def draw_date_score():
# dir_name 에는 보간값 있는 폴더 이름 적기
st = time.time()
# 프리셋 적용
preset_ds()
plt.title(f"소녀전선 한국서버 <허수미궁+> 등급컷 변화 그래프")
# 점, 그래프 그리기
ds_plot_in100([1, 10, 50, 100], marker='o', mfc='w')
ds_plot([5, 10, 15, 20, 30, 40, 50], marker='o', mfc='w')
# 가로선 그리기
draw_axhline(200000, '황금요정 확정지급 점수\n200,000점')
draw_axhline(400000, '최고등급 보상 확정지급 점수\n400,000점')
# 범례
plt.legend(bbox_to_anchor=(1, 0.5), loc="center left")
plt.figtext(0.10, 0.04, "36베이스 - 소녀전선 데이터베이스 https://girlsfrontline.kr", ha="left", va="top", alpha=0.5, size=12)
plt.figtext(0.88, 0.04, "구글 설문 및 36베이스 카카오톡 봇으로 표본 조사중입니다. 많이 참여해주세요.", ha="right", va="top", alpha=0.5, size=12)
# 저장
# plt.show()
plt.savefig(f'../image/{event_name}/date_score/{datetime.date.today()}.png')
shutil.copy(f'../image/{event_name}/date_score/{datetime.date.today()}.png', "../docs/recent.png")
print(f">>> {time.time() - st} secs.")
return
def plot_3panel(X1,
X2,
X3,
Y,
xlims1=None,
xlims2=None,
xlims3=None,
ymax=None,
X1lab='dBZ',
X2lab='ZDR',
X3lab=r'Kdp (dB km$^{-1}$)',
ylab=None,
label=True,
labelTx=' ',
labelpos=None):
"""Create a 3-panel vertical plot of reflectivity, differential reflectivity,
and specific differential phase.
"""
fig, (ax1, ax2, vax3) = plt.subplots(1, 3, sharey=True)
if xlims1 is None:
xlims1 = (-20, 30.)
if xlims2 is None:
xlims2 = (-1.5, 1.5)
if xlims3 is None:
xlims3 = (.2, .4)
if ymax is None:
ymax = 10.
ax1.plot(X1, Y, color='k')
ax2.plot(X2, Y, color='k')
ax3.plot(X3, Y, color='k')
ax1.set_xlim(xlims1)
ax2.set_xlim(xlims2)
ax3.set_xlim(xlims3)
ax1.set_xlabel(X1lab)
ax2.set_xlabel(X2lab)
ax3.set_xlabel(X3lab)
# Set y axis characteristics
ax1.set_ylim(0., ymax)
if ylab is None:
ax1.set_ylabel('Altitude (km)')
else:
ax1.set_ylabel(ylab)
ax1.vlines(0, 0, ymax)
ax2.vlines(0, 0, ymax)
ax1.xaxis.grid(color='k', ls=':', lw=1)
ax2.xaxis.grid(color='k', ls=':', lw=1)
ax3.xaxis.grid(color='k', ls=':', lw=1)
ax1.yaxis.grid(color='k', ls=':', lw=.5)
ax2.yaxis.grid(color='k', ls=':', lw=.5)
ax3.yaxis.grid(color='k', ls=':', lw=.5)
# Add label to above plot unless location specified
if label:
if labelpos is None:
labelpos = (.15, .91)
plt.figtext(labelpos[0], labelpos[1], labelTx)
return fig, ax1, ax2, ax3
def plot_zdr_rhv(X1,
X2,
Y,
xlims1=None,
xlims2=None,
ymax=None,
label=True,
labelTx=' ',
labelpos=None):
"""Create a vertical plot of differential reflectivity and copolar correlation
coefficient.
"""
fig, ax = plt.subplots()
axes = [ax, ax.twiny()]
if xlims1 is None:
xlims1 = (-1.5, 1.5)
if xlims2 is None:
xlims2 = (.8, 1.)
if ymax is None:
ymax = 10.
axes[0].plot(X1, Y, label='Differential Reflectivity', color='b')
axes[1].plot(X2, Y, label='CoPolar Correlation Coefficient', color='r')
axes[0].set_xlim(xlims1)
axes[1].set_xlim(xlims2)
axes[0].set_xlabel('Differential Reflectivity (dB)')
axes[1].set_xlabel('CoPolar Correlation Coefficient')
axes[0].tick_params(axis='x', colors='b')
axes[1].tick_params(axis='x', colors='r')
axes[0].xaxis.label.set_color('b')
axes[1].xaxis.label.set_color('r')
axes[0].set_ylim(0., ymax)
axes[0].set_ylabel('Altitude (km)')
axes[0].vlines(0, 0, ymax)
axes[0].xaxis.grid(color='b', ls=':', lw=1)
axes[1].xaxis.grid(color='r', ls=':', lw=1)
axes[0].yaxis.grid(color='k', ls=':', lw=.5)
handles1, labels1 = axes[0].get_legend_handles_labels()
handles2, labels2 = axes[1].get_legend_handles_labels()
plt.legend(
[handles1[0], handles2[0]],
['Differential Reflectivity', 'CoPolar Correlation Coefficient'],
loc=6,
fontsize=11)
# Add label to lower left in plot unless location specified
if label:
if labelpos is None:
labelpos = (.15, .15)
plt.figtext(labelpos[0], labelpos[1], labelTx)
return fig, ax, axes
def plot_add_stats(instance=None, avg=None, sd=None, points=None,
good_samples=None, tot_samples=None, labelpos=None):
"""Add text to the figure that contains statistics."""
if labelpos is None:
labelpos=(.15, .7)
if instance == 'single':
plt.figtext(labelpos[0], labelpos[1],
"Avg Zdr = %g\nStd Dev = %g\nPoints = %g\n"%(avg, sd, points))
elif instance == 'multi':
plt.figtext(labelpos[0], labelpos[1],
"Avg Zdr = %g\nStd Dev = %g\nSamples = %g used of %g total\nPoints = %g\n"%
(avg, sd, good_samples, tot_samples, points))
else:
print "Need to supply either single or multiple run statistics!!"
def plot_reg(x, y, out_file):
f, ax = plt.subplots(figsize=(6.5, 6.5))
sns.despine(f, left=True, bottom=True)
i = np.logical_and(np.isfinite(x), np.isfinite(y))
x = x[i]
y = y[i]
sns.regplot(x, y, ax=ax)
r = np.polyfit(x, y, 1)
print(i.sum())
print(r)
filename = os.path.basename(out_file)
plt.title(filename[:-4])
plt.figtext(0.1, 0.95, 'a = {:0.4f}'.format(r[0]))
plt.figtext(0.1, 0.90, 'b = {:0.4f}'.format(r[1]))
plt.savefig(out_file)
def plot_3panel(X1, X2, X3, Y,
xlims1=None, xlims2=None, xlims3=None, ymax=None,
X1lab='dBZ', X2lab='ZDR', X3lab=r'Kdp (dB km$^{-1}$)', ylab=None,
label=True, labelTx=' ', labelpos=None):
"""Create a 3-panel vertical plot of reflectivity, differential reflectivity,
and specific differential phase.
"""
fig, (ax1, ax2, vax3) = plt.subplots(1, 3, sharey=True)
if xlims1 is None:
xlims1 = (-20, 30.)
if xlims2 is None:
xlims2 = (-1.5, 1.5)
if xlims3 is None:
xlims3 = (.2, .4)
if ymax is None:
ymax = 10.
ax1.plot(X1, Y, color='k')
ax2.plot(X2, Y, color='k')
ax3.plot(X3, Y, color='k')
ax1.set_xlim(xlims1)
ax2.set_xlim(xlims2)
ax3.set_xlim(xlims3)
ax1.set_xlabel(X1lab)
ax2.set_xlabel(X2lab)
ax3.set_xlabel(X3lab)
# Set y axis characteristics
ax1.set_ylim(0., ymax)
if ylab is None:
ax1.set_ylabel('Altitude (km)')
else:
ax1.set_ylabel(ylab)
ax1.vlines(0,0,ymax)
ax2.vlines(0,0,ymax)
ax1.xaxis.grid(color='k', ls=':', lw=1)
ax2.xaxis.grid(color='k', ls=':', lw=1)
ax3.xaxis.grid(color='k', ls=':', lw=1)
ax1.yaxis.grid(color='k', ls=':', lw=.5)
ax2.yaxis.grid(color='k', ls=':', lw=.5)
ax3.yaxis.grid(color='k', ls=':', lw=.5)
# Add label to above plot unless location specified
if label:
if labelpos is None:
labelpos = (.15,.91)
plt.figtext(labelpos[0], labelpos[1], labelTx)
return fig, ax1, ax2, ax3
def __init__(self, poll, parties, elections=None, join_coalitions=True):
plt.rcParams['figure.figsize'] = (12, 6)
self._fig, ax = plt.subplots()
plt.rcParams['xtick.labelsize'] = 16
plt.rcParams['axes.labelweight'] = 'bold'
plt.rcParams['font.weight'] = 'normal'
plt.rcParams['xtick.major.pad']='16'
plt.rcParams['axes.titlesize'] = 20
plt.rcParams['axes.titleweight'] = 'bold'
parties_votes = []
for i, p in enumerate(parties.parties.values()):
parties_votes.append((p, poll.get_party(p,join_coalitions)))
parties_votes.sort(key=lambda x: x[1], reverse=True)
parties_votes = []
for i, p in enumerate(parties.parties.values()):
parties_votes.append((p, poll.get_party(p,join_coalitions)))
parties_votes.sort(key=lambda x: x[1], reverse=True)
width = 0.6
left_lim = 0.1
plt.title(poll.pollster + poll.date.strftime(' - %-d %b'), loc='left', x=0, y=1.1, fontdict={'ha':'left'})
names = []
for i, (p, votes) in enumerate(parties_votes):
a = ax.bar(left_lim+i, votes, width=width, color=p.color, edgecolor='none')
ax.text(left_lim+i+width/2, votes-4, '{0}%'.format(votes),
fontdict={'weight':'bold', 'color':'w', 'fontsize':'20', 'ha':'center', 'va':'center'})
names.append(p.short_name)
if elections:
vot =elections.get_party(p,join_coalitions)
if a:
plt.plot([left_lim+i-0.1*width, left_lim+i+width+0.1*width], [vot, vot], color=[0.2,0.2,0.2], linewidth=3)
idx = np.arange(len(parties.parties))+width/2 + left_lim
ax.set_xticks(idx)
ax.set_xlim([0, idx[-1]+width/2 + left_lim])
ax.set_xticklabels(names);
ax.spines['top'].set_visible(False)
ax.spines['right'].set_visible(False)
ax.spines['left'].set_visible(False)
ax.xaxis.set_ticks_position('none')
ax.yaxis.set_ticks_position('none')
if poll.error:
plt.figtext(0.125,.94,'({}% error)'.format(poll.error), fontdict={'fontsize': 12})
def draw_plot(states, times, caption):
try:
with plt.xkcd():
#plt.style.use('fivethirtyeight')
fig, ax = plt.subplots(nrows=1, ncols=1, sharex=True, sharey=True)
fig.suptitle('Spring damping over time', fontsize=18, fontweight='bold')
displacement = [n[0] for n in states]
ax.plot(times, displacement)
ax.set_xlabel('Time (s)')
ax.set_ylabel('Displacement (m)')
ax.axis('tight')
figtext(.52, .15, caption)
plt.show()
except Exception as ex:
print(ex)
def plot_zdr_rhv(X1, X2, Y, xlims1=None, xlims2=None, ymax=None,
label=True, labelTx=' ', labelpos=None):
"""Create a vertical plot of differential reflectivity and copolar correlation
coefficient.
