def disc_norm():
x = np.linspace(-3,3,100)
y = st.norm.pdf(x,0,1)
fig, ax = plt.subplots()
fig.canvas.draw()
ax.plot(x,y)
fill1_x = np.linspace(-2,-1.5,100)
fill1_y = st.norm.pdf(fill1_x,0,1)
fill2_x = np.linspace(-1.5,-1,100)
fill2_y = st.norm.pdf(fill2_x,0,1)
ax.fill_between(fill1_x,0,fill1_y,facecolor = 'blue', edgecolor = 'k',alpha = 0.75)
ax.fill_between(fill2_x,0,fill2_y,facecolor = 'blue', edgecolor = 'k',alpha = 0.75)
for label in ax.get_yticklabels():
label.set_visible(False)
for tick in ax.get_xticklines():
tick.set_visible(False)
for tick in ax.get_yticklines():
tick.set_visible(False)
plt.rc("font", size = 16)
plt.xticks([-2,-1.5,-1])
labels = [item.get_text() for item in ax.get_xticklabels()]
labels[0] = r"$v_k$"
labels[1] = r"$\varepsilon_k$"
labels[2] = r"$v_{k+1}$"
ax.set_xticklabels(labels)
plt.ylim([0, .45])
plt.savefig('discnorm.pdf')
plt.clf()
def plots(i,tcodnt, temp, forecast,added_tcodnt,n_steps,path, rsdlsc,rsdlpctgc, sqrpctgc,a,b,c,d,e):
fig=mp.figure(figsize=[15,6])#5:2,89mm
grid=mp.GridSpec(3,36,wspace=1,hspace=0.4)
ax=mp.subplot(grid[:2,:18])
cpplot(i,tcodnt, temp, forecast,added_tcodnt,n_steps,path)
#rscplot(i,tcodnt, rsdlsc, rsdlpctgc, sqrpctgc,path)
ax=mp.subplot(grid[2,:18])
im1=colorbar(ax,tcodnt, rsdlsc,i,0,-1,c**2)
ax.set_yticks([])
ax=mp.subplot(grid[2,21:35])
im2=colorbar(ax,tcodnt, rsdlsc,i,a,b,int(c/2))
ax.set_yticks([])
ax=mp.subplot(grid[:2,21:35])
partial_plot_for_ahead_interval(i,tcodnt, temp, forecast,added_tcodnt,n_steps,path,rsdlpctgc,a,b)
ax1=mp.subplot(grid[:,35])
clb1=mp.colorbar(im2,cax=ax1,extend='both')
#clb1.set_label('residuals',fontsize=12,color='grey')
ax2=mp.subplot(grid[:,18])
clb2=mp.colorbar(im1,cax=ax2,extend='both')
clb1.set_label('residuals',fontsize=size)
# ax=mp.subplot(grid[:2,32:35])
# partial_plot_for_ahead_interval(i,tcodnt, temp, forecast,added_tcodnt,n_steps,path,rsdlpctgc,d,e)
# ax=mp.subplot(grid[2,32:35])
# im3=colorbar(ax,tcodnt, rsdlsc,i,d,e,int(c/5))
# ax.set_yticks([])
# ax3=mp.subplot(grid[:,35])
# clb3=mp.colorbar(im3,cax=ax3,extend='both')
# clb3.set_label('residuals',fontsize=size,color='grey')
mp.savefig((str(path)+'\\'+'results'+'\\'+'Accuracy_Graph_%d'+'.jpg')%i,format='jpg',dpi=2000)
def plot_figure(data, row_labels, col_labels, abs_val, plot_bin, labels, time, logInterval):
colors = ['#0077FF', '#FF0000', '#00FF00', 'magenta']
cmaps = []
for i in colors:
cmaps.append(mpl.colors.LinearSegmentedColormap.from_list('m1',['black',i]))
dim, rows, cols = data.shape
vmax = np.amax(data)
vmin = np.amin(data)
fig, ax = plt.subplots()
c = np.zeros([rows, cols, 4])
for i in range(dim):
c = np.add(c, cmaps[i]((data[i]-vmin)/(vmax-vmin)))
c = np.clip(c, 0, 1)
pc = ax.imshow(c, aspect='auto', interpolation='none')
#ax.set_title(labels[0])
fig.text(0.5, 0.04, 'Bin # along rod length', ha='center',
fontsize=fontsize)
fig.text(0.0, 0.5, 'Time (s)', va='center', rotation='vertical',
fontsize=fontsize)
#ax.add_patch(Rectangle((0.5, time/logInterval), cols-1, 10, edgecolor='w',
# facecolor='none'))
#ax.add_patch(Rectangle((bin_id, 0.5/logInterval), 1, rows-0.5/logInterval,
# edgecolor='w', facecolor='none'))
#plt.savefig('kymo.png', bbox_inches='tight')
plt.savefig('3rods_1long_kymo.pdf')
plt.show()
def make_fish(zoom=False):
plt.close(1)
plt.figure(1, figsize=(6, 4))
plt.plot(plot_limits['pitch'], plot_limits['rolldev'], '-g', lw=3)
plt.plot(plot_limits['pitch'], -plot_limits['rolldev'], '-g', lw=3)
plt.plot(pitch.midvals, roll.midvals, '.b', ms=1, alpha=0.7)
p, r = make_ellipse() # pitch, off nominal roll
plt.plot(p, r, '-c', lw=2)
gf = -0.08 # Fudge on pitch value for illustrative purposes
plt.plot(greta['pitch'] + gf, -greta['roll'], '.r', ms=1, alpha=0.7)
plt.plot(greta['pitch'][-1] + gf, -greta['roll'][-1], 'xr', ms=10, mew=2)
if zoom:
plt.xlim(46.3, 56.1)
plt.ylim(4.1, 7.3)
else:
plt.ylim(-22, 22)
plt.xlim(40, 180)
plt.xlabel('Sun pitch angle (deg)')
plt.ylabel('Sun off-nominal roll angle (deg)')
plt.title('Mission off-nominal roll vs. pitch (5 minute samples)')
plt.grid()
plt.tight_layout()
plt.savefig('fish{}.png'.format('_zoom' if zoom else ''))
def plot_scatter_matrix(df, plotdir):
"Plot scatter matrix."
print('plotting scatter matrix, this may take a while')
plt.clf()
pd_scatter_matrix(df, figsize=(16,16))
plt.suptitle("Scatter Matrix", fontsize=14)
plt.savefig(plotdir + 'scatter_matrix.png')
def scree_plot(pca_obj, fname=None):
'''
Scree plot for variance & cumulative variance by component from PCA.
Arguments:
- pca_obj: a fitted sklearn PCA instance
- fname: path to write plot to file
Output:
- scree plot
'''
components = pca_obj.n_components_
variance = pca.explained_variance_ratio_
plt.figure()
plt.plot(np.arange(1, components + 1), np.cumsum(variance), label='Cumulative Variance')
plt.plot(np.arange(1, components + 1), variance, label='Variance')
plt.xlim([0.8, components]); plt.ylim([0.0, 1.01])
plt.xlabel('No. Components', labelpad=11); plt.ylabel('Variance Explained', labelpad=11)
plt.legend(loc='best')
plt.tight_layout()
if fname is not None:
plt.savefig(fname)
plt.close()
else:
plt.show()
return
def draw_ranges_for_parameters(data, title='', save_path='./pictures/'):
parameters = data.columns.values.tolist()
# remove flight name parameter
for idx, parameter in enumerate(parameters):
if parameter == 'flight_name':
del parameters[idx]
flight_names = np.unique(data['flight_name'])
print len(flight_names)
for parameter in parameters:
plt.figure()
axis = plt.gca()
# ax.set_xticks(numpy.arange(0,1,0.1))
axis.set_yticks(flight_names)
axis.tick_params(labelright=True)
axis.set_ylim([94., 130.])
plt.grid()
plt.title(title)
plt.xlabel(parameter)
plt.ylabel('flight name')
colors = iter(cm.rainbow(np.linspace(0, 1,len(flight_names))))
for flight in flight_names:
temp = data[data.flight_name == flight][parameter]
plt.plot([np.min(temp), np.max(temp)], [flight, flight], c=next(colors), linewidth=2.0)
plt.savefig(save_path+title+'_'+parameter+'.jpg')
plt.close()
def test_minimized_rasterized():
# This ensures that the rasterized content in the colorbars is
# only as thick as the colorbar, and doesn't extend to other parts
# of the image. See #5814. While the original bug exists only
# in Postscript, the best way to detect it is to generate SVG
# and then parse the output to make sure the two colorbar images
# are the same size.
from xml.etree import ElementTree
np.random.seed(0)
data = np.random.rand(10, 10)
fig, ax = plt.subplots(1, 2)
p1 = ax[0].pcolormesh(data)
p2 = ax[1].pcolormesh(data)
plt.colorbar(p1, ax=ax[0])
plt.colorbar(p2, ax=ax[1])
buff = io.BytesIO()
plt.savefig(buff, format='svg')
buff = io.BytesIO(buff.getvalue())
tree = ElementTree.parse(buff)
width = None
for image in tree.iter('image'):
if width is None:
width = image['width']
else:
if image['width'] != width:
assert False
def do_plot(mode, content, wide):
global style
style.apply(mode, content, wide)
data = np.load("data/prr_AsAu_%s%s.npz"%(content, wide))
AU, TAU = np.meshgrid(-data["Au_range_dB"], data["tau_range"])
Zu = data["PRR_U"]
Zs = data["PRR_S"]
assert TAU.shape == AU.shape == Zu.shape, "The inputs TAU, AU, PRR_U must have the same shape for plotting!"
plt.clf()
if mode in ("sync",):
# Plot the inverse power ratio, sync signal is stronger for positive ratios
CSf = plt.contourf(TAU, AU, Zs, levels=(0.0, 0.2, 0.4, 0.6, 0.8, 0.9, 1.0), colors=("1.0", "0.75", "0.5", "0.25", "0.15", "0.0"), origin="lower")
CS2 = plt.contour(CSf, colors = ("r",)*5+("w",), linewidths=(0.75,)*5+(1.0,), origin="lower", hold="on")
else:
CSf = plt.contourf(TAU, AU, Zs, levels=(0.0, 0.2, 0.4, 0.6, 0.8, 0.9, 1.0), colors=("1.0", "0.75", "0.5", "0.25", "0.15", "0.0"), origin="lower")
CS2f = plt.contour(CSf, levels=(0.0, 0.2, 0.4, 0.6, 0.8, 1.0), colors=4*("r",)+("w",), linewidths=(0.75,)*4+(1.0,), origin="lower", hold="on")
#CS2f = plt.contour(TAU, -AU, Zu, levels=(0.9, 1.0), colors=("0.0",), linewidths=(1.0,), origin="lower", hold="on")
if content in ("unif",):
CSu = plt.contourf(TAU, AU, Zu, levels=(0.2, 1.0), hatches=("////",), colors=("0.75",), origin="lower")
CS2 = plt.contour(CSu, levels=(0.2,), colors = ("r",), linewidths=(1.0,), origin="lower", hold="on")
style.annotate(mode, content, wide)
plt.axis([data["tau_range"][0], data["tau_range"][-1], -data["Au_range_dB"][-1], -data["Au_range_dB"][0]])
plt.ylabel(r"Signal power ratio ($\mathrm{SIR}$)", labelpad=2)
plt.xlabel(r"Time offset $\tau$ ($/T$)", labelpad=2)
plt.savefig("pdf/prrc2_%s_%s%s_z.pdf"%(mode, content, wide))
def vis_result(image, seg, gt, title1='Segmentation', title2='Ground truth', savefile=None):
indices = np.where(seg >= 0.5)
indices_gt = np.where(gt >= 0.5)
im_norm = image / image.max()
rgb_image = color.gray2rgb(im_norm)
multiplier = [0., 1., 1.]
multiplier_gt = [1., 1., 0.]
im_seg = rgb_image.copy()
im_gt = rgb_image.copy()
im_seg[indices[0], indices[1], :] *= multiplier
im_gt[indices_gt[0], indices_gt[1], :] *= multiplier_gt
fig = plt.figure()
a = fig.add_subplot(1, 2, 1)
plt.imshow(im_seg)
a.set_title(title1)
a = fig.add_subplot(1, 2, 2)
plt.imshow(im_gt)
a.set_title(title2)
if savefile is None:
plt.show()
else:
plt.savefig(savefile)
plt.close()
def Test(self):
test_Dir = "Result";
if not os.path.exists(test_Dir):
os.makedirs(test_Dir);
test_Label_List = [0,1,2,3,4,5,6,7,8,9,0,1,2,3,4,5];
test_Label_Pattern = np.zeros((16, 10));
test_Label_Pattern[np.arange(16), test_Label_List] = 1;
feed_Dict = {
self.noise_Placeholder: np.random.uniform(-1., 1., size=[16, self.noise_Size]),
self.label_for_Fake_Placeholder: test_Label_Pattern,
self.is_Training_Placeholder: False
}; #Batch is constant in the test.
global_Step, mnist_List = self.tf_Session.run(self.test_Tensor_List, feed_dict = feed_Dict);
fig = plt.figure(figsize=(4, 4))
gs = gridspec.GridSpec(4, 4)
gs.update(wspace=0.05, hspace=0.05)
for index, mnist in enumerate(mnist_List):
ax = plt.subplot(gs[index])
plt.axis('off')
ax.set_xticklabels([])
ax.set_yticklabels([])
ax.set_aspect('equal')
plt.imshow(mnist.reshape(28, 28), cmap='Greys_r')
plt.savefig('%s/S%d.png' % (test_Dir, global_Step), bbox_inches='tight');
plt.close();
def run_test(fld, seeds, plot2d=True, plot3d=True, add_title="",
view_kwargs=None, show=False, scatter_mpl=False, mesh_mvi=True):
interpolated_fld = viscid.interp_trilin(fld, seeds)
seed_name = seeds.__class__.__name__
if add_title:
seed_name += " " + add_title
try:
if not plot2d:
raise ImportError
from viscid.plot import vpyplot as vlt
from matplotlib import pyplot as plt
plt.clf()
# plt.plot(seeds.get_points()[2, :], fld)
mpl_plot_kwargs = dict()
if interpolated_fld.is_spherical():
mpl_plot_kwargs['hemisphere'] = 'north'
vlt.plot(interpolated_fld, **mpl_plot_kwargs)
plt.title(seed_name)
plt.savefig(next_plot_fname(__file__, series='2d'))
if show:
plt.show()
if scatter_mpl:
plt.clf()
vlt.plot2d_line(seeds.get_points(), fld, symdir='z', marker='o')
plt.savefig(next_plot_fname(__file__, series='2d'))
if show:
plt.show()
except ImportError:
pass
try:
if not plot3d:
raise ImportError
from viscid.plot import vlab
_ = get_mvi_fig(offscreen=not show)
try:
if mesh_mvi:
mesh = vlab.mesh_from_seeds(seeds, scalars=interpolated_fld)
mesh.actor.property.backface_culling = True
except RuntimeError:
pass
pts = seeds.get_points()
p = vlab.points3d(pts[0], pts[1], pts[2], interpolated_fld.flat_data,
scale_mode='none', scale_factor=0.02)
vlab.axes(p)
vlab.title(seed_name)
if view_kwargs:
vlab.view(**view_kwargs)
vlab.savefig(next_plot_fname(__file__, series='3d'))
if show:
vlab.show(stop=True)
except ImportError:
pass
def default_run(self):
"""
Plots the results, saves the figure, and finally displays it from simulating codewords with Sum-prod and Max-prod
algorithms across variance levels. This combines the results in one plot.
