def colorbar_index(ncolors, cmap, orientation="vertical"):
cmap = cmap_discretize(cmap, ncolors)
mappable = cm.ScalarMappable(cmap=cmap)
mappable.set_array([])
mappable.set_clim(-0.5, ncolors+0.5)
colorbar = plt.colorbar(mappable, orientation=orientation)
colorbar.set_ticks(np.linspace(0, ncolors, ncolors))
colorbar.set_ticklabels(range(ncolors))
return colorbar
def generate_table(table_data, rows, columns):
df = DataFrame(table_data, index=rows, columns=columns)
base = 0
colorings = []
#colorings.append([base]*(len(rows)+1))
for column in columns:
vals = df[column].values
normal = normalize(vals.min() - 1, vals.max() + 1)
m = cm.ScalarMappable(
norm=matplotlib.colors.Normalize(vmin=vals.min(), vmax=vals.max()))
m.set_cmap("YlGn")
col_colors = m.to_rgba(vals)
print col_colors
colorings.append(col_colors)
#colorings.append(list(np.transpose(cm.hot(normal(vals)))[1]))
colorings = np.transpose(colorings, (1, 0, 2))
print colorings.shape
fig = figure(figsize=(15, 8))
ax = fig.add_subplot(111, frameon=True, xticks=[], yticks=[])
#print colorings
vals = df.values
the_table = table(cellText=vals,
rowLabels=df.index,
colLabels=df.columns,
colWidths=[0.13] * vals.shape[1],
loc='center',
cellColours=colorings,
fontsize=15)
#nrows, ncols = len(rows)+1, len(columns)+1
#hcell, wcell = 1, 1
#hpad, wpad = .5, 0
#fig = figure(figsize=(ncols*wcell+wpad, nrows*hcell+hpad))
#fig = figure()
#ax = fig.add_subplot(111)
#ax.axis('off')
#ax.table(cellText=table_data,
# rowLabels=rows,
# colLabels=columns,
# loc='center')
show()
close()
def plot_spikes(df, sample_type, ax=None, mi=None, mx=None):
if ax is None:
fig, ax = plt.subplots()
else:
fig = None
x = df[df['Sample Type'] == sample_type]['x']
y = df[df['Sample Type'] == sample_type]['z']
s = df[df['Sample Type'] == sample_type]['volume']
if mi is None:
mi = min(s)
mx = max(s)
norm = np.array([((i - mi) / (mx - mi)) * 100 for i in s])
colors_to_use = cm.rainbow(norm / max(norm))
colmap = cm.ScalarMappable(cmap=cm.rainbow)
colmap.set_array(colors_to_use)
t = ax.scatter(x, y, c=colors_to_use, s=norm, marker='o')
ax.set_xlim(150, 400)
if fig is not None:
fig.colorbar(colmap)
return (fig, ax)
return colmap
def plot_spike(df, spikename, ax=None, mi=None, mx=None):
if ax is None:
fig, ax = plt.subplots()
x = df[df['Sample name'] == spikename]['x']
y = df[df['Sample name'] == spikename]['z']
s = df[df['Sample name'] == spikename]['volume']
if mi is None:
mi = min(s)
mx = max(s)
norm = np.array([((i - mi) / (mx - mi)) * 75 for i in s])
colors_to_use = cm.rainbow(norm / max(norm))
colmap = cm.ScalarMappable(cmap=cm.rainbow)
colmap.set_array(colors_to_use)
ax.scatter(x, y, c=colors_to_use, s=norm, marker='o')
ax.set_xlim(0, 512)
fid = list(df[df['Sample name'] == spikename]['folderid'])[0]
ax.set_title('{0}\n{1}'.format(spikename, fid))
# if fig:
# fig.colorbar(colmap)
# return (fig, ax)
return colmap
def get_param_param_scores(param1,
param2,
param3=None,
dataPath=os.getcwd(),
score=0,
model=None):
param1_vals = []
param2_vals = []
param3_vals = []
score_vals = []
eachPoint = {} # dict of list as point coordinate : score list
model_pattern = re.compile("LG14modelID.*:\ *(\d+).")