"""
fig, ax = plt.subplots()
axes = [ax, ax.twiny()]
if xlims1 is None:
xlims1 = (-1.5, 1.5)
if xlims2 is None:
xlims2 = (.8, 1.)
if ymax is None:
ymax = 10.
axes[0].plot(X1, Y, label='Differential Reflectivity', color='b')
axes[1].plot(X2, Y, label='CoPolar Correlation Coefficient', color='r')
axes[0].set_xlim(xlims1)
axes[1].set_xlim(xlims2)
axes[0].set_xlabel('Differential Reflectivity (dB)')
axes[1].set_xlabel('CoPolar Correlation Coefficient')
axes[0].tick_params(axis='x', colors='b')
axes[1].tick_params(axis='x', colors='r')
axes[0].xaxis.label.set_color('b')
axes[1].xaxis.label.set_color('r')
axes[0].set_ylim(0., ymax)
axes[0].set_ylabel('Altitude (km)')
axes[0].vlines(0, 0, ymax)
axes[0].xaxis.grid(color='b', ls=':', lw=1)
axes[1].xaxis.grid(color='r', ls=':', lw=1)
axes[0].yaxis.grid(color='k', ls=':', lw=.5)
handles1, labels1 = axes[0].get_legend_handles_labels()
handles2, labels2 = axes[1].get_legend_handles_labels()
plt.legend([handles1[0], handles2[0]],
['Differential Reflectivity','CoPolar Correlation Coefficient'],
loc=6, fontsize =11)
# Add label to lower left in plot unless location specified
if label:
if labelpos is None:
labelpos = (.15, .15)
plt.figtext(labelpos[0], labelpos[1], labelTx)
return fig, ax, axes
def pressSat(event):
tempData=np.nan_to_num(theData.data)
maxHarg=np.argmax(tempData[:,1])
minHarg=np.argmin(tempData[:,1])
'''linear fit to saturated data (+- 25 points from max/min field)
'''
highFit=np.polyfit(theData.data[maxHarg-25:maxHarg+25,1],theData.data[maxHarg-25:maxHarg+25,2],1)
lowFit=np.polyfit(theData.data[minHarg-25:minHarg+25,1],theData.data[minHarg-25:minHarg+25,2],1)
''' Average intercept
'''
fitSat=(highFit[1]-lowFit[1])/2
''' display ms
'''
txtSat='ms = '+str(fitSat)
plt.figtext(0.75, 0.4,txtSat)
theData.fitSat=fitSat
def pressSat(event):
tempData=np.nan_to_num(theData.data)
maxHarg=np.argmax(tempData[:,1])
minHarg=np.argmin(tempData[:,1])
'''linear fit to saturated data (+- 25 points from max/min field)
'''
highFit=np.polyfit(theData.data[maxHarg-25:maxHarg+25,1],theData.data[maxHarg-25:maxHarg+25,2],1)
lowFit=np.polyfit(theData.data[minHarg-25:minHarg+25,1],theData.data[minHarg-25:minHarg+25,2],1)
''' Average intercept
'''
fitSat=(highFit[1]-lowFit[1])/2
''' display ms
'''
txtSat='ms = '+str(fitSat)
plt.figtext(0.75, 0.4,txtSat)
theData.fitSat=fitSat
def plot_add_stats(instance=None,
avg=None,
sd=None,
points=None,
good_samples=None,
tot_samples=None,
labelpos=None):
"""Add text to the figure that contains statistics."""
if labelpos is None:
labelpos = (.15, .7)
if instance == 'single':
plt.figtext(
labelpos[0], labelpos[1],
"Avg Zdr = %g\nStd Dev = %g\nPoints = %g\n" % (avg, sd, points))
elif instance == 'multi':
plt.figtext(
labelpos[0], labelpos[1],
"Avg Zdr = %g\nStd Dev = %g\nSamples = %g used of %g total\nPoints = %g\n"
% (avg, sd, good_samples, tot_samples, points))
else:
print "Need to supply either single or multiple run statistics!!"
def print_info(self):
try:
pat_surname, pat_firstname = self.dicom.PatientName.split('^')
except ValueError:
pat_surname = self.dicom.PatientName
pat_firstname = ''
pat_name = ' '.join((pat_surname, pat_firstname.title()))
pat_id = self.dicom.PatientID
pat_sex = self.dicom.PatientSex
pat_bdate = datetime.strptime(
self.dicom.PatientBirthDate, '%Y%m%d').strftime("%e %b %Y")
info = "%s (%s) sex: %s\nbirthdate: %s" % (pat_name, pat_id,
pat_sex, pat_bdate)
plt.figtext(0.08, 0.865, info, fontsize=12)
info = "duration: %s s | samples: %s | sample freq.: %s/s" % (
self.duration,
self.samples,
self.sampling_frequency)
plt.figtext(0.08, 0.02, info, fontsize=10)
info = "%s mm/s | %s mm/mV" % (self.mm_s, self.mm_mv)
plt.figtext(0.68, 0.02, info, fontsize=10)
plt.figtext(0.5, 0.865, self.legend(), fontsize=10)
info = 'E. O. Ospedali Galliera\nECG date: '
date_str = (self.dicom.InstanceCreationDate +
self.dicom.InstanceCreationTime)
info += datetime.strftime(datetime.strptime(date_str,
'%Y%m%d%H%M%S'),
'%d %b %Y %H:%M')
plt.figtext(0.03, 0.94, info, fontsize=12)
def draw_per_score(date, gets=[0, 10, 20, 40, 50]):
st = time.time()
# 그래프 기초 설정
preset_ps()
plt.title(f"소녀전선 한국서버 <허수미궁+> {date} 분포 그래프")
# 점, 그래프 그리기
ps_scatter(date, marker='s', label="전체 표본")
ps_plot(date, annotate=gets, label="예상 점수 그래프")
# 가로선 그리기
draw_axhline(200000, '황금요정 확정지급 점수\n200,000점')
draw_axhline(400000, '최고등급 보상 확정지급 점수\n400,000점')
# 범례
plt.legend(loc=1)
plt.figtext(0.10, 0.04, "36베이스 - 소녀전선 데이터베이스 https://girlsfrontline.kr", ha="left", va="top", alpha=0.5, size=12)
plt.figtext(0.94, 0.04, "구글 설문 및 36베이스 카카오톡 봇으로 표본 조사중입니다. 많이 참여해주세요.", ha="right", va="top", alpha=0.5, size=12)
# 저장
# plt.show()
plt.savefig(f'../image/{event_name}/per_score/{date}.png')
print(f">>> {time.time() - st} secs.")
return
def add_header(text_1="", text_2="", text_3="", fontsize=15):
"""
Add text footer to a figure.
Author: Albenis Pérez Alarcón
contact:[email protected]
Parameters
----------
text_1 : str
text_2 : str
text_3 : str
Returns
-------
`matplotlib.image.FigureImage`
The `matplotlib.image.FigureImage` instance created
"""
coords = plt.gca().get_position().get_points()
plt.figtext((coords[0, 0] + 0.50) / 2.0,
0.97,
text_1,
horizontalalignment='center',
verticalalignment='center',
fontsize=fontsize,
fontweight="bold")
plt.figtext((coords[0, 0] + 1.5) / 2.0,
0.97,
text_2,
horizontalalignment='center',
verticalalignment='center',
fontsize=fontsize,
fontweight="bold")
plt.figtext((coords[0, 0] + 0.44) / 2.0,
0.93,
text_3,
horizontalalignment='center',
verticalalignment='center',
fontsize=fontsize - 2)
return
def add_footer(text_1="", text_2="", text_3="", fontsize=13):
"""Add footer to a figure.
Add text footer to a figure.
Author: Albenis Pérez Alarcón
contact:[email protected]
Parameters
----------
text_1 : str
text_2 : str
text_3 : str
text to put in the figure, all text are lower center
Returns
-------
`matplotlib.image.FigureImage`
The `matplotlib.image.FigureImage` instance created
"""
coords = plt.gca().get_position().get_points()
plt.figtext((coords[0, 0] + 1.) / 2.0,
0.09,
text_1,
fontsize=fontsize,
horizontalalignment='center',
fontweight='bold')
plt.figtext((coords[0, 0] + 1.) / 2.0,
0.07,
text_2,
horizontalalignment='center',
verticalalignment='center',
fontsize=fontsize)
plt.figtext((coords[0, 0] + 1.) / 2.0,
0.03,
text_3,
horizontalalignment='center',
verticalalignment='center',
fontsize=fontsize)
return
def plot_(fig, l1, l2, t):
plt.figure(fig)
plt.xlabel(l1)
plt.ylabel(l2)
plt.title(t)
j = 0
for i in range(df.shape[1]):
df = df.rename(columns={i: header[i]})
if header[i] in continuous:
dist = df[header[i]].sort_values()
plot_(j, 'values', header[i], header[i])
dist.plot.hist(bins=20)
plt.figtext(1, 0.4, df[header[i]].describe())
else:
dist = df[header[i]].value_counts(sort=False)
miss = [' Not in universe', ' ?', ' Not in universe or children', ' Not in universe under 1 year old']
m = 0
for k in miss:
if k in dist.index.tolist():
m = +dist[k]
dist = dist.drop(k)
dist = dist * 100. / df.shape[0]
if df[header[i]].dtype == 'int64':
plot_(j, 'categories', 'Frequency', header[i])
df[header[i]].hist(bins=50)
else:
plot_(j, 'categories', 'Percentage', header[i])
dist.plot.bar()
#ablated_fitness[1] = '#cc7a00'
connect(axnet2, DA, DD, "arc3,rad= 0.00", Rs, ablated_fitness[6])
connect(axnet2, AS, DA, "arc3,rad= 0.00", Rs, ablated_fitness[0])
connect(axnet2, AS, VD, "arc3,rad= 0.00", Rs, ablated_fitness[1])
connect(axnet2, DA, DB, "arc3,rad= 0.00", Rs, ablated_fitness[2])
connect(axnet2, DB, AS, "arc3,rad= 0.00", Rs, ablated_fitness[3])
connect(axnet2, VD, VA, "arc3,rad= 0.00", Rs, ablated_fitness[4])
connect(axnet2, VD, VB, "arc3,rad= 0.00", Rs, ablated_fitness[5])
connect(axnet2, VB, DD, "arc3,rad= 0.00", Rs, ablated_fitness[7])
connect(axnet2, VA, DD, "arc3,rad= 0.00", Rs, ablated_fitness[8])
Gapjunction(axnet2, VD, DD, "arc3,rad= 0.0", Rs, ablated_fitness[9])
for ax in [axnet1, axnet2]:
ax.set_xlim(-0.5, 10.5)
ax.set_ylim(-1.0, 19.5)
ax.axis('off')
ax.set_aspect('equal')
####################################################################
####################################################################
fz = 88
plt.figtext(0.02, 0.94, 'A', ha='center', va='center', fontsize=fz)
plt.figtext(0.22, 0.94, 'B', ha='center', va='center', fontsize=fz)
plt.figtext(0.62, 0.94, 'C', ha='center', va='center', fontsize=fz)
fig.subplots_adjust(left=0.02, bottom=0.15, right=1.00, top=1.00)
plt.savefig('dv_propagation.png', dpi=100)
plt.savefig('dv_propagation.pdf')
#######################################################################
#######################################################################
def age_plot(dataname2age2num, age2pval, age2label, outfn, plot_type='bar',
title='', output_png=False, scale_x=False, xlabel='Age',
methods_str=''):
""" """
ages = sorted(age2label.keys())
fig = plt.figure()
ax1 = fig.add_subplot(111)
plt.subplots_adjust(bottom=0.27)
width = 0.35
plt.xlabel(xlabel)
plt.ylabel('Fraction')
# hack to make sure background is last if present
data_names = []; bgs = []
for name in sorted(dataname2age2num):
if 'ackground' in name:
bgs.append(name)
else:
data_names.append(name)
data_names += bgs
dataname2avgdepth = {}
for dataname_idx, name in enumerate(data_names):
# compute average depth, age, and total number of proteins
N = 0.
avg_depth = 0.
avg_age = 0.
