dyf

from allensdk.api.queries.rma_api import RmaApi
import allensdk.core.json_utilities as ju


all_structs = []

root = RmaApi().model_query("Structure", criteria="[graph_id$eq1],[acronym$eqgrey]")[0]

all_structs.append(root)

dyf

from allensdk.core.mouse_connectivity_cache import MouseConnectivityCache
mcc = MouseConnectivityCache(manifest_file="/data/dynamic-brain-workshop/mouse_connectivity_cache/manifest.json",
                             resolution=10)
tv, _ = mcc.get_template_volume()
fig, ax = plt.subplots(figsize=(10,10))
plt.imshow(tv[:,515,:], cmap='gray')
plt.show()

dyf

import matplotlib.pyplot as plt
import numpy as np
import matplotlib.patches as mpatch
from matplotlib.collections import PatchCollection
import matplotlib.colors as mcolors
import matplotlib.colorbar 
import matplotlib.gridspec as gridspec

def mega_paw_plot(sdata_list=None, sdata_bg_list=None, cdata_list=None, 
                  cmap=None, clim=None, 

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import matplotlib.pyplot as plt
import imageio
import numpy as np
from scipy.signal import medfilt

# from here
# https://www.nasa.gov/multimedia/imagegallery/image_feature_539.html
im = imageio.imread('jupiter_bottom.jpg')
off = [16,-1]
rtrim = 200

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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],

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

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', 

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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.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

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: