def run_analysis(filename,mode,method):
click.echo('Reading file : %s'%filename)
data = IOfile.parsing_input_file(filename)
click.echo('Creating class...')
theclass = TFC(data)
click.echo('Calculating transfer function using %s method'%method)
if method=='tf_kramer286_sh':
theclass.tf_kramer286_sh()
elif method=='tf_knopoff_sh':
theclass.tf_knopoff_sh()
elif method=='tf_knopoff_sh_adv':
theclass.tf_knopoff_sh_adv()
plt.plot(theclass.freq,np.abs(theclass.tf[0]),label=method)
plt.xlabel('frequency (Hz)')
plt.ylabel('Amplification')
plt.yscale('log')
plt.xscale('log')
plt.grid(True,which='both')
plt.legend(loc='best',fancybox=True,framealpha=0.5)
#plt.axis('tight')
plt.autoscale(True,axis='x',tight=True)
plt.tight_layout()
plt.savefig('test.png', format='png')
click.echo(click.style('Calculation has been finished!',fg='green'))
def plot(self, y, *args, **kwargs):
'''
Plot something vs this frequency
This plots whateve is given vs. `self.f_scaled` and then
calls `labelXAxis`.
'''
try:
if len(shape(y))>2:
# perhapsthe dimensions are empty, try to squeeze it down
y= y.squeeze()
if len(shape(y))>2:
# the dimensions are full, so lets loop and plot each
for m in range(shape(y)[1]):
for n in range(shape(y)[2]):
self.plot(y[:,m,n], *args, **kwargs)
return
if len(y)==len(self):
pass
else:
raise IndexError(['thing to plot doesn\'t have same'
' number of points as f'])
except(TypeError):
y = y*npy.ones(len(self))
plot(self.f_scaled, y,*args, **kwargs)
autoscale(axis='x', tight=True)
self.labelXAxis()
def getValueGFP(self, radius=10, name='', plot=False):
mean = []
movie = np.zeros((self.images[0].shape[0],
self.images[0].shape[1] * self.lengthSeq))
if plot:
pylab.figure(figsize=(6, 22))
for index, im in enumerate(self.images):
center = [(self.params[index][1] + self.params[index][1 + 6]) / 2.,
(self.params[index][2] + self.params[index][2 + 6]) / 2.]
GFP = segmentationClass.Segmentation(im.image)
GFP.defineFG()
GFP.smooth_corr()
mask = GFP.rond_mask(center, radius)
val = np.sum(mask * GFP.smooth) / 1. / np.sum(mask)
#val = np.average(GFP.smooth)
movie[:,
index * im.shape[1]:(index + 1) * im.shape[1]] = GFP.smooth
mean.append(val)
if plot:
pylab.subplot(len(self.images), 2, 2 * index + 1)
pylab.imshow(GFP.smooth, 'gray')
#pylab.title("t = {0}".format())
pylab.axis('off')
pylab.subplot(len(self.images), 2, 2 * index + 2)
pylab.imshow(mask, 'gray')
pylab.autoscale(False)
pylab.axis('off')
pylab.plot(self.params[index][2::6], self.params[index][1::6],
'ro')
pylab.title('{0:.0f}'.format(val))
if plot:
pylab.savefig(name)
pylab.close()
return np.sum(nlargest(3, mean)) / 3., movie
def __init__(self, strictness=1):
self.on = False
self.pts = []
self.marks = []
self.fig = pl.gcf()
self.ax = pl.gca()
pl.autoscale(enable=False)
self.cid_move = self.fig.canvas.mpl_connect('motion_notify_event',
self.onmove)
self.cid_click = self.fig.canvas.mpl_connect('button_release_event',
self.onclick)
self.cid_exit = self.fig.canvas.mpl_connect('axes_leave_event',
self.onexit)
self.cid_keyup = self.fig.canvas.mpl_connect('key_release_event',
self.on_keyup)
img = self.ax.get_images()[0].get_array().view(np.ndarray)
img = (img - img.min()) / (img.max() - img.min())
img *= 255
img = img.astype(np.uint8)
edge_img = cv2.Canny(img, img.mean(),
img.mean() + strictness * img.std())
self.edge_pts = np.argwhere(edge_img)
self.fig.canvas.start_event_loop(timeout=-1)
def plot_cpu_usr_sys(dstat_dict):
figs = [x for x in dstat_dict.keys() if "cpu" in x]
if not figs:
print "No CPU data available to plot"
datetimes = [DT.datetime.strptime(t, "%d-%m %H:%M:%S")
for t in dstat_dict['time']]
hfmt = dates.DateFormatter('%H:%M:%S')
if len(figs) == 1:
plots = [plots]
for i in range(len(figs)):
f, plots = pl.subplots(1)
plots.plot(datetimes, dstat_dict[figs[i]]['usr'], 'r-', label="usr",
linewidth=.5)
plots.plot(datetimes, dstat_dict[figs[i]]['sys'], 'b-', label="sys",
linewidth=.5)
plots.set_title(figs[i]+" usr/sys")
plots.legend(loc='best')
plots.xaxis.set_major_locator(dates.MinuteLocator())
plots.xaxis.set_major_formatter(hfmt)
pl.xticks(rotation='vertical')
pl.subplots_adjust(bottom=.15)
pl.autoscale()
fil = figs[i]+"-usr-sys.svg"
print fil
pl.savefig(fil, format="svg")
def render_image(img):
print("rerendering..")
plt.clf()
plt.imshow(img)
plt.draw()
pl.autoscale(False)
print("OK")
def go(self):
self.rayss.append(self.bundles.generate_rays())
l = []
for k in self.rayss:
for i in k:
for j in self.lenses:
j.propagate_ray(i)
l.append(i.vertices())
for j in l:
x = []
y = []
z = []
for k in j:
x.append(k[0])
y.append(k[1])
z.append(k[2])
pl.figure(4)
pl.title("Ray displayed in x/z plane")
pl.xlabel("z displacement (mm)")
pl.ylabel("x displacement (mm)")
pl.plot(z, x, 'r')
pl.autoscale(enable=True, axis='y')
pl.autoscale(enable=True, axis='x')
pl.grid()
pl.show()
def plot(self, y, *args, **kwargs):
'''
Plot something vs this frequency
This plots whateve is given vs. `self.f_scaled` and then
calls `labelXAxis`.
'''
try:
if len(shape(y)) > 2:
# perhapsthe dimensions are empty, try to squeeze it down
y = y.squeeze()
if len(shape(y)) > 2:
# the dimensions are full, so lets loop and plot each
for m in range(shape(y)[1]):
for n in range(shape(y)[2]):
self.plot(y[:, m, n], *args, **kwargs)
return
if len(y) == len(self):
pass
else:
raise IndexError([
'thing to plot doesn\'t have same'
' number of points as f'
])
except (TypeError):
y = y * npy.ones(len(self))
plot(self.f_scaled, y, *args, **kwargs)
autoscale(axis='x', tight=True)
self.labelXAxis()
def main():
title = 'MoS$_2$-1ML (VASP-PAW-PBE.Mo_pv)'
xlabel = [
'$\mathrm{\Gamma}$', '$\mathrm{K}$', '$\mathrm{M}$',
'$\mathrm{\Gamma}$'
]
xlabelpos = [1, 21, 31, 48]
ylimit = [-6.5, 5.5]
yminor = 4
[nkpt, nband, nion, kpt, ev, proj] = read_procar()
efermi = get_efermi()
[econ, eval] = find_edges(ev, efermi + 1)
eshift = eval
fig = pl.gcf()
fig.set_size_inches(5, 6)
fig.subplots_adjust(bottom=0.05, left=0.12, top=0.94, right=0.96)
fig.set_dpi(300)
fig.suptitle(title, fontsize=13)
ax = pl.gca()
mpl.rcParams['font.sans-serif'] = 'Arial' #'Helvetica'
pl.ylabel('Energy (eV)', fontsize=12)
pl.xticks(xlabelpos, xlabel, size=12)
pl.yticks(size=10)
ax.yaxis.set_minor_locator(mpl.ticker.AutoMinorLocator(yminor))
pl.autoscale(enable=True, axis='y')
pl.tick_params(axis='y',
which='major',
direction='out',
length=3,
width=0.8,
left='on',
right='off',
pad=5)
pl.tick_params(axis='y',
which='minor',
direction='out',
length=2,
width=0.5,
left='on',
right='off')
pl.tick_params(axis='x', which='both', top='off', bottom='off')
for xline in xlabelpos:
pl.axvline(x=xline, color='k', linewidth=0.6)
x = np.arange(ev.shape[1]) + 1
for i in range(ev.shape[0]):
pl.plot(x, ev[i, :] - eshift, 'k-')
plot_projection(proj, ev, [1], [5, 6, 7, 8, 9], eshift, 'b')
plot_projection(proj, ev, [2, 3], [2, 3, 4], eshift, 'r')
pl.scatter(-99, -99, marker='o', c='b', alpha=0.5, label='Mo d')
pl.scatter(-99, -99, marker='o', c='r', alpha=0.5, label='S p')
pl.xlim(x.min(), x.max())
pl.ylim(ylimit)
pl.axhline(y=eval - eshift, color='g', linestyle='--')
pl.axhline(y=econ - eshift, color='g', linestyle='--')
mpl.rcParams['pdf.fonttype'] = 42
pl.legend(loc=1, prop={'size': 8})
pl.savefig('band_proj.pdf')
def getValueGFP(self, radius = 10, name = '', plot = False):
mean = []
movie = np.zeros((self.images[0].shape[0], self.images[0].shape[1]*self.lengthSeq))
if plot:
pylab.figure(figsize = (6,22))
for index, im in enumerate(self.images):
center = [(self.params[index][1] + self.params[index][1+6])/2., (self.params[index][2] + self.params[index][2+6])/2.]
