repo stringlengths 2 99 | file stringlengths 14 239 | code stringlengths 20 3.99M | file_length int64 20 3.99M | avg_line_length float64 9.73 128 | max_line_length int64 11 86.4k | extension_type stringclasses 1
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ZINBAE | ZINBAE-master/ZINBAE.py | """
Implementation of ZINBAE model
"""
from time import time
import numpy as np
from keras.models import Model
import keras.backend as K
from keras.engine.topology import Layer, InputSpec
from keras.layers import Dense, Input, GaussianNoise, Layer, Activation, Lambda, Multiply, BatchNormalization, Reshape, Concatenate... | 10,280 | 39.636364 | 154 | py |
ZINBAE | ZINBAE-master/loss.py | import numpy as np
import tensorflow as tf
from keras import backend as K
def _nan2zero(x):
return tf.where(tf.is_nan(x), tf.zeros_like(x), x)
def _nan2inf(x):
return tf.where(tf.is_nan(x), tf.zeros_like(x)+np.inf, x)
def _nelem(x):
nelem = tf.reduce_sum(tf.cast(~tf.is_nan(x), tf.float32))
return tf... | 4,141 | 30.142857 | 122 | py |
ZINBAE | ZINBAE-master/layers.py | from keras.engine.topology import Layer
from keras.layers import Lambda
from keras import backend as K
import tensorflow as tf
class ConstantDispersionLayer(Layer):
'''
An identity layer which allows us to inject extra parameters
such as dispersion to Keras models
'''
def __init__(... | 1,798 | 32.314815 | 98 | py |
ZINBAE | ZINBAE-master/ZINBAE0.py | """
Implementation of scDeepCluster for scRNA-seq data
"""
from time import time
import numpy as np
from keras.models import Model
import keras.backend as K
from keras.engine.topology import Layer, InputSpec
from keras.layers import Dense, Input, GaussianNoise, Layer, Activation, Lambda, Multiply, BatchNormalization, ... | 8,888 | 39.040541 | 154 | py |
ZINBAE | ZINBAE-master/preprocess.py |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import pickle, os, numbers
import numpy as np
import scipy as sp
import pandas as pd
import scanpy.api as sc
from sklearn.model_selection import train_test_split
from sklearn.preprocessing import scale
#TO... | 4,580 | 33.969466 | 112 | py |
incremental-ks | incremental-ks-master/IncrementalKS/Pure Python/IKS.py | from Treap import Treap
from math import log
class IKS:
def __init__(self):
self.treap = None
self.n = [0, 0]
@staticmethod
def KSThresholdForPValue(pvalue, N):
'''Threshold for KS Test given a p-value
Args:
pval (float): p-value.
N (int): the size of the samples.
Returns:
... | 3,778 | 29.475806 | 199 | py |
incremental-ks | incremental-ks-master/IncrementalKS/Pure Python/Treap.py | from random import random
class Treap:
def __init__(self, key, value = 0):
self.key = key
self.value = value
self.priority = random()
self.size = 1
self.height = 1
self.lazy = 0
self.max_value = value
self.min_value = value
self.left = None
self.right = None
@staticmethod
... | 3,699 | 21.02381 | 64 | py |
incremental-ks | incremental-ks-master/IncrementalKS/Python C++ Wrapper/ForgettingBuffer.py | class Node:
def __init__(self, value):
self.value = value
self.next = None
class ForgettingBuffer:
def __init__(self, values):
self.first = None
self.last = None
for val in values:
if self.first == None:
self.first = Node(val)
self.last = self.first
else:
se... | 930 | 18.808511 | 40 | py |
incremental-ks | incremental-ks-master/IncrementalKS/Python C++ Wrapper/IKS.py | from cffi import FFI
ffi = FFI()
ffi.cdef("""
typedef struct {
void * pointer;
} IKS_WrappedPointer;
IKS_WrappedPointer IKS_NewGeneratorWithSeed(unsigned seed);
IKS_WrappedPointer IKS_NewGenerator(void);
void IKS_DeleteGenerator(IKS_WrappedPointer pointer);
IKS_WrappedPointer IKS_NewIKS(IKS_WrappedPointer gen... | 4,612 | 30.813793 | 199 | py |
pyterpol | pyterpol-master/grid_to_binary.py |
import os
import argparse
import numpy as np
def main():
ps = argparse.ArgumentParser()
ps.add_argument('--remove', action='store_true', default=False, help='Removes ascii files.')
