dyf

import csv

def hex_str_to_rgb(hex_str):
    """ convert a hex string (e.g. "FFFFFF") to an RGB dictionary """
    val = int(hex_str, 16)
    return { 
        'r': val & 0x0000ff,
        'g': (val & 0x00ff00) >> 8,
        'b': val >> 16
        }

dyf

from allensdk.config import enable_console_log
from allensdk.api.queries.rma_api import RmaApi
from allensdk.api.queries.image_download_api import ImageDownloadApi

# print download messages to your console
enable_console_log()

# instantiate api classes for downloading metadata/images
image_api = ImageDownloadApi()
rma_api = RmaApi()

dyf

from allensdk.core.mouse_connectivity_cache import MouseConnectivityCache

# pick from 10, 25, 50, 100 for resolution
mcc = MouseConnectivityCache(manifest_file='mcc/manifest.json', resolution=10)

# careful, these will get read into memory
av, _ = mcc.get_annotation_volume()
tv, _ = mcc.get_template_volume()

dyf

import json
from allensdk.core.structure_tree import StructureTree

file_name = "C:/Users/davidf/Downloads/mouse-brain-ontology.json"
structures = json.load(open(file_name,'r'))

# workaround for a bug in StructureTree.clean_structures that I just found
for s in structures:
    s['id'] = int(s['id'])
    s['structure_sets'] = []

dyf

import requests
import shutil
from IPython.display import HTML

url = 'https://media.giphy.com/media/demgpwJ6rs2DS/giphy.gif'
file_name = 'img.gif'

# download
response = requests.get(url, stream=True)
with open(file_name, 'wb') as out_file:

dyf

from allensdk.brain_observatory.locally_sparse_noise import LocallySparseNoise
from allensdk.core.brain_observatory_cache import BrainObservatoryCache
import allensdk.brain_observatory.stimulus_info as stiminfo


experiment_id = 12345 # dummy id
analysis_file = '/path/to/analysis.h5'

boc = BrainObservatoryCache(manifest_file='boc/manifest.json')
data_set = boc.get_ophys_experiment_data(experiment_id)

dyf

from allensdk.core.brain_observatory_cache import BrainObservatoryCache
boc = BrainObservatoryCache(manifest_file='boc/manifest.json')

containers = boc.get_experiment_containers(include_failed=True)

tagged_containers = [ c for c in containers if c['tags'] ]
for tc in tagged_containers:
    print(tc['id'], tc['tags'])

dyf

from allensdk.core.brain_observatory_cache import BrainObservatoryCache
from allensdk.config import enable_console_log
from allensdk.api.queries.rma_api import RmaApi
import matplotlib.pyplot as plt

# print out API queries 
enable_console_log()

# download experiments with passing eye tracking
results = RmaApi().model_query('OphysExperiment', 

dyf

from allensdk.core.mouse_connectivity_cache import MouseConnectivityCache
import nrrd

mcc = MouseConnectivityCache(manifest_file="/data/dynamic-brain-workshop/mouse_connectivity_cache/mouse_connectivity_manifest.json")
exps = mcc.get_experiments()
pd, _ = mcc.get_projection_density(exps[0]['id'])

nrrd.write('some_file.nrrd', pd, options={ 'encoding': 'raw' })

dyf

require 'csv'

def read_swc(file_path)
    rows = CSV.read(file_path, col_sep: ' ')
    
    good_rows = rows.select { |row| not row[0].starts_with?('#') }

    return good_rows.collect do |row|
      {
        'id' => row[0],