def ColLegManager(colours=None, legend=None, N=None):
# If no dict of colours_map or legend or N has been entered
if not colours:
colours = None
if not legend:
legend = None
if not N:
N = len(legend) + 1
# Constructing list of indexes for alphabetically ordered molecule names in 'legend'
if legend is not None:
order = np.argsort(legend)
print("Order_of_mol_names: ", list(order))
def ColMatcher(*names):
for name in names:
if mol.find(name) != -1:
cols.append(key)
return cols
cols = []
if colours is not None:
# Sorting molecules by colours:
for mol in legend:
for key in list(colours.keys()):
cmap = colours[key]
if isinstance(cmap, (list, tuple)):
ColMatcher(*cmap)
else:
ColMatcher(cmap)
print("Input_legend: ", legend)
print("Matched_col_maps: ", cols)
# Creating list of different colour shades from selected colour map for each molecule:
paintings = [0] * len(cols)
# Matching different shades from selected colour map for each molecule, the gradient respects the alphabetical
# order of the molecules' names (first molecule is always the darkest, the shade gets lighter with each next)
q = 0
num_of_col = len(Counter(cols).keys())
for num in range(0, num_of_col):
clr = cols[order[q]]
numocc = cols.count(clr)
gradient = np.linspace(0.2, 1, 2 * numocc + 1)
for i in range(0, numocc):
loc = order[i + q]
paintings[loc] = plt.get_cmap(clr)(1 - gradient[i])
q = q + numocc
# Default setting - gradient of colours of preset colour map
if colours is None:
paintings = [0] * N
gradient = np.linspace(0.2, 1, N)
j = 0
for o in order:
paintings[o] = plt.get_cmap('inferno_r')(1 - gradient[j])
j = j + 1
return [order, paintings]
def multiplot_hexbin(b, s):
f1 = 'DER_mass_transverse_met_lep'
f2 = 'DER_mass_MMC'
f3 = 'DER_mass_jet_jet'
f4 = 'DER_pt_h'
feature_pairs = list(itertools.combinations([f1, f2, f3, f4], 2))
feature_pairs_ = list(itertools.chain(*zip(feature_pairs, feature_pairs)))
b_clean = b[(b[f1] != -999.0) & (b[f2] != -999.0) & (b[f3] != -999.0) &
(b[f4] != -999.0)]
s_clean = s[(s[f1] != -999.0) & (s[f2] != -999.0) & (s[f3] != -999.0) &
(s[f4] != -999.0)]
plt.figure(figsize=(15, 15))
multiplot_range = xrange(6)
for i, k in zip(multiplot_range, feature_pairs_[0:6]):
plt.subplot(str(32) + str(i + 1))
if i % 2:
plot_hexbin(s_clean, s_clean['Weight'], plt.get_cmap('Reds'), k)
else:
plot_hexbin(b_clean, b_clean['Weight'], plt.get_cmap('Blues'), k)
plt.tight_layout()
filename = '../Graphs/scatter1.png'
print 'Saving plot in ' + filename
plt.savefig(filename)
plt.figure(figsize=(15, 15))
multiplot_range = xrange(6)
for i, k in zip(multiplot_range, feature_pairs_[6:12]):
plt.subplot(str(32) + str(i + 1))
if i % 2:
plot_hexbin(s_clean, s_clean['Weight'], plt.get_cmap('Reds'), k)
else:
plot_hexbin(b_clean, b_clean['Weight'], plt.get_cmap('Blues'), k)
plt.tight_layout()
filename = '../Graphs/scatter2.png'
print 'Saving plot in ' + filename
plt.savefig(filename)
def get_cmap(cmap=None):
"""Get the color map.
Parameters
----------
cmap: str, mpl.colors.Colormap
The colormap can be provided as the name (should be in matplotlib or cmocean colormaps),
or as matplotlib colormap object.
Returns
-------
colormap:mpl.colors.Colormap
Matplotlib colormap object.
"""
if cmap:
if isinstance(cmap, (mpl.colors.Colormap)):
colormap = cmap
elif cmap in cmo.cmapnames:
colormap = cmo.cmap_d[cmap]
elif cmap in plt.colormaps():
colormap = plt.get_cmap(cmap)
else:
raise ValueError(
"Get unrecognised name for the colormap `{}`. Colormaps should be from standard matplotlib set of from cmocean package."
.format(cmap))
else:
colormap = plt.get_cmap("Spectral_r")
return colormap
def plot_spectrogram_to_numpy2(spectrogram1, spectrogram2, save_name):
fig, (ax1, ax2) = plt.subplots(nrows=2,
ncols=1,
figsize=(3, 3),
sharex=True,
sharey=True)
im = ax1.imshow(spectrogram1,
vmin=-11.53,
vmax=-0.5,
aspect="auto",
origin="lower",
cmap=plt.get_cmap('magma'),
interpolation='none')
plt.colorbar(im, ax=ax1)
plt.xlabel("Frames")
plt.ylabel("Channels")
plt.tight_layout()
ax2 = plt.subplot(2, 1, 2)
im2 = ax2.imshow(spectrogram2,
vmin=-11.53,
vmax=-0.5,
aspect="auto",
origin="lower",
cmap=plt.get_cmap('magma'),
interpolation='none')
plt.colorbar(im2, ax=ax2)
plt.xlabel("Frames")
plt.ylabel("Channels")
plt.tight_layout()
plt.savefig(save_name)
def plot_sun_image(img, filename, wavelength, title = '', vmin=0.0, vmax = 1.0):
if wavelength == 'hmi':
cmap = plt.get_cmap('hmimag')
else:
cmap = plt.get_cmap('sdoaia{}'.format(wavelength))
plt.title(title)
plt.imshow(img,cmap=cmap,origin='lower',vmin=vmin, vmax=vmax)
plt.savefig(filename)
plt.close("all")
def draw_mask(img, mask, blend=.5, cmap=None, interp='cubic'):
if not cmap:
import matplotlib.pylab as plt
cmap = plt.get_cmap('jet')
if isinstance(cmap, str):
import matplotlib.pylab as plt
cmap = plt.get_cmap(cmap)
if mask.shape[:2] != img.shape[:2]:
mask = imresize(mask, img.shape[:2], interp=interp)
return (cmap(mask)[:, :, :3] * 255 * blend + img *
(1 - blend)).round().astype('uint8')
def visualize(model, latent_dim, rangee, epoch):
viz = []
random_index = np.random.randint(len(X)-1)
X_random = X[random_index]
zi, zi_std = model.encode(torch.Tensor(X_random))
for j in range(latent_dim): # for each latent
buf = []
for i in rangee: # updating the z by adding the value in rangee
x = zi.clone()
x[j] += i
zi2 = torch.zeros(latent_dim)
gen_imgs = model.decode(model.reparameterize_static(x, zi2))
gen_imgs_np = gen_imgs.data.numpy()
buf.append(gen_imgs_np)
viz.append(buf)
lw = 2
N, M = 5, int(latent_dim / 5) # latent_dim = M x N.