ps.add_argument('--overwrite', action='store_true', default=False, help='Overwrites binary files -- mandatory for every mach... | 1,998 | 34.696429 | 140 | py |
pyterpol | pyterpol-master/fitting/fitter.py | import os
import nlopt
import emcee
# import warnings
import numpy as np
from scipy.optimize import fmin
from scipy.optimize import fmin_slsqp
try:
from scipy.optimize import differential_evolution
except ImportError as ex:
print ex
differential_evolution = None
from pyterpol.synthetic.auxiliary import parl... | 20,033 | 31.842623 | 114 | py |
pyterpol | pyterpol-master/fitting/interface.py | import copy
import corner
# import sys
import warnings
import numpy as np
import matplotlib.pyplot as plt
from scipy import stats
from pyterpol.synthetic.makespectrum import SyntheticGrid
from pyterpol.observed.observations import ObservedSpectrum
from pyterpol.fitting.parameter import Parameter
from pyterpol.fitting.p... | 151,519 | 35.127802 | 120 | py |
pyterpol | pyterpol-master/synthetic/auxiliary.py | import numpy as np
import matplotlib.pyplot as plt
from astropy.constants import c
from scipy.interpolate import splrep
from scipy.interpolate import splev
from scipy.interpolate import bisplrep
from scipy.interpolate import bisplev
from scipy.interpolate import RectBivariateSpline
from scipy.interpolate import Interpo... | 10,363 | 24.033816 | 115 | py |
pyterpol | pyterpol-master/synthetic/makespectrum.py | import os
import sys
import copy
import warnings
import numpy as np
import matplotlib.pyplot as plt
from astropy.constants import c
from auxiliary import is_within_interval
from auxiliary import instrumental_broadening
from auxiliary import interpolate_spec
from auxiliary import interpolate_block_faster
from auxiliary ... | 45,773 | 34.319444 | 119 | py |
pyterpol | pyterpol-master/synthetic/defaults.py | # defaults settings - for more utility, this was transfered
# to init
import os, inspect
curdir = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe())))
# DEFINITIONS OF GRIDS OF RELATIVE SPECTRA
gridDirectory = os.path.join("/".join(curdir.split('/')[:-1]), 'grids')
# name of the file containing r... | 2,466 | 34.242857 | 120 | py |
pyterpol | pyterpol-master/plotting/plotting.py | import copy
import matplotlib.pyplot as plt
import matplotlib.gridspec as gs
import numpy as np
from scipy.stats import norm
from pyterpol.synthetic.auxiliary import read_text_file
def get_walker(db, nchain, nwalker, niter):
"""
Retrieves a walker from the chain.
:param db:
:param nchain:
:param n... | 9,041 | 22.42487 | 95 | py |
pyterpol | pyterpol-master/pyterpol_examples/Interface/output/example.py | """
This tutorial serves as demonstration of how to fit observed
spectra with Pyterpol.
Our observed spectra were created with the old C++ version of the
code. We have three spectra of a binary consisting of
primary: teff = 25000, g = 4.2, , vrot = 150, lr = 0.7, z = 1.0
secondary: teff = 18000, g = 4.2, , vrot = 50, ... | 5,219 | 47.333333 | 146 | py |
pyterpol | pyterpol-master/pyterpol_examples/Interface/setup/example.py | """
This tutorial serves as demonstration of how to set up an Interface.
Our observed spectra were created with the old C++ version of the
code. We have three spectra of a binary consisting of
primary: teff = 25000, g = 4.2, , vrot = 150, lr = 0.7, z = 1.0
secondary: teff = 18000, g = 4.2, , vrot = 50, lr = 0.3, z = 1.... | 9,099 | 51.601156 | 151 | py |
pyterpol | pyterpol-master/pyterpol_examples/Interface/fit/example.py | """
This tutorial serves as demonstration of how to fit observed
spectra with Pyterpol.
Our observed spectra were created with the old C++ version of the
code. We have three spectra of a binary consisting of
primary: teff = 25000, g = 4.2, , vrot = 150, lr = 0.7, z = 1.0
secondary: teff = 18000, g = 4.2, , vrot = 50, ... | 8,806 | 45.845745 | 146 | py |
pyterpol | pyterpol-master/pyterpol_examples/SyntheticSpectrum/example.py | """
This is a tutorial script how to handle the class Synthetic Spectrum.
"""
import pyterpol
import numpy as np
import matplotlib.pyplot as plt
# Load the spectrum using the library numpy
wave, intens = np.loadtxt('grid.dat', unpack=True, usecols=[0,1])
# The synthetic spectrum can be created either from arrays
ss =... | 1,449 | 25.851852 | 92 | py |
pyterpol | pyterpol-master/pyterpol_examples/SyntheticGrid/example.py | """
This script serves a demonstration of the class SyntheticGrid.
"""
# import the library
import pyterpol
import matplotlib.pyplot as plt
# The handling of the synthetic grid is shadowed from the user,
# therefore the interaction of the user with the grid should
# restrict to only few methods.
# How to create a gri... | 2,610 | 31.6375 | 83 | py |
pyterpol | pyterpol-master/pyterpol_examples/observed_spectra_fitting/v746cas/v746cas_2.py | """
V746Cas - fitting of a observed spectra.
This example also show, ho we can proceed if
we want to fit parameters step by step.
"""
import pyterpol
import matplotlib.pyplot as plt
def inspect_spectra(f):
ifile = open(f, 'r')
slist = ifile.readlines()
ifile.close()
for rec in slist:
ifile = ... | 2,974 | 28.455446 | 90 | py |
pyterpol | pyterpol-master/pyterpol_examples/observed_spectra_fitting/v746cas/v746cas.py | """
V746Cas - fitting of a observed spectra.
This example also show, ho we can proceed if
we want to fit parameters step by step.
"""
import pyterpol
import matplotlib.pyplot as plt
def inspect_spectra(f):
ifile = open(f, 'r')
slist = ifile.readlines()
ifile.close()
for rec in slist:
ifile = ... | 2,974 | 28.455446 | 90 | py |
pyterpol | pyterpol-master/pyterpol_examples/observed_spectra_fitting/v746cas_2/v746cas_2.py | """
V746Cas - fitting of a observed spectra.
This example also show, ho we can proceed if
we want to fit parameters step by step.
"""
import pyterpol
import numpy as np
import matplotlib.pyplot as plt
def inspect_spectra(f):
"""
Plots all spectra.
