 3, 8)
PL.cla()
interval = max(theWorld.pop_expertise) - min(theWorld.pop_expertise)
step = 0.05
b = [
min(theWorld.pop_expertise) + step * i
for i in range(int(interval / step) + 1)
]
if theWorld.pop_expertise:
PL.hist(theWorld.pop_expertise, bins=b, color='cyan')
# PL.axis()
PL.title("population counts by foraging expertise")
PL.hold(True)
PL.subplot(4, 3, 9)
PL.cla()
PL.plot(theWorld.median_storage, color='black')
PL.title("Median food stored")
PL.hold(True)
PL.subplot(4, 3, 10)
PL.cla()
PL.plot(theWorld.hoover, color='black')
PL.title("Hoover index")
PL.hold(True)
PL.subplot(4, 3, 10)
PL.cla()
PL.plot(theWorld.avg_food_stored, color='black')
PL.title("average food stored")
PL.hold(False)
plots.tight_layout()
plots.canvas.manager.window.update()
PL.figure(1)
drt_l_out = np.array(drt_l_out)
drt_u_mean.append(np.mean(drt_u_out))
drt_u_std.append(np.std(drt_u_out))
drt_l_mean.append(np.mean(drt_l_out))
drt_l_std.append(np.std(drt_l_out))
drt_u_mean = np.array(drt_u_mean)
drt_l_mean = np.array(drt_l_mean)
drt_u_std = np.array(drt_u_std)
drt_l_std = np.array(drt_l_std)
residuals_u = (drt_u_mean - drt_in) / drt_u_std
residuals_l = (drt_l_mean - drt_in) / drt_l_std
##- Setup figures
plt.ion()
plt.rcParams.update({'font.size': 14})
colors = [
'#396AB1', '#DA7C30', '#3E9651', '#CC2529', '#535154', '#6B4C9A',
'#922428', '#948B3D'
]
##- Plot bias figure
fig, ax = plt.subplots(nrows=2, ncols=1, figsize=(8, 8))
fig.subplots_adjust(hspace=0.5)
ax[0].set_title(
fr'$\Delta r$, 1000000 realisations, rt={rt_in}, rp={rp_in}')
ax[0].plot(drt_in, drt_in, color=colors[4], ls=':')
ax[0].errorbar(drt_in,
drt_u_mean,
yerr=drt_u_std,
def modified_XOR(kernel, degree, C, sdev):
import svm
sv = svm.svm(kernel, degree=degree, C=C)
#sv = svm.svm(kernel='poly',degree=3,C=0.2)
#sv = svm.svm(kernel='rbf',C=0.1)
#sv = svm.svm(kernel='poly',degree=3)
#sdev = 0.4 #0.3 #0.1
m = 100
X = sdev * np.random.randn(m, 2)
X[m / 2:, 0] += 1.
X[m / 4:m / 2, 1] += 1.
X[3 * m / 4:, 1] += 1.
targets = -np.ones((m, 1))
targets[:m / 4, 0] = 1.
targets[3 * m / 4:, 0] = 1.
#targets = (np.where(X[:,0]*X[:,1]>=0,1,-1)*np.ones((1,np.shape(X)[0]))).T
sv.train_svm(X, targets)
Y = sdev * np.random.randn(m, 2)
Y[m / 2:, 0] += 1.
Y[m / 4:m / 2, 1] += 1.
Y[3 * m / 4:m, 1] += 1.
test = -np.ones((m, 1))
test[:m / 4, 0] = 1.
test[3 * m / 4:, 0] = 1.
#test = (np.where(Y[:,0]*Y[:,1]>=0,1,-1)*np.ones((1,np.shape(Y)[0]))).T
#print test.T
output = sv.classifier(Y, soft=False)
#print output.T
#print test.T
err1 = np.where((output == 1.) & (test == -1.))[0]
err2 = np.where((output == -1.) & (test == 1.))[0]
print kernel, C
print "Class 1 errors ", len(err1), " from ", len(test[test == 1])
print "Class 2 errors ", len(err2), " from ", len(test[test == -1])
print "Test accuracy ", 1. - (float(len(err1) + len(err2))) / (
len(test[test == 1]) + len(test[test == -1]))
pl.ion()
pl.figure()
l1 = np.where(targets == 1)[0]
l2 = np.where(targets == -1)[0]
pl.plot(X[sv.sv, 0], X[sv.sv, 1], 'o', markeredgewidth=5)
pl.plot(X[l1, 0], X[l1, 1], 'ko')
pl.plot(X[l2, 0], X[l2, 1], 'wo')
l1 = np.where(test == 1)[0]
l2 = np.where(test == -1)[0]
pl.plot(Y[l1, 0], Y[l1, 1], 'ks')
pl.plot(Y[l2, 0], Y[l2, 1], 'ws')
step = 0.1
f0, f1 = np.meshgrid(
np.arange(np.min(X[:, 0]) - 0.5,
np.max(X[:, 0]) + 0.5, step),
np.arange(np.min(X[:, 1]) - 0.5,
np.max(X[:, 1]) + 0.5, step))
out = sv.classifier(np.c_[np.ravel(f0), np.ravel(f1)], soft=True).T
out = out.reshape(f0.shape)
pl.contour(f0, f1, out, 2)
pl.axis('off')
pl.show()
def loopEvents(RUNID, boardID, att):
DISPLAY = 0
print('DISPLAY = ', DISPLAY)
pl.ion()
filename = "C" + RUNID + "_b" + boardID + ".data.txt"
#datafile = '../data/ulastai/'+filename
datafile = '/home/martineau/GRAND/GRANDproto35/data/ulastai/' + filename
print('Scanning', datafile)
with open(datafile, "r") as f:
evts = f.read().split('-----------------')
nevts = len(evts) - 1
print('Number of events:', nevts)
time.sleep(1)
date = []
board = np.zeros(shape=(np.size(evts)), dtype=np.int32)
TS2 = np.zeros(shape=(np.size(evts)))
TS1PPS = np.zeros(shape=(np.size(evts)))
TS1Trig = np.zeros(shape=(np.size(evts)))
SSS = np.zeros(shape=(np.size(evts)), dtype=np.int32)
EvtId = np.zeros(shape=(np.size(evts)), dtype=np.int32)
TrigPattern = np.zeros(shape=(np.size(evts)))
imax = np.zeros(shape=(nevts, 3), dtype=int)
Amax = np.zeros(shape=(nevts, 3))
mub = np.zeros(shape=(nevts, 3))
sigb = np.zeros(shape=(nevts, 3))
j = 0
# Index of array filling (because date & data are "append")
for i in range(1, nevts + 1):
if float(i) / 100 == int(i / 100):
print('Event', i, '/', nevts)
evt = evts[i]
evtsplit = evt.split('\n')
if np.size(evtsplit) > 8: # Event is of normal size
date.append(evtsplit[1])
IP = evtsplit[2][3:]
board[j] = int(IP[-2:])
TS2[j] = int(
evtsplit[3][4:]
) # time elapsed since last PPS (125MHz clock <=> 8ns counter)
tt = int(evtsplit[4][11:]) # phase in 8ns slot fr trigger
TS1Trig[i] = get_1stone(hex(tt))
tpps = int(evtsplit[5][7:])
TS1PPS[j] = get_1stone(hex(tpps)) # phase in 8ns slot for PPS
SSS[j] = int(evtsplit[6][4:]) # Elapsed seconds since start
EvtId[j] = int(evtsplit[7][3:])
TrigPattern[j] = int(evtsplit[8][12:])
# Data
raw = evtsplit[9:][:] #raw data
raw2 = raw[0].split(" ") # Cut raw data list into samples
raw2 = raw2[0:np.size(raw2) - 1] # Remove last element (empty)
hraw2 = [hex(int(a)) for a in raw2] # TRansfer back to hexadecimal
draw = [twos_comp(int(a, 16), 12) for a in hraw2] #2s complements
draw = np.array(draw) * 1. / 2048 # in Volts
nsamples = len(draw) / 4 # Separate data to each channel
offset = nsamples / 2.0
thisEvent = np.reshape(draw, (4, nsamples))
#data.append(thisEvent) # Write to data list ... Not needed here
if DISPLAY:
print('Event ', j, 'at date', date[j])
t = np.array(range(np.shape(thisEvent)[1]))
t = t * 10e-3 #in mus
pl.figure(j)
pl.subplot(311)
pl.plot(t[3:], thisEvent[0][3:])
pl.ylabel('Amplitude [LSB]')
pl.grid(True)
pl.subplot(312)
pl.ylabel('Amplitude [LSB]')
pl.plot(t[3:], thisEvent[1][3:])
pl.grid(True)
pl.subplot(313)
pl.plot(t[3:], thisEvent[2][3:])
pl.xlabel('Time [mus]')
pl.ylabel('Amplitude [LSB]')
pl.grid(True)
pl.suptitle('Board {0} Event {1}'.format(board[j], EvtId[j]))
pl.show()
raw_input()
pl.close(j)
for k in [0, 1, 2]:
nz = np.where(thisEvent[k][:] != 0)
imax[j, k] = np.argmax(thisEvent[k][:])
Amax[j, k] = thisEvent[k][imax[j, k]]
mub[j, k] = np.mean(thisEvent[k][nz])
sigb[j, k] = np.std(thisEvent[k][nz])
j = j + 1
else:
print('Error! Empty event', i)
boards = set(board[np.where(board > 0)])
print('Boards in run:', list(boards))
j = 0
m = np.empty([len(boards), 3])
em = np.empty([len(boards), 3])
for id in boards:
sel = np.where(board == id)
for k in [0, 1, 2]:
pl.figure(1)
subpl = 311 + k
pl.subplot(subpl)
a = mub[sel, k][0]
pl.hist(a, 100)
if k == 0:
pl.title('Board {0}'.format(id))
if k == 2:
pl.xlabel('Mean amplitude')
pl.grid(True)
pl.figure(2)
subpl = 311 + k
pl.subplot(subpl)
b = sigb[sel, k][0]
pl.hist(b, 100)
if k == 0:
pl.title('Board {0}'.format(id))
if k == 2:
pl.xlabel('Std dev')
pl.grid(True)
#Pack up results
m[j, k] = np.mean(a)
em[j, k] = np.mean(b)
print('Channel', k, ': mean=', m[j, k], '; stddev=', em[j, k])
j = j + 1
return {'m': m, 'em': em}
def spectrum_image(avg_num, direction):
pylab.ion()
[Burleigh_WM, Burleigh_WM_bool] = Initialise_Burleigh_WM()
[SpecAn, SpecAn_Bool] = Initialise_HP8560E_SpecAn()
#set the spectrum analyser scanning
HP8560E_SpecAn_Trigger('FREE', 'CONTS', SpecAn)
