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help='draw 2D box')
parser.add_argument('--draw_bev', default=False, action='store_true',
help='draw Birds eye view')
args = parser.parse_args()
args.select_seq = [args.select_seq] if isinstance(args.select_seq,
int) else args.select_seq
print(' '.join(sys.argv))
return args
args = parse_args()
# Global Variable
sns.set(style="darkgrid")
FONT = cv2.FONT_HERSHEY_SIMPLEX
FOURCC = cv2.VideoWriter_fourcc(*'mp4v')
OUTPUT_PATH = cfg.OUTPUT_PATH
FOV_H = 60
NEAR_CLIP = 0.15
if args.dataset == 'gta':
W = cfg.GTA.W # 1920
H = cfg.GTA.H # 1080
resW = W // 2
resH = H // 2
FOCAL_LENGTH = cfg.GTA.FOCAL_LENGTH # 935.3074360871937
else:
W = cfg.KITTI.W # 1248
H = cfg.KITTI.H # 384
resW = W
def plotHistogram(values, xlabel=None, ylabel=None, title=None, xmin=None, xmax=None,
extra=None, extraColor='grey', extraLoc='right',
hist=True, showCI=False, showMean=False, showMedian=False,
color=None, shade=False, kde=True, show=True, filename=None):
fig = plt.figure()
style = "white"
colorSet = "Set1"
sns.set_style(style)
sns.set_palette(colorSet, desat=0.6)
red, blue, green, purple = sns.color_palette(colorSet, n_colors=4)
color = blue if color is None else color
count = values.count()
bins = count // 10 if count > 150 else (count // 5 if count > 50 else (count // 2 if count > 20 else None))
sns.distplot(values, hist=hist, bins=bins, kde=kde, color=color, kde_kws={'shade': shade})
#sns.axlabel(xlabel=xlabel, ylabel=ylabel)
if xlabel:
plt.xlabel(xlabel) # , size='large')
if ylabel:
plt.ylabel(ylabel) # , size='large')
sns.despine()
def plot_umap(trainer):
latent_seq, latent_fish = trainer.get_latent()
latent2d = umap.UMAP().fit_transform(np.concatenate([latent_seq, latent_fish]))
latent2d_seq = latent2d[: latent_seq.shape[0]]
latent2d_fish = latent2d[latent_seq.shape[0] :]
data_seq, data_fish = [p.gene_dataset for p in trainer.all_dataset]
colors = sns.color_palette(n_colors=30)
plt.figure(figsize=(25, 10))
ax = plt.subplot(1, 3, 1)
ax.scatter(*latent2d_seq.T, color="r", label="seq", alpha=0.5, s=0.5)
ax.scatter(*latent2d_fish.T, color="b", label="osm", alpha=0.5, s=0.5)
ax.legend()
ax = plt.subplot(1, 3, 2)
labels = data_seq.labels.ravel()
for i, label in enumerate(data_seq.cell_types):
ax.scatter(
*latent2d_seq[labels == i].T,
color=colors[i],
label=label[:12],
alpha=0.5,
s=5
)
mmsb_degree = np.load('figures/mmsb_sparse_degree.npy')
kron_degree = np.load('figures/kron_degree.npy')
ba_degree = np.load('figures/ba_degree.npy')
real_clustering = np.load('figures/real_clustering.npy')
graphrnn_rnn_clustering = np.load('figures/graphrnn_rnn_clustering.npy')
graphrnn_mlp_clustering = np.load('figures/graphrnn_mlp_clustering.npy')
mmsb_clustering = np.load('figures/mmsb_sparse_clustering.npy')
kron_clustering = np.load('figures/kron_clustering.npy')
ba_clustering = np.load('figures/ba_clustering.npy')
plt.switch_backend('agg')
sns.set()
sns.set_style("ticks")
sns.set_context("poster",font_scale=1.4,rc={"lines.linewidth": 3.5})
fig = plt.figure()
plt.ylim(0, 0.1)
plt.xlim(0, 50)
plt.tight_layout()
current_size = fig.get_size_inches()
fig.set_size_inches(current_size[0]*1.5, current_size[1]*1.5)
degree_plot = sns.distplot(real_degree,hist=False,rug=False,norm_hist=True,label='Real')
degree_plot = sns.distplot(ba_degree,hist=False,rug=False,norm_hist=True,label='B-A')
degree_plot = sns.distplot(kron_degree,hist=False,rug=False,norm_hist=True,label='Kronecker')
degree_plot = sns.distplot(mmsb_degree,hist=False,rug=False,norm_hist=True,label='MMSB')
degree_plot = sns.distplot(graphrnn_mlp_degree,hist=False,rug=False,norm_hist=True,label='GraphRNN-S')
degree_plot = sns.distplot(graphrnn_rnn_degree,hist=False,rug=False,norm_hist=True,label='GraphRNN')
degree_plot.set(xlabel='degree', ylabel='probability density')
print("Prob exactly 2: " + str(prob_exactly_2))
print("Prob exactly 1: " + str(prob_exactly_1))
print("Prob never uninterpretable: " + str(prob_exactly_0))
"""attn_perf_overlap_for_model('yahoo')
attn_perf_overlap_for_model('imdb')
attn_perf_overlap_for_model('amazon')
attn_perf_overlap_for_model('yelp')"""
try:
sns.set(font_scale=1.5)
sns.set_style("whitegrid")
except:
pass
def make_2x2_2boxplot_set(list1_of_two_vallists_to_boxplot, list2_of_two_vallists_to_boxplot,
list3_of_two_vallists_to_boxplot, list4_of_two_vallists_to_boxplot, list_of_colorlabels,