:return:
"""
if not os.path.exists("./graphs"):
os.makedirs("./graphs")
self.save_time = str(int(time.time()))
self.simulate(Decoder.SUM_PROD)
self.compute_error()
plt.plot([math.log10(x) for x in self.variance_levels], [math.log10(y) for y in self.bit_error_probability],
"ro-", label="Sum-Prod")
self.simulate(Decoder.MAX_PROD)
self.compute_error()
plt.plot([math.log10(x) for x in self.variance_levels], [math.log10(y) for y in self.bit_error_probability],
"g^--", label="Max-Prod")
plt.legend(loc=2)
plt.title("Hamming Decoder Factor Graph Simulation Results\n" +
r"$\log_{10}(\sigma^2)$ vs. $\log_{10}(P_e)$" + " for Max-Prod & Sum-Prod Algorithms\n" +
"Sample Size n = %(codewords)s Codewords \n Variance Levels = %(levels)s"
% {"codewords": str(self.iterations), "levels": str(self.variance_levels)})
plt.xlabel("$\log_{10}(\sigma^2)$")
plt.ylabel(r"$\log_{10}(P_e)$")
plt.savefig("graphs/%(time)s-max-prod-sum-prod-%(num_codewords)s-codewords-variance-bit_error_probability.png" %
{"time": self.save_time,
"num_codewords": str(self.iterations)}, bbox_inches="tight")
plt.show()
def build_hist(self, coverage, show=False, save=False, save_fn="max_hist_plot"):
"""
Build a histogram to determine what the maxes look & visualize match_count
Might be used to determine a resonable threshold
@param coverage: the average coverage for an single nt
@param show: Show visualization with match maxes
@param save_fn: Save to disk with this file name or else it will be the default
@return: the histogram array
"""
#import matplotlib
#matplotlib.use("Agg")
import matplotlib.pyplot as plt
maxes = self.match_count.max(1) # get maxes along 1st dim
h = plt.hist(maxes, bins=self.match_count.shape[0]) # figure out where the majority
plt.ylabel("Frequency")
plt.xlabel("Count per index")
plt.title("Frequency count histogram")
if show: plt.show()
if save: plt.savefig(save_fn, dpi=160, frameon=False)
return h[0]
def compare_chebhist(dname, mylambda, c, Nbin = 25):
if mylambda == 'Do not exist':
print('--!!Warning: eig file does not exist, can not display compare histgram')
else:
mylambda = 1 - mylambda
lmin = max(min(mylambda), -1)
lmax = min(max(mylambda), 1)
# print c
cheb_file_content = '\n'.join([str(st) for st in c])
x = np.linspace(lmin, lmax, Nbin + 1)
y = plot_chebint(c, x)
u = (x[1:] + x[:-1]) / 2
v = y[1:] - y[:-1]
plt.clf()
plt.hold(True)
plt.hist(mylambda,Nbin)
plt.plot(u, v, "r.", markersize=10)
plt.hold(False)
plt.show()
filename = 'data/' + dname + '.png'
plt.savefig(filename)
cheb_filename = 'data/' + dname + '.cheb'
f = open(cheb_filename, 'w+')
f.write(cheb_file_content)
f.close()
def plotErrorBars(dict_to_plot, x_lim, y_lim, xlabel, y_label, title, out_file, margin=[0.05, 0.05], loc=2):
plt.title(title)
plt.xlabel(xlabel)
plt.ylabel(y_label)
if y_lim is None:
y_lim = [1 * float("Inf"), -1 * float("Inf")]
max_val_seen_y = y_lim[1] - margin[1]
min_val_seen_y = y_lim[0] + margin[1]
print min_val_seen_y, max_val_seen_y
max_val_seen_x = x_lim[1] - margin[0]
min_val_seen_x = x_lim[0] + margin[0]
handles = []
for k in dict_to_plot:
means, stds, x_vals = dict_to_plot[k]
min_val_seen_y = min(min(np.array(means) - np.array(stds)), min_val_seen_y)
max_val_seen_y = max(max(np.array(means) + np.array(stds)), max_val_seen_y)
min_val_seen_x = min(min(x_vals), min_val_seen_x)
max_val_seen_x = max(max(x_vals), max_val_seen_x)
handle = plt.errorbar(x_vals, means, yerr=stds)
handles.append(handle)
print max_val_seen_y
plt.xlim([min_val_seen_x - margin[0], max_val_seen_x + margin[0]])
plt.ylim([min_val_seen_y - margin[1], max_val_seen_y + margin[1]])
plt.legend(handles, dict_to_plot.keys(), loc=loc)
plt.savefig(out_file)
def plot_precision_recall_n(y_true, y_scores, model_name):
'''
Takes the model, plots precision and recall curves
'''
precision_curve, recall_curve, pr_thresholds = precision_recall_curve(y_true, y_scores)
precision_curve = precision_curve[:-1]
recall_curve = recall_curve[:-1]
pct_above_per_thresh = []
number_scored = len(y_scores)
for value in pr_thresholds:
num_above_thresh = len(y_scores[y_scores >= value])
pct_above_thresh = num_above_thresh / float(number_scored)
pct_above_per_thresh.append(pct_above_thresh)
pct_above_per_thresh = np.array(pct_above_per_thresh)
plt.clf()
fig, ax1 = plt.subplots()
ax1.plot(pct_above_per_thresh, precision_curve, 'b')
ax1.set_xlabel('percent of population')
ax1.set_ylabel('precision', color='b')
ax2 = ax1.twinx()
ax2.plot(pct_above_per_thresh, recall_curve, 'r')
ax2.set_ylabel('recall', color='r')
name = model_name
plt.title(name)
plt.savefig("Eval/{}.png".format(name))
def display(spectrum):
template = np.ones(len(spectrum))
#Get the plot ready and label the axes
pyp.plot(spectrum)
max_range = int(math.ceil(np.amax(spectrum) / standard_deviation))
for i in range(0, max_range):
pyp.plot(template * (mean + i * standard_deviation))
pyp.xlabel('Units?')
pyp.ylabel('Amps Squared')
pyp.title('Mean Normalized Power Spectrum')
if 'V' in Options:
pyp.show()
if 'v' in Options:
tokens = sys.argv[-1].split('.')
filename = tokens[0] + ".png"
input = ''
if os.path.isfile(filename):
input = input("Error: Plot file already exists! Overwrite? (y/n)\n")
while input != 'y' and input != 'n':
input = input("Please enter either \'y\' or \'n\'.\n")
if input == 'y':
pyp.savefig(filename)
else:
print("Plot not written.")
else:
pyp.savefig(filename)
def export(data, F, k):
'''Write data to a png image
Arguments
---------
data : numpy.ndarray
array containing the data to be written as png image
F : float
feed rate of the current configuration
k : float
rate constant of the current configuration
'''
figsize = tuple(s / 72.0 for s in data.shape)
fig = plt.figure(figsize=figsize, dpi=72.0, facecolor='white')
fig.add_axes([0, 0, 1, 1], frameon=False)
plt.xticks([])
plt.yticks([])
plt.imshow(data, cmap=plt.cm.RdBu_r, interpolation='bicubic')
plt.gci().set_clim(0, 1)
filename = './study/F{:03d}-k{:03d}.png'.format(int(1000*F), int(1000*k))
plt.savefig(filename, dpi=72.0)
plt.close()
def draw_img_for_viewing_ice(self):
#print "Press 'p' to save PNG."
global colmax
global colmin
fig = P.figure(num=None, figsize=(13.5, 5), dpi=100, facecolor='w', edgecolor='k')
cid1 = fig.canvas.mpl_connect('key_press_event', self.on_keypress_for_viewing)
cid2 = fig.canvas.mpl_connect('button_press_event', self.on_click)
canvas = fig.add_subplot(121)
canvas.set_title(self.filename)
self.axes = P.imshow(self.inarr, origin='lower', vmax = colmax, vmin = colmin)
self.colbar = P.colorbar(self.axes, pad=0.01)
self.orglims = self.axes.get_clim()
canvas = fig.add_subplot(122)
canvas.set_title("Angular Average")
maxAngAvg = (self.inangavg).max()
numQLabels = len(eDD.iceHInvAngQ.keys())+1
labelPosition = maxAngAvg/numQLabels
for i,j in eDD.iceHInvAngQ.iteritems():
P.axvline(j,0,colmax,color='r')
P.text(j,labelPosition,str(i), rotation="45")
labelPosition += maxAngAvg/numQLabels
P.plot(self.inangavgQ, self.inangavg)
P.xlabel("Q (A-1)")
P.ylabel("I(Q) (ADU/srad)")
pngtag = original_dir + "peakfit-gdvn_%s.png" % (self.filename)
P.savefig(pngtag)
print "%s saved." % (pngtag)
P.close()
def draw_stat(actual_price, action):
price_list = []
x_list = []
# idx = np.where(actual_price == 0)[0]
# print idx
# print actual_price[np.where(actual_price < 2000)]
# idx = [0] + idx.tolist()
# print idx
# for i in range(len(idx)-1):
# price_list.append(actual_price[idx[i]+1:idx[i+1]-1])
# x_list.append(range(idx[i]+i+1, idx[i+1]+i-1))
# for i in range(len(idx)-1):
# print x_list[i]
# print price_list[i]
# plt.plot(x_list[i], price_list[i], 'r')
x_list = range(1,50)
price_list = actual_price[1:50]
plt.plot(x_list, price_list, 'k')
for i in range(1, 50):
style = 'go'
if action[i] == 1:
style = 'ro'
plt.plot(i, actual_price[i], style)
plt.ylim(2140, 2144.2)
# plt.show()
plt.savefig("action.png")
def make_bar(
x,
y,
f_name,
title=None,
legend=None,
x_label=None,
y_label=None,
x_ticks=None,
y_ticks=None,
):
fig = plt.figure()
if title is not None:
plt.title(title, fontsize=16)
if x_label is not None:
plt.ylabel(x_label)
if y_label is not None:
plt.xlabel(y_label)
if x_ticks is not None:
plt.xticks(x, x_ticks)
if y_ticks is not None:
plt.yticks(y_ticks)
plt.bar(x, y, align="center")
if legend is not None:
plt.legend(legend)
plt.savefig(f_name)
plt.close(fig)
def main():
parser = argparse.ArgumentParser(description="""Compute subset of users who rated at
least 10 movies and plot fraction of users satisfied
as a function of inventory size.""")
parser.add_argument("infilename",
help="Read from this file.", type=open)
args = parser.parse_args()
ratings = read_inputs(args.infilename)
ratings = ratings.drop("timestamp", axis=1)
movie_rankings = find_movie_rankings(ratings)
ratings = ratings.drop("rating", axis=1)
user_rankings = find_user_rankings(ratings, movie_rankings)
num_users = user_rankings.user_id.unique().size
num_movies = movie_rankings.shape[0]
user_rankings = clean_rankings(user_rankings)
us_levels_100 = find_satisfaction(user_rankings, num_users, num_movies)
us_levels_90 = find_satisfaction(user_rankings, num_users, num_movies, satisfaction_level=0.9)
rc('text', usetex=True)
plt.title('Percent of Users Satisfied vs Inventory Size in the MovieLens Dataset')
plt.xlabel('Inventory Size')
plt.ylabel('Percent of Users Satisfied')
plt.plot(us_levels_100, 'b', label=r'$100\% \ satisfaction$')
plt.plot(us_levels_90, 'r--', label=r'$90\% \ satisfaction$')
plt.legend()
d = datetime.datetime.now().isoformat()
plt.savefig('user_satisfaction_%s.png' % d)
def plot_jacobian(A, name, cmap= plt.cm.coolwarm, normalize=True, precision=1e-6):
"""
Customized visualization of jacobian matrices for observing
sparsity patterns
"""
plt.figure()
fig, ax = plt.subplots()
if normalize is True:
plt.imshow(A, interpolation='none', cmap=cmap,
norm = mpl.colors.Normalize(vmin=-1.,vmax=1.))
else:
plt.imshow(A, interpolation='none', cmap=cmap)
plt.colorbar(format=ticker.FuncFormatter(fmt))
ax.spy(A, marker='.', markersize=0, precision=precision)
ax.spines['right'].set_visible(True)
ax.spines['bottom'].set_visible(True)
ax.xaxis.set_ticks_position('top')
ax.yaxis.set_ticks_position('left')
xlabels = np.linspace(0, A.shape[0], 5, True, dtype=int)
ylabels = np.linspace(0, A.shape[1], 5, True, dtype=int)
plt.xticks(xlabels)
plt.yticks(ylabels)
plt.savefig(name, bbox_inches='tight', pad_inches=0.05)
plt.close()
return
def plot(self, path, num_bins=0):
"""
draw a histogram to represent the data
:param num_bins: number of bars, default is (Number different word in the file )/ 2,
if it is too large take 50 as default (see '#default of num_bins')
"""
# plot data
mu = self.Average # mean of distribution
sigma = self.StdE # standard deviation of distribution
if num_bins == 0: # default of num_bins
num_bins = min([round(self.NumWord / 2), 50])
# print num_bins
# the histogram of the data
n, bins, patches = plt.hist(self.WordCount.values(), num_bins, normed=1, facecolor='green', alpha=0.5)
# add a 'best fit' line
y = mlab.normpdf(bins, mu, sigma)
plt.plot(bins, y, 'r--')
plt.xlabel('Word Count')
plt.ylabel('Probability(how many words have this word count)')
plt.title(r'Histogram of word count: $\mu=' + str(self.Average) + '$, $\sigma=' + str(self.StdE) + '$')
# Tweak spacing to prevent clipping of ylabel
plt.subplots_adjust(left=0.15)
plt.savefig(path)
plt.close()
def make_entity_plot(filename, title, fixed_noip, fixed_ip, dynamic_noip, dynamic_ip):
plt.figure(figsize=(12,5))
plt.title("Settings comparison - " + title)
plt.xlabel('Time (ms)', fontsize=12)
plt.xlim([0,62000])
x = 0
barwidth = 0.5
bargroupspacing = 1.5
fixed_noip_mean,fixed_noip_conf = conf_stats(fixed_noip)
fixed_ip_mean,fixed_ip_conf = conf_stats(fixed_ip)
dynamic_noip_mean,dynamic_noip_conf = conf_stats(dynamic_noip)
dynamic_ip_mean,dynamic_ip_conf = conf_stats(dynamic_ip)
values = [fixed_noip_mean,fixed_ip_mean,dynamic_noip_mean, dynamic_ip_mean]
errs = [fixed_noip_conf,fixed_ip_conf,dynamic_noip_conf, dynamic_ip_conf]
y_pos = numpy.arange(len(values))
plt.barh(y_pos, values, xerr=errs, align='center', color=['r', 'b', 'r', 'b'], ecolor='black', alpha=0.7)
plt.yticks(y_pos, ["Fixed | no I.P.", "Fixed | I.P.", "Dynamic | no I.P.", "Dynamic | I.P."])