[SpecAn_BW, SpecAn_Sweeptime
] = HP8560E_SpecAn_Resbandwidth_Sweeptime(resbandwidth, sweeptime, SpecAn)
[SpecAn_Centre,
SpecAn_Span] = HP8560E_SpecAn_Centre_Span(centre, span, SpecAn)
[SpecAn_track, SpecAn_Power] = HP8560E_SpecAn_RF(tracking_gen, RF_power,
SpecAn)
#need initial x_axis measurements to generate output array
x_axis_data = np.arange(centre - span / 2, centre + span / 2, span / 601)
#load in the offset from InGaAs detector and Modulator response
amplitude_offset = np.loadtxt(
"C:\\Users\\Milos\Desktop\\Er_Experiment_Interface_Code\\amplitude_offset.csv",
delimiter=",")
compensated_array = np.zeros((avg_num, 601), dtype=float)
c = 299792453
Burleigh_WM.write("FETC:SCAL:WAV?")
laser_wavelength = np.float(Burleigh_WM.read())
#convert x axis from frequency to wavelength
if direction == 'pos':
wavelength_values = x_axis_data * ((laser_wavelength**2) /
(c * 10**9)) + laser_wavelength
frequency_values = -x_axis_data + (c * 10**9) / laser_wavelength
else:
wavelength_values = -x_axis_data * ((laser_wavelength**2) /
(c * 10**9)) + laser_wavelength
frequency_values = x_axis_data + (c * 10**9) / laser_wavelength
#now we collect the data trace
for i in range(avg_num):
plt.clf()
#collect data from spectrum analyser
SpecAn.write("TRA?")
binary_string = SpecAn.read_raw()
hex_string = binascii.b2a_hex(binary_string)
spec_data_temp = np.zeros(601)
for j in range(601):
spec_data_temp[j] = int('0x' + hex_string[j * 4:j * 4 + 4], 0)
compensated_data = np.subtract(spec_data_temp, amplitude_offset)
compensated_array[i, :] = compensated_data[:]
plt.plot(wavelength_values, compensated_data)
plt.pause(0.01)
#turn off RF so it stops burning
[SpecAn_track, SpecAn_Power] = HP8560E_SpecAn_RF('OFF', RF_power, SpecAn)
#average the above runs into one array
avg_spec_data = np.average(compensated_array, 0)
#print avg_spec_data
plt.clf()
pylab.ioff()
foldername = 'spin polarisation image'
filename = 'unpolarised-negative direction'
if direction == 'pos':
save_data(filename, foldername, laser_wavelength, avg_spec_data,
wavelength_values, frequency_values)
plt.plot(wavelength_values - 1538, avg_spec_data)
plt.xlim(wavelength_values[1] - 1538, wavelength_values[-1] - 1538)
plt.show()
else:
save_data(filename, foldername, laser_wavelength,
np.flipud(avg_spec_data), np.flipud(wavelength_values),
np.flipud(frequency_values))
plt.plot(np.flipud(wavelength_values) - 1538, np.flipud(avg_spec_data))
plt.xlim(wavelength_values[-1] - 1538, wavelength_values[1] - 1538)
plt.show()
#! /usr/bin/env python
# encoding: UTF-8
from astropy.table import Table
import numpy as np
import pylab as pt
from matplotlib.backends.backend_pdf import PdfPages
from gammapy.utils.energy import EnergyBounds
from method_fit import *
from method_plot import *
import yaml
import sys
pt.ion()
"""
./plot_spectra.py "config_crab.yaml"
plot la valeur des differentes composantes utilisees pour le fit morpho
"""
input_param = yaml.load(open(sys.argv[1]))
#Input param fit and source configuration
image_size = input_param["general"]["image_size"]
extraction_region = input_param["param_fit"]["extraction_region"]
freeze_bkg = input_param["param_fit"]["freeze_bkg"]
source_name = input_param["general"]["source_name"]
name_method_fond = input_param["general"]["name_method_fond"]
name = "_region_" + str(extraction_region) + "pix"
if freeze_bkg:
name += "_bkg_fix"
else:
name += "_bkg_free"
for_integral_flux = input_param["exposure"]["for_integral_flux"]
for i in xrange(X.size):
griddata.addSample([X.ravel()[i], Y.ravel()[i]], [0])
griddata._convertToOneOfMany(
) # this is still needed to make the fnn feel comfy
for i in range(20):
trainer.trainEpochs(1)
trnresult = percentError(trainer.testOnClassData(), trndata['class'])
tstresult = percentError(trainer.testOnClassData(dataset=tstdata),
tstdata['class'])
print "epoch: %4d" % trainer.totalepochs, \
" train error: %5.2f%%" % trnresult, \
" test error: %5.2f%%" % tstresult
out = fnn.activateOnDataset(griddata)
out = out.argmax(axis=1) # the highest output activation gives the class
out = out.reshape(X.shape)
figure(1)
ioff() # interactive graphics off
clf() # clear the plot
hold(True) # overplot on
for c in [0, 1, 2]:
here, _ = where(tstdata['class'] == c)
plot(tstdata['input'][here, 0], tstdata['input'][here, 1], 'o')
if out.max() != out.min(): # safety check against flat field
contourf(X, Y, out) # plot the contour
ion() # interactive graphics on
draw() # update the plot
ioff()
show()
def aux_basic(self, dirname, rc):
"""Helper function -- to assure that all filehandlers
get closed so we could remove trash directory.
Otherwise -- .nfs* files on NFS-mounted drives cause problems
"""
report = rc('UnitTest report',
title="Sample report for testing",
path=dirname)
isdummy = isinstance(report, DummyReport)
verbose.handlers = [report]
verbose.level = 3
verbose(1, "Starting")
verbose(2, "Level 2")
if not isdummy:
self.assertTrue(len(report._story) == 2,
msg="We should have got some lines from verbose")
if __debug__:
odhandlers = debug.handlers
debug.handlers = [report]
oactive = debug.active
debug.active = ['TEST'] + debug.active
debug('TEST', "Testing report as handler for debug")
if not isdummy:
self.assertTrue(len(report._story) == 4,
msg="We should have got some lines from debug")
debug.active = oactive
debug.handlers = odhandlers
os.makedirs(dirname)
if externals.exists('pylab plottable'):
if not isdummy:
clen = len(report._story)
import pylab as pl
pl.ioff()
pl.close('all')
pl.figure()
pl.plot([1, 2], [3, 2])
pl.figure()
pl.plot([2, 10], [3, 2])
pl.title("Figure 2 must be it")
report.figures()
if not isdummy:
self.assertTrue(
len(report._story) == clen+2,
msg="We should have got some lines from figures")
report.text("Dugi bugi")
# make sure we don't puke on xml like text with crap
report.text("<kaj>$lkj&*()^$%#%</kaj>")
report.text("locals:\n%s globals:\n%s" % (`locals()`, `globals()`))
# bloody XML - just to check that there is no puke
report.xml("<b>Dugi bugi</b>")
report.save()
if externals.exists('pylab'):
import pylab as pl
pl.close('all')
pl.ion()
pass
def pvhist(self, ns=0, nbins=20):
print "nsamp", self.nsamp[ns]
pylab.ion()
pylab.hist(numpy.array(self.pvs[ns]), nbins)
def kepbls(infile,
outfile,
datacol,
errcol,
minper,
maxper,
mindur,
maxdur,
nsearch,
nbins,
plot,
clobber,
verbose,
logfile,
status,
cmdLine=False):
# startup parameters
numpy.seterr(all="ignore")
status = 0
labelsize = 32
ticksize = 18
xsize = 16
ysize = 8
lcolor = '#0000ff'
lwidth = 1.0
fcolor = '#ffff00'
falpha = 0.2
# log the call
hashline = '----------------------------------------------------------------------------'
kepmsg.log(logfile, hashline, verbose)
call = 'KEPBLS -- '
call += 'infile=' + infile + ' '
call += 'outfile=' + outfile + ' '
call += 'datacol=' + str(datacol) + ' '
call += 'errcol=' + str(errcol) + ' '
call += 'minper=' + str(minper) + ' '
call += 'maxper=' + str(maxper) + ' '
call += 'mindur=' + str(mindur) + ' '
call += 'maxdur=' + str(maxdur) + ' '
call += 'nsearch=' + str(nsearch) + ' '
call += 'nbins=' + str(nbins) + ' '
plotit = 'n'
if (plot): plotit = 'y'
call += 'plot=' + plotit + ' '
overwrite = 'n'
if (clobber): overwrite = 'y'
call += 'clobber=' + overwrite + ' '
chatter = 'n'
if (verbose): chatter = 'y'
call += 'verbose=' + chatter + ' '
call += 'logfile=' + logfile
kepmsg.log(logfile, call + '\n', verbose)
# start time
kepmsg.clock('KEPBLS started at', logfile, verbose)
