repo stringlengths 2 99 | file stringlengths 13 225 | code stringlengths 0 18.3M | file_length int64 0 18.3M | avg_line_length float64 0 1.36M | max_line_length int64 0 4.26M | extension_type stringclasses 1
value |
|---|---|---|---|---|---|---|
RoadDamageDetector | RoadDamageDetector-master/utils/dataset_util.py | # Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | 2,617 | 29.091954 | 80 | py |
RoadDamageDetector | RoadDamageDetector-master/utils/object_detection_evaluation.py | # Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | 26,696 | 42.269044 | 80 | py |
RoadDamageDetector | RoadDamageDetector-master/utils/np_box_list_test.py | # Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | 5,183 | 37.117647 | 80 | py |
RoadDamageDetector | RoadDamageDetector-master/utils/np_box_ops.py | # Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | 3,320 | 32.887755 | 80 | py |
RoadDamageDetector | RoadDamageDetector-master/utils/test_utils.py | # Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | 4,576 | 31.692857 | 80 | py |
RoadDamageDetector | RoadDamageDetector-master/utils/config_util_test.py | # Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | 18,834 | 45.853234 | 80 | py |
code-nerf | code-nerf-main/optimize.py |
import sys, os
ROOT_DIR = os.path.abspath(os.path.join('', 'src'))
sys.path.insert(0, os.path.join(ROOT_DIR))
import argparse
from utils import str2bool
from optimizer import Optimizer
if __name__ == '__main__':
arg_parser = argparse.ArgumentParser(description="CodeNeRF")
arg_parser.add_argument("--gpu",d... | 1,624 | 39.625 | 105 | py |
code-nerf | code-nerf-main/train.py |
import sys, os
ROOT_DIR = os.path.abspath(os.path.join('', 'src'))
sys.path.insert(0, os.path.join(ROOT_DIR))
import argparse
from trainer import Trainer
if __name__ == '__main__':
arg_parser = argparse.ArgumentParser(description="CodeNeRF")
arg_parser.add_argument("--gpu",dest="gpu",required=True)
a... | 1,201 | 34.352941 | 95 | py |
code-nerf | code-nerf-main/src/utils.py |
import imageio
import numpy as np
import torch
# import json
# from torchvision import transforms
import os
def get_rays(H, W, focal, c2w):
i, j = torch.meshgrid(torch.linspace(0, W - 1, W), torch.linspace(0, H - 1, H))
i = i.t()
j = j.t()
dirs = torch.stack([(i - W * .5) / focal, -(j - H * .5) / foc... | 2,512 | 34.394366 | 94 | py |
code-nerf | code-nerf-main/src/model.py | import torch
import torch.nn as nn
def PE(x, degree):
y = torch.cat([2.**i * x for i in range(degree)], -1)
w = 1
return torch.cat([x] + [torch.sin(y) * w, torch.cos(y) * w], -1)
class CodeNeRF(nn.Module):
def __init__(self, shape_blocks = 2, texture_blocks = 1, W = 256,
num_xyz_fre... | 2,360 | 43.54717 | 83 | py |
code-nerf | code-nerf-main/src/data.py |
import imageio
import numpy as np
import torch
# import json
# from torchvision import transforms
import os
def load_poses(pose_dir, idxs=[]):
txtfiles = np.sort([os.path.join(pose_dir, f.name) for f in os.scandir(pose_dir)])
posefiles = np.array(txtfiles)[idxs]
srn_coords_trans = np.diag(np.array([1, -1... | 3,451 | 37.786517 | 92 | py |
code-nerf | code-nerf-main/src/trainer.py |
import numpy as np
import torch
import torch.nn as nn
import json
from data import SRN
from utils import get_rays, sample_from_rays, volume_rendering, image_float_to_uint8
from model import CodeNeRF
from torch.utils.data import DataLoader
from torch.utils.tensorboard import SummaryWriter
import os
import math
import ... | 8,307 | 46.204545 | 121 | py |
code-nerf | code-nerf-main/src/optimizer.py |
import numpy as np
import torch
import torch.nn as nn
import json
from data import SRN
from utils import get_rays, sample_from_rays, volume_rendering, image_float_to_uint8
from skimage.metrics import structural_similarity as compute_ssim
from model import CodeNeRF
from torch.utils.data import DataLoader
from torch.ut... | 11,915 | 47.636735 | 134 | py |
pynbody | pynbody-master/setup.py | import codecs
import distutils
import os
import shutil
import subprocess
import sys
import tempfile
from os import path
import numpy.distutils.misc_util
from Cython.Build import build_ext
from Cython.Compiler.Options import get_directive_defaults
from setuptools import Extension, setup
get_directive_defaults()['langu... | 7,627 | 32.603524 | 98 | py |
pynbody | pynbody-master/tests/sph_image_test.py | import pickle
from pathlib import Path
import numpy as np
import numpy.testing as npt
import pylab as p
import pytest
import pynbody
test_folder = Path(__file__).parent
def setup_module():
global f
f = pynbody.load("testdata/g15784.lr.01024")
h = f.halos()
# hard-code the centre so we're not implici... | 4,603 | 32.362319 | 118 | py |
pynbody | pynbody-master/tests/array_test.py | import pynbody
SA = pynbody.array.SimArray
import numpy as np
import pytest
def test_pickle():
import pickle
x = SA([1, 2, 3, 4], units='kpc')