GFP = segmentationClass.Segmentation(im.image)
GFP.defineFG()
GFP.smooth_corr()
mask = GFP.rond_mask(center, radius)
val = np.sum(mask*GFP.smooth)/1. /np.sum(mask)
#val = np.average(GFP.smooth)
movie[:,index*im.shape[1]:(index+1)*im.shape[1]] = GFP.smooth
mean.append(val)
if plot:
pylab.subplot(len(self.images),2,2*index+1)
pylab.imshow(GFP.smooth, 'gray')
#pylab.title("t = {0}".format())
pylab.axis('off')
pylab.subplot(len(self.images),2,2*index+2)
pylab.imshow(mask, 'gray')
pylab.autoscale(False)
pylab.axis('off')
pylab.plot(self.params[index][2::6], self.params[index][1::6], 'ro')
pylab.title('{0:.0f}'.format(val))
if plot:
pylab.savefig(name)
pylab.close()
return np.sum(nlargest(3, mean))/3., movie
def ax_pianoroll(title='notes'):
'''Twelve named semitones on the x-axis, one octave.'''
pl.cla()
pl.title(title)
pl.xticks(pl.frange(0, 1, npts=12, closed=0), 'C. C# D. D# E. F. F# G. G# A. A# B.'.split())
pl.yticks(pl.arange(24))
pl.grid(True, axis='x')
pl.xlim(-.5/12,11.5/12)
pl.autoscale(True,axis='y')
def plot_locpot_z(lattice_constant, a, elements, numofatoms, atom_pos, locpot):
import matplotlib as mpl
mpl.use("PDF")
import pylab as pl
potz = np.empty([locpot.shape[2]])
for z in range(locpot.shape[2]):
potz[z] = locpot[:, :, z].sum() / locpot.shape[0] / locpot.shape[1]
# print '{0:4d} {1:12.6f}'.format(z,potz[z])
sz = np.linalg.norm(a[2]) * lattice_constant
# print potz.max()
# Plot Setting
pl.title('LOCPOT', size=12)
pl.xlabel('Z', size=10)
pl.ylabel('Local potential (eV)', size=10)
xminor = 4
yminor = 4
fig = pl.gcf()
fig.set_size_inches(5, 3)
fig.subplots_adjust(bottom=0.14, left=0.12, top=0.88, right=0.95)
fig.set_dpi(300)
mpl.rcParams['font.sans-serif'] = 'Arial'
ax = pl.gca()
ax.xaxis.set_minor_locator(mpl.ticker.AutoMinorLocator(xminor))
ax.yaxis.set_minor_locator(mpl.ticker.AutoMinorLocator(yminor))
pl.xticks(size=8)
pl.yticks(size=8)
pl.tick_params(axis='x',
which='major',
direction='in',
length=3,
width=1,
top='on',
bottom='on',
pad=6)
pl.tick_params(axis='y',
which='major',
direction='in',
length=3,
width=1,
left='on',
right='on',
pad=6)
pl.autoscale(enable=True, axis='x')
pl.autoscale(enable=True, axis='y')
# Plot
z = np.arange(potz.shape[0]) / float(potz.shape[0])
pl.plot(z, potz, '-', label='locpot_z')
# pl.legend(loc=1,prop={'size':8})
pl.savefig('locpot_z.pdf')
return
def csv_reader(self, mode):
if(mode == 1):
if(test):
inputFile = self.testFileName
else:
inputFile = self.filename
else:
inputFile = self.filename
with open(inputFile, 'r') as csv_file:
reader = csv.reader(csv_file, delimiter = ',')
Hour = [];
Minute = [];
Time = [];
RawIR = [];
Blinks = [];
ActualBlinks = [];
# Skips the first line which does not contain data
next(reader)
for row in reader:
if mode == 2:
Hour.append(float(row[0]))
Minute.append(float(row[1]))
elif mode==1:
Blinks.append(float(row[4]))
ActualBlinks.append(float(row[5]))
#####CHANGE THIS NICOLE
if(float(row[2])<49):
Time.append(float(row[2])+60)
else:
Time.append(float(row[2]))
RawIR.append(float(row[3]))
if mode ==1:
totalOpTime = max(Time) - min(Time)
print "Average Sampling Frequency: "
print len(Time)/totalOpTime
if(self.MatchedBlinks != 0 and self.ActualBlinks != 0 and self.DetectedBlinks !=0):
print "Accuracy of Blink Detection: " + str(self.MatchedBlinks/self.ActualBlinks)
print "# of Actual Blinks: " + str(self.ActualBlinks)
print "# of Detected Blinks: " + str(self.DetectedBlinks)
pl.rcParams.update({'font.size': 18})
pl.figure(1)
pl.xlabel("Time(s)")
pl.ylabel("IR Values")
pl.title("IR Blink Sensor Results")
pl.plot(Time, RawIR, linewidth = 2, color = 'gray')
pl.autoscale()
pl.plot(Time, Blinks, linewidth = 2, color = 'red')
pl.plot(Time, ActualBlinks, linewidth = 2, color = 'blue')
pl.show()
else:
return [Time, RawIR, Hour, Minute]
def save_maxima(image, new_x, new_y, dist, outpath, nameCondition):
pylab.close('all')
pylab.imshow(image)
pylab.axis('off')
pylab.autoscale(False)
for i in xrange(len(new_x)):
points = pylab.plot(new_x[i], new_y[i], 'wo')
squares = pylab.gca().add_patch(pylab.Rectangle((new_x[i] - dist/2, new_y[i] - dist/2), dist, dist, edgecolor = 'w', alpha = 0.3, lw = 3))
pylab.savefig("{0}/found_maxima_n{1}_{2}.png".format(outpath, len(new_x), nameCondition))
pylab.close()
def draw_the_track_cross_section(image, crossection_points):
track_polygon = get_polygon(crossection_points)
cross_section = get_image_cross_section(image, track_polygon)
pylab.plot(map(lambda pixel: 255 - pixel[2], cross_section))
pylab.ylim(0, 255)
pylab.xlim(0, len(cross_section))
pylab.xticks([])
pylab.autoscale(False)
pylab.show()
def bargraph_cfd(xitems, yitems, figname, xLabel, yLabel):
#fig = plt.figure(dpi=100)
plt.bar(arange(len(xitems)), yitems, align='center')
plt.autoscale(True, axis='both')
plt.tight_layout(pad=7.0)
plt.xticks(arange(len(xitems)), xitems, rotation=90)
plt.xlabel(xLabel)
plt.ylabel(yLabel)
plt.title(figname)
plt.savefig(IOtools.results_rootpath+os.sep+figname+".png")
def analyse_connectivity(sheet_name,proj_name,lhi):
or_bins = numpy.linspace(0,numpy.pi/2,30)
projection = topo.sim[sheet_name].projections()[proj_name]
or_pref = topo.sim[projection.src.name].sheet_views['OrientationPreference'].view()[0]*numpy.pi
or_pref_target = topo.sim[projection.dest.name].sheet_views['OrientationPreference'].view()[0]*numpy.pi
domain_orientation_connection_strength = numpy.zeros((30,1))
pinwheel_orientation_connection_strength = numpy.zeros((30,1))
pinwheels = numpy.where(lhi.flatten()<0.1)[0]
domains = numpy.where(lhi.flatten()>0.9)[0]
for i in pinwheels:
cf = projection.cfs.flatten()[i]
this_or = or_pref_target.flatten()[i]
ors = cf.input_sheet_slice.submatrix(or_pref).flatten()
weights = numpy.multiply(cf.weights,cf.mask).flatten()
for j,k in enumerate(numpy.digitize(circular_dist(ors,this_or,numpy.pi),or_bins)):
print k
pinwheel_orientation_connection_strength[k-1] += weights[j]
for i in domains:
cf = projection.cfs.flatten()[i]
this_or = or_pref_target.flatten()[i]
ors = cf.input_sheet_slice.submatrix(or_pref).flatten()
weights = numpy.multiply(cf.weights,cf.mask).flatten()
for j,k in enumerate(numpy.digitize(circular_dist(ors,this_or,numpy.pi),or_bins)):
domain_orientation_connection_strength[k-1] += weights[j]
import pylab
pylab.figure()
pylab.subplot(2,1,1)
pylab.hold('on')
pylab.plot(numpy.linspace(0,numpy.pi/2,30,endpoint=False)+numpy.pi/2/60,pinwheel_orientation_connection_strength,'k',linewidth=2.0)
pylab.plot(numpy.linspace(0,numpy.pi/2,30,endpoint=False)+numpy.pi/2/60,pinwheel_orientation_connection_strength,'ko')
pylab.title(proj_name,fontsize=20)
pylab.autoscale(tight=True)
pylab.title('pinwheels')
pylab.subplot(2,1,2)
pylab.hold('on')
pylab.plot(numpy.linspace(0,numpy.pi/2,30,endpoint=False)+numpy.pi/2/60,domain_orientation_connection_strength,'k',linewidth=2.0)
pylab.plot(numpy.linspace(0,numpy.pi/2,30,endpoint=False)+numpy.pi/2/60,domain_orientation_connection_strength,'ko')
pylab.title(proj_name,fontsize=20)
pylab.autoscale(tight=True)
pylab.title('domains')
from param import normalize_path
pylab.savefig(normalize_path('PPconnectivity: ' + proj_name + str(topo.sim.time()) + '.png'));
def plot_locpotc(lpc, ef, sc):
import matplotlib as mpl
mpl.use("PDF")
import pylab as pl
# Plot Setting
# pl.title('LOCPOT',size=12)
pl.xlabel('c axis ($\mathrm{\AA}$)', size=12)
pl.ylabel('Local potential (eV)', size=12)
xminor = 5
yminor = 5
fig = pl.gcf()
fig.set_size_inches(6, 4)
fig.subplots_adjust(bottom=0.13, left=0.10, top=0.96, right=0.97)
fig.set_dpi(300)
mpl.rcParams['font.sans-serif'] = 'Arial'
ax = pl.gca()
ax.xaxis.set_minor_locator(mpl.ticker.AutoMinorLocator(xminor))
ax.yaxis.set_minor_locator(mpl.ticker.AutoMinorLocator(yminor))
pl.xticks(size=10)
pl.yticks(size=10)
pl.tick_params(axis='x',
which='major',
direction='in',
length=3,
width=1,
top='on',
bottom='on',
pad=6)
pl.tick_params(axis='y',
which='major',
direction='in',
length=3,
width=1,
left='on',
right='on',
pad=6)
ax.margins(0.1)
pl.autoscale(enable=True, axis='x')
pl.autoscale(enable=True, axis='y')
pl.xlim([0, sc])
# Plot
pl.plot(lpc[:, 1] * sc, lpc[:, 2] - ef, '-', label='locpot_c')
pl.axhline(y=0.0, color='g', linestyle='--')
# pl.legend(loc=1,prop={'size':8})
pl.savefig('locpotc.pdf')
return
def save_spectrogram(wav_file, spectrogram_path):
sound_info, frame_rate = get_wav_info(wav_file)
pylab.figure(num = None, figsize = (19, 12), frameon = False)
pylab.subplot(111)
pylab.specgram(sound_info, Fs = frame_rate)
pylab.gca().get_yaxis().set_visible(False)
pylab.gca().get_xaxis().set_visible(False)
pylab.gca().set_yticklabels([])
pylab.gca().set_xticklabels([])
pylab.gca().set_axis_off()
pylab.axis('off')
pylab.autoscale(False)
pylab.subplots_adjust(top = 1, bottom = 0, right = 1, left = 0, hspace = 0, wspace = 0)
# extent = pylab.gca().get_window_extent().transformed(pylab.gcf().dpi_scale_trans.inverted())
pylab.savefig(spectrogram_path, bbox_inches = 'tight', pad_inches = -0.05)
def main():
'''Exemple d'utilisation de la fonction d'affichage d'un astre phase vue depuis la Terre'''
w,h = pylab.figaspect(1.)
