def line_pie_chart():
"""円グラフを画像として作成するためのメソッド"""
data = [1011, 530, 355, 200, 40, 11]
label = [
'hoge(' + str(1011) + ')', 'fuga(' + str(530) + ')',
'piyo(' + str(355) + ')', 'pugya(' + str(200) + ')',
'dododododododo(' + str(40) + ')', 'ga(' + str(11) + ')'
]
###綺麗に書くためのおまじない###
plt.style.use('ggplot')
plt.rcParams.update({'font.size': 15})
###各種パラメータ###
size = (9, 5) # 凡例を配置する関係でsizeは横長にしておきます。(横9、縦5)
col = cm.Spectral(np.arange(len(data)) /
float(len(data))) # color指定はcolormapから好みのものを。
###pie###
plt.figure(figsize=size, dpi=100)
plt.pie(data,
colors=col,
counterclock=False,
startangle=90,
autopct=lambda p: '{:.1f}%'.format(p) if p >= 5 else '')
plt.subplots_adjust(left=0, right=0.7)
plt.legend(label,
fancybox=True,
loc='center left',
bbox_to_anchor=(0.9, 0.5))
plt.axis('equal')
plt.savefig('../../config/img/figure.png',
bbox_inches='tight',
pad_inches=0.05)
def plot_pcoords(df, labels, tag, path_to_plot):
columns_to_drop = [col for col in df.columns if col not in labels]
df = df.drop(axis=1, labels=columns_to_drop)
_, axes = plt.subplots(ncols=len(labels) - 1,
sharey=False,
figsize=(20, 8))
for i, ax in enumerate(axes):
for ix in df.index:
ax.plot(
[0, 1],
df.loc[ix, labels[i]:labels[i + 1]].astype(float),
c=cm.Spectral(df.loc[ix, "Value"]),
)
ax.set_xlim((0, 1))
ax.set_ylim((-0.05, 1.05))
try:
label = labels[i].split("_")[1]
except:
label = labels[i]
ax.set_xticklabels([label])
ax = plt.twinx(axes[-1])
ax.set_xticks([0, 1])
ax.set_ylim((-0.05, 1.05))
ax.set_xlim((0, 1))
ax.set_xticklabels([labels[-2], labels[-1]])
plt.subplots_adjust(wspace=0)
plt.savefig(f"{path_to_plot}/pcoords_{tag}.pdf")
plt.close()
def Draw(silhouette_avg, sample_silhouette_values, X, y, k):
# 创建一个 subplot with 1-row 2-column
fig, ax1 = plt.subplots(1)
fig.set_size_inches(18, 7)
# 第一个 subplot 放轮廓系数点
# 范围是[-1, 1]
ax1.set_xlim([-0.1, 1])
# 后面的 (k + 1) * 10 是为了能更明确的展现这些点
ax1.set_ylim([0, len(X) + (k + 1)])
y_lower = 0
for i in range(k): # 分别遍历这几个聚类
ith_cluster_silhouette_values = sample_silhouette_values[y == i]
ith_cluster_silhouette_values.sort()
size_cluster_i = ith_cluster_silhouette_values.shape[0]
y_upper = y_lower + size_cluster_i
color = cm.Spectral(float(i) / k) # 搞一款颜色
ax1.fill_betweenx(np.arange(y_lower, y_upper),
0,
ith_cluster_silhouette_values,
facecolor=color,
edgecolor=color,
alpha=0.7) # 这个系数不知道干什么的
# 在轮廓系数点这里加上聚类的类别号
ax1.text(-0.05, y_lower + 0.5 * size_cluster_i, str(i))
# 计算下一个点的 y_lower y轴位置
y_lower = y_upper
# 在图里搞一条垂直的评论轮廓系数虚线
ax1.axvline(x=silhouette_avg, color='red', linestyle="--")
plt.show()
def silhouette(Ks, km, df, output_path):
score_file = Path(output_path, 'sil_avg.txt')
silfile = open(score_file,
'w') # save the average silhouette score for all clusters
# following lists all indexed by k
kmeans = [km0.fit(df) for km0 in km]
labels = [m.labels_ for m in kmeans]
#print('type of labels', type(labels))
#print('shape of labels', len(labels))
#print('each array size', labels[0].shape)
#print('3rd array: ', labels[3])
sil_avg = [silhouette_score(df, label)
for label in labels] # average silhouette score for all samples
for k in range(len(kmeans)):
line = 'For n_cluster = %d, average silhouette score = %.5f\n' % (
k + 2, sil_avg[k])
silfile.write(line)
print(line)
sil_each = [silhouette_samples(df, label)
for label in labels] # sil score for every sample
#print('type and shape of sil_each', type(sil_each[1]), sil_each[1].shape)
for n_cluster in Ks:
k = Ks.index(n_cluster)
# for each k, plot individual figure for silhouette value distribution over all samples
fig = plt.plot()
plt.xlim([-1, 1])
plt.ylim([0, len(df) + (n_cluster + 1) * 10
]) # (n_cluster+1) * 10 is the blank between clusters
low_y = 0
print('%d clusters' % n_cluster)
for i in range(n_cluster):
ith_cluster_sil_values = sil_each[k][labels[k] == i]
#print('type and shape of %d th_cluster_sil_values' % i, type(ith_cluster_sil_values), ith_cluster_sil_values.shape)
ith_cluster_sil_values.sort()
size_cluster_i = ith_cluster_sil_values.shape[0]
high_y = low_y + size_cluster_i
color = cm.Spectral(float(i) /
n_cluster) # spread color for each cluster
plt.fill_betweenx(np.arange(low_y, high_y),
0,
ith_cluster_sil_values,
facecolor=color,
edgecolor=color)
plt.text(-0.05, low_y + 0.5 * size_cluster_i, str(
i)) # text label cluster number in the middle of each cluster
low_y = high_y + 10
plt.title('Silhouette scores for clusters with %d clusters' %
n_cluster)
plt.xlabel('Silhouette coefficient values')
plt.ylabel('Cluster labels')
plt.axvline(
x=sil_avg[k], color='red',
linestyle='--') # add vertical line to show average sil score
plt.savefig(Path(output_path, ('sil%d.eps' % n_cluster)))
plt.show()
def out_graph(amount_map, price_jpy):
amount = list(amount_map.values())
c_code = list(amount_map.keys())
total_jpy = 0.0
values = {}
for code in c_code:
if price_jpy[code] != False:
values[code] = amount_map[code] * price_jpy[code]
total_jpy += amount_map[code] * price_jpy[code]
label = [
"{c}(JPY:{v:,d}) {a:,f}".format(c=c,
v=int(amount_map[c] * price_jpy[c]),
a=amount_map[c]) for c in c_code
]
plt.style.use("ggplot")
plt.rcParams.update({"font.size": 15})
size = (9, 5)
col = cm.Spectral(np.arange(len(amount)) / float(len(amount)))
def make_autopct(values):
def my_autopct(pct):
total = sum(values)
val = int(round(pct * total / 100.0))
return "{p:.2f}%".format(p=pct) if val > 100000 else ""
return my_autopct
plt.figure(figsize=size, dpi=100)
plt.pie(list(values.values()),
colors=col,
counterclock=False,
startangle=90,
autopct=make_autopct(list(values.values())))
plt.subplots_adjust(left=0, right=0.7)
plt.legend(label,
fancybox=True,
loc="center left",
bbox_to_anchor=(0.9, 0.5))
plt.axis("equal")
plt.text(-1.7, 1, "{:,d}JPY".format(int(total_jpy)), fontsize=14)
plt.savefig("pie_graph.png", bbox_inches="tight", pad_inches=0.05)
def createPiechart(data, label, title, figpath):
###綺麗に書くためのおまじない###
plt.style.use('ggplot')
plt.rcParams.update({'font.size':15})
###各種パラメータ###
size=(7,3.5) #凡例を配置する関係でsizeは横長にしておきます。
col=cm.Spectral(np.arange(len(data))/float(len(data))) #color指定はcolormapから好みのものを。
###pie###
plt.figure(figsize=size,dpi=100)
plt.title(title)
plt.pie(data,colors=col,counterclock=False,startangle=90,autopct=lambda p:'{:.1f}%'.format(p) if p>=1.0 else '')
plt.subplots_adjust(left=0,right=0.7)
plt.legend(label,fancybox=True,loc='center left',bbox_to_anchor=(0.9,0.5))
plt.axis('equal')
plt.savefig(figpath,bbox_inches='tight',pad_inches=0.05)
def pie_chart(data: list, label: list, file_name: str):
plt.style.use('ggplot')
plt.rcParams.update({'font.size': 15})
size = (18, 10) # 凡例を配置する関係でsizeは横長にしておきます。
col = cm.Spectral(np.arange(len(data)) / float(len(data)))
plt.figure(figsize=size, dpi=100)
plt.pie(data,
colors=col,
counterclock=False,
startangle=90,
autopct=lambda p: '{:0.1f}%'.format(p) if p >= 5 else '')
plt.subplots_adjust(left=0, right=0.7)
plt.legend(label,
fancybox=True,
loc='center left',
bbox_to_anchor=(0.9, 0.5))
plt.axis('equal')
plt.savefig(f"{file_name}", bbox_inches='tight', pad_inches=0.05)
return True
def find_data_DBSCAN(plt, sample, epsln, minSam, title):
X = sample[['latitude', 'longitude']]
# Run DBSCAN on the samples
# Need to tweak eps
db = DBSCAN(eps=epsln, min_samples=minSam).fit(X)
core_samples_mask = np.zeros_like(db.labels_, dtype=bool)
core_samples_mask[db.core_sample_indices_] = True
labels = db.labels_
# Number of clusters in labels, ignoring noise if present.
n_clusters_ = len(set(labels)) - (1 if -1 in labels else 0)
print(f'Estimated number of clusters for {title}: {n_clusters_}')
# Black removed and is used for noise instead.
unique_labels = set(labels)
colors = [
cm.Spectral(each) for each in np.linspace(0, 1, len(unique_labels))
]
for k, col in zip(unique_labels, colors):
if k == -1:
# Black used for noise.
col = [0, 0, 0, 1]
class_member_mask = (labels == k)
xy = X[class_member_mask & core_samples_mask]
plt.plot(xy.latitude,
xy.longitude,
'.',
markerfacecolor=tuple(col),
markeredgecolor='k',
markersize=14)
xy = X[class_member_mask & ~core_samples_mask]
plt.plot(xy.latitude,
xy.longitude,
'.',
markerfacecolor=tuple(col),
markeredgecolor='k',
markersize=6)
plt.set_title(f'{title}:{n_clusters_}')
def plot_hyperboloid(current_ax=None, style='surface', title='$Hyperboloid$'):
""" Apply hyperboloid mapping to sample grid and plot figure """
if current_ax == None:
fig = plt.figure(figsize=plt.figaspect(1))
ax = fig.gca(projection='3d')
else:
ax = current_ax
X = np.arange(-2, 2, 0.2)
Y = np.arange(-2, 2, 0.2)
X, Y = np.meshgrid(X, Y)
Z = np.sqrt(X**2 + Y**2 + 1)
if style == 'wireframe':
ax.plot_wireframe(X, Y, Z, rstride=2, cstride=2, linewidth=1, edgecolor='black')
else:
zcolors = Z - min(Z.flat)
zcolors = zcolors/max(zcolors.flat)
ax.plot_surface(X, Y, Z, rstride=1, cstride=1, facecolors=cm.Spectral(zcolors), linewidth=1)
ax.set_title(title, size=20)
ax.set_xlabel('$x$')
ax.set_ylabel('$y$')
ax.set_zlabel('$z$');
def plot(preprocess):
labels, data = dataset.get(subset="train",
preprocess=preprocess,
categories=categories,
verbose=True)
labels = np.array(labels)
print "Getting TF IDF weights"
vec = TfidfVectorizer(max_df=0.5,
max_features=10000,
min_df=2,
stop_words='english',
use_idf=True,
ngram_range=(1, 1))
X = vec.fit_transform(data)
print(repr(X))
print "Reducing dimensions to 50"
X_reduced = TruncatedSVD(n_components=50, random_state=0).fit_transform(X)
X_embedded = PCA(n_components=2).fit_transform(X_reduced)
names = np.unique(labels)
print names
num_clusters = len(names)
fig = plt.figure(frameon=False)
colors = iter(cm.Spectral(np.linspace(0, 1, num_clusters)))
for name in names:
X = X_embedded[labels == name]
plt.scatter(X[:, 0], X[:, 1], marker='x', label=name)
plt.title("PCA (Preprocessed)" if preprocess else "PCA")
plt.xticks([])
plt.yticks([])
plt.legend()
def create_pie_fig(count, label, savename):
plt.style.use('ggplot')
plt.rcParams.update({'font.size': 18})
#日本語対応FONT
plt.rcParams['font.family'] = 'IPAPGothic'
size = (8, 8)
col = cm.Spectral(np.arange(len(count)) /
float(len(count))) #color指定はcolormapから好みのものを。
plt.figure(figsize=size, dpi=200)
plt.pie(count,
colors=col,
counterclock=False,
startangle=90,
autopct=lambda p: '{:.1f}%'.format(p) if p >= 5 else '')
plt.subplots_adjust(left=0, right=0.9)
plt.legend(label,
fancybox=True,
loc='center left',
bbox_to_anchor=(0.9, 0.5))
plt.axis('equal')
plt.savefig(savename, bbox_inches='tight', pad_inches=0.05)
def plot_basis_scatter(embedding, ax):
# A hack because we now that each embedding consists of
# 3 clusters of 1000 points each. These clusters are also
# ordered (1st cluster: 0:999, 2nd: 1000:2000, 3rd: 2000:3000)
xx = embedding[:, 0]
yy = embedding[:, 1]
num_basis = 3 # Rock, paper, scissors
colors = cm.Spectral(np.linspace(0, 1, num_basis))
basis_borders = [0, 1000, 2000]
xx_basis_1 = xx[:basis_borders[1]]
yy_basis_1 = yy[:basis_borders[1]]
xx_basis_2 = xx[basis_borders[1]:basis_borders[2]]
yy_basis_2 = yy[basis_borders[1]:basis_borders[2]]
xx_basis_3 = xx[basis_borders[2]:]
yy_basis_3 = yy[basis_borders[2]:]
ax.scatter(xx_basis_1, yy_basis_1, color=colors[0])
ax.scatter(xx_basis_2, yy_basis_2, color=colors[1])
ax.scatter(xx_basis_3, yy_basis_3, color=colors[2])
def plot_isovist_sec_by_pt(ax, frames):
area_isovist = []
plotpt_x = []
plotpt_y = []
texts = []
for line in tqdm(frames):
# framelineに分割点がなかった場合
if isinstance(line.isovist_sec, type(None)):
pass
else:
isovists = [_ for _ in line.isovist_sec if not isinstance(_.positon, type(None))]
if len(isovists) == 0: # 分割面で道路が見つからなかった場合
pass
else:
for i in isovists:
area_isovist.append(i.isovist.area)
plotpt_x.append(i.positon.x)
plotpt_y.append(i.positon.y)
texts.append("{}:{}".format(line.id, i.id))
for i, area in enumerate(area_isovist):
ax.scatter(plotpt_x[i], plotpt_y[i], color=cm.Spectral(area / max(area_isovist)))
ax.text(plotpt_x[i], plotpt_y[i], texts[i], c='b')
def save_latent_vis(path, data, classes, encoder, epoch, num_classes):
z = encoder.predict(data)
fig = plt.figure()
ax = fig.add_subplot(111)
colors = cm.Spectral(np.linspace(0, 1, num_classes))
xx = z[:, 0]
yy = z[:, 1]
labels = range(num_classes)
# plot the 2D data points
for i in range(num_classes):
ax.scatter(xx[labels == i],
yy[labels == i],
color=colors[i],
label=labels[i],
s=5)
plt.axis('tight')
plt.savefig(path + '_latent_vis_%d.png' % (epoch + 1))
def plot_graph(self):
X = self.X
plot_fig = plt.figure(figsize=(5, 5))
plt.xlim(-1, 1)
plt.ylim(-1, 1)
if self.cen and self.clusters:
cen = self.cen
clus = self.clusters
K = self.K
for m, clu in clus.items():
cs = cm.Spectral(1. * m / self.K)
plt.plot(cen[m][0], cen[m][1], 'o', marker='*', \
markersize=12, color=cs)
plt.plot(list(zip(*clus[m]))[0], list(zip(*clus[m]))[1], '.', \
markersize=8, color=cs, alpha=0.5)
else:
plt.plot(list(zip(*X))[0], list(zip(*X))[1], '.', alpha=0.5)
plot_title = 'K-means Clustering'
plot_pars = 'N=%s, K=%s' % (str(self.N), str(self.K))
plt.title('\n'.join([plot_pars, plot_title]), fontsize=16)
plt.savefig('kpp_N%s_K%s.png' % (str(self.N), str(self.K)), \
bbox_inches='tight', dpi=200)
def pie(label, data):
# 書式
plt.style.use('ggplot')
plt.rcParams.update({'font.size': 15})
# 各種パラメータ
size = (9, 5)
col = cm.Spectral(np.arange(len(data)) / float(len(data)))
# pie
plt.figure(figsize=size, dpi=100)
plt.pie(data,
colors=col,
counterclock=False,
startangle=90,
autopct=lambda p: '{:.1f}%'.format(p) if p >= 5 else '')
plt.subplots_adjust(left=0, right=0.7)
plt.legend(label,
fancybox=True,
loc='center left',
bbox_to_anchor=(0.9, 0.5))
plt.axis('equal')
plt.savefig('tt_wr.png', bbox_inches='tight', pad_inches=0.05)
plt.show()
fh.setLevel(logging.DEBUG)
ch = logging.StreamHandler() # console handler
ch.setLevel(logging.DEBUG)
formatter = logging.Formatter(
'%(asctime)s - %(name)s - %(levelname)s - %(message)s')
ch.setFormatter(formatter)
fh.setFormatter(formatter)
logger.addHandler(fh)
logger.addHandler(ch)
logger.info('Initializing %s', __name__)
colors = [
cm.RdBu(0.85),
cm.RdBu(0.7),
cm.PiYG(0.7),
cm.Spectral(0.38),
cm.Spectral(0.25)
]
if __name__ == '__main__':
# parameter setting
gps_dir = s.GPS_DIR
gps_counter_file = s.GPS_COUNTER_FILE
TWEET_COUNTER_FILE = s.TWEET_COUNTER_FILE
timestart = s.TIMESTART
timestart_text = s.TIMESTART_TEXT
timeend = s.TIMEEND
timeend_text = s.TIMEEND_TEXT
aoi = s.AOI
unit_temporal = s.UNIT_TEMPORAL
# unit_spatial = s.UNIT_SPATIAL
# Compute the silhouette scores for each sample
sample_silhouette_values = silhouette_samples(X_norm, cluster_labels)
y_lower = 10
for i in range(n_clusters):
# Aggregate the silhouette scores for samples belonging to
# cluster i, and sort them
ith_cluster_silhouette_values = \
sample_silhouette_values[cluster_labels == i]
ith_cluster_silhouette_values.sort()
size_cluster_i = ith_cluster_silhouette_values.shape[0]
y_upper = y_lower + size_cluster_i
color = cm.Spectral(float(i) / n_clusters)
ax1.fill_betweenx(np.arange(y_lower, y_upper),
0,
ith_cluster_silhouette_values,
facecolor=color,
edgecolor=color,
alpha=0.7)
# Label the silhouette plots with their cluster numbers at the middle
ax1.text(-0.05, y_lower + 0.5 * size_cluster_i, str(i))
# Compute the new y_lower for next plot
y_lower = y_upper + 10 # 10 for the 0 samples
ax1.set_title("The silhouette plot for the various clusters.")