:param f:
:return:
"""
ifile = open(f, 'r')
... | 3,716 | 24.993007 | 89 | py |
pyterpol | pyterpol-master/pyterpol_examples/observed_spectra_fitting/v746cas_2/v746cas_eval_mcmc.py | import pyterpol
# check convergence of individual parameters
pyterpol.Interface.plot_convergence_mcmc('chain.dat', figname='mcmc_convergence.png')
# plot covariance of radiative parameters
pyterpol.Interface.plot_covariances_mcmc('chain.dat', parameters=['vrot', 'teff', 'logg'], figname='mcmc_correlations.png')
# pl... | 514 | 38.615385 | 123 | py |
pyterpol | pyterpol-master/pyterpol_examples/observed_spectra_fitting/v746cas_2/ondrejov/mask_tell.py | import sys
import numpy as np
tellbase = [
[6522., 6525.5],
[6530., 6538.5],
[6541.8, 6550.37],
[6551.75, 6554.9],
[6557., 6560],
[6563.6, 6564.8],
[6568.38, 6576.3],
[6580.2, 6588.2],
[6594.2, 6596.],
[6598.8, 6603.4]
]
def remove_telluric(f):
"""
Removes intervals def... | 770 | 15.404255 | 56 | py |
pyterpol | pyterpol-master/pyterpol_examples/ObservedList/example.py | """
This example demonstrates how to prepare observations.
"""
import pyterpol
# create a blank list
ol = pyterpol.ObservedList()
# now we are ready to attach some data - lets have a look at the data first
# the spectrum is not a KOREL spectrum, so we do not have to pass additional
# information
obs1 = pyterpol.Obse... | 2,934 | 34.361446 | 104 | py |
pyterpol | pyterpol-master/pyterpol_examples/StarList/example.py | """
This script demonstrates capabilities of the StarList class.
"""
import pyterpol
# create an empty class
sl = pyterpol.StarList()
# pyterpol knows a set of parameters, which are given to a component
# these parameters are teff, logg, z, lr, vrot and rv. Therefore
# adding component is possible by just calling:
s... | 2,079 | 31 | 107 | py |
pyterpol | pyterpol-master/pyterpol_examples/disentangled_spectra_fitting/hd81357/hd81357_plot.py | """
This shows how to evaluate the outcome of the fitting
We were fitting the disentangled spectra of the secondary.
"""
import pyterpol
# 1) Load the last session - create an empty Interface
itf = pyterpol.Interface()
# fill it with teh last session
itf.load('hd81357.sav')
# 2) Have a look at the comparisons
itf.pl... | 627 | 20.655172 | 58 | py |
pyterpol | pyterpol-master/pyterpol_examples/disentangled_spectra_fitting/hd81357/hd81357.py | """
Real life demonstration. HD81357 is an interacting binary.
Its secondary is a Roche-lobe filling star, which is probably
losing its mass. We obtained disentangled spectra of the secondary
in two spectral regions. Here is an estimate of its radiative properties.
"""
# import numpy as np
import pyterpol
## 1) Creat... | 5,610 | 39.366906 | 154 | py |
pyterpol | pyterpol-master/pyterpol_examples/Fitter/example.py | """
This function demonstrates usage of the class Fitter.
"""
import pyterpol
import numpy as np
import matplotlib.pyplot as plt
import time
# define a function that will be minimized
def func(x):
"""
Polynomial of order 4
:param x:
:param p:
:return:
"""
x = x[0]
return 0.5*x**4 - 2*x... | 2,764 | 28.105263 | 89 | py |
pyterpol | pyterpol-master/pyterpol_examples/RegionList/example.py | """
This script demonstrates capabilities of the RegionList class.
"""
import pyterpol
# create an empty class
rl = pyterpol.RegionList()
# add a region - the simplest way
rl.add_region(wmin=4300, wmax=4500)
# add a region, define name
rl.add_region(wmin=6200, wmax=6600, identification='red')
# for some reason we ... | 1,879 | 35.153846 | 89 | py |
pyterpol | pyterpol-master/grids_ABS/ready_phoenix.py |
"""
ready_phoenix.py
Convert Phoenix synthetic spectra from FITS to DAT.
"""
__author__ = "Miroslav Broz (miroslav.broz@email.cz)"
__version__ = "Jun 23rd 2016"
import sys
import numpy as np
from scipy.interpolate import splrep, splev
from astropy.io import fits
from pyterpol.synthetic.auxiliary import instrumenta... | 2,065 | 20.747368 | 97 | py |
pyterpol | pyterpol-master/observed/observations.py | import warnings
import numpy as np
import matplotlib.pyplot as plt
from scipy.interpolate import splrep
from scipy.interpolate import splev
# repeat userwarnings
warnings.simplefilter('always', UserWarning)
class ObservedSpectrum:
"""
A wrapper class for the observed spectra.