fig = pylab.figure(figsize = (int(2. * w), int(2. * h)))
ax = fig.add_subplot(111, axisbg = '0.1') # 0.1 c'est gris fonce
pylab.xlabel('alt')
pylab.ylabel('az')
astre = ephem.Moon()
obs = ephem.city('Paris')
obs.date = '2013/3/16 21:000:00'
astre.compute(obs)
pylab.title('Moon Phase ('+str(astre.phase)+') - '+str(obs.date))
# ra_dec = False : Apparent topocentric position represented by the properties : ra and dec, and alt and az.
object_phase (ax, obs, False, astre, astre.alt * 180. / math.pi, astre.az * 180. / math.pi, astre.size / 1000., '0.2', '0.85')
pylab.autoscale()
pylab.show()
def save_maxima(image, new_x, new_y, dist, outpath, nameCondition):
pylab.close('all')
pylab.imshow(image)
pylab.axis('off')
pylab.autoscale(False)
for i in xrange(len(new_x)):
points = pylab.plot(new_x[i], new_y[i], 'wo')
squares = pylab.gca().add_patch(
pylab.Rectangle((new_x[i] - dist / 2, new_y[i] - dist / 2),
dist,
dist,
edgecolor='w',
alpha=0.3,
lw=3))
pylab.savefig("{0}/found_maxima_n{1}_{2}.png".format(
outpath, len(new_x), nameCondition))
pylab.close()
def plot_muscle_activity(filepath, exc=None, act=None):
"""Plots provided muscle activity and saves to a pdf file.
Parameters
----------
filepath: string
Path name of pdf file to print to.
exc: pandas DataFrame
DataFrame containing muscle excitation and muscle name information.
act: pandas DataFrame
DataFrame containing muscle activation and muscle name information.
"""
if (exc is None) and (act is None):
raise Exception("Please provide either excitation or "
"activation information")
elif act is None:
N = len(exc.columns)
else:
N = len(act.columns)
# Create plots
num_rows = 5
num_cols = np.ceil(float(N) / num_rows)
fig = pl.figure(figsize=(11, 8.5))
for i in range(N):
pl.subplot(num_rows, num_cols, i + 1)
if not (exc is None):
pl.plot(exc.index, exc[exc.columns[i]], label='e')
if not (act is None):
pl.plot(act.index, act[act.columns[i]], label='a')
pl.ylim(0, 1)
if i == 1:
pl.legend(frameon=False, fontsize=8)
if not (exc is None):
pl.title(exc.columns[i], fontsize=8)
else:
pl.title(act.columns[i], fontsize=8)
pl.autoscale(enable=True, axis='x', tight=True)
pl.xticks([])
pl.yticks([])
pl.tight_layout()
pl.savefig(filepath)
pl.close(fig)
def show_fft(self, samples=1000, channel=0, clock_rate = 2000.0):
import pylab as pl
task = self.AnalogInputTask()
task.create_voltage_channel('Dev1/ai1', terminal = 'rse', min_val=-10, max_val=10) # current amplifier
task.configure_timing_sample_clock(rate = clock_rate)
task.start()
data = task.read(samples, fill_mode='group_by_channel',timeout=1000)
del task
myfft = np.fft.fftshift(np.fft.fft(data[channel]))
freq = np.fft.fftshift(np.fft.fftfreq(len(data[0]),1.0/clock_rate))
pl.xlim((0,clock_rate/2))
pl.autoscale(axis='y')
pl.ylim(ymin=0)
pl.plot(freq,myfft)
pl.show()
def plot_bootstraps(origin,
bootstraps,
labels,
ellipse_level=0.95,
scatter_alpha=0.5,
colors=None):
fig = pl.figure(figsize=(14, 10))
ax = pl.axes(aspect=1)
#ax = pl.axes([-1, -1, 1, 1])
default_colors = "bgrcmyk" # TODO
for i, l in enumerate(labels):
# random color -- do better than random but so they stay distinct and
# not limited by predefined set of colors
# c = np.random.rand(3,1)
c = (colors or default_colors)[i % len(default_colors)]
# scatter plot all the bootstrap samples
bs = bootstraps[:, i]
if scatter_alpha:
ax.scatter(bs[:, 0], bs[:, 1], c=c[0], alpha=scatter_alpha)
# plot original 'center'
x, y = origin[i][:2]
ax.plot(x, y, 'o', label=l, markeredgewidth=2, markerfacecolor=c[0])
ax.text(x,
y,
l,
fontsize=12,
bbox=dict(facecolor='white', alpha=0.8),
color=c[0],
horizontalalignment='center',
verticalalignment='center')
# plot ellipse
if ellipse_level:
# estimate mean/cov for bootstraps
_make_ellipse(bs.mean(0)[:2],
np.cov(bs, rowvar=0)[:2, :2],
ax,
level=ellipse_level,
color=c)
# and now plot all the sample points we got
#break
# pl.legend()
pl.autoscale(tight=False)
def generate_dataset_for_GAN():
# Create data directories if not already there
if not os.path.exists("./gaussian_images"):
os.makedirs("./gaussian_images")
if not os.path.exists("./sinusoidal_images"):
os.makedirs("./sinusoidal_images")
# Instantiate generator
generator = imgen.Image_Generator()
plt.rcParams['savefig.pad_inches'] = 0
plt.autoscale(tight=True)
# Create 1000 Gaussian images with random onehot pixels
for x in range(0, 1000):
image = generator.create_image(np.random.randint(6), 0.25, 0.0625,
(64, 64), "gaussian")
# Save images to the ./gaussian_images directory
plt.imshow(image, cmap="gray", interpolation="nearest", vmin=0, vmax=1)
plt.xticks([])
plt.yticks([])
plt.savefig("gaussian_images/gaussian" + str(x) + ".png",
bbox_inches="tight",
pad_inches=0,
transparent=True,
dpi=136.9)
# Create 1000 sinusoidal images with random onehot pixels
for x in range(0, 1000):
image = generator.create_image(np.random.randint(6), 0.25, 0.0625,
(512, 512), "sinusoidal")
# Save images to the ./sinusoidal_images directory
plt.imshow(image, cmap="gray", interpolation="nearest", vmin=0, vmax=1)
plt.xticks([])
plt.yticks([])
plt.savefig("sinusoidal_images/sinusoidal" + str(x) + ".png",
bbox_inches="tight",
pad_inches=0,
transparent=True,
dpi=136.9)
def __init__(self, strictness=1):
self.on = False
self.pts = []
self.marks = []
self.fig = pl.gcf()
self.ax = pl.gca()
pl.autoscale(enable=False)
self.cid_move = self.fig.canvas.mpl_connect('motion_notify_event', self.onmove)
self.cid_click = self.fig.canvas.mpl_connect('button_release_event', self.onclick)
self.cid_exit = self.fig.canvas.mpl_connect('axes_leave_event', self.onexit)
self.cid_keyup = self.fig.canvas.mpl_connect('key_release_event', self.on_keyup)
img = self.ax.get_images()[0].get_array().view(np.ndarray)
img = (img-img.min())/(img.max()-img.min())
img *= 255
img = img.astype(np.uint8)
edge_img = cv2.Canny(img, img.mean(), img.mean()+strictness*img.std())
self.edge_pts = np.argwhere(edge_img)
self.fig.canvas.start_event_loop(timeout=-1)
def plot(self, y, *args, **kwargs):
'''
Plot something vs this frequency
This plots whateve is given vs. `self.f_scaled` and then
calls `labelXAxis`.