ax1.set_xlabel("The silhouette coefficient values")
def plot_benchmark_simple(rmses_spherical, model_description, lead_times, input_dir, output_dir, \
title=True, filename=None, names=[]):
"""
Plot rmse of different models vs Weyn et al
:param rmses_spherical: list of xarrays or xarray
:param model_description: string
:param lead_times: xarray
:param input_dir: string
:param output_dir: string
:param title: boolean
:param filename: string
:param names: if rmses_spherical is a list, names should be a list of same length with the name of each model
:return:
"""
lead_times0 = np.arange(6, lead_times[-1]+6, 6)
colors = cm.Spectral(np.linspace(0,1,len(rmses_spherical)))
xlabels = [str(t) if t%4 == 0 else '' for t in lead_times] if lead_times[0] < 12 else lead_times
# RMSE baselines
rmses_weyn = xr.open_dataset(input_dir + 'rmses_weyn.nc').rename({'z500':'z', 't850':'t'})
f, axs = plt.subplots(1, 2, figsize=(17, 6))
if title:
f.suptitle('RMSE between forecast and observation as a function of forecast time', fontsize=24, y=1.07)
axs[0].plot(lead_times0, rmses_weyn.z.values[:len(lead_times0)], label='Weyn 2020', linestyle='-')
axs[1].plot(lead_times0, rmses_weyn.t.values[:len(lead_times0)], label='Weyn 2020', linestyle='-')
if len(names) == 0:
axs[0].plot(lead_times, rmses_spherical.z.values, label='Ours', color='black', marker='o')
axs[1].plot(lead_times, rmses_spherical.t.values, label='Ours', color='black', marker='o')
else:
for rmse, name, c in zip(rmses_spherical, names, colors):
axs[0].plot(lead_times, rmse.z.values, label=name, color=c, marker='o')
axs[1].plot(lead_times, rmse.t.values, label=name, color=c, marker='o')
axs[0].set_ylabel('RMSE [$m^2 s^{−2}$]', fontsize=18)
axs[0].set_xlabel('Forecast time [h]', fontsize=18)
axs[0].set_title('Z500', fontsize=22)
axs[0].tick_params(axis='both', which='major', labelsize=16)
axs[0].set_xticks(lead_times)
axs[0].set_xticklabels(xlabels, fontsize=16)
axs[0].legend(loc='upper left', fontsize=15)
axs[1].set_ylabel('RMSE [K]', fontsize=18)
axs[1].set_xlabel('Forecast time [h]', fontsize=18)
axs[1].set_title('T850', fontsize=22)
axs[1].set_xticks(lead_times)
axs[1].set_xticklabels(xlabels, fontsize=16)
axs[1].tick_params(axis='both', which='major', labelsize=16)
axs[1].legend(loc='upper left', fontsize=15)
if not filename:
filename = model_description + '_benchmark.png'
plt.tight_layout()
plt.savefig(output_dir + filename, bbox_inches='tight')
plt.show()
k,
"the best run is",
ds,
"but this has an anomcorr of",
bestano,
"which indicates this may not be suitable for phasing.",
)
best_results += [(k, bestano, ds)]
except:
print("No data at", k, "A passed the sanity check.")
x_val = [x[0] for x in best_results]
y_val = [x[1] for x in best_results]
c_val = [x[2] for x in best_results]
fig, ax = plt.subplots(1, 1)
ax.scatter(x_val, y_val, c=cm.Spectral([i * 10 for i in c_val]))
ax.plot(x_val, y_val, "b-")
plt.axhline(y=9, color="r", linestyle="--")
ax.invert_xaxis()
plt.show()
fig.savefig("ResolutionVsAnomcorr.jpg", dpi=600)
best_run = mode(c_val)
print("\nThe best run appears to be number", best_run)
os.mkdir("best")
shutil.copy2(
os.path.join(path, str(best_run)) + "/XSCALE.INP", os.path.join(path, "best")
)
subprocess.run(["xscale_par"], cwd=os.path.join(path, "best"))
def draw_tracks(self, frame_clr):
drawable_tracks = self.get_drawable_tracks()
for index, tr in enumerate(drawable_tracks):
track_color = tuple(256 * x for x in cm.Spectral(index * 100 % 255)[0:3])
cv2.polylines(frame_clr, [np.int32([tup[0:2] for tup in tr])], False, track_color)
x0 = np.array([10, 10]) # initial condition
A = np.array([
[0, 1], # system dynamics matrix
[0, 0]
])
B = np.array([[0], [1]]) # b matrix
K = np.array([[-2, -3]]) # control law
track = odeint(linear_sys, x0, t, args=(A, B, K))
fig = plt.figure(figsize=(10, 5))
plt.style.use('seaborn-deep')
# temp = cm.winter(t / 10)
# plt.plot(track[:, 0], track[:, 1], lw=3, c=cm.hot(t / 10))
plt.subplot(1, 2, 1)
plt.scatter(track[:, 0], track[:, 1], linewidths=0.5, c=cm.Spectral(t / 5))
plt.xlabel('x1')
plt.ylabel('x2')
plt.subplot(1, 2, 2)
plt.plot(t, track[:, 0], lw=3, label='x1')
plt.plot(t, track[:, 1], lw=3, label='x2')
plt.xlabel('t')
plt.legend()
# plt.savefig('./linear_fdc.png')
plt.show()
# ==========================
# plot the phase of the dynamics system
num_steps = 11
Y, X = np.mgrid[-25:25:(num_steps * 1j), -25:25:(num_steps * 1j)]
# print(data)
# compare the trajectory with nonlinear-RL
# phase
plt.style.use('seaborn-deep')
fig = plt.figure(figsize=(8, 6))
num_steps = 11
g = 10
res = [-0.067, 0.00078, -0.031, -15.41, -9.28]
Y, X = np.mgrid[-4 * sqrt(g):4 * sqrt(g):(num_steps * 1j),
-pi:pi:(num_steps * 1j)]
U = Y
V = res[0] * X * X + res[1] * Y * Y + res[2] * X * Y + res[3] * X + res[
4] * Y + g * np.sin(X)
speed = np.sqrt(U**2 + V**2)
plt.streamplot(X, Y, U, V, color=speed, cmap='PuBu', density=2)
plt.scatter(data[0],
data[1],
s=30,
c=cm.Spectral(
np.linspace(0,
len(data[0]) * 0.1, len(data[0])) / 40))
plt.plot(data[0], data[1], color='C2', lw=2)
plt.xlabel('x1')
plt.ylabel('x2')
plt.xlim([-pi, pi])
plt.ylim([-4 * sqrt(g), 4 * sqrt(g)])
plt.savefig('./nonlinear_mpc.png')
plt.show()
from mpl_toolkits.mplot3d import axes3d
from matplotlib import cm
def squares_sum(w0, w1):
return w0**2 + w0 * w1 + w1**2
w0, w1 = np.meshgrid(np.arange(-2, 2, 0.1), np.arange(-2, 2, 0.1))
J = squares_sum(w0, w1)
J = (J - J.min()) / (J.max() - J.min()
) # normalization - to match colormap spectre
colors = cm.Spectral(J)
rcount, ccount, _ = colors.shape
fig = plt.figure()
ax = fig.gca(projection='3d')
surf = ax.plot_surface(w0,
w1,
J,
rcount=rcount,
ccount=ccount,
facecolors=colors,
shade=False)
surf.set_facecolor((0, 0, 0, 0))
ax.set_xlabel('$w_0$')
ax.set_ylabel('$w_1$')
def df_input(dfUniprot=DataFrame([])):
num_phylum = len(dfUniprot.PHYLUM.drop_duplicates())
from matplotlib import cm
set3 = [
matplotlib.colors.rgb2hex(tuple(i))
for i in cm.Set3(np.arange(12) / 12.)
]
set2 = [
matplotlib.colors.rgb2hex(tuple(i))
for i in cm.Set2(np.arange(8) / 8.)
]
set1 = [
matplotlib.colors.rgb2hex(tuple(i))
for i in cm.Set1(np.arange(9) / 9.)
]
pastel2 = [
matplotlib.colors.rgb2hex(tuple(i))
for i in cm.Pastel2(np.arange(8) / 8.)
]
pastel1 = [
matplotlib.colors.rgb2hex(tuple(i))
for i in cm.Pastel1(np.arange(9) / 9.)
]
dark2 = [
matplotlib.colors.rgb2hex(tuple(i))
for i in cm.Dark2(np.arange(8) / 8.)
]
paired = [
matplotlib.colors.rgb2hex(tuple(i))
for i in cm.Paired(np.arange(12) / 12.)
]
accent = [
matplotlib.colors.rgb2hex(tuple(i))
for i in cm.Accent(np.arange(8) / 8.)
]
spectral = [
matplotlib.colors.rgb2hex(tuple(i))
for i in cm.Spectral(np.arange(11) / 11.)
]
tab20 = [
matplotlib.colors.rgb2hex(tuple(i))
for i in cm.tab20(np.arange(20) / 20.)
]
tab20b = [
matplotlib.colors.rgb2hex(tuple(i))
for i in cm.tab20b(np.arange(20) / 20.)
]
tab20c = [
matplotlib.colors.rgb2hex(tuple(i))
for i in cm.tab20c(np.arange(20) / 20.)
]
Colors1 = set2 + set1 + dark2 + paired + accent + spectral + tab20 + tab20b + tab20c
Colors2 = accent + spectral + tab20 + tab20b + tab20c + set1 + set2 + dark2 + paired
Colors3 = dark2 + paired + accent + spectral + tab20 + tab20b + tab20c + set1 + set2
Colors4 = tab20b + tab20c + set1 + set2 + dark2 + paired + accent + spectral + tab20
Colors5 = spectral + tab20 + tab20b + tab20c + set1 + set2 + dark2 + paired + accent
pie_colors = {
'Set3': cm.Set3(np.arange(12) / 12.),
'Set2': cm.Set2(np.arange(8) / 8.),
'Set1': cm.Set1(np.arange(9) / 9.),
'Pastel2': cm.Pastel2(np.arange(8) / 8.),
'Pastel1': cm.Pastel1(np.arange(9) / 9.),
'Dark2': cm.Dark2(np.arange(8) / 8.),
'Paired': cm.Paired(np.arange(12) / 12.),
'Accent': cm.Accent(np.arange(8) / 8.),
'Spectral': cm.Spectral(np.arange(11) / 11.),
'tab20': cm.tab20(np.arange(20) / 20.),
'tab20b': cm.tab20b(np.arange(20) / 20.),
'tab20c': cm.tab20c(np.arange(20) / 20.)