# is duration greater than one bin in the phased light curve?
if float(nbins) * maxdur / 24.0 / maxper <= 1.0:
message = 'WARNING -- KEPBLS: ' + str(
maxdur) + ' hours transit duration < 1 phase bin when P = '
message += str(maxper) + ' days'
kepmsg.warn(logfile, message)
# test log file
logfile = kepmsg.test(logfile)
# clobber output file
if clobber: status = kepio.clobber(outfile, logfile, verbose)
if kepio.fileexists(outfile):
message = 'ERROR -- KEPBLS: ' + outfile + ' exists. Use clobber=yes'
status = kepmsg.err(logfile, message, verbose)
# open input file
if status == 0:
instr, status = kepio.openfits(infile, 'readonly', logfile, verbose)
if status == 0:
tstart, tstop, bjdref, cadence, status = kepio.timekeys(
instr, infile, logfile, verbose, status)
# fudge non-compliant FITS keywords with no values
if status == 0:
instr = kepkey.emptykeys(instr, file, logfile, verbose)
# read table structure
if status == 0:
table, status = kepio.readfitstab(infile, instr[1], logfile, verbose)
# filter input data table
if status == 0:
work1 = numpy.array(
[table.field('time'),
table.field(datacol),
table.field(errcol)])
work1 = numpy.rot90(work1, 3)
work1 = work1[~numpy.isnan(work1).any(1)]
# read table columns
if status == 0:
intime = work1[:, 2] + bjdref
indata = work1[:, 1]
inerr = work1[:, 0]
# test whether the period range is sensible
if status == 0:
tr = intime[-1] - intime[0]
if maxper > tr:
message = 'ERROR -- KEPBLS: maxper is larger than the time range of the input data'
status = kepmsg.err(logfile, message, verbose)
# prepare time series
if status == 0:
work1 = intime - intime[0]
work2 = indata - numpy.mean(indata)
# start period search
if status == 0:
srMax = numpy.array([], dtype='float32')
transitDuration = numpy.array([], dtype='float32')
transitPhase = numpy.array([], dtype='float32')
dPeriod = (maxper - minper) / nsearch
trialPeriods = numpy.arange(minper,
maxper + dPeriod,
dPeriod,
dtype='float32')
complete = 0
print ' '
for trialPeriod in trialPeriods:
fracComplete = float(complete) / float(len(trialPeriods) -
1) * 100.0
txt = '\r'
txt += 'Trial period = '
txt += str(int(trialPeriod))
txt += ' days ['
txt += str(int(fracComplete))
txt += '% complete]'
txt += ' ' * 20
sys.stdout.write(txt)
sys.stdout.flush()
complete += 1
srMax = numpy.append(srMax, 0.0)
transitDuration = numpy.append(transitDuration, numpy.nan)
transitPhase = numpy.append(transitPhase, numpy.nan)
trialFrequency = 1.0 / trialPeriod
# minimum and maximum transit durations in quantized phase units
duration1 = max(int(float(nbins) * mindur / 24.0 / trialPeriod), 2)
duration2 = max(
int(float(nbins) * maxdur / 24.0 / trialPeriod) + 1,
duration1 + 1)
# 30 minutes in quantized phase units
halfHour = int(0.02083333 / trialPeriod * nbins + 1)
# compute folded time series with trial period
work4 = numpy.zeros((nbins), dtype='float32')
work5 = numpy.zeros((nbins), dtype='float32')
phase = numpy.array(
((work1 * trialFrequency) -
numpy.floor(work1 * trialFrequency)) * float(nbins),
dtype='int')
ptuple = numpy.array([phase, work2, inerr])
ptuple = numpy.rot90(ptuple, 3)
phsort = numpy.array(sorted(ptuple, key=lambda ph: ph[2]))
for i in range(nbins):
elements = numpy.nonzero(phsort[:, 2] == float(i))[0]
work4[i] = numpy.mean(phsort[elements, 1])
work5[i] = math.sqrt(
numpy.sum(numpy.power(phsort[elements, 0], 2)) /
len(elements))
# extend the work arrays beyond nbins by wrapping
work4 = numpy.append(work4, work4[:duration2])
work5 = numpy.append(work5, work5[:duration2])
# calculate weights of folded light curve points
sigmaSum = numpy.nansum(numpy.power(work5, -2))
omega = numpy.power(work5, -2) / sigmaSum
# calculate weighted phased light curve
s = omega * work4
# iterate through trial period phase
for i1 in range(nbins):
# iterate through transit durations
for duration in range(duration1, duration2 + 1, int(halfHour)):
# calculate maximum signal residue
i2 = i1 + duration
sr1 = numpy.sum(numpy.power(s[i1:i2], 2))
sr2 = numpy.sum(omega[i1:i2])
sr = math.sqrt(sr1 / (sr2 * (1.0 - sr2)))
if sr > srMax[-1]:
srMax[-1] = sr
transitDuration[-1] = float(duration)
transitPhase[-1] = float((i1 + i2) / 2)
# normalize maximum signal residue curve
bestSr = numpy.max(srMax)
bestTrial = numpy.nonzero(srMax == bestSr)[0][0]
srMax /= bestSr
transitDuration *= trialPeriods / 24.0
BJD0 = numpy.array(transitPhase * trialPeriods / nbins,
dtype='float64') + intime[0] - 2454833.0
print '\n'
# clean up x-axis unit
if status == 0:
ptime = copy(trialPeriods)
xlab = 'Trial Period (days)'
# clean up y-axis units
if status == 0:
pout = copy(srMax)
ylab = 'Normalized Signal Residue'
# data limits
xmin = ptime.min()
xmax = ptime.max()
ymin = pout.min()
ymax = pout.max()
xr = xmax - xmin
yr = ymax - ymin
ptime = insert(ptime, [0], [ptime[0]])
ptime = append(ptime, [ptime[-1]])
pout = insert(pout, [0], [0.0])
pout = append(pout, 0.0)
# plot light curve
if status == 0 and plot:
plotLatex = True
try:
params = {
'backend': 'png',
'axes.linewidth': 2.5,
'axes.labelsize': labelsize,
'axes.font': 'sans-serif',
'axes.fontweight': 'bold',
'text.fontsize': 12,
'legend.fontsize': 12,
'xtick.labelsize': ticksize,
'ytick.labelsize': ticksize
}
rcParams.update(params)
except:
plotLatex = False
if status == 0 and plot:
pylab.figure(figsize=[xsize, ysize])
pylab.clf()
# plot data
ax = pylab.axes([0.06, 0.10, 0.93, 0.87])
# force tick labels to be absolute rather than relative
pylab.gca().xaxis.set_major_formatter(
pylab.ScalarFormatter(useOffset=False))
pylab.gca().yaxis.set_major_formatter(
pylab.ScalarFormatter(useOffset=False))
# rotate y labels by 90 deg
labels = ax.get_yticklabels()
pylab.setp(labels, 'rotation', 90)
# plot curve
if status == 0 and plot:
pylab.plot(ptime[1:-1],
pout[1:-1],
color=lcolor,
linestyle='-',
linewidth=lwidth)
pylab.fill(ptime, pout, color=fcolor, linewidth=0.0, alpha=falpha)
pylab.xlabel(xlab, {'color': 'k'})
pylab.ylabel(ylab, {'color': 'k'})
pylab.grid()
# plot ranges
if status == 0 and plot:
pylab.xlim(xmin - xr * 0.01, xmax + xr * 0.01)
if ymin >= 0.0:
pylab.ylim(ymin - yr * 0.01, ymax + yr * 0.01)
else:
pylab.ylim(1.0e-10, ymax + yr * 0.01)
# render plot
if status == 0 and plot:
if cmdLine:
pylab.show()
else:
pylab.ion()
pylab.plot([])
pylab.ioff()
# append new BLS data extension to the output file
if status == 0:
col1 = Column(name='PERIOD',
format='E',
unit='days',
array=trialPeriods)
col2 = Column(name='BJD0',
format='D',
unit='BJD - 2454833',
array=BJD0)
col3 = Column(name='DURATION',
format='E',
unit='hours',
array=transitDuration)
col4 = Column(name='SIG_RES', format='E', array=srMax)
cols = ColDefs([col1, col2, col3, col4])
instr.append(new_table(cols))
instr[-1].header.cards['TTYPE1'].comment = 'column title: trial period'
instr[-1].header.cards[
'TTYPE2'].comment = 'column title: trial mid-transit zero-point'
instr[-1].header.cards[
'TTYPE3'].comment = 'column title: trial transit duration'