'''
try:
if len(y)==len(self):
pass
else:
raise IndexError(['thing to plot doesnt have same'
' number of points as f'])
except(TypeError):
y = y*npy.ones(len(self))
plot(self.f_scaled, y,*args, **kwargs)
autoscale(axis='x', tight=True)
self.labelXAxis()
def _analyse_push_pull_connectivity(sheet_name,proj_name):
or_bins = numpy.linspace(0,numpy.pi,31)
phase_bins = numpy.linspace(0,numpy.pi*2,31)
projection = topo.sim[sheet_name].projections()[proj_name]
or_pref = topo.sim[projection.src.name].sheet_views['OrientationPreference'].view()[0]*numpy.pi
phase_pref = topo.sim[projection.src.name].sheet_views['PhasePreference'].view()[0]*numpy.pi*2
or_pref_target = topo.sim[projection.dest.name].sheet_views['OrientationPreference'].view()[0]*numpy.pi
phase_pref_target = topo.sim[projection.dest.name].sheet_views['PhasePreference'].view()[0]*2*numpy.pi
phase_connection_strength = numpy.zeros((30,1))
orientation_connection_strength = numpy.zeros((30,1))
for (i,cf) in enumerate(projection.cfs.flatten()):
this_or = or_pref_target.flatten()[i]
this_phase = phase_pref_target.flatten()[i]
ors = cf.input_sheet_slice.submatrix(or_pref).flatten()
phases = cf.input_sheet_slice.submatrix(phase_pref).flatten()
weights = numpy.multiply(cf.weights,cf.mask).flatten()
for j,k in enumerate(numpy.digitize(circular_dist(ors,this_or,numpy.pi),or_bins)):
orientation_connection_strength[k-1] += weights[j]
for j,k in enumerate(numpy.digitize(circular_dist(phases,this_phase,2*numpy.pi),phase_bins)):
phase_connection_strength[k-1] += weights[j]
import pylab
pylab.figure()
pylab.subplot(2,1,1)
pylab.hold('on')
pylab.plot(numpy.linspace(0,numpy.pi,30,endpoint=False)+numpy.pi/60,orientation_connection_strength,'k',linewidth=2.0)
pylab.plot(numpy.linspace(0,numpy.pi,30,endpoint=False)+numpy.pi/60,orientation_connection_strength,'ko')
pylab.title(proj_name,fontsize=20)
pylab.autoscale(tight=True)
pylab.subplot(2,1,2)
pylab.hold('on')
pylab.plot(numpy.linspace(0,numpy.pi*2,30,endpoint=False)+2*numpy.pi/60,phase_connection_strength,'k',linewidth=2.0)
pylab.plot(numpy.linspace(0,numpy.pi*2,30,endpoint=False)+2*numpy.pi/60,phase_connection_strength,'ko')
pylab.autoscale(tight=True)
from param import normalize_path
pylab.savefig(normalize_path('PPconnectivity: ' + proj_name + str(topo.sim.time()) + '.png'));
def show_sig(rtransform, start, end, rate, subsample): interval = end - start subsample = subsample[:interval] intpersec = rate/interval sig = filter(lambda x:x>1, rtransform) if not len(sig): return print start/float(rate) print sig subplot(3,1,1) axis([start, end, -0.5, 0.5]) plot(xrange(start, end), subsample) subplot(3,1,2) xlim(0,rate) autoscale(axis='y') plot(xrange(0, rate), rtransform) subplot(3,1,3) xlim(0,rate) autoscale(axis='y') plot(xrange(0, rate), smooth(rtransform, 10)) show()
def plotStock(dates, symbol, name, trades, turnovers, amounts, masterAmounts):
masterAmounts = numpy.array(masterAmounts)
amounts = numpy.array(amounts)
numpy.seterr(all='ignore')
masters = (masterAmounts / amounts) * 100
masters[numpy.isnan(masters)] = 0
masterAmounts = masterAmounts / 10000000
turnovers = pylab.array(turnovers)
turnovers = turnovers * 100
pylab.figure(figsize=(16,10), dpi=200)
pylab.subplot(3,1,1)
pylab.title(symbol + ' ' + name + ' (' + dates[-1] + ')')
pylab.plot(trades, color = 'black', label = u'收盘价格')
pylab.ylabel(u'价格')
pylab.legend(loc = 'upper left')
pylab.autoscale(True, 'both', None)
pylab.grid(True)
pylab.subplot(3,1,2)
pylab.plot(masterAmounts, color = 'red', label = u'主力流入')
pylab.ylabel(u'千万')
pylab.legend(loc = 'upper left')
pylab.autoscale(True, 'both', None)
pylab.grid(True)
pylab.subplot(3,1,3)
pylab.plot(masters, color = 'blue', label = u'主力占比')
# pylab.plot(turnovers, color = 'green', label = u'换手率')
pylab.xlabel(u'日期')
pylab.ylabel(u'百分比-100%')
pylab.legend(loc = 'upper left')
pylab.autoscale(True, 'both', None)
pylab.grid(True)
pylab.savefig(symbol, dpi=200)
def plot(self, y, *args, **kwargs):
'''
Plot something vs this frequency
This plots whateve is given vs. `self.f_scaled` and then
calls `labelXAxis`.
'''
try:
if len(y) == len(self):
pass
else:
raise IndexError([
'thing to plot doesn\'t have same'
' number of points as f'
])
except (TypeError):
y = y * npy.ones(len(self))
plot(self.f_scaled, y, *args, **kwargs)
autoscale(axis='x', tight=True)
self.labelXAxis()
def draw2D(self, title, image=[]):
pylab.figure()
if image == []:
pylab.imshow(self.image, 'gray')
else:
pylab.imshow(image, 'gray')
pylab.axis('off')
pylab.autoscale(False)
for i in xrange(self.nComponents):
xeq = lambda t: self.params[6 * i + 3] * np.cos(t) * np.cos(self.params[6 * i + 5]) + self.params[
6 * i + 4] * np.sin(
t) * np.sin(self.params[6 * i + 5]) + self.params[6 * i + 1]
yeq = lambda t: - self.params[6 * i + 3] * np.cos(t) * np.sin(self.params[6 * i + 5]) + self.params[
6 * i + 4] * np.sin(
t) * np.cos(self.params[6 * i + 5]) + self.params[6 * i + 2]
t = np.linspace(0, 2 * np.pi, 100)
x = xeq(t)
y = yeq(t)
pylab.scatter(self.params[6 * i + 2], self.params[6 * i + 1], color='k')
pylab.plot(y.astype(int), x.astype(int), self.colors[i] + '-')
pylab.savefig(title)
pylab.close()
def pos_analysis(data):
"""
Analyze position.
"""
tmerc_map = create_map(data.GPS_Lon.values, data.GPS_Lat.values)
gps_y, gps_x = tmerc_map(data.GPS_Lon.values, data.GPS_Lat.values)
gpos_y, gpos_x = tmerc_map(data.GPOS_Lon.values, data.GPOS_Lat.values)
gpsp_y, gpsp_x = tmerc_map(
data.GPSP_Lon[pl.isfinite(data.GPSP_Lon.values)].values,
data.GPSP_Lat[pl.isfinite(data.GPSP_Lat.values)].values)
pl.plot(gpos_y, gpos_x, '.', label='est')
pl.plot(gps_y, gps_x, 'x', label='GPS')
pl.plot(gpsp_y, gpsp_x, 'ro', label='cmd')
pl.xlabel('E, m')
pl.ylabel('N, m')
pl.grid()
pl.autoscale(True, 'both', True)
pl.legend(loc='best')
return locals()
def plot_reserve_activity(filepath, reserves):
"""Plots provided reservec acutator activations and saves to a pdf file.
Parameters
----------
filepath: string
Path name of pdf file to print to.
reserves: pandas DataFrame
DataFrame containing reserve activity and name information.
"""
fig = pl.figure()
NR = len(reserves.columns)
for i in range(NR):
pl.subplot(NR, 1, i + 1)
pl.plot(reserves.index, reserves[reserves.columns[i]])
pl.ylim(-1, 1)
pl.title(reserves.columns[i], fontsize=8)
pl.axhline(0)
pl.autoscale(enable=True, axis='x', tight=True)
pl.tight_layout()
pl.savefig(filepath)
pl.close(fig)
def main():
pl.title('MoS$_2$-1ML (VASP-PAW-PBE.Mo_pv)',fontsize=12)
xlabel=['$\mathrm{\Gamma}$','$\mathrm{K}$','$\mathrm{M}$','$\mathrm{\Gamma}$']
xlabelpos=[1,21,31,48]
ef = get_efermi()
ylimit=[-7,6]
yminor=4
fig=pl.gcf()
fig.set_size_inches(5,6)
fig.subplots_adjust(bottom=0.05,left=0.12, top=0.95, right=0.96)
fig.set_dpi(300)
ax = pl.gca()
mpl.rcParams['font.sans-serif']='Arial' #'Helvetica'
pl.ylabel('Energy (eV)',fontsize=10)
pl.xticks(xlabelpos,xlabel,size=10)
pl.yticks(size=9)
ax.yaxis.set_minor_locator(mpl.ticker.AutoMinorLocator(yminor))
pl.autoscale(enable=True,axis='y')
pl.tick_params(axis='y',which='major',direction='out',length=4, width=1,left='on',right='off',pad=5)
pl.tick_params(axis='y',which='minor',direction='out',length=3, width=0.5,left='on',right='off')
pl.tick_params(axis='x',which='both',top='off',bottom='off')
for xline in xlabelpos:
pl.axvline(x=xline,color='k',linewidth=0.6)
ev=read_eigenvalues_vasp()
x=ev[0,:]
econ,eval=find_edges(ev,ef)
print 'E_fermi: {0} Band edges: {1} {2}'.format(ef,econ,eval)
for i in range(ev.shape[0]-1):
pl.plot(x,ev[i+1,:]-eval,'k-')
pl.xlim(x.min(),x.max())
pl.ylim(ylimit)
pl.axhline(y=econ-eval,color='g',linestyle='--')
pl.axhline(y=0.0,color='g',linestyle='--')
mpl.rcParams['pdf.fonttype']=42
pl.savefig('band.pdf')
#figure()
#figure(facecolor="white")
fig.set_facecolor("white")
#print 'U =',u[0:4],x[0:4],y[0:4]
subplot(311)
bounds = [0, 1, 100]
img = imshow(transpose(u),
origin='lower',
cmap='jet',
extent=[-2.0, 18.0, -4.0, 4.0])
#imshow(u,cmap='jet')
#colorbar(img, cmap=cmap, norm=norm, boundaries=bounds, ticks=[0, 5, 10])
#colorbar(boundaries=bounds)
#clim(0,1)
autoscale()
colorbar()
subplot(312)
xlabel('x/D')
ylabel('1 - U/Uinf')
ylim([0, 1])
plt, = plot(x, cline)
#fig.tight_layout()
def update(val):
ct = sct.val
ti = sti.val
mean_sfr[ix][iy] = np.mean(np.log10(sfrall[sel]))
mean_z[ix][iy] = np.mean(zall[sel])
mean_zcold[ix][iy] = np.mean(np.log10(zcoldall[sel]))
# pl.matshow(mean_sfr)
ssel = np.where((zall > _z-zbin/2.) &
(zall < _z+zbin/2.))