"""
def __init__(self, w... | 15,903 | 33.498915 | 118 | py |
davis2017-evaluation | davis2017-evaluation-master/setup.py | from setuptools import setup
import sys
if sys.version_info < (3, 6):
sys.exit('Sorry, only Python >= 3.6 is supported')
setup(
python_requires='>=3.6, <4',
install_requires=[
'Pillow>=4.1.1',
'networkx>=2.0',
'numpy>=1.12.1',
'opencv-python>=4.0.0.21',
'pandas>=0.2... | 506 | 23.142857 | 54 | py |
davis2017-evaluation | davis2017-evaluation-master/evaluation_method.py | import os
import sys
from time import time
import argparse
import numpy as np
import pandas as pd
from davis2017.evaluation import DAVISEvaluation
default_davis_path = '/path/to/the/folder/DAVIS'
time_start = time()
parser = argparse.ArgumentParser()
parser.add_argument('--davis_path', type=str, help='Path to the DA... | 3,492 | 49.623188 | 118 | py |
davis2017-evaluation | davis2017-evaluation-master/evaluation_codalab.py | import sys
import os.path
from time import time
import numpy as np
import pandas
from davis2017.evaluation import DAVISEvaluation
task = 'semi-supervised'
gt_set = 'test-dev'
time_start = time()
# as per the metadata file, input and output directories are the arguments
if len(sys.argv) < 3:
input_dir = "input_di... | 4,122 | 42.861702 | 140 | py |
davis2017-evaluation | davis2017-evaluation-master/davis2017/utils.py | import os
import errno
import numpy as np
from PIL import Image
import warnings
from davis2017.davis import DAVIS
def _pascal_color_map(N=256, normalized=False):
"""
Python implementation of the color map function for the PASCAL VOC data set.
Official Matlab version can be found in the PASCAL VOC devkit
... | 6,009 | 33.342857 | 110 | py |
davis2017-evaluation | davis2017-evaluation-master/davis2017/results.py | import os
import numpy as np
from PIL import Image
import sys
class Results(object):
def __init__(self, root_dir):
self.root_dir = root_dir
def _read_mask(self, sequence, frame_id):
try:
mask_path = os.path.join(self.root_dir, sequence, f'{frame_id}.png')
return np.arr... | 1,236 | 37.65625 | 111 | py |
davis2017-evaluation | davis2017-evaluation-master/davis2017/metrics.py | import math
import numpy as np
import cv2
def db_eval_iou(annotation, segmentation, void_pixels=None):
""" Compute region similarity as the Jaccard Index.
Arguments:
annotation (ndarray): binary annotation map.
segmentation (ndarray): binary segmentation map.
void_pixels (ndarray)... | 6,823 | 33.464646 | 137 | py |
davis2017-evaluation | davis2017-evaluation-master/davis2017/evaluation.py | import sys
from tqdm import tqdm
import warnings
warnings.filterwarnings("ignore", category=RuntimeWarning)
import numpy as np
from davis2017.davis import DAVIS
from davis2017.metrics import db_eval_boundary, db_eval_iou
from davis2017 import utils
from davis2017.results import Results
from scipy.optimize import linea... | 6,143 | 54.351351 | 143 | py |
davis2017-evaluation | davis2017-evaluation-master/davis2017/davis.py | import os
from glob import glob
from collections import defaultdict
import numpy as np
from PIL import Image
class DAVIS(object):
SUBSET_OPTIONS = ['train', 'val', 'test-dev', 'test-challenge']
TASKS = ['semi-supervised', 'unsupervised']
DATASET_WEB = 'https://davischallenge.org/davis2017/code.html'
V... | 5,514 | 43.837398 | 130 | py |
mapalignment | mapalignment-master/projects/mapalign/evaluate_funcs/evaluate_utils.py | import sys
import numpy as np
sys.path.append("../../utils")
import polygon_utils
def compute_batch_polygon_distances(gt_polygons_batch, aligned_disp_polygons_batch):
# Compute distances
distances = np.sqrt(np.sum(np.square(aligned_disp_polygons_batch - gt_polygons_batch), axis=-1))
min = np.nanmin(dis... | 2,799 | 36.333333 | 100 | py |
mapalignment | mapalignment-master/projects/mapalign/dataset_utils/preprocess_bradbury_buildings_multires.py | import sys
import os
import json
import math
import skimage.transform
import skimage.draw
import numpy as np
# from PIL import Image, ImageDraw
# Image.MAX_IMAGE_PIXELS = 200000000
import tensorflow as tf
import config_bradbury_buildings_multires as config
sys.path.append("../../../data/bradbury_buildings_roads_he... | 17,281 | 47.68169 | 163 | py |
mapalignment | mapalignment-master/projects/mapalign/dataset_utils/preprocess_aerial_image_multires.py | import sys
import os
import math
import json
import random
import skimage.transform
import numpy as np
import tensorflow as tf
import config_aerial_image_multires as config
sys.path.append("../../../data/AerialImageDataset")
import read
# sys.path.append("../utils")
# import visualization
sys.path.append("../../u... | 16,812 | 46.360563 | 182 | py |
mapalignment | mapalignment-master/projects/mapalign/dataset_utils/dataset_multires.py | import sys
import os
import math
import tensorflow as tf
sys.path.append("../utils") # Mapalign sub-projects utils
import visualization
import skimage.io
sys.path.append("../../utils") # Projects utils
import tf_utils
import python_utils
STRING_QUEUE_CAPACITY = 4000
MIN_QUEUE_EXAMPLES = 2000
def all_items_are... | 27,745 | 47.422339 | 197 | py |
mapalignment | mapalignment-master/projects/mapalign/utils/visualization.py | import os
import sys
import numpy as np