instr[-1].header.cards[
'TTYPE4'].comment = 'column title: normalized signal residue'
instr[-1].header.cards['TFORM1'].comment = 'column type: float32'
instr[-1].header.cards['TFORM2'].comment = 'column type: float64'
instr[-1].header.cards['TFORM3'].comment = 'column type: float32'
instr[-1].header.cards['TFORM4'].comment = 'column type: float32'
instr[-1].header.cards['TUNIT1'].comment = 'column units: days'
instr[-1].header.cards[
'TUNIT2'].comment = 'column units: BJD - 2454833'
instr[-1].header.cards['TUNIT3'].comment = 'column units: hours'
instr[-1].header.update('EXTNAME', 'BLS', 'extension name')
instr[-1].header.update('PERIOD', trialPeriods[bestTrial],
'most significant trial period [d]')
instr[-1].header.update('BJD0', BJD0[bestTrial] + 2454833.0,
'time of mid-transit [BJD]')
instr[-1].header.update('TRANSDUR', transitDuration[bestTrial],
'transit duration [hours]')
instr[-1].header.update('SIGNRES', srMax[bestTrial] * bestSr,
'maximum signal residue')
# history keyword in output file
if status == 0:
status = kepkey.history(call, instr[0], outfile, logfile, verbose)
instr.writeto(outfile)
# close input file
if status == 0:
status = kepio.closefits(instr, logfile, verbose)
# print best trial period results
if status == 0:
print ' Best trial period = %.5f days' % trialPeriods[bestTrial]
print ' Time of mid-transit = BJD %.5f' % (BJD0[bestTrial] +
2454833.0)
print ' Transit duration = %.5f hours' % transitDuration[
bestTrial]
print ' Maximum signal residue = %.4g \n' % (srMax[bestTrial] * bestSr)
# end time
if (status == 0):
message = 'KEPBLS completed at'
else:
message = '\nKEPBLS aborted at'
kepmsg.clock(message, logfile, verbose)
import sys
sys.path.insert(0, '..')
import numpy as np
import pylab as pb
from gp import chgp
from gp import hgp
import kern
pb.ion()
#build a double-hierarchy HGP
#1) construct the data
genenames = ['foo', 'bar', 'baz', 'bex']
Nrep = 5
Ngene = len(genenames)
Nd = [np.random.randint(2, 8) for i in range(Nrep)]
X = [np.random.randn(Ndi, 1) for Ndi in Nd]
[xx.sort(0) for xx in X]
Y = [[
np.sin(xx) + 0.3 * np.sin(xx + 5 * np.random.rand()) +
0.5 * np.sin(xx + 10. * gs) + 0.05 * np.random.randn(Ndi, 1)
for Ndi, xx in zip(Nd, X)
] for g, gs in enumerate([np.random.randn() for i in range(Ngene)])]
#2) construct the pdata
pdata_chgp = np.vstack(
[np.tile([[str(i)]], (Ndi, 1)) for i, Ndi in enumerate(Nd)])
pdata_rep = np.tile(pdata_chgp, (Ngene, 1))
pdata_gene = np.vstack(
[np.tile([[str(i)]],
np.vstack(X).shape) for i in range(Ngene)])
from __future__ import absolute_import
import theano
import matplotlib
if 'MACOSX' in matplotlib.get_backend().upper():
matplotlib.use('TKAgg')
import pylab as py
py.ion() ## Turn on plot visualization
import gzip, pickle
import numpy as np
from PIL import Image
import cv2
import keras.backend as K
K.set_image_dim_ordering('th')
from keras.layers import Input, merge, TimeDistributed, LSTM, GRU, RepeatVector
from keras.models import Sequential, Model
from keras.layers.core import Flatten, Dense, Dropout, Activation, Reshape
from keras.initializations import normal, identity, he_normal, glorot_normal, glorot_uniform, he_uniform
from keras.layers.normalization import BatchNormalization
import threading
############# Define Data Generators ################
class ImageNoiseDataGenerator(object):
'''Generate minibatches with
realtime data augmentation.
'''
def __init__(self, corruption_level=0.5):
self.__dict__.update(locals())
self.p = corruption_level
def lsm_matching(patch, lsm_search, pointAdjusted, lsm_buffer, thresh=0.001):
# source code from Ellen Schwalbe rewritten for Python
#x1, y1 of patch (template); x2, y2 of search area (little bit bigger)
add_val = 1
px = patch.shape[1]
py = patch.shape[0]
n = px * py
dif_patch_lsm_size_x = (lsm_search.shape[1] - patch.shape[1]) / 2
dif_patch_lsm_size_y = (lsm_search.shape[0] - patch.shape[0]) / 2
p_shift_ini = pointImg()
p_shift_ini.x = np.int(lsm_search.shape[1] / 2)
p_shift_ini.y = np.int(lsm_search.shape[0] / 2)
#approximation
U = np.asarray(
[np.int(lsm_search.shape[1] / 2),
np.int(lsm_search.shape[0] / 2)],
dtype=np.float)
# #tx, ty, alpha
# U = np.asarray([np.int(lsm_search.shape[1]/2), np.int(lsm_search.shape[0]/2),
# np.float(0)], dtype=np.float)
A = np.zeros((n, U.shape[0]))
l = np.zeros((n, 1))
for i in range(100): #number of maximum iterations
lsm_search = contrastAdaption(patch, lsm_search)
lsm_search = brightnessAdaption(patch, lsm_search)
#calculate gradient at corresponding (adjusting) position U
count = 0
img_test_search = np.zeros((lsm_search.shape[0], lsm_search.shape[1]))
img_test_patch = np.zeros((patch.shape[0], patch.shape[1]))
for x1 in range(px):
for y1 in range(py):
if (U[0] - p_shift_ini.x < -(lsm_buffer + dif_patch_lsm_size_x)
or U[0] - p_shift_ini.x >
lsm_search.shape[1] + lsm_buffer - 1
or U[1] - p_shift_ini.y <
-(lsm_buffer + dif_patch_lsm_size_y)
or U[1] - p_shift_ini.y >
lsm_search.shape[0] + lsm_buffer - 1):
print(count, i)
print('patch out of search area')
return 1 / 0
x2 = x1 + U[
0] - p_shift_ini.x + dif_patch_lsm_size_x #shift to coordinate system of lsm_search
y2 = y1 + U[1] - p_shift_ini.y + dif_patch_lsm_size_y
# #rotation and translation
# x2 = x1 * np.cos(U[2]) - y1 * np.sin(U[2]) + U[0]-p_shift_ini.x + dif_patch_lsm_size_x
# y2 = x1 * np.sin(U[2]) + y1 * np.cos(U[2]) + U[1]-p_shift_ini.y + dif_patch_lsm_size_y
g1 = patch[int(y1), int(x1)]
g2 = interopolateGreyvalue(lsm_search, x2, y2)
img_test_patch[y1, x1] = g1
img_test_search[int(y2), int(x2)] = g2
plt.ion()
#translation x
gx1 = interopolateGreyvalue(lsm_search, x2 - add_val, y2)
gx2 = interopolateGreyvalue(lsm_search, x2 + add_val, y2)
#translation y
gy1 = interopolateGreyvalue(lsm_search, x2, y2 - add_val)
gy2 = interopolateGreyvalue(lsm_search, x2, y2 + add_val)
# #rotation
# galpha1 = interopolateGreyvalue(lsm_search, x2, y2, 1)
# galpha2 = interopolateGreyvalue(lsm_search, x2, y2, -1)
plt.close('all')
if g1 < 0 or g2 < 0 or gx1 < 0 or gy1 < 0 or gx2 < 0 or gy2 < 0:
print(count, i)
print('error during gradient calculation')
return 1 / 0
l[count] = g2 - g1
#translation
A[count, 0] = gx1 - gx2
A[count, 1] = gy1 - gy2
# #rotation
# A[count, 2] = galpha1-galpha2
count = count + 1
#perform adjustment with gradients
dx_lsm, s0 = adjustmentGradient(A, l)
#adds corrections to the values of unknowns
SUM = 0
for j in range(U.shape[0]):
U[j] = U[j] + dx_lsm[j]
SUM = SUM + np.abs(dx_lsm[j])
# print SUM, U, dx_lsm
#stops the iteration if sum of additions is very small
if (SUM < thresh):
pointAdjusted.x = U[0]
pointAdjusted.y = U[1]
pointAdjusted.s0 = s0
pointAdjusted.usedObserv = n
return pointAdjusted
print('adjustment not converging')
return -1
def plotgauge(gaugeno, plotdata, verbose=False):
#==========================================
"""
Plot all requested plots for a single gauge from the computation.