}
circle_colors = {
'Colors1': Colors1[0:num_phylum],
'Colors2': Colors2[0:num_phylum],
'Colors3': Colors3[0:num_phylum],
'Colors4': Colors4[0:num_phylum],
'Colors5': Colors5[0:num_phylum]
}
def tax_colors(color_list=circle_colors['Colors1'], taxx=dfUniprot):
tax_cols = [
'Entry', 'Tax_ID', 'KINGDOM', 'PHYLUM', 'CLASS', 'ORDER', 'FAMILY',
'GENUS', 'SPECIES', 'Organism'
]
new2 = taxx[tax_cols].drop_duplicates()
#>>>>>>>>>>>>>>>>>>>>>>>>>>>
phylum0 = new2.groupby(['PHYLUM'
]).Entry.count().reset_index().sort_values(
by='Entry',
ascending=False).reset_index(drop=True)
asign_color = {}
for i, j in zip(phylum0.PHYLUM, color_list):
if i == 'NA':
asign_color[i] = 'black'
else:
asign_color[i] = j
phylum0['phy_col'] = list(asign_color.values())
# distribución de Class
phylum1 = new2.groupby(['PHYLUM', 'CLASS']).Entry.count().reset_index()
class0 = []
class0_colors = []
for i in phylum0.PHYLUM:
for j in phylum1.PHYLUM:
if i == j:
class0_colors.append(asign_color[j])
class0.append(phylum1[phylum1.PHYLUM == i].sort_values(
by='Entry', ascending=False).reset_index(drop=True))
else:
pass
class1 = pd.concat(class0).drop_duplicates()
class1['class_col'] = class0_colors
class0_colors_corregido = []
for index, row in class1.iterrows():
if row.PHYLUM == 'NA':
if row.CLASS == 'NA':
class0_colors_corregido.append(row.class_col)
else:
class0_colors_corregido.append('grey')
else:
if row.CLASS == 'NA':
class0_colors_corregido.append('black')
else:
class0_colors_corregido.append(row.class_col)
class1['class_col'] = class0_colors_corregido
class11 = class1.groupby(['CLASS'
]).Entry.sum().reset_index().sort_values(
by='Entry',
ascending=False).reset_index(drop=True)
class11 = class11.merge(class1[['CLASS',
'class_col']].drop_duplicates(),
on='CLASS',
how='left')
# distribución de Order
phylum2 = new2.groupby(['PHYLUM', 'CLASS',
'ORDER']).Entry.count().reset_index()
order0 = []
order0_colors = []
for i in phylum0.PHYLUM:
for j in phylum2.PHYLUM:
if i == j:
order0_colors.append(asign_color[j])
order0.append(phylum2[phylum2.PHYLUM == i].sort_values(
by='Entry', ascending=False).reset_index(drop=True))
else:
pass
order1 = pd.concat(order0).drop_duplicates()
order1['order_col'] = order0_colors
order0_colors_corregido = []
for index, row in order1.iterrows():
if row.PHYLUM == 'NA':
if row.ORDER == 'NA':
order0_colors_corregido.append(row.order_col)
else:
order0_colors_corregido.append('grey')
else:
if row.ORDER == 'NA':
order0_colors_corregido.append('black')
else:
order0_colors_corregido.append(row.order_col)
order1['order_col'] = order0_colors_corregido
order11 = order1.groupby(['ORDER'
]).Entry.sum().reset_index().sort_values(
by='Entry',
ascending=False).reset_index(drop=True)
order11 = order11.merge(order1[['ORDER',
'order_col']].drop_duplicates(),
on='ORDER',
how='left')
# distribución de Genus
phylum3 = new2.groupby(['PHYLUM', 'CLASS', 'ORDER',
'GENUS']).Entry.count().reset_index()
genus0 = []
genus0_colors = []
for i in phylum0.PHYLUM:
for j in phylum3.PHYLUM:
if i == j:
genus0_colors.append(asign_color[j])
genus0.append(phylum3[phylum3.PHYLUM == i].sort_values(
by='Entry', ascending=False).reset_index(drop=True))
else:
pass
genus1 = pd.concat(genus0).drop_duplicates()
genus1['genus_col'] = genus0_colors
genus0_colors_corregido = []
for index, row in genus1.iterrows():
if row.PHYLUM == 'NA':
if row.GENUS == 'NA':
genus0_colors_corregido.append(row.genus_col)
else:
genus0_colors_corregido.append('grey')
else:
if row.GENUS == 'NA':
genus0_colors_corregido.append('black')
else:
genus0_colors_corregido.append(row.genus_col)
genus1['genus_col'] = genus0_colors_corregido
genus11 = genus1.groupby(['GENUS'
]).Entry.sum().reset_index().sort_values(
by='Entry',
ascending=False).reset_index(drop=True)
genus11 = genus11.merge(genus1[['GENUS',
'genus_col']].drop_duplicates(),
on='GENUS',
how='left')
# distribución de Organism
phylum4 = new2.groupby(
['PHYLUM', 'CLASS', 'ORDER', 'GENUS',
'Organism']).Entry.count().reset_index()
org0 = []
org0_colors = []
for i in phylum0.PHYLUM:
for j in phylum4.PHYLUM:
if i == j:
org0_colors.append(asign_color[j])
org0.append(phylum4[phylum4.PHYLUM == i].sort_values(
by='Entry', ascending=False).reset_index(drop=True))
else:
pass
org1 = pd.concat(org0).drop_duplicates()
org1['org_col'] = org0_colors
org0_colors_corregido = []
for index, row in org1.iterrows():
if row.PHYLUM == 'NA':
if row.Organism == 'NA':
org0_colors_corregido.append(row.org_col)
else:
org0_colors_corregido.append('grey')
else:
if row.Organism == 'NA':
org0_colors_corregido.append('black')
else:
org0_colors_corregido.append(row.org_col)
org1['org_col'] = org0_colors_corregido
org11 = org1.groupby(['Organism'
]).Entry.sum().reset_index().sort_values(
by='Entry',
ascending=False).reset_index(drop=True)
org11 = org11.merge(org1[['Organism', 'org_col']].drop_duplicates(),
on='Organism',
how='left')
os.makedirs('tax', exist_ok=True)
return phylum0.to_csv('tax/phylum0.tsv', sep = '\t', index = None),\
class1.to_csv('tax/class1.tsv', sep = '\t', index = None),\
class11.to_csv('tax/class11.tsv', sep = '\t', index = None),\
order1.to_csv('tax/order1.tsv', sep = '\t', index = None),\
order11.to_csv('tax/order11.tsv', sep = '\t', index = None),\
genus1.to_csv('tax/genus1.tsv', sep = '\t', index = None),\
genus11.to_csv('tax/genus11.tsv', sep = '\t', index = None),\
org1.to_csv('tax/org1.tsv', sep = '\t', index = None),\
org11.to_csv('tax/org11.tsv', sep = '\t', index = None)
alfas = {
'Lineage*': [1, 1, 1, 1, 1],
'Phylum': [1, 0.3, 0.3, 0.3, 0.3],
'Class': [0.3, 1, 0.3, 0.3, 0.3],
'Order': [0.3, 0.3, 1, 0.3, 0.3],
'Genus': [0.3, 0.3, 0.3, 1, 0.3],
'Species': [0.3, 0.3, 0.3, 0.3, 1],
'Gradient1*': [1, 0.85, 0.7, 0.55, 0.4],
'Gradient2*': [0.4, 0.55, 0.7, 0.85, 1],
'Attenuate*': [0.3, 0.3, 0.3, 0.3, 0.3],
'None*': [0, 0, 0, 0, 0]
}
def circle_lineage(alphas=alfas['Phylum']):
#fig, ax = plt.subplots(111, facecolor= 'white')
#fig, ax = plt.subplot(111)
phylum0 = pd.read_csv('tax/phylum0.tsv', sep='\t').fillna('NA')
class1 = pd.read_csv('tax/class1.tsv', sep='\t').fillna('NA')
order1 = pd.read_csv('tax/order1.tsv', sep='\t').fillna('NA')
genus1 = pd.read_csv('tax/genus1.tsv', sep='\t').fillna('NA')
org1 = pd.read_csv('tax/org1.tsv', sep='\t').fillna('NA')
radio = 0.5
linaje = [phylum0, class1, order1, genus1, org1]
#colores = [list(asign_color.values()), class0_colors, order0_colors, genus0_colors, org0_colors]
colores = ['phy_col', 'class_col', 'order_col', 'genus_col', 'org_col']
pat = []
size = -.205
for i, j, k in zip(linaje, colores, alphas):
size += .205
patches, texts = plt.pie(
i.Entry,
radius=radio + size,
labels=None,
labeldistance=0.8,
rotatelabels=True,
colors=
i[j], # new_colors(valor = len(i.Entry), col = 'nipy_spectral'),
wedgeprops=dict(width=0.2, edgecolor='white', alpha=k),
textprops=dict(size=10))
pat.append(patches)
#plt.legend(pat[0], df_phylum.PHYLUM, loc=2,fontsize=13,labelspacing = 0.4,
# bbox_to_anchor=(1.05, 1),frameon=False)
plt.gca().set(aspect='equal')
plt.title('Root', fontsize=10, x=0.5, y=0.465)
plt.text(-1.8,
1.35,
'Lineage',
fontsize=15,
ha='left',
va='center',
color='black')
#plt.title('Lineage',fontsize=20, fontweight='bold', x = -0.17, y = 1)
#plt.text(1.1, 1.35, linaje_seleccionado, fontsize = 15, ha='left', va='center',
# color='black')
#>>>>>>>>>>>>>>>>>>>>>>>
#### insetplot
#ax2 = plt.axes([0.1, 0.66, 0.13, 0.14])
ax2 = plt.axes([-0.07, 1.71, 0.17, 0.18])
logo = [20, 20, 20, 20, 20, 20, 20, 20]
logo_col = [
'white', 'white', 'black', 'white', 'white', 'white', 'white',
'white'
]
logo_col1 = [
'white', 'white', 'black', 'black', 'black', 'black', 'black',
'black'
]
radio = 0.5
linaje = [logo, logo, logo, logo, logo]
colores = [logo_col1, logo_col, logo_col, logo_col, logo_col]
name_linaje = ['Phylum', 'Class', 'Order', 'Genus', 'Species']
pat = []
size = -.44
pos = -.18
for i, j, k, l in zip(linaje, colores, name_linaje, alphas):
pos += .47
size += .44
ax2.pie(i,
radius=radio + size,
labels=None,
colors=j,
wedgeprops=dict(width=0.35, edgecolor='white', alpha=l),
textprops=dict(size=10))
ax2.text(0.1,
pos,
k,
fontsize=9,
ha='left',
va='center',
fontweight='bold',
alpha=l) #color='black'
def barras_tax(df=DataFrame([]),
column=0,
dim=111,
title='',
row_num=10,
color=['#ff7f0e'],
size_x=8,
size_y=10,
ylabel_text='',
xlabel=10,