import cv2
current_filepath = os.path.dirname(os.path.realpath(__file__))
sys.path.append(os.path.join(current_filepath, "../../utils"))
import python_utils
import polygon_utils
# Try importing pyplot:
display_is_available = python_utils.get_display_availability()
use_pyplot = ... | 13,891 | 40.717718 | 173 | py |
mapalignment | mapalignment-master/projects/mapalign/mapalign_multires/main.py | # Quicky align the OSM data of your images with this script
import sys
import os
import argparse
import skimage.io
import numpy as np
import test
sys.path.append("../../utils")
import run_utils
import print_utils
import geo_utils
CONFIG = "config"
IMAGE = "geo_images/test_image.tif"
SHAPEFILE = None
BATCH_SIZE = 1... | 8,129 | 31.390438 | 176 | py |
mapalignment | mapalignment-master/projects/mapalign/mapalign_multires/5_model_buildings.py | import os.path
import numpy as np
import bpy, bmesh
import config
OUTPUT_BASE_DIRPATH = os.path.join(config.PROJECT_DIR, "3d_buildings/leibnitz")
SCALE = 0.1
IMAGE_HEIGHT = 12360 * 0.5 # In meters
IMAGE_WIDTH = 17184 * 0.5 # In meters
UV_SCALE = (1 / (IMAGE_HEIGHT * SCALE), 1 / (IMAGE_WIDTH * SCALE)) # (u, v)... | 1,792 | 27.460317 | 79 | py |
mapalignment | mapalignment-master/projects/mapalign/mapalign_multires/model_utils.py | from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import math
import sys
import tensorflow as tf
sys.path.append("../../utils")
import tf_utils
import print_utils
DEBUG = False
SUMMARY = False
def print_debug(obj):
if DEBUG:
print_utils.print_... | 20,710 | 44.820796 | 185 | py |
mapalignment | mapalignment-master/projects/mapalign/mapalign_multires/loss_utils.py | from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import sys
import numpy as np
import tensorflow as tf
sys.path.append("../../utils")
import tf_utils
def displacement_error(gt, preds, level_loss_coefs, polygon_map, disp_loss_params):
"""
:param g... | 9,420 | 44.73301 | 125 | py |
mapalignment | mapalignment-master/projects/mapalign/mapalign_multires/multires_pipeline.py | import sys
import skimage.transform
import skimage.io
import numpy as np
import model
sys.path.append("../../utils")
import run_utils
import polygon_utils
import print_utils
def rescale_data(image, polygons, scale):
downsampled_image = skimage.transform.rescale(image, scale, order=3, preserve_range=True, multic... | 6,435 | 47.390977 | 186 | py |
mapalignment | mapalignment-master/projects/mapalign/mapalign_multires/4_compute_building_heights.py | import os.path
import sys
import math
import itertools
import numpy as np
import config
sys.path.append("../../utils")
import geo_utils
DATASET_DIR = os.path.join(config.PROJECT_DIR, "../../../data/stereo_dataset")
RAW_DIR = os.path.join(DATASET_DIR, "raw/leibnitz")
INPUT_DIR = "test/stereo_dataset_real_displacemen... | 4,526 | 40.154545 | 174 | py |
mapalignment | mapalignment-master/projects/mapalign/mapalign_multires/download_pretrained.py | import os.path
import urllib.request
import zipfile
ressource_filename_list = ["runs.igarss2019.zip"]
ressource_dirpath_url = "https://www-sop.inria.fr/members/Nicolas.Girard/downloads/mapalignment"
script_filepath = os.path.realpath(__file__)
zip_download_dirpath = os.path.join(os.path.dirname(script_filepath), "ru... | 953 | 35.692308 | 102 | py |
mapalignment | mapalignment-master/projects/mapalign/mapalign_multires/1_train.py | from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import sys
import tensorflow as tf
import os
import model
sys.path.append(os.path.join("../dataset_utils"))
import dataset_multires
sys.path.append("../../utils")
import python_utils
import run_utils
flags... | 9,943 | 44.2 | 146 | py |
mapalignment | mapalignment-master/projects/utils/tf_utils.py | import tensorflow as tf
from tensorflow.python.framework.ops import get_gradient_function
import math
import numpy as np
def get_tf_version():
return tf.__version__
def bytes_feature(value):
return tf.train.Feature(bytes_list=tf.train.BytesList(value=[value]))
def int64_feature(value):
return tf.train... | 9,356 | 35.694118 | 155 | py |
mapalignment | mapalignment-master/projects/utils/viz_utils.py | import sys
import numpy as np
sys.path.append("../../utils")
import polygon_utils
import skimage.io
import cv2
def save_plot_image_polygon(filepath, image, polygons):
spatial_shape = image.shape[:2]
polygons_map = polygon_utils.draw_polygon_map(polygons, spatial_shape, fill=False, edges=True,
... | 1,610 | 34.021739 | 98 | py |
mapalignment | mapalignment-master/projects/utils/dataset_utils.py | import os
import tensorflow as tf
class TFRecordShardWriter:
def __init__(self, filepath_format, max_records_per_shard):
self.filepath_format = filepath_format
self.max_records_per_shard = max_records_per_shard
self.current_shard_record_count = 0 # To know when to switch to a new file
... | 1,079 | 36.241379 | 83 | py |
mapalignment | mapalignment-master/projects/utils/python_utils.py |
import os
import errno
import json
from jsmin import jsmin
def module_exists(module_name):
try:
__import__(module_name)
except ImportError:
return False
else:
return True
def choose_first_existing_path(path_list):
for path in path_list:
if os.path.exists(os.path.expa... | 2,600 | 24.5 | 136 | py |