The plots are requested by setting attributes of plotdata
to ClawPlotFigure objects with plot_type="each_gauge".
"""
if verbose:
gaugesoln = plotdata.getgauge(gaugeno)
print ' Plotting gauge %s at x = %s, y = %s ... ' \
% (gaugeno, gaugesoln.location[0], gaugesoln.location[1])
if plotdata.mode() == 'iplotclaw':
pylab.ion()
try:
plotfigure_dict = plotdata.plotfigure_dict
except:
print '*** Error in plotgauge: plotdata missing plotfigure_dict'
print '*** This should not happen'
return None
if len(plotfigure_dict) == 0:
print '*** Warning in plotgauge: plotdata has empty plotfigure_dict'
print '*** Apparently no figures to plot'
# initialize current_data containing data that will be passed
# to beforegauge, aftergauge, afteraxes commands
current_data = clawdata.ClawData()
current_data.add_attribute("user", {}) # for user specified attributes
# to avoid potential conflicts
current_data.add_attribute('plotdata', plotdata)
current_data.add_attribute('gaugeno', gaugeno)
# call beforegauge if present, which might define additional
# attributes in current_data or otherwise set up plotting for this
# gauge.
beforegauge = getattr(plotdata, 'beforegauge', None)
if beforegauge:
if isinstance(beforegauge, str):
# a string to be executed
exec(beforegauge)
else:
# assume it's a function
try:
output = beforegauge(current_data)
if output: current_data = output
except:
print '*** Error in beforegauge ***'
raise
# iterate over each single plot that makes up this gauge:
# -------------------------------------------------------
if plotdata._mode == 'iplotclaw':
gaugesoln = plotdata.getgauge(gaugeno)
print ' Plotting Gauge %s at x = %s, y = %s ... ' \
% (gaugeno, gaugesoln.location[0], gaugesoln.location[1])
requested_fignos = plotdata.iplotclaw_fignos
else:
requested_fignos = plotdata.print_fignos
plotted_fignos = []
plotdata = set_show(plotdata) # set _show attributes for which figures
# and axes should be shown.
# loop over figures to appear for this gauge:
# -------------------------------------------
for figname in plotdata._fignames:
plotfigure = plotdata.plotfigure_dict[figname]
if (not plotfigure._show) or (plotfigure.type != 'each_gauge'):
continue # skip to next figure
figno = plotfigure.figno
if requested_fignos != 'all':
if figno not in requested_fignos:
continue # skip to next figure
plotted_fignos.append(figno)
if not plotfigure.kwargs.has_key('facecolor'):
# use Clawpack's default bg color (tan)
plotfigure.kwargs['facecolor'] = '#ffeebb'
# create figure and set handle:
plotfigure._handle = pylab.figure(num=figno, **plotfigure.kwargs)
pylab.ioff()
if plotfigure.clf_each_gauge:
pylab.clf()
try:
plotaxes_dict = plotfigure.plotaxes_dict
except:
print '*** Error in plotgauge: plotdata missing plotaxes_dict'
print '*** This should not happen'
return None
if (len(plotaxes_dict) == 0) or (len(plotfigure._axesnames) == 0):
print '*** Warning in plotgauge: plotdata has empty plotaxes_dict'
print '*** Apparently no axes to plot in figno ', figno
# loop over axes to appear on this figure:
# ----------------------------------------
for axesname in plotfigure._axesnames:
plotaxes = plotaxes_dict[axesname]
if not plotaxes._show:
continue # skip this axes if no items show
# create the axes:
axescmd = getattr(plotaxes, 'axescmd', 'subplot(1,1,1)')
axescmd = 'plotaxes._handle = pylab.%s' % axescmd
exec(axescmd)
pylab.hold(True)
# loop over items:
# ----------------
for itemname in plotaxes._itemnames:
plotitem = plotaxes.plotitem_dict[itemname]
outdir = plotitem.outdir
if outdir is None:
outdir = plotdata.outdir
gaugesoln = plotdata.getgauge(gaugeno, outdir)
current_data.add_attribute('gaugesoln', gaugesoln)
current_data.add_attribute('q', gaugesoln.q)
current_data.add_attribute('t', gaugesoln.t)
if plotitem._show:
try:
output = plotgauge1(gaugesoln, plotitem, current_data)
if output: current_data = output
if verbose:
print ' Plotted plotitem ', itemname
except:
print '*** Error in plotgauge: problem calling plotgauge1'
traceback.print_exc()
return None
# end of loop over plotitems
for itemname in plotaxes._itemnames:
plotitem = plotaxes.plotitem_dict[itemname]
pylab.title("%s at gauge %s" % (plotaxes.title, gaugeno))
# call an afteraxes function if present:
afteraxes = getattr(plotaxes, 'afteraxes', None)
if afteraxes:
if isinstance(afteraxes, str):
# a string to be executed
exec(afteraxes)
else:
# assume it's a function
try:
current_data.add_attribute("plotaxes", plotaxes)
current_data.add_attribute("plotfigure",
plotaxes._plotfigure)
output = afteraxes(current_data)
if output: current_data = output
except:
print '*** Error in afteraxes ***'
raise
if plotaxes.scaled:
pylab.axis('scaled')
# set axes limits:
if (plotaxes.xlimits is not None) & (type(plotaxes.xlimits)
is not str):
try:
pylab.xlim(plotaxes.xlimits[0], plotaxes.xlimits[1])
except:
pass # let axis be set automatically
if (plotaxes.ylimits is not None) & (type(plotaxes.ylimits)
is not str):
try:
pylab.ylim(plotaxes.ylimits[0], plotaxes.ylimits[1])
except:
pass # let axis be set automatically
# end of loop over plotaxes
# end of loop over plotfigures
# call an aftergauge function if present:
aftergauge = getattr(plotdata, 'aftergauge', None)
if aftergauge:
if isinstance(aftergauge, str):
# a string to be executed
exec(aftergauge)
else:
# assume it's a function
try:
output = aftergauge(current_data)
if output: current_data = output
except:
print '*** Error in aftergauge ***'
raise
if plotdata.mode() == 'iplotclaw':
pylab.ion()
for figno in plotted_fignos:
pylab.figure(figno)
pylab.draw()
if verbose:
print ' Done with plotgauge for gauge %i' % (gaugeno)
# print the figure(s) to file(s) if requested:
if (plotdata.mode() != 'iplotclaw') & plotdata.printfigs:
# iterate over all figures that are to be printed:
for figno in plotted_fignos:
printfig(gaugeno=gaugeno, figno=figno, \
format=plotdata.print_format, plotdir=plotdata.plotdir,\
verbose=verbose)
return current_data
0,
but_h,
fun=callback.Xfrew)
bfrew = mybut('<<', fig, button_layout_cursor, y0, 0, but_h, fun=callback.frew)
brew = mybut('<', fig, button_layout_cursor, y0, 0, but_h, fun=callback.rew)
bshot = mybut('12345',
fig,
button_layout_cursor,
y0,
0,
but_h,
fun=callback.shot)
bfwd = mybut('>', fig, button_layout_cursor, y0, 0, but_h, fun=callback.fwd)
bffwd = mybut('>>', fig, button_layout_cursor, y0, 0, but_h, fun=callback.ffwd)
bXffwd = mybut('>>>',
fig,
button_layout_cursor,
y0,
0,
but_h,
fun=callback.Xffwd)
if oldinter: pl.ion()
# this is sort of initialisation code, but needed to be in a function
if HaveTix: ShotWid()
callback.redraw()
pl.show()
kwargs = dict(nwalkers=args.nwalkers,nburn=args.nburn,
nsteps=args.nsteps,nthreads=args.nthreads, sigmaprior=args.sigmaprior)
samples,sampler = mcmc(vel,velerr,**kwargs)
mean,std = scipy.stats.norm.fit(vel)
print '%-05s : %.2f'%('mean',mean)
print '%-05s : %.2f'%('std',std)
intervals = []
for i,name in enumerate(PARAMS.keys()):
peak,[low,high] = peak_interval(samples[name],alpha=alpha)
print "%-05s : %.2f [%.2f,%.2f]"%(name,peak,low,high)
intervals.append([low,high])
if args.plot:
try:
import pylab as plt
fig = plot(samples,intervals,sigma_clip=4)
plt.ion(); plt.show()
outfile = os.path.splitext(args.infile)[0]+'.pdf'
warnings.filterwarnings('ignore')
plt.savefig(outfile)
warnings.resetwarnings()
except ImportError as e:
msg = '\n '+e.message
msg +='\n Failed to create plot.'
