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sneakers-the-rat
e89e8cf913 Merge branch 'main' of https://git.jon-e.net/jonny/scrape-dandi 2023-10-30 12:18:16 -07:00
sneakers-the-rat
3effed9bdd plotting 2023-10-30 12:18:07 -07:00
5 changed files with 561 additions and 1 deletions
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@ -160,3 +160,5 @@ cython_debug/
# option (not recommended) you can uncomment the following to ignore the entire idea folder. # option (not recommended) you can uncomment the following to ignore the entire idea folder.
#.idea/ #.idea/
metadata.json
log.txt

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poetry.lock generated
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@ -507,6 +507,135 @@ files = [
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] ]
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tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"]
[[package]] [[package]]
name = "pycparser" name = "pycparser"
version = "2.21" version = "2.21"
@ -1620,6 +2058,20 @@ core = ["blessed", "jsonschema (>=3.0.0)"]
full = ["blessed", "jsonschema (>=3.0.0)", "pytest", "pytest-timeout"] full = ["blessed", "jsonschema (>=3.0.0)", "pytest", "pytest-timeout"]
tests = ["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"
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diagrams = ["jinja2", "railroad-diagrams"]
[[package]] [[package]]
name = "python-dateutil" name = "python-dateutil"
version = "2.8.2" version = "2.8.2"
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packaging = ">=20"
setuptools = "*"
typing-extensions = "*"
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docs = ["entangled-cli[rich]", "mkdocs", "mkdocs-entangled-plugin", "mkdocs-material", "mkdocstrings[python]", "pygments"]
rich = ["rich"]
test = ["build", "pytest", "rich", "wheel"]
[[package]] [[package]]
name = "six" name = "six"
version = "1.16.0" version = "1.16.0"
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[metadata] [metadata]
lock-version = "2.0" lock-version = "2.0"
python-versions = "^3.11" python-versions = "^3.11"
content-hash = "255b26438bcdaa14b4614da06a257e5d344691e5248c07e90e1fa4032045a5c4" content-hash = "0b2410046c8281d17cfe2c2d93fe3fa2f52aa6213755d5b33c6054ebf59576fe"

1
pyproject.toml
View file

@ -14,6 +14,7 @@ scrape-dandi = "scrape_dandi:main"
[tool.poetry.dependencies] [tool.poetry.dependencies]
python = "^3.11" python = "^3.11"
dandi = "^0.56.2" dandi = "^0.56.2"
matplotlib = "^3.8.0"
[build-system] [build-system]

44
scrape_dandi/metadata.py Normal file
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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()

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scrape_dandi/plot.py Normal file
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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)