mapalignment | mapalignment-master/projects/utils/image_utils.py | from io import BytesIO
import math
import numpy as np
from PIL import Image
import skimage.draw
import python_utils
CV2 = False
if python_utils.module_exists("cv2"):
import cv2
CV2 = True
if python_utils.module_exists("matplotlib.pyplot"):
import matplotlib.pyplot as plt
def get_image_size(filepath):
... | 8,487 | 34.514644 | 148 | py |
mapalignment | mapalignment-master/projects/utils/print_utils.py | class bcolors:
HEADER = '\033[95m'
OKBLUE = '\033[94m'
OKGREEN = '\033[92m'
WARNING = '\033[93m'
FAIL = '\033[91m'
DEBUG = '\033[31;40m'
ENDC = '\033[0m'
BOLD = '\033[1m'
UNDERLINE = '\033[4m'
def print_info(string):
print(bcolors.OKBLUE + string + bcolors.ENDC)
def print_suc... | 1,293 | 19.21875 | 65 | py |
mapalignment | mapalignment-master/projects/utils/polygon_utils.py | import math
import random
import numpy as np
import scipy.spatial
from PIL import Image, ImageDraw, ImageFilter
import skimage
import python_utils
if python_utils.module_exists("skimage.measure"):
from skimage.measure import approximate_polygon
if python_utils.module_exists("shapely"):
from shapely import g... | 42,079 | 36.437722 | 131 | py |
mapalignment | mapalignment-master/projects/utils/geo_utils.py | import numpy as np
import time
import json
import os.path
from osgeo import gdal, ogr
from osgeo import osr
import overpy
# from fiona.crs import from_epsg
# import fiona
from pyproj import Proj, transform
import polygon_utils
import math_utils
import print_utils
QUERY_BASE = \
"""
<osm-script timeout="900"... | 12,156 | 32.86351 | 187 | py |
mapalignment | mapalignment-master/projects/utils/math_utils.py | import numpy as np
import time
import sklearn.datasets
import skimage.transform
import python_utils
import image_utils
# if python_utils.module_exists("matplotlib.pyplot"):
# import matplotlib.pyplot as plt
CV2 = False
if python_utils.module_exists("cv2"):
import cv2
CV2 = True
# import multiprocessing
... | 11,176 | 31.873529 | 147 | py |
mapalignment | mapalignment-master/data/mapping_challenge_dataset/read.py | import sys
sys.path.append("../utils")
import visualization
from pycocotools.coco import COCO
from pycocotools import mask as cocomask
import numpy as np
import skimage.io as io
import matplotlib.pyplot as plt
import pylab
import random
import os
FOLD_LIST = ["train", "val"]
IMAGES_DIRPATH_FORMAT = "{}/images" # v... | 3,220 | 29.102804 | 103 | py |
mapalignment | mapalignment-master/data/AerialImageDataset/convert_npy_to_shp.py | import os.path
import sys
import read
FILE_DIRNAME = os.getcwd()
sys.path.append(os.path.join(FILE_DIRNAME, "../../projects/utils"))
import geo_utils
RAW_DIRPATH = os.path.join(FILE_DIRNAME, "raw")
IMAGE_INFO_LIST = [
{
"city": "bloomington",
"numbers": list(range(1, 37)),
},
{
... | 2,189 | 25.071429 | 168 | py |
mapalignment | mapalignment-master/data/AerialImageDataset/fetch_gt_polygons.py | import sys
import os
import numpy as np
sys.path.append("../../../projects/utils")
import python_utils
import polygon_utils
import geo_utils
DIR_PATH_LIST = ["./raw/train", "./raw/test"]
IMAGE_DIR_NAME = "images"
IMAGE_EXTENSION = "tif"
GT_POLYGONS_DIR_NAME = "gt_polygons"
def load_gt_polygons(image_filepath):... | 2,053 | 29.656716 | 115 | py |
mapalignment | mapalignment-master/data/AerialImageDataset/read.py | import os.path
import csv
import sys
import numpy as np
import skimage.io
CITY_METADATA_DICT = {
"bloomington": {
"fold": "test",
"pixelsize": 0.3,
"numbers": list(range(1, 37)),
},
"bellingham": {
"fold": "test",
"pixelsize": 0.3,
"numbers": list(range(1, 3... | 4,120 | 26.657718 | 115 | py |
mapalignment | mapalignment-master/data/bradbury_buildings_roads_height_dataset/download.py | import os.path
import urllib.request
import zipfile
BASE_URL = 'https://figshare.com/collections/Aerial_imagery_object_identification_dataset_for_building_and_road_detection_and_building_height_estimation/3290519'
FILE_URL_FORMAT = "https://ndownloader.figshare.com/articles/{}/versions/1"
FILE_METADATA_LIST = [
{
... | 1,842 | 24.957746 | 161 | py |
mapalignment | mapalignment-master/data/bradbury_buildings_roads_height_dataset/read.py | import os.path
import csv
import numpy as np
import skimage.io
CITY_METADATA_DICT = {
"Arlington": {
"pixelsize": 0.3,
"numbers": [1, 2, 3],
},
"Atlanta": {
"pixelsize": 0.1524,
"numbers": [1, 2, 3],
},
"Austin": {
"pixelsize": 0.1524,
"numbers": ... | 5,849 | 29.952381 | 118 | py |
cowrie | cowrie-master/setup.py |
from setuptools import setup
try:
import twisted
except ImportError:
raise SystemExit("twisted not found. Make sure you "
"have installed the Twisted core package.")
setup(
packages=["cowrie", "twisted"],
include_package_data=True,
package_dir={"": "src"},
package_data={... | 642 | 22.814815 | 88 | py |
cowrie | cowrie-master/src/twisted/plugins/cowrie_plugin.py | # All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
# notice, this list of conditions and the following disclaimer.
# notice, this list of conditions and the following disclaimer in the
# doc... | 10,607 | 38.434944 | 110 | py |
cowrie | cowrie-master/src/cowrie/_version.py | """
Provides cowrie version information.
