plotting
This commit is contained in:
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debbadc939
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5 changed files with 561 additions and 1 deletions
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@ -160,3 +160,5 @@ cython_debug/
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# option (not recommended) you can uncomment the following to ignore the entire idea folder.
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#.idea/
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metadata.json
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log.txt
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poetry.lock
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@ -507,6 +507,135 @@ files = [
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{file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"},
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]
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[[package]]
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name = "contourpy"
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version = "1.1.0"
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description = "Python library for calculating contours of 2D quadrilateral grids"
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optional = false
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python-versions = ">=3.8"
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[package.dependencies]
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[package.extras]
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bokeh = ["bokeh", "selenium"]
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docs = ["furo", "sphinx-copybutton"]
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mypy = ["contourpy[bokeh,docs]", "docutils-stubs", "mypy (==1.2.0)", "types-Pillow"]
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|
||||
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|
||||
|
||||
[package.dependencies]
|
||||
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|
||||
|
||||
[package.extras]
|
||||
bokeh = ["bokeh", "selenium"]
|
||||
docs = ["furo", "sphinx (>=7.2)", "sphinx-copybutton"]
|
||||
mypy = ["contourpy[bokeh,docs]", "docutils-stubs", "mypy (==1.4.1)", "types-Pillow"]
|
||||
test = ["Pillow", "contourpy[test-no-images]", "matplotlib"]
|
||||
test-no-images = ["pytest", "pytest-cov", "wurlitzer"]
|
||||
|
||||
[[package]]
|
||||
name = "cryptography"
|
||||
version = "41.0.4"
|
||||
|
|
@ -552,6 +681,21 @@ ssh = ["bcrypt (>=3.1.5)"]
|
|||
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|
||||
test-randomorder = ["pytest-randomly"]
|
||||
|
||||
[[package]]
|
||||
name = "cycler"
|
||||
version = "0.12.1"
|
||||
description = "Composable style cycles"
|
||||
optional = false
|
||||
python-versions = ">=3.8"
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|
||||
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||||
[package.extras]
|
||||
docs = ["ipython", "matplotlib", "numpydoc", "sphinx"]
|
||||
tests = ["pytest", "pytest-cov", "pytest-xdist"]
|
||||
|
||||
[[package]]
|
||||
name = "dandi"
|
||||
version = "0.56.2"
|
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|
@ -686,6 +830,71 @@ files = [
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name = "fonttools"
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||||
description = "Tools to manipulate font files"
|
||||
optional = false
|
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||||
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|
||||
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|
||||
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||||
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|
||||
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|
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|
||||
{file = "Pillow-10.1.0-pp39-pypy39_pp73-manylinux_2_28_x86_64.whl", hash = "sha256:1fafabe50a6977ac70dfe829b2d5735fd54e190ab55259ec8aea4aaea412fa0b"},
|
||||
{file = "Pillow-10.1.0-pp39-pypy39_pp73-win_amd64.whl", hash = "sha256:3b834f4b16173e5b92ab6566f0473bfb09f939ba14b23b8da1f54fa63e4b623f"},
|
||||
{file = "Pillow-10.1.0.tar.gz", hash = "sha256:e6bf8de6c36ed96c86ea3b6e1d5273c53f46ef518a062464cd7ef5dd2cf92e38"},
|
||||
]
|
||||
|
||||
[package.extras]
|
||||
docs = ["furo", "olefile", "sphinx (>=2.4)", "sphinx-copybutton", "sphinx-inline-tabs", "sphinx-removed-in", "sphinxext-opengraph"]
|
||||
tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"]
|
||||
|
||||
[[package]]
|
||||
name = "pycparser"
|
||||
version = "2.21"
|
||||
|
|
@ -1620,6 +2058,20 @@ core = ["blessed", "jsonschema (>=3.0.0)"]
|
|||
full = ["blessed", "jsonschema (>=3.0.0)", "pytest", "pytest-timeout"]
|
||||
tests = ["pytest", "pytest-timeout"]
|
||||
|
||||
[[package]]
|
||||
name = "pyparsing"
|
||||
version = "3.1.1"
|
||||
description = "pyparsing module - Classes and methods to define and execute parsing grammars"