ylabel=10,
size_title=15,
size_bartxt=10,
sep=1.2):
if len(df) == 0:
print('Data frame sin datos')
else:
#plt.subplot(dim, facecolor= 'white')
barWidth = 0.9
if row_num == len(df):
ejey = list(df.iloc[0:len(df), 1])
val = max(ejey)
ejex = list(df.iloc[0:len(df), column])
colores = list(df.iloc[0:len(df), 2])
borde = list(
np.repeat('white', len(df.iloc[0:row_num, column])))
linea = list(np.repeat(0, len(df.iloc[0:row_num, column])))
if row_num < len(df):
ejey = list(df.iloc[0:row_num,
1]) + [df.iloc[row_num:len(df), 1].sum()]
val = max(ejey)
ejex = list(df.iloc[0:row_num, column]) + ['Others']
borde = list(
np.repeat('white', len(df.iloc[0:row_num,
column]))) + ['black']
colores = list(df.iloc[0:row_num, 2]) + ['linen']
linea = list(np.repeat(0, len(df.iloc[0:row_num,
column]))) + [1]
if row_num > len(df):
ejey = list(df.iloc[0:len(df), 1])
val = max(ejey)
ejex = list(df.iloc[0:len(df), column])
borde = list(
np.repeat('white', len(df.iloc[0:row_num, column])))
colores = list(df.iloc[0:len(df), 2])
linea = list(np.repeat(0, len(df.iloc[0:row_num, column])))
for i, j, k, l, m in zip(ejex, ejey, borde, colores, linea):
plt.barh(i,
j,
color=l,
align='center',
height=0.7,
linewidth=m,
alpha=1,
edgecolor=k)
plt.gca().spines['right'].set_visible(False)
plt.gca().spines['top'].set_visible(False)
plt.gca().spines['bottom'].set_position(('data', -0.6))
plt.gca().spines['left'].set_visible(False)
plt.title(title, size=size_title, loc='left')
plt.tick_params(axis="y", color="gray")
plt.yticks(size=size_y)
v1 = -50
v2 = 0
v3 = 0
for i in range(10000):
v1 += 50
v2 += 50
v3 += 10
if v1 <= max(list(ejey)) < v2:
#print(v3, v1, val, v2)
escala = v3
plt.xticks(range(0, val, escala), size=size_x) #fontweight='bold'
plt.ylabel(ylabel_text, size=ylabel)
plt.xlabel("Number of Proteins", size=xlabel)
#plt.tick_params(top = 'on', bottom = 'on', right = 'on', left = 'on')
#plt.tick_params(axis='x', which='both', bottom=False, top=False, labelbottom=False)
for j, k in zip(ejey, range(0, len(ejey))):
plt.text(j + sep,
k - 0.2,
j,
size=size_bartxt,
ha='left',
color='black')
import ipywidgets as widgets
from ipywidgets import interact, interactive, fixed, interact_manual, Button, HBox, VBox, IntSlider, Label, IntRangeSlider
from ipywidgets import Checkbox, RadioButtons
from ipywidgets import Button, Layout
alfas = {
'Lineage*': [1, 1, 1, 1, 1],
'Phylum': [1, 0.3, 0.3, 0.3, 0.3],
'Class': [0.3, 1, 0.3, 0.3, 0.3],
'Order': [0.3, 0.3, 1, 0.3, 0.3],
'Genus': [0.3, 0.3, 0.3, 1, 0.3],
'Species': [0.3, 0.3, 0.3, 0.3, 1],
'Gradient1*': [1, 0.85, 0.7, 0.55, 0.4],
'Gradient2*': [0.4, 0.55, 0.7, 0.85, 1],
'Attenuate*': [0.3, 0.3, 0.3, 0.3, 0.3],
'None*': [0, 0, 0, 0, 0]
}
plotss = ['Phylum', 'Class', 'Order', 'Genus', 'Species']
posicion_subplots = []
n = 0.9
while n < 2:
n += 0.1
posicion_subplots.append(np.around(n, 1))
color_a6 = widgets.Dropdown(options=list(circle_colors.keys()),
value='Colors1',
description='Colors:',
disabled=False,
button_style='',
layout=Layout(width='20%', height='25px'))
a6 = widgets.Dropdown(options=list(alfas.keys()),
description='Chart 1:',
value='Phylum',
disabled=False,
button_style='',
layout=Layout(width='20%', height='25px'))
a61 = widgets.Dropdown(options=plotss,
description='Chart 2:',
disabled=False,
button_style='',
layout=Layout(width='20%', height='25px'))
pos_sub1 = widgets.Dropdown(options=posicion_subplots,
value=1.3,
description='xloc1:',
disabled=False,
layout=Layout(width='15%', height='25px'))
pos_sub2 = widgets.Dropdown(options=posicion_subplots,
value=1.3,
description='xloc2:',
disabled=False,
layout=Layout(width='15%', height='25px'))
b6 = widgets.Dropdown(options=list(range(0, 101)),
value=10,
description='rows1:',
disabled=False,
layout=Layout(width='15%', height='25px'))
c6 = widgets.Dropdown(options=list(range(0, 101)),
value=10,
description='rows2:',
disabled=False,
layout=Layout(width='15%', height='25px'))
z6 = widgets.ToggleButton(value=False,
description='Save Chart',
disabled=False,
button_style='',
tooltip='Description')
o6 = widgets.Dropdown(options=[0, 0.25, 0.5, 0.75] + list(range(0, 201)),
value=3,
description='sep1:',
disabled=False,
layout=Layout(width='15%', height='25px'))
o61 = widgets.Dropdown(options=[0, 0.25, 0.5, 0.75] + list(range(0, 201)),
value=3,
description='sep2:',
disabled=False,
layout=Layout(width='15%', height='25px'))
d6 = widgets.Dropdown(options=list(range(0, 51)),
value=8,
description='size_y1:',
disabled=False,
layout=Layout(width='15%', height='25px'))
d61 = widgets.Dropdown(options=list(range(0, 51)),
value=8,
description='size_y2:',
disabled=False,
layout=Layout(width='15%', height='25px'))
g6 = widgets.Dropdown(options=list(range(0, 51)),
value=8,
description='bartxt1:',
disabled=False,
layout=Layout(width='15%', height='25px'))
g61 = widgets.Dropdown(options=list(range(0, 51)),
value=8,
description='bartxt2:',
disabled=False,
layout=Layout(width='15%', height='25px'))
xxx = Button(layout=Layout(width='5%', height='25px'), disabled=True)
xxx.style.button_color = 'white'
yyy = Button(layout=Layout(width='94%', height='5px'), disabled=True)
yyy.style.button_color = 'red'
ww = widgets.HBox([color_a6, xxx, z6])
w6 = widgets.HBox([
a6,
b6,
o6,
d6,
g6,
pos_sub1,
])
w7 = widgets.HBox([
a61,
c6,
o61,
d61,
g61,
pos_sub2,
])
w8 = widgets.VBox([w6, w7, yyy])
######
def col(color_a6):
tax_colors(color_list=circle_colors[color_a6], taxx=dfUniprot)
out7 = widgets.interactive_output(col, {'color_a6': color_a6})
def box1(a6, a61, pos_sub1, pos_sub2, b6, c6, z6, o6, o61, d6, d61, g6,
g61):
yetiquetas_plot1 = {
'Lineage*': 'Phylum',
'Phylum': 'Phylum',
'Class': 'Class',
'Order': 'Order',
'Genus': 'Genus',
'Species': 'Species',
'Gradient1*': 'Phylum',
'Gradient2*': 'Phylum',
'Attenuate*': 'Phylum',
'None*': 'Phylum'
}
plots1 = {
'Lineage*': pd.read_csv('tax/phylum0.tsv', sep='\t').fillna('NA'),
'Phylum': pd.read_csv('tax/phylum0.tsv', sep='\t').fillna('NA'),
'Class': pd.read_csv('tax/class11.tsv', sep='\t').fillna('NA'),
'Order': pd.read_csv('tax/order11.tsv', sep='\t').fillna('NA'),
'Genus': pd.read_csv('tax/genus11.tsv', sep='\t').fillna('NA'),
'Species': pd.read_csv('tax/org11.tsv', sep='\t').fillna('NA'),
'Gradient1*': pd.read_csv('tax/phylum0.tsv',
sep='\t').fillna('NA'),
'Gradient2*': pd.read_csv('tax/phylum0.tsv',
sep='\t').fillna('NA'),
'Attenuate*': pd.read_csv('tax/phylum0.tsv',
sep='\t').fillna('NA'),
'None*': pd.read_csv('tax/phylum0.tsv', sep='\t').fillna('NA')
}
plots2 = {
'Phylum': pd.read_csv('tax/phylum0.tsv', sep='\t').fillna('NA'),
'Class': pd.read_csv('tax/class11.tsv', sep='\t').fillna('NA'),
'Order': pd.read_csv('tax/order11.tsv', sep='\t').fillna('NA'),
'Genus': pd.read_csv('tax/genus11.tsv', sep='\t').fillna('NA'),
'Species': pd.read_csv('tax/org11.tsv', sep='\t').fillna('NA')
}
ax3 = plt.axes([pos_sub2, .97, .3, 0.55])
##>>>>>>>>>>> grafico circular
ax = plt.axes([0, 1, 0.9, 1])
circle_lineage(alphas=alfas[a6])
##>>>>>>>>>>> grafico 1
#ax2 = plt.axes([pos_sub1, 1.51, .3, 0.55])
ax2 = plt.axes([pos_sub1, 1.63, .3, 0.4]) #>>>>>>>>>>
barras_tax(
plots1[a6],
#barras_tax(tax_colors(color_list = circle_colors['Spectral'])[0],
row_num=b6,
color=plots1[a6].iloc[0:b6, 2],
sep=o6,
size_y=d6,
size_bartxt=g6,
ylabel_text=yetiquetas_plot1[a6],
ylabel=10)
##>>>>>>>>>>> grafico 2
ax3 = plt.axes([pos_sub2, .97, .3, 0.55])
barras_tax(
plots2[a61],
#barras_tax(tax_colors(color_list = circle_colors['Spectral'])[0],
row_num=c6,
color=plots2[a61].iloc[0:b6, 2],
sep=o61,
size_y=d61,
size_bartxt=g61,
ylabel_text=yetiquetas_plot1[a61],
ylabel=10)
##>>>>>>>>>>>> save
if z6 == True:
import datetime
plt.savefig('img/Lineage' +
datetime.datetime.now().strftime('%d.%B.%Y_%I-%M%p') +
'.png',
dpi=900,
bbox_inches='tight')
else:
pass
out6 = widgets.interactive_output(
box1, {
'a6': a6,
'a61': a61,
'pos_sub1': pos_sub1,
'pos_sub2': pos_sub2,
'b6': b6,
'c6': c6,
'z6': z6,
'o6': o6,
'o61': o61,
'd6': d6,
'd61': d61,
'g6': g6,
'g61': g61
})
import warnings
warnings.filterwarnings("ignore")
return display(VBox([yyy, ww, w8, out6]))
def plot_cluster(
db_cluster: DBSCAN,
data: pd.DataFrame,
x_predict: np.ndarray,
plot_label: str = None,
plot_features: Tuple[int, int] = (0, 1),
verbose: bool = False,
cut_off: int = 3,
xlabel: str = None,
ylabel: str = None,
):
"""
Plot clustered data as scatter chart.