warnings.warn(msg)
import scipy as sc
output = sc.test('all', raise_warnings='release')
import pylab as gr
import matplotlib as mpl
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from matplotlib.widgets import Slider, Button, RadioButtons
import scipy.io as sio
import sympy as sy
from analysis1 import GetLocalExtrema
gr.ion()
x, p = sy.symbols('x p')
a, pa, r, xr = sy.symbols('a pa r xr')
h = sy.symbols('h')
dpAP = a * (pa - p) + h * (1 - p)
dxAP = r * x * (xr - x) + p * (1 - x)
dp = a * (p - pa)
dx = r * x * (xr - x)
# Stimulus
pars = {
'timeStart': 0.0,
'timeMax': 500.0,
'timeStep': 1e-3,
'tauX': 75.0,
'tauP': 75.0,
'asynX': 1.0,
'asynP': 0.3,
'kP': 0.0,
def performFeatureTracking(template_size,
search_area,
initCooTemplate,
templateImage,
searchImage,
shiftSearchArea,
performLSM=True,
lsm_buffer=3,
thresh=0.001,
subpixel=False,
plot_result=False):
#template_size: np.array([template_width, template_height])
#search_area: np.array([search_area_x_CC, search_area_y_CC])
#initCooTemplate: np.array([x,y])
#shiftSearchArea: np.array([shiftFromCenter_x, shiftFromCenter_y])
template_width = template_size[0]
template_height = template_size[1]
search_area_x = search_area[0]
search_area_y = search_area[1]
shiftSearchArea_x = shiftSearchArea[0]
shiftSearchArea_y = shiftSearchArea[1]
#check if template sizes even and correct correspondingly
if int(template_width) % 2 == 0:
template_width = template_width + 1
if int(template_height) % 2 == 0:
template_height = template_height + 1
if int(search_area_x) % 2 == 0:
search_area_x = search_area_x + 1
if int(search_area_y) % 2 == 0:
search_area_y = search_area_y + 1
#get patch clip
if plot_result:
plt.imshow(templateImage)
plt.plot(initCooTemplate[0], initCooTemplate[1], "r.", markersize=10)
plt.waitforbuttonpress()
plt.cla()
plt.close('all')
try:
patch, _ = getTemplate(templateImage, initCooTemplate, template_width,
template_height, True)
except Exception as e:
# _, _, exc_tb = sys.exc_info()
# print(e, 'line ' + str(exc_tb.tb_lineno))
print('template patch reaches border')
return 1 / 0
#shift search area to corresponding position considering movement direction
templateCoo_init_shift = np.array([
initCooTemplate[0] + shiftSearchArea_x,
initCooTemplate[1] + shiftSearchArea_y
])
#get lsm search clip
try:
search_area, lowerLeftCoo_lsm_search = getTemplate(
searchImage, templateCoo_init_shift, search_area_x, search_area_y,
True)
except Exception as e:
# _, _, exc_tb = sys.exc_info()
# print(e, 'line ' + str(exc_tb.tb_lineno))
print('search patch reaches border')
return 1 / 0
if plot_result:
plt.ion()
CC_xy = crossCorrelation(search_area, patch, lowerLeftCoo_lsm_search,
plot_result, subpixel)
if CC_xy[0] == -999:
return 1 / 0
if plot_result:
plt.close('all')
print(CC_xy)
TrackedFeature = CC_xy
if performLSM:
#perform least square matching (subpixel accuracy possible)
try:
lsm_search, lowerLeftCoo_lsm_search = getTemplate(
searchImage, CC_xy, search_area_x, search_area_y, True)
except Exception as e:
# _, _, exc_tb = sys.exc_info()
# print(e, 'line ' + str(exc_tb.tb_lineno))
print('lsm patch reaches border')
return 1 / 0
if plot_result:
plt.imshow(lsm_search)
plt.waitforbuttonpress()
plt.close('all')
pointAdjusted_ = pointAdjusted()
try:
result_lsm = lsm_matching(patch, lsm_search, pointAdjusted_,
lsm_buffer, thresh)
print('sigma LSM tracking: ' + str(result_lsm.s0))
if plot_result:
plt.imshow(searchImage, cmap='gray')
plt.plot(result_lsm.y + lowerLeftCoo_lsm_search[0],
result_lsm.x + lowerLeftCoo_lsm_search[1],
"b.",
markersize=10)
plt.waitforbuttonpress()
plt.close('all')
TrackedFeature = np.asarray([result_lsm.x, result_lsm.y])
except Exception as e:
# _, _, exc_tb = sys.exc_info()
# print(e, 'line ' + str(exc_tb.tb_lineno))
print('lsm failed')
return TrackedFeature
def main():
p = ArgumentParser()
p.add_argument('filename', help='Path to csv file containing the results.')
p.add_argument('baseline', help='Path to csv file containing the results.')
p.add_argument('--accuracy', required=1)
p.add_argument('--runtime', required=1)
p.add_argument('--data', choices=('train', 'dev'), default='dev')
# p.add_argument('--save')
args = p.parse_args()
df = pandas.read_csv(args.filename)
RUNTIME = '%s_new_policy_%s' % (args.data, args.runtime)
ACCURACY = '%s_new_policy_%s' % (args.data, args.accuracy)
df.sort_values(RUNTIME, inplace=1, ascending=False)
[grammar] = df.args_grammar.unique()
print 'Grammar: %s' % grammar
assert not df.empty
print df[[ACCURACY, RUNTIME, 'tradeoff', 'jobid']]
rescale = 1 / df[RUNTIME].max()
ax = pl.figure().add_subplot(111)
#pl.axes(frameon=0)
#pl.grid()
ax.spines['top'].set_visible(False)
ax.spines['right'].set_visible(False)
ax.spines['left'].set_visible(False)
ax.spines['bottom'].set_visible(False)
B = pandas.read_csv(args.baseline)
df = df[(df.args_accuracy == args.accuracy)
& (df.args_runtime == args.runtime)
& (df.args_classifier == 'LOGISTIC')]
# filter out points we didn't use from the baseline.
used = []
for _, lols in df.iterrows():
[ix] = B[B.tradeoff == lols.args_initializer_penalty].index
used.append(ix)
B = B.ix[used]
lambda_cone(B[ACCURACY],
B[RUNTIME] * rescale,
ax,
c=c_baseline,
conesize=0.05)
lols_front = []
for _, lols in df.iterrows():
penalty = lols.args_initializer_penalty
init = B[B.tradeoff == penalty]
assert len(init) == 1
x = float(init[RUNTIME] * rescale)
y = float(init[ACCURACY])
tradeoff = lols.tradeoff / rescale
# baseline vector (target direction)
arrow(x, y, tradeoff, offset=-0.05, c=c_vec_baseline, ax=ax)
# baseline point
ax.scatter([B[RUNTIME] * rescale], [B[ACCURACY]],
c=c_vec_baseline,
lw=0,
s=9)
# LOLS learning curve (squirt)
squirt = pandas.read_csv(lols.log)
ax.scatter(squirt[RUNTIME] * rescale,
squirt[ACCURACY],
lw=0,
c=c_lols,
s=8,
alpha=.5)
print 'acc iter1: %g init: %g' % (
squirt[squirt.iteration == 1][ACCURACY], init[ACCURACY])
print 'run iter1: %g init: %g' % (
squirt[squirt.iteration == 1][RUNTIME], init[RUNTIME])
assert abs(
float(squirt[squirt.iteration == 1][ACCURACY]) -
float(init[ACCURACY])) < 1e-3
assert abs(
float(squirt[squirt.iteration == 1][RUNTIME]) -
float(init[RUNTIME])) < 1e-3
# re-do early stopping
early_stop = squirt[ACCURACY] - squirt[RUNTIME] * squirt.tradeoff
lols = squirt.ix[early_stop.argmax()]
# lols = squirt.ix[squirt.iteration.argmax()]
if abs(x - lols[RUNTIME] * rescale) + abs(y - lols[ACCURACY]) > 1e-10:
# LOLS vector
ax.annotate("",
xy=(lols[RUNTIME] * rescale, lols[ACCURACY]),
xytext=(x, y),
arrowprops=dict(arrowstyle="->",
lw=2,
color=c_vec_lols,
connectionstyle="arc3"))
else:
print colors.yellow % 'no lols vector for this point'
print abs(x -
lols[RUNTIME] * rescale) + abs(y - lols[ACCURACY]), abs(
x - lols[RUNTIME] * rescale), abs(y - lols[ACCURACY])
print 'early stop iteration', lols.iteration
print early_stop
# LOLS vector end point (early stopping
ax.scatter([lols[RUNTIME] * rescale], [lols[ACCURACY]],
c=c_vec_lols,
s=13)