cmap = plt.get_cmap('RdYlGn_r')
colors = cmap(np.linspace(0, 1.0,len(rangee)).tolist())
fig, axs = plt.subplots(M, N, sharex=True, sharey=True, figsize=(int(N*4), int(M*4)))
lantent_idx = 0
for i in range(M): # M: rows
for j in range(N): # N: columns
axs[i, j].plot(X_random, ls = '--', color = 'black', label='sample')
ts = np.array(viz[lantent_idx]).T
for k, value in enumerate(rangee):
axs[i, j].plot(ts[:,k], lw=lw, color=colors[k], label='z_%s+=%s'%(lantent_idx, rangee[k]))
axs[i, j].set_title('Updating z_%s, and others fixed'%lantent_idx)
axs[i, j].legend(bbox_to_anchor=(0, 0.02), loc=3, borderaxespad=0.2, ncol=2)
lantent_idx += 1
fig.suptitle('Training: epoch_%s with total %s latent states = %s'%(epoch,latent_dim, str(np.round(zi.tolist(),2))))
fig.savefig(figure_path + '/epoch_%s.png'%epoch, format="png")
def __init__(self,
obs_df,
ref_name,
var_name,
period,
how=np.mean,
annual_rule='A'):
self.period = period
self.var_name = var_name
self.ref_name = ref_name
self.aggr_how = how
self.annual_rule = annual_rule
obs_df = obs_df.loc[(obs_df.index >= period[0])
& (obs_df.index <= period[-1])]
self.obs = New()
self.obs.data = obs_df
self.obs.freq = infer_freq(obs_df)
if self.obs.freq != 'y':
self.obs.monthly = self.obs.data.resample(rule='m',
how=self.aggr_how)
self.obs.annual = self.obs.data.resample(rule='A', how=self.aggr_how)
# self.obs.freq = infer_freq(obs_df)
self.models = ObjectDict()
self._cmap = plt.get_cmap('gist_rainbow')
self.selection = Selector([])
def simulate_sequence(D, L, iterations, min_size, max_size, step_size, loop_avoid, reflect):
poly = Polymer(D, L, loop_avoid, reflect=reflect)
data = []
for N in range(min_size,max_size, step_size):
print N #Poor's man progress bar
data_per_N = []
bad_number = 0
for i in range(iterations):
(last, count, grid) = poly.create_polymer(N)
dist = linalg.norm(last - poly.start_point)
#print [dist,count,N]
df = pd.DataFrame({"dist":[dist], "N": [N], "count" : [count]})
data.append(df)
#Save some example realization.
if i == 10 and D == 2:
pylab.figure()
pylab.imshow(grid, cmap=pylab.get_cmap("binary"), interpolation="none")
pylab.savefig("realization_N=%d_self_avoid=%d" % (N, loop_avoid))
bad_ratio = 1.0*bad_number/iterations
if bad_ratio > 0.02:
print "To many bads with N=%d. Bad ratio %.3f" % (N, bad_ratio)
#draw_distribution(D,L,N,iterations,loop_avoid, data_per_N)
#R2 = (data_per_N**2).mean()
#data.append((R2, N))
data = pd.concat(data)
return data
def ShowSlice(vals, min_val, max_val):
import matplotlib.pyplot as plt
# tell imshow about color map so that only set colors are used
img = plt.imshow(vals,cmap = plt.get_cmap('gray'),vmin=min_val, vmax=max_val)
plt.show()
def plot_3d(arr, colorsMap='jet'):
def make_2d_to_3d_array(arr1):
x = []
y = []
z = []
for i in range(0, len(arr1)):
for j in range(0, len(arr1[0])):
x.append(i)
y.append(j)
z.append(arr1[i][j])
return [x, y, z]
points = make_2d_to_3d_array(arr)
cm = plt.get_cmap(colorsMap)
cNorm = matplotlib.colors.Normalize(vmin=min(points[2]),
vmax=max(points[2]))
scalarMap = cmx.ScalarMappable(norm=cNorm, cmap=cm)
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
ax.scatter(points[0], points[1], points[2], c=scalarMap.to_rgba(points[2]))
scalarMap.set_array(points[2])
cbar = fig.colorbar(scalarMap)
cbar.ax.tick_params(labelsize=20)
ax.tick_params(axis='x', labelsize=20)
ax.tick_params(axis='y', labelsize=20)
ax.tick_params(axis='z', labelsize=20)
# ax.set_xlabel("X direction",fontsize = 20)
# ax.set_ylabel("Y direction",fontsize = 20)
# ax.set_zlabel("Temperature",fontsize = 20)
plt.show()
def showImagesGrid(imageDatas,
colCnt=None,
rowCnt=None,
gap=0.03,
sigsize=5,
cmap=None):
plt.figure(figsize=(sigsize, sigsize))
imgSize = len(imageDatas)
if cmap is None:
cmap = plt.get_cmap('gray')
if rowCnt is None:
if colCnt is None:
colCnt = math.ceil(math.sqrt(imgSize))
rowCnt = colCnt
for idx in range(imgSize):
plt.subplot(colCnt, rowCnt, idx + 1)
plt.imshow(imageDatas[idx], cmap=cmap)
plt.axis("off")
plt.subplots_adjust(left=0.1,
bottom=0.1,
right=0.9,
top=0.9,
wspace=gap,
hspace=gap)
plt.show()
def __init__(self,name):
self.name=name
self.log=False
self.filter=lambda x:x
self.vmin=None
self.vmax=None
self._norm=None
self.compression=6
self.set_depth(8)
m=CM_RE.match(name)
if m!=None:
LOG.debug("%s -> %s",name,repr(m.groups()))
cmap,min_val,max_val,under_color,over_color,bad_color=m.groups()
if cmap.endswith('-log'):
self.filter=np.log10
self.log=True
cmap=cmap[:-4]
self.cmap=get_cmap(cmap)
if min_val and max_val:
self.set_minmax(float(min_val),float(max_val))
if under_color: self.cmap.set_under('#'+under_color[:6],alpha=int(under_color[6:],16)/255.0 if under_color[6:] else 1.0)
if over_color: self.cmap.set_over('#'+over_color[:6],alpha=int(over_color[6:],16)/255.0 if over_color[6:] else 1.0)
if bad_color: self.cmap.set_bad('#'+bad_color[:6],alpha=int(bad_color[6:],16)/255.0 if bad_color[6:] else 1.0)
try:
from PIL import Image
self.Image=Image
self._write=self._write_pil
LOG.debug('Using PIL for image writing')
except ImportError:
self._write=self._write_png
LOG.debug('Using PNG for image writing')
def plot_param_by_run(self, bins, h, lbl, logscale=False, ax=None):
#runs = np.linspace(self.runs[0]-0.5, self.runs[-1]+0.5, self.nrun+1)
runs = np.linspace(0.5, self.nrun + 0.5, self.nrun + 1)
hmn = np.min(h[h > 0])
hmn = 1e-4
y, x = np.meshgrid(runs, bins, indexing='ij')
plt.rc('text', usetex=True)
plt.rc('font', family='serif', size=16)
if ax is None:
fig = plt.figure(figsize=(16, 4))
ax = fig.gca()
cmap = plt.get_cmap()
cmap.set_bad(cmap(0))
ax.pcolor(x, y, h, norm=LogNorm(), vmin=hmn, cmap=cmap)
if logscale:
ax.set_xscale('log')
ax.set_ylim(self.nrun + 0.5, 0.5)
ax.set_xlabel(lbl)
ax.set_ylabel("run")
#ax.get_xaxis().set_major_formatter(LogFormatterExponent())
#ax.get_xaxis().set_minor_formatter(ScalarFormatter())
ax.set_yticks(runs[:-1] + 0.5)
ax.set_yticklabels(self.runs, fontsize=14)
def plot_image(img, img_number, row0, col0, img_size, vmin=0, vmax=600):
"""
Plot 6x6 or 8x8 background image
:param img: current bgd image, always 8x8
:param img_number: number of image, or number of time frame,
to fetch appropriate item from row0/col0
:param row0: list with size=nframes containing IMGROW0
:param row0: list with size=nframes containing IMGCOL0
:img_size: image size, 8px for ER, 6px for Science,
to fetch and plot bgd image part used for bgd subtraction
"""
r_min, r_max, c_min, c_max = patch_coords(row0, col0, img_size)
# +3 chosen arbitrary, to plot a bit larger area
data = vmin * np.ones((c_max - c_min + 3, r_max - r_min + 3))
dr = row0[img_number] - r_min
dc = col0[img_number] - c_min
data[dr:dr + img_size, dc:dc + img_size] = img[:img_size, :img_size]
im = plt.imshow(data,
cmap=plt.get_cmap('hot'),
interpolation='none',
origin='lower',
vmin=vmin,
vmax=vmax)
return im
def get_colormap(ptype, units="mm/h", colorscale="pysteps"):
"""
Function to generate a colormap (cmap) and norm.