for age in dataname2age2num[name]:
N += dataname2age2num[name][age]
avg_depth += (age * dataname2age2num[name][age])
try:
avg_age += (float(age2label[age]) * dataname2age2num[name][age])
except ValueError:
avg_age += (age * dataname2age2num[name][age])
avg_age /= N
avg_depth /= N
# plot data
heights = []
x_base = []
for age_idx, age in enumerate(ages):
if age in dataname2age2num[name] and \
dataname2age2num[name][age] != 0.0:
heights.append(dataname2age2num[name][age] / N)
x_base.append(age if scale_x else age_idx)
else:
heights.append(0.0)
x_base.append(age if scale_x else age_idx)
# line or bar plot
if plot_type == 'line':
line_color = '#990000' if dataname_idx % 2 == 0 else 'black'
ax1.plot(x_base, heights, 'x-', label='%s (N=%d)' % (name, N),
linewidth=2, mew=3, markersize=8, color=line_color)
else:
r = numpy.array(x_base, dtype='float_')
bar_color = '#990000' if dataname_idx % 2 == 1 else 'black'
r += .03 if dataname_idx % 2 == 1 else -.03
ax1.bar(r - width * (1-dataname_idx), heights, width,
label='%s (N=%d)' % (name, N), color=bar_color)
# now set up axes limits and ticks
ax1.set_xticks(x_base)
x_range = x_base[-1] - x_base[0]
pad = max(.03 * x_range, 1)
ax1.set_xlim(x_base[0] - pad, x_base[-1] + pad)
ymin = ax1.viewLim.ymin
ymax = ax1.viewLim.ymax
y_range = ymax - ymin
ax1.set_ylim(-.05 * y_range, ymax + (.23 * y_range))
leg = ax1.legend(prop={'size': 12}, loc='upper left', numpoints=1)
leg.get_frame().set_fill(False)
#leg.draw_frame(False)
# write p-value *'s
for age_idx, age in enumerate(ages):
if age in age2pval:
pval_str = ''
if .01 < age2pval[age] < 0.05:
pval_str = '*'
elif .001 < age2pval[age] <= 0.01:
pval_str = '**'
elif age2pval[age] <= 0.001:
pval_str = '***'
ax1.text(age if scale_x else age_idx, ymin - (.025 * y_range),
pval_str, horizontalalignment='center',
verticalalignment='center', weight='bold')
# set x_tick names
labels = []
for age in ages:
if age in age2label:
label = age2label[age]
if label != str(age):
labels.append('%s (%d)' % (label, age))
else:
labels.append('%d' % age)
else:
labels.append('')
xtickNames = plt.setp(ax1, xticklabels = labels)
plt.setp(xtickNames, fontsize=10)
plt.setp(xtickNames, rotation=30)
plt.setp(xtickNames, horizontalalignment='right')
title_obj = plt.title(title, fontsize=12)
plt.figtext(0.07, 0.01, '[DB: '+methods_str+']', size=9)
plt.savefig(outfn)
if output_png: plt.savefig(outfn.replace('.pdf', '.png'))
return
def print_info(self, interpretation):
"""Print info about the patient and about the ecg signals.
"""
try:
pat_surname, pat_firstname = self.dicom.PatientName.decode('ISO-8859-1').split('^')
except ValueError:
pat_surname = self.dicom.PatientName
pat_firstname = ''
pat_name = ' '.join((pat_surname, pat_firstname.title()))
pat_age = self.dicom.get('PatientAge', '').strip('Y')
pat_id = self.dicom.PatientID
pat_sex = self.dicom.PatientSex
try:
pat_bdate = datetime.strptime(
self.dicom.PatientBirthDate, '%Y%m%d').strftime("%e %b %Y")
except ValueError:
pat_bdate = ""
# Strip microseconds from acquisition date
regexp = "\.\d+$"
acquisition_date_no_micro = re.sub(
regexp, '', self.dicom.AcquisitionDateTime)
acquisition_date = datetime.strftime(
datetime.strptime(
acquisition_date_no_micro, '%Y%m%d%H%M%S'),
'%d %b %Y %H:%M'
)
info = "%s\n%s: %s\n%s: %s\n%s: %s (%s %s)\n%s: %s" % (
pat_name,
i18n.pat_id,
pat_id,
i18n.pat_sex,
pat_sex,
i18n.pat_bdate,
pat_bdate,
pat_age,
i18n.pat_age,
i18n.acquisition_date,
acquisition_date
)
plt.figtext(0.08, 0.87, info, fontsize=8)
plt.figtext(0.30, 0.87, self.legend(), fontsize=8)
if interpretation:
plt.figtext(0.45, 0.87, self.interpretation(), fontsize=8)
info = "%s: %s s %s: %s Hz" % (
i18n.duration, self.duration,
i18n.sampling_frequency,
self.sampling_frequency
)
plt.figtext(0.08, 0.025, info, fontsize=8)
info = INSTITUTION
if not info:
info = self.dicom.get('InstitutionName', '')
plt.figtext(0.38, 0.025, info, fontsize=8)
# TODO: the lowpass filter 0.05-40 Hz will have to became a parameter
info = "%s mm/s %s mm/mV 0.05-40 Hz" % (self.mm_s, self.mm_mv)
plt.figtext(0.76, 0.025, info, fontsize=8)
def feature_by_age_boxplot(age2vals, age2label, outfn, title='', xlabel='Age',
ylabel='Value', scale_x = False, output_png=False,
methods_str=''):
fig = plt.figure()
if len(age2vals.keys()) > 1:
fig_width = fig.get_figwidth()
fig_height = fig.get_figheight()
fig.set_figwidth(fig_width * 1.7)
fig.set_figheight(fig_height * 1.2)
ax1 = fig.add_subplot(111)
plt.subplots_adjust(bottom=0.26)
ages = sorted(age2label.keys())
box_data = []
box_pos = []
for i, age in enumerate(ages):
if age in age2vals:
box_data.append(age2vals[age])
box_pos.append(age if scale_x else i)
else:
box_data.append([])
box_pos.append(age if scale_x else i)
bp = plt.boxplot(box_data, widths=.6, sym='', patch_artist=True,
positions=box_pos)
plt.setp(bp['boxes'], color='#99CCFF', edgecolor="black", lw=1)
#plt.setp(bp['boxes'], color='darkkhaki', edgecolor="black", lw=1)
plt.setp(bp['whiskers'], color='black', lw=1)
plt.setp(bp['medians'], color='black', lw=1.5)
plt.setp(bp['caps'], color='black', lw=1)
for i, age in enumerate(ages):
x_pos = age if scale_x else i
if age in age2vals:
ax1.plot(x_pos, numpy.average(age2vals[age]), 'x', color='red',
markersize=6, markeredgewidth=1.5)
if age2label:
labels = []
for age in ages:
if age < 0:
labels.append('')
elif age in age2label:
np = len(age2vals[age]) if age in age2vals else 0
labels.append('%s (%d)' % (age2label[age], age))
#labels.append('%s (n=%d)' % (age2label[age], np))
else:
labels.append('')
xtickNames = plt.setp(ax1, xticklabels = labels)
plt.setp(xtickNames, fontsize=10)
plt.setp(xtickNames, rotation=45)
plt.setp(xtickNames, horizontalalignment='right')
ymin = ax1.viewLim.ymin
ymax = ax1.viewLim.ymax
y_range = ymax - ymin
#ax1.set_ylim(-.05 * ymin, 1.05 * ymax)
ax1.set_ylim(ymin - (.02 * y_range), ymax + (.02 * y_range))
xmin = ax1.viewLim.xmin
xmax = ax1.viewLim.xmax
x_range = xmax - xmin
pad = .02 * x_range
ax1.set_xlim(xmin - pad, xmax + pad)
plt.xlabel(xlabel)
plt.ylabel(ylabel)
plt.title(title)
plt.figtext(0.1, 0.01, '[DB: '+methods_str+']', size=10)
plt.savefig(outfn)
if output_png: plt.savefig(outfn.replace('.pdf', '.png'))
return
for i in range(1, ceval):
xeval = -cset[i] / mset[i]
yeval = mset[i - 1] * xeval + cset[i - 1]
plt.plot([xeval, xeval], [0, yeval], '.k', ms=13)
plt.plot([xeval, xeval], [0, yeval], '.g', ms=9)
wl += (yeval) / 22. / (ceval - 1)
wavelength[ind] = wl
ax1.set_xlim(0, 350)
#####################################
plt.figtext(0.053,
0.93,
'wavelength ~= %.2f worm length' % (wl),
ha='left',
va='center',
fontsize=20)
fig.subplots_adjust(left=0.05, bottom=0.04, right=0.98, top=0.96)
plt.savefig('wavelength_figures/plot_sel_%d.png' % ind)
### The script fails in this 7 solution, they were calculated manually.
#wavelength[48] = 0.7
#wavelength[52] = 0.75
#wavelength[60] = 0.9
#wavelength[67] = 0.8
#wavelength[72] = 0.8
#wavelength[97] = 0.85
#wavelength[100] = 0.8
def plot_clades_relationships(clade_pairs, folder, remove_highest=0):
ds = get_dataset('Stool')
ds = compute_relative_values(ds)
# Use numeric Tree. We will discreteze relevant values ourselves
# and plot the numeric correlations
tree = Tree(ds)
same_lineages = 0
for clade_1, clade_2 in clade_pairs:
# Get the nodes in the phylogenetic tree
from_node = tree.node_for_clade_name(clade_1)
to_node = tree.node_for_clade_name(clade_2)
if from_node.is_in_lineage(to_node):
same_lineages += 1
title_text = 'Relative clade abundances'
title(title_text)
# find from-to bacteria abundances
xs = []
ys = []
# Get the total abundance for hte clades in the tree
abundance_from = tree.abundance_column_in_subtree(from_node)
abundance_to = tree.abundance_column_in_subtree(to_node)
x_zeroes = 0
y_zeroes = 0
# List the in-sample values for each sample
for index, _row in enumerate(ds[1:]):
from_abundance = abundance_from[index]
to_abundance = abundance_to[index]
if from_abundance == 0.0:
x_zeroes += 1
if to_abundance == 0.0:
y_zeroes += 1
# if from_abundance < 0.01 and to_abundance < 0.01:
xs.append(from_abundance)
ys.append(to_abundance)
# else:
# xs.append(0.0)
# ys.append(0.0)
if remove_highest > 0.0:
xs, ys = pairwise_remove_highest_values(remove_highest, xs, ys)
ys, xs = pairwise_remove_highest_values(remove_highest, ys, xs)
# All data was eventyally removed
if len(xs) == 0:
print 'Warning. lowest values:%f removed all data from caldes:%s-%s' % (remove_highest, from_node.name, to_node.name)
continue
print 'x zeroes: ', x_zeroes
print 'y zeroes: ', y_zeroes
grid(True)
text_x = 0.67
sample_points = 'Sample points: %d' % len(xs)
figtext(text_x, 0.85, sample_points, fontsize=10)
from_clade = from_node.name.replace('|', '-')
to_clade = to_node.name.replace('|', '-')
xlabel(from_clade, fontsize=10)
ylabel(to_clade, fontsize=10)
disc_x, discrete_xs = discretize_row(xs, maxent_discretization_splitter)
disc_y, discrete_ys = discretize_row(ys, maxent_discretization_splitter)
# plot discretization lines
a, b = [disc_x, disc_x], [-0.001, max(ys)]
c, d = [-0.001, max(xs)], [disc_y, disc_y]
plot(a, b, c='r')
plot(c, d, c='r')
# Discrete bin sizes
pairs = zip(discrete_ys, discrete_xs)
_00 = '00: ' + str(len([x for x in pairs if x == (0,0)]))
_01 = '01: ' + str(len([x for x in pairs if x == (0,1)]))
_10 = '10: ' + str(len([x for x in pairs if x == (1,0)]))
_11 = '11: ' + str(len([x for x in pairs if x == (1,1)]))
figtext(text_x, 0.82, _00, fontsize=10)
figtext(text_x, 0.79, _01, fontsize=10)
figtext(text_x, 0.76, _10, fontsize=10)
figtext(text_x, 0.73, _11, fontsize=10)
phi_coeff, phi_r = pearsonr(discrete_xs, discrete_ys)
phi = 'phi: %f, %f' % (phi_coeff, phi_r)
figtext(text_x, 0.70, phi, fontsize=10)
# Depth of nodes in the phylogenetic tree
from_depth = 'x depth: %d' % from_node.depth
to_depth = 'y depth: %d' % to_node.depth
figtext(text_x, 0.67, from_depth, fontsize=10)
figtext(text_x, 0.64, to_depth, fontsize=10)
# Discretization values
median_x = 'splitter x: %f' % disc_x
median_y = 'splitter y: %f' % disc_y
figtext(text_x, 0.61, median_x, fontsize=10)
figtext(text_x, 0.58, median_y, fontsize=10)
# Same lineage
same_lineage = 'False'
if tree.nodes_have_same_lineage(from_node, to_node):
same_lineage = ' True'
figtext(text_x, 0.55, 'Same lineage: ' + same_lineage, fontsize=10)
# Pearson and spearman correlations
try:
pearson = pearsonr(xs, ys)
spearman = spearmanr(xs, ys)
pearson = 'Pearson: %.3f, %.3f' % (pearson[0], pearson[1])
spearman = 'Spearman: %.3f, %.3f' % (spearman[0], spearman[1])
figtext(text_x, 0.52, pearson, fontsize=10)
figtext(text_x, 0.49, spearman, fontsize=10)
except Exception, e:
print e
print 'clades1: ', from_node.name
print 'clades2: ', to_node.name
print 'xs: %s', xs
print 'ys: %s', ys
# vals = vals[:-20]
scatter(xs, ys, s=1, color='#0066FF')
file_name = folder + from_node.name.replace('|', '-').replace('/', '%') + '---' + to_node.name.replace('|', '-').replace('/', '%')
# file_name = os.path.join(dir, file_name)
# print '[RESULT] ', file_name
# print vals
savefig(file_name)
close()
def GeneByGeneOutput(setOfAligns,parameters):
logging.info('Making the GBG plots...')