param1Val_pattern = re.compile(str(param1) + ".*:\ *(\d+[\.\d*]*).*")
param2Val_pattern = re.compile(str(param2) + ".*:\ *(\d+[\.\d*]*).*")
param3Val_pattern = re.compile(str(param3) + ".*:\ *(\d+[\.\d*]*).*")
for fName in os.listdir(dataPath):
dirPath = os.path.join(dataPath, fName)
if os.path.isdir(dirPath) and fName.startswith("2017"):
try:
with open(os.path.join(dirPath, "score.txt"),
"r") as scoreFile:
obt_score = float(scoreFile.readline().rstrip())
except Exception:
continue
if obt_score < float(score):
continue
# If the score is ok
# lets check the model nb by getting the modelParams
with open(dirPath + "/modelParams.py", 'r') as paramsFile:
Paramsdata = paramsFile.readlines()
# only getting the results of the expected model
if (not model is None):
mod = int(
model_pattern.findall(
filter(lambda x: model_pattern.search(x),
Paramsdata)[0])[0])
if (mod != model):
continue
# get values
point = []
try:
val1 = float(
param1Val_pattern.findall(
filter(lambda x: param1Val_pattern.search(x),
Paramsdata)[0])[0])
param1_vals.append(val1)
point.append(val1)
except IndexError: # if there were no result : the variable name is wrong
reason = "------------- ERROR : Wrong variable name [" + str(
param1) + "]"
print reason
return plot_print_wrong(axis, reason)
try:
val2 = float(
param2Val_pattern.findall(
filter(lambda x: param2Val_pattern.search(x),
Paramsdata)[0])[0])
param2_vals.append(val2)
point.append(val2)
except IndexError: # if there were no result : the variable name is wrong
reason = "------------- ERROR : Wrong variable name [" + str(
param2) + "]"
print reason
return plot_print_wrong(axis, reason)
if not param3 is None:
try:
val3 = float(
param3Val_pattern.findall(
filter(lambda x: param3Val_pattern.search(x),
Paramsdata)[0])[0])
param3_vals.append(val3)
point.append(val3)
except IndexError: # if there were no result : the variable name is wrong
reason = "------------- ERROR : Wrong variable name [" + str(
param3) + "]"
print reason
return plot_print_wrong(axis, reason)
# saving every score for each point
point = tuple(point)
if eachPoint.has_key(point):
eachPoint[point].append(obt_score)
else:
eachPoint[point] = [obt_score]
score_vals.append(obt_score)
# end for
score_vals = np.array(score_vals)
colmap = cm.ScalarMappable(cmap=cm.hsv)
colmap.set_array(score_vals)
return param1_vals, param2_vals, param3_vals, eachPoint, score_vals, colmap
def fig2_b(df_orig, ax=None, mi=None, mx=None, use_fig=False, fig=None):
df = df_orig.copy(deep=True)
mono_names = list(
filter(lambda n: True if 'wild' not in n else False,
einkorn['Sample name'].unique()))[:13]
mono_names.extend(
list(
filter(lambda n: True if 'wild' in n else False,
einkorn['Sample name'].unique())))
df = df[df['Sample name'].isin(mono_names)]
df.ix[df['Sample Type'] == 'T. monococcum',
'x'] = df[df['Sample Type'] == 'T. monococcum']['x'] + 512
if ax is None:
fig, ax = plt.subplots()
x = df['x']
y = df['z']
s = df['volume']
if mi is None:
mi = min(s)
mx = max(s)
norm = np.array([((i - mi) / (mx - mi)) * 100 for i in s])
colors_to_use = cm.rainbow(norm / max(norm))
colmap = cm.ScalarMappable(cmap=cm.rainbow)
colmap.set_array(colors_to_use)
t = ax.scatter(x, y, c=colors_to_use, s=norm, marker='o')
if not use_fig:
colbar = fig.colorbar(colmap, ticks=[0, 0.5, 1])
colbar.ax.set_yticklabels([
r'{0:3.2f}mm$^3$'.format(mi),
r'{0:3.2f}mm$^3$'.format(df['volume'].mean()),
r'{0:3.2f}mm$^3$'.format(mx)