Parameters
----------
ptype : {'intensity', 'depth', 'prob'}, optional
Type of the map to plot: 'intensity' = precipitation intensity field,
'depth' = precipitation depth (accumulation) field,
'prob' = exceedance probability field.
units : {'mm/h', 'mm', 'dBZ'}, optional
Units of the input array. If ptype is 'prob', this specifies the unit of
the intensity threshold.
colorscale : {'pysteps', 'STEPS-BE', 'BOM-RF3'}, optional
Which colorscale to use. Applicable if units is 'mm/h', 'mm' or 'dBZ'.
Returns
-------
cmap : Colormap instance
colormap
norm : colors.Normalize object
Colors norm
clevs: list(float)
List of precipitation values defining the color limits.
clevs_str: list(str)
List of precipitation values defining the color limits (with correct
number of decimals).
"""
if ptype in ["intensity", "depth"]:
# Get list of colors
color_list, clevs, clevs_str = _get_colorlist(units, colorscale)
cmap = colors.LinearSegmentedColormap.from_list(
"cmap", color_list, len(clevs) - 1
)
if colorscale == "BOM-RF3":
cmap.set_over("black", 1)
if colorscale == "pysteps":
cmap.set_over("darkred", 1)
if colorscale == "STEPS-BE":
cmap.set_over("black", 1)
norm = colors.BoundaryNorm(clevs, cmap.N)
cmap.set_bad("gray", alpha=0.5)
cmap.set_under("none")
return cmap, norm, clevs, clevs_str
if ptype == "prob":
cmap = copy.copy(plt.get_cmap("OrRd", 10))
cmap.set_bad("gray", alpha=0.5)
cmap.set_under("none")
clevs = np.linspace(0, 1, 11)
clevs[0] = 1e-3 # to set zeros to transparent
norm = colors.BoundaryNorm(clevs, cmap.N)
clevs_str = [f"{clev:.1f}" for clev in clevs]
return cmap, norm, clevs, clevs_str
return cm.get_cmap("jet"), colors.Normalize(), None, None
def makePlot(iFile, title, pltz, c):
roiMat = []
for l in iFile:
roiMat.append(l)
roiMat = np.array(roiMat)
roiMat = roiMat.astype(np.float)
axes = plt.subplot2grid((4,1), (c, 0))
pltz.append(axes)
#pltz[c].set_title(title)
#_#_#_#_#_#
cmap = plt.get_cmap(lut=np.nanmax(roiMat)-np.nanmin(roiMat)+1)
pltz[c].matshow(roiMat, aspect='auto', cmap=cmap, vmin=0, vmax=40)
#pltz[c].colorbar(label='Count')
if c == 3:
pltz[c].set_xlabel('ROI')
pltz[c].set_ylabel(title)
if c == 0:
pltz[c].set_xticks(range(30))
pltz[c].set_xticklabels(["1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24", "25", "26", "27", "28", "29", "30"])
else:
pltz[c].set_xticklabels([])
pltz[c].set_yticks(range(7))
pltz[c].set_yticklabels(["E", "G", "L", "M", "R", "S", "W"], rotation =90)
for asd, cas in enumerate(roiMat):
for sdf, c in enumerate(cas):
plt.text(sdf-.4, asd+.2, int(c), fontsize=8)
def plot_value_function(self, value_function, prefix, v_folder):
fig, ax = plt.subplots(subplot_kw=dict(projection='3d'))
X, Y = np.meshgrid(np.arange(self.config.input_size[1]),
np.arange(self.config.input_size[0]))
reproj_value_function = value_function.reshape(
self.config.input_size[0], self.config.input_size[1])
"""Build the support"""
for i in range(len(X)):
for j in range(int(len(X[i]) / 2)):
tmp = X[i][j]
X[i][j] = X[i][len(X[i]) - j - 1]
X[i][len(X[i]) - j - 1] = tmp
cm.jet(
np.random.rand(reproj_value_function.shape[0],
reproj_value_function.shape[1]))
ax.plot_surface(X,
Y,
reproj_value_function,
rstride=1,
cstride=1,
cmap=plt.get_cmap('jet'))
plt.gca().view_init(elev=30, azim=30)
plt.savefig(
os.path.join(v_folder,
"SuccessorFeatures" + prefix + 'value_function.png'))
plt.close()
def get_cmap(cmap_name):
"""Return matplotlib colormap object.
From matplotlib.cm or cmocean.
Additional custom colormap for salinity is provided:
- "custom_salinity1"
"""
cm.register_cmap(name='cubehelix3',
data=mpl._cm.cubehelix(gamma=1.0, s=2.0, r=1.0, h=3))
if cmap_name in cmo.cmapnames:
colormap = cmo.cmap_d[cmap_name]
elif cmap_name in plt.colormaps():
colormap = plt.get_cmap(cmap_name)
elif cmap_name == "custom_salinity1":
colormap = shiftedcolormap(cm.get_cmap("cubehelix3"),
start=0,
midpoint=0.89,
stop=0.9,
name='shiftedcmap')
else:
raise ValueError('Get unrecognised name for the colormap `{}`.\
Colormaps should be from standard matplotlib \
set or from cmocean package.'.format(cmap_name))
return colormap
def getPolyFit(deg=6):
#{{{docstring
"""
Get the polynomial fit
Parameters
----------
deg : int
Degree of polynomial to use
Returns
-------
p : array
The polynomial coefficients in ascending order.
NOTE: This is revesered as compared to np.polyfit
polyStr : str
String of the polynomial function.
Meant to use in a C++ program.
"""
#}}}
cmap = plt.get_cmap("viridis")
p = np.polyfit(TeEV, nuEN, deg)
# polyfit gives coefficients of highest polynomial first
p = p[::-1]
polyStr = ""
for i in range(deg + 1):
polyStr += "{:+f}*pow(Te0_, {})\n".format(p[i], i)
if polyStr[0] == "+":
polyStr = polyStr[1:]
polyStr = "nuEN = (nn/2.5e-19)*(\n" + polyStr
polyStr += ");"
return p, polyStr
def make_prediction(i):
test_img = test_images[i]
test_data= x_test[[i], :]
plt.imshow(test_img, cmap=plt.get_cmap('gray'))
plt.title("Model Prediction: {}".format(num_to_text[model.predict_classes(test_data)[0]]))
plt.show()
def ShowSlice(vals, min_val, max_val):
import matplotlib.pyplot as plt
# tell imshow about color map so that only set colors are used
img = plt.imshow(vals,cmap = plt.get_cmap('gray'),vmin=min_val, vmax=max_val)
plt.show()
def plot_value_function(self, value_function, prefix, folder=None):
if folder is None:
folder = self.summary_path
'''3d plot of a value function.'''