assert str(x.units) == 'kpc'
y = pickle.loads(pickle.dumps(x))
assert y[3] == 4
assert str(y.units) == 'kpc'
def test_issue255() :
r = SA(0.5, 'a... | 4,790 | 24.897297 | 107 | py |
pynbody | pynbody-master/tests/units_test.py | import numpy.testing as npt
import pynbody
from pynbody import units
def numacc(a, b, tol=1.e-9):
print(a, b)
assert abs(a - b) < a * tol
def test_units_conversion():
numacc(units.kpc.in_units(units.Mpc), 0.001)
numacc(units.Mpc.in_units(units.kpc), 1000)
numacc(units.yr.in_units(units.Myr), 1... | 2,311 | 28.265823 | 79 | py |
pynbody | pynbody-master/tests/subfindhdf_gadget4_test.py | from os.path import isfile
import h5py
import numpy as np
import pynbody
def setup_module():
global snap, halos, subhalos, htest, snap_arepo, halos_arepo, subhalos_arepo, htest_arepo
snap = pynbody.load('testdata/testL10N64/snapshot_000.hdf5')
halos = pynbody.halo.Gadget4SubfindHDFCatalogue(snap)
su... | 13,096 | 38.095522 | 116 | py |
pynbody | pynbody-master/tests/test_profile.py | import numpy as np
import numpy.testing as npt
import pynbody
np.random.seed(1)
def make_fake_bar(npart=100000, max=1, min=-1, barlength=.8, barwidth=0.05, phi=0, fraction=0.2):
x = np.random.sample(int(npart*fraction))*(max-min) + min
y = np.random.sample(int(npart*fraction))*(max-min) + min
xbar = np... | 2,747 | 28.548387 | 97 | py |
pynbody | pynbody-master/tests/ramses_test.py | import os
import numpy as np
import pytest
import pynbody
def setup_module():
global f
f = pynbody.load("testdata/ramses_partial_output_00250")
def test_lengths():
assert len(f.gas) == 152667
assert len(f.star) == 2655
assert len(f.dm) == 51887
def test_properties():
np.testing.assert_alm... | 17,652 | 40.438967 | 116 | py |
pynbody | pynbody-master/tests/subfind_test.py | import numpy as np
from numpy.testing import assert_allclose
import pynbody
def setup_module():
global snap, halos, groups
snap = pynbody.load("testdata/subfind/snapshot_019")
halos = snap.halos(subs=True)
groups = snap.halos()
def teardown_module():
global snap, halos, groups
del snap, hal... | 2,947 | 42.352941 | 122 | py |
pynbody | pynbody-master/tests/filter_test.py | import numpy as np
import numpy.testing as npt
import pytest
import pynbody
def setup_module():
global f
f = pynbody.new(1000)
f['pos'] = np.random.normal(scale=1.0, size=f['pos'].shape)
f['vel'] = np.random.normal(scale=1.0, size=f['vel'].shape)
f['mass'] = np.random.uniform(1.0, 10.0, size=f['m... | 2,736 | 26.37 | 80 | py |
pynbody | pynbody-master/tests/bridge_test.py | import numpy as np
import pynbody
def test_order_bridge():
f1 = pynbody.new(dm=1000)
f2 = pynbody.new(dm=3000)
f1['iord'] = np.arange(5, 2005, 2, dtype=int)
f2['iord'] = np.arange(3000, dtype=int)
b = pynbody.bridge.OrderBridge(f1, f2)
h1 = f1[:50:2]
assert b(h1).ancestor is f2
asse... | 4,933 | 37.850394 | 164 | py |
pynbody | pynbody-master/tests/adaptahop_test.py | import numpy as np
import pytest
from scipy.io import FortranFile as FF
import pynbody
from pynbody.halo.adaptahop import AdaptaHOPCatalogue, NewAdaptaHOPCatalogue
# Note: we do not use a module-wide fixture here to prevent caching of units
@pytest.fixture
def f():
yield pynbody.load("testdata/output_00080")
@... | 5,950 | 28.904523 | 95 | py |
pynbody | pynbody-master/tests/derived_arrays_test.py | import numpy as np
import pynbody
def setup_module():
global f, h
f = pynbody.new(dm=1000, star=500, gas=500, order='gas,dm,star')
f['pos'] = pynbody.array.SimArray(np.random.normal(scale=1.0, size=f['pos'].shape), units='kpc')
f['vel'] = pynbody.array.SimArray(np.random.normal(scale=1.0, size=f['vel... | 4,439 | 39 | 112 | py |
pynbody | pynbody-master/tests/import_test.py | def test_import_plot_module():
import pynbody
pl_dir = dir(pynbody.plot)
im = pynbody.plot.sph.image
assert callable(im)
| 137 | 22 | 31 | py |
pynbody | pynbody-master/tests/partial_tipsy_test.py | import numpy as np
import pytest
import pynbody
def test_indexing():
f1 = pynbody.load("testdata/g15784.lr.01024")
np.random.seed(1)
for test_len in [100, 10000, 20000]:
for i in range(5):
subindex = np.random.permutation(np.arange(0, len(f1)))[:test_len]
subindex.sort()
... | 1,131 | 25.325581 | 78 | py |
pynbody | pynbody-master/tests/ahf_halos_test.py | import glob
import os.path
import shutil
import stat
import subprocess
import numpy as np
import pynbody
def test_load_ahf_catalogue():
f = pynbody.load("testdata/g15784.lr.01024")
h = pynbody.halo.AHFCatalogue(f)
assert len(h)==1411
def test_load_ahf_catalogue_non_gzipped():
subprocess.call(["gunz... | 3,948 | 41.923913 | 150 | py |
pynbody | pynbody-master/tests/subarray_test.py | import gc
import pickle
import numpy as np
import pynbody
def test_pickle():
import pickle
f = pynbody.new(10)
f['blob'] = np.arange(10)
s = f[[3, 6, 7]]
assert (s['blob'] == [3, 6, 7]).all(
), "Preliminary check to testing pickle failed!"