h = 2.0 # plot hieght
l = 4.0 # plot width
MB = 0.05 # percent buffer from side
LB = 0.01 # percent buffer for corner
seq1len = setOfAligns.seqOfInt.length
colors = ['b','g','r','c','m']
plotNum = 0
plots = 0
GBGdata = open(parameters['OUTFILE'] + '/images/GBGdata.txt','wb')
GBGdata.write('GBGX.pdf:ts1!ts2!ts3!ts4!\n')
numToExpect = 0
for pAlign in setOfAligns.aligns:
if len(pAlign.localAligns) > 0:
numToExpect += 1
for pAlign in setOfAligns.aligns:
if len(pAlign.localAligns) > 0:
if plotNum%4 == 0:
fig = plt.figure(figsize=(22,17))
plots += 1
plt.figtext(0.5, 0.965, 'Local Alignments for soi: ' + setOfAligns.seqOfInt.name + ', test seqs (' + str(1+(plots-1)*4) + '-' + str(min(4+(plots-1)*4,numToExpect)) + '/' + str(numToExpect), ha='center', color='black', weight='bold', size='large')
gbgstring = 'GBG' + str(plots) + '.pdf:'
ax = []
ax.append(fig.add_subplot(411))
plotNum = 0
else:
ax.append(fig.add_subplot(411+plotNum%4))
seq2len = pAlign.testSeq.length
seq1las = []
seq2las = []
seqRatio = []
scoreRolling = 0
for locA in pAlign.localAligns:
for i in range(len(locA.SOIrange)):
seq1las.append(locA.SOIrange[i])
seq2las.append(locA.TSrange[i])
if setOfAligns.seqOfInt.dataDepths != 0:
scoreSum = sum(locA.fullScoreVec[locA.SOIrange[i][0]:locA.SOIrange[i][1]])
else:
scoreSum = sum(locA.fullScoreVec[locA.SOIrange[i][0]:locA.SOIrange[i][1]])
seqRatio.append(scoreSum/float(locA.SOIrange[i][1]-locA.SOIrange[i][0]))
scoreRolling += scoreSum
totRatio = [scoreRolling/float(seq1len),scoreRolling/float(seq2len)]
if seq1len <= seq2len:
rL = 0.3 # relitive y start of lower
rU = 0.7 # relitive y start of higher
ratio = (seq2len - seq1len)/float(2*seq2len)
s1xm = MB + ratio
s1xx = 1 - MB - ratio
else:
rL = 0.7 # relitive y start of lower
rU = 0.3 # relitive y start of higher
ratio = (seq1len - seq2len)/float(2*seq1len)
s1xm = MB + ratio
s1xx = 1 - MB - ratio
# top, smaller line
ax[plotNum].axhline(y = rU*h, xmin = s1xm, xmax = s1xx, color='black')
ax[plotNum].plot([s1xm*l,s1xm*l],[rU*h - 3*MB, rU*h + 3*MB],color='black') # left bound
ax[plotNum].plot([s1xx*l,s1xx*l],[rU*h - 3*MB, rU*h + 3*MB],color='black') # right bound
ax[plotNum].axhline(y = rU*h - 3*MB, xmin = s1xm, xmax = s1xm + LB, color='black') # left lower corner
ax[plotNum].axhline(y = rU*h + 3*MB, xmin = s1xm, xmax = s1xm + LB, color='black') # left upper corner
ax[plotNum].axhline(y = rU*h - 3*MB, xmin = s1xx, xmax = s1xx - LB, color='black') # right lower corner
ax[plotNum].axhline(y = rU*h + 3*MB, xmin = s1xx, xmax = s1xx - LB, color='black') # right upper corner
# bottom, larger line
ax[plotNum].axhline(y = rL*h, xmin = MB, xmax = 1 - MB, color='black') # main line
ax[plotNum].plot([MB*l,MB*l],[rL*h - 3*MB, rL*h + 3*MB],color='black') # left bound
ax[plotNum].plot([(1 - MB)*l,(1 - MB)*l],[rL*h - 3*MB, rL*h + 3*MB],color='black') # right bound
ax[plotNum].axhline(y = rL*h - 3*MB, xmin = MB, xmax = MB + LB, color='black') # left lower corner
ax[plotNum].axhline(y = rL*h + 3*MB, xmin = MB, xmax = MB + LB, color='black') # left upper corner
ax[plotNum].axhline(y = rL*h - 3*MB, xmin = 1 - MB, xmax = 1 - (MB + LB), color='black') # right lower corner
ax[plotNum].axhline(y = rL*h + 3*MB, xmin = 1 - MB, xmax = 1 - (MB + LB), color='black') # right upper corner
if seq1len <= seq2len:
ax[plotNum].text(MB*l - MB/2*l, rL*h, '0',verticalalignment='center') # left text, bot
ax[plotNum].text((1 - MB)*l + MB/4*l, rL*h + 3*MB, str(seq2len),verticalalignment='center') # right text1, bot
ax[plotNum].text((1 - MB)*l + MB/4*l, rL*h - 3*MB, str(totRatio[1])[0:5],verticalalignment='center') # right text2, bot
ax[plotNum].text(s1xm*l - MB/2*l, rU*h, '0',verticalalignment='center') # left text, top
ax[plotNum].text(s1xx*l + MB/4*l, rU*h + 3*MB, str(seq1len),verticalalignment='center') # right text1, top
ax[plotNum].text(s1xx*l + MB/4*l, rU*h - 3*MB, str(totRatio[0])[0:5],verticalalignment='center') # right text2, top
else:
ax[plotNum].text(MB*l - MB/2*l, rL*h, '0',verticalalignment='center') # left text, bot
ax[plotNum].text((1 - MB)*l + MB/4*l, rL*h + 3*MB, str(seq1len),verticalalignment='center') # right text1, bot
ax[plotNum].text((1 - MB)*l + MB/4*l, rL*h - 3*MB, str(totRatio[0])[0:5],verticalalignment='center') # right text2, bot
ax[plotNum].text(s1xm*l - MB/2*l, rU*h, '0',verticalalignment='center') # left text, top
ax[plotNum].text(s1xx*l + MB/4*l, rU*h + 3*MB, str(seq2len),verticalalignment='center') # right text1, top
ax[plotNum].text(s1xx*l + MB/4*l, rU*h - 3*MB, str(totRatio[1])[0:5],verticalalignment='center') # right text2, top
# local alignments
for i in range(len(seq1las)):
if seq1len <= seq2len:
ax[plotNum].text(l*(MB + (1 - 2*MB)*seq2las[i][0]/float(seq2len) + MB + (1 - 2*MB)*seq2las[i][1]/float(seq2len) + s1xm + (1 - 2*MB)*seq1las[i][0]/float(seq2len) + s1xm + (1 - 2*MB)*seq1las[i][1]/float(seq2len))/4.0,(rL*h - 10*MB + rL*h - 10*MB + rU*h + 5*MB + rU*h + 5*MB)/4.0,str(seqRatio[i])[0:4],horizontalalignment='center')
ax[plotNum].axhspan(rU*h - 3*MB, rU*h + 3*MB, xmin = s1xm + (1 - 2*MB - 2*ratio)*seq1las[i][0]/float(seq1len), xmax = s1xm + (1 - 2*MB - 2*ratio)*seq1las[i][1]/float(seq1len), facecolor = colors[i%5], alpha = 0.35) # top seq
ax[plotNum].axhspan(rL*h - 3*MB, rL*h + 3*MB, xmin = MB + (1 - 2*MB)*seq2las[i][0]/float(seq2len), xmax = MB + (1 - 2*MB)*seq2las[i][1]/float(seq2len), facecolor = colors[i%5], alpha = 0.35) # bot seq
ax[plotNum].plot([l*(s1xm + (1 - 2*MB - 2*ratio)*seq1las[i][0]/float(seq1len)),l*(MB + (1 - 2*MB)*seq2las[i][0]/float(seq2len))],[rU*h - 3*MB,rL*h + 3*MB],color = 'black', alpha = 0.35) # left line
ax[plotNum].plot([l*(s1xm + (1 - 2*MB - 2*ratio)*seq1las[i][1]/float(seq1len)),l*(MB + (1 - 2*MB)*seq2las[i][1]/float(seq2len))],[rU*h - 3*MB,rL*h + 3*MB],color = 'black', alpha = 0.35) # right line
ax[plotNum].text(l*(MB + .01 + (1 - 2*MB)*seq2las[i][0]/float(seq2len)),rL*h - 10*MB,str(seq2las[i][0]),horizontalalignment='center') # lower left text
ax[plotNum].text(l*(MB - .01 + (1 - 2*MB)*seq2las[i][1]/float(seq2len)),rL*h - 10*MB,str(seq2las[i][1]),horizontalalignment='center') # lower right text
ax[plotNum].text(l*(s1xm + .01 + (1 - 2*MB - 2*ratio)*seq1las[i][0]/float(seq1len)),rU*h + 5*MB,str(seq1las[i][0]),horizontalalignment='center') # upper left text
ax[plotNum].text(l*(s1xm - .01 + (1 - 2*MB - 2*ratio)*seq1las[i][1]/float(seq1len)),rU*h + 5*MB,str(seq1las[i][1]),horizontalalignment='center') # upper right text
else:
ax[plotNum].text(l*(MB + (1 - 2*MB)*seq1las[i][0]/float(seq1len) + MB + (1 - 2*MB)*seq1las[i][1]/float(seq1len) + s1xm + (1 - 2*MB)*seq2las[i][0]/float(seq1len) + s1xm + (1 - 2*MB)*seq2las[i][1]/float(seq1len))/4.0,(rL*h - 10*MB + rL*h - 10*MB + rU*h + 5*MB + rU*h + 5*MB)/4.0,str(seqRatio[i])[0:4],horizontalalignment='center')
ax[plotNum].axhspan(rU*h - 3*MB, rU*h + 3*MB, xmin = s1xm + (1 - 2*MB - 2*ratio)*seq2las[i][0]/float(seq2len), xmax = s1xm + (1 - 2*MB - 2*ratio)*seq2las[i][1]/float(seq2len), facecolor = colors[i%5], alpha = 0.35) # top seq
ax[plotNum].axhspan(rL*h - 3*MB, rL*h + 3*MB, xmin = MB + (1 - 2*MB)*seq1las[i][0]/float(seq1len), xmax = MB + (1 - 2*MB)*seq1las[i][1]/float(seq1len), facecolor = colors[i%5], alpha = 0.35) # bot seq
ax[plotNum].plot([l*(s1xm + (1 - 2*MB - 2*ratio)*seq2las[i][0]/float(seq2len)),l*(MB + (1 - 2*MB)*seq1las[i][0]/float(seq1len))],[rU*h + 3*MB,rL*h - 3*MB],color = 'black', alpha = 0.35) # left line
ax[plotNum].plot([l*(s1xm + (1 - 2*MB - 2*ratio)*seq2las[i][1]/float(seq2len)),l*(MB + (1 - 2*MB)*seq1las[i][1]/float(seq1len))],[rU*h + 3*MB,rL*h - 3*MB],color = 'black', alpha = 0.35) # right line
ax[plotNum].text(l*(MB + .01 + (1 - 2*MB)*seq1las[i][0]/float(seq1len)),rL*h + 5*MB,str(seq1las[i][0]),horizontalalignment='center') # lower left text
ax[plotNum].text(l*(MB - .01 + (1 - 2*MB)*seq1las[i][1]/float(seq1len)),rL*h + 5*MB,str(seq1las[i][1]),horizontalalignment='center') # lower right text
ax[plotNum].text(l*(s1xm + .01 + (1 - 2*MB - 2*ratio)*seq2las[i][0]/float(seq2len)),rU*h - 10*MB,str(seq2las[i][0]),horizontalalignment='center') # upper left text
ax[plotNum].text(l*(s1xm - .01 + (1 - 2*MB - 2*ratio)*seq2las[i][1]/float(seq2len)),rU*h - 10*MB,str(seq2las[i][1]),horizontalalignment='center') # upper right text
ax[plotNum].set_ylim(0,h)
ax[plotNum].set_xlim(0,l)
ax[plotNum].set_yticklabels([])
ax[plotNum].set_xticklabels([])
ax[plotNum].set_yticks([])
ax[plotNum].set_xticks([])
plt.xlabel(pAlign.testSeq.name + ' rf ' + str(pAlign.localAligns[0].offset), multialignment='center')
gbgstring += pAlign.testSeq.name
if (plotNum+1)%4 == 0 and plotNum > 1:
gbgstring += '\n'
GBGdata.write(gbgstring)
fig.savefig(parameters['OUTFILE'] + '/images/GBG' + str(plots) + '.png', bbox_inches='tight', pad_inches=0.03)
fig.savefig(parameters['OUTFILE'] + '/images/GBG' + str(plots) + '.pdf')
logging.debug('Made GBG plot ' + str(plots))
else:
gbgstring += '!'