fig, ax = plt.subplots(subplot_kw=dict(projection='3d'))
X, Y = np.meshgrid(np.arange(self.config.input_size[1]),
np.arange(self.config.input_size[0]))
Z = value_function.reshape(self.config.input_size[0],
self.config.input_size[1])
for i in range(len(X)):
for j in range(int(len(X[i]) / 2)):
tmp = X[i][j]
X[i][j] = X[i][len(X[i]) - j - 1]
X[i][len(X[i]) - j - 1] = tmp
my_col = cm.jet(np.random.rand(Z.shape[0], Z.shape[1]))
ax.plot_surface(X,
Y,
Z,
rstride=1,
cstride=1,
cmap=plt.get_cmap('jet'))
plt.gca().view_init(elev=30, azim=30)
plt.savefig(
os.path.join(folder,
"SuccessorFeatures" + prefix + 'value_function.png'))
plt.close()
def plotBasisFunctions(self, eigenvalues, eigenvectors):
"""3d plot of the basis function. Right now I am plotting eigenvectors,
so each coordinate of the eigenvector correspond to the value to be
plotted for the correspondent state."""
for i in range(len(eigenvalues)):
fig, ax = plt.subplots(subplot_kw=dict(projection="3d"))
X, Y = np.meshgrid(np.arange(self.numRows),
np.arange(self.numCols))
Z = eigenvectors[:, i].reshape(self.numCols, self.numRows)
for ii in range(len(X)):
for j in range(len(X[ii]) // 2):
tmp = X[ii][j]
X[ii][j] = X[ii][len(X[ii]) - j - 1]
X[ii][len(X[ii]) - j - 1] = tmp
my_col = cm.jet(np.random.rand(Z.shape[0], Z.shape[1]))
ax.plot_surface(X,
Y,
Z,
rstride=1,
cstride=1,
cmap=plt.get_cmap("jet"))
plt.gca().view_init(elev=30, azim=30)
plt.savefig(self.outputPath + str(i) + "_eig" + ".png")
plt.close()
plt.plot(eigenvalues, "o")
plt.savefig(self.outputPath + "eigenvalues.png")
def visualize_model(self):
'''
VISUALIZATION
TO DO: qualitative analysis of a confusion matrix from the 2d display
'''
plt.figure( figsize=(7,7))
cm = plt.get_cmap('viridis')
colors = iter( cm( np.linspace(0,1,10)))
for digit in range(10):
# train_images = x_train[ train_digit_indices[digit]]
# train_vector = base_network.predict( train_images)
# train_vector = np.mean( train_vector, axis=0)
# test_images = x_test[ test_digit_indices[digit]]
# test_vector = base_network.predict( test_images)
# test_vector = np.mean( test_vector, axis=0)
# print( train_vector, test_vector)
color = next(colors)
# plt.quiver( 0,0 , *train_vector, label='%d train'%digit, color=color)
# plt.quiver( 0,0, *test_vector, label='%d test'%digit, color=color)
# plt.plot( *train_vector.reshape(2,1), label='%d train'%digit, color=color, marker=r'$%d$'%digit, markersize=22, ls='none')
# plt.plot( *test_vector.reshape(2,1), label='%d train'%digit, color=color, marker=r'$%d$'%digit, markersize=22, ls='none')
# running for train, test concatenation (because we checked similarity)
images = np.concatenate( (self.x_train[ self.train_digit_indices[digit]], self.x_test[ self.test_digit_indices[digit]]), axis=0)
vector = self.base_network.predict( images, batch_size=128)
# vector = np.mean( vector, axis=0)
# plt.plot( *vector.reshape(2,1), label='%d'%digit, color=color, marker=r'$%d$'%digit, markersize=22, ls='none')
# PLOTTING DISTRIBUTION INSTEAD
x, y = vector.T
sns.kdeplot(x, y, shade=True, shade_lowest=False, color=color, label=digit)
plt.legend(ncol=2)
plt.xticks( [])
plt.yticks( [])
plt.tight_layout()
plt.show()
def plotValueFunction(self, valueFunction, prefix):
'''3d plot of a value function.'''
fig, ax = plt.subplots(subplot_kw=dict(projection='3d'))
X, Y = np.meshgrid(np.arange(self.numCols), np.arange(self.numRows))
Z = valueFunction.reshape(self.numRows, self.numCols)
for i in range(len(X)):
for j in range(int(len(X[i]) / 2)):
tmp = X[i][j]
X[i][j] = X[i][len(X[i]) - j - 1]
X[i][len(X[i]) - j - 1] = tmp
my_col = cm.jet(np.random.rand(Z.shape[0], Z.shape[1]))
ax.plot_surface(X,
Y,
Z,
rstride=1,
cstride=1,
cmap=plt.get_cmap('jet'))
plt.gca().view_init(elev=30, azim=30)
plt.savefig(
os.path.join(self.outputPath,
"SuccessorFeatures" + prefix + 'value_function.png'))
plt.close()
def multicolcheck(pipeline,
subsample=0.03,
dA=20,
xrange=[-1000, 3000],
yrange=[-1000, 6000]):
p = pipeline
plt.figure()
plt.subplot(1, 2, 1)
estimator = scatterdens(p['fitResults_Ag'],
p['fitResults_Ar'],
subsample=subsample,
s=10)
plt.xlim(xrange)
plt.ylim(yrange)
x1d = np.arange(xrange[0], xrange[1], dA)
y1d = np.arange(yrange[0], yrange[1], dA)
x2d = x1d[:, None] * np.ones_like(y1d)[None, :]
y2d = np.ones_like(x1d)[:, None] * y1d[None, :]
imd = estimator.evaluate([x2d.flatten(), y2d.flatten()])
imd2d = imd.reshape(x2d.shape)
imd2d /= imd2d.max()
#plt.figure()
plt.subplot(1, 2, 2)
plt.imshow(imd2d[:, ::-1].transpose(),
cmap=plt.get_cmap('jet'),
extent=[xrange[0], xrange[1], yrange[0], yrange[1]])
plt.grid(True)
return imd2d
def draw_matrix_user_ranking(df_stat, higher_better=False, fig=None):
""" show matrix as image, sorted per column and unique colour per user
:param DF df_stat: table where index are users and columns are scoring
:param bool higher_better: ranking such that larger value is better
:return Figure:
>>> import pandas as pd
>>> df = pd.DataFrame(np.random.random((5, 3)), columns=list('abc'))
>>> fig = draw_matrix_user_ranking(df)
"""
ranking = compute_matrix_user_ranking(df_stat, higher_better)
if fig is None:
fig, _ = plt.subplots(
figsize=np.array(df_stat.as_matrix().shape[::-1]) * 0.35)
ax = fig.gca()
arange = np.linspace(-0.5, len(df_stat) - 0.5, len(df_stat) + 1)
norm = plt_colors.BoundaryNorm(arange, len(df_stat))
fmt = plt_ticker.FuncFormatter(lambda x, pos: df_stat.index[x])
draw_heatmap(ranking,
np.arange(1,
len(df_stat) + 1),
df_stat.columns,
ax=ax,
cmap=plt.get_cmap('nipy_spectral', len(df_stat)),
norm=norm,
cbar_kw=dict(ticks=range(len(df_stat)), format=fmt),
cbarlabel='Users')
ax.set_ylabel('Ranking')
return fig
def plot_runs(runs):
""" Plot population evolutions
"""
ts = range(len(runs[0]))
cmap = plt.get_cmap('viridis')
for i, r in enumerate(runs):
mean, var = zip(*r)
bm, cm = zip(*mean)
bv, cv = zip(*var)
color = cmap(float(i)/len(runs))
plt.errorbar(ts, bm, fmt='-', yerr=bv, c=color)
plt.errorbar(ts, cm, fmt='--', yerr=cv, c=color)
plt.title('population evolution overview')
plt.xlabel('time')
plt.ylabel('value')
plt.ylim((0, 1))
plt.plot(0, 0, '-', c='black', label='benefit value')
plt.plot(0, 0, '--', c='black', label='cost value')
plt.legend(loc='best')
plt.savefig('result.pdf')
plt.show()
def plot_IR_distribution(self, bR, bI, H, ax=None):
plt.rc('text', usetex=False)
plt.rc('font', family='serif', size=16)
plt.rc('xtick', labelsize=14)
plt.rc('ytick', labelsize=14)
plt.rc('axes', labelsize=16)
plt.rc('axes', titlesize=16)
if ax is None:
fig = plt.figure(figsize=(8, 6))
ax = fig.gca()
cmap = plt.get_cmap()
cmap.set_bad(cmap(0))
x, y = np.meshgrid(bR, bI)
im = ax.pcolor(x, y, H, norm=LogNorm(), cmap=cmap)
ax.set_yscale('log')
ax.set_xscale('log')
ax.set_ylabel(self.lbl[1])
ax.set_xlabel(self.lbl[2])
return im
def colorize(vector,cmap='plasma', vmin=None, vmax=None):
"""Convert a vector to RGBA colors.