reloaded = pickle.loads(pickle.dumps(s['blob'])... | 1,492 | 24.305085 | 74 | py |
pynbody | pynbody-master/tests/transformation_test.py | import copy
import gc
import numpy as np
import numpy.testing as npt
import pytest
import pynbody
def setup_module():
global f, original
f = pynbody.new(dm=1000)
f['pos'] = np.random.normal(scale=1.0, size=f['pos'].shape)
f['vel'] = np.random.normal(scale=1.0, size=f['vel'].shape)
f['mass'] = n... | 3,328 | 26.512397 | 74 | py |
pynbody | pynbody-master/tests/tipsy_test.py | import glob
import os
import numpy as np
import pytest
import pynbody
from pynbody.dependencytracker import DependencyError
def setup_module():
X = glob.glob("testdata/test_out.*")
for z in X:
os.unlink(z)
global f, h
f = pynbody.load("testdata/g15784.lr.01024")
h = f.halos()
def tear... | 15,081 | 36.056511 | 115 | py |
pynbody | pynbody-master/tests/rockstar_test.py | import numpy as np
import numpy.testing as npt
import pytest
import pynbody
def setup_module():
# create a dummy gadget file
global f, h
f = pynbody.new(dm=2097152)
f['iord'] = np.arange(2097152)
f.properties['z']=1.6591479493605812
f._filename = "testdata/rockstar/snapshot_015"
h = f.hal... | 1,401 | 32.380952 | 110 | py |
pynbody | pynbody-master/tests/utils_test.py | import time
import numpy as np
import numpy.testing as npt
import pynbody
def random_slice(max_pos=1000, max_step=10):
import random
a = random.randint(0, max_pos)
b = random.randint(0, max_pos)
return slice(min(a, b), max(a, b), random.randint(1, max_step))
def test_intersect_slices():
"""Uni... | 6,074 | 29.074257 | 86 | py |
pynbody | pynbody-master/tests/ramses_new_ptcl_format_test.py | import glob
import os
import warnings
import numpy as np
import pynbody
sink_filename = "testdata/ramses_new_format_partial_output_00001/sink_00001.csv"
sink_filename_moved = sink_filename+".temporarily_moved"
import pytest
def setup_module():
global f
f = pynbody.load("testdata/ramses_new_format_partial_... | 5,249 | 37.602941 | 125 | py |
pynbody | pynbody-master/tests/pyread_gadget_hdf5.py | """Routine for reading Gadget3 HDF5 output files."""