plt.savefig(output_file(filename))
plt.clf()
def plot_dpi_dpr_distribution(args, dpis, dprs, diagnoses):
print log.INFO, 'Plotting estimate distributions...'
diagnoses = np.array(diagnoses)
diagnoses[(0.25 <= diagnoses) & (diagnoses <= 0.75)] = 0.5
# Setup plot
fig, ax = plt.subplots()
pt.setup_axes(plt, ax)
biomarkers_str = args.method if args.biomarkers is None else ', '.join(args.biomarkers)
ax.set_title('DP estimation using {0} at {1}'.format(biomarkers_str, ', '.join(args.visits)))
ax.set_xlabel('DP')
ax.set_ylabel('DPR')
plt.scatter(dpis, dprs, c=diagnoses, edgecolor='none', s=25.0,
vmin=0.0, vmax=1.0, cmap=pt.progression_cmap,
alpha=0.5)
# Plot legend
# noinspection PyUnresolvedReferences
rects = [mpl.patches.Rectangle((0, 0), 1, 1, fc=pt.color_cn + (0.5,), linewidth=0),
mpl.patches.Rectangle((0, 0), 1, 1, fc=pt.color_mci + (0.5,), linewidth=0),
mpl.patches.Rectangle((0, 0), 1, 1, fc=pt.color_ad + (0.5,), linewidth=0)]
labels = ['CN', 'MCI', 'AD']
legend = ax.legend(rects, labels, fontsize=10, ncol=len(rects), loc='upper center', framealpha=0.9)
legend.get_frame().set_edgecolor((0.6, 0.6, 0.6))
# Draw or save the plot
plt.tight_layout()
if args.plot_file is not None:
plt.savefig(args.plot_file, transparent=True)
else:
plt.show()
plt.close(fig)
def plot_wav_fft(wav_filename, desc=None):
plt.clf()
plt.figure(num=None, figsize=(6, 4))
sample_rate, X = scipy.io.wavfile.read(wav_filename)
spectrum = np.fft.fft(X)
freq = np.fft.fftfreq(len(X), 1.0 / sample_rate)
plt.subplot(211)
num_samples = 200.0
plt.xlim(0, num_samples / sample_rate)
plt.xlabel("time [s]")
plt.title(desc or wav_filename)
plt.plot(np.arange(num_samples) / sample_rate, X[:num_samples])
plt.grid(True)
plt.subplot(212)
plt.xlim(0, 5000)
plt.xlabel("frequency [Hz]")
plt.xticks(np.arange(5) * 1000)
if desc:
desc = desc.strip()
fft_desc = desc[0].lower() + desc[1:]
else:
fft_desc = wav_filename
plt.title("FFT of %s" % fft_desc)
plt.plot(freq, abs(spectrum), linewidth=5)
plt.grid(True)
plt.tight_layout()
rel_filename = os.path.split(wav_filename)[1]
plt.savefig("%s_wav_fft.png" % os.path.splitext(rel_filename)[0],
bbox_inches='tight')
def make_overview_plot(filename, title, noip_arrs, ip_arrs):
plt.title("Inner parallelism - " + title)
plt.ylabel('Time (ms)', fontsize=12)
x = 0
barwidth = 0.5
bargroupspacing = 1.5
for z in zip(noip_arrs, ip_arrs):
noip,ip = z
noip_mean,noip_conf = conf_stats(noip)
ip_mean,ip_conf = conf_stats(ip)
b_noip = plt.bar(x, noip_mean, barwidth, color='r', yerr=noip_conf, ecolor='black', alpha=0.7)
x += barwidth
b_ip = plt.bar(x, ip_mean, barwidth, color='b', yerr=ip_conf, ecolor='black', alpha=0.7)
x += bargroupspacing
plt.xticks([0.5, 2.5, 4.5], ['50k', '100k', '200k'], rotation='horizontal')
fontP = FontProperties()
fontP.set_size('small')
plt.legend([b_noip, b_ip], \
('no inner parallelism', 'inner parallelism'), \
prop=fontP, loc='upper center', bbox_to_anchor=(0.5, -0.05), fancybox=True, shadow=True, ncol=2)
plt.ylim([0,62000])
plt.savefig(output_file(filename))
plt.clf()
def make_line(
x,
y,
f_name,
title=None,
legend=None,
x_label=None,
y_label=None,
x_ticks=None,
y_ticks=None,
):
fig = plt.figure()
if title is not None:
plt.title(title, fontsize=16)
if x_label is not None:
plt.ylabel(x_label)
if y_label is not None:
plt.xlabel(y_label)
if x_ticks is not None:
plt.xticks(x, x_ticks)
if y_ticks is not None:
plt.yticks(y_ticks)
if isinstance(y[0], list):
for data in y:
plt.plot(x, data)
else:
plt.plot(x, y)
if legend is not None:
plt.legend(legend)
plt.savefig(f_name)
plt.close(fig)
fig, ax = plt.subplots()
sns.barplot(data=rmses_ens2)
ax.set(ylabel='RMSE', title="mean=%.3f, CI=%.3f-%.3f"%(mean_ens2, CI_ens2[0], CI_ens2[1]))
plt.xticks()
plt.savefig("plots/multiply_%s_rmse.pdf"%neuron_type)
print('rmses: ', rmses_ens, rmses_ens_out, rmses_ens2)
print('means: ', mean_ens, mean_ens_out, mean_ens2)
print('confidence intervals: ', CI_ens, CI_ens_out, CI_ens2)
np.savez('data/multiply_%s_results.npz'%neuron_type, rmses_ens=rmses_ens, rmses_ens_out=rmses_ens_out, rmses_ens2=rmses_ens2)
return rmses_ens2
# rmses_lif = run(neuron_type=LIF())
# rmses_alif = run(neuron_type=AdaptiveLIFT())
# rmses_wilson = run(neuron_type=WilsonEuler(), dt=0.00005)
# rmses_durstewitz = run(neuron_type=DurstewitzNeuron())
# , load_w="data/multiply_w.npz", load_df="data/multiply_DurstewitzNeuron()_df.npz")
rmses_lif = np.load("data/multiply_LIF()_results.npz")['rmses_ens2']
rmses_alif = np.load("data/multiply_AdaptiveLIFT()_results.npz")['rmses_ens2']
rmses_wilson = np.load("data/multiply_WilsonEuler()_results.npz")['rmses_ens2']
rmses_durstewitz = np.load("data/multiply_DurstewitzNeuron()_results.npz")['rmses_ens2']
rmses = np.vstack((rmses_lif, rmses_alif, rmses_wilson, rmses_durstewitz))
nt_names = ['LIF', 'ALIF', 'Wilson', 'Durstewitz']
fig, ax = plt.subplots()
sns.barplot(data=rmses.T)
ax.set(ylabel='RMSE')
plt.xticks(np.arange(len(nt_names)), tuple(nt_names), rotation=0)
plt.savefig("figures/multiply_all_rmses.pdf")
train_source,
train_steps,
epochs = bc_config.EPOCHS,
validation_data = test_source,
validation_steps = validation_steps)
timestamp = strftime('%d-%b-%y_%H:%M:%S')
try:
os.mkdir(bc_config.MODEL_DIR)
except FileExistsError:
pass
model.save(bc_config.MODEL_DIR + '/' + timestamp + '.h5')
if bc_config.PLOT_LOSSES:
import matplotlib.pyplot as plt
plt.plot(history.history['loss'])
plt.plot(history.history['val_loss'])
plt.title('Model Loss')
plt.ylabel('Loss')
plt.xlabel('Epoch')
plt.legend(['Train Loss', 'Val. Loss'], loc='upper left')
try:
os.mkdir(bc_config.PLOT_DIR)
except FileExistsError:
pass
plt.savefig(bc_config.PLOT_DIR + '/' + timestamp + '.png')
print('done')
def main(fig_num, invert=False):
if fig_num == '1':
# Subplots: http://aplpy.readthedocs.io/en/stable/howto_subplot.html
fig = plt.figure(
figsize=(7, 5)) # height > optimal aspect ratio has no effect
# MOST image alone to show structure (varying dark/bright regions)
fmost = aplpy.FITSFigure(XMMPATH + '/../most/G309.2-0.6.fits',
figure=fig,
subplot=(1, 2, 1))
fmost.recenter(ra2deg(13, 46, 40),
-62.87,
width=18. / 60,
height=18. / 60)
fmost_cmap = 'afmhot'
if invert:
fmost_cmap += '_r'
fmost.show_colorscale(vmin=1e-4,
vmax=2e-1,
stretch='arcsinh',
cmap=fmost_cmap)
# MOST beam notes:
# - must specify parameters or else constructor will unsuccessfully
# search for FITS keywords BMAJ, BMIN, BPA.
# - hatching is too sparse at our image size, and so has no effect
# Reference: Whiteoak & Green, 1996A&AS..118..329W
fmost.add_beam(major=42. / np.sin(-62.9 * np.pi / 180) * u.arcsecond,
minor=42 * u.arcsecond,
angle=0,
corner='bottom left',
hatch=None,
pad=1,
color='white')
if invert:
fmost.beam.set_edgecolor('black')
fmost.beam.set_facecolor('gray')
format_ticks_and_labels(fmost, invert=invert)
#fmost.tick_labels.hide_y()
#fmost.axis_labels.hide_y()
# Broadband X-ray image with sparse MOST contours to guide the eye
# Base image has 2.5" pixels and is smoothed with 2px Gaussian (5")
fxmm = aplpy.FITSFigure(
XMMPATH +
'/repro_merged_no_holes/corrected-800-3300_bin0_gauss2.fits',
figure=fig,
subplot=(1, 2, 2))
fxmm.recenter(ra2deg(13, 46, 40),
-62.87,
width=18. / 60,
height=18. / 60)
# Weird bug:
# vmin=9e-6,vmax=5e-5 works w/colorbar, but vmin=1e-5,vmax=5e-5 fails
fxmm_cmap = 'cubehelix'
if invert:
fxmm_cmap += '_r'
# Idea: log scale here to show faint emission; linear show in full fov
# image to show sources
#fxmm.show_colorscale(vmin=0.2e-5, vmax=2e-5, stretch='linear',cmap=fxmm_cmap)
fxmm.show_colorscale(vmin=2e-6,
vmax=4e-5,
stretch='log',
cmap=fxmm_cmap)
# TODO get colorbars working for both subplots
# https://github.com/aplpy/aplpy/issues/119
# Warning: bottom colorbar not fully implemented =(
#fxmm.add_colorbar(location='right', log_format=True)
#fxmm.colorbar.set_font(size='small')