Parameters
----------
vector : array
Array of values to be represented by relative colors
cmap : str (optional)
Matplotlib Colormap name
vmin : float (optional)
Minimum value for color normalization. Defaults to np.min(vector)
vmax : float (optional)
Maximum value for color normalization. Defaults to np.max(vector)
Returns
-------
vcolors : np.ndarray
Array of RGBA colors
scalarmap : matplotlib.cm.ScalarMappable
ScalerMap to convert values to colors
cNorm : matplotlib.colors.Normalize
Color normalization
"""
if vmin is None: vmin = np.min(vector)
if vmax is None: vmax = np.max(vector)
cm = plt.get_cmap(cmap)
cNorm = colors.Normalize(vmin=vmin, vmax=vmax)
scalarmap = cmx.ScalarMappable(norm=cNorm, cmap=cm)
vcolors = scalarmap.to_rgba(vector)
return vcolors,scalarmap,cNorm
def random_colormap(N, colormap='jet', name='random', seed=None):
"""
Create a random ordered colormap. Default settings creates a colormap named 'random'
using the jet colormap.
Parameters
-----------
N : int
Number of bins in the colormap.
colormap : str (optional)
Name of matplotlib colormap
name : str (optional)
Name of the colormap
seed : int or None
Random seed
Returns
--------
cmap : matplotlib.colors.ListedColormap object
"""
if seed is not None:
np.random.seed(seed)
vals = np.arange(0, 1, 1 / N)
np.random.shuffle(vals)
cmap = plt.get_cmap(colormap)
cmap_random = ListedColormap(cmap(vals), name=name)
return cmap_random
def plot_line_colored(x, y, t, w=None, color=None, cmap=None):
import numpy as np
from matplotlib.collections import LineCollection
# Create a set of line segments so that we can color them individually
# This creates the points as a N x 1 x 2 array so that we can stack points
# together easily to get the segments. The segments array for line collection
# needs to be numlines x points per line x 2 (x and y)
points = np.array([x, y]).T.reshape(-1, 1, 2)
segments = np.concatenate([points[:-1], points[1:]], axis=1)
extra = {}
if w is None: extra['linewidths'] = w
# Create the line collection object, setting the colormapping parameters.
# Have to set the actual values used for colormapping separately.
lc = LineCollection(segments,
cmap=p.get_cmap(cmap),
**extra
#norm=p.Normalize(0, 10)
)
lc.set_array(t)
lc.set_linewidth(w)
if color is not None:
lc.set_color(color)
p.gca().add_collection(lc)
def over_plot_googlemap(self):
import folium
from folium import plugins
import matplotlib.colors as colors
import matplotlib.cm as cmx
colorMap = plt.get_cmap('cool')
cNorm = colors.Normalize(vmin=1920, vmax=1990)
scalarMap = cmx.ScalarMappable(norm=cNorm, cmap=colorMap)
x = self.dic_nodes['x']; y = self.dic_nodes['y']
Lead = 10**np.array( self.dic_nodes['value'] ) - 1.
Year = self._generate_new_value(tag='Year Built')
map = folium.Map(location=[43.0125, -83.6875], zoom_start=13)
for i in range(len(x)):
colorVal = scalarMap.to_rgba(Year[i])
colorVal = colors.rgb2hex(colorVal)
radius = 40*np.sqrt(Lead[i])
disc = 'Expected Lead : %i\n'%Lead[i] +\
'Expected Year : %i\n'%Year[i]
folium.CircleMarker([y[i], x[i]], radius=radius,
popup=disc, color=None,
fill_color=colorVal).add_to(map)
map.create_map(path='prediction.html')
def pie_plot_important_activities_2018(
): # pie_plot_important_activities_2018(kaggleSurveyDF_2018, schemaSurveyDF_2018 ):
responseCountsList = []
responseOptionsTextListAnnotated = [
'Analyze and understand data',
'Use ML services to improve product or wokflows',
'Build/run data infrastructure',
'Apply ML to new areas and build prototypes',
'Research/advance state of the art in ML',
'Other / None of these activities are important to my role'
]
responseCountsList = [9532, 5481, 5233, 7233, 4934, 4663]
plt.figure()
plt.pie(x=responseCountsList,
labels=responseOptionsTextListAnnotated,
startangle=90,
autopct='%1.1f%%',
wedgeprops={
'linewidth': 1,
'edgecolor': 'white'
},
colors=np.array(plt.get_cmap('tab20').colors))
plt.title(
'What activities make up an important part of your role at work?')
plt.show()
def draw_custom(G,
pos=None,
node_size=1000,
edge_width=3,
font_size=12,
node_color='white',
color_map='Blues',
edge_label=None):
"""Draw the graph G using Matplotlib.
Draw the graph with Matplotlib with options for node positions,
labeling, titles, and many other drawing features.
"""
if not pos:
pos = nx.circular_layout(G)
nx.draw_networkx_nodes(G, pos, node_color=node_color, node_size=node_size)
nx.draw_networkx_edges(G,
pos,
width=edge_width,
edge_color=range(nx.number_of_edges(G)),
edge_cmap=plt.get_cmap(color_map),
edge_vmin=-10,
edge_vmax=10)
nx.draw_networkx_labels(G, pos, font_size=font_size)
nx.draw_networkx_edge_labels(G,
pos,
edge_labels=nx.get_edge_attributes(
G, edge_label))
plt.axis('off')
def plot_basis_function(args, x_range, y_range, basis, prefix):
"""
Plots 3d graph where the x and y coordinates represent the grid and the z axis encodes the value to be depicted.
One could use this to look at q-values, for example. In my work, I've used this plot to show proto-value functions,
the successor representation, or eigenvectors.