import fnmatch
import os
import h5py
import numpy
import pandas as pd
__author__ = 'Alan Duffy'
__email__ = 'mail@alanrduffy.com'
__version__ = '0.1.0'
def pyread_gadget_hdf5(filename, ptype, var_name, sub_dir=None,\
smooth=None,cgsunits=None,physunits=None,... | 18,632 | 40.778027 | 126 | py |
pynbody | pynbody-master/tests/gravity_test.py | import numpy as np
import numpy.testing as npt
import pynbody
def test_gravity():
f = pynbody.load("testdata/g15784.lr.01024")
h = f.halos()
pynbody.analysis.angmom.faceon(h[1])
pro = pynbody.analysis.profile.Profile(
h[1], type='equaln', nbins=50, rmin='100 pc', rmax='50 kpc')
v_circ_co... | 2,887 | 39.111111 | 90 | py |
pynbody | pynbody-master/tests/family_test.py | import numpy as np
import pynbody
def test_pickle():
# Regression test for issue 80
import pickle
assert pickle.loads(pickle.dumps(pynbody.family.gas)) is pynbody.family.gas
def test_family_array_dtype() :
# test for issue #186
f = pynbody.load('testdata/g15784.lr.01024.gz')
f.g['rho'] = np.... | 1,282 | 35.657143 | 120 | py |
pynbody | pynbody-master/tests/gadget_test.py | import numpy as np
import pytest
import pynbody
def setup_module():
global snap
snap = pynbody.load("testdata/test_g2_snap")
def teardown_module():
global snap
del snap
def test_construct():
"""Check the basic properties of the snapshot"""
assert (np.size(snap._files) == 2)
assert(sna... | 7,056 | 31.671296 | 96 | py |
pynbody | pynbody-master/tests/halotools_test.py | import glob
import os
import time
import numpy as np
import pytest
import pynbody
def setup_module():
global f, h
f = pynbody.load("testdata/g15784.lr.01024")
h = f.halos()
def teardown_module():
global f, h
del f, h
def test_center():
global f, h
with pynbody.analysis.halo.center(h[... | 2,825 | 34.772152 | 121 | py |
pynbody | pynbody-master/tests/snapshot_test.py | import weakref
import numpy as np
import pytest
import pynbody
def setup_module():
global f, h
f = pynbody.new(dm=1000, star=500, gas=500, order='gas,dm,star')
f['pos'] = np.random.normal(scale=1.0, size=f['pos'].shape)
f['vel'] = np.random.normal(scale=1.0, size=f['vel'].shape)
f['mass'] = np.r... | 6,673 | 24.76834 | 103 | py |
pynbody | pynbody-master/tests/gadgethdf_test.py | import shutil
from itertools import chain
import h5py
import numpy as np
import pytest
import pynbody
def setup_module() :
global snap,subfind
snap = pynbody.load('testdata/Test_NOSN_NOZCOOL_L010N0128/data/snapshot_103/snap_103.hdf5')
subfind = pynbody.load('testdata/Test_NOSN_NOZCOOL_L010N0128/data/sub... | 8,441 | 39.782609 | 166 | py |
pynbody | pynbody-master/tests/grafic_test.py | import numpy as np
import numpy.testing as npt
import pytest
import pynbody
def setup_module():
global f
f = pynbody.load("testdata/grafic_test/")
def test_vel():
npt.assert_allclose(f['vel'][::10], [[-14.57081223, 25.25094223, -4.56839371],
[ -7.05367327, -32.75279617, 22.61590385],
... | 1,775 | 33.153846 | 107 | py |
pynbody | pynbody-master/tests/cosmology_test.py | import numpy as np
import numpy.testing as npt
import pynbody
def test_a_to_t():
"""Test scalefactor -> time conversion for accuracy. See also issue #479"""
f = pynbody.new() # for default cosmology
ipoints = pynbody.analysis.cosmology._interp_points
interp_a = np.linspace(0.005, 1.0, ipoints+1) # en... | 1,095 | 38.142857 | 119 | py |
pynbody | pynbody-master/tests/nchilada_test.py | import numpy as np
import numpy.testing as npt
import pynbody
correct_pos_3000 = np.array([[4.80664825e+01, -8.99647751e+01,
3.74038162e+01],
[-5.44153690e+00,
1.38918352e+00, -4.13906145e+00],
... | 11,304 | 48.366812 | 84 | py |
pynbody | pynbody-master/tests/theoretical_profile.py | import numpy as np
import numpy.testing as npt
import pytest
import pynbody
from pynbody.array import SimArray
def setup_module():
global halo_boundary, rs, rhos, mass, c, NFW1, NFW2
halo_boundary = SimArray(347., units="kpc")
rs = SimArray(10, units="kpc")
rhos = SimArray(1e8, units="Msol kpc**-3")... | 4,717 | 42.284404 | 118 | py |
pynbody | pynbody-master/tests/sph_smooth_test.py | from pathlib import Path
import numpy as np
import numpy.testing as npt
import pytest
import pynbody
def setup_module():
global f
f = pynbody.load("testdata/g15784.lr.01024")
# for compatibility with original results, pretend the box
# is not periodic
del f.properties['boxsize']
def teardown_m... | 7,056 | 31.37156 | 134 | py |
pynbody | pynbody-master/docs/conf.py | #
# pynbody documentation build configuration file, created by
# sphinx-quickstart on Mon Oct 3 11:57:24 2011.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All configuration values ha... | 8,294 | 31.027027 | 89 | py |
pynbody | pynbody-master/docs/tutorials/example_code/velocity_vectors.py | import matplotlib.pylab as plt
import pynbody
import pynbody.plot.sph as sph
# load the snapshot and set to physical units
s = pynbody.load('testdata/g15784.lr.01024.gz')
s.physical_units()
# load the halos
h = s.halos()
# center on the largest halo and align the disk
pynbody.analysis.angmom.sideon(h[1])
# create ... | 1,002 | 33.586207 | 92 | py |
pynbody | pynbody-master/docs/tutorials/example_code/do_pictures.py | diskgas=s.gas[diskf]
### Make pictures:
try:
pp.sph.image(h[i].gas,filename=simname+'.facegas.png',width=30)