pl.close()
a1 = pl.figure(1)
pl.imshow(mean_sfr,extent=[pmin,pmax,tmin,tmax],interpolation='nearest')
pl.xticks(np.arange(pmin,pmax,10))
pl.yticks(np.arange(tmin,tmax,10))
pl.xlabel('deg')
pl.ylabel('deg')
pl.autoscale(False)
pl.plot(theta[ssel],phi[ssel],'.',color='gray',alpha=0.5)
cbar = pl.colorbar()
cbar.set_label(r'$\log({\rm SFR} [M_{\odot}/yr)]$',rotation=270)
pl.text(10,10,r'$'+trunc(_z-zbin/2.,1)+'<z<'+trunc(_z+zbin/2.,1)+'$',bbox=dict(facecolor='0.85', alpha=0.85),fontsize=18)
pl.savefig('sfr_iz'+trunc(iz,0)+'.png',bbox_inches='tight',dpi=350)
pl.close(a1)
# pl.matshow(mean_zcold)
a2 = pl.figure(2)
pl.imshow(mean_zcold,extent=[pmin,pmax,tmin,tmax],interpolation='nearest')
pl.xticks(np.arange(pmin,pmax,10))
pl.yticks(np.arange(tmin,tmax,10))
pl.xlabel('deg')
pl.ylabel('deg')
pl.autoscale(False)
def plot(self, trace_filters=None, spike_filters=None, xlim=None, ylim=None, legend=False, xlabel=None, xscale=None, fig_trace_kwargs=None, fig_event_kwargs=None):
import pylab
import mreorg
import numpy as np
trace_filters = trace_filters or []
spike_filters = spike_filters or []
fig_trace_kwargs = fig_trace_kwargs or {}
fig_event_kwargs = fig_event_kwargs or {}
tr_figs = []
for filt in trace_filters:
fig = pylab.figure(**fig_trace_kwargs)
tr_figs.append(fig)
trs = self.filter_traces(filt)
print 'Plotting:', filt, len(trs)
for res in trs:
if xlim:
time_mask = np.logical_and(
res.raw_data.time_pts>xlim[0],
res.raw_data.time_pts<xlim[1],
)
time, data = res.raw_data.time_pts[time_mask], res.raw_data.data_pts[time_mask]
else:
time, data = res.raw_data.time_pts, res.raw_data.data_pts
if xscale is not None:
time = time * xscale
pylab.plot(time, data,'-', label=','.join(res.tags), ms=2 )
if len(trs)==0:
pylab.close(fig)
else:
pylab.ylabel(filt)
if legend:
pylab.legend()
if ylim:
pylab.ylim(*ylim)
else:
pylab.autoscale(axis='y')
if xlabel is not None:
pylab.xlabel(xlabel)
mreorg.PM.save_figure(figname=filt)
mreorg.PM.save_active_figures()
spike_figs = []
for filt in spike_filters:
f2 = pylab.figure(**fig_event_kwargs)
spike_figs.append(f2)
#trs = self.filter_events(filt)
trs = list(it.chain( *[f.filter_events(filt) for f in self.results_files] ) )
trs = self.filter_events(filt)
print ' -- plotting:', filt, len(trs)
for i,res in enumerate(trs):
evt_times = res.times
pylab.plot( evt_times, i+ 0*evt_times, 'x', label=','.join(res.tags))
if xlim:
pylab.xlim(*xlim)
pylab.ylabel(filt)
if legend:
pylab.legend()
if ylim:
pylab.ylim(*ylim)
else:
pylab.ylim(0, len(trs))
mreorg.PM.save_active_figures()
return tr_figs, spike_figs
# loadtext actually comes from numpy, which pylab has.
wave,fnu,sig = pylab.loadtxt(infile, skiprows=3, usecols=(0,1,2), unpack=True)
# for plotting purposes, multiply by scale factor to bring to order unity
factor = 1E29
fnu *= factor
sig *= factor
# If continuum file exists, grab it, for later plotting, fitting of EW.
if(os.path.exists(contfile)):
pixcont, wavcont, concont = numpy.loadtxt(contfile,comments="#", usecols=(0,1,2), unpack=True)
concont *=factor
# JRR simplify, just make 1 plot
start = 2600
end = 3700
pylab.plot(wave[start:end], fnu[start:end], lincolor, linestyle='steps') # plot spectrum
pylab.plot(wave[start:end], sig[start:end], errcolor, linestyle='steps') # plot 1 sigma uncert spectrum
pylab.autoscale(axis='x', tight=True)
# If continuum file exists, plot the continuum
if(os.path.exists(contfile)):
this = numpy.where((wavcont > wave[start]) & (wavcont < wave[end]))
pylab.plot(wavcont[this[0]], concont[this[0]], 'y', linestyle='steps') # plot this portion of the continuum
# Here is where simple linear interpolation of continuum should go, to have continuum values at every wavelength.
# Next, look up the EW formula.
# Next, define boundaries, where EW goes positive again on either side.
# Next, sum up the EW for every pixel within the boundaries
# Finally, print it up.
def chooseAnchors(spec, method):
stime = time.time()
if method == 1:
# original
spec *= spec
cutoff = args.anchorThresh * np.std(spec)
t3 = np.where(spec < cutoff)
t4 = np.where(spec >= cutoff)
spec[t3] = 0
print "cutoff val:", cutoff
print "below cutoff:", len(t3[0])
print "over cutoff:", len(t4[0])
tmp = np.delete(spec.flatten(), np.where(spec.flatten() < cutoff))
if args.showPlots:
h = np.histogram(tmp, bins=100)
pylab.bar(h[1][1:], h[0])
pylab.autoscale()
pylab.show()
# return anchor points
log.info("ChooseAnchor(1) time: %fs" % (time.time() - stime))
tmp[np.where(tmp > 0)] = 1
return tmp
elif method == 2:
# non squared (Better)
cutoff = args.anchorThresh * np.std(spec)
# swing everything positive
spec = abs(spec)
belowCut = np.where(spec < cutoff)
aboveCut = np.where(spec >= cutoff)
spec[belowCut] = 0
print "cutoff val:", cutoff
#print "below cutoff:",len(belowCut[0])
#print "over cutoff(Anchors):",len(aboveCut[0])
if args.showPlots:
spec2 = spec.copy()
spec2[np.where(spec2 > 0)] = np.log(spec2[np.where(spec2 > 0)])
img = pylab.imshow(np.transpose(spec2))
pylab.colorbar(img)
pylab.show()
print spec.shape
#tmp=np.delete(spec,np.where(spec<cutoff))
spec[np.where(spec < cutoff)] = 0
spec[np.where(spec >= cutoff)] = 1
#print tmp.flatten().shape
#print np.min(tmp), np.max(tmp)
if args.showPlots:
print "Final distribution of Anchors:"
h = np.histogram(tmp, bins=100)
pylab.bar(h[1][1:], h[0])
pylab.autoscale()
pylab.show()
# return anchor points
#tmp[np.where(tmp>0)]=1
log.info("ChooseAnchor(2) time: %fs" % (time.time() - stime))
return spec
elif method == 3:
# method as described in github worldveil/dejavu/fingerprint.py
# generate binary mask
binMask = generate_binary_structure(2, 1)
grownBinMask = iterate_structure(binMask, args.footprintSize)
filter = maximum_filter(spec, footprint=grownBinMask)
local_max = filter == spec
background = (spec == 0)
eroded_background = binary_erosion(background,
structure=grownBinMask,
border_value=1)
# Boolean mask of arr2D with True at peaks
detected_peaks = local_max - eroded_background
return detected_peaks.astype(int)
else:
print "you fail"
exit()
end = race_start+datetime.timedelta(days=1, hours=12)
import time
now = time.time()
print "loading data"
samples = load_messages(0x402, "Bus Voltage", start, end)
print "loaded data",
print "took %s seconds to load %d data points" % (time.time() - now, len(samples))
now = time.time()
print "simplifying via vertical line test"
samples = list(simplify_by_extrema(samples))
print "simplified to %d data points in %s seconds" % (len(samples), time.time() - now)
now = time.time()
print "simplifying via ramer-douglas-peucker"
trans = transform_to_screen(samples, [to_utc(start), to_utc(end)], [40.0, 140.0], 600, 600)
trans_simple = simplify_ramer_douglas_peucker(list(trans), 2.0)
samples = list(transform_to_sample(trans_simple, [to_utc(start), to_utc(end)], [40.0, 140.0], 600, 600))
print "simplified to %d data points in %s seconds" % (len(samples), time.time() - now)
times =[x[0] for x in samples]
voltages = [x[1] for x in samples]
pylab.autoscale(False)
pylab.plot(times, voltages)
pylab.axis([start, end, 40.0, 140.0])
pylab.show()
ax = pylab.subplot(111)
p1 = ax.bar(x,y, align='center')
pylab.setp(p1, color='#3333B3')
for xx,yy in zip(x,y):
pylab.annotate('%.2f' % yy, xy=(xx, yy), xytext=(0,2), textcoords='offset points', ha='center', va='bottom', fontproperties=font)