## TODO WARNING: tick labeling not good.
##fxmm.colorbar.set_axis_label_text(r'Counts $s^{-1}$') # Give in text
##fxmm.colorbar.set_axis_label_font(size='small')
most = fits.open(XMMPATH + '/../most/G309.2-0.6.fits')
#lev = np.linspace(0.02, 0.2, 10)
#lev = np.logspace(np.log10(0.01), np.log10(0.2), 10)
lev = np.logspace(-2, -0.5,
4) # Sparse log contours, 0.01 to 0.1*sqrt(10)
lev_color = 'cyan'
if invert:
lev_color = 'gray'
fxmm.show_contour(data=most, levels=lev, colors=lev_color, alpha=1)
format_ticks_and_labels(fxmm, invert=invert)
fxmm.tick_labels.hide_y()
fxmm.axis_labels.hide_y()
fxmm.refresh()
fig.tight_layout()
fig.canvas.draw()
if invert:
plt.savefig('fig_snr_xmm_most_invert.pdf', dpi=300)
else:
plt.savefig('fig_snr_xmm_most.pdf', dpi=300)
elif fig_num == '2':
# Subplots: http://aplpy.readthedocs.io/en/stable/howto_subplot.html
fig = plt.figure(
figsize=(8, 10)) # height > optimal aspect ratio has no effect
cmap = 'afmhot'
if invert:
cmap = 'cubehelix_r'
#cmap += '_r'
# Broadband X-ray image with point source extractions
# and interpolation
f = aplpy.FITSFigure(
XMMPATH +
'/repro_merged_no_holes/corrected-800-3300_bin0_gauss2.fits',
figure=fig,
subplot=(1, 2, 1))
g = aplpy.FITSFigure(
XMMPATH + '/repro_merged/corrected-800-3300_bin0_gauss2.fits',
figure=fig,
subplot=(1, 2, 2))
for aplfig in [f, g]:
aplfig.recenter(ra2deg(13, 46, 40),
-62 - 52. / 60,
width=30. / 60,
height=36. / 60)
#aplfig.show_colorscale(vmin=1e-6, vmax=4e-5, stretch='log',cmap=cmap)
aplfig.show_colorscale(vmin=0.2e-5,
vmax=3e-5,
stretch='linear',
cmap=cmap)
format_ticks_and_labels(aplfig, invert=invert)
aplfig.ticks.set_color('black') # Because of FOV image
if not invert:
axleft_ticks = aplfig._ax1.yaxis.get_ticklines()
axright_ticks = aplfig._ax2.yaxis.get_ticklines()
axleft_minorticks = aplfig._ax1.yaxis.get_minorticklines()
axright_minorticks = aplfig._ax2.yaxis.get_minorticklines()
axleft_ticks[4].set_color('white')
axleft_ticks[6].set_color('white')
axright_ticks[5].set_color('white')
for idx in [18, 20, 22, 24, 26, 28, 30, 32, 34, 36]:
axleft_minorticks[idx].set_color('white')
for idx in [17, 19, 21, 23]:
axright_minorticks[idx].set_color('white')
g.tick_labels.hide_y()
g.axis_labels.hide_y()
f.show_regions('regs-plot/all_point_sources.reg')
#f.show_regions('regs/ann_000_100.reg')
#f.show_regions('regs-plot/circ_200.reg')
#f.show_regions('regs-plot/circ_300.reg')
f.show_regions(
'regs/src.reg') # Equivalent to circ_400, but changed color/width
#f.show_regions('regs-plot/circ_500.reg')
f.show_regions('regs/bkg.reg') # Yes, do show background
#f.image.figure.tight_layout() # Use the matplotlib figure instance
fig.tight_layout()
fig.canvas.draw()
if invert:
plt.savefig('fig_snr_fullfov_invert.pdf',
dpi=300) # Drops into CWD
else:
plt.savefig('fig_snr_fullfov.pdf', dpi=300) # Drops into CWD
elif fig_num == '3':
fig = plt.figure(figsize=(7, 5))
cmap_lf = 'cubehelix'
if invert:
cmap_lf += '_r'
cmap_ew = 'afmhot'
if invert:
cmap_ew += '_r'
mg_line = aplpy.FITSFigure(
XMMPATH + '/repro_merged/mg_lineflux_bin8_gauss2.fits',
figure=fig,
subplot=(2, 3, 1))
si_line = aplpy.FITSFigure(
XMMPATH + '/repro_merged/si_lineflux_bin8_gauss2.fits',
figure=fig,
subplot=(2, 3, 2))
s_line = aplpy.FITSFigure(XMMPATH +
'/repro_merged/s_lineflux_bin8_gauss2.fits',
figure=fig,
subplot=(2, 3, 3))
mg_eqw = aplpy.FITSFigure(XMMPATH +
'/repro_merged/mg_eqwidth_bin16_gauss2.fits',
figure=fig,
subplot=(2, 3, 4))
si_eqw = aplpy.FITSFigure(XMMPATH +
'/repro_merged/si_eqwidth_bin16_gauss2.fits',
figure=fig,
subplot=(2, 3, 5))
s_eqw = aplpy.FITSFigure(XMMPATH +
'/repro_merged/s_eqwidth_bin16_gauss2.fits',
figure=fig,
subplot=(2, 3, 6))
mg_line.show_colorscale(vmin=0,
vmax=3e-6,
stretch='arcsinh',
cmap=cmap_lf)
si_line.show_colorscale(vmin=0,
vmax=3e-6,
stretch='arcsinh',
cmap=cmap_lf)
s_line.show_colorscale(vmin=0,
vmax=3e-6,
stretch='arcsinh',
cmap=cmap_lf)
mg_eqw.show_colorscale(vmin=0,
vmax=250,
stretch='linear',
cmap=cmap_ew)
si_eqw.show_colorscale(vmin=0,
vmax=1000,
stretch='linear',
cmap=cmap_ew)
s_eqw.show_colorscale(vmin=0,
vmax=1000,
stretch='linear',
cmap=cmap_ew)
for im in [mg_line, si_line, s_line, mg_eqw, si_eqw, s_eqw]:
im.recenter(ra2deg(13, 46, 40),
-62.87,
width=18. / 60,
height=18. / 60)
format_ticks_and_labels(im, invert=invert)
im.ticks.hide()
im.tick_labels.hide()
im.axis_labels.hide()
most = fits.open(XMMPATH + '/../most/G309.2-0.6.fits')
lev = [1e-2]
lev_color = 'cyan'
if invert:
lev_color = 'gray'
for im in [mg_line, si_line, s_line, mg_eqw, si_eqw, s_eqw]:
im.show_contour(data=most, levels=lev, colors=lev_color, alpha=0.7)
text_color = 'white'
if invert:
text_color = 'black'
if invert:
mg_line.add_label(0.96,
0.92,
'1.3--1.4 keV',
relative=True,
horizontalalignment='right',
size='small',
color='black')
si_line.add_label(0.96,
0.92,
'1.8--1.9 keV',
relative=True,
horizontalalignment='right',
size='small',
color='black')
s_line.add_label(0.96,
0.92,
'2.4--2.5 keV',
relative=True,
horizontalalignment='right',
size='small',
color='black')
else:
mg_line.add_label(0.96,
0.92,
'1.3--1.4 keV',
relative=True,
horizontalalignment='right',
size='small',
color='black',
backgroundcolor='white')
si_line.add_label(0.96,
0.92,
'1.8--1.9 keV',
relative=True,
horizontalalignment='right',
size='small',
color='black',
backgroundcolor='white')
s_line.add_label(0.96,
0.92,
'2.4--2.5 keV',
relative=True,
horizontalalignment='right',
size='small',
color='black',
backgroundcolor='white')
# MEH -- too awkward.
# mg_line.add_label(0.96, 0.78, '1.3--1.4 keV', relative=True, horizontalalignment='right', size='small', color=text_color)
# si_line.add_label(0.96, 0.78, '1.8--1.9 keV', relative=True, horizontalalignment='right', size='small', color=text_color)
# s_line.add_label( 0.96, 0.78, '2.4--2.5 keV', relative=True, horizontalalignment='right', size='small', color=text_color)
mg_eqw.add_label(0.96,
0.92,
'Mg EW',
relative=True,
horizontalalignment='right',
size='small',
color=text_color)
si_eqw.add_label(0.96,
0.92,
'Si EW',
relative=True,
horizontalalignment='right',
size='small',
color=text_color)
s_eqw.add_label(0.96,
0.92,
'S EW',
relative=True,
horizontalalignment='right',
size='small',
color=text_color)
mg_eqw.add_colorbar(location='bottom')
mg_eqw.colorbar.set_font(size='small')
#mg_eqw.colorbar.set_axis_label_text(r'Equivalent width, eV')
#mg_eqw.colorbar.set_axis_label_font(size='small')
mg_eqw.colorbar.set_ticks([0, 50, 100, 150, 200, 250])
si_eqw.add_colorbar(location='bottom')
si_eqw.colorbar.set_font(size='small')
#si_eqw.colorbar.set_axis_label_text(r'Equivalent width, eV')
#si_eqw.colorbar.set_axis_label_font(size='small')
si_eqw.colorbar.set_ticks([0, 200, 400, 600, 800, 1000])
s_eqw.add_colorbar(location='bottom')
s_eqw.colorbar.set_font(size='small')
#s_eqw.colorbar.set_axis_label_text(r'Equivalent width, eV')
#s_eqw.colorbar.set_axis_label_font(size='small')
s_eqw.colorbar.set_ticks([0, 200, 400, 600, 800, 1000])
# Scalebar label commanding does not work :(
#s_eqw.add_scalebar(1 * u.arcmin) # 1 arcminute scalebar
#s_eqw.scalebar.set_label('1 arcmin.')
#s_eqw.scalebar.set_corner('top right')
#s_eqw.scalebar.set_font(size='small')
#if invert:
# s_eqw.scalebar.set_color('black')
#else:
# s_eqw.scalebar.set_color('white')
fig.tight_layout()
fig.canvas.draw()
if invert:
plt.savefig('fig_lineflux_eqwidth_invert.pdf', dpi=300)
else:
plt.savefig('fig_lineflux_eqwidth.pdf', dpi=300)
elif fig_num == '4':
# RGB image of Mg line flux, Si/S eq width
aplpy.make_rgb_image([
XMMPATH + '/repro_merged/mg_lineflux_bin16_gauss2.fits',
XMMPATH + '/repro_merged/si_eqwidth_bin16_gauss2.fits',
XMMPATH + '/repro_merged/s_eqwidth_bin16_gauss2.fits'
],
'fig_rgb_soft_eqwidth.png',
vmin_r=1e-7,
vmax_r=1e-6,
stretch_r='log',
vmin_g=0,
vmax_g=800,
stretch_g='linear',
vmin_b=0,
vmax_b=800,
stretch_b='linear',
make_nans_transparent=True)
fig = plt.figure(figsize=(3, 5))
f = aplpy.FITSFigure(XMMPATH +
'/repro_merged/mg_lineflux_bin16_gauss2.fits',
figure=fig)
f.recenter(ra2deg(13, 46, 40), -62.87, width=18. / 60, height=18. / 60)
f.show_rgb('fig_rgb_soft_eqwidth.png')
format_ticks_and_labels(f, invert=False)
f.ticks.hide()
f.tick_labels.hide()
f.axis_labels.hide()
most = fits.open(XMMPATH + '/../most/G309.2-0.6.fits')
lev = [1e-2]
lev_color = 'magenta'
f.show_contour(data=most, levels=lev, colors=lev_color, alpha=0.7)
f.show_regions('regs/core.reg')
f.show_regions('regs/lobe_ne.reg')
f.show_regions('regs/lobe_sw.reg')
f.show_regions('regs/ridge_nw.reg')
f.show_regions('regs/ridge_se.reg')
f.add_label(0.52, 0.34, 'Core', relative=True, size=8, color='white')
f.add_label(0.09,
0.74,
'Lobe NE',
relative=True,
size=8,
color='white')
f.add_label(0.87,
0.75,
'Ridge NW',
relative=True,
size=8,
color='white')
f.add_label(0.10,
0.22,
'Ridge SE',
relative=True,
size=8,
color='white')
f.add_label(0.55,
0.05,
'Lobe SW',
relative=True,
size=8,
color='white')
fig.tight_layout()
fig.canvas.draw()
plt.savefig('fig_rgb_soft_eqwidth.pdf', dpi=300)
else:
raise Exception("Invalid figure number")
import time
dataset = pd.read_csv("dataset1.txt", header = None,delim_whitespace=True)
X = np.array(dataset[dataset.columns[0:dataset.shape[1]]])
x = np.array(dataset[dataset.columns[0:dataset.shape[1]-1]])
y =np.array(dataset[dataset.columns[dataset.shape[1]-1]])
from sklearn.cross_validation import train_test_split
from sklearn.cluster import KMeans
kmeans = KMeans()
kmeans = kmeans.fit(X)
k = len(kmeans.cluster_centers_)
labels = kmeans.labels_
centroids = kmeans.cluster_centers_
from matplotlib import pyplot
for i in range(k):
ds = X[np.where(labels==i)]
pyplot.plot(ds[:,0],ds[:,1],'o')
lines = pyplot.plot(centroids[i,0],centroids[i,1],'kx')
pyplot.setp(lines,ms=15.0)
print("The number of clusters are ",k)
pyplot.savefig("plot3.png")
fout.close()
# Loss variables
step_list = np.array(step_list)
train_loss_list = np.array(train_loss_list)
# for some reason, dev_loss_list.shape = [Ndev , 4]
dev_loss_list = np.array(dev_loss_list)
# Plot
plt.figure()
plt.plot(step_list, train_loss_list, label='Train')
plt.plot(step_list, dev_loss_list[:,0], label='Dev')
plt.xlabel('Step')
plt.ylabel('Loss')
plt.legend(loc = 'upper right')
plt.savefig(f'figs/channel/loss2_{seed_no}.png', bbox_inches='tight')
plt.figure()
plt.semilogx(y_test * Re, b_pred[:,0,1],'x', label='TBNN')
plt.semilogx(y_raw * Re, bij_raw[:,0,1],'-',label='DNS')
plt.ylabel(r'$b_{12}$')
plt.xlabel(r'$y^+$')
plt.legend(loc='lower left')
plt.savefig(f'figs/channel/tbnn2_log_{seed_no}.png', bbox_inches='tight')
plt.figure()
plt.plot(y_test, b_pred[:,0,1],'x', label='TBNN')
plt.plot(y_raw, bij_raw[:,0,1],'-',label='DNS')
plt.ylabel(r'$b_{12}$')
plt.xlabel(r'$y$')
def graph_sas_curve(filename, x, y, title_text, x_lab, y_lab,
x_min, x_max, y_min, y_max, **kwargs):
"""
Outputs graph of x and y to a pdf file. x and y are intended to be functions
of the magnitude of scattering vector, q, and intensity, I. Values that are
computed from the graph (outputs)
and range of R? * qfit written on graph
@type x: numpy array
@param x: Function of the scattering vector magnitude, q, used for the
x-axis of the plot.
@type y: numpy array
@param y: Function of the scattered intensity, I, used for the y-axis
of the plot.
@type x_lab: string
@param x_lab: Label for the x-axis of the plot.
@type y_lab: string
@param y_lab: Label for the y-axis of the plot.
@type x_min: float
@param x_min: Minimum value to plot on x-axis.
@type x_max: float
@param x_max: Maximum value to plot on x-axis.
@type y_min: float
@param y_min: Minimum value to plot on x-axis.
@type y_max: float
@param y_max: Maximum value to plot on x-axis.
@keyword fit_coeffs: Fit coefficients for a linear fit from a numpy polyfit
of the input x and y values.
@keyword outputs: Text of values that should be added to plot (e.g. Rg).
@keyword rq_range: Text detailing the R*q values over the range of any
fit performed on the x, y values.
@keyword mask: Numpy style mask to select points used in fit so that
these can be highlighted in the plot.