pp.sph.image(h[i].star,filename=simname+'.facestar.png',width=30)
pp.sph.image(diskgas,qty='temp',filename=simname+'.tempgasdiskface.png',
width=30,vmin=3,vmax=7)
s.gas['hiden'] ... | 2,045 | 48.902439 | 76 | py |
pynbody | pynbody-master/docs/tutorials/example_code/rotcurve.py | from os import environ
import matplotlib.pylab as plt
import pynbody
# load the snapshot and set to physical units
s = pynbody.load('testdata/g15784.lr.01024.gz')
# load the halos
h = s.halos()
# center on the largest halo and align the disk
pynbody.analysis.angmom.faceon(h[1])
# create a profile object for the s... | 943 | 28.5 | 82 | py |
pynbody | pynbody-master/docs/tutorials/example_code/do_plots.py | ### Make plots
try:
pp.sbprofile(h[i],filename=simname+'.sbprof.png',center=False)
pp.sfh(h[i],filename=simname+'.sfh.png',nbins=500)
pp.rotation_curve(h[i],filename=simname+'.rc.png',quick=True,
rmax ='40 kpc',center=False)
pp.rotation_curve(h[i],filename=simname+'.rcparts.png',quick=True,
... | 948 | 46.45 | 79 | py |
pynbody | pynbody-master/docs/tutorials/example_code/density_slice.py | import matplotlib.pylab as plt
import pynbody
import pynbody.plot.sph as sph
# load the snapshot and set to physical units
s = pynbody.load('testdata/g15784.lr.01024.gz')
s.physical_units()
# load the halos
h = s.halos()
# center on the largest halo and align the disk
pynbody.analysis.angmom.faceon(h[1])
#create a... | 416 | 22.166667 | 66 | py |
pynbody | pynbody-master/docs/tutorials/example_code/do_images.py | diskgas=s.gas[diskf]
### Make pictures:
try:
pp.sph.image(h[i].gas,filename=simname+'.facegas.png',width=30)
pp.sph.image(h[i].star,filename=simname+'.facestar.png',width=30)
pp.sph.image(diskgas,qty='temp',filename=simname+'.tempgasdiskface.png',
width=30,vmin=3,vmax=7)
s.gas['hiden'] ... | 2,005 | 50.435897 | 76 | py |
pynbody | pynbody-master/docs/tutorials/example_code/star_render.py | import matplotlib.pylab as plt
import pynbody
# load the snapshot and set to physical units
s = pynbody.load('testdata/g15784.lr.01024.gz')
s.physical_units()
# load the halos
h = s.halos()
# center on the largest halo and align the disk
pynbody.analysis.angmom.sideon(h[1])
#create an image using the default bands... | 375 | 21.117647 | 50 | py |
pynbody | pynbody-master/docs/tutorials/example_code/density_profile.py | import matplotlib.pylab as plt
import pynbody
# load the snapshot and set to physical units
s = pynbody.load('testdata/g15784.lr.01024.gz')
# load the halos
h = s.halos()
# center on the largest halo and align the disk
pynbody.analysis.angmom.faceon(h[1])
# convert all units to something reasonable (kpc, Msol etc)... | 1,024 | 27.472222 | 82 | py |
pynbody | pynbody-master/docs/tutorials/example_code/rcs.py | import glob
import pickle
import sys
import matplotlib.pyplot as plt
import numpy as np
import pynbody
runs = ['c.1td.05rp.1','mugs','esn1.2','td.01c.1rp.1','rp.175','noradpres','2crasy']
labels = ['Fiducial','MUGS','120% SN energy','Low Diffusion','High Diffusion','No ESF',
'High ESF']
cs = ['r','k','c','... | 1,046 | 29.794118 | 87 | py |
pynbody | pynbody-master/docs/tutorials/example_code/do_preamble.py | import glob
import os
import pickle
import sys
import numpy as np
import pynbody
import pynbody.analysis.profile as profile
import pynbody.filt as filt
import pynbody.plot as pp
import pynbody.plot.sph
import pynbody.units as units
simname = sys.argv[1] # use first argument as simulation name to analyze
pp.plt.ion... | 1,443 | 34.219512 | 86 | py |
pynbody | pynbody-master/docs/tutorials/example_code/do_data.py | Jtot = np.sqrt(((np.multiply(h[i]['j'].transpose(),h[i]['mass']).sum(axis=1))**2).sum()) # calculate angular momentum
W = np.sum(h[i]['phi']*h[i]['mass']) # halo potential energy
K = np.sum(h[i]['ke']*h[i]['mass']) # halo kinetic energy
absE = np.fabs(W+K) # total halo energy
mvir=np.sum(h[i]['mass'].in_... | 2,337 | 54.666667 | 128 | py |
pynbody | pynbody-master/docs/tutorials/example_code/temperature_slice.py | import matplotlib.pylab as plt
import pynbody
import pynbody.plot.sph as sph
# load the snapshot and set to physical units
s = pynbody.load('testdata/g15784.lr.01024.gz')
s.physical_units()
# load the halos
h = s.halos()
# center on the largest halo and align the disk
pynbody.analysis.angmom.sideon(h[1])
#create a... | 451 | 24.111111 | 88 | py |
pynbody | pynbody-master/docs/tutorials/example_code/density_integrated.py | import matplotlib.pylab as plt
import pynbody
import pynbody.plot.sph as sph
# load the snapshot and set to physical units
s = pynbody.load('testdata/g15784.lr.01024.gz')
s.physical_units()
# load the halos
h = s.halos()
# center on the largest halo and align the disk
pynbody.analysis.angmom.faceon(h[1])
#create a... | 452 | 24.166667 | 73 | py |
pynbody | pynbody-master/docs/sphinxext/docscrape_sphinx.py | import inspect
import pydoc
import re
import textwrap
from docscrape import ClassDoc, FunctionDoc, NumpyDocString
class SphinxDocString(NumpyDocString):
# string conversion routines
def _str_header(self, name, symbol='`'):
return ['.. rubric:: ' + name, '']
def _str_field_list(self, name):
... | 4,237 | 29.056738 | 76 | py |
pynbody | pynbody-master/docs/sphinxext/ipython_directive.py | r"""Sphinx directive to support embedded IPython code.