Parameters
----------
db_cluster : DBSCAN
DBScan Cluster (from SkLearn DBSCAN).
data : pd.DataFrame
Dataframe containing original data.
x_predict : np.ndarray
The DBSCAN predict numpy array
plot_label : str, optional
If set the column to use to label data points
(the default is None)
plot_features : Tuple[int, int], optional
Which two features in x_predict to plot (the default is (0, 1))
verbose : bool, optional
Verbose execution with some extra info
(the default is False)
cut_off : int, optional
The cluster size below which items are considered outliers
(the default is 3)
xlabel : str, optional
x-axis label (the default is None)
ylabel : str, optional
y-axis label (the default is None)
"""
max_idx = x_predict.shape[1] - 1
if plot_features[0] >= x_predict.shape[1]:
raise ValueError(
"plot_features[0] index must be a value from 0 to {}.".format(max_idx)
)
if plot_features[1] >= x_predict.shape[1]:
raise ValueError(
"plot_features[1] index must be a value from 0 to {}.".format(max_idx)
)
if plot_features[0] == plot_features[1]:
mssg = "plot_features indexes must be 2 different values in range 0 to"
raise ValueError(mssg + f" {max_idx}.")
labels = db_cluster.labels_
core_samples_mask = np.zeros_like(labels, dtype=bool)
# pylint: disable=unsupported-assignment-operation
# (assignment of numpy array is valid)
core_samples_mask[db_cluster.core_sample_indices_] = True
unique_labels = set(labels)
# pylint: disable=no-member
# Spectral color map does exist
colors = [cm.Spectral(each) for each in np.linspace(0, 1, len(unique_labels))]
# Number of clusters in labels, ignoring noise if present.
n_clusters_ = len(set(labels)) - (1 if -1 in labels else 0)
n_noise_ = list(labels).count(-1)
_, counts = np.unique(labels, return_counts=True)
if verbose:
print("Estimated number of clusters: %d" % n_clusters_)
print("Estimated number of noise points: %d" % n_noise_)
# print("Silhouette Coefficient: %0.3f"
# % metrics.silhouette_score(x_predict, labels))
if not isinstance(data, pd.DataFrame):
plot_label = None
elif plot_label is not None and plot_label not in data:
plot_label = None
p_label = None
for cluster_id, color in zip(unique_labels, colors):
if cluster_id == -1:
# Black used for noise.
color = [0, 0, 0, 1]
class_member_mask = labels == cluster_id
cluster_size = counts[cluster_id]
marker_size = cluster_size
marker = "o"
font_size = "small"
alpha = 0.4
if cluster_size < cut_off:
marker = "+"
marker_size = 10
font_size = "large"
alpha = 1.0
first_row = data[class_member_mask].iloc[0]
xy_pos = x_predict[class_member_mask & core_samples_mask]
plt.plot(
xy_pos[:, plot_features[0]],
xy_pos[:, plot_features[1]],
marker,
markerfacecolor=tuple(color),
markersize=marker_size,
)
if plot_label:
if not first_row.empty and plot_label in first_row:
p_label = first_row[plot_label]
try:
plt.annotate(
s=p_label,
xy=(xy_pos[0, plot_features[0]], xy_pos[0, plot_features[1]]),
fontsize=font_size,
alpha=alpha,
)
except IndexError:
pass
plt.xlabel(xlabel)
plt.ylabel(ylabel)
plt.title("Estimated number of clusters: %d" % n_clusters_)
plt.show()
return plt
#Average degree
N = G.order()
K = G.size()
avg_d = float(N) / K
avg_degree = 'Average degree: %.4f ' % (avg_d)
# Plot: Degree_centrality
plt.figure()
ax1 = plt.subplot(211)
plt.title('Degree centrality for nodes', fontsize=12)
a_lenght = np.arange(len(degc_value))
plt.bar(a_lenght[:50],
degc_value[:50],
color=cm.Spectral(degc_value),
align='center')
plt.xticks(a_lenght, degc_key, size='small', rotation=45)
plt.tick_params(axis='x', labelsize=4)
plt.tick_params(axis='y', labelsize=8)
plt.autoscale(enable=True, axis='both', tight=None)
#Top degree centrality:
topTable(degc_key, degc_value, 10)
plt.text(len(degc_value) * 0.75,
max(degc_value) * 0.4,
avg_degree,
bbox={
'facecolor': 'blue',
'alpha': 0.25,
'pad': 10
def extractData(self):
import matplotlib
import matplotlib.pyplot as plt
import matplotlib.cm as cm
from matplotlib.font_manager import FontProperties
self.plt = plt
data = {}
data["filename_plot"] = ""
webpage = open(self.source.getTmpPath())
strwebpage = webpage.read()
tree = lxml.html.parse(StringIO.StringIO(strwebpage))
rowlist = tree.findall(".//item")
StartDates = []
Jobs = [[0 for t in range(len(rowlist) - 1)]
for c in range(len(self.cat_names))]
for i in range(1, len(rowlist)):
ThisData = {key: 0 for key in self.tags}
for j in range(len(rowlist[i])):
if rowlist[i][j].tag == 's_date':
StartDates.append(rowlist[i][j].text_content())
else:
if rowlist[i][j].tag in self.tags:
ThisData[rowlist[i]
[j].tag] = rowlist[i][j].text_content()
for key, value in ThisData.iteritems():
Jobs[self.tags.index(key)][i - 1] = int(value)
# Calculate derived statistics
minJobs = [0 for c in range(len(self.cat_names))]
maxJobs = [0 for c in range(len(self.cat_names))]
avgJobs = [0 for c in range(len(self.cat_names))]
JobFractions = [[0 for t in range(len(StartDates))]
for c in range(len(self.cat_names))]
AggrJobsEval = 0
EvalFraction = 0.0
JobsEval = [0 for c in range(len(self.cat_names))]
JobFractionsEval = [0 for c in range(len(self.cat_names))]
JobsEvalColor = ['' for c in range(len(self.cat_names))]
for t in range(len(StartDates)):
Jobs[len(self.cat_names) - 1][t] = 0
for c in range(len(self.cat_names) - 1):
Jobs[len(self.cat_names) - 1][t] += Jobs[c][t]
for t in range(
len(StartDates) - 1,
len(StartDates) - 1 - self.eval_interval, -1):
for c in range(len(self.cat_names)):
JobsEval[c] += Jobs[c][t]
for c in range(len(self.cat_names)):
minJobs[c] = min(Jobs[c])
maxJobs[c] = max(Jobs[c])
for t in range(len(StartDates)):
if Jobs[len(self.cat_names) - 1][t] > 0:
JobFractions[c][t] = 100.0 * Jobs[c][t] / float(
Jobs[len(self.cat_names) - 1][t])
else:
JobFractions[c][t] = 0.0
avgJobs[c] += Jobs[c][t]
avgJobs[c] /= len(StartDates)
if JobsEval[len(self.cat_names) - 1] > 0:
JobFractionsEval[c] = 100.0 * JobsEval[c] / float(
JobsEval[len(self.cat_names) - 1])
else:
JobFractionsEval[c] = 0.0
# Calculate evaluation statistic
for item in self.eval_categories:
AggrJobsEval += JobsEval[self.cat_names.index(item)]
if JobsEval[len(self.cat_names) - 1] > 0:
EvalPercentage = 100.0 * AggrJobsEval / float(
JobsEval[len(self.cat_names) - 1])
else:
EvalPercentage = 0.0
# Set module status according to evaluation statistic
data['status'] = 1.0
if JobsEval[len(self.cat_names) - 1] >= self.eval_job_threshold:
if self.eval_warn_threshold[0] == '<':
if EvalPercentage <= self.eval_warn_threshold[1]:
data['status'] = 0.5
elif self.eval_warn_threshold[0] == '>':
if EvalPercentage >= self.eval_warn_threshold[1]:
data['status'] = 0.5
if self.eval_crit_threshold[0] == '<':
if EvalPercentage <= self.eval_crit_threshold[1]:
data['status'] = 0.0
elif self.eval_crit_threshold[0] == '>':
if EvalPercentage >= self.eval_crit_threshold[1]:
data['status'] = 0.0
# Color summary subtable cells in column evaluation according to module status
for item in self.eval_categories:
if data['status'] == 0.5:
JobsEvalColor[self.cat_names.index(item)] = 'warning'
elif data['status'] == 0.0:
JobsEvalColor[self.cat_names.index(item)] = 'critical'
# Save subtable data
for c in range(len(self.cat_names)):
self.statistics_db_value_list.append({
'CatName':
self.cat_names[c],
'JobsEval':
JobsEval[c],
'JobFracsEval':
'%.1f' % JobFractionsEval[c],
'JobsEvalColor':
JobsEvalColor[c],
'JobsCurrentHour':
Jobs[c][len(StartDates) - 1],
'JobFracsCurrentHour':
'%.1f' % JobFractions[c][len(StartDates) - 1],
'JobsLastHour':
Jobs[c][len(StartDates) - 2],
'JobFracsLastHour':
'%.1f' % JobFractions[c][len(StartDates) - 2],
'MinJobs':
minJobs[c],
'MaxJobs':
maxJobs[c],
'AvgJobs':
avgJobs[c]
})
# Function to convert raw time data given in UTC to local time zone
def ChangeTimeZone(TimeStringIn, InFormatString, OutFormatString):
Date = datetime.strptime(TimeStringIn, InFormatString).replace(
tzinfo=pytz.utc).astimezone(pytz.timezone('Europe/Berlin'))
return (Date.strftime(OutFormatString))
# Change times from utc to local
StartDatesRaw = StartDates[:]
for t in range(len(StartDates)):
StartDates[t] = ChangeTimeZone(StartDates[t], "%d-%b-%y %H:%M:%S",
"%d-%b-%y %H:%M:%S")
data['InstanceTitle'] = self.config['name']
data['IntervalStart'] = ChangeTimeZone(
tree.find(".//start").text_content().split(".")[0],
"%Y-%m-%d %H:%M:%S", "%d-%b-%y %H:%M:%S")
data['IntervalEnd'] = ChangeTimeZone(
tree.find(".//end").text_content().split(".")[0],
"%Y-%m-%d %H:%M:%S", "%d-%b-%y %H:%M:%S")
data['CurrentHourStart'] = StartDates[len(StartDates) -
1].split(' ')[1]
data['CurrentHourEnd'] = data['IntervalEnd'].split(' ')[1]
data['LastHourStart'] = StartDates[len(StartDates) - 2].split(' ')[1]
data['LastHourEnd'] = StartDates[len(StartDates) - 1].split(' ')[1]
data['EvaluationStart'] = StartDates[len(StartDates) -
self.eval_interval].split(' ')[1]
data['EvaluationEnd'] = data['IntervalEnd'].split(' ')[1]
######################################################################
### Plot data
#Colors = ['MidnightBlue', 'SteelBlue', 'LightSkyBlue', 'SeaGreen', \
# 'LightGreen', 'DarkKhaki', 'PaleGoldenrod', 'Khaki', 'LightSalmon', \
# 'Crimson', 'Maroon']
Colors = []
for i in range(len(self.cat_names) - 1):
# for list of colormaps see http://wiki.scipy.org/Cookbook/Matplotlib/Show_colormaps
Colors.append(
cm.Spectral(1.0 - i / max(float(len(self.cat_names) - 2), 1.0),
1))
# Colors.append(cm.spectral((i+1)/float(len(self.cat_names)-0), 1))
# Colors.append(cm.jet(i/float(len(self.cat_names)-2), 1))
# Colors.append(cm.gist_earth((i+1)/float(len(self.cat_names)-1), 1))
# Colors.append(cm.RdBu(1.0 - i/float(len(self.cat_names)-2), 1))
# Colors.append(cm.YlGnBu(1.0 - i/float(len(self.cat_names)-2), 1))
nbins = len(StartDates)
if nbins == 0:
# break image creation if there are no jobs
data[
'error_string'] = "No plot is generated because data source contains no jobs to be displayed."
