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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)
layers = [ { 'id': 900000000, 'acronym': 'Isocortex1', 'name': 'Isocortex layer 1', 'color_hex_triplet': '7fc97f' },
{ 'id': 900000001, 'acronym': 'Isocortex2/3', 'name': 'Isocortex layer 2/3', 'color_hex_triplet': 'beaed4' },
{ 'id': 900000002, 'acronym': 'Isocortex4', 'name': 'Isocortex layer 4', 'color_hex_triplet': 'fdc086' },
{ 'id': 900000003, 'acronym': 'Isocortex5', 'name': 'Isocortex layer 5', 'color_hex_triplet': 'ffff99' },
{ 'id': 900000004, 'acronym': 'Isocortex6a', 'name': 'Isocortex layer 6a', 'color_hex_triplet': '386cb0' },
{ 'id': 900000005, 'acronym': 'Isocortex6b', 'name': 'Isocortex layer 6b', 'color_hex_triplet': 'f0027f' } ]
all_structs += layers
for layer in layers:
layer['structure_id_path'] = '/%d/%d/' % (root['id'], layer['id'])
layer['parent_structure_id'] = root['id']
structs = RmaApi().model_query("Structure", criteria="structure_sets[name$eq'%s']"%layer['name'])
for struct in structs:
struct['structure_id_path'] = '/%d/%d/%d/' % (root['id'], layer['id'], struct['id'])
struct['color_hex_triplet'] = layer['color_hex_triplet']
struct['parent_structure_id'] = layer['id']
all_structs += structs
# Generate structure similar to the one returned by the http://api.brain-map.org/api/v2/data/Structure/query.json
content = {
"msg": all_structs,
"num_rows": len(all_structs),
"start_row": 0,
"success": True,
"total_rows": len(all_structs)
}
ju.write("layer_structures.json", content)
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