pylab.xticks(x, x, fontproperties=font2)
pylab.yticks(fontproperties=font2)
pylab.title('The percentage of shortest path changes\n for each O-D pair on Chicago Sketch', fontproperties=font2)
pylab.xlabel('Number of times the shortest path for an O-D pair \nchanged 0, 1, 2, 3, $\ldots$, times, out of 26 iterations', fontproperties=font2)
pylab.ylabel('Percentage of total number of O-D pairs', fontproperties=font2)
pylab.autoscale(enable=True, axis='x')
pdf.savefig(fig, bbox_inches='tight')
#------------------------------
counts =[]
with open('sp_change_berlin', 'r') as f:
for line in f:
o, d, count = map(int, line.split())
counts.append(count)
x, y = map(list,zip(*Counter(counts).items()))
x = map(lambda t:t-1, x)
y = map(lambda t:100*t/49688.0, y)
x = x[:16]
y = y[:16]
def plotedi(fn, saveplot=False, component=None):
edi = MTedi.Edi()
try:
edi.readfile(fn)
except:
print '\n\tERROR - not a valid EDI file: {0}\n'.format(fn)
sys.exit()
# if saveplot is True:
# import matplotlib
# matplotlib.use('Agg')
import pylab
lo_comps = []
if component is not None:
'n' in component.lower()
try:
if 'n' in component.lower():
lo_comps.append('n')
except:
pass
try:
if 'e' in component.lower():
lo_comps.append('e')
except:
pass
if len(lo_comps) == 0:
lo_comps = ['n', 'e']
res_te = []
res_tm = []
phi_te = []
phi_tm = []
reserr_te = []
reserr_tm = []
phierr_te = []
phierr_tm = []
for r in edi.Z.resistivity:
res_te.append(r[0, 1])
res_tm.append(r[1, 0])
for p in edi.Z.phase:
phi_te.append(p[0, 1] % 90)
phi_tm.append(p[1, 0] % 90)
if pylab.np.mean(phi_te) > 90 and pylab.np.mean(phi_tm) > 90:
phi_te = [i % 90 for i in phi_te]
phi_tm = [i % 90 for i in phi_tm]
for r in edi.Z.resistivity_err:
reserr_te.append(r[0, 1])
reserr_tm.append(r[1, 0])
for p in edi.Z.phase_err:
phierr_te.append(p[0, 1])
phierr_tm.append(p[1, 0])
periods = 1. / edi.freq
resplotelement_xy = None
resplotelement_yx = None
axes = pylab.figure('EDI ' + fn)
ax1 = pylab.subplot(211)
if 'n' in lo_comps:
resplotelement_xy = pylab.errorbar(periods,
res_te,
reserr_te,
marker='x',
c='b',
fmt='x')
if 'e' in lo_comps:
resplotelement_yx = pylab.errorbar(periods,
res_tm,
reserr_tm,
marker='x',
c='r',
fmt='x')
pylab.xscale('log', nonposx='clip')
pylab.yscale('log', nonposy='clip')
minval = pylab.min(pylab.min(res_te, res_tm))
maxval = pylab.max(pylab.max(res_te, res_tm))
pylab.xlim(0.5 * pylab.min(periods), 2 * pylab.max(periods))
# ylim([0.1,100])
pylab.ylim([minval / 10, maxval * 10])
pylab.autoscale(False)
pylab.ylabel(r' $\rho$ (in $\Omega m$)')
pylab.setp(ax1.get_xticklabels(), visible=False)
# share x only
ax2 = pylab.subplot(212, sharex=ax1)
pylab.autoscale(False)
# ylim(-45,135)
if 'n' in lo_comps:
pylab.errorbar(periods, phi_te, phierr_te, marker='x', c='b', fmt='x')
if 'e' in lo_comps:
pylab.errorbar(periods, phi_tm, phierr_tm, marker='x', c='r', fmt='x')
pylab.ylabel('Phase angle ($\degree$)')
pylab.xlabel('Period (in s)')
pylab.plot([pylab.xlim()[0], pylab.xlim()[1]], [45, 45], '-.', c='0.7')
pylab.ylim([-0, 90])
ax1.legend([resplotelement_xy, resplotelement_yx],
['$E_{X}/B_Y$', '$E_Y/B_X$'],
loc=2,
ncol=1,
numpoints=1,
markerscale=0.8,
frameon=True,
labelspacing=0.3,
prop={'size': 8},
fancybox=True,
shadow=False)
pylab.tight_layout()
if saveplot is True:
pylab.ioff()
outfn = op.splitext(fn)[0] + '.png'
pylab.savefig(outfn, bbox_inches='tight')
pylab.close('all')
pylab.ion()
return outfn
else:
pylab.ion()
pylab.show(block=True)
return None
cdf = NP.cumsum(hist * delta)
print(cdf[-1])
# assert False
# print(E_series.min())
# print(E_series.max())
import pylab as PL
PL.plot(bin_centers,
cdf)
PL.autoscale(axis='x', tight=True)
PL.show()
# print(len(E_series))
# print(E_series.min())
# print(E_series.max())
# import pylab as PL
# PL.hist(E_series.)
# N = 1024
# days_to_seconds = 60 * 60 * 24
# periods = NP.linspace(0.9 * days_to_seconds, 1.1 * days_to_seconds, N)
score_ts = clf.score(X_ts, Y_ts)
# Display scores and errors of each set
if classifier is 'rfc':
print 'Error from level '+str(l)+' from RandomForestClassifier'
elif classifier is 'dtc':
print 'Error from level '+str(l)+' from DecisionTreeClassifier'
print "LS error: "+str((1-score_ls)*100)+"%"
print "TS error: "+str((1-score_ts)*100)+"%"
if classifier is 'dtc':
print 'Node count: '+str(clf.tree_.node_count)
print 'Depth of the tree: '+str(depth(clf.tree_))
print "------------------"
errors.append((1-score_ts)*100)
pl.xlabel('Levels')
pl.ylabel('Error (%)')
if classifier is 'rfc':
pl.title(r'Error on TS from RandomForestClassifier (n=1000)')
elif classifier is 'dtc':
pl.title(r'Error on TS from DecisionTreeClassifier')
pl.bar(np.arange(len(errors)),errors, color='blue', align='center')
pl.autoscale(tight=True)
pl.xticks(range(0,15),range(1,16), size='small')
pl.yticks(range(0,30,5), range(0,30,5), size='small')
if classifier is 'rfc':
pl.savefig('mean_error_TS_rfc_game.png')
elif classifier is 'dtc':
pl.savefig('mean_error_TS_dtc_game.png')
x = np.random.uniform(0, 4 * np.pi, size=200)
y = np.cos(x) + np.random.random(size=len(x))
#%%
# Compute a lowess smoothing of the data
smoothed = sm.nonparametric.lowess(exog=x, endog=y, frac=0.2)
type(smoothed) # numpy.ndarray
smoothed.shape # (200, 2)
smoothed
# Plot the fit line
fig, ax = pylab.subplots()
ax.scatter(x, y)
ax.plot(smoothed[:, 0], smoothed[:, 1], c="k")
pylab.autoscale(enable=True, axis="x", tight=True)
#%%
# Compute a lowess smoothing of the data
smoothed = sm.nonparametric.lowess(exog=x,
endog=y,
xvals=np.linspace(0, 4 * np.pi, 20),
frac=0.2)
type(smoothed) # numpy.ndarray
smoothed.shape # (20, )
np.array([np.linspace(0, 4 * np.pi, 20), smoothed])
# Plot the fit line
fig, ax = pylab.subplots()
ax.scatter(x, y)
C['spike_syn']), np.std(C['spike_syn'])
vol_syn[j], st_vol_syn = np.mean(C['vol_syn']), np.std(
C['vol_syn'])
mean[j], st_mean[j] = moments[0], st_moments[0]
var[j], st_var[j] = moments[1], st_moments[1]
stdv[j], st_stdv[j] = moments[2], st_moments[2]
skw[j], st_skw[j] = moments[3], st_moments[3]
kurt[j], st_kurt[j] = moments[4], st_moments[4]
else:
print 'something was wrong'
exit(0)
colors = ['k', 'maroon', "crimson", "y", 'royalblue', 'magenta']
fig, ax = pl.subplots(nrows=2, ncols=3, figsize=(12, 8))
pl.autoscale(enable=True, axis='y', tight=True)
x = std_noise
ax[0, 0].errorbar(x,
vol_syn,
yerr=st_vol_syn,
fmt='-o',
c=colors[0],
elinewidth=1,
ecolor='g')
ax[1, 0].errorbar(x,
spike_syn,
yerr=st_spike_syn,
fmt='-o',
c=colors[1],
elinewidth=1,
ecolor='g')
def main(experiment):
swapped = False
use_geodesic = True
experiments = dict(
cat = dict(
file1 = 'meshes/tosca/cat0.mat',
file2 = 'meshes/tosca/cat2.mat',
mu = [0.7],
Ks = np.arange(10, 50, 5),
),
david = dict(
file1 = 'meshes/tosca_holes/david0_halfed.obj',
file2 = 'meshes/tosca_holes/david10_nolegs_nohead.obj',
mu = [0.7],
Ks = np.arange(10, 50, 5),
),
hand = dict(
file1 = 'meshes/hand_868.obj',
file2 = 'meshes/hand_868_holes2.obj',
mu = [5.0],
Ks = np.arange(10, 50, 2),
),
)
if experiment not in experiments:
print "Usage: python %s <experiment>" % sys.argv[0]
print "where experiment is one of: %s" % (', '.join(experiments.keys()))
sys.exit(1)
exp = experiments[experiment]
file1, file2 = exp['file1'], exp['file2']
mu, Ks = exp['mu'], exp['Ks']
print "this will take a while..."