data["filename_plot"] = ""
else:
ind = np.arange(nbins) # the x locations for the groups
width = 1.00 # the width of the bars: can also be len(x) sequence
max_val = maxJobs[len(self.cat_names) - 1]
xlabels = [0] * nbins
for i in range(0, nbins):
if i % 2 == 0:
DateLabel = StartDates[i].split(' ')[0].split('-')
TimeLabel = StartDates[i].split(' ')[1].split(':')
xlabels[i] = DateLabel[0] + '-' + DateLabel[1] + '\n' + \
TimeLabel[0] + ':' + TimeLabel[1]
else:
xlabels[i] = ''
# calculate bottom levels in order to enforce stacking
cat_bottoms = [[0 for t in range(len(StartDates))]
for c in range(len(self.cat_names) - 1)]
for cSet in range(1, len(self.cat_names) - 1):
for cGet in range(0, cSet):
for t in range(len(StartDates)):
cat_bottoms[cSet][t] += Jobs[cGet][t]
# Create figure and plot job numbers of the different categories
fig = self.plt.figure(figsize=(10, 5.8))
axis = fig.add_subplot(111)
p = [
axis.bar(ind,
Jobs[c],
width,
color=(getcolor(self.cat_names[c]) or Colors[c]),
bottom=cat_bottoms[c])
for c in range(len(self.cat_names) - 1)
]
# Prepare legend entries
p_leg = []
cat_leg = []
for i in range(len(p) - 1, -1, -1):
p_leg.append(p[i][0])
cat_leg.append(self.cat_names[i])
# Configure plot layout
fontTitle = FontProperties()
fontTitle.set_size('medium')
axis.set_title('24 hours from ' + data['IntervalStart'] + ' to ' \
+ data['IntervalEnd'] + ' (all times are local)',
fontproperties=fontTitle)
axis.set_position([0.10, 0.12, 0.68, 0.82])
axis.set_ylabel('Number of Jobs')
axis.set_xticks(ind + 0.0 * width / 2.0)
axis.set_xticklabels(xlabels, rotation='vertical')
axis.set_autoscaley_on(False)
axis.set_ylim([0, (max_val + 1.0) * 1.05])
fontLegend = FontProperties()
fontLegend.set_size('small')
axis.legend(p_leg,
cat_leg,
bbox_to_anchor=(1.02, 0.5),
loc=6,
ncol=1,
borderaxespad=0.,
prop=fontLegend)
fig.savefig(hf.downloadService.getArchivePath(
self.run, self.instance_name + "_jobs_dist.png"),
dpi=91)
data["filename_plot"] = self.instance_name + "_jobs_dist.png"
return data
import networkx as nx
import nxviz as nxv
#####
from matplotlib import cm
words = ['Biological Process', 'Molecular Function', 'Cellular Component']
pie_colors = {
'Set3': cm.Set3(np.arange(12) / 12.),
'Set2': cm.Set2(np.arange(8) / 8.),
'Set1': cm.Set1(np.arange(9) / 9.),
'Pastel2': cm.Pastel2(np.arange(8) / 8.),
'Pastel1': cm.Pastel1(np.arange(9) / 9.),
'Dark2': cm.Dark2(np.arange(8) / 8.),
'Paired': cm.Paired(np.arange(12) / 12.),
'Accent': cm.Accent(np.arange(8) / 8.),
'Spectral': cm.Spectral(np.arange(11) / 11.)
}
colors = {
'#8DD3C7': pie_colors['Set3'][0:1],
'#FFFFB3': pie_colors['Set3'][1:2],
'#BEBADA': pie_colors['Set3'][2:3],
'#FB8072': pie_colors['Set3'][3:4],
'#80B1D3': pie_colors['Set3'][4:5],
'#FDB462': pie_colors['Set3'][5:6],
'#B3DE69': pie_colors['Set3'][6:7],
'#FCCDE5': pie_colors['Set3'][7:8],
'#D9D9D9': pie_colors['Set3'][8:9],
'#BC80BD': pie_colors['Set3'][9:10],
'#CCEBC5': pie_colors['Set3'][10:11],
'#FFED6F': pie_colors['Set3'][11:12]
}
def extractData(self):
# set rack names and associated clusters
rack_001_010 = {
'rack_string': 'gridka_rack001-010',
'clusters': map(lambda x: '%03d' % (x+1), range(0,10))}
rack_011_020 = {
'rack_string': 'gridka_rack011-020',
'clusters': map(lambda x: '%03d' % (x+1), range(10,20))}
rack_021_030 = {
'rack_string': 'gridka_rack021-030',
'clusters': map(lambda x: '%03d' % (x+1), range(20,30))}
rack_101_110 = {
'rack_string': 'gridka_rack101-110',
'clusters': map(lambda x: '%03d' % (x+1), range(100,110))}
rack_111_120 = {
'rack_string': 'gridka_rack111-120',
'clusters': map(lambda x: '%03d' % (x+1), range(110,120))}
racks = [rack_001_010, rack_011_020, rack_021_030, rack_101_110, rack_111_120]
import matplotlib.pyplot as plt
import matplotlib.cm as cm
from matplotlib.font_manager import FontProperties
self.plt = plt
data = {}
data["filename_plot"] = ""
with open(self.source.getTmpPath()) as webpage:
rawdata = json.load(webpage)
# Function to convert raw time data given in UTC to local time zone
def ChangeTimeZone(TimeStringIn, InFormatString, OutFormatString):
Date = datetime.strptime(TimeStringIn, InFormatString).replace(
tzinfo=pytz.utc).astimezone(pytz.timezone('Europe/Berlin'))
return(Date.strftime(OutFormatString))
data['IntervalEnd'] = ChangeTimeZone(rawdata['meta']['date2'][0],
"%Y-%m-%d %H:%M:%S", "%d-%b-%y %H:%M:%S")
IntervalEnd = datetime.strptime(data['IntervalEnd'], "%d-%b-%y %H:%M:%S")
IntervalStart = IntervalEnd - timedelta(hours = self.eval_time)
data['IntervalStart'] = IntervalStart.strftime("%d-%b-%y %H:%M:%S")
#filter rawdata for jobs finished in eval_time or still running
if self.eval_time != 24:
for item in rawdata['jobs']:
try:
date = datetime.strptime(item['FinishedTimeStamp'], "%Y-%m-%dT%H:%M:%S").replace(
tzinfo=pytz.utc).astimezone(pytz.timezone('Europe/Berlin'))
if date < IntervalStart:
rawdata['jobs'].remove(item)
except Exception:
pass
# Prepare different attribute values (either use those indicated in
# config file or loop over data and get all different categories)
AttributeValues = []
if self.eval_attribute_value <> '':
AttributeValues.append(self.eval_attribute_value)
if self.attribute_values <> '':
AddAttributeValues = self.attribute_values.split('|')
for i in range(len(AddAttributeValues)):
if AddAttributeValues[i] not in AttributeValues:
AttributeValues.append(AddAttributeValues[i])
else:
for item in rawdata['jobs']:
if item[self.attribute] not in AttributeValues:
AttributeValues.append(item[self.attribute])
# Get all different primary and secondary keys for the selected attribute values
PrimaryKeys = []
SecondaryKeys = []
for item in rawdata['jobs']:
if item[self.attribute] in AttributeValues:
if item[self.primary_key] not in PrimaryKeys:
PrimaryKeys.append(item[self.primary_key])
if self.use_secondary_key == True:
SecondaryKeys.append(item[self.secondary_key])
# Get job numbers from raw data
Jobs = [[0 for k in range(len(PrimaryKeys))] for a in range(len(AttributeValues))]
for item in rawdata['jobs']:
if item[self.attribute] in AttributeValues:
Jobs[AttributeValues.index(item[self.attribute])][
PrimaryKeys.index(item[self.primary_key])] += 1
# Get total number of jobs across all categories per node
TotalJobsPerNode = [0 for k in range(len(PrimaryKeys))]
for k in range(len(PrimaryKeys)):
for a in range(len(AttributeValues)):
TotalJobsPerNode[k] += Jobs[a][k]