This directive allows pasting of entire interactive IPython sessions, prompts
and all, and their code will actually get re-executed at doc build time, with
all prompts renumbered sequentially. It also allows you to input code as a pure
python input by giving the a... | 27,656 | 31.807829 | 141 | py |
pynbody | pynbody-master/docs/sphinxext/apigen.py | """Attempt to generate templates for module reference with Sphinx
XXX - we exclude extension modules
To include extension modules, first identify them as valid in the
``_uri2path`` method, then handle them in the ``_parse_module`` script.
We get functions and classes by parsing the text of .py files.
Alternatively w... | 15,622 | 35.417249 | 79 | py |
pynbody | pynbody-master/docs/sphinxext/numpydoc.py | """
========
numpydoc
========
Sphinx extension that handles docstrings in the Numpy standard format. [1]
It will:
- Convert Parameters etc. sections to field lists.
- Convert See Also section to a See also entry.
- Renumber references.
- Extract the signature from the docstring, if it can't be determined otherwise.... | 4,068 | 32.628099 | 90 | py |
pynbody | pynbody-master/docs/sphinxext/docscrape.py | """Extract reference documentation from the NumPy source tree.
"""
import inspect
import pydoc
import re
import textwrap
from warnings import warn
from StringIO import StringIO
4
class Reader(object):
"""A line-based string reader.
"""
def __init__(self, data):
"""
Parameters
--... | 14,810 | 28.740964 | 80 | py |
pynbody | pynbody-master/docs/sphinxext/ipython_console_highlighting.py | """reST directive for syntax-highlighting ipython interactive sessions.
XXX - See what improvements can be made based on the new (as of Sept 2009)
'pycon' lexer for the python console. At the very least it will give better
highlighted tracebacks.
"""
#-----------------------------------------------------------------... | 4,144 | 35.681416 | 87 | py |
pynbody | pynbody-master/docs/sphinxext/inheritance_diagram.py | r"""
Defines a docutils directive for inserting inheritance diagrams.
Provide the directive with one or more classes or modules (separated
by whitespace). For modules, all of the classes in that module will
be used.
Example::
Given the following classes:
class A: pass
class B(A): pass
class C(A): pass
... | 13,635 | 32.258537 | 103 | py |
pynbody | pynbody-master/pynbody/transformation.py | import weakref
import numpy as np
from . import snapshot
class Transformation:
def __init__(self, f, defer=False):
if isinstance(f, snapshot.SimSnap):
self.sim = f
self.next_transformation = None
elif isinstance(f, Transformation):
self.sim = None
... | 5,675 | 25.773585 | 118 | py |
pynbody | pynbody-master/pynbody/derived.py | """
derived
=======
Holds procedures for creating new arrays from existing ones, e.g. for
getting the radial position. For more information see :ref:`derived`.
"""
import functools
import logging
import time
import numpy as np
from . import analysis, array, config, units
from .snapshot import SimSnap
logger = log... | 8,269 | 25.59164 | 109 | py |
pynbody | pynbody-master/pynbody/array.py | """
array
=====
Defines a shallow wrapper around numpy.ndarray for extra functionality like unit-tracking.
For most purposes, the differences between numpy.ndarray and
array.SimArray are not important. However, when units are specified
(by setting the ``units`` attribute), the behaviour is slightly
different. In part... | 37,590 | 30.50964 | 129 | py |
pynbody | pynbody-master/pynbody/family.py | """
family
======
This module defines the Family class which represents
families of particles (e.g. dm, gas, star particles).
New Family objects are automatically registered so that
snapshots can use them in the normal syntax (snap.dm,
snap.star, etc).
In practice the easiest way to make use of the flexibility
this ... | 2,974 | 24.869565 | 80 | py |
pynbody | pynbody-master/pynbody/units.py | """
units
=====
The pynbody units module consists of a set of classes for tracking units.
It relates closely to the :mod:`~pynbody.array` module, which defines
an extension to numpy arrays which carries unit information.
Making units
------------
Units are generated and used at various points through the pynbody
f... | 24,362 | 27.494737 | 187 | py |
pynbody | pynbody-master/pynbody/filt.py | """
filt
====
Defines and implements 'filters' which allow abstract subsets
of data to be specified.