# show ugly read arrow to the last point.
if 0:
last = squirt.ix[squirt.iteration.argmax()]
ax.annotate("",
xy=(last[RUNTIME] * rescale, last[ACCURACY]),
xytext=(x, y),
arrowprops=dict(arrowstyle="->",
lw=2,
color='r',
connectionstyle="arc3"))
lols_front.append([lols[RUNTIME] * rescale, lols[ACCURACY]])
# LOLS pareto frontier.
xx, yy = zip(*lols_front)
show_frontier(xx,
yy,
c=c_vec_lols,
alpha=0.4,
zorder=10,
interpolation='linear-convex',
ax=ax)
# tick labels.
xx = B[RUNTIME] * rescale
#xx = np.linspace(xx.min(), xx.max(), 12)
if args.runtime == 'pops':
ax.set_xlabel(r'runtime (avg constituents built)')
elif args.runtime == 'mask':
ax.set_xlabel('runtime (avg spans allowed)')
elif args.runtime == 'pushes':
ax.set_xlabel('Runtime (Avg $|E|$)')
pl.xticks(xx, ['%.f' % (x / rescale) for x in xx], rotation=45)
# show all learning curves.
if 0:
pl.figure()
for _, lols in df.iterrows():
squirt = pandas.read_csv(lols.log)
#pl.figure()
#pl.plot(squirt[RUNTIME]*rescale, squirt[ACCURACY])
R = squirt[ACCURACY] - squirt.tradeoff * squirt[RUNTIME]
pl.plot(squirt.iteration, R)
#xx=B[ACCURACY]
#pl.yticks(xx, ['%.3f' % (x) for x in xx])
pl.ion()
pl.show()
# # not ready for prime time because axes limits aren't set.
# if args.save:
# save = True
# if path(args.save).exists():
# save = False
# print bold % colors.yellow % "File exists (%s)" % args.save
# print bold % colors.yellow % "Overwrite existing file [y/N]?",
# if raw_input().strip().lower() in ('y','yes'):
# save = True
# if save:
# print bold % colors.yellow % "Saved file %s" % args.save
# pl.savefig(args.save)
t = ['Controlled experiments (dev)']
[G] = df.args_grammar.unique()
if 'medium' in G:
t.append('small grammar')
elif 'big' in G:
t.append('big grammar')
[RO] = df.args_roll_out.unique()
if 'CP' in RO:
t.append('$r_{\\textit{CP}}$')
elif 'DP' in RO:
t.append('$r_{\\textit{DP}}$')
elif 'BF' in RO:
t.append('$r_{\\textit{BF}}$')
elif 'HY' in RO:
t.append('$r_{\\textit{HY}}$')
if args.accuracy == 'expected_recall_avg':
ax.set_ylabel('accuracy (expected binarized recall)')
elif args.accuracy == 'evalb_avg':
ax.set_ylabel('accuracy (avg single-sentence F1)')
#pl.title(', '.join(t))
print B[[ACCURACY, RUNTIME]]
ax.figure.tight_layout()
pl.ioff()
pl.show()
def create_images_png(filename, outfilename='Default'):
"""Creates the original, clean, and mask images in single a PNG.
Useful for checking how well LACosmic worked.
You may want to adjust the size of the "cut" images so to
capture your source star.
Parameters:
filename : string
Name of the original FITS image, including the path.
outfilename : string, optional
Name of the outfile PNG.
Returns:
nothing
Outputs:
PNG file. ``<file rootname>.png`` by default.
Shows both full frame images and "cut" images of the source.
"""
pylab.ioff()
# create page for plots
page_width = 21.59 / 2
page_height = 27.94 / 2
fig = pylab.figure(figsize=(page_width, page_height))
file_clean = (filename.split('.fits')[0] + '.clean.fits')
file_mask = (filename.split('.fits')[0] + '.mask.fits')
scmax = 7000 # scale_max for raw and clean
scmin = 3 # scale_min for raw and clean
# Plot the original image
pylab.subplot(3, 2, 1, aspect='equal') # 311
image_orig = fits.open(filename)
image_orig_ext = image_orig[1].data
image_orig_scaled = img_scale.log(image_orig_ext, \
scale_min=scmin, \
scale_max=scmax)
plt_orig = pylab.imshow(image_orig_scaled, aspect='equal')
pylab.title('Original (SCI)')
# Plot cut of original image
pylab.subplot(3, 2, 2, aspect='equal')
image_orig_cut = img_scale.log(image_orig_ext[175:275,175:275], \
scale_min=scmin, \
scale_max=scmax)
plt_orig_cut = pylab.imshow(image_orig_cut, aspect='equal')
pylab.title('Original (SCI)')
image_orig.close()
# Plot the mask image
pylab.subplot(3, 2, 3) #312
image_mask = fits.open(file_mask)
image_mask_ext = image_mask[0].data
plt_orig = pylab.imshow(image_mask_ext, aspect='equal', vmin=-2,
vmax=1) #-2, -5
pylab.title('Mask')
# Plot cut of the mask image
pylab.subplot(3, 2, 4)
plt_mask_cut = pylab.imshow(image_mask_ext[175:275,175:275], \
aspect='equal', vmin=-2, vmax=1)
pylab.title('Mask')
image_mask.close()
# Plot the LACosmic-cleaned image
pylab.subplot(3, 2, 5) #313
image_clean = fits.open(file_clean)
image_clean_ext = image_clean[0].data
image_clean_scaled = img_scale.log(image_clean_ext, \
scale_min=scmin, \
scale_max=scmax)
plt_clean = pylab.imshow(image_clean_scaled, aspect='equal')
pylab.title('Clean')
#Plot cut of the LACosmic-cleaned image
pylab.subplot(3, 2, 6)
image_clean_cut = img_scale.log(image_clean_ext[175:275,175:275], \
scale_min=scmin, scale_max=scmax)
plt_clean_cut = pylab.imshow(image_clean_cut, aspect='equal')
pylab.title('Clean')
image_clean.close()
if outfilename == 'Default':
pylab.savefig(filename.split('.fits')[0] + '.png')
else:
pylab.savefig(outfilename)
pylab.close()
pylab.ion()
def view_patches_bar(Yr, A, C, b, f, d1, d2, YrA=None, img=None):
"""view spatial and temporal components interactively
Parameters:
-----------
Yr: np.ndarray
movie in format pixels (d) x frames (T)
A: sparse matrix
matrix of spatial components (d x K)
C: np.ndarray
matrix of temporal components (K x T)
b: np.ndarray
spatial background (vector of length d)
f: np.ndarray
temporal background (vector of length T)
d1,d2: np.ndarray
frame dimensions
YrA: np.ndarray
ROI filtered residual as it is given from update_temporal_components
If not given, then it is computed (K x T)
img: np.ndarray
background image for contour plotting. Default is the image of all spatial components (d1 x d2)
"""
pl.ion()
if 'csc_matrix' not in str(type(A)):
A = csc_matrix(A)
if 'array' not in str(type(b)):
b = b.toarray()
nr, T = C.shape
nb = f.shape[0]
nA2 = np.sqrt(np.array(A.power(2).sum(axis=0))).squeeze()
if YrA is None:
Y_r = spdiags(old_div(1, nA2), 0, nr, nr) * (A.T.dot(Yr) -
(A.T.dot(b)).dot(f) -
(A.dot(A)).dot(C)) + C
else:
Y_r = YrA + C
if img is None:
img = np.reshape(np.array(A.mean(axis=1)), (d1, d2), order='F')
fig = pl.figure(figsize=(10, 10))
axcomp = pl.axes([0.05, 0.05, 0.9, 0.03])
ax1 = pl.axes([0.05, 0.55, 0.4, 0.4])
ax3 = pl.axes([0.55, 0.55, 0.4, 0.4])
ax2 = pl.axes([0.05, 0.1, 0.9, 0.4])
s_comp = Slider(axcomp, 'Component', 0, nr + nb - 1, valinit=0)
vmax = np.percentile(img, 98)
def update(val):
i = np.int(np.round(s_comp.val))
print(('Component:' + str(i)))
if i < nr:
ax1.cla()
imgtmp = np.reshape(A[:, i].toarray(), (d1, d2), order='F')
ax1.imshow(imgtmp, interpolation='None', cmap=pl.cm.gray)
ax1.set_title('Spatial component ' + str(i + 1))
ax1.axis('off')
ax2.cla()
ax2.plot(np.arange(T), Y_r[i], 'c', linewidth=3)
ax2.plot(np.arange(T), C[i], 'r', linewidth=2)
ax2.set_title('Temporal component ' + str(i + 1))
ax2.legend(labels=['Filtered raw data', 'Inferred trace'])
ax3.cla()
ax3.imshow(img, interpolation='None', cmap=pl.cm.gray, vmax=vmax)
imgtmp2 = imgtmp.copy()
imgtmp2[imgtmp2 == 0] = np.nan
ax3.imshow(imgtmp2,
interpolation='None',
alpha=0.5,
cmap=pl.cm.hot)
ax3.axis('off')
else:
ax1.cla()
bkgrnd = np.reshape(b[:, i - nr], (d1, d2), order='F')
ax1.imshow(bkgrnd, interpolation='None')
ax1.set_title('Spatial background ' + str(i + 1 - nr))
ax1.axis('off')
ax2.cla()
ax2.plot(np.arange(T), np.squeeze(np.array(f[i - nr, :])))
ax2.set_title('Temporal background ' + str(i + 1 - nr))
def arrow_key_image_control(event):
if event.key == 'left':
new_val = np.round(s_comp.val - 1)
if new_val < 0:
new_val = 0
s_comp.set_val(new_val)
elif event.key == 'right':
new_val = np.round(s_comp.val + 1)
if new_val > nr + nb:
new_val = nr + nb
s_comp.set_val(new_val)
else:
pass
s_comp.on_changed(update)
s_comp.set_val(0)
fig.canvas.mpl_connect('key_release_event', arrow_key_image_control)
pl.show()
def mollzoom(map=None,
fig=None,
rot=None,
coord=None,
unit='',
xsize=800,
title='Mollweide view',
nest=False,
min=None,
max=None,
flip='astro',
remove_dip=False,
remove_mono=False,
gal_cut=0,
format='%g',
cmap=None,
norm=None,
hold=False,
margins=None,
sub=None):
"""Interactive mollweide plot with zoomed gnomview.