# Calculate module status
# a 'node' is the class of grouping, i.e. one line in the plot (a host, a workflow, ...)
data['status'] = 1.0
if self.eval_threshold > -1:
TotalEval = 0
if self.eval_mode == 1: # total jobs evaluation (total number of jobs at different nodes are compared to all nodes)
Statistics = [TotalJobsPerNode[k] for k in range(len(PrimaryKeys))]
for k in range(len(PrimaryKeys)):
TotalEval += Statistics[k]
elif self.eval_mode == 2: # global category evaluation (jobs in specified category is summed across all nodes)
i = AttributeValues.index(self.eval_attribute_value)
Statistics = 0
for k in range(len(PrimaryKeys)):
Statistics += Jobs[i][k]
TotalEval += TotalJobsPerNode[k]
elif self.eval_mode == 3: # local category evaluation (individual nodes are checked for specific category)
i = AttributeValues.index(self.eval_attribute_value)
Statistics = [Jobs[i][k] for k in range(len(PrimaryKeys))]
for k in range(len(PrimaryKeys)):
TotalEval += Statistics[k]
elif self.eval_mode == 4: # per node evaluation (individual nodes are checked for specific category and compared with all categories of the node)
i = AttributeValues.index(self.eval_attribute_value)
Statistics = [Jobs[i][k] for k in range(len(PrimaryKeys))]
if TotalEval >= self.eval_threshold:
if self.eval_mode == 1: # total jobs evaluation
if self.eval_threshold_warning > -1:
for k in range(len(PrimaryKeys)):
if 100.0 * Statistics[k] / float(TotalEval) >= float(
self.eval_threshold_warning):
data['status'] = 0.5
if self.eval_threshold_critical > -1:
for k in range(len(PrimaryKeys)):
if 100.0 * Statistics[k] / float(TotalEval) >= float(
self.eval_threshold_critical):
data['status'] = 0.0
elif self.eval_mode == 2: # global category evaluation
if self.eval_threshold_warning > -1:
if 100.0 * Statistics / float(TotalEval) >= float(
self.eval_threshold_warning):
data['status'] = 0.5
if self.eval_threshold_critical > -1:
if 100.0 * Statistics / float(TotalEval) >= float(
self.eval_threshold_critical):
data['status'] = 0.0
elif self.eval_mode == 3: # local category evaluation
if self.eval_threshold_warning > -1:
for k in range(len(PrimaryKeys)):
if 100.0 * Statistics[k] / float(TotalEval) >= float(
self.eval_threshold_warning):
data['status'] = 0.5
if self.eval_threshold_critical > -1:
for k in range(len(PrimaryKeys)):
if 100.0 * Statistics[k] / float(TotalEval) >= float(
self.eval_threshold_critical):
data['status'] = 0.0
elif self.eval_mode == 4: # per node evaluation
count = 0
if self.eval_threshold_warning > -1:
for k in range(len(PrimaryKeys)):
if 100.0 * Statistics[k] / float(TotalJobsPerNode[k]) >= float(
self.eval_threshold_warning):
data['status'] = 0.5
if self.eval_threshold_critical > -1:
for k in range(len(PrimaryKeys)):
if 100.0 * Statistics[k] / float(TotalJobsPerNode[k]) >= float(
self.eval_threshold_critical):
count += 1
if count <= 1:
data['status'] = 0.5
else:
data['status'] = 0.0
################################################################
### Plot data
# Get filtered subset of job numbers to plot
PlotIndices = []
if self.plot_filter_attribute_value in AttributeValues:
AttributeValueIndex = AttributeValues.index(
self.plot_filter_attribute_value)
CountsSet = set(Jobs[AttributeValueIndex])
Counts = [c for c in CountsSet]
Counts.sort(reverse=True)
for c in range(len(Counts)):
for k in range(len(PrimaryKeys)):
if Jobs[AttributeValueIndex][k] == Counts[c]:
PlotIndices.append(k)
else:
CountsSet = set(TotalJobsPerNode)
Counts = [c for c in CountsSet]
Counts.sort(reverse=True)
for c in range(len(Counts)):
for k in range(len(PrimaryKeys)):
if TotalJobsPerNode[k] == Counts[c]:
PlotIndices.append(k)
nbins = min(self.plot_filter_node_number, len(PlotIndices))
# Sort counts and get self.plot_filter_node_number highest
FilteredJobs = [[0 for k in range(nbins)] for a in AttributeValues]
TotalFilteredJobs = [0 for k in range(nbins)]
for a in range(len(AttributeValues)):
for k in range(nbins):
FilteredJobs[a][k] = Jobs[a][PlotIndices[k]]
TotalFilteredJobs[k] += FilteredJobs[a][k]
# Write filtered data to database
for k in range(nbins-1,-1,-1): # same ordering as in plot
for a in range(len(AttributeValues)-1,-1,-1): # same ordering as in plot
SubtableEntry = {
'PrimaryKey': PrimaryKeys[PlotIndices[k]],
'PrimaryKeyURL': '',
'SecondaryKey': '',
'AttributeValue': AttributeValues[a],
'AttributeData': FilteredJobs[a][k]}
if self.use_secondary_key == True:
SubtableEntry['SecondaryKey'] = SecondaryKeys[PlotIndices[k]]
if self.table_link_url <> '':
if self.primary_key == 'WNHostName':
cluster = PrimaryKeys[PlotIndices[k]].upper().split('-')
for r in range(len(racks)):
if len(cluster) > 1 and cluster[0]!='UNKNOWN' and cluster[1] in racks[r]['clusters']:
SubtableEntry['PrimaryKeyURL'] = self.table_link_url.\
replace('RACK', racks[r]['rack_string']).\
replace('CLUSTER', cluster[0] + '-' + cluster[1]).\
replace('HOST', PrimaryKeys[PlotIndices[k]])
elif self.primary_key == 'TaskMonitorId':
SubtableEntry['PrimaryKeyURL'] = self.table_link_url.\
replace('TASKMONITORID', PrimaryKeys[PlotIndices[k]].replace('wmagent_', ''))
self.statistics_db_value_list.append(SubtableEntry)
# calculate bottom levels in order to enforce stacking
Bottoms = [[0 for k in range(nbins)] for c in range(
len(AttributeValues))]
for cSet in range(1,len(AttributeValues)):
for cGet in range(0,cSet):
for k in range(nbins):
Bottoms[cSet][k] += FilteredJobs[cGet][k]
Colors = []
for i in range(len(AttributeValues)):
# for list of colormaps see http://wiki.scipy.org/Cookbook/Matplotlib/Show_colormaps
Colors.append(cm.Spectral(1.0 - i/max(float(len(AttributeValues)-1), 1.0), 1))
if nbins == 0:
# break image creation if there are no jobs
data['error_string'] = "No plot is generated because data source contains no jobs to be displayed."
data["filename_plot"] = ""
else:
max_width = max(TotalFilteredJobs)
xlabels = [0]*nbins
pos = np.arange(nbins)+0.5
fig = self.plt.figure(figsize=(self.image_width,self.image_height))
axis = fig.add_subplot(111)
p = [axis.barh(pos, FilteredJobs[a], left=Bottoms[a], align='center',
height=0.6, color= (getcolor(AttributeValues[a]) or Colors[a])) for a in range(len(AttributeValues))]
#fontyAxis = FontProperties()
#fontyAxis.set_size('small')
axis.set_yticks(pos)
#axis.set_yticklabels(xlabels, fontproperties=fontyAxis)
axis.set_yticklabels('')
fontyLabels = FontProperties()
fontyLabels.set_size('small')
fontyLabels.set_weight('bold')
for i in range(nbins):
xlabels[i] = PrimaryKeys[PlotIndices[i]]
if self.use_secondary_key == True:
xlabels[i] += ' (' + SecondaryKeys[PlotIndices[i]] + ')'
if self.plot_ylabels_ellipsis > 0 and len(xlabels[i]) > self.plot_ylabels_ellipsis + 3:
xlabels[i] = xlabels[i][:self.plot_ylabels_ellipsis] + '...'
if self.plot_ylabels_linebreak > 0 and len(xlabels[i]) > self.plot_ylabels_linebreak:
xlabels[i] = xlabels[i][:self.plot_ylabels_linebreak] + '\n' + xlabels[i][self.plot_ylabels_linebreak:]
plt.text(0.03*max_width, pos[i], '%s'%xlabels[i], ha='left', va='center', fontproperties = fontyLabels)
if self.eval_threshold > -1 and TotalEval >= self.eval_threshold:
if self.plot_line_warning == 1 and self.eval_threshold_warning >= 0:
axis.axvline(TotalEval * self.eval_threshold_warning / 100.0,
color='Yellow',lw=2)
if self.plot_line_critical == 1 and self.eval_threshold_critical >= 0:
axis.axvline(TotalEval * self.eval_threshold_critical / 100.0,
color='Red',lw=3)
# Prepare legend entries
p_leg = []
cat_leg = []
for i in range(len(p)-1,-1,-1):
p_leg.append(p[i][0])
cat_leg.append(AttributeValues[i])
# Configure plot layout
fontTitle = FontProperties()
fontTitle.set_size('medium')
axis.set_title('%s hours from ' %self.eval_time + data['IntervalStart'] + ' to ' \
+ data['IntervalEnd'] + ' (all times are local)',
fontproperties=fontTitle)
axis.set_position([self.plot_left,0.08,self.plot_width,0.86])
axis.set_xlabel('Number of Jobs')
fontLegend = FontProperties()
fontLegend.set_size('small')
axis.legend(p_leg, cat_leg, bbox_to_anchor=(1.02, 0.5), loc=6, ncol=1,
borderaxespad=0., prop = fontLegend)
fig.savefig(hf.downloadService.getArchivePath(self.run,
self.instance_name + "_jobs_dist.png"), dpi=91)
data["filename_plot"] = self.instance_name + "_jobs_dist.png"
data['PrimaryKey'] = self.primary_key
data['SecondaryKey'] = self.secondary_key
data['Attribute'] = self.attribute
return data