plotNum += 1
gbgstring += '\n'
GBGdata.write(gbgstring)
fig.savefig(parameters['OUTFILE'] + '/images/GBG' + str(plots) + '.png', bbox_inches='tight', pad_inches=0.03)
fig.savefig(parameters['OUTFILE'] + '/images/GBG' + str(plots) + '.pdf')
logging.debug('Made GBG plot ' + str(plots))
GBGdata.close()
vmin=-10,
vmax=10,
origin='lower',
interpolation='none')
ax1.set_xticks([])
ax1.set_yticks([6, 16, 41])
ax1.set_yticklabels(['Head', 'Neck', 'Tail'], fontsize=22)
ax1.set_xticks([0, 200, 400, 600])
ax1.set_xticklabels(['0', '10', '20', '30'], fontsize=22)
ax1.set_xlim(0, 600)
ax1.set_ylim(-0.5, 48.5)
ax1.set_xlabel('Time (s)', fontsize=22)
# ax1.set_ylabel('Body axis', fontsize = 22)
plt.figtext(0.5,
0.955,
'Inactivated anterior half of the body, Ind %d' % ind,
fontsize=24,
va='center',
ha='center')
#calculate amplitud as in Fouad 2017
amplitude_fouad = np.zeros(3)
head, neck, tail = 7, 17, 42
L = 100.
p = 0
for position in [head, neck, tail]:
dt = 1 / 20.
dk = np.diff(curv[:, position])
amplitude_fouad[p] = np.sqrt(L * np.mean(dk**2) / dt)
p += 1
np.savetxt('../../data/amplitude_fouad_BWM_%d' % ind, amplitude_fouad)
fontsize=fz)
axnet3.annotate('',
xy=(0.3, yloc),
xycoords='axes fraction',
xytext=(0.95, yloc),
arrowprops=dict(arrowstyle=lstyle_inter,
color='k',
linewidth=1))
##################################################################
######################################################################
xpos = 0.015, 0.340, 0.675
ypos = [0.94, 0.43]
fzl = 70
letters = ['A', 'B', 'C']
[
plt.figtext(xpos[i],
ypos[0],
letters[i],
fontsize=fzl,
ha='center',
va='center') for i in range(3)
]
#[plt.figtext(xpos[i], ypos[1], 'B%d'%(i+1), fontsize = fzl, ha = 'center', va = 'center') for i in range(3)]
######################################################################
fig.subplots_adjust(left=0.02, bottom=0.00, right=0.98, top=1.02)
plt.savefig('phase_delay.png' % (), dpi=100)
plt.savefig('phase_delay.pdf')
#plt.savefig('phase_delay.svg')
def main():
infilenames = [
"mc_ttbar.dat", "zipfile_save_data_400k.zip",
"regular_save_data_400k.npy", "compressed_save_data_400k.npz",
"pickle_save_data_400k.dat", "onebyonesixty400k.npz",
"onebyonesixty400kcompressed.npz", "fourbyforty400k.npz",
"fourbyforty400kcompressed.npz", "thirtytwobyfive400k.npz",
"thirtytwobyfive400kcompressed.npz"
]
#infilenames = ["mc_ttbar.dat", "onebyonesixty400k.npz"]
#infilenames = [ "onebyonesixty400k.npz"]
#infilenames = ["mc_ttbar.dat","zipfile_save_data_400k.zip"]
#infilenames = ["mc_dy_1000collisions.dat"]
#infilenames = ["thirtytwobyfive400k.npz", "thirtytwobyfive400kcompressed.npz"]
read_times = []
process_times = []
#infilenames = ["thirtytwobyfive400kcompressed.npz", "mc_ttbar.dat"]
for i, infilename in enumerate(infilenames):
print infilename
infile = open(infilename)
collisions = None
start_time = time()
if infilename[0] == 'm':
collisions = cms_tools.get_collisions(infile)
elif infilename[0] == 'z':
collisions = cms_tools.get_collisions(infile)
elif infilename[0] == 'r':
collisions = cms_tools.get_array_collisions(infile)
elif infilename[0] == 'c':
collisions = cms_tools.get_compressed_collisions(infile)
elif infilename[0] == 'p':
collisions = cms_tools.get_pickle_collisions(infile)
elif infilename[0] == 'o':
collisions = cms_tools.get_onebyonesixty_collisions(infile)
elif infilename[0] == 'f':
collisions = cms_tools.get_fourbyforty_collisions(infile)
elif infilename[0] == 't':
collisions = cms_tools.get_thirtytwobyfive_collisions(infile)
#print "type collisions: ",type(collisions)
#print "# collisions: %d" % (len(collisions))
time_to_read_in_data = time() - start_time
read_times.append(time_to_read_in_data)
start_time = time()
masses = do_some_standard_analysis(collisions)
print "type masses: ", type(masses)
time_to_process_data = time() - start_time
process_times.append(time_to_process_data)
# print collisions[0]
# Make a diagnostic plot.
masses = np.array(masses)
plt.figure()
plt.hist(masses[masses > 0], bins=100, range=(0, 80))
plt.xlim(0, 80)
plt.figtext(0.4, 0.8, infilename, size=18)
name = "diagnostic_plot_%s.png" % (infilename.split('.')[0])
plt.savefig(name)
#plt.show()
print read_times
print process_times
for n, r, p in zip(infilenames, read_times, process_times):
print "%-40s %5.2f %5.2f" % (n, r, p)
plt.figure()
plt.plot(read_times, 'ko')
plt.xlim(-1, len(read_times))
plt.figure()
plt.plot(process_times, 'ro')
plt.xlim(-1, len(process_times))
points = []
for name in infilenames:
points.append(os.path.getsize(name))
plt.figure()
for i, (point, name) in enumerate(zip(points, infilenames)):
plt.plot(i, point, 'o', markersize=20, label=name)
plt.legend()
plt.xlim(-1, len(points))
for i in range(len(points)):
plt.plot(points[i],
process_times[i],
'o',
markersize=15,
label=infilenames[i])
plt.legend()
plt.ylabel('mag Y [G]')
plt.subplot(1, 3, 3)
plt.plot(power_resampled[idx], magZ_body[idx], 'yo', power_resampled[idx],
pz[idx][0] * power_resampled[idx] + pz[idx][1], '--k')
plt.xlabel('current [kA]')
plt.ylabel('mag Z [G]')
# display results
plt.figtext(0.24,
0.03,
'CAL_MAG{}_XCOMP: {:.3f} {}'.format(calibration_instance[idx],
factor * px[idx][0], unit),
horizontalalignment='center',
fontsize=12,
multialignment='left',
bbox=dict(boxstyle="round",
facecolor='#D8D8D8',
ec="0.5",
pad=0.5,
alpha=1),
fontweight='bold')
plt.figtext(0.51,
0.03,
'CAL_MAG{}_YCOMP: {:.3f} {}'.format(calibration_instance[idx],
factor * py[idx][0], unit),
horizontalalignment='center',
fontsize=12,
multialignment='left',
bbox=dict(boxstyle="round",
facecolor='#D8D8D8',
RC0 = sc.array([R0, C0])
pops, infodict = integrate.odeint(dCR_dt, RC0, t, full_output=True)
print(infodict['message']) # >>> 'Integration successful.'
f1 = p.figure() # Open empty figure object
p.plot(t, pops[:, 0], 'g-', label='Resource density') # Plot
p.plot(t, pops[:, 1], 'b-', label='Consumer density')
p.grid()
p.legend(loc='best')
p.xlabel('Time')
p.ylabel('Population density')
p.title('Consumer-Resource population dynamics')
p.figtext(.79, .58, " r =" + str(r) + "\n a =" + str(a) + "\n z = " + str(z)
+ "\n e = " + str(e) + "\n K = " + str(K))
# p.show() # To display the figure
# Plot consumer density against resource density
f2 = p.figure()
p.plot(pops[:, 0], pops[:, 1], 'r-', label='Consumer density')
p.grid()
p.xlabel('Resource density')
p.ylabel('Consumer density')
p.title('Consumer-Resource population dynamics')
p.figtext(.79, .58, " r =" + str(r) + "\n a =" + str(a) + "\n z = " + str(z)
+ "\n e = " + str(e) + "\n K = " + str(K))
# p.show() # To display the figure
# Save both figures into a single pdf
def cmdline_chart_compare(db, options, *args):
import matplotlib
matplotlib.use('Agg')
import numpy as np
import matplotlib.pylab as plt
labels = []
timing_sets = []
command_names = None
run_kinds = parse_timings_selections(db, *args)
# iterate the timings selections and accumulate data
for run_kind in run_kinds:
query = TimingQuery(db, run_kind)
timings = query.get_timings()
if not timings:
print("No timings for %s" % run_kind.label())
continue
labels.append(run_kind.label())
timing_sets.append(timings)
# it only makes sense to compare those commands that have timings
# in the first selection, because that is the one everything else
# is compared to. Remember the first selection's command names.
if not command_names:
command_names = query.get_sorted_command_names()
if len(timing_sets) < 2:
bail("Not enough timings")
if options.command_names:
command_names = [
name for name in command_names if name in options.command_names
]
chart_path = options.chart_path
if not chart_path:
chart_path = 'compare_' + '_'.join(
[filesystem_safe_string(l) for l in labels]) + '.svg'
N = len(command_names)
M = len(timing_sets) - 1
if M < 2:
M = 2
group_positions = np.arange(N) # the y locations for the groups
dist = 1. / (1. + M)
height = (1. - dist) / M # the height of the bars
fig = plt.figure(figsize=(12, 5 + 0.2 * N * M))
plot1 = fig.add_subplot(121)
plot2 = fig.add_subplot(122)
left = timing_sets[0]
# Iterate timing sets. Each loop produces one bar for each command name
# group.
for label_i, label in enumerate(labels[1:], 1):
right = timing_sets[label_i]
if not right:
continue
for cmd_i, command_name in enumerate(command_names):
if command_name not in right:
#skip
continue
left_N, left_min, left_max, left_avg = left[command_name]
right_N, right_min, right_max, right_avg = right[command_name]
div_avg = 100. * (do_div(left_avg, right_avg) - 1.0)
if div_avg <= 0:
col = '#55dd55'
else:
col = '#dd5555'
diff_val = do_diff(left_avg, right_avg)
ofs = (dist + height) / 2. + height * (label_i - 1)
barheight = height * (1.0 - dist)
y = float(cmd_i) + ofs
plot1.barh((y, ), (div_avg, ),
barheight,
color=col,
edgecolor='white')
plot1.text(0.,
y + height / 2.,
'%s %+5.1f%%' % (label, div_avg),
ha='right',
va='center',
size='small',
rotation=0,
family='monospace')
plot2.barh((y, ), (diff_val, ),
barheight,
color=col,
edgecolor='white')
plot2.text(0.,
y + height / 2.,
'%s %+6.2fs' % (label, diff_val),
ha='right',
va='center',
size='small',
rotation=0,
family='monospace')
for p in (plot1, plot2):
xlim = list(p.get_xlim())
if xlim[1] < 10.:
xlim[1] = 10.