"""
fit_coeffs = kwargs.get('fitcoeffs', None)
outputs = kwargs.get('outputs', None)
rq_range = kwargs.get('rqrange', None)
mask = kwargs.get('mask', None)
# Plot the input x, y values and if provided a fit line
# output is used to display values calculated from fit (Rg, Rxs?, R?*q over
# fit values) on the plot
plt.figure(figsize=(8, 6), dpi=300)
ax = plt.subplot(111, xlabel=x_lab, ylabel=y_lab, title=title_text,
xlim=(x_min, x_max), ylim=(y_min, y_max))
plt.scatter(x, y, s=5)
for item in ([ax.title, ax.xaxis.label, ax.yaxis.label]):
item.set_fontsize(15)
ax.tick_params(axis='both', which='major', labelsize=12)
# Plot linear fit and highlight points used in its construction
if fit_coeffs is not None:
# Plot the fit line along the whole x range shown in teh plot
fitLine = np.poly1d(fit_coeffs)
x_points = np.linspace(x_min, x_max, 300)
plt.plot(x_points, fitLine(x_points))
# Highlight points used in the fit
if mask is None:
plt.scatter(x, y, s=30)
else:
plt.scatter(x[mask], y[mask], s=30)
plt.annotate(outputs + '\n' + rq_range, xy=(0.45, 0.85),
xycoords='axes fraction')
plt.savefig(filename)
def run(n_neurons=60, t=10, t_test=10, n_trains=10, n_encodes=20, n_tests=10,
f=DoubleExp(1e-3, 3e-2), f_out=DoubleExp(1e-3, 1e-1),
dt=0.001, neuron_type=LIF(), reg=1e-2, penalty=0.5, load_w=None, load_df=None):
d_ens = np.zeros((n_neurons, 1))
f_ens = f
w_ens = None
e_ens = None
w_ens2 = None
e_ens2 = None
f_smooth = DoubleExp(1e-2, 2e-1)
print('\nNeuron Type: %s'%neuron_type)
if isinstance(neuron_type, DurstewitzNeuron):
if load_w:
w_ens = np.load(load_w)['w_ens']
else:
print('Optimizing ens1 encoders')
for nenc in range(n_encodes):
print("encoding trial %s"%nenc)
stim_func1, stim_func2 = make_normed_flipped(value=1.4, t=t, N=1, f=f, seed=nenc)
data = go(d_ens, f_ens, n_neurons=n_neurons, t=t, f=f, stim_func1=stim_func1, stim_func2=stim_func2, neuron_type=neuron_type, w_ens=w_ens, e_ens=e_ens, L=True)
w_ens = data['w_ens']
e_ens = data['e_ens']
np.savez('data/multiply_w.npz', w_ens=w_ens, e_ens=e_ens)
fig, ax = plt.subplots()
sns.distplot(np.ravel(w_ens), ax=ax)
ax.set(xlabel='weights', ylabel='frequency')
plt.savefig("plots/tuning/multiply_%s_w_ens.pdf"%neuron_type)
a_ens = f_smooth.filt(data['ens'], dt=dt)
a_supv = f_smooth.filt(data['supv'], dt=dt)
for n in range(n_neurons):
fig, ax = plt.subplots(1, 1)
ax.plot(data['times'], a_supv[:,n], alpha=0.5, label='supv')
ax.plot(data['times'], a_ens[:,n], alpha=0.5, label='ens')
ax.set(ylim=((0, 40)))
plt.legend()
plt.savefig('plots/tuning/multiply_ens_nenc_%s_activity_%s.pdf'%(nenc, n))
plt.close('all')
if load_df:
load = np.load(load_df)
d_ens = load['d_ens']
d_out1 = load['d_out1']
taus_ens = load['taus_ens']
taus_out1 = load['taus_out1']
f_ens = DoubleExp(taus_ens[0], taus_ens[1])
f_out1 = DoubleExp(taus_out1[0], taus_out1[1])
else:
print('Optimizing ens1 filters and decoders')
stim_func1, stim_func2 = make_normed_flipped(value=1.2, t=t, N=n_trains, f=f, seed=0)
data = go(d_ens, f_ens, n_neurons=n_neurons, t=t*n_trains, f=f, dt=dt, neuron_type=neuron_type,
stim_func1=stim_func1, stim_func2=stim_func2, w_ens=w_ens)
d_ens, f_ens, taus_ens = df_opt(data['x'][:,0]*data['x'][:,1], data['ens'], f, dt=dt, penalty=penalty, reg=reg, name='multiply_%s'%neuron_type)
d_ens = d_ens.reshape((n_neurons, 1))
d_out1, f_out1, taus_out1 = df_opt(data['x'], data['ens'], f_out, dt=dt, name='multiply_%s'%neuron_type)
np.savez('data/multiply_%s_df.npz'%neuron_type, d_ens=d_ens, taus_ens=taus_ens, d_out1=d_out1, taus_out1=taus_out1)
times = np.arange(0, 1, 0.0001)
fig, ax = plt.subplots()
ax.plot(times, f.impulse(len(times), dt=0.0001), label=r"$f^x, \tau_1=%.3f, \tau_2=%.3f$" %(-1./f.poles[0], -1./f.poles[1]))
ax.plot(times, f_ens.impulse(len(times), dt=0.0001), label=r"$f^{ens}, \tau_1=%.3f, \tau_2=%.3f, d: %s/%s$"
%(-1./f_ens.poles[0], -1./f_ens.poles[1], np.count_nonzero(d_ens), n_neurons))
ax.set(xlabel='time (seconds)', ylabel='impulse response', ylim=((0, 10)))
ax.legend(loc='upper right')
plt.tight_layout()
plt.savefig("plots/multiply_%s_filters_ens.pdf"%neuron_type)
times = np.arange(0, 1, 0.0001)
fig, ax = plt.subplots()
ax.plot(times, f_out.impulse(len(times), dt=0.0001), label=r"$f^{out}, \tau=%.3f, \tau_2=%.3f$" %(-1./f_out.poles[0], -1./f_out.poles[1]))
ax.plot(times, f_out1.impulse(len(times), dt=0.0001), label=r"$f^{out1}, \tau_1=%.3f, \tau_2=%.3f, d: %s/%s$"
%(-1./f_out1.poles[0], -1./f_out1.poles[1], np.count_nonzero(d_out1), n_neurons))
ax.set(xlabel='time (seconds)', ylabel='impulse response', ylim=((0, 10)))
ax.legend(loc='upper right')
plt.tight_layout()
plt.savefig("plots/multiply_%s_filters_out1.pdf"%neuron_type)
a_ens = f_ens.filt(data['ens'], dt=dt)
x = f.filt(data['x'][:,0]*data['x'][:,1], dt=dt).ravel()
xhat_ens = np.dot(a_ens, d_ens).ravel()
rmse_ens = rmse(xhat_ens, x)
fig, ax = plt.subplots()
ax.plot(data['times'], x, linestyle="--", label='x')
ax.plot(data['times'], xhat_ens, label='ens, rmse=%.3f' %rmse_ens)
ax.set(xlabel='time (s)', ylabel=r'$\mathbf{x}$', title="train ens1")
plt.legend(loc='upper right')
plt.savefig("plots/multiply_%s_ens1_train.pdf"%neuron_type)
a_ens = f_out1.filt(data['ens'], dt=dt)
x_out = f_out.filt(data['x'], dt=dt)
xhat_ens_out = np.dot(a_ens, d_out1)
rmse_ens_out1 = rmse(xhat_ens_out[:,0], x_out[:,0])
rmse_ens_out2 = rmse(xhat_ens_out[:,1], x_out[:,1])
fig, ax = plt.subplots()
ax.plot(data['times'], x_out[:,0], linestyle="--", label='x_0')
ax.plot(data['times'], x_out[:,1], linestyle="--", label='x_1')
ax.plot(data['times'], xhat_ens_out[:,0], label='ens_0, rmse=%.3f' %rmse_ens_out1)
ax.plot(data['times'], xhat_ens_out[:,1], label='ens_1, rmse=%.3f' %rmse_ens_out2)
ax.set(xlabel='time (s)', ylabel=r'$\mathbf{x}$', title="train ens1")
plt.legend(loc='upper right')
plt.savefig("plots/multiply_%s_ens1_out_train.pdf"%neuron_type)
if isinstance(neuron_type, DurstewitzNeuron):
if load_w:
w_ens2 = np.load(load_w)['w_ens2']
else:
print('Optimizing ens2 encoders')
for nenc in range(n_encodes):
print("encoding trial %s"%nenc)
stim_func1, stim_func2 = make_normed_flipped(value=1.4, t=t, N=1, f=f, seed=nenc)
data = go(d_ens, f_ens, n_neurons=n_neurons, t=t, f=f, stim_func1=stim_func1, stim_func2=stim_func2, neuron_type=neuron_type, w_ens=w_ens, w_ens2=w_ens2, e_ens2=e_ens2, L2=True)
w_ens2 = data['w_ens2']
e_ens2 = data['e_ens2']
np.savez('data/multiply_w.npz', w_ens=w_ens, e_ens=e_ens, w_ens2=w_ens2, e_ens2=e_ens2)
fig, ax = plt.subplots()
sns.distplot(np.ravel(w_ens2), ax=ax)
ax.set(xlabel='weights', ylabel='frequency')
plt.savefig("plots/tuning/multiply_%s_w_ens2.pdf"%neuron_type)
a_ens = f_smooth.filt(data['ens2'], dt=dt)
a_supv = f_smooth.filt(data['supv2'], dt=dt)
for n in range(30):
fig, ax = plt.subplots(1, 1)
ax.plot(data['times'], a_supv[:,n], alpha=0.5, label='supv2')
ax.plot(data['times'], a_ens[:,n], alpha=0.5, label='ens2')
ax.set(ylim=((0, 40)))
plt.legend()
plt.savefig('plots/tuning/multiply_ens2_nenc_%s_activity_%s.pdf'%(nenc, n))
plt.close('all')
if load_df:
load = np.load(load_df)
d_out2 = load['d_out2']
taus_out2 = load['taus_out2']
f_out2 = DoubleExp(taus_out2[0], taus_out2[1])
else:
print('Optimizing ens2 filters and decoders')
stim_func1, stim_func2 = make_normed_flipped(value=1.2, t=t, N=n_trains, f=f, seed=0)
data = go(d_ens, f_ens, n_neurons=n_neurons, t=t*n_trains, f=f, dt=dt, neuron_type=neuron_type,
stim_func1=stim_func1, stim_func2=stim_func2, w_ens=w_ens, w_ens2=w_ens2)
d_out2, f_out2, taus_out2 = df_opt(data['x2'], data['ens2'], f_out, dt=dt, name='multiply_%s'%neuron_type)
np.savez('data/multiply_%s_df.npz'%neuron_type, d_ens=d_ens, taus_ens=taus_ens, d_out1=d_out1, taus_out1=taus_out1, d_out2=d_out2, taus_out2=taus_out2)
times = np.arange(0, 1, 0.0001)
fig, ax = plt.subplots()
ax.plot(times, f_out.impulse(len(times), dt=0.0001), label=r"$f^{out}, \tau=%.3f, \tau_2=%.3f$" %(-1./f_out.poles[0], -1./f_out.poles[1]))
ax.plot(times, f_out2.impulse(len(times), dt=0.0001), label=r"$f^{out2}, \tau_1=%.3f, \tau_2=%.3f, d: %s/%s$"
%(-1./f_out2.poles[0], -1./f_out2.poles[1], np.count_nonzero(d_out2), 30))
ax.set(xlabel='time (seconds)', ylabel='impulse response', ylim=((0, 10)))
ax.legend(loc='upper right')
plt.tight_layout()
plt.savefig("plots/multiply_%s_filters_out2.pdf"%neuron_type)
a_ens2 = f_out2.filt(data['ens2'], dt=dt)
x2 = f_out.filt(data['x2'], dt=dt)
xhat_ens2 = np.dot(a_ens2, d_out2)
rmse_ens2 = rmse(xhat_ens2, x2)
fig, ax = plt.subplots()
ax.plot(data['times'], x2, linestyle="--", label='x')
ax.plot(data['times'], xhat_ens2, label='ens2, rmse=%.3f' %rmse_ens2)
ax.set(xlabel='time (s)', ylabel=r'$\mathbf{x}$', title="train ens2")
plt.legend(loc='upper right')
plt.savefig("plots/multiply_%s_ens2_train.pdf"%neuron_type)
rmses_ens = np.zeros((n_tests))
rmses_ens_out = np.zeros((n_tests))
rmses_ens2 = np.zeros((n_tests))
for test in range(n_tests):
print('test %s' %test)
stim_func1, stim_func2 = make_normed_flipped(value=1.0, t=t_test, N=1, f=f, seed=100+test)
data = go(d_ens, f_ens, n_neurons=n_neurons, t=t_test, f=f, dt=dt, neuron_type=neuron_type,
stim_func1=stim_func1, stim_func2=stim_func2, w_ens=w_ens, w_ens2=w_ens2)
a_ens = f_ens.filt(data['ens'], dt=dt)
x = f.filt(data['x'][:,0]*data['x'][:,1], dt=dt).ravel()
xhat_ens = np.dot(a_ens, d_ens).ravel()
rmse_ens = rmse(xhat_ens, x)
a_ens_out = f_out1.filt(data['ens'], dt=dt)
x_out = f_out.filt(data['x'], dt=dt)
xhat_ens_out = np.dot(a_ens, d_out1)
rmse_ens_out = rmse(xhat_ens_out, x_out)
rmse_ens_out1 = rmse(xhat_ens_out[:,0], x_out[:,0])
rmse_ens_out2 = rmse(xhat_ens_out[:,1], x_out[:,1])
a_ens2 = f_out2.filt(data['ens2'], dt=dt)
x2 = f_out.filt(data['x2'], dt=dt)
xhat_ens2 = np.dot(a_ens2, d_out2)
rmse_ens2 = rmse(xhat_ens2, x2)
rmses_ens[test] = rmse_ens
rmses_ens_out[test] = rmse_ens_out
rmses_ens2[test] = rmse_ens2
fig, ax = plt.subplots()
ax.plot(data['times'], x_out[:,0], linestyle="--", label='x_0')
ax.plot(data['times'], x_out[:,1], linestyle="--", label='x_1')
ax.plot(data['times'], xhat_ens_out[:,0], label='ens_0, rmse=%.3f' %rmse_ens_out1)
ax.plot(data['times'], xhat_ens_out[:,1], label='ens_1, rmse=%.3f' %rmse_ens_out2)
ax.set(xlabel='time (s)', ylabel=r'$\mathbf{x}$', title="test ens1 out")
plt.legend(loc='upper right')
plt.savefig("plots/multiply_%s_ens1_out_test_%s.pdf"%(neuron_type, test))
fig, ax = plt.subplots()
ax.plot(data['times'], x, linestyle="--", label='x')
ax.plot(data['times'], xhat_ens, label='ens, rmse=%.3f' %rmse_ens)
ax.set(xlabel='time (s)', ylabel=r'$\mathbf{x}$', title="test ens1")
plt.legend(loc='upper right')
plt.savefig("plots/multiply_%s_ens1_test_%s.pdf"%(neuron_type, test))
fig, ax = plt.subplots()
ax.plot(data['times'], x2, linestyle="--", label='x')
ax.plot(data['times'], xhat_ens2, label='ens2, rmse=%.3f' %rmse_ens2)
ax.set(xlabel='time (s)', ylabel=r'$\mathbf{x}$', title="test ens2")
plt.legend(loc='upper right')
plt.savefig("plots/multiply_%s_ens2_test_%s.pdf"%(neuron_type, test))
plt.close('all')
mean_ens = np.mean(rmses_ens)
mean_ens_out = np.mean(rmses_ens_out)
mean_ens2 = np.mean(rmses_ens2)
CI_ens = sns.utils.ci(rmses_ens)
CI_ens_out = sns.utils.ci(rmses_ens_out)
CI_ens2 = sns.utils.ci(rmses_ens2)
fig, ax = plt.subplots()
sns.barplot(data=rmses_ens2)
ax.set(ylabel='RMSE', title="mean=%.3f, CI=%.3f-%.3f"%(mean_ens2, CI_ens2[0], CI_ens2[1]))
plt.xticks()
plt.savefig("plots/multiply_%s_rmse.pdf"%neuron_type)
print('rmses: ', rmses_ens, rmses_ens_out, rmses_ens2)
print('means: ', mean_ens, mean_ens_out, mean_ens2)
print('confidence intervals: ', CI_ens, CI_ens_out, CI_ens2)
np.savez('data/multiply_%s_results.npz'%neuron_type, rmses_ens=rmses_ens, rmses_ens_out=rmses_ens_out, rmses_ens2=rmses_ens2)
return rmses_ens2
for i in xrange(M):
plt.scatter(Xdd[i],Ydd[i],c = colors[i], facecolor='0.5', lw = 0,label = 'cluster'+str(i+1));
plt.scatter(train1[:,0],train1[:,1],c = 'k',label = 'train class 1');
plt.scatter(train2[:,0],train2[:,1],c = 'r',label = 'train class 2');
plt.xlabel('Feature 1')
plt.ylabel('Feature 2')
plt.title('Dataset5, k means clustering,iteration:'+str(iter)+'clusters = '+str(M))
plt.legend(loc='best')
plt.xlim(xx.min(), xx.max())
plt.ylim(yy.min(), yy.max())
plt.xticks(())
plt.yticks(())
plt.savefig("kmeansnormal1(b)"+str(iter)+"-"+str(M)+".png", bbox_inches='tight')
plt.close(fig)
z = np.zeros((N,M))
for n in xrange(N):
minindex = 0
minval = LA.norm(np.subtract(X_train[n],mu[0]))
for i in xrange(M):
a = LA.norm(np.subtract(X_train[n],mu[i]))
if(minval>a):
minval = a
minindex = i
z[n][minindex] = 1
newmu = np.zeros((M,size[1]))
flag = 0
n = 10
plt.figure(figsize=(20, 4))
for i in range(1, n):
# display original
ax = plt.subplot(2, n, i)
plt.imshow(x_train[i+4*13*150].reshape(32, 32, 3))
ax.get_xaxis().set_visible(False)
ax.get_yaxis().set_visible(False)
# display reconstruction
ax = plt.subplot(2, n, i + n)
plt.imshow(x_train_noisy[i+4*13*150].reshape(32, 32, 3))
ax.get_xaxis().set_visible(False)
ax.get_yaxis().set_visible(False)
plt.show()
plt.savefig('saves/cdA_gblur_noisy_vis.png')
"""Constructing the Model"""
import keras
from keras import losses
from keras.models import Model, load_model
from keras.layers import Input, Dense, Conv2D, MaxPooling2D, UpSampling2D, concatenate
L = 5 # Total number of layers
S = 2 # Number of shared layers
F = [16, 32, 64, 128, 256] # Number of clean filters including input
# Clean different encoding layers
inp = Input(shape=(32, 32, 3))
enc = inp
for i in range(L-S):
ax1.spines['bottom'].set_position(('data', 0.0))
ax1.spines['top'].set_color('none')
# buffer layer annotation
#ax1.axvspan(5.0, 30.0, ymin=0.049, alpha=1.0, color=Grey, zorder=0)
#ax1.axvline(x=5.0, color=Grey)
#ax1.axvline(x=30.0, color=Grey)
ax1.text(6.5, 0.15,
r"Buffer layer") # , color=Grey) # bbox=dict(facecolor=Grey))
ax1.annotate(s='',
xy=(5.0, 0.11),
xytext=(30.0, 0.11),
arrowprops=dict(arrowstyle='|-|',
linewidth=0.75,
shrinkA=0.0,
shrinkB=0.0,
edgecolor=Grey))
# plot mode interactive (1) or pdf (2)
if plot != 2:
plt.tight_layout()
plt.show()
else:
fig.tight_layout()
#fnam = fnam.replace(".dat", "viscous.pdf")
plt.savefig(fnamout, transparent=True)
print('Written file:', fnamout)
fig.clf()
print("Done!")