"""
# This file is auto-generated! Do not edit!
# Use `python -m incremental.update cowrie` to change this file.
from __future__ import annotations
from incremental import Version
__version__ = Version("cowrie", 2, 5, 0)
__all__: list[str] = ["__version__"]
| 303 | 20.714286 | 64 | py |
cowrie | cowrie-master/src/cowrie/output/xmpp.py | from __future__ import annotations
import json
import string
from random import choice
from wokkel import muc
from wokkel.client import XMPPClient
from wokkel.xmppim import AvailablePresence
from twisted.application import service
from twisted.python import log
from twisted.words.protocols.jabber import jid
from twis... | 2,986 | 29.479592 | 84 | py |
cowrie | cowrie-master/src/cowrie/output/rethinkdblog.py | from __future__ import annotations
import time
from datetime import datetime
import rethinkdb as r
import cowrie.core.output
from cowrie.core.config import CowrieConfig
def iso8601_to_timestamp(value):
return time.mktime(datetime.strptime(value, "%Y-%m-%dT%H:%M:%S.%fZ").timetuple())
RETHINK_DB_SEGMENT = "outp... | 1,526 | 30.163265 | 85 | py |
cowrie | cowrie-master/src/cowrie/output/reversedns.py | from __future__ import annotations
from functools import lru_cache
import ipaddress
from twisted.internet import defer
from twisted.names import client, error
from twisted.python import log
import cowrie.core.output
from cowrie.core.config import CowrieConfig
class Output(cowrie.core.output.Output):
"""
Ou... | 3,128 | 28.242991 | 88 | py |
cowrie | cowrie-master/src/cowrie/output/mysql.py | """
MySQL output connector. Writes audit logs to MySQL database
"""
from __future__ import annotations
from twisted.enterprise import adbapi
from twisted.internet import defer
from twisted.python import log
import cowrie.core.output
from cowrie.core.config import CowrieConfig
import mysql.connector
class Reconnec... | 11,175 | 37.143345 | 102 | py |
cowrie | cowrie-master/src/cowrie/output/telegram.py | # Simple Telegram Bot logger
import treq
from twisted.python import log
import cowrie.core.output
from cowrie.core.config import CowrieConfig
class Output(cowrie.core.output.Output):
"""
telegram output
"""
def start(self):
self.bot_token = CowrieConfig.get("output_telegram", "bot_token")
... | 2,326 | 34.8 | 86 | py |
cowrie | cowrie-master/src/cowrie/output/influx.py | from __future__ import annotations
import re
from influxdb import InfluxDBClient
from influxdb.exceptions import InfluxDBClientError
from twisted.python import log
import cowrie.core.output
from cowrie.core.config import CowrieConfig
class Output(cowrie.core.output.Output):
"""
influx output
"""
d... | 7,285 | 31.968326 | 87 | py |
cowrie | cowrie-master/src/cowrie/output/virustotal.py | # All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
# notice, this list of conditions and the following disclaimer.
# notice, this list of conditions and the following disclaimer in the
# doc... | 18,353 | 35.416667 | 117 | py |
cowrie | cowrie-master/src/cowrie/output/jsonlog.py | # All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
# notice, this list of conditions and the following disclaimer.
# notice, this list of conditions and the following disclaimer in the
# doc... | 2,770 | 36.958904 | 75 | py |
cowrie | cowrie-master/src/cowrie/output/hpfeeds3.py | """
Output plugin for HPFeeds
"""
from __future__ import annotations
import json
import logging
from hpfeeds.twisted import ClientSessionService
from twisted.internet import endpoints, ssl
from twisted.internet import reactor
from twisted.python import log
import cowrie.core.output
from cowrie.core.config import C... | 4,221 | 34.478992 | 87 | py |
cowrie | cowrie-master/src/cowrie/output/csirtg.py | from __future__ import annotations
import os
import sys
from datetime import datetime
from twisted.python import log
import cowrie.core.output
from cowrie.core.config import CowrieConfig
token = CowrieConfig.get("output_csirtg", "token", fallback="a1b2c3d4")
if token == "a1b2c3d4":
log.msg("output_csirtg: token ... | 2,714 | 26.15 | 86 | py |
cowrie | cowrie-master/src/cowrie/output/mongodb.py | from __future__ import annotations
import pymongo
from twisted.python import log
import cowrie.core.output
from cowrie.core.config import CowrieConfig
class Output(cowrie.core.output.Output):
"""
mongodb output
"""
def insert_one(self, collection, event):
try:
object_id = collec... | 5,057 | 37.318182 | 106 | py |
cowrie | cowrie-master/src/cowrie/output/discord.py | """
Simple Discord webhook logger
"""
from __future__ import annotations
import json
from io import BytesIO
from twisted.internet import reactor
from twisted.internet.ssl import ClientContextFactory
from twisted.web import client, http_headers
from twisted.web.client import FileBodyProducer
import cowrie.core.outpu... | 1,486 | 26.537037 | 75 | py |
cowrie | cowrie-master/src/cowrie/output/graylog.py | """
Simple Graylog HTTP Graylog Extended Log Format (GELF) logger.