# make sure the zero line is far enough right so that the annotations
# fit inside the chart. About half the width should suffice.
if xlim[0] > -xlim[1]:
xlim[0] = -xlim[1]
p.set_xlim(*xlim)
p.set_xticks((0, ))
p.set_yticks(group_positions + (height / 2.))
p.set_yticklabels(())
p.set_ylim((len(command_names), 0))
p.grid()
plot1.set_xticklabels(('+-0%', ), rotation=0)
plot1.set_title('Average runtime change from %s in %%' % labels[0],
size='medium')
plot2.set_xticklabels(('+-0s', ), rotation=0)
plot2.set_title('Average runtime change from %s in seconds' % labels[0],
size='medium')
margin = 1. / (2 + N * M)
titlemargin = 0
if options.title:
titlemargin = margin * 1.5
fig.subplots_adjust(left=0.005,
right=0.995,
wspace=0.3,
bottom=margin,
top=1.0 - margin - titlemargin)
ystep = (1.0 - 2. * margin - titlemargin) / len(command_names)
for idx, command_name in enumerate(command_names):
ylabel = '%s\nvs. %.1fs' % (command_name, left[command_name][3])
ypos = 1.0 - margin - titlemargin - ystep / M - ystep * idx
plt.figtext(0.5,
ypos,
command_name,
ha='center',
va='top',
size='medium',
weight='bold')
plt.figtext(0.5,
ypos - ystep / (M + 1),
'%s\n= %.2fs' % (labels[0], left[command_name][3]),
ha='center',
va='top',
size='small')
if options.title:
plt.figtext(0.5,
1. - titlemargin / 2,
options.title,
ha='center',
va='center',
weight='bold')
plt.savefig(chart_path)
print('wrote chart file:', chart_path)
def plot_bacteria_hist(folder, depth=6, mid_quantile=False):
"""
Saves a histogram of abundances binned
:return:
"""
# Get the stool dataset and discretize it
ds = parser.get_dataset()
ds = compute_relative_values(ds)
t = Tree(ds)
ds = t.dataset_at_depth(depth)
# Get header names to priint on the plots
headers = ds[0][2:]
for index, header in enumerate(headers):
node = t.node_for_clade_name(header)
abundances = t.abundance_column_in_subtree(node)
abundances = [round(x,3) for x in abundances]
if mid_quantile:
abundances.sort()
abundances = abundances[int(len(abundances)*0.25): -int(len(abundances)*0.25)]
xlabel('Relative abundance')
ylabel('Bin size')
title_text = header.replace('/','-').replace('|', '-')
title(title_text)
binwidth = 0.001
bins, bin_sizes, patches = hist(abundances, bins=np.arange(min(abundances), max(abundances) + binwidth, binwidth), color='#0066FF')
# Write discretized values
threshold, discretized_abundances = discretize_row(abundances, maxent_discretization_splitter)
_0 = '0: ' + str(len([x for x in discretized_abundances if x == 0]))
_1 = '1: ' + str(len([x for x in discretized_abundances if x == 1]))
text_x = 0.7
smaples_text = 'Samples: %d' % len(abundances)
figtext(text_x, 0.85, smaples_text, fontsize=10)
threshold_text = 'Splitter: %f' % threshold
figtext(text_x, 0.82, threshold_text, fontsize=10)
figtext(text_x, 0.79, _0, fontsize=10)
figtext(text_x, 0.76, _1, fontsize=10)
# Draw threshold line
max_bin = len(abundances)
if len(bins) != 0:
max_bin = max(bins)
a, b = [threshold, threshold], [0, max_bin]
plot(a, b, c='r')
grid(True)
# Write max and avg
# max_abundance = 'max: %f' % max(abundances)
# avg_abundance = 'avg: %f' % (sum(abundances) / float(len(abundances)))
# figtext(text_x, 0.76, max_abundance, fontsize=10)
# figtext(text_x, 0.73, avg_abundance, fontsize=10)
# write variance
# variance = 'var: %f' % tvar(abundances)
# figtext(text_x, 0.70, variance, fontsize=10)
# Save fig to folder
if not (os.path.exists(folder)):
os.makedirs(folder)
file_name = os.path.join(folder, title_text)
print 'Hist: ', file_name
savefig(file_name)
close()
plt.title('2D Background Frequency', fontsize=14)
H, xedges, yedges = np.histogram2d(bkg_template[1],bkg_template[0],bins=50,range=[[0,1],[0,1]])
imbkg = plt.imshow(H, interpolation='nearest', origin='low', extent=[xedges[0], xedges[-1], yedges[0], yedges[-1]])
ax = plt.gca()
divider = make_axes_locatable(ax)
cax = divider.append_axes("right", size="5%", pad=0.05)
cbar = plt.colorbar(cax=cax)
cbar.ax.set_ylabel('Frequency')
plt.savefig('2D_Histograms.png')
#plt.ylim(0,10)
#plt.xlim(12,21)
txt = 'Figure A: The location of a sphere in both radius density plots indidcates the location of a data point for the background and signal datasets. \nThe radius of the sphere indicates the neighbor density of the particular datapoint. Note how the radii of the background points are \ngenerally the same and the points are scattered throughout the plot in the signal plot the points are concentrated in the center and those \nclosest to the center have the largest radii indicated that they have the largest neighbor densities in the center of the plot.'
fig_template = plt.figure(figsize=(12,6))
fig_template.add_subplot(1,2,1)
plt.figtext(.5, -.01,txt, horizontalalignment='center',verticalalignment='center')
plt.scatter(data[0],data[1],s=sigFD*50,alpha=0.1)
plt.xlim(0,1)
plt.ylim(0,1)
plt.xlabel('Signal Dataset #1')
plt.ylabel('Signal Dataset #2')
plt.title('Signal Function Density', fontsize=14)
fig_template.add_subplot(1,2,2)
plt.scatter(data[0],data[1],s=bkgFD*50,alpha=0.1)
plt.xlim(0,1)
plt.ylim(0,1)
plt.xlabel('Background Dataset 1')
plt.ylabel('Background Dataset 2')
plt.title('Background Function Density', fontsize=14)
plt.savefig('bubble_plots.png')
ax22 = plt.subplot(gm[60:77, 97:175])
####################
axo1 = plt.subplot(gm[:52, 200:288])
axoc = plt.subplot(gm[:52, 291:294])
axo2 = plt.subplot(gm[60:77, 200:288])
#########################################################################################
selected, wt, ns, bwm, wt2, ns2, bwm2, curv, curv_prof, speeds_mean = np.load(
'myfile.npy')
#######################################################################
x1, x2, x3, y1, y2 = 0.015, 0.31, 0.61, 0.96, 0.30
letters = [[x1, y1, 'A'], [x1, y2, 'B'], [x2, y1, 'C'], [x2, y2, 'D'],
[x3, y1, 'E'], [x3, y2, 'F']]
for l in letters:
plt.figtext(l[0], l[1], l[2], fontsize=34, ha='center', va='center')
#########################################################################################
#######################################################################
control, headparal, midbodyparal, edge = '#1b9e77', '#d95f02', '#7570b3', 'k'
[head, neck, tail] = [0, 1, 2]
ax1.scatter(1 * np.ones(15),
wt[:, head],
lw=0.5,
s=100,
color=control,
edgecolors=edge,
label='Control') #wild type head amplitude
ax1.scatter(2 * np.ones(15),
ns[:, head],
lw=0.5,
def skydip(data,
averagepol=True,
tsky=300.,
plot=False,
temperature=288,
pressure=101325.,
humidity=0.5):
"""Determine the opacity from a set of 'skydip' obervations.
This can be any set of observations over a range of elevations,
but will ususally be a dedicated (set of) scan(s).
Return a list of 'n' opacities for 'n' IFs. In case of averagepol
being 'False' a list of 'n*m' elements where 'm' is the number of
polarisations, e.g.
nIF = 3, nPol = 2 => [if0pol0, if0pol1, if1pol0, if1pol1, if2pol0, if2pol1]
The opacity is determined by fitting a first order polynomial to:
Tsys(airmass) = p0 + airmass*p1
where
airmass = 1/sin(elevation)
tau = p1/Tsky
Parameters:
data: a list of file names or scantables or a single
file name or scantable.
averagepol: Return the average of the opacities for the polarisations
This might be useful to set to 'False' if one polarisation
is corrupted (Mopra). If set to 'False', an opacity value
per polarisation is returned.
tsky: The sky temperature (default 300.0K). This might
be read from the data in the future.
plot: Plot each fit (airmass vs. Tsys). Default is 'False'
"""
# quiten output
verbose = rcParams["verbose"]
rcParams["verbose"] = False
try:
if plot:
from matplotlib import pylab
scan = _import_data(data)
f = fitter()
f.set_function(poly=1)
sel = selector()
basesel = scan.get_selection()
inos = scan.getifnos()
pnos = scan.getpolnos()
opacities = []
om = model(temperature, pressure, humidity)
for ino in inos:
sel.set_ifs(ino)
opacity = []
fits = []
airms = []
tsyss = []
if plot:
pylab.cla()
pylab.ioff()
pylab.clf()
pylab.xlabel("Airmass")
pylab.ylabel(r"$T_{sys}$")
for pno in pnos:
sel.set_polarisations(pno)
scan.set_selection(basesel + sel)
freq = scan.get_coordinate(0).get_reference_value() / 1e9
freqstr = "%0.4f GHz" % freq
tsys = scan.get_tsys()
elev = scan.get_elevation()
airmass = [1. / math.sin(i) for i in elev]
airms.append(airmass)
tsyss.append(tsys)
f.set_data(airmass, tsys)
f.fit()
fits.append(f.get_fit())
params = f.get_parameters()["params"]
opacity.append(params[1] / tsky)
if averagepol:
opacities.append(sum(opacity) / len(opacity))
else:
opacities += opacity
if plot:
colors = ['b', 'g', 'k']
n = len(airms)
for i in range(n):
pylab.plot(airms[i], tsyss[i], 'o', color=colors[i])
pylab.plot(airms[i], fits[i], '-', color=colors[i])
pylab.figtext(0.7,
0.3 - (i / 30.0),
r"$\tau_{fit}=%0.2f$" % opacity[i],
color=colors[i])
if averagepol:
pylab.figtext(0.7,
0.3 - (n / 30.0),
r"$\tau_{avg}=%0.2f$" % opacities[-1],
color='r')
n += 1
pylab.figtext(0.7,
0.3 - (n / 30.0),
r"$\tau_{model}=%0.2f$" %
om.get_opacities(freq * 1e9),
color='grey')
pylab.title("IF%d : %s" % (ino, freqstr))
pylab.ion()
pylab.draw()
raw_input("Hit <return> for next fit...")
sel.reset()
scan.set_selection(basesel)
if plot:
pylab.close()
return opacities
finally:
rcParams["verbose"] = verbose
vmin=-10,
vmax=10,
origin='lower')
ax1.set_xlim(0, 120)
ax1.set_xticks([0, 40, 80, 120])
ax1.set_xticklabels([])
ax1.set_yticks([1, 21])
ax1.set_yticklabels(['', ''])
ax1.text(-1, 1, 'Head', va='center', ha='right', fontsize=fzl)
ax1.text(-1, 21, 'Tail', va='center', ha='right', fontsize=fzl)
############ Velocity #######
###############################
s = np.where(np.array(sel) == 23)[0]
ax2.plot(np.linspace(0, 10, len(v[s][0])), 1000 * v[s][0], 'k', linewidth=3)
ax2.axhline(y=0.22, linestyle='--', color='r')
ax2.set_ylim(0.05, 0.35)
ax2.set_xlim(0, 6)
ax2.set_yticks([0.1, 0.2, 0.3])
ax2.set_ylabel('Velocity (mm/s)', fontsize=fzl, labelpad=24)
ax2.set_xlabel('Time (s)', fontsize=fzl, labelpad=22)
###############################
fz = 70
plt.figtext(0.018, 0.95, 'A', fontsize=fz, ha='center', va='center')
plt.figtext(0.018, 0.46, 'B', fontsize=fz, ha='center', va='center')
plt.figtext(0.460, 0.95, 'C', fontsize=fz, ha='center', va='center')
###############################
fig.subplots_adjust(left=0.08, bottom=0.02, right=1.0, top=0.98)
plt.savefig('behavior.png', dpi=100)
plt.savefig('behavior.pdf')
def GeneCDFplots(setOfAligns, numGenes,parameters):
logging.info('Making the CDF plots (This may take a while)...')