# load meshes
verts1, tris1, verts2, tris2, ij = load_shape_pair(file1, file2, check=False, normalize=False)
if swapped: # swapped?
verts2, tris2, verts1, tris1 = verts1, tris1, verts2, tris2
ij = ij[:,::-1]
if use_geodesic:
D = compute_geodesic_distance_matrix(verts1, tris1)
eigenvector_algorithms = [
('MHB', partial(cmm.manifold_harmonics, scaled=False)),
]
for cmu in mu:
name = 'CMHB' if len(mu) == 1 else 'CMHB %f' % (cmu)
eigenvector_algorithms.append(
(name, partial(
cmm.compressed_manifold_modes,
mu=cmu, maxiter=10000, verbose=0, scaled=False)))
mapping_algorithms = [
('rotation', partial(align.optimal_rotation, allow_reflection=True)),
#('permutation', partial(align.optimal_permutation, allow_reflection=True)),
]
print "computing basis functions (first mesh)"
runs = [(K, name, algo) for K in Ks for name, algo in eigenvector_algorithms]
Phis1 = Parallel(-1)(
delayed(algo)(verts1, tris1, K)
for K, name, algo in runs)
print "computing basis functions (second mesh)"
Phis2 = Parallel(-1)(
delayed(algo)(verts2, tris2, K)
for K, name, algo in runs)
# run for different number of eigenfunctions K
errors_per_mapping_algorithm = defaultdict(lambda: defaultdict(list))
C_by_mapping_algorithm = defaultdict(lambda: defaultdict(list))
for (K, eigenvector_algorithm_name, algo), Phi1, Phi2 in zip(runs, Phis1, Phis2):
for mapping_algorithm_name, mapping_algorithm in mapping_algorithms:
# compute the mapping between the eigenfunctions
C = mapping_algorithm(Phi1[ij[:,0]].T, Phi2[ij[:,1]].T)
Phi1_rot = np.dot(C, Phi1.T).T
# for all points in shape 2 where there is a correspondence to shape 1 (all j),
# find corresponding point i in shape 1
tree = cKDTree(Phi1_rot)
distance_eigenspace, nearest = tree.query(Phi2[ij[:, 1]])
ij_corr = np.column_stack((ij[:,0], nearest))
# compute error
if use_geodesic:
errors = D[ij_corr[:,0], ij_corr[:,1]]
else:
errors = veclen(verts1[ij_corr[:, 0]] - verts1[ij_corr[:,1]])
mean_error = np.mean(errors)
errors_per_mapping_algorithm[mapping_algorithm_name][eigenvector_algorithm_name].append(mean_error)
C_by_mapping_algorithm[mapping_algorithm_name][eigenvector_algorithm_name].append(C)
print "%s/%s (K=%d) %.2f" % (mapping_algorithm_name, eigenvector_algorithm_name, K, mean_error)
for mapping_algorithm_name, C_by_trial in C_by_mapping_algorithm.iteritems():
for trial_name, Cs in C_by_trial.iteritems():
# just use the last rotation matrix computed
C = Cs[-2]
pl.figure(mapping_algorithm_name + '_' + trial_name, figsize=(4,3.5))
plot_functional_map(reorder_functional_map(C), newfig=False)
pl.subplots_adjust(left=0.01, right=1, top=0.95, bottom=0.05)
show_correspondence(
verts1, tris1, verts2, tris2, ij,
points=5, color_only_correspondences=True,
colormap='Paired', #offset_factor=(-1.8, +0.0, 0.),
show_spheres=False, blend_factor=1.0, block=False)
for mapping_algorithm_name, errors_per_trial in errors_per_mapping_algorithm.iteritems():
#pl.rcParams.update({'font.size': 6})
pl.figure(mapping_algorithm_name + '_' + file1 + '_' + file2, figsize=(2.5,2.5))
pl.rc('text', usetex=False)
style_by_name = dict(
CMHB=dict(c=(6/255., 50/255., 100/255.), lw=2),
MHB=dict(c=(121/255., 6/255., 34/255.), lw=1)
)
for trial_name, errors in sorted(errors_per_trial.items(), key=lambda (k,v): k):
print trial_name, errors
style = style_by_name.get(trial_name, {})
pl.plot(Ks, errors, label=trial_name, **style)
pl.locator_params(nbins=4)
pl.legend().draggable()
pl.autoscale(tight=True)
pl.ylim(bottom=0)
pl.grid()
pl.xlabel(r'$K$')
pl.ylabel(r'geodesic error')
pl.tight_layout()
pl.show()
def draw2D_new(self, title, image=[]):
tt=np.array(self.image.shape)/50.
pylab.figure(figsize=tt, dpi=50.)
if image == []:
pylab.imshow(self.image, 'gray')
else:
pylab.imshow(image, 'gray')
pylab.axis('off')
pylab.autoscale(False)
for i in xrange(self.nComponents):
k1 = np.array([[self.params[6 * i + 3] ** 2, self.params[6 * i + 3] * self.params[6 * i + 4] * self.params[6 * i + 5]],
[self.params[6 * i + 3] * self.params[6 * i + 4] * self.params[6 * i + 5], self.params[6 * i + 4] ** 2]])
w1, v1 = np.linalg.eig(k1)
idx = w1.argsort()
w1 = w1[idx]
v1 = v1[:, idx]
angle=-(np.arctan(v1[1][1]/v1[0][1]))+np.pi#x+2*(pi/4-x)+pi/2#since in the image X and Y are inverted, so need to minus 90 degree and flip around pi/4
#print angle
w2 = np.zeros((1 , 2))
w2[0,1] = np.sqrt(2)*np.max([self.params[6 * i + 3], self.params[6 * i + 4]])
w2[0,0] = w2[0,1]*w1[0]/w1[1]
xeq = lambda t: w2[0,1] * np.cos(t) * np.cos(angle) + w2[0,0] * np.sin(
t) * np.sin(angle) + self.params[6 * i + 1]
yeq = lambda t: - w2[0,1] * np.cos(t) * np.sin(angle) + w2[0,0] * np.sin(
t) * np.cos(angle) + self.params[6 * i + 2]
t = np.linspace(0, 2 * np.pi, 100)
x = xeq(t)
y = yeq(t)
pylab.scatter(self.params[6 * i + 2], self.params[6 * i +1], color=self.colors[i], s=2)
pylab.plot(y.astype(int), x.astype(int), self.colors[i] + '-')
pylab.plot([self.params[6 * i + 2], yeq(0)],[self.params[6 * i + 1],xeq(0)],self.colors[i]+'-')
#draw for inipara before optimization
k1 = np.array([[self.inipara[6 * i + 3] ** 2, self.inipara[6 * i + 3] * self.inipara[6 * i + 4] * self.inipara[6 * i + 5]],
[self.inipara[6 * i + 3] * self.inipara[6 * i + 4] * self.inipara[6 * i + 5], self.inipara[6 * i + 4] ** 2]])
w1, v1 = np.linalg.eig(k1)
idx = w1.argsort()
w1 = w1[idx]
v1 = v1[:, idx]
angle=-(np.arctan(v1[1][1]/v1[0][1]))+np.pi#x+2*(pi/4-x)+pi/2#since in the image X and Y are inverted, so need to minus 90 degree and flip around pi/4
w2 = np.zeros((1 , 2))
w2[0,1] = np.sqrt(2)*np.max([self.inipara[6 * i + 3], self.inipara[6 * i + 4]])
w2[0,0] = w2[0,1]*w1[0]/w1[1]
xeq = lambda t: w2[0,1] * np.cos(t) * np.cos(angle) + w2[0,0] * np.sin(
t) * np.sin(angle) + self.inipara[6 * i + 1]
yeq = lambda t: - w2[0,1] * np.cos(t) * np.sin(angle) + w2[0,0] * np.sin(
t) * np.cos(angle) + self.inipara[6 * i + 2]
t = np.linspace(0, 2 * np.pi, 100)
x = xeq(t)
y = yeq(t)
x=x[0::5]
y=y[0::5]
pylab.scatter(self.inipara[6 * i + 2], self.inipara[6 * i +1], color=self.colors[i], s=1)
pylab.plot(y.astype(int), x.astype(int), self.colors[i] + '--')
pylab.plot([self.inipara[6 * i + 2], yeq(0)],[self.inipara[6 * i + 1],xeq(0)],self.colors[i]+'-')
if self.nComponents==3:
minind=np.argmin([np.linalg.norm(self.params[1:3]-self.params[7:9]),np.linalg.norm(self.params[1:3]-self.params[13:15]),np.linalg.norm(self.params[7:9]-self.params[13:15])])
if minind==0:
cenind=[1,7]
elif minind==1:
cenind=[1,13]
else:
cenind=[7,13]
pylab.plot([self.params[cenind[0]+1],self.params[cenind[1]+1]], [self.params[cenind[0]],self.params[cenind[1]]], '-m')
pylab.savefig(title,bbox_inches='tight', pad_inches=0)
pylab.close()
for i in range(expert.cluster_num):
expert.plot_model(partition=i, show_plot=False, save_fig_folder=folder_name) #(i==expert.cluster_num-1))
pl.figure(expert.cluster_num+1)
pl.plot(prediction_error_history)
pl.title("Prediction Error History")
pl.xlabel("time")
pl.ylabel("Prediction Error")
save_figure.save(folder_name+"/Prediction Error History")
pl.figure(expert.cluster_num+2)
pl.hist(state1_history)
pl.title("Resultant State Histogram")
pl.xlabel("State")
pl.ylabel("# of Occurrence")
pl.autoscale(True)
save_figure.save(folder_name+"/Resultant State Histogram")
pl.figure(expert.cluster_num+3)
pl.hist2d(state0_history, action0_history)
pl.title("Initial State vs Initial Action Histogram")
pl.xlabel("State")
pl.ylabel("Action")
pl.colorbar()
save_figure.save(folder_name+"/Initial State vs Initial Action Histogram")
#print("Most common Action")
def most_common(lst):
return max(set(lst), key=lst.count)
bin_num = 100
bin_size = int(len(action0_history)/bin_num)
#! /usr/bin/env python
# -*- coding: utf-8 -*-
import pylab as pl
import numpy as np
weka = [0, 0, 1.5, 0.5, 9, 0, 0, 3, 0, 0.5, 5, 14, 15.5, 2, 12]
# Main
if __name__ == "__main__":
pl.xlabel('Levels')
pl.ylabel('Error (%)')
pl.title(
r'Error on 10-fold cross-validation with functional tree from Weka')
pl.bar(np.arange(len(weka)), weka, color='blue', align='center')
pl.autoscale(tight=True, axis='x')
pl.xticks(np.arange(0, 15), range(1, 16), size='small')
pl.yticks(range(0, 55, 5), range(0, 55, 5), size='small')
pl.savefig('weka_ft_game.png')
pl.savefig('weka_ft_game.eps')
#! /usr/bin/env python
# -*- coding: utf-8 -*-
import pylab as pl
import numpy as np
databases = ['IRIS','BREASTCANCER','PIMA','VEHICLE','LANDSAT']
weka = [5,2.86,23.29,22.45,14.18]
# Main
if __name__ == "__main__":
pl.xlabel('Databases')
pl.ylabel('Error (%)')
pl.title(r'Error on 10-fold cross-validation with functional tree from Weka')
pl.bar(np.arange(len(weka)),weka, color='blue', align='center')
pl.autoscale(tight=True, axis='x')
pl.xticks(range(len(databases)),databases, size='small')
pl.yticks(range(0,70,5), range(0,70,5), size='small')
pl.savefig('weka_ft_learning.png')
pl.savefig('weka_ft_learning.eps')
def getGFPband(self, name='', time=-1, width=70, plot=True, save=True):
results = []
for index, im in enumerate(self.images):
dx, dy = np.indices(im.shape)
c1 = (int(self.params[index][1]), int(self.params[index][2]))
c2 = (int(self.params[index][1 + 6]),
int(self.params[index][2 + 6]))
center = [(self.params[index][1] + self.params[index][1 + 6]) / 2.,
(self.params[index][2] + self.params[index][2 + 6]) / 2.]