def plot(rewards):
clear_output(True)
plt.figure(figsize=(20, 5))
plt.plot(rewards)
plt.savefig('td3_lstm.png')
def _plot_and_save_attention(self, att_w, filename):
plt = self.draw_attention_plot(att_w)
plt.savefig(filename)
plt.close()
d_mean_list.append( dagger_results['returns']['mean'] )
d_std_list.append( dagger_results['returns']['std'] )
c_mean_dict[envname] = np.array(c_mean_list, dtype = np.float32)
c_std_dict[envname] = np.array(c_std_list, dtype = np.float32)
d_mean_dict[envname] = np.array(d_mean_list, dtype = np.float32)
d_std_dict[envname] = np.array(d_std_list, dtype = np.float32)
expert_results_fname = os.path.join(expert_results_folder, 'train_' + envname +'.pkl')
with open(expert_results_fname, 'rb') as f:
expert_results = pickle.loads(f.read())
e_mean = np.array(expert_results['returns']['mean'])
lines0 = plt.errorbar(x, c_mean_dict[envname], c_std_dict[envname],color='r', linewidth=2.0, label='Behavioral Cloning')
lines1 = plt.errorbar(x, d_mean_dict[envname], d_std_dict[envname], color='g', linewidth=2.0, label='Dagger')
lines2 = plt.plot(x, e_mean * np.ones_like(d_mean_dict[envname]) )
plt.setp(lines2, color='b', linewidth=2.0, label='Expert')
plt.ylabel('Reward')
plt.xlabel('# rollouts/ Dagger iterations')
plt.legend()
plt.savefig(os.path.join(out_folder,'%s.png'%(envname)), bbox_inches='tight')
plt.clf()
label=False)
ax3.set_title('d={}'.format(d_list[2]))
fig.subplots_adjust(left=None,
bottom=None,
right=None,
top=None,
wspace=None,
hspace=None)
fig.legend(loc="lower right", ncol=3)
fig.text(0.5,
0.04,
'number of iterations \n ({} pass x {} samples)'.format(1, N),
ha='center')
fig.suptitle('Sharp prior:' + r'$\sigma_0={}$'.format(sigma0))
plt.savefig('./outputs/KL_HighDim_sharpPrior')
if 'HD2' in Test:
# sensitivity to dimension with Flat prior sigma0=1
sigma0 = 30
mu0 = 0
d_list = [30, 70, 100]
N = 500
s = 2
c = 0
seed = 10
fig = plt.figure(num, figsize=set_size(ratio=0.5))
num = num + 1
ax1 = fig.add_subplot(131)
XP_HighDim(np.array([ax1]),
def main(weather_data_dir, katkam_dir):
weather_files = os.listdir(weather_data_dir)
df = pd.concat((pd.read_csv(os.path.join(weather_data_dir, f), header=14, parse_dates=['Date/Time']) for f in weather_files))
df = df[df['Weather'].notnull()]
weather_df = df[['Date/Time', 'Time', 'Weather']].copy()
images = katkam_dir + '/*.*'
x_images = io.imread_collection(images)
images = pd.DataFrame({'filename': x_images.files, 'img': np.arange(0, len(x_images.files)) })
images['Date/Time'] = pd.to_datetime(images['filename'].str.extract('-([0-9]+)\.', expand=False), format='%Y%m%d%H%M%S')
images = images.merge(weather_df, on='Date/Time')
images['Weather'] = images['Weather'].apply(transform_weather)
data = []
target = []
filenames = []
# need to do this for loop to get the images out of x_images or else we'd need to load the whole
# x_images array instead of just the images we have data for
for i, x in images.iterrows():
matrix = rgb2gray(x_images[x['img']])
matrix = np.reshape(matrix, (192*256))
data.append(matrix)
target.append(x['Weather'].split(','))
filenames.append(x['filename'])
mlb = MultiLabelBinarizer()
y_enc = mlb.fit_transform(target)
X_train, X_test, y_train, y_test, idx1, idx2 = train_test_split(np.array(data), y_enc, np.array(filenames))
model = make_pipeline(
PCA(250),
KNeighborsClassifier(n_neighbors=15)
)
model.fit(X_train, y_train)
predicted = model.predict(X_test)
print("KNN Model Score: %f" % model.score(X_test, y_test))
result = np.empty(predicted.shape[0], dtype=np.bool)
for i, (x,y) in enumerate(zip(predicted, y_test)):
result[i] = np.array_equal(x,y)
wrong = mlb.inverse_transform(predicted[~result])
real = mlb.inverse_transform(y_test[~result])
results_df = pd.DataFrame({'filename': idx2[~result], 'predicted': wrong, 'actual': real})
aggregated = results_df.groupby(['predicted', 'actual']).count().rename(columns={'filename': 'Predicted Incorrectly'})
aggregated.plot.bar()
plt.tight_layout()
plt.legend()
plt.savefig('errors.png')
correct = mlb.inverse_transform(predicted[result])
real = mlb.inverse_transform(y_test[result])
results_df = pd.DataFrame({'filename': idx2[result], 'predicted': correct, 'actual': real})
aggregated = results_df.groupby(['predicted', 'actual']).count().rename(columns={'filename': 'Predicted Correctly'})
aggregated.plot.bar()
plt.tight_layout()
plt.legend()
plt.savefig('correct.png')
ax[0].set_ylabel("Total A \n Concentration \n [mol/L]",fontsize=15)
ax[1].set_ylabel("Total A \n Sorbed Concent. \n [mol/m3]",fontsize=15)
ax[2].set_title("Langmuir and Freundlich sorption models",fontsize=15)
ax[3].set_xlabel("Distance (m)",fontsize=15)
ax[2].set_ylabel("Total B, C \n Concentration \n [mol/L]",fontsize=15)
ax[3].set_ylabel("Total B, C \n Sorbed Concent. \n [mol/m3]",fontsize=15)
ax[0].legend(loc='upper right',fontsize=10)
ax[1].legend(loc='upper right',fontsize=10)
ax[0].set_xlim(left=30,right=70)
ax[1].set_xlim(left=30,right=70)
ax[2].legend(loc='upper right',fontsize=10)
ax[3].legend(loc='upper right',fontsize=8)
ax[2].set_xlim(left=30,right=70)
ax[3].set_xlim(left=30,right=70)
# plot adjustments
plt.tight_layout()
plt.subplots_adjust(left=0.20,bottom=0.15,right=0.95,top=0.90)
plt.suptitle("Amanzi 1D "+root.title()+" Benchmark at 50 years",x=0.57,fontsize=20)
plt.tick_params(axis='both', which='major', labelsize=15)
# pyplot.show()
plt.savefig(root+"_1d.png",format="png")
# plt.close()
# finally:
# pass
for site in datasetObjects:
print site, datasetObjects[site].data
x = datasetObjects[site].getAgeValues()
y = datasetObjects[site].getElevationValues()
n = len(datasetObjects[site].getAgeValues())
plt.plot(x, y, mapSiteToColour(site) + 's', label=site+" n=%i" % n, markersize=4.0)
datasetModels[site] = siteModelConnectTheDots(datasetObjects[site])
##plt.title("Plot of Elevation by Age\nRaw Data only")
plt.ylabel('Elevation (m IGLD1985)')
plt.xlabel('Age Before Present (years)')
plt.legend(loc=2, prop={'size': 17})
plt.savefig('./theDataRaw.png')
plt.close()
############################################################################
############################################################################
## create the raw plot with the model included #############################
for ds in datasetObjects:
print ds, datasetObjects[ds].data
x = datasetObjects[ds].getAgeValues()
y = datasetObjects[ds].getElevationValues()
plt.plot(x, y, mapSiteToColour(ds) + 's', label="%s, n=%i" % (ds, len(x)), markersize=4.0)
for d in datasets:
def main():
with timer('load data'):
df = pd.read_csv(FOLD_PATH)
with timer('preprocessing'):
train_df, val_df = df[df.fold_id != FOLD_ID], df[df.fold_id == FOLD_ID]
train_augmentation = Compose([
Flip(p=0.5),
OneOf(
[
#ElasticTransform(p=0.5, alpha=120, sigma=120 * 0.05, alpha_affine=120 * 0.03),
GridDistortion(p=0.5),
OpticalDistortion(p=0.5, distort_limit=2, shift_limit=0.5)
],
p=0.5),
#OneOf([
# ShiftScaleRotate(p=0.5),
## RandomRotate90(p=0.5),
# Rotate(p=0.5)
#], p=0.5),
OneOf([
Blur(blur_limit=8, p=0.5),
MotionBlur(blur_limit=8, p=0.5),
MedianBlur(blur_limit=8, p=0.5),
GaussianBlur(blur_limit=8, p=0.5)
],
p=0.5),
OneOf(
[
#CLAHE(clip_limit=4, tile_grid_size=(4, 4), p=0.5),
RandomGamma(gamma_limit=(100, 140), p=0.5),
RandomBrightnessContrast(p=0.5),
RandomBrightness(p=0.5),
RandomContrast(p=0.5)
],
p=0.5),
OneOf([
GaussNoise(p=0.5),
Cutout(num_holes=10, max_h_size=10, max_w_size=20, p=0.5)
],
p=0.5)
])
val_augmentation = None
train_dataset = SeverDataset(train_df,
IMG_DIR,
IMG_SIZE,
N_CLASSES,
id_colname=ID_COLUMNS,
transforms=train_augmentation)
val_dataset = SeverDataset(val_df,
IMG_DIR,
IMG_SIZE,
N_CLASSES,
id_colname=ID_COLUMNS,
transforms=val_augmentation)
train_loader = DataLoader(train_dataset,
batch_size=BATCH_SIZE,
shuffle=True,
num_workers=2)
val_loader = DataLoader(val_dataset,
batch_size=BATCH_SIZE,
shuffle=False,
num_workers=2)
del train_df, val_df, df, train_dataset, val_dataset
gc.collect()
with timer('create model'):
model = smp.Unet('densenet201',
encoder_weights='imagenet',
classes=N_CLASSES)
model.to(device)
criterion = torch.nn.BCEWithLogitsLoss()
optimizer = torch.optim.Adam(model.parameters(), lr=3e-4)
scheduler_cosine = CosineAnnealingLR(optimizer,
T_max=CLR_CYCLE,
eta_min=3e-5)
scheduler = GradualWarmupScheduler(optimizer,
multiplier=1.1,
total_epoch=CLR_CYCLE * 2,
after_scheduler=scheduler_cosine)
model, optimizer = amp.initialize(model,
optimizer,
opt_level="O1",
verbosity=0)
with timer('train'):
train_losses = []
valid_losses = []
best_model_loss = 999
best_model_ep = 0
checkpoint = 0
for epoch in range(1, EPOCHS + 1):
if epoch % (CLR_CYCLE * 2) == 0:
if epoch != 0:
y_val = y_val.reshape(-1, N_CLASSES, IMG_SIZE[0],
IMG_SIZE[1])
best_pred = best_pred.reshape(-1, N_CLASSES, IMG_SIZE[0],
IMG_SIZE[1])
for i in range(N_CLASSES):
th, score, _, _ = search_threshold(
y_val[:, i, :, :], best_pred[:, i, :, :])
LOGGER.info(
'Best loss: {} Best Dice: {} on epoch {} th {} class {}'
.format(round(best_model_loss, 5), round(score, 5),
best_model_ep, th, i))
checkpoint += 1
best_model_loss = 999
LOGGER.info("Starting {} epoch...".format(epoch))
tr_loss = train_one_epoch(model, train_loader, criterion,
optimizer, device)
train_losses.append(tr_loss)
LOGGER.info('Mean train loss: {}'.format(round(tr_loss, 5)))
valid_loss, val_pred, y_val = validate(model, val_loader,
criterion, device)
valid_losses.append(valid_loss)
LOGGER.info('Mean valid loss: {}'.format(round(valid_loss, 5)))
scheduler.step()
if valid_loss < best_model_loss:
torch.save(
model.state_dict(),
'{}_fold{}_ckpt{}.pth'.format(EXP_ID, FOLD_ID, checkpoint))
best_model_loss = valid_loss
best_model_ep = epoch
best_pred = val_pred
del val_pred
gc.collect()
with timer('eval'):
y_val = y_val.reshape(-1, N_CLASSES, IMG_SIZE[0], IMG_SIZE[1])
best_pred = best_pred.reshape(-1, N_CLASSES, IMG_SIZE[0], IMG_SIZE[1])
for i in range(N_CLASSES):
th, score, _, _ = search_threshold(y_val[:, i, :, :],
best_pred[:, i, :, :])
LOGGER.info(
'Best loss: {} Best Dice: {} on epoch {} th {} class {}'.
format(round(best_model_loss, 5), round(score, 5),
best_model_ep, th, i))
xs = list(range(1, len(train_losses) + 1))
plt.plot(xs, train_losses, label='Train loss')
plt.plot(xs, valid_losses, label='Val loss')
plt.legend()
plt.xticks(xs)
plt.xlabel('Epochs')
plt.savefig("loss.png")
def get_thresholds(in_dat,
interactive=False,
plot_events=False,
fig_path=None,
prefix=None):
"""Guess distance threshold for event filtering
Analyse the events in the first million of Hi-C pairs in the library, plot
the occurrences of each event type according to number of restriction
fragments, and ask user interactively for the minimum threshold for uncuts
and loops.