"""
from __future__ import annotations
import json
import time
from io import BytesIO
from twisted.internet import reactor
from twisted.internet.ssl import ClientContextFactory
from twisted.web import client, http_headers
from twisted.web.client impo... | 1,607 | 26.254237 | 75 | py |
cowrie | cowrie-master/src/cowrie/output/abuseipdb.py | # Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the "Software"),
# to deal in the Software without restriction, including without limitation
# and/or sell copies of the Software, and to permit persons to whom the
# Software is furnish... | 18,525 | 36.275654 | 89 | py |
cowrie | cowrie-master/src/cowrie/output/datadog.py | """
Simple Datadog HTTP logger.
"""
from __future__ import annotations
import json
import platform
from io import BytesIO
from twisted.internet import reactor
from twisted.internet.ssl import ClientContextFactory
from twisted.python import log
from twisted.web import client, http_headers
from twisted.web.client impo... | 2,286 | 30.763889 | 86 | py |
cowrie | cowrie-master/src/cowrie/output/crashreporter.py | """
Cowrie Crashreport
This output plugin is not like the others.
It has its own emit() function and does not use cowrie eventid's
to avoid circular calls
"""
from __future__ import annotations
import json
import treq
from twisted.internet import defer
from twisted.logger._levels import LogLevel
from twisted.pytho... | 2,005 | 24.392405 | 86 | py |
cowrie | cowrie-master/src/cowrie/output/elasticsearch.py | # Simple elasticsearch logger
from __future__ import annotations
from typing import Any
from elasticsearch import Elasticsearch, NotFoundError
import cowrie.core.output
from cowrie.core.config import CowrieConfig
class Output(cowrie.core.output.Output):
"""
elasticsearch output
"""
index: str
... | 4,393 | 33.873016 | 94 | py |
cowrie | cowrie-master/src/cowrie/output/localsyslog.py | # All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
# notice, this list of conditions and the following disclaimer.
# notice, this list of conditions and the following disclaimer in the
# doc... | 2,683 | 36.277778 | 78 | py |
cowrie | cowrie-master/src/cowrie/output/threatjammer.py |
"""
Cowrie plugin for reporting login attempts via the ThreatJammer.com Report API.
"ThreatJammer.com is a tool to track and detect attacks" <https://threatjammer.com>
"""
__author__ = "Diego Parrilla Santamaria"
__version__ = "0.1.0"
import datetime
from typing import Optional
from collections.abc import Generator... | 7,010 | 32.545455 | 111 | py |
cowrie | cowrie-master/src/cowrie/output/dshield.py | """
Send SSH logins to SANS DShield.
See https://isc.sans.edu/ssh.html
"""
from __future__ import annotations
import base64
import hashlib
import hmac
import re
import time
import dateutil.parser
import requests
from twisted.internet import reactor
from twisted.internet import threads
from twisted.python import log... | 6,123 | 33.994286 | 100 | py |
cowrie | cowrie-master/src/cowrie/output/splunk.py |
"""
Splunk HTTP Event Collector (HEC) Connector.
Not ready for production use.
JSON log file is still recommended way to go
"""
from __future__ import annotations
import json
from io import BytesIO
from typing import Any
from twisted.internet import reactor
from twisted.internet.ssl import ClientContextFactory
from... | 3,647 | 30.179487 | 88 | py |
cowrie | cowrie-master/src/cowrie/output/sqlite.py | from __future__ import annotations
import sqlite3
from typing import Any
from twisted.enterprise import adbapi
from twisted.internet import defer
from twisted.python import log
import cowrie.core.output
from cowrie.core.config import CowrieConfig
class Output(cowrie.core.output.Output):
"""
sqlite output
... | 7,367 | 33.919431 | 102 | py |
cowrie | cowrie-master/src/cowrie/output/textlog.py | # All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
# notice, this list of conditions and the following disclaimer.
# notice, this list of conditions and the following disclaimer in the
# doc... | 2,383 | 38.733333 | 80 | py |
cowrie | cowrie-master/src/cowrie/output/redis.py | from __future__ import annotations
import json
from configparser import NoOptionError
import redis
import cowrie.core.output
from cowrie.core.config import CowrieConfig
SEND_METHODS = {
"lpush": lambda redis_client, key, message: redis_client.lpush(key, message),
"rpush": lambda redis_client, key, message: r... | 1,797 | 27.539683 | 87 | py |
cowrie | cowrie-master/src/cowrie/output/misp.py | from __future__ import annotations
import warnings
from functools import wraps
from pathlib import Path
from pymisp import MISPAttribute, MISPEvent, MISPSighting
from twisted.python import log
import cowrie.core.output
from cowrie.core.config import CowrieConfig
try:
from pymisp import ExpandedPyMISP as PyMISP
... | 4,393 | 31.308824 | 85 | py |
cowrie | cowrie-master/src/cowrie/output/slack.py | # All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
# notice, this list of conditions and the following disclaimer.
# notice, this list of conditions and the following disclaimer in the
# doc... | 2,394 | 35.287879 | 75 | py |
cowrie | cowrie-master/src/cowrie/output/cuckoo.py | # All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
# notice, this list of conditions and the following disclaimer.
# notice, this list of conditions and the following disclaimer in the
# doc... | 5,799 | 33.52381 | 88 | py |
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