])
x1 = [300, 800]
squad = ['T. beoticum', 'T. monococcum']
ax.set_xticks(x1)
ax.set_xticklabels(squad, minor=False)
return (fig, ax)
else:
colbar = fig.colorbar(colmap, ticks=[0, 0.5, 1], ax=ax)
colbar.ax.set_yticklabels([
r'{0:3.2f}mm$^3$'.format(mi),
r'{0:3.2f}mm$^3$'.format(df['volume'].mean()),
r'{0:3.2f}mm$^3$'.format(mx)
])
x1 = [300, 800]
squad = ['T. beoticum', 'T. monococcum']
ax.set_xticks(x1)
ax.set_xticklabels(squad, minor=False)
return colmap
sns.distplot(initLoss)
plt.savefig(os.path.join(foldername, 'costs-dist.jpg'))
x = np.arange(len(initLoss))
sns.jointplot(x=x, y=initLoss)
plt.savefig(os.path.join(foldername, 'costs-seq.jpg'))
arr = np.array(list_ball[:len(initLoss)])
x = arr[:, 0]
y = arr[:, 1]
z = arr[:, 2]
fig = plt.figure(figsize=(8, 6))
ax = fig.add_subplot(111, projection='3d')
n = 100
cmap = cm.RdGy
colors = cmap(initLoss / max(initLoss))
colmap = cm.ScalarMappable(cmap=cmap)
colmap.set_array(initLoss)
yg = ax.scatter(x, y, z, c=colors, marker='o')
cb = fig.colorbar(colmap)
plt.savefig(os.path.join(foldername, 'viz_errors.jpg'))
plt.show()
np.set_printoptions(suppress=True,
formatter={'float_kind': '{:.20f},'.format},
linewidth=100) # Try to print 4 numbers on one line
# ----------------------------------------------------------------------------
# STEP1: Optimize R
# ----------------------------------------------------------------------------
if args.step == 1:
print(
print "size of X is: ", X.shape
print "size of Y is: ", Y.shape
Z=[[-58,-59.5,-65,-71,-76,-80,-84], [-65,-67,-71,-75.5,-80,-83,-85.5],[-72,-73,-75,-79,-82,-84,-87],[-75,-77,-80,-81,-84,-85.5,-90]]
'''Z=[]
Z.append([-58,-61,-66,-83,-69,-63,-58])
Z.append([-66, -69, -74, -86, -74, -69.5, -66.5])
Z.append([-75, -76, -81, -90, -85, -75.5, -72])
Z.append([-76, -80, -84, -91, -88, -83, -78])'''
print Z
#ax.plot_surface(X, Y, Z,cmap=cm.RdBu,vmin=-100, vmax=-50)
A = np.arange(-90, -50, 2)
ax.plot_trisurf(X.flatten(), Y.flatten(), np.array(Z).flatten(), color="Red", cmap='winter', shade=True, linewidth="0.7")
ax.set_xlabel('X coordinate')
ax.set_ylabel('Y coordinate')
ax.set_zlabel('Power')
m = cm.ScalarMappable(cmap=cm.winter)
m.set_array(A)
plt.colorbar(m)
# Plotting Power vs x,y,z in the case of single antenna
"""fig2 = plt.figure()
ax2 = fig2.add_subplot(111, projection='3d')
Z2 = []
Z2.append([-58,-59.5,-65,-71,-76,-80,-84])
Z2.append([-65,-67,-71,-75.5,-80,-83,-85.5])
Z2.append([-72,-73,-75,-79,-82,-84,-87])
Z2.append([-75,-77,-80,-81,-84,-85.5,-90])
ax2.plot_trisurf(X.flatten(), Y.flatten(), np.array(Z2).flatten(), color="Red", cmap='hot', shade=True, linewidth="0.7")
root = int(sqrt(num_concepts))
if root * root >= num_concepts:
columns = root
rows = root
elif root * (root + 1) >= num_concepts:
columns = root + 1
rows = root
else:
columns = root + 1
rows = root
# for each concept, create a colored scatter plot of all unlabeled data points
counter = 1
for label, memberships in validation_memberships.items():
colors = cm.jet(memberships)
colmap = cm.ScalarMappable(cmap=cm.jet)
colmap.set_array(memberships)
ax = fig.add_subplot(rows, columns, counter)
if ltn.default_type == "cuboid":
# also plot the actual box
import matplotlib.patches as patches
import shapely.geometry
from matplotlib.path import Path
def _path_for_core(cuboids, d1, d2):
"""Creates the 2d path for a complete core."""
polygon = None
for cuboid in cuboids:
p_min = cuboid[0]