lensoi = setOfAligns.seqOfInt.length
colors = ['b','g','r','c','m']
if numGenes > len(setOfAligns.testSeqs)/setOfAligns.seqOfInt.readingFrames or numGenes < 1:
numGenes = len(setOfAligns.testSeqs)*setOfAligns.seqOfInt.readingFrames
geneCount = 0
plots = 0
CDFdata = open(parameters['OUTFILE'] + '/images/CDFdata.txt','wb')
CDFdata.write('CDFX.pdf:soi!testseq\n')
for pAlign in setOfAligns.aligns:
if len(pAlign.localAligns) > 0:
if geneCount < numGenes:
geneCount += 1
plotNum = 0
totalForLocA = 0
for locA in pAlign.localAligns:
totalForLocA += 1
# get density ratio
seqRatio = []
if setOfAligns.seqOfInt.dataDepths != 0:
for i in range(len(locA.SOIrange)):
scoreSum = (sum(locA.fullScoreVec[locA.SOIrange[i][0]:locA.SOIrange[i][1]]))
seqRatio.append(scoreSum/float(locA.SOIrange[i][1]-locA.SOIrange[i][0]))
else:
for i in range(len(locA.SOIrange)):
scoreSum = (sum(locA.fullScoreVec[locA.SOIrange[i][0]:locA.SOIrange[i][1]]))
seqRatio.append(scoreSum/float(locA.SOIrange[i][1]-locA.SOIrange[i][0]))
# make the empty plot, 4 per page
if plotNum%4 == 0:
fig = plt.figure(figsize=(22,17))
plt.figtext(0.5, 0.965, 'Local Alignments for soi: ' + setOfAligns.seqOfInt.name + ' vs ' + pAlign.testSeq.name + ' rf ' + str(pAlign.localAligns[0].offset), ha='center', color='black', weight='bold', size='large')
ax = []
ax.append(fig.add_subplot(811))
ax.append(fig.add_subplot(812))
plotNum = 0
plots += 1
else:
ax.append(fig.add_subplot(811+(plotNum%4)*2))
ax.append(fig.add_subplot(811+(plotNum%4)*2+1))
# make the upper plot, the match vector
temp = numpy.zeros(lensoi)
for i in range(len(locA.SOIrange)):
temp[locA.SOIrange[i][0]:locA.SOIrange[i][1]] = 2*numpy.ones(locA.SOIrange[i][1]-locA.SOIrange[i][0])
ax[plotNum*2].pcolor(numpy.reshape(numpy.array(locA.fullScoreVec) + temp,(1,lensoi)))
# plot the cdfs
ax[plotNum*2+1].plot(locA.cdfL)
ax[plotNum*2+1].plot(locA.cdfR)
for i in range(len(locA.SOIrange)):
ax[plotNum*2+1].axvspan(locA.SOIrange[i][0],locA.SOIrange[i][1], facecolor = 'r', alpha = 0.35)
# mark off the intron area
intronArea = numpy.asarray(numpy.asarray(locA.cdfL) == numpy.asarray(locA.cdfR),dtype=numpy.int32)
ranges = rangeFinder(intronArea)
for i in range(len(ranges)):
ax[plotNum*2+1].axvspan(ranges[i][0],ranges[i][1], facecolor = 'm', alpha = 0.35)
#ax[plotNum*2+1].text((locA.SOIrange[0]+locA.SOIrange[1])/2.0,(max(max(locA.cdfL),max(locA.cdfR)) + min(min(locA.cdfL),min(locA.cdfR)))/2*1.66,str(seqRatio)[0:4],verticalalignment='center',horizontalalignment='center')
# make the tick marks
ax[plotNum].set_yticklabels([])
ax[plotNum*2].set_yticks([])
prevTicks = []
prevLabs = []
for i in range(len(locA.SOIrange)):
prevTicks.extend([locA.SOIrange[i][0],(locA.SOIrange[i][0]+locA.SOIrange[i][1])/2.0,locA.SOIrange[i][1]])
prevLabs.extend([str(locA.SOIrange[i][0]),str(seqRatio[i])[0:4],str(locA.SOIrange[i][1])])
newXticks, newXtickLabels = intronAdderXticks(prevTicks,prevLabs,ranges)
ax[plotNum*2].set_xticks(newXticks)
ax[plotNum*2].set_xticklabels(newXtickLabels)
#ax[plotNum*2].set_xticks([locA.SOIrange[0],(locA.SOIrange[0]+locA.SOIrange[1])/2.0,locA.SOIrange[1]])
#ax[plotNum*2].set_xticklabels([str(locA.SOIrange[0]),str(seqRatio)[0:4],str(locA.SOIrange[1])])
ax[plotNum*2+1].set_yticklabels([])
ax[plotNum*2+1].set_yticks([])
ax[plotNum*2].set_xlim(0,lensoi)
ax[plotNum*2+1].set_xlim(0,lensoi)
plotNum += 1
#plt.show()
if ((plotNum)%4 == 0 and plotNum > 1) or totalForLocA == len(pAlign.localAligns):
#print plotNum, (plotNum)%4, totalForLocA, len(pAlign.localAligns)
CDFdata.write('CDF' + str(plots) + '.pdf:' + setOfAligns.seqOfInt.name + '!' + pAlign.testSeq.name + '\n')
fig.savefig(parameters['OUTFILE'] + '/images/CDF' + str(plots) + '.png', bbox_inches='tight', pad_inches=0.03)
fig.savefig(parameters['OUTFILE'] + '/images/CDF' + str(plots) + '.pdf')
logging.debug('Made CDF plot ' + str(plots) + '...')
#return 0
else:
#plt.show()
CDFdata.close()
return 0
CDFdata.close()
qry_c = ''
for w in qry_raw:
qry_c += w + ' '
cap = ('DOC: ' + '\n'.join(
[''.join(doc_c[idx:idx + CH])
for idx in range(0, len(doc_c), CH)]) + '\n\n' + 'QRY: ' + '\n'.join([
''.join(qry_c[idx:idx + CH]) for idx in range(0, len(qry_c), CH)
]) + '\n' + 'ANS: ' + ''.join(text[6].rstrip()))
num_lines = cap.count('\n')
if num_lines < 10: bot = 0.35
elif num_lines < 13: bot = 0.40
elif num_lines < 16: bot = 0.45
elif num_lines < 19: bot = 0.50
else: bot = 0.55
fig.subplots_adjust(bottom=bot)
plt.figtext(
0.06,
0.0,
cap,
weight='medium',
)
# add colorbar
fig.subplots_adjust(right=0.95)
cbar_ax = fig.add_axes([0.97, bot, 0.01, 0.90 - bot])
fig.colorbar(im, cax=cbar_ax)
#plt.show()
plt.savefig(root_dir + '%s.png' % X[0], bbox_inches='tight')
plt.close()
numb_growing_in_rad += 1
else:
ax10.plot(curv_profile_rad[ind], color='green')
for ax in [ax0, ax10]:
ax.set_xlim(pos_norm, n_seg - 1)
ax.set_xticks([])
ax.set_yticks([0.5, 1.0, 1.5, 2.0])
ax.set_ylim(0.4, 2.1)
ax.set_ylabel('Normalized curvature', fontsize=15)
ax10.set_xticks([1 + pos_norm, n_seg - 2])
ax10.set_xticklabels(['Head', 'Tail'], fontsize=15)
plt.figtext(0.5,
0.96,
'Negative slope N=%d' % (numb_growing_in_rad),
color='k',
fontsize=20,
ha='center')
plt.figtext(0.5,
0.485,
'Positive slope N=%d' % (nsel - numb_growing_in_rad),
color='k',
fontsize=20,
ha='center')
fig.subplots_adjust(left=0.09, bottom=0.05, right=0.99, top=0.95)
plt.savefig('plot_2.png', dpi=200)
def cmdline_chart_compare(db, options, *args):
import matplotlib
matplotlib.use('Agg')
import numpy as np
import matplotlib.pylab as plt
labels = []
timing_sets = []
command_names = None
run_kinds = parse_timings_selections(db, *args)
# iterate the timings selections and accumulate data
for run_kind in run_kinds:
query = TimingQuery(db, run_kind)
timings = query.get_timings()
if not timings:
print "No timings for %s" % run_kind.label()
continue
labels.append(run_kind.label())
timing_sets.append(timings)
# it only makes sense to compare those commands that have timings
# in the first selection, because that is the one everything else
# is compared to. Remember the first selection's command names.
if not command_names:
command_names = query.get_sorted_command_names()
if len(timing_sets) < 2:
bail("Not enough timings")
if options.command_names:
command_names = [name for name in command_names
if name in options.command_names]
chart_path = options.chart_path
if not chart_path:
chart_path = 'compare_' + '_'.join(
[ filesystem_safe_string(l) for l in labels ]
) + '.svg'
N = len(command_names)
M = len(timing_sets) - 1
if M < 2:
M = 2
group_positions = np.arange(N) # the y locations for the groups
dist = 1. / (1. + M)
height = (1. - dist) / M # the height of the bars
fig = plt.figure(figsize=(12, 5 + 0.2*N*M))
plot1 = fig.add_subplot(121)
plot2 = fig.add_subplot(122)
left = timing_sets[0]
# Iterate timing sets. Each loop produces one bar for each command name
# group.
for label_i,label in enumerate(labels[1:],1):
right = timing_sets[label_i]
if not right:
continue
for cmd_i, command_name in enumerate(command_names):
if command_name not in right:
#skip
continue
left_N, left_min, left_max, left_avg = left[command_name]
right_N, right_min, right_max, right_avg = right[command_name]
div_avg = 100. * (do_div(left_avg, right_avg) - 1.0)
if div_avg <= 0:
col = '#55dd55'
else:
col = '#dd5555'
diff_val = do_diff(left_avg, right_avg)
ofs = (dist + height) / 2. + height * (label_i - 1)
barheight = height * (1.0 - dist)
y = float(cmd_i) + ofs
plot1.barh((y, ),
(div_avg, ),
barheight,
color=col, edgecolor='white')
plot1.text(0., y + height/2.,
'%s %+5.1f%%' % (label, div_avg),
ha='right', va='center', size='small',
rotation=0, family='monospace')
plot2.barh((y, ),
(diff_val, ),
barheight,
color=col, edgecolor='white')
plot2.text(0., y + height/2.,
'%s %+6.2fs' % (label, diff_val),
ha='right', va='center', size='small',
rotation=0, family='monospace')
for p in (plot1, plot2):
xlim = list(p.get_xlim())
if xlim[1] < 10.:
xlim[1] = 10.
# make sure the zero line is far enough right so that the annotations
# fit inside the chart. About half the width should suffice.
if xlim[0] > -xlim[1]:
xlim[0] = -xlim[1]
p.set_xlim(*xlim)
p.set_xticks((0,))
p.set_yticks(group_positions + (height / 2.))
p.set_yticklabels(())
p.set_ylim((len(command_names), 0))
p.grid()
plot1.set_xticklabels(('+-0%',), rotation=0)
plot1.set_title('Average runtime change from %s in %%' % labels[0],
size='medium')
plot2.set_xticklabels(('+-0s',), rotation=0)
plot2.set_title('Average runtime change from %s in seconds' % labels[0],
size='medium')
margin = 1./(2 + N*M)
titlemargin = 0
if options.title:
titlemargin = margin * 1.5
fig.subplots_adjust(left=0.005, right=0.995, wspace=0.3, bottom=margin,
top=1.0-margin-titlemargin)
ystep = (1.0 - 2.*margin - titlemargin) / len(command_names)
for idx,command_name in enumerate(command_names):
ylabel = '%s\nvs. %.1fs' % (
command_name,
left[command_name][3])
ypos=1.0 - margin - titlemargin - ystep/M - ystep * idx
plt.figtext(0.5, ypos,
command_name,
ha='center', va='top',
size='medium', weight='bold')
plt.figtext(0.5, ypos - ystep/(M+1),
'%s\n= %.2fs' % (
labels[0], left[command_name][3]),
ha='center', va='top',
size='small')
if options.title:
plt.figtext(0.5, 1. - titlemargin/2, options.title, ha='center',
va='center', weight='bold')
plt.savefig(chart_path)
print 'wrote chart file:', chart_path
plt.xticks([0, min(durations), max(durations)], ['0', str(int(math.ceil(min(durations)))), str(int(math.ceil(max(durations))))])
plt.xlabel('Time since start (s)')
for tick in ax.xaxis.get_major_ticks():
tick.tick1On = False
tick.tick2On = False
#ax.tick_params(top='off', right='off')
#ax.spines['top'].set_color('none')
#ax.spines['right'].set_color('none')
# ax = plt.subplot(212, frame_on=False)
# plt.plot(xseries2, yseries2, 'r-')
# plt.xlim(0, math.ceil(max(duration1, duration2)))
# plt.ylim(0, 21)
# ax.tick_params(top='off', right='off')
# plt.xticks([0, math.ceil(duration1), math.ceil(duration2)])
# plt.yticks([0, 20], ['0', '20'])
# #ax.spines['top'].set_color('none')
# #ax.spines['right'].set_color('none')
# plt.ylabel('Hadoop')
# plt.xticks((0, math.ceil(min(duration1, duration2)), math.ceil(max(duration1, duration2))), ('0', str(int(math.ceil(min(duration1, duration2)))), str(int(math.ceil(max(duration1, duration2))))))
plt.figtext(0.0, (0.2+0.95)/2, 'Number of chunks', rotation='vertical', verticalalignment='center')
plt.savefig('smithwaterman-util.pdf', format='pdf')
def skydip(data, averagepol=True, tsky=300., plot=False,
temperature=288, pressure=101325., humidity=0.5):
"""Determine the opacity from a set of 'skydip' obervations.