Parameters:
-----------
map : float, array-like shape (Npix,)
An array containing the map,
supports masked maps, see the `ma` function.
if None, use map with inf value (white map), useful for
overplotting
fig : a figure number.
Default: create a new figure
rot : scalar or sequence, optional
Describe the rotation to apply.
In the form (lon, lat, psi) (unit: degrees) : the point at
longitude *lon* and latitude *lat* will be at the center. An additional rotation
of angle *psi* around this direction is applied.
coord : sequence of character, optional
Either one of 'G', 'E' or 'C' to describe the coordinate
system of the map, or a sequence of 2 of these to rotate
the map from the first to the second coordinate system.
unit : str, optional
A text describing the unit of the data. Default: ''
xsize : int, optional
The size of the image. Default: 800
title : str, optional
The title of the plot. Default: 'Mollweide view'
nest : bool, optional
If True, ordering scheme is NESTED. Default: False (RING)
min : float, optional
The minimum range value
max : float, optional
The maximum range value
flip : {'astro', 'geo'}, optional
Defines the convention of projection : 'astro' (default, east towards left, west towards right)
or 'geo' (east towards roght, west towards left)
remove_dip : bool, optional
If :const:`True`, remove the dipole+monopole
remove_mono : bool, optional
If :const:`True`, remove the monopole
gal_cut : float, scalar, optional
Symmetric galactic cut for the dipole/monopole fit.
Removes points in latitude range [-gal_cut, +gal_cut]
format : str, optional
The format of the scale label. Default: '%g'
"""
import pylab
# create the figure (if interactive, it will open the window now)
f = pylab.figure(fig, figsize=(10.5, 5.4))
extent = (0.02, 0.25, 0.56, 0.72)
# Starting to draw : turn interactive off
wasinteractive = pylab.isinteractive()
pylab.ioff()
try:
if map is None:
map = np.zeros(12) + np.inf
map = pixelfunc.ma_to_array(map)
ax = PA.HpxMollweideAxes(f,
extent,
coord=coord,
rot=rot,
format=format,
flipconv=flip)
f.add_axes(ax)
if remove_dip:
map = pixelfunc.remove_dipole(map,
gal_cut=gal_cut,
nest=nest,
copy=True,
verbose=True)
elif remove_mono:
map = pixelfunc.remove_monopole(map,
gal_cut=gal_cut,
nest=nest,
copy=True,
verbose=True)
ax.projmap(map,
nest=nest,
xsize=xsize,
coord=coord,
vmin=min,
vmax=max,
cmap=cmap,
norm=norm)
im = ax.get_images()[0]
b = im.norm.inverse(np.linspace(0, 1, im.cmap.N + 1))
v = np.linspace(im.norm.vmin, im.norm.vmax, im.cmap.N)
if matplotlib.__version__ >= '0.91.0':
cb = f.colorbar(ax.get_images()[0],
ax=ax,
orientation='horizontal',
shrink=0.5,
aspect=25,
ticks=PA.BoundaryLocator(),
pad=0.05,
fraction=0.1,
boundaries=b,
values=v)
else:
# for older matplotlib versions, no ax kwarg
cb = f.colorbar(ax.get_images()[0],
orientation='horizontal',
shrink=0.5,
aspect=25,
ticks=PA.BoundaryLocator(),
pad=0.05,
fraction=0.1,
boundaries=b,
values=v)
ax.set_title(title)
ax.text(0.86,
0.05,
ax.proj.coordsysstr,
fontsize=14,
fontweight='bold',
transform=ax.transAxes)
cb.ax.text(1.05,
0.30,
unit,
fontsize=14,
fontweight='bold',
transform=cb.ax.transAxes,
ha='left',
va='center')
f.sca(ax)
## Gnomonic axes
#extent = (0.02,0.25,0.56,0.72)
g_xsize = 600
g_reso = 1.
extent = (0.60, 0.04, 0.38, 0.94)
g_ax = PA.HpxGnomonicAxes(f,
extent,
coord=coord,
rot=rot,
format=format,
flipconv=flip)
f.add_axes(g_ax)
if remove_dip:
map = pixelfunc.remove_dipole(map,
gal_cut=gal_cut,
nest=nest,
copy=True)
elif remove_mono:
map = pixelfunc.remove_monopole(map,
gal_cut=gal_cut,
nest=nest,
copy=True)
g_ax.projmap(map,
nest=nest,
coord=coord,
vmin=min,
vmax=max,
xsize=g_xsize,
ysize=g_xsize,
reso=g_reso,
cmap=cmap,
norm=norm)
im = g_ax.get_images()[0]
b = im.norm.inverse(np.linspace(0, 1, im.cmap.N + 1))
v = np.linspace(im.norm.vmin, im.norm.vmax, im.cmap.N)
if matplotlib.__version__ >= '0.91.0':
cb = f.colorbar(g_ax.get_images()[0],
ax=g_ax,
orientation='horizontal',
shrink=0.5,
aspect=25,
ticks=PA.BoundaryLocator(),
pad=0.08,
fraction=0.1,
boundaries=b,
values=v)
else:
cb = f.colorbar(g_ax.get_images()[0],
orientation='horizontal',
shrink=0.5,
aspect=25,
ticks=PA.BoundaryLocator(),
pad=0.08,
fraction=0.1,
boundaries=b,
values=v)
g_ax.set_title(title)
g_ax.text(-0.07,
0.02,
"%g '/pix, %dx%d pix" %
(g_ax.proj.arrayinfo['reso'], g_ax.proj.arrayinfo['xsize'],
g_ax.proj.arrayinfo['ysize']),
fontsize=12,
verticalalignment='bottom',
transform=g_ax.transAxes,
rotation=90)
g_ax.text(-0.07,
0.8,
g_ax.proj.coordsysstr,
fontsize=14,
fontweight='bold',
rotation=90,
transform=g_ax.transAxes)
lon, lat = np.around(g_ax.proj.get_center(lonlat=True),
g_ax._coordprec)
g_ax.text(0.5,
-0.03,
'on (%g,%g)' % (lon, lat),
verticalalignment='center',
horizontalalignment='center',
transform=g_ax.transAxes)
cb.ax.text(1.05,
0.30,
unit,
fontsize=14,
fontweight='bold',
transform=cb.ax.transAxes,
ha='left',
va='center')
# Add graticule info axes
grat_ax = pylab.axes([0.25, 0.02, 0.22, 0.25])
grat_ax.axis('off')
# Add help text
help_ax = pylab.axes([0.02, 0.02, 0.22, 0.25])
help_ax.axis('off')
t = help_ax.transAxes
help_ax.text(0.1,
0.8,
'r/t .... zoom out/in',
transform=t,
va='baseline')
help_ax.text(0.1,
0.65,
'p/v .... print coord/val',
transform=t,
va='baseline')
help_ax.text(0.1,
0.5,
'c ...... go to center',
transform=t,
va='baseline')
help_ax.text(0.1,
0.35,
'f ...... next color scale',
transform=t,
va='baseline')
help_ax.text(0.1,
0.2,
'k ...... save current scale',
transform=t,
va='baseline')
help_ax.text(0.1,
0.05,
'g ...... toggle graticule',
transform=t,
va='baseline')
f.sca(g_ax)
# Set up the zoom capability
zt = ZoomTool(map,
fig=f.number,
nest=nest,
cmap=cmap,
norm=norm,
coord=coord)
finally:
pylab.draw()
if wasinteractive:
pylab.ion()