|
||||
optional = false
|
||||
python-versions = ">=3.6.8"
|
||||
files = [
|
||||
{file = "pyparsing-3.1.1-py3-none-any.whl", hash = "sha256:32c7c0b711493c72ff18a981d24f28aaf9c1fb7ed5e9667c9e84e3db623bdbfb"},
|
||||
{file = "pyparsing-3.1.1.tar.gz", hash = "sha256:ede28a1a32462f5a9705e07aea48001a08f7cf81a021585011deba701581a0db"},
|
||||
]
|
||||
|
||||
[package.extras]
|
||||
diagrams = ["jinja2", "railroad-diagrams"]
|
||||
|
||||
[[package]]
|
||||
name = "python-dateutil"
|
||||
version = "2.8.2"
|
||||
|
|
@ -2053,6 +2505,27 @@ docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments
|
|||
testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pip (>=19.1)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-ruff", "pytest-timeout", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
|
||||
testing-integration = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "packaging (>=23.1)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
|
||||
|
||||
[[package]]
|
||||
name = "setuptools-scm"
|
||||
version = "8.0.4"
|
||||
description = "the blessed package to manage your versions by scm tags"
|
||||
optional = false
|
||||
python-versions = ">=3.8"
|
||||
files = [
|
||||
{file = "setuptools-scm-8.0.4.tar.gz", hash = "sha256:b5f43ff6800669595193fd09891564ee9d1d7dcb196cab4b2506d53a2e1c95c7"},
|
||||
{file = "setuptools_scm-8.0.4-py3-none-any.whl", hash = "sha256:b47844cd2a84b83b3187a5782c71128c28b4c94cad8bfb871da2784a5cb54c4f"},
|
||||
]
|
||||
|
||||
[package.dependencies]
|
||||
packaging = ">=20"
|
||||
setuptools = "*"
|
||||
typing-extensions = "*"
|
||||
|
||||
[package.extras]
|
||||
docs = ["entangled-cli[rich]", "mkdocs", "mkdocs-entangled-plugin", "mkdocs-material", "mkdocstrings[python]", "pygments"]
|
||||
rich = ["rich"]
|
||||
test = ["build", "pytest", "rich", "wheel"]
|
||||
|
||||
[[package]]
|
||||
name = "six"
|
||||
version = "1.16.0"
|
||||
|
|
@ -2338,4 +2811,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
|
|||
[metadata]
|
||||
lock-version = "2.0"
|
||||
python-versions = "^3.11"
|
||||
content-hash = "255b26438bcdaa14b4614da06a257e5d344691e5248c07e90e1fa4032045a5c4"
|
||||
content-hash = "0b2410046c8281d17cfe2c2d93fe3fa2f52aa6213755d5b33c6054ebf59576fe"
|
||||
|
|
|
|||
|
|
@ -14,6 +14,7 @@ scrape-dandi = "scrape_dandi:main"
|
|||
[tool.poetry.dependencies]
|
||||
python = "^3.11"
|
||||
dandi = "^0.56.2"
|
||||
matplotlib = "^3.8.0"
|
||||
|
||||
|
||||
[build-system]
|
||||
|
|
|
|||
44
scrape_dandi/metadata.py
Normal file
44
scrape_dandi/metadata.py
Normal file
|
|
@ -0,0 +1,44 @@
|
|||
from dandi.cli.cmd_ls import ls
|
||||
import io
|
||||
import sys
|
||||
import json
|
||||
from click.exceptions import ClickException
|
||||
from scrape_dandi import DANDI_ID, MAX_DANDISET
|
||||
from tqdm import trange
|
||||
from multiprocessing import Pool
|
||||
|
||||
def dset_ls(dset: int) -> dict:
|
||||
orig = sys.stdout
|
||||
capturer = io.StringIO()
|
||||
metadata = {}
|
||||
try:
|
||||
sys.stdout = capturer
|
||||
ls.main([DANDI_ID.format(dset), '--format', 'json'], standalone_mode=False)
|
||||
metadata = json.loads(capturer.getvalue())[0]
|
||||
except ClickException:
|
||||
pass
|
||||
finally:
|
||||
sys.stdout = orig
|
||||
return metadata
|
||||
|
||||
def get_all_meta() -> dict:
|
||||
meta = {}
|
||||
|
||||
try:
|
||||
for i in trange(MAX_DANDISET):
|
||||
this_meta = dset_ls(i)
|
||||
if this_meta:
|
||||
meta[i] = this_meta
|
||||
finally:
|
||||
return meta
|
||||
|
||||
def get_and_save_meta(file:str='metadata.json'):
|
||||
|
||||
#try:
|
||||
meta = get_all_meta()
|
||||
#finally:
|
||||
with open(file, 'w') as jfile:
|
||||
json.dump(meta, jfile)
|
||||
|
||||
if __name__ == '__main__':
|
||||
get_and_save_meta()
|
||||
40
scrape_dandi/plot.py
Normal file
40
scrape_dandi/plot.py
Normal file
|
|
@ -0,0 +1,40 @@
|
|||
from matplotlib import pyplot as plt
|
||||
import matplotlib.ticker as tkr
|
||||
import numpy as np
|
||||
import json
|
||||
|
||||
def sizeof_fmt(x, pos):
|
||||
if x<0:
|
||||
return ""
|
||||
for x_unit in ['bytes', 'kB', 'MB', 'GB', 'TB']:
|
||||
if x < 1024.0:
|
||||
return "%3.1f %s" % (x, x_unit)
|
||||
x /= 1024.0
|
||||
|
||||
def plot_sizes(meta:dict):
|
||||
x = np.arange(np.max([int(k) for k in meta.keys()]))
|
||||
y = np.array([meta.get(str(i), {}).get('size', 0) for i in x])
|
||||
|
||||
cumulative = np.cumsum(y)
|
||||
#cumulative = cumulative / np.max(cumulative)
|
||||
|
||||
y[y<1000000000] = 0
|
||||
|
||||
fig, ax = plt.subplots(2,1)
|
||||
ax[0].bar(x, y)
|
||||
ax[0].set_yscale('log')
|
||||
|
||||
ax[0].yaxis.set_major_formatter(tkr.FuncFormatter(sizeof_fmt))
|
||||
|
||||
ax[1].plot(x, cumulative)
|
||||
ax[1].yaxis.set_major_formatter(tkr.FuncFormatter(sizeof_fmt))
|
||||
plt.show()
|
||||
|
||||
if __name__ == "__main__":
|
||||
with open('metadata.json', 'r') as jfile:
|
||||
meta = json.load(jfile)
|
||||
|
||||
del meta['108']
|
||||
|
||||
|
||||
plot_sizes(meta)
|
||||
Loading…
Reference in a new issue