Example Python script to download atlas background images from #AllenBrainAtlasAPI #AtlasDownload

download_atlas_background_images.py

import urllib, json
import os

# 
# Example python code to download atlas background images
#
# Read the Allen Brain Atlas API documentation:
# http://help.brain-map.org/display/api/Atlas+Drawings+and+Ontologies
#
# In the table find the atlas that you looking for.
# Take note of the "Atlas ID"
#

# Specify output directory for files
output_directory = "temp/background_image"

# Specify downsample factor
downsample = 6

# Copy "Atlas ID" here
atlas_id = 265297126

# RMA query to find images for atlas
query_url = "http://api.brain-map.org/api/v2/data/query.json?criteria=model::AtlasImage"
query_url += ",rma::criteria,[annotated$eqtrue]"
query_url += ",atlas_data_set(atlases[id$eq%d])" % (atlas_id)
query_url += ",rma::options[order$eq'sub_images.section_number'][num_rows$eqall]"

response = urllib.urlopen(query_url)
images = json.loads(response.read())['msg']

# make output directory
if not os.path.exists( output_directory ) :
    os.makedirs( output_directory )

# loop through each image
for i in images :

    print i['section_number']

    # downsampled images 
    image_url  = "http://api.brain-map.org/api/v2/section_image_download/%d?" % (i['id'])
    image_url += "downsample=%d" % (downsample)
    image_path = os.path.join( output_directory, '%04d_%d.jpg' % (i['section_number'],i['id'])   )
    urllib.urlretrieve(image_url, image_path)