product = (dx - c1[0]) * (c2[1] - c1[1]) + (dy - c1[1]) * (c1[0] -
c2[0])
orthProduct = (dx - c1[0]) * (c1[0] - c2[0]) + (dy - c1[1]) * (
c1[1] - c2[1])
distance = np.sqrt((dx - c1[0])**2 +
(dy - c1[1])**2) * np.sign(orthProduct)
product = np.abs(product)
mask = np.zeros(im.shape)
mask[product < np.percentile(product, 5)] = 1
X = distance[mask == 1].flatten()
Y = im.image[mask == 1].flatten()
Z = zip(X, Y)
Z.sort()
Xsort, Ysort = zip(*Z)
Xsort = np.array(Xsort)
c1proj = np.argmax(Xsort == 0)
c2proj = np.argmax(Xsort == distance[c2[0], c2[1]])
try:
s = Sequence(Ysort, [c1proj, c2proj], r=width)
s.hScale()
out = s.vScale()
except IndexError:
out = np.zeros(2 * width)
#print "--- debug ---"
if plot:
pylab.figure(figsize=(17, 6))
pylab.subplot(1, 3, 2)
pylab.imshow(distance * mask)
pylab.title("Distance")
pylab.autoscale(False)
pylab.axis('off')
pylab.plot(self.params[index][2::6],
self.params[index][1::6],
'ro',
label="centres des cellules")
pylab.legend(numpoints=1)
pylab.subplot(1, 3, 1)
pylab.title("GFP")
pylab.imshow(im.image, 'gray')
pylab.autoscale(False)
pylab.axis('off')
pylab.plot(self.params[index][2::6],
self.params[index][1::6],
'ro',
label="centres des cellules")
pylab.legend(numpoints=1)
pylab.subplot(1, 3, 3)
pylab.plot(Ysort, 'r')
pylab.axvline(x=c1proj)
pylab.axvline(x=c2proj)
pylab.xlabel("Distance")
pylab.ylabel("Fluorescence (GFP)")
if save:
pylab.savefig("{0}_t{1:02d}.png".format(
name, time + index))
else:
pylab.show()
pylab.close('all')
results.append(out)
return results, c1, c2
def divideangle(self, tSelect): # compute division angle after detecting cell division
if tSelect > 0 and tSelect < len(self.listObj):
params2 = self.listObj[tSelect][0].params
params3 = self.listObj[tSelect][1].params
angleFind = angle.AngleFinder(3, params3)
a, distDaughtercells, rightOrder = angleFind.getAngle_gaussian()
th_dist=25
if rightOrder and (distDaughtercells <= th_dist):
#fileout.write(",TAU{0},ORDER{1},DIST{2},T{3},A{4}\n".format(traj.tau, str(rightOrder)[0], distDaughtercells, tSelect, a))
plotflag=1
if plotflag:
pylab.figure()
for indexIm in range(-2, 1):
pylab.subplot(2, 3, indexIm+3)
if tSelect+indexIm > 0:
imfilePrevious = glob("edga_*_t{0:04d}.tif".format(tSelect+indexIm))
try:
imagePrevious = cv2.imread(imfilePrevious[0], cv.CV_LOAD_IMAGE_UNCHANGED)
if len(imagePrevious.shape) == 3:
print imagePrevious.shape, len(imagePrevious.shape)
imagePrevious = imagePrevious[:,:,0]
pylab.imshow(imagePrevious, 'gray')
pylab.axis('off')
except IndexError:
print "no image at ", "edga_*s{0}_t{1:04d}.tif".format( 'dir', tSelect+indexIm)
pass
pylab.title("t = {0}".format(tSelect+indexIm))
imfile = glob("edga_*_t{0:04d}.tif".format(tSelect+indexIm))
if len(imfile) > 1:
print "too many images"
raise IndexError
try:
image = cv2.imread(imfile[0], cv.CV_LOAD_IMAGE_UNCHANGED)
if len(image.shape) == 3:
image = image[:,:,0]
pylab.subplot(2,3,4)
pylab.imshow(image, 'gray')
pylab.axis('off')
pylab.autoscale(False)
angleFind.draw()
pylab.title("angle={0:.0f} degree".format(a*180./np.pi))
pylab.subplot(2,3,5)
pylab.imshow(image, 'gray')
pylab.axis('off')
pylab.autoscale(False)
angleFind.draw2D_new()
pylab.subplot(2,3,6)
pylab.imshow(image, 'gray')
pylab.axis('off')
pylab.autoscale(False)
GaussClasses.GaussianObject(2, params=params2).draw2D_new()
except IndexError:
print "no image at : ", "edga_*s{0}_t{1:04d}.tif".format('dir', tSelect+indexIm)
pylab.title("t = {0}".format(tSelect))
#pylab.legend()
#pylab.savefig("../angle_s{0}_x{1:03d}_y{2:03d}_t{3:03d}.png".format('dir', int(x), int(y), int(tSelect)))
pylab.savefig("../angle_t{0:03d}.png".format(int(tSelect)))
pylab.close()
return a*180./np.pi
def getGFPband(self, name = '', time = -1, width = 70, plot = True, save = True):
results = []
for index, im in enumerate(self.images):
dx, dy = np.indices(im.shape)
c1 = (int(self.params[index][1]), int(self.params[index][2]))
c2 = (int(self.params[index][1+6]), int(self.params[index][2+6]))
center = [(self.params[index][1] + self.params[index][1+6])/2., (self.params[index][2] + self.params[index][2+6])/2.]
product = (dx -c1[0])*(c2[1] - c1[1]) + (dy - c1[1])*(c1[0] - c2[0])
orthProduct = (dx -c1[0])*(c1[0] - c2[0]) + (dy - c1[1])*(c1[1] - c2[1])
distance = np.sqrt((dx - c1[0])**2 + (dy - c1[1])**2) * np.sign(orthProduct)
product = np.abs(product)
mask = np.zeros(im.shape)
mask[product < np.percentile(product, 5)] = 1
X = distance[mask == 1].flatten()
Y = im.image[mask == 1].flatten()
Z = zip(X, Y)
Z.sort()
Xsort, Ysort = zip(*Z)
Xsort = np.array(Xsort)
c1proj = np.argmax(Xsort == 0)
c2proj = np.argmax(Xsort == distance[c2[0], c2[1]])
try:
s = Sequence(Ysort, [c1proj, c2proj], r = width)
s.hScale()
out = s.vScale()
except IndexError:
out = np.zeros(2*width)
#print "--- debug ---"
if plot:
pylab.figure(figsize = (17,6))
pylab.subplot(1,3,2)
pylab.imshow(distance*mask)
pylab.title("Distance")
pylab.autoscale(False)
pylab.axis('off')
pylab.plot(self.params[index][2::6], self.params[index][1::6], 'ro', label = "centres des cellules")
pylab.legend(numpoints = 1)
pylab.subplot(1,3,1)
pylab.title("GFP")
pylab.imshow(im.image, 'gray')
pylab.autoscale(False)
pylab.axis('off')
pylab.plot(self.params[index][2::6], self.params[index][1::6], 'ro', label = "centres des cellules")
pylab.legend(numpoints = 1)
pylab.subplot(1,3,3)
pylab.plot(Ysort, 'r')
pylab.axvline(x = c1proj)
pylab.axvline(x = c2proj)
pylab.xlabel("Distance")
pylab.ylabel("Fluorescence (GFP)")
if save:
pylab.savefig("{0}_t{1:02d}.png".format(name, time+index))
else:
pylab.show()
pylab.close('all')
results.append(out)
return results, c1, c2