Parameters
----------
in_dat: str
Path to the .pairs file containing Hi-C pairs.
interactive: bool
If True, plots are diplayed and thresholds are required interactively.
plot_events : bool
Whether to show the plot
fig_path : str
Path where the figure will be saved. If None, the figure will be
diplayed interactively.
prefix : str
If the library has a name, it will be shown on plots.
Returns
-------
dictionary
dictionary with keys "uncuts" and "loops" where the values are the
corresponding thresholds entered by the user.
"""
thr_uncut = None
thr_loop = None
max_sites = 50
# Map of event -> legend name of event for intrachromosomal pairs.
legend = {
"++": "++ (weird)",
"--": "-- (weird)",
"+-": "+- (uncuts)",
"-+": "-+ (loops)",
}
colors = {"++": "#222222", "+-": "r", "--": "#666666", "-+": "tab:orange"}
n_events = {event: np.zeros(max_sites) for event in legend}
i = 0
# open the file for reading (just the first 1 000 000 lines)
with open(in_dat, "r") as pairs:
for line in pairs:
# Skip header lines
if line.startswith("#"):
continue
i += 1
# Only use the first million pairs to estimate thresholds
if i == 1000000:
break
# Process Hi-C pair into a dictionary
p = process_read_pair(line)
# Type of event and number of restriction site between reads
etype = p["type"]
nsites = p["nsites"]
# Count number of events for intrachrom pairs
if etype != "inter" and nsites < max_sites:
n_events[etype][nsites] += 1
def plot_event(n_events, legend, name):
"""Plot the frequency of a given event types over distance."""
plt.xlim([-0.5, 15])
plt.plot(
range(n_events[name].shape[0]),
n_events[name],
"o-",
label=legend[name],
linewidth=2.0,
c=colors[name],
)
if interactive:
# PLot:
try:
plt.figure(0)
for event in legend:
plot_event(n_events, legend, event)
plt.grid()
plt.xlabel("Number of restriction fragment(s)")
plt.ylabel("Number of events")
plt.yscale("log")
plt.legend()
plt.show(block=False)
except Exception:
logger.error(
"Unable to show plots, skipping figure generation. Perhaps "
"there is no Xserver running ? (might be due to windows "
"environment). Try running without the interactive option.")
# Asks the user for appropriate thresholds
print(
"Please enter the number of restriction fragments separating "
"reads in a Hi-C pair below or at which loops and "
"uncuts events will be excluded\n",
file=sys.stderr,
)
thr_uncut = int(input("Enter threshold for the uncuts events (+-):"))
thr_loop = int(input("Enter threshold for the loops events (-+):"))
try:
plt.clf()
except Exception:
pass
else:
# Estimate thresholds from data
for event in n_events:
fixed = n_events[event]
fixed[fixed == 0] = 1
n_events[event] = fixed
all_events = np.log(np.array(list(n_events.values())))
# Compute median occurences at each restriction sites
event_med = np.median(all_events, axis=0)
# Compute MAD, to have a robust estimator of the expected deviation
# from median at long distances
mad = np.median(abs(all_events - event_med))
exp_stdev = mad / 0.67449
# Iterate over sites, from furthest to frag+2
for site in range(max_sites)[:1:-1]:
# For uncuts and loops, keep the last (closest) site where the
# deviation from other events <= expected_stdev
if (abs(np.log(n_events["+-"][site]) - event_med[site]) <=
exp_stdev):
thr_uncut = site
if (abs(np.log(n_events["-+"][site]) - event_med[site]) <=
exp_stdev):
thr_loop = site
if thr_uncut is None or thr_loop is None:
raise ValueError(
"The threshold for loops or uncut could not be estimated. "
"Please try running with -i to investigate the problem.")
logger.info("Filtering with thresholds: uncuts={0} loops={1}".format(
thr_uncut, thr_loop))
if plot_events:
try:
plt.figure(1)
plt.xlim([-0.5, 15])
# Draw colored lines for events to discard
plt.plot(
range(0, thr_uncut + 1),
n_events["+-"][:thr_uncut + 1],
"o-",
c=colors["+-"],
label=legend["+-"],
)
plt.plot(
range(0, thr_loop + 1),
n_events["-+"][:thr_loop + 1],
"o-",
c=colors["-+"],
label=legend["-+"],
)
plt.plot(
range(0, 2),
n_events["--"][:2],
"o-",
c=colors["--"],
label=legend["--"],
)
plt.plot(
range(0, 2),
n_events["++"][:2],
"o-",
c=colors["++"],
label=legend["++"],
)
# Draw black lines for events to keep
plt.plot(
range(thr_uncut, n_events["+-"].shape[0]),
n_events["+-"][thr_uncut:],
"o-",
range(thr_loop, n_events["-+"].shape[0]),
n_events["-+"][thr_loop:],
"o-",
range(1, n_events["--"].shape[0]),
n_events["--"][1:],
"o-",
range(1, n_events["++"].shape[0]),
n_events["++"][1:],
"o-",
label="kept",
linewidth=2.0,
c="g",
)
plt.grid()
plt.xlabel("Number of restriction site(s)")
plt.ylabel("Number of events")
plt.yscale("log")
# Remove duplicate "kept" entries in legend
handles, labels = plt.gca().get_legend_handles_labels()
by_label = OrderedDict(zip(labels, handles))
plt.legend(by_label.values(), by_label.keys())
# Show uncut and loop threshold as vertical lines
plt.axvline(x=thr_loop, color=colors["-+"])
plt.axvline(x=thr_uncut, color=colors["+-"])
if prefix:
plt.title(
"Library events by distance in {}".format(prefix))
plt.tight_layout()
if fig_path:
plt.savefig(fig_path)
else:
plt.show(block=False)
# plt.clf()
except Exception:
logger.error(
"Unable to show plots, skipping figure generation. Is "
"an X server running? (might be due to windows "
"environment). Try running without the plot option.")
return thr_uncut, thr_loop
def plotGradientConfidenceIntervals(giaRegressionsByCombo, keys, giaRegressionDescriptions, outputPathDict):
def plotInterval(ax, y, xstart, xstop, intervalLabel, colord, colords):
"""Plot interval at y from xstart to xstop with given color."""
ax.hlines(y, xstart, xstop, colords, lw=7)
ax.hlines(y, xstart, xstop, colord, lw=3, label=intervalLabel)
## plots the interval in the colours of both sites
outputPath = convertListToRelativePath([outputPathDict[setting] for setting in getCurrentSettingOptions()])
y = 0
## used in spacing out the intervals for each site vertically through the
## graph
fig,ax = plt.subplots(1)
for combo in keys:
y += 1
combo1 = combo.split('-')[0]
combo2 = combo.split('-')[1].split(':')[0]
order = combo.split('-')[1].split(':')[1]
if(order == 'forward'):
direct = combo1
modelled = combo2
else:
direct = combo2
modelled = combo1
est = giaRegressionsByCombo[combo]['gradientEstimator']
ciStart = giaRegressionsByCombo[combo]['gradient'][0]
ciEnd = giaRegressionsByCombo[combo]['gradient'][1]
if(est < 0):
est = -est
ciStart = -ciStart
ciEnd = -ciEnd
if(order == 'forward'):
plotInterval(ax, y, ciStart, ciEnd, "", mapSiteToColour(direct), mapSiteToColour(modelled))
else:
plotInterval(ax, y, ciStart, ciEnd, "", mapSiteToColour(direct), mapSiteToColour(modelled))
ax.vlines(est, y+0.3, y-0.3, mapSiteToColour(direct), lw=4)
ax.set_xlabel('GIA (m/year)')
ax.set_xlim([0,0.009])
plt.yticks(list(np.arange(1, len(keys)+1, 1.0)), [giaRegressionDescriptions[key] for key in keys], rotation=0)
fileNameIdentifier = "_".join([outputPathDict[setting] for setting in getCurrentSettingOptions()])
plt.title("95p Confidence intervals on GIA\nfilters: %s" % fileNameIdentifier)
for item in ax.get_yticklabels():
item.set_fontsize(8)
outputFilePath = filePathOnRelativePath(outputPath+"gias/", fileName='intervals', ext="png")
print "Saving gia intervals plot at '%s'" % outputFilePath
verifyPath(outputPath+"gias/")
plt.savefig(outputFilePath,bbox_inches='tight')
outputFilePath = filePathOnRelativePath(outputPath+"gias/", fileName='%s_intervals' % fileNameIdentifier, ext="png")
print "Saving gia intervals plot at '%s'" % outputFilePath
plt.savefig(outputFilePath,bbox_inches='tight')
plt.close()
gamma : float
Width of Lorententzian component
kt : float
Thermal energy. If >0, will compute transitions from vibrationally
excited states. Default 0.
n_max : int
Largest vibrational number in final manifold. If not supplied, a guess
is provided, but may not be adequate.
m_max : int
Largest vibrational number in orginal manifold. If not supplied, a guess
is provided, but may not be adequate.
"""
return amp*vibronic_ls(-x+x0, s, sigma, gamma, e_vib, kt=kt, **kw)
x = np.linspace(1.8, 2.5, 1000)
e0 = 2.17
s = 0.5
sigma = 0.01
gamma = 0.001
e_vib = 0.07
y1 = vibronic_emission(x, 1, e0, s, sigma, gamma, e_vib, 0)
y2 = vibronic_emission(x, 1, e0, s, sigma, gamma, e_vib, 0.025)
y3 = vibronic_emission(x, 1, e0, s, sigma, gamma, e_vib, 0.2)
plt.figure()
plt.plot(x, y1, label="kT=0")
plt.plot(x, y2, label="kT=RT")
plt.plot(x, y3, label="kT=200 meV")
plt.legend()
plt.savefig("fc_emission.png", dpi=150)
def filter_events(
in_dat,
out_filtered,
thr_uncut,
thr_loop,
plot_events=False,
fig_path=None,
prefix=None,
):
"""Filter events (loops, uncuts and weirds)
Filter out spurious intrachromosomal Hi-C pairs from input file. +- pairs
with reads closer or at the uncut threshold and -+ pairs with reads closer
or at the loop thresholds are excluded from the ouput file. -- and ++ pairs
with both mates on the same fragments are also discarded. All others are
written.
Parameters
----------
in_dat : file object
File handle in read mode to the 2D BED file containing Hi-C pairs.
out_filtered : file object
File handle in write mode the output filtered 2D BED file.
thr_uncut : int
Minimum number of restriction sites between reads to keep an
intrachromosomal +- pair.
thr_loop : int
Minimum number of restriction sites between reads to keep an
intrachromosomal -+ pair.
plot_events : bool
If True, a plot showing the proportion of each type of event will be
shown after filtering.
fig_path : str
Path where the figure will be saved. If None, figure is displayed
interactively.
prefix : str
If the library has a name, it will be shown on plots.
"""
n_uncuts = 0
n_loops = 0
n_weirds = 0
lrange_intra = 0
lrange_inter = 0
# open the files for reading and writing
with open(in_dat, "r") as pairs, open(out_filtered, "w") as filtered:
for line in pairs: # iterate over each line
# Copy header lines to output
if line.startswith("#"):
filtered.write(line)
continue
p = process_read_pair(line)
line_to_write = ("\t".join(
map(
str,
(
p["readID"],
p["chr1"],
p["pos1"],
p["chr2"],
p["pos2"],
p["strand1"],
p["strand2"],
p["frag1"],
p["frag2"],
),
)) + "\n")
if p["chr1"] == p["chr2"]:
# Do not report ++ and -- pairs on the same fragment (impossible)
if p["frag1"] == p["frag2"] and p["strand1"] == p["strand2"]:
n_weirds += 1
elif p["nsites"] <= thr_loop and p["type"] == "-+":
n_loops += 1
elif p["nsites"] <= thr_uncut and p["type"] == "+-":
n_uncuts += 1
else:
lrange_intra += 1
filtered.write(line_to_write)
if p["chr1"] != p["chr2"]:
lrange_inter += 1
filtered.write(line_to_write)
if lrange_inter > 0:
ratio_inter = round(
100 * lrange_inter / float(lrange_intra + lrange_inter), 2)
else:
ratio_inter = 0
# Log quick summary of operation results
kept = lrange_intra + lrange_inter
discarded = n_loops + n_uncuts + n_weirds
total = kept + discarded
logger.info("Proportion of inter contacts: {0}% (intra: {1}, "
"inter: {2})".format(ratio_inter, lrange_intra, lrange_inter))
logger.info(
"{0} pairs discarded: Loops: {1}, Uncuts: {2}, Weirds: {3}".format(
discarded, n_loops, n_uncuts, n_weirds))
logger.info("{0} pairs kept ({1}%)".format(
kept, round(100 * kept / (kept + discarded), 2)))
# Visualize summary if requested by user
if plot_events:
try:
# Plot: make a square figure and axes to plot a pieChart:
plt.figure(2, figsize=(6, 6))
# The slices will be ordered and plotted counter-clockwise.
fracs = [n_uncuts, n_loops, n_weirds, lrange_intra, lrange_inter]
# Format labels to include event names and proportion
labels = list(
map(
lambda x: (x[0] + ": %.2f%%") % (100 * x[1] / total),
[
("Uncuts", n_uncuts),
("Loops", n_loops),
("Weirds", n_weirds),
("3D intra", lrange_intra),
("3D inter", lrange_inter),
],
))
colors = ["salmon", "lightskyblue", "yellow", "palegreen", "plum"]
patches, _ = plt.pie(fracs, colors=colors, startangle=90)
plt.legend(patches, labels, loc=2)
if prefix:
plt.title(
"Distribution of library events in {}".format(prefix),
bbox={
"facecolor": "1.0",
"pad": 5
},
)
plt.text(
0.3,
1.15,
"Threshold Uncuts =" + str(thr_uncut),
fontdict=None,
withdash=False,
)
plt.text(
0.3,
1.05,
"Threshold Loops =" + str(thr_loop),
fontdict=None,
withdash=False,
)
plt.text(
-1.5,
-1.2,
"Total number of reads =" + str(total),
fontdict=None,
withdash=False,
)
plt.text(
-1.5,
-1.3,
"Ratio inter/(intra+inter) =" + str(ratio_inter) + "%",
fontdict=None,
withdash=False,
)
percentage = round(
100 * float(lrange_inter + lrange_intra) /
(n_loops + n_uncuts + n_weirds + lrange_inter + lrange_intra))
plt.text(
-1.5,
-1.4,
"selected reads = {0}%".format(percentage),
fontdict=None,
withdash=False,
)
if fig_path:
plt.savefig(fig_path)
else:
plt.show()
plt.clf()
except Exception:
logger.error(
"Unable to show plots. Perhaps there is no Xserver running ?"