list_of_two_color_tuples, labels_for_4_boxplot_sets):
pass
def make_4_4boxplot_set(list1_of_four_vallists_to_boxplot, list2_of_four_vallists_to_boxplot,
list3_of_four_vallists_to_boxplot, list4_of_four_vallists_to_boxplot, list_of_colorlabels,
list_of_four_color_tuples, labels_for_4_boxplot_sets):
pass
def draw_group_boxplot(name_list,data_list1,data_list2, label ='Dice Score',titile=None, fpth=None ):
df = get_df_from_list(name_list,data_list1,data_list2)
df = df[['Group', 'Longitudinal', 'Cross-subject']]
dd = pd.melt(df, id_vars=['Group'], value_vars=['Longitudinal', 'Cross-subject'], var_name='task')
fig, ax = plt.subplots(figsize=(15, 8))
sn=sns.boxplot(x='Group', y='value', data=dd, hue='task', palette='Set2',ax=ax)
#sns.palplot(sns.color_palette("Set2"))
sn.set_xlabel('')
sn.set_ylabel(label)
# plt.xticks(rotation=45)
ax.yaxis.grid(True)
leg=plt.legend(prop={'size': 18},loc=4)
leg.get_frame().set_alpha(0.2)
for item in ([ax.title, ax.xaxis.label, ax.yaxis.label] +
ax.get_xticklabels() + ax.get_yticklabels()):
item.set_fontsize(20)
for tick in ax.get_xticklabels():
tick.set_rotation(30)
if fpth is not None:
plt.savefig(fpth,dpi=500, bbox_inches = 'tight')
plt.close('all')
else:
np.linalg.norm(p_hat - dcsbm_P) ** 2
# heatmap(dcsbe.p_mat_, inner_hier_labels=labels)
# heatmap(dcsbm_P, inner_hier_labels=labels)
import seaborn as sns
plt.figure()
sns.scatterplot(
x=latent[:, 0], y=latent[:, 1], hue=dcsbe.vertex_assignments_, linewidth=0
)
#%%
from graspy.embed import LaplacianSpectralEmbed, AdjacencySpectralEmbed
plt.style.use("seaborn-white")
sns.set_palette("Set1")
plt.figure(figsize=(10, 10))
sns.set_context("talk", font_scale=1.5)
sns.scatterplot(x=latent[:, 0], y=latent[:, 1], hue=labels, linewidth=0)
plt.axis("square")
ase = AdjacencySpectralEmbed(n_components=2)
lse = LaplacianSpectralEmbed(n_components=2, form="R-DAD", regularizer=1)
ase_latent = ase.fit_transform(graph)
lse_latent = lse.fit_transform(graph)
plt.figure(figsize=(10, 10))
sns.scatterplot(x=ase_latent[:, 0], y=ase_latent[:, 1], hue=labels, linewidth=0)
plt.axis("square")
plt.figure(figsize=(10, 10))
sns.scatterplot(x=lse_latent[:, 0], y=lse_latent[:, 1], hue=labels, linewidth=0)
plt.axis("square")
# A PSD matrix can be created as follows, though is not used in the test.
# H = H @ H.t()
eigenvalues = A.symeig(H)[0]
spectrum_norm = A.max(eigenvalues)
H /= spectrum_norm
K = 1024
n_vec = 1
eigs = matrix_ops.lanczos_spectrum_approx(H, 100, K, n_vec)
eig_ref = A.symeig(H)[0]
import seaborn as sns
from matplotlib import pyplot as plt
import pandas as pd
plt.figure()
sns.distplot(A.eval(eig_ref), bins=50, norm_hist=True, kde=False)
sns.lineplot(data=pd.DataFrame(A.eval(eigs), index=np.linspace(-1, 1, K)) )
plt.savefig("lanczos_wigner.jpg")
dataset.isna().sum()
dataset = dataset.dropna()
origin = dataset.pop('Origin')
dataset['USA'] = (origin == 1)*1.0
dataset['Europe'] = (origin == 2)*1.0
dataset['Japan'] = (origin == 3)*1.0
dataset.tail()
train_dataset = dataset.sample(frac=0.8, random_state=0)
test_dataset = dataset.drop(train_dataset.index)
sns.pairplot(
train_dataset[["MPG", "Cylinders", "Displacement", "Weight"]], diag_kind="kde")
train_stats = train_dataset.describe()
train_stats.pop("MPG")
train_stats = train_stats.transpose()
train_stats
train_labels = train_dataset.pop('MPG')
test_labels = test_dataset.pop('MPG')
def norm(x):
return (x - train_stats['mean']) / train_stats['std']
from __future__ import print_function
import argparse
import sys
import os
import toolshed as ts
sys.path.insert(0, os.path.join(os.path.dirname(__file__), ".."))
from itertools import groupby, cycle
from operator import itemgetter
import matplotlib
matplotlib.use('Agg')
from matplotlib import pyplot as plt
try:
import seaborn as sns
sns.set_context("paper")
sns.set_style("dark", {'axes.linewidth': 1})
except ImportError:
pass
import numpy as np
from cpv._common import bediter, get_col_num, genomic_control
def chr_cmp(a, b):
a, b = a[0], b[0]
a = a.lower().replace("_", ""); b = b.lower().replace("_", "")
achr = a[3:] if a.startswith("chr") else a
bchr = b[3:] if b.startswith("chr") else b
try:
return cmp(int(achr), int(bchr))
except ValueError:
if achr.isdigit() and not bchr.isdigit(): return -1
if bchr.isdigit() and not achr.isdigit(): return 1