:param args: list of all arguments passed at the execution so we can access the paths we are interested at
:param x_range: one of the dimensions of the grid world
:param y_range: the other dimension of the grid world
:param basis: actual values to be plotted
:param prefix: string that will be used as the filename of the generated graph
"""
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
# fig, ax = plt.subplots(subplot_kw=dict(projection='3d'))
data_x, data_y = np.meshgrid(np.arange(y_range), np.arange(x_range))
data_z = basis.reshape(x_range, y_range)
for ii in range(len(data_x)):
for j in range(int(len(data_x[ii]) / 2)):
tmp = data_x[ii][j]
data_x[ii][j] = data_x[ii][len(data_x[ii]) - j - 1]
data_x[ii][len(data_x[ii]) - j - 1] = tmp
ax.plot_surface(data_x,
data_y,
data_z,
rstride=1,
cstride=1,
cmap=plt.get_cmap('jet'))
plt.gca().view_init(elev=30, azim=30)
plt.gca().set_zlim(-1.0, 1.0)
plt.savefig(args.output + prefix + '.png')
plt.close()
plt.clf()
def plot(lon, lat, var1, var2, actions, ax, fig, **kwargs):
aspect = kwargs.get('aspect', None)
height = kwargs.get('height')
width = kwargs.get('width')
norm = kwargs.get('norm')
cmap = get_cmap(kwargs.get('cmap', 'jet'))
cmin = kwargs.get('cmin', "None")
cmax = kwargs.get('cmax', "None")
magnitude = kwargs.get('magnitude', 'False')
if var1 is not None:
if var2 is not None:
mag = np.sqrt(var1**2 + var2**2)
else:
if magnitude == 'False':
mag = var1
else:
mag = np.abs(var1)
mag = mag.squeeze()
if "pcolor" in actions:
fig.set_figheight(height/80.0)
fig.set_figwidth(width/80.0)
pcolor(lon, lat, mag, ax, cmin, cmax, cmap)
if "facets" in actions:
fig.set_figheight(height/80.0)
fig.set_figwidth(width/80.0)
pcolor(lon, lat, mag, ax, cmin, cmax, cmap)
elif "filledcontours" in actions:
fig.set_figheight(height/80.0)
fig.set_figwidth(width/80.0)
fcontour(lon, lat, mag, ax, norm, cmin, cmax, cmap)
elif "contours" in actions:
fig.set_figheight(height/80.0)
fig.set_figwidth(width/80.0)
contour(lon, lat, mag, ax, norm, cmin, cmax, cmap)
#elif "facets" in actions:
# fig.set_figheight(height/80.0)
# fig.set_figwidth(width/80.0)
# facet(lon, lat, mag, ax)
elif "vectors" in actions:
fig.set_figheight(height/80.0/aspect)
fig.set_figwidth(width/80.0)
vectors(lon, lat, var1, var2, mag, ax, norm, cmap, magnitude)
elif "unitvectors" in actions:
fig.set_figheight(height/80.0/aspect)
fig.set_figwidth(width/80.0)
unit_vectors(lon, lat, var1, var2, mag, ax, norm, cmap, magnitude)
elif "streamlines" in actions:
fig.set_figheight(height/80.0/aspect)
fig.set_figwidth(width/80.0)
m = kwargs.get('basemap')
lonmin = kwargs.get("lonmin")
latmin = kwargs.get("latmin")
lonmax = kwargs.get("lonmax")
latmax = kwargs.get("latmax")
streamlines(lon, lat, var1, var2, mag, ax, norm, cmap, magnitude, m, lonmin, latmin, lonmax, latmax)
elif "barbs" in actions:
fig.set_figheight(height/80.0/aspect)
fig.set_figwidth(width/80.0)
barbs(lon, lat, var1, var2, mag, ax, norm, cmin, cmax, cmap, magnitude)
def plotConfiguration(conf):
cmap = plt.get_cmap('viridis')
fig, ax = plt.subplots()
for i in range(0,conf.orbitals):
ax.plot(conf.configurations[0:conf.beads,i,1],range(0,conf.beads),"o",color=cmap(i*1./conf.orbitals));
return {"fig":fig,"ax":ax}
def plotIntensity(data): #plots intensity in color map
plot = data.sumPols().getData()
if len(plot.shape) != 2: #check if waterfall file is valid
sys.exit("Waterplot may only plot waterfall files")
vmin, vmax = vlim(plot) #get color scale
if isinstance(data, Data.SpecData):
t_all = data.getTrange()
f_all = data.getFrange()
plt.imshow(plot.T, aspect='auto', interpolation='nearest',
origin='lower', cmap=plt.get_cmap('Greys'),
extent= t_all + f_all, vmin=vmin, vmax=vmax)
elif isinstance(data, Data.Data):
plt.imshow(plot.T, aspect='auto', interpolation='nearest',
origin='lower', cmap=plt.get_cmap('Greys'),
vmin=vmin, vmax=vmax)
plt.show()
def plot_sun_image(img, filename, wavelength=193, title = ''):
#cmap = plt.get_cmap('sdoaia{}'.format(wavelength))
cmap = plt.get_cmap('sohoeit195')
plt.title(title)
cax = plt.imshow(img,cmap=cmap,origin='lower',vmin=0, vmax=3000)#,vmin=vmin, vmax=vmax)
plt.gcf().colorbar(cax)
plt.savefig(filename)
plt.close("all")
def group_causality(sig_list, condition, freqs, ROI_labels=None,
out_path=None, submount=10):
"""
Make group causality analysis, by evaluating significant matrices across
subjects.
----------
sig_list: list
The path list of individual significant causal matrix.
condition: string
One condition of the experiments.
freqs: list
The list of interest frequency band.
min_subject: string
The subject for the common brain space.
submount: int
Significant interactions come out at least in 'submount' subjects.
"""
print 'Running group causality...'
set_directory(out_path)
sig_caus = []
for f in sig_list:
sig_cau = np.load(f)
print sig_cau.shape[-1]
sig_caus.append(sig_cau)
sig_caus = np.array(sig_caus)
sig_group = sig_caus.sum(axis=0)
plt.close()
for i in xrange(len(sig_group)):
fmin, fmax = freqs[i][0], freqs[i][1]
cau_band = sig_group[i]
# cau_band[cau_band < submount] = 0
cau_band[cau_band < submount] = 0
# fig, ax = pl.subplots()
cmap = plt.get_cmap('hot', cau_band.max()+1-submount)
cmap.set_under('gray')
plt.matshow(cau_band, interpolation='nearest', vmin=submount, cmap=cmap)
if ROI_labels == None:
ROI_labels = np.arange(cau_band.shape[0]) + 1
pl.xticks(np.arange(cau_band.shape[0]), ROI_labels, fontsize=9, rotation='vertical')
pl.yticks(np.arange(cau_band.shape[0]), ROI_labels, fontsize=9)
# pl.imshow(cau_band, interpolation='nearest')
# pl.set_cmap('BlueRedAlpha')
np.save(out_path + '/%s_%s_%sHz.npy' %
(condition, str(fmin), str(fmax)), cau_band)
v = np.arange(submount, cau_band.max()+1, 1)
# cax = ax.scatter(x, y, c=z, s=100, cmap=cmap, vmin=10, vmax=z.max())
# fig.colorbar(extend='min')
plt.colorbar(ticks=v, extend='min')
# pl.show()
plt.savefig(out_path + '/%s_%s_%sHz.png' %
(condition, str(fmin), str(fmax)), dpi=300)
plt.close()
return
def colors(numcolors,map='spectral'):
std_col = ['r','b','g','m']
if numcolors <= 4:
return std_col[:numcolors]
cm=plt.get_cmap(map)
col = []