"(might be due to windows environment) skipping figure "
"generation.")
import numpy
import matplotlib.pyplot as plt
x = numpy.linspace(-3, 3, 100)
y1 = numpy.sin(x)
y2 = numpy.exp(x)
plt.plot(x, y1, color="green", marker="o")
plt.plot(x, y2, color="blue", marker="+", linewidth=3, linestyle="None")
plt.xlabel("argumenty")
plt.ylabel("wartości")
plt.legend(["sin(x)", "exp(x)"])
plt.ylim([-1, 1])
plt.savefig("wykresik.png")
plt.show()
from q30 import read_wakati
from collections import Counter
import matplotlib.pyplot as plt
from matplotlib.font_manager import FontProperties
wakati_list = read_wakati()
words = Counter([wakati['surface'] for sentence in wakati_list for wakati in sentence]).most_common()
words_cnt = [int(word[1]) for word in words]
words_ctx = [word[0] for word in words]
plt.hist(words_cnt, bins=50, range=(0, 50))
plt.savefig('fig38.jpg')
###########
# 模範解答 #
###########
from collections import Counter
import matplotlib.pyplot as plt
from q30 import get_neko_morphemes
morphemes_list = get_neko_morphemes()
words = Counter([morpheme["base"] for morphemes in morphemes_list for morpheme in morphemes]).most_common()
_, word_count = list(zip(*words))
plt.rcParams["font.family"] = "IPAexGothic"
plt.hist(word_count, bins=50, range=(1, 50))
plt.savefig("fig38.png")
def plot():
import matplotlib.pyplot as plt
with open('results.pkl') as f:
results, parser, initial_hypergrad = pickle.load(f)
# ----- Nice versions of Alpha and beta schedules for paper -----
fig = plt.figure(0)
fig.clf()
ax = fig.add_subplot(411)
#ax.set_title('Alpha learning curves')
for cur_results, name in zip(results['log_alphas'][-1].T, parser.names):
if name[0] == 'weights':
ax.plot(np.exp(cur_results), 'o-', label=name)
#ax.set_xlabel('Learning Iteration', fontproperties='serif')
low, high = ax.get_ylim()
ax.set_ylim([0, high])
ax.set_ylabel('Step size', fontproperties='serif')
ax.set_xticklabels([])
ax.legend(numpoints=1,
loc=1,
frameon=False,
bbox_to_anchor=(1.0, 0.5),
prop={
'family': 'serif',
'size': '12'
})
ax = fig.add_subplot(412)
#ax.set_title('Alpha learning curves')
for cur_results, name in zip(results['invlogit_betas'][-1].T,
parser.names):
if name[0] == 'weights':
ax.plot(logit(cur_results), 'o-', label=name)
low, high = ax.get_ylim()
ax.set_ylim([0, 1])
ax.set_xlabel('Learning Iteration', fontproperties='serif')
ax.set_ylabel('Momentum', fontproperties='serif')
ax = fig.add_subplot(413)
#ax.set_title('Alpha learning curves')
for cur_results, name in zip(results['log_alphas'][-1].T, parser.names):
if name[0] == 'biases':
ax.plot(np.exp(cur_results), 'o-', label=name)
#ax.set_xlabel('Learning Iteration', fontproperties='serif')
low, high = ax.get_ylim()
ax.set_ylim([0, high])
ax.set_ylabel('Step size', fontproperties='serif')
ax.set_xticklabels([])
ax.legend(numpoints=1,
loc=1,
frameon=False,
bbox_to_anchor=(1.0, 0.5),
prop={
'family': 'serif',
'size': '12'
})
ax = fig.add_subplot(414)
#ax.set_title('Alpha learning curves')
for cur_results, name in zip(results['invlogit_betas'][-1].T,
parser.names):
if name[0] == 'biases':
ax.plot(logit(cur_results), 'o-', label=name)
low, high = ax.get_ylim()
ax.set_ylim([0, 1])
ax.set_xlabel('Learning Iteration', fontproperties='serif')
ax.set_ylabel('Momentum', fontproperties='serif')
fig.set_size_inches((6, 8))
#plt.show()
plt.savefig('alpha_beta_paper.png')
plt.savefig('alpha_beta_paper.pdf', pad_inches=0.05, bbox_inches='tight')
fig.clf()
fig.set_size_inches((6, 8))
# ----- Primal learning curves -----
ax = fig.add_subplot(311)
ax.set_title('Primal learning curves')
for i, y in enumerate(results['learning_curves']):
ax.plot(y['learning_curve'], 'o-', label='Meta iter {0}'.format(i))
ax.set_xlabel('Epoch number')
ax.set_ylabel('Negative log prob')
#ax.legend(loc=1, frameon=False)
ax = fig.add_subplot(312)
ax.set_title('Meta learning curves')
losses = ['train_loss', 'valid_loss', 'tests_loss']
for loss_type in losses:
ax.plot(results[loss_type], 'o-', label=loss_type)
ax.set_xlabel('Meta iter number')
ax.set_ylabel('Negative log prob')
ax.legend(loc=1, frameon=False)
ax = fig.add_subplot(313)
ax.set_title('Meta-gradient magnitude')
ax.plot(results['meta_grad_magnitude'],
'o-',
label='Meta-gradient magnitude')
ax.plot(results['meta_grad_angle'], 'o-', label='Meta-gradient angle')
ax.set_xlabel('Meta iter number')
ax.set_ylabel('Meta-gradient Magnitude')
ax.legend(loc=1, frameon=False)
plt.savefig('learning_curves.png')
# ----- Learning curve info -----
fig.clf()
ax = fig.add_subplot(311)
ax.set_title('Primal learning curves')
for i, y in enumerate(results['learning_curves']):
ax.plot(y['grad_norm'], 'o-', label='Meta iter {0}'.format(i))
ax.set_xlabel('Epoch number')
#ax.legend(loc=1, frameon=False)
ax.set_title('Grad norm')
ax = fig.add_subplot(312)
for i, y in enumerate(results['learning_curves']):
ax.plot(y['weight_norm'], 'o-', label='Meta iter {0}'.format(i))
ax.set_xlabel('Epoch number')
ax.legend(loc=1, frameon=False)
ax.set_title('Weight norm')
ax = fig.add_subplot(313)
for i, y in enumerate(results['learning_curves']):
ax.plot(y['velocity_norm'], 'o-', label='Meta iter {0}'.format(i))
ax.set_xlabel('Epoch number')
ax.set_title('Velocity norm')
ax.legend(loc=1, frameon=False)
plt.savefig('extra_learning_curves.png')
# ----- Alpha and beta schedules -----
fig.clf()
ax = fig.add_subplot(211)
ax.set_title('Alpha learning curves')
for i, y in enumerate(results['log_alphas']):
ax.plot(y, 'o-', label="Meta iter {0}".format(i))
ax.set_xlabel('Primal iter number')
#ax.set_ylabel('Log alpha')
ax.legend(loc=1, frameon=False)
ax = fig.add_subplot(212)
ax.set_title('Beta learning curves')
for y in results['invlogit_betas']:
ax.plot(y, 'o-')
ax.set_xlabel('Primal iter number')
ax.set_ylabel('Inv logit beta')
plt.savefig('alpha_beta_curves.png')
# ----- Init scale and L2 reg -----
fig.clf()
ax = fig.add_subplot(211)
ax.set_title('Init scale learning curves')
for i, y in enumerate(zip(*results['log_param_scale'])):
if parser.names[i][0] == 'weights':
ax.plot(y, 'o-', label=parser.names[i])
ax.set_xlabel('Meta iter number')
ax.set_ylabel('Log param scale')
ax.legend(loc=1, frameon=False)
ax = fig.add_subplot(212)
ax.set_title('Init scale learning curves')
for i, y in enumerate(zip(*results['log_param_scale'])):
if parser.names[i][0] == 'biases':
ax.plot(y, 'o-', label=parser.names[i])
ax.set_xlabel('Meta iter number')
ax.set_ylabel('Log param scale')
ax.legend(loc=1, frameon=False)
plt.savefig('scale_and_reg.png')
# Pressure at transit radius as function of wavelength:
sigma = 3.0 # Gauss-convolve for better-looking plots
p = sip.interp1d(rad1[::-1], press[::-1])
pt1 = p(gaussf(rp1, sigma))
p = sip.interp1d(rad2[::-1], press[::-1])
pt2 = p(gaussf(rp2, sigma))
p = sip.interp1d(rad3[::-1], press[::-1])
pt3 = p(gaussf(rp3, sigma))
# Photospheric pressure modulation spectrum:
lw = 1.5
plt.figure(-25)
plt.clf()
ax = plt.subplot(111)
plt.semilogy(1e4/pyrat.spec.wn, pt3, lw=lw, color="orange",
label=r"$100\times\,{\rm solar}$")
plt.semilogy(1e4/pyrat.spec.wn, pt2, lw=lw, color="sienna",
label=r"$1.0\times\,{\rm solar}$")
plt.semilogy(1e4/pyrat.spec.wn, pt1, lw=lw, color="k",
label=r"$0.1\times\,{\rm solar}$")
plt.axvspan(0.74, 1.01, color="0.80")
plt.xlim(0.5, 1.2)
plt.ylim(3, 3e-7)
plt.legend(loc="upper right", fontsize=15)
plt.ylabel(r"$\rm Pressure\ \ (bar)$", fontsize=16)
plt.xlabel(r"$\rm Wavelength\ \ (um)$", fontsize=16)
plt.savefig("../plots/WASP49b_clear_spectra.ps")
#%%
pnl[['yhat_lstm_1','y']].plot(figsize=(20,10))
#%%
sample_yhat = pnl[['yhat_lstm_0','yhat_lstm_1']].values
y_raw = pnl.y.values
#%%
plt.figure(figsize=(10,5))
sns.distplot(y_raw[sample_yhat.argmax(axis=1)==1],color="r",bins=30,kde=True)
sns.distplot(y_raw[sample_yhat.argmax(axis=1)==0],color="b",bins=30,kde=True)
plt.savefig("HIGH_CHG_7")
plt.show()
#%%
from importlib import reload
import model.DataReg as DR
# reload(model.DataReg)
dr = DR.DataReg()
x0,ks = dr.plotROC(sample_yhat[:,1],pnl.y.apply(lambda x: 1 if x>=0 else 0).values)
#%%
x0
opt = Adam(lr=INIT_LR, decay=INIT_LR/EPOCHS)
model.compile(loss="binary_crossentropy", optimizer=opt, metrics=["accuracy"])
#train model
print("[INFO] training model...")
H = model.fit_generator(aug.flow(trainX, trainY, batch_size=BS), validation_data=(testX,testY), steps_per_epoch=len(trainX) // BS, epochs = EPOCHS, verbose=1)
#save the model to disk
print("[INFO] serializing network...")
model.save(args["model"])
# save the label binarizer to disk
print("[INFO] serializing label binarizer...")
f = open(args["labelbin"], "wb")
f.write(pickle.dumps(lb))
f.close()
#plot the training loss and accuracy
plt.style.use("ggplot")
plt.figure()
N = EPOCHS
plt.plot(np.arange(0,N), H.history["loss"], label="train_loss")
plt.plot(np.arange(0,N), H.history["val_loss"], label="val_loss")
plt.plot(np.arange(0,N), H.history["acc"], label="train_acc")
plt.plot(np.arange(0,N), H.history["val_acc"], label="val_acc")
plt.title("Training Loss and Accuracy")
plt.xlabel("Epochs #")
plt.ylabel("Loss/Accuracy")
plt.legend(loc="upper left")
plt.savefig(args["plot"])
data_list_2 = list()
# fig = plt.figure()
fig2 = plt.figure()
# ax = fig.add_subplot(111)
ax = fig2.add_subplot(121)
ax2 = fig2.add_subplot(122)
# for path in paths_list:
for pb_path, shu_path in zip(paths, paths_2):
no, pb, legend = calculate_graph_data(pb_path)
esfe, shu, seg = calculate_graph_data(shu_path)
#legend_str = path[0].split('/')[-1]
#legend = legend_str.split('_')[0]
ax.plot(shu[0], shu[1])
ax2.plot(pb[0], pb[1])
#plt.xlim((-0.6,0))
#plt.ylim((-0.06, 0.02))
#plt.legend(loc = 'lower right')
#plt.title('E.coli MG1655 Pseudo starting at 10^5 CFU/ml after 5 hours Incubation with 1mM Resazurin')
ax.set_xlabel('Voltage vs AgAgCl (V)')
ax.set_ylabel('Current (mA)')
ax2.set_xlabel('Voltage vs AgAgCl (V)')
plt.savefig(os.path.join(directory2, 'MB_ITO_17-5-17.png'), dpi=300)
plt.show()
print "total time", time.time() - start_time
print "Surface temperatures:", surface_temperatures
print "Luminosities:", stars_luminosities
print "Masses:", stars_masses
print "Radii:", stars_radii
plt.figure(1)
plt.plot(surface_temperatures, stars_luminosities)
plt.xscale('log')
plt.yscale('log')
plt.gca().invert_xaxis()
plt.xlabel('Surface Temperatures (K)')
plt.ylabel('Luminosity ($L/L_{sun}$)')
plt.title('Main Sequence: Hertzsprung-Russell Diagram')
plt.savefig("main_sequence.png")
plt.figure(2)
plt.plot(stars_masses, stars_luminosities, '.')
#plt.xscale('log')
plt.yscale('log')
plt.gca().invert_xaxis()
plt.xlabel('Masses ($M/M_{sun}$)')
plt.ylabel('Luminosity ($L/L_{sun}$)')
plt.title('Main Sequence: Luminosity versus Mass')
plt.savefig("main_sequence_luminosities_masses.png")
plt.figure(3)
plt.plot(stars_masses, stars_radii, '.')
#plt.xscale('log')
#plt.yscale('log')