This can be any set of observations over a range of elevations,
but will ususally be a dedicated (set of) scan(s).
Return a list of 'n' opacities for 'n' IFs. In case of averagepol
being 'False' a list of 'n*m' elements where 'm' is the number of
polarisations, e.g.
nIF = 3, nPol = 2 => [if0pol0, if0pol1, if1pol0, if1pol1, if2pol0, if2pol1]
The opacity is determined by fitting a first order polynomial to:
Tsys(airmass) = p0 + airmass*p1
where
airmass = 1/sin(elevation)
tau = p1/Tsky
Parameters:
data: a list of file names or scantables or a single
file name or scantable.
averagepol: Return the average of the opacities for the polarisations
This might be useful to set to 'False' if one polarisation
is corrupted (Mopra). If set to 'False', an opacity value
per polarisation is returned.
tsky: The sky temperature (default 300.0K). This might
be read from the data in the future.
plot: Plot each fit (airmass vs. Tsys). Default is 'False'
"""
# quiten output
verbose = rcParams["verbose"]
rcParams["verbose"] = False
try:
if plot:
from matplotlib import pylab
scan = _import_data(data)
f = fitter()
f.set_function(poly=1)
sel = selector()
basesel = scan.get_selection()
inos = scan.getifnos()
pnos = scan.getpolnos()
opacities = []
om = model(temperature, pressure, humidity)
for ino in inos:
sel.set_ifs(ino)
opacity = []
fits = []
airms = []
tsyss = []
if plot:
pylab.cla()
pylab.ioff()
pylab.clf()
pylab.xlabel("Airmass")
pylab.ylabel(r"$T_{sys}$")
for pno in pnos:
sel.set_polarisations(pno)
scan.set_selection(basesel+sel)
freq = scan.get_coordinate(0).get_reference_value()/1e9
freqstr = "%0.4f GHz" % freq
tsys = scan.get_tsys()
elev = scan.get_elevation()
airmass = [ 1./math.sin(i) for i in elev ]
airms.append(airmass)
tsyss.append(tsys)
f.set_data(airmass, tsys)
f.fit()
fits.append(f.get_fit())
params = f.get_parameters()["params"]
opacity.append(params[1]/tsky)
if averagepol:
opacities.append(sum(opacity)/len(opacity))
else:
opacities += opacity
if plot:
colors = ['b','g','k']
n = len(airms)
for i in range(n):
pylab.plot(airms[i], tsyss[i], 'o', color=colors[i])
pylab.plot(airms[i], fits[i], '-', color=colors[i])
pylab.figtext(0.7,0.3-(i/30.0),
r"$\tau_{fit}=%0.2f$" % opacity[i],
color=colors[i])
if averagepol:
pylab.figtext(0.7,0.3-(n/30.0),
r"$\tau_{avg}=%0.2f$" % opacities[-1],
color='r')
n +=1
pylab.figtext(0.7,0.3-(n/30.0),
r"$\tau_{model}=%0.2f$" % om.get_opacities(freq*1e9),
color='grey')
pylab.title("IF%d : %s" % (ino, freqstr))
pylab.ion()
pylab.draw()
raw_input("Hit <return> for next fit...")
sel.reset()
scan.set_selection(basesel)
if plot:
pylab.close()
return opacities
finally:
rcParams["verbose"] = verbose
def cupper(self, event):
theta = np.linspace(-np.pi / 2, np.pi / 2, 1000)
Lx = np.array([0.2, 0.4, 0.6])
Ly = np.linspace(-1, 1, 1000)
fig = plt.figure(
"Rectangular_x_Beam_pattern",
figsize=(22, 12),
facecolor="white",
edgecolor="blue",
)
fig.set_size_inches(15, 10)
P_rectangular1 = np.sin((np.pi * Lx[0] / wavelength[2]) * np.sin(theta)) / (
(np.pi * Lx[0] / wavelength[2]) * np.sin(theta)
)
P_rectangular2 = np.sin((np.pi * Lx[1] / wavelength[2]) * np.sin(theta)) / (
(np.pi * Lx[1] / wavelength[2]) * np.sin(theta)
)
P_rectangular3 = np.sin((np.pi * Lx[2] / wavelength[2]) * np.sin(theta)) / (
(np.pi * Lx[2] / wavelength[2]) * np.sin(theta)
)
ax = plt.subplot(131)
plt.figtext(
0.5,
0.5,
z,
style="italic",
wrap=True,
horizontalalignment="center",
fontsize=18,
color="gray",
)
plt.plot(
np.degrees(theta),
10 * np.log10((P_rectangular1 / np.amax(P_rectangular1)) ** 2),
"b",
label="0.2m",
)
plt.xlabel(r"Angle $\theta$($\circ$)")
plt.ylabel("Power(dB)")
plt.yticks(np.linspace(-40, 0, 5))
plt.ylim([-40, 0])
plt.grid(True)
plt.title("Dx = 0.2 m")
ax = plt.subplot(132)
plt.plot(
np.degrees(theta),
10 * np.log10((P_rectangular2 / np.amax(P_rectangular2)) ** 2),
"g",
label="0.4m",
)
plt.xlabel(r"Dy $\theta$($\circ$)")
plt.ylabel("Power(dB)")
plt.yticks(np.linspace(-40, 0, 5))
plt.ylim([-40, 0])
plt.grid(True)
plt.title("Dx = 0.4 m")
ax = plt.subplot(133)
plt.plot(
np.degrees(theta),
10 * np.log10((P_rectangular3 / np.amax(P_rectangular3)) ** 2),
"purple",
label=" 0.6 m",
)
plt.xlabel("Dy ( m )")
plt.ylabel(r"Power $\theta$($\circ$)")
plt.yticks(np.linspace(-40, 0, 5))
plt.ylim([-40, 0])
plt.grid(True)
plt.title("Dx = 0.6 m")
plt.tight_layout()
plt.savefig("Rectangular_x_Beam_pattern.png")
plt.show()
plt.subplot(2, 3, 6)
plt.plot(thrust_resampled[idx], magZ_body[idx], 'yo',
thrust_resampled[idx],
pz_th[idx][0] * thrust_resampled[idx] + pz_th[idx][1], '--k')
plt.xlabel('thrust []')
plt.ylabel('mag Z [G]')
# display results
plt.figtext(
0.24,
0.03,
'Thrust CAL_MAG{}_XCOMP: {:.3f}[G] \nCurrent CAL_MAG{}_XCOMP: {:.3f}[G/kA]'
.format(calibration_instance[idx], px_th[idx][0],
calibration_instance[idx], -px_curr[idx][0]),
horizontalalignment='center',
fontsize=12,
multialignment='left',
bbox=dict(boxstyle="round",
facecolor='#D8D8D8',
ec="0.5",
pad=0.5,
alpha=1),
fontweight='bold')
plt.figtext(
0.51,
0.03,
'Thrust CAL_MAG{}_YCOMP: {:.3f}[G] \nCurrent CAL_MAG{}_YCOMP: {:.3f}[G/kA]'
.format(calibration_instance[idx], py_th[idx][0],
calibration_instance[idx], -py_curr[idx][0]),
horizontalalignment='center',
plt.close('all')
fig = plt.figure(figsize=[12, 6])
gm = gridspec.GridSpec(100, 190)
ax2 = plt.subplot(gm[:, :])
h = ax2.hist(1. / curvature,
bins=20,
range=[0, 2100],
orientation="vertical",
color='b')
ax2.set_xlim(0, 2100)
#ax2.yaxis.tick_right()
#ax2.yaxis.set_label_position("right")
ax2.set_ylabel('Counts', fontsize=18, rotation=270, labelpad=13)
ax2.set_ylim(0, 15)
ax2.set_xlabel('Curvature (1/m)', fontsize=18, labelpad=2)
#ax0.set_xticks([])
#ax2.set_yticks([25, 50, 75, 100])
#ax2.get_children()[19].set_facecolor('r')
plt.figtext(0.5,
0.94,
'Trayectory curvature distribution',
fontsize=20,
va='center',
ha='center')
plt.savefig('trayectory_curvature_distribution.png')
def print_info(self, interpretation):
"""Print info about the patient and about the ecg signals.
"""
try:
pat_surname, pat_firstname = self.dicom.PatientName.decode('ISO-8859-1').split('^')
except ValueError:
pat_surname = self.dicom.PatientName
pat_firstname = ''
pat_name = ' '.join((pat_surname, pat_firstname.title()))
pat_age = self.dicom.get('PatientAge', '').strip('Y')
pat_id = self.dicom.PatientID
pat_sex = self.dicom.PatientSex
try:
pat_bdate = datetime.strptime(
self.dicom.PatientBirthDate, '%Y%m%d').strftime("%e %b %Y")
except ValueError:
pat_bdate = ""
acquisition_date = datetime.strftime(datetime.strptime(
self.dicom.AcquisitionDateTime, '%Y%m%d%H%M%S'), '%d %b %Y %H:%M')
info = "%s\n%s: %s\n%s: %s\n%s: %s (%s %s)\n%s: %s" % (
pat_name,
i18n.pat_id,
pat_id,
i18n.pat_sex,
pat_sex,
i18n.pat_bdate,
pat_bdate,
pat_age,
i18n.pat_age,
i18n.acquisition_date,
acquisition_date
)
plt.figtext(0.08, 0.87, info, fontsize=8)
plt.figtext(0.30, 0.87, self.legend(), fontsize=8)
if interpretation:
plt.figtext(0.45, 0.87, self.interpretation(), fontsize=8)
info = "%s: %s s %s: %s Hz" % (
i18n.duration, self.duration,
i18n.sampling_frequency,
self.sampling_frequency
)
plt.figtext(0.08, 0.025, info, fontsize=8)
info = INSTITUTION
if not info:
info = self.dicom.get('InstitutionName', '')
plt.figtext(0.38, 0.025, info, fontsize=8)
# TODO: the lowpass filter 0.05-40 Hz will have to became a parameter
info = "%s mm/s %s mm/mV 0.05-40 Hz" % (self.mm_s, self.mm_mv)
plt.figtext(0.76, 0.025, info, fontsize=8)
10 * np.log10((P_rectangular2 / np.amax(P_rectangular2)) ** 2),
"g",
label="0.4m",
)
plt.xlabel(r"Dy $\theta$($\circ$)")
plt.ylabel("Power(dB)")
plt.yticks(np.linspace(-40, 0, 5))
plt.ylim([-40, 0])
plt.grid(True)
plt.title("Dx = 0.4 m")
ax = plt.subplot(133)
plt.figtext(
0.5,
0.5,
z,
style="italic",
wrap=True,
horizontalalignment="center",
fontsize=18,
color="gray",
)
plt.plot(
np.degrees(theta),
10 * np.log10((P_rectangular3 / np.amax(P_rectangular3)) ** 2),
"purple",
label=" 0.6 m",
)
plt.xlabel("Dy ( m )")
plt.ylabel(r"Power $\theta$($\circ$)")
plt.yticks(np.linspace(-40, 0, 5))
plt.ylim([-40, 0])
plt.grid(True)
all_crit)
###################
c = venn3(subsets=sets,
set_labels=('Ablations', 'Posture', 'Trayectory'),
ax=ax4,
alpha=0.65)
for text in c.set_labels:
text.set_fontsize(18)
for text in c.subset_labels:
text.set_fontsize(18)
plt.figtext(0.09,
0.92,
'A and B class neuron ablation analysis',
fontsize=22,
bbox={
'facecolor': colors[0],
'alpha': 0.5,
'pad': 18
})
plt.figtext(0.62,
0.92,
'Body posture analysis',
fontsize=22,
bbox={
'facecolor': colors[1],
'alpha': 0.5,
'pad': 18
})
plt.figtext(0.132,
0.4,