for i in range(numcolors):
col.append(cm(1.*i/numcolors))
return col
def showGraph(graph):
G_adj = adjacencyList(np.array(graph))
G = nx.DiGraph(G_adj)
# nx.write_adjlist(G_adj, )
#initialze Figure
pos = nx.spring_layout(G)
nx.draw_networkx_nodes(G, pos, cmap=plt.get_cmap('jet'))
nx.draw_networkx_edges(G, pos, edge_color='b', arrows=True)
plt.show()
def plot_matrix(matrix):
fig = plt.figure()
ax = fig.add_subplot(111)
ax.set_title("colorMap")
vmax = np.max(np.max(matrix), -1 * np.min(matrix))
plt.imshow(matrix, interpolation="none", cmap=plt.get_cmap("seismic"), vmin=-1 * vmax, vmax=vmax)
ax.set_aspect("equal")
plt.colorbar(orientation="vertical")
plt.show()
def color_by_prop(propArr, nbins):
colorArr = []
for icl in xrange(nbins):
colorArr.append(plt.get_cmap("hsv")(float(icl)/(nbins)))
color_id_Arr = N.zeros_like(propArr)
#propbins = N.logspace(N.log10(colorprops*0.99), N.log10(colorprops*1.01), ncolor+1)
p_ids, p_bins = pTdf.group_by_prop(propArr, takelog=True, fixed_interval=True, bins=[])
return p_ids, p_bins, colorArr
def __init__(self,vmin=None,vmax=None,
filter=lambda x:x,
depth=8,compression=None,
colormap=plt.get_cmap('jet'),
over_color=None, over_alpha=1.0,
under_color=None, under_alpha=1.0,
bad_color=None, bad_alpha=1.0,
gamma=1.0):
self.filter=filter
if vmin!=None and vmax!=None:
self.set_minmax(float(vmin),float(vmax))
else:
self.vmin=None
self.vmax=None
self._norm=None
if compression!=None:
compression=int(compression)
self.compression=compression
self.set_depth(int(depth))
if isinstance(colormap,str):
self.colormap=plt.get_cmap(colormap)
else:
self.colormap=colormap
if over_color!=None:
try:
int(over_color,16)
over_color='#'+over_color
except ValueError:
pass
self.colormap.set_over(over_color,alpha=float(over_alpha))
if under_color!=None:
try:
int(under_color,16)
under_color='#'+under_color
except ValueError:
pass
self.colormap.set_under(under_color,alpha=float(under_alpha))
if bad_color!=None:
self.colormap.set_bad(bad_color,alpha=float(bad_alpha))
self.colormap.set_gamma(float(gamma))
def _plot_colormap(self,cm):
r=Renderer(colormap=plt.get_cmap(cm))
name=os.path.join(self.dir,cm+"_h.png")
if not os.path.exists(name):
f=open(name,'wb')
r.write_h_colorbar(f)
f.close()
name=os.path.join(self.dir,cm+"_v.png")
if not os.path.exists(name):
f=open(name,'wb')
r.write_v_colorbar(f)
f.close()
def plot_2d(params_dir):
model_dirs = [name for name in os.listdir(params_dir)
if os.path.isdir(os.path.join(params_dir, name))]
if len(model_dirs) == 0:
model_dirs = [params_dir]
colors = plt.get_cmap('plasma')
plt.figure(figsize=(20, 10))
ax = plt.subplot(111)
ax.set_xlabel('Learning Rate')
ax.set_ylabel('Error rate')
i = 0
for model_dir in model_dirs:
model_df = pd.DataFrame()
for param_path in glob.glob(os.path.join(params_dir,
model_dir) + '/*.h5'):
param = dd.io.load(param_path)
gd = {'learning rate': param['hyperparameters']['learning_rate'],
'momentum': param['hyperparameters']['momentum'],
'dropout': param['hyperparameters']['dropout'],
'val. objective': param['best_epoch']['validate_objective']}
model_df = model_df.append(pd.DataFrame(gd, index=[0]),
ignore_index=True)
if i != len(model_dirs) - 1:
ax.scatter(model_df['learning rate'],
model_df['val. objective'],
s=128,
marker=(i+3, 0),
edgecolor='black',
linewidth=model_df['dropout'],
label=model_dir,
c=model_df['momentum'],
cmap=colors)
else:
im = ax.scatter(model_df['learning rate'],
model_df['val. objective'],
s=128,
marker=(i+3, 0),
edgecolor='black',
linewidth=model_df['dropout'],
label=model_dir,
c=model_df['momentum'],
cmap=colors)
i += 1
plt.colorbar(im, label='Momentum')
plt.legend()
plt.show()
plt.savefig('{}.eps'.format(os.path.join(IMAGES_DIRECTORY, 'params2d')), format='eps', dpi=1000)
plt.close()
def visualize(y_true,y_pred,img):
score = accuracy_score(y_true, y_pred)
print '\n accuracy score : ', score
h, w = img.shape
target_pred = y_pred.reshape(h, w)
target_true = y_true.reshape(h, w)
fig1 = plt.figure(1)
plt.imshow(img, cmap=plt.get_cmap('gray'))
plt.hold(True)
plt.imshow(target_pred, alpha=0.7)
plt.title('Predicted target - accuracy_score : %s' % round(score, 3))
fig2 = plt.figure(2)
plt.imshow(img, cmap=plt.get_cmap('gray'))
plt.hold(True)
plt.imshow(target_true, alpha=0.7)
plt.title('True target')
plt.show()
def __display_clusters(centers, clusters, iterations, name, suffix, place):
fig = pylab.figure()
ax = fig.add_subplot(111)
N = len(centers)
colors_id = numpy.array(range(N), dtype=numpy.float32) / (N - 1)
cm = pylab.get_cmap('jet')
colors = cm(colors_id)
cid = 0
for c in clusters:
for p in c:
x = p[0]
if p.shape[0] > 1:
y = p[1]
else:
y = 0
ax.scatter([x], [y], c=colors[cid], marker='o')
cid += 1
cid = 0
for c in centers:
x = c[0]
if c.shape[0] > 1:
y = c[1]
else:
y = 0
ax.scatter([x], [y], c=colors[cid], s=200, marker='^')
cid += 1
#ax.set_ylabel('True positive rate')
#ax.set_xlabel('False positive rate')
title = name + ' clustering'
title += '\n' + filename
title += ' [' + place + '] '
title += ' [iterations=' + str(iterations)
if data_size != 0:
title += ' data size=' + str(data_size)
title += ']'
ax.set_title(title)
ofname = filename + suffix + "_clustering_" + name + "_" + place
pylab.savefig(ofname + ".pdf")
pylab.savefig(ofname + ".eps")
pylab.savefig(ofname + ".svg")
def draw_cool_graph(G, fig_no=1, node_size=100):
colors = [deg for _, deg in G.degree_iter()]
fig = plt.figure(fig_no)
fig.clear()
nx.draw_spring(G,
node_color=colors,
vmin=min(colors),
vmax=max(colors),
cmap=plt.get_cmap('cool'),
node_size=node_size,
alpha=.5,
width=.3,
edge_color="#FFFFFF"
)
fig.set_facecolor("#000000")
return fig
def plot(lon, lat, lonn, latn, nv, var1, var2, actions, m, ax, fig, **kwargs):
patch1 = None
aspect = kwargs.get('aspect', None)
height = kwargs.get('height')
width = kwargs.get('width')
norm = kwargs.get('norm')
cmap = get_cmap(kwargs.get('cmap', 'jet'))
cmin = kwargs.get('cmin', "None")
cmax = kwargs.get('cmax', "None")
magnitude = kwargs.get('magnitude', "False")
topology_type = kwargs.get('topology_type', 'node')
fig.set_figheight(height/80.0)
fig.set_figwidth(width/80.0)
