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Ben Dichter bendichter

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@bendichter
bendichter / zarr_metadata.py
Last active July 4, 2024 15:52
Create zarr metadata to read arbitrary binary file
import numpy as np
import json
import base64
def _add_dataset_to_rfs(
rfs: dict,
shape: list[int],
dtype: np.dtype,
dset_name: str,
@bendichter
bendichter / constrained_array.py
Created January 8, 2024 20:04
constrainedarray
from typing import Tuple, Type, Any, Union, Optional
from pydantic import BaseModel
import numpy as np
def get_shape(data):
"""
Get the shape of various data structures: NumPy array, h5py dataset, Zarr dataset, or a nested list of arbitrary depth.
Parameters
@bendichter
bendichter / convert_ephys_dandiset_to_bids.ipynb
Last active December 18, 2023 15:06
convert_ephys_dandiset_to_bids
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@bendichter
bendichter / rest_neuro_papers.ipynb
Created October 19, 2022 11:32
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@bendichter
bendichter / grouped_barplot.py
Last active July 15, 2022 18:34
plot a grouped barplot
import matplotlib.pyplot as plt
import numpy as np
from typing import List, Optional
def grouped_barplot(
data,
clabels: List[str],
xlabels: List[str],
@bendichter
bendichter / jit_plotter.py
Created July 7, 2022 21:02
from itertools import chain, repeat
from bisect import bisect_left
from datetime import datetime, timedelta
import numpy as np
import matplotlib.pyplot as plt
data = [
{
@bendichter
bendichter / git_timesheet.py
Last active July 7, 2022 20:55
# first run:
#
#!git log --all --numstat --pretty=format:'--%h--%ad--%aN' --no-renames > git.log
import datetime
import matplotlib.pyplot as plt
import pandas as pd
from pprint import pprint
import matplotlib.ticker
@bendichter
bendichter / dandi cli log
Created June 1, 2022 16:58
2022-06-01 11:34:17,098 [ INFO] Logs saved in /Users/bendichter/Library/Logs/dandi-cli/20220601153356Z-59646.log
(base) MacBook-Pro-3:~ bendichter$ dandi download https://dandiarchive.org/dandisets/000053/versions/"draft"/assets/?path="sub-npJ3/sub-npJ3_ses-20190504_behavior.nwb"
(base) MacBook-Pro-3:~ bendichter$
(base) MacBook-Pro-3:~ bendichter$
(base) MacBook-Pro-3:~ bendichter$
(base) MacBook-Pro-3:~ bendichter$ dandi download https://dandiarchive.org/dandisets/000053/versions/"draft"/assets/?path="sub-npJ3/sub-npJ3_ses-20190504_behavior.nwb"
(base) MacBook-Pro-3:~ bendichter$
(base) MacBook-Pro-3:~ bendichter$ cat /Users/bendichter/Library/Logs/dandi-cli/20220601153356Z-59646.log
2022-06-01T11:33:56-0400 [INFO ] dandi 59646:8602854912 dandi v0.40.0, hdmf v3.2.1, pynwb v2.0.1, h5py v3.1.0
2022-06-01T11:33:56-0400 [INFO ] dandi 59646:8602854912 sys.argv = ['/Users/bendichter/opt/miniconda3/bin/dandi', 'download', 'https://dandiarchive.org/dandisets/000053/versions/draft/assets/?path=sub-npJ3/
@bendichter
bendichter / download_figshare_collection.py
Created April 27, 2022 21:36
Iterate over an entire collection and download each file from each article
import os
import json
import requests
from tqdm import tqdm
from urllib.request import urlretrieve
BASE_URL = 'https://api.figshare.com/v2'
def download_collection(collection_id, destination):
@bendichter
bendichter / h5pytree.py
Last active March 23, 2022 00:54
draw tree structure of h5py File
import h5py
def print_group(group: h5py.Group):
name = group.name.split('/')[-1]
return f"{name} ({len(group.keys())} objects)/"
def print_dataset(dataset: h5py.Dataset):
name = dataset.name.split('/')[-1]
return f"{name} {dataset.shape}, {dataset.dtype}"