See the `filter tutorial
<http://pynbody.github.io/pynbody/tutorials/filters.html>`_ for some
sample usage.
"""
import pickle
import numpy as np
from . import _util, family, units
class Filter:
def __init... | 10,427 | 25.738462 | 122 | py |
pynbody | pynbody-master/pynbody/configuration.py | import logging
import multiprocessing
import os
import warnings
def _get_config_parser_with_defaults():
# Create config dictionaries which will be required by subpackages
import configparser
config_parser = configparser.ConfigParser()
config_parser.optionxform = str
config_parser.read(
os.... | 4,328 | 37.651786 | 200 | py |
pynbody | pynbody-master/pynbody/util.py | """
util
====
Various utility routines used internally by pynbody.
"""
import fractions
import gzip
import logging
import math
import os
import struct
import sys
import threading
import time
import numpy as np
from . import units
from .array import SimArray
logger = logging.getLogger('pynbody.util')
from ._util ... | 17,864 | 26.191781 | 105 | py |
pynbody | pynbody-master/pynbody/dependencytracker.py | import threading
class DependencyError(RuntimeError):
pass
class DependencyContext:
def __init__(self, tracker, name):
self.tracker = tracker
self.name = name
def __enter__(self):
self.tracker._calculation_lock.__enter__()
if self.name in self.tracker._current_calculation... | 1,736 | 28.948276 | 74 | py |
pynbody | pynbody-master/pynbody/__init__.py | """
pynbody
=======
A light-weight, portable, format-transparent analysis framework
for N-body and SPH astrophysical simulations.
For more information, either build the latest documentation included
in our git repository, or view the online version here:
http://pynbody.github.io/pynbody/
"""
import sys
if sys.vers... | 2,460 | 24.905263 | 95 | py |
pynbody | pynbody-master/pynbody/simdict.py | """
simdict
=======
This submodule defines an augmented dictionary class
(:class:`SimDict`) for :class:`~pynbody.snapshot.SimSnap` properties
where entries need to be managed e.g. for defining default entries,
or for ensuring consistency between equivalent properties like
redshift and scalefactor.
By default, a :cla... | 2,417 | 22.705882 | 79 | py |
pynbody | pynbody-master/pynbody/bridge/__init__.py | """
bridge
======
The bridge module has tools for connecting different outputs. For instance,
it's possible to take a subview (e.g. a halo) from one snapshot and 'push'
it into the other. This is especially useful if the two snapshots are
different time outputs of the same simulation.
Once connected, bridge called o... | 13,047 | 41.090323 | 230 | py |
pynbody | pynbody-master/pynbody/chunk/__init__.py | """
chunk
=====
Methods for describing parts of files to load.
This module provides generalized logic for getting parts of sequential data off disk.
It is for internal use. If you want to write a loader that supports partial loading,
it will make it a lot easier.
The steps for loading particle data are as follows
... | 16,235 | 36.238532 | 111 | py |
pynbody | pynbody-master/pynbody/extern/cython_fortran_utils.py | from . import _cython_fortran_utils
FortranFile = _cython_fortran_utils.FortranFile
| 85 | 20.5 | 47 | py |
pynbody | pynbody-master/pynbody/extern/__init__.py | 0 | 0 | 0 | py | |
pynbody | pynbody-master/pynbody/bc_modules/__init__.py | # Dummy file
| 13 | 6 | 12 | py |
pynbody | pynbody-master/pynbody/gravity/tree.py | """Gravity Tree. Builds tree based on pkdgrav2"""
try:
from .. import pkdgrav
except ImportError:
# pkdgrav2 never works at the moment, and the warning below
# confuses/annoys people
pass
#import warnings
#warnings.warn("Unable to import PKDGrav gravity solver. Most likely this means either tha... | 1,595 | 30.92 | 350 | py |
pynbody | pynbody-master/pynbody/gravity/calc.py | import math
import warnings
import numpy as np
from .. import array, config, units
from ..util import eps_as_simarray, get_eps
from . import tree
from ._gravity import direct
def all_direct(f, eps=None):
phi, acc = direct(f, f['pos'].view(np.ndarray), eps)
f['phi'] = phi
f['acc'] = acc
def all_pm(f, e... | 5,075 | 28.005714 | 120 | py |
pynbody | pynbody-master/pynbody/gravity/__init__.py | from . import calc
| 19 | 9 | 18 | py |
pynbody | pynbody-master/pynbody/plot/sph.py | """
sph
===
routines for plotting smoothed quantities
"""
import matplotlib
import numpy as np
import pylab as p
from .. import config, sph, units as _units
def sideon_image(sim, *args, **kwargs):
"""
Rotate the simulation so that the disc of the passed halo is
side-on, then make an SPH image by pas... | 17,830 | 31.898524 | 136 | py |
pynbody | pynbody-master/pynbody/plot/gas.py | """
gas
===
Functions for plotting gas quantities
"""
import logging
import matplotlib.pyplot as plt
import numpy as np
from ..analysis import angmom, halo, profile
from ..units import Unit
from .generic import hist2d
logger = logging.getLogger('pynbody.plot.gas')