if var1 is not None:
if var2 is not None:
mag = np.sqrt(var1**2 + var2**2)
else:
if magnitude == "True":
mag = np.abs(var1)
else:
mag = var1
mag = mag.squeeze()
if "facets" in actions:
facet(lon, lat, lonn, latn, mag, nv, m, ax, norm, cmin, cmax, cmap, topology_type, kwargs)
elif "vectors" in actions:
vectors(lon, lat, lonn, latn, var1, var2, mag, nv, m, ax, norm, cmap, magnitude, topology_type)
elif "unitvectors" in actions:
unit_vectors(lon, lat, lonn, latn, var1, var2, mag, nv, m, ax, norm, cmap, magnitude, topology_type)
#elif "streamlines" in actions:
# streamlines(lon, lat, lonn, latn, var1, var2, mag, m, ax, norm, cmap, magnitude, topology_type)
elif "barbs" in actions:
barbs(lon, lat, lonn, latn, var1, var2, mag, m, ax, norm, cmin, cmax, cmap, magnitude, topology_type)
else:
lonmin = kwargs.get("lonmin")
latmin = kwargs.get("latmin")
lonmax = kwargs.get("lonmax")
latmax = kwargs.get("latmax")
dataset = kwargs.get("dataset")
continuous = kwargs.get("continuous")
projection = kwargs.get("projection")
if "pcolor" in actions:
fig, m = pcolor(lon, lat, lonn, latn, mag, nv, m, ax, norm, cmap, topology_type, fig, height, width, lonmin, latmin, lonmax, latmax, dataset, continuous, projection)
elif "filledcontours" in actions:
fig, m = fcontour(lon, lat, lonn, latn, mag, nv, m, ax, norm, cmin, cmax, cmap, topology_type, fig, height, width, lonmin, latmin, lonmax, latmax, dataset, continuous, projection)
elif "contours" in actions:
fig, m = contour(lon, lat, lonn, latn, mag, nv, m, ax, norm, cmin, cmax, cmap, topology_type, fig, height, width, lonmin, latmin, lonmax, latmax, dataset, continuous, projection)
return fig, m
def make_xy_plot(graph, tag_1, tag_2):
import matplotlib.pyplot as plt
import matplotlib.colors as colors
import matplotlib.cm as cmx
Lead = np.log10( np.array(self.data['Lead (ppb)']) + 1.0 )
plt.figure(figsize=(20,20))
jet = plt.get_cmap('seismic')
cNorm = colors.Normalize(vmin=0.3, vmax=1.3)
scalarMap = cmx.ScalarMappable(norm=cNorm, cmap=jet)
for x, y, col in zip(np.array(self.data[tag_1]),
np.array(self.data[tag_2]), Lead):
colorVal = scalarMap.to_rgba(col)
plt.plot(x, y, '.', color=colorVal)
plt.savefig('./output/graph_vis/Lead.png', bbox_inches='tight')
def __init__(
self,
colour=None,
symbol=None,
label=None,
level_names=None,
colour_map=None,
colour_bar_title=None,
size=5,
colours=None):
self.colour = colour
self.symbol = symbol
self.label = label
self.level_names = level_names
self.colour_map = get_cmap(colour_map)
self.colour_bar_title = colour_bar_title
self.size = size
self.colours = colours
def plot_color_multigraph(G, graph_colors, n_rows, n_cols, node_size=100, fig_no=1):
fig = plt.figure(fig_no)
fig.clear()
for k, (name, colors) in enumerate(graph_colors):
plt.subplot(n_rows, n_cols, k + 1)
plt.title(name, color='white')
nx.draw_graphviz(G, # this is expensive but at least it's consistent.
node_color=colors,
vmin=min(colors),
vmax=max(colors),
cmap=plt.get_cmap('cool'),
alpha=.5,
width=.3,
edge_color="#FFFFFF",
node_size=node_size
)
fig.set_facecolor("#000000")
return fig
def sliderupdate(val):
val = int(val)
nonzeroc = len(np.nonzero(self.mmc.classvec_ws)[0])
if val > nonzeroc:
claims = val - nonzeroc
newclazz = 1
elif val < nonzeroc:
claims = nonzeroc - val
newclazz = 0
else: return
print 'Claimed', claims, 'points for class', newclazz #val, nonzeroc, claims
self.claims = claims
mmc.claim_n_points(claims, newclazz)
steepness_vector = mmc.compute_steepness_vector()
X = [steepness_vector, steepness_vector]
self.slider_axis2.imshow(X, cmap=plt.get_cmap("Oranges"))
self.slider_axis2.set_aspect('auto')
self.redrawall(newslider = False) #HACK!
self.prevnewclazz = newclazz
def init(self, data_len):
""" Initialize plots. """
self._t = 0
self._data_len = data_len
self._data = np.empty((0, data_len))
cm = plt.get_cmap('spectral')
self._plots = []
for i in range(data_len):
color = cm(1.0 * i / data_len)
alpha = self._alphas[i] if self._alphas is not None else 1.0
label = self._labels[i] if self._labels is not None else str(i)
self._plots.append(
self._ax.plot([], [], color=color, alpha=alpha, label=label)[0]
)
self._ax.set_xlim(0, self._time_window)
self._ax.set_ylim(0, 1)
self._ax.legend(loc='upper left', bbox_to_anchor=(0, 1.15))
self._init = True
def plot_contour_2d(xi, yi, zi, x=None, y=None, var=None, norm=False, figsize=None):
if x is None:
x = []
if y is None:
y = []
if figsize is None:
figsize = (w, golden_mean * w)
fig = plt.figure(figsize=figsize, facecolor='white')
ax = fig.add_subplot(1, 1, 1)
xig, yig = np.meshgrid(xi, yi)
x_min, y_min = map(np.nanmin, (xi, yi))
x_max, y_max = map(np.nanmax, (xi, yi))
ax.set_ylim([y_min, y_max])
ax.set_xlim([x_min, x_max])
ax.set_xlabel("Packet Emission Rate (pps)")
ax.set_ylabel("Average Node Separation (m)")
if norm:
vmin, vmax = 0.0, 1.0
else:
vmin = np.nanmin(abs(zi))
vmax = np.nanmax(abs(zi))
cset = ax.contourf(zi, alpha=0.75, # hatches=['+','x','-', '/', '\\', '//'],
cmap=plt.get_cmap('hot_r'),
vmin=vmin, vmax=vmax,
extent=[x_min, x_max, y_min, y_max]
)
cbar = fig.colorbar(cset)
if var is not None:
# ax.set_title("{} with varying Packet Emission and Node Separations".format(var))
cbar.set_label(var)
if len(x) and len(y):
ax.scatter(x, y, color='k', marker='.', s=1)
# ax.clabel(cset,inline=1)
return fig
def plot_field_2D(file,out=None,filter=lambda d:d,cmap_func=lambda min,max: plt.get_cmap('jet'),opts={}):
if out==None: out=os.path.dirname(file)
LOG.debug('Plotting file %s to %s',file,out)
# Open the hdf5 data
h5file=h5py.File(file,'r')
try:
field=h5file.attrs['field']
# Get the 2D data, timesteps, x and z
dset=h5file['/data']
dmax=dset.attrs['max']
dmin=dset.attrs['min']
cmap=cmap_func(dmin,dmax)
frames=h5file['/frame']
path, ext = os.path.splitext(file) # get the prefix_fieldname
# extent=(left,right,bottom,top)
x=h5file['x'].value
z=h5file['z'].value
extent=(0,(x[0]+x[-1])/1e3,0,(z[0]+z[-1])/1e3)
figname=os.path.join(out,os.path.basename(path)+'%05d.png')
plot_frames_2D(frames,dset.value[:,:,0,:],figname,mm=(dmin,dmax),title=field,filter=filter,cmap=cmap,extent=extent)
finally:
h5file.close()