def rho_T(sim, rho_units=None, rho_range=None,... | 3,676 | 28.416 | 125 | py |
pynbody | pynbody-master/pynbody/plot/profile.py | """
profile
=======
"""
import logging
import numpy as np
import pylab as p
from .. import config, filt, units
from ..analysis import angmom, halo, profile
logger = logging.getLogger('pynbody.plot.profile')
def rotation_curve(sim, center=True, r_units='kpc',
v_units='km s^-1', disk_height='10... | 6,830 | 27.227273 | 91 | py |
pynbody | pynbody-master/pynbody/plot/stars.py | """
stars
=====
"""
import logging
import warnings
import matplotlib
import matplotlib.pyplot as plt
import numpy as np
from .. import array, filt, units, units as _units
from ..analysis import angmom, profile
from ..sph import Kernel2D, render_spherical_image
from .sph import image
logger = logging.getLogger('py... | 41,698 | 29.661029 | 199 | py |
pynbody | pynbody-master/pynbody/plot/generic.py | """
generic
=======
Flexible and general plotting functions
"""
import numpy as np
import pylab as plt
import pynbody
from .. import config
from ..array import SimArray
from ..units import NoUnit
def qprof(sim, qty='metals', weights=None, q=(0.16, 0.5, 0.84),
ax=False, ylabel=None, xlog=False, ylog=Fa... | 19,317 | 28.137255 | 107 | py |
pynbody | pynbody-master/pynbody/plot/util.py | """
util
====
Utility functions for the plotting module
"""
import numpy as np
import scipy as sp
import scipy.signal
import scipy.sparse
def fast_kde(x, y, kern_nx=None, kern_ny=None, gridsize=(100, 100),
extents=None, nocorrelation=False, weights=None, norm = False, **kwargs):
"""
A faster ... | 6,364 | 30.509901 | 89 | py |
pynbody | pynbody-master/pynbody/plot/__init__.py | import imp
from . import gas, generic, metals, profile, stars, util
imp.reload(profile)
imp.reload(generic)
imp.reload(stars)
imp.reload(gas)
imp.reload(metals)
imp.reload(util)
from .gas import rho_T, temp_profile
from .generic import fourier_map, gauss_kde, hist2d, qprof
from .metals import mdf, ofefeh
from .profi... | 488 | 26.166667 | 69 | py |
pynbody | pynbody-master/pynbody/plot/metals.py | """
metals
======
"""
import numpy as np
from .generic import gauss_kde
def mdf(sim, filename=None, clear=True, range=[-5, 0.3], axes=False, **kwargs):
'''
Metallicity Distribution Function
Plots a metallicity distribution function to the best of
matplotlib's abilities. Unfortunately, the "nor... | 1,882 | 22.835443 | 96 | py |
pynbody | pynbody-master/pynbody/snapshot/nchilada.py | """
nchilada
========
Implements classes and functions for handling nchilada files. You rarely
need to access this module directly as it will be invoked
automatically via pynbody.load.
"""
import os
import struct
import warnings
import xml.dom.minidom
import numpy as np
from .. import chunk, family, units
from .... | 7,561 | 35.708738 | 131 | py |
pynbody | pynbody-master/pynbody/snapshot/gadgethdf.py | """
gadgethdf
=========
Implementation of backend reader for GadgetHDF files by Andrew Pontzen.
The gadget array names are mapped into pynbody array mes according
to the mappings given by the config.ini section [gadgethdf-name-mapping].
The gadget particle groups are mapped into pynbody families according
to the m... | 38,390 | 35.183789 | 173 | py |
pynbody | pynbody-master/pynbody/snapshot/snapshot_util.py | """
util
====
Utility functions for the snapshot module.
"""
import logging
from functools import reduce
from .. import array, units
logger = logging.getLogger('pynbody.snapshot')
class ContainerWithPhysicalUnitsOption:
"""
Defines an abstract class that has properties and arrays
that can be converte... | 4,046 | 29.428571 | 117 | py |
pynbody | pynbody-master/pynbody/snapshot/gadget.py | """
gadget
======
Implements classes and functions for handling gadget files; you rarely
need to access this module directly as it will be invoked
automatically via pynbody.load.
"""
import configparser
import copy
import errno
import itertools
import struct
import sys
import warnings
import numpy as np
from .. ... | 52,546 | 42.57131 | 149 | py |
pynbody | pynbody-master/pynbody/snapshot/tipsy.py | """tipsy
=====
Implements classes and functions for handling tipsy files. You rarely
need to access this module directly as it will be invoked
automatically via pynbody.load.
**Input**:
*filename*: file name string
**Optional Keywords**:
*paramfile*: string specifying the parameter file to load. If not
specified,... | 63,527 | 36.042566 | 145 | py |
pynbody | pynbody-master/pynbody/snapshot/namemapper.py | import configparser
import sys
from .. import config_parser
def setup_name_maps(config_name, gadget_blocks=False, with_alternates=False):
name_map = {}
rev_name_map = {}
alternates = {}
try:
for a, b in config_parser.items(config_name):
if sys.version_info[0] == 2:
... | 1,903 | 29.709677 | 111 | py |
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