def __init__(self):
SvgApi.__init__(
self
) # https://github.com/AllenInstitute/AllenSDK/blob/master/allensdk/api/queries/svg_api.py
ImageDownloadApi.__init__(
self
) # https://github.com/AllenInstitute/AllenSDK/blob/master/allensdk/api/queries/image_download_api.py
self.annsetsapi = AnnotatedSectionDataSetsApi(
) # https://github.com/AllenInstitute/AllenSDK/blob/master/allensdk/api/queries/annotated_section_data_sets_api.py
self.oapi = OntologiesApi(
) # https://github.com/AllenInstitute/AllenSDK/blob/master/allensdk/api/queries/ontologies_api.py
# Get metadata about atlases
self.atlases = pd.DataFrame(self.oapi.get_atlases_table())
self.atlases_names = sorted(list(self.atlases['name'].values))
self.mouse_coronal_atlas_id = int(self.atlases.loc[
self.atlases['name'] == "Mouse, P56, Coronal"].id.values[0])
self.mouse_sagittal_atlas_id = int(self.atlases.loc[
self.atlases['name'] == "Mouse, P56, Sagittal"].id.values[0])
self.mouse_3D_atlas_id = int(self.atlases.loc[
self.atlases['name'] == "Mouse, Adult, 3D Coronal"].id.values[0])
# Get metadata about products
if connected_to_internet():
self.products = pd.DataFrame(
send_query(
"http://api.brain-map.org/api/v2/data/query.json?criteria=model::Product"
))
self.mouse_brain_reference_product_id = 12
self.mouse_brain_ish_data_product_id = 1
self.products_names = sorted(list(self.products["name"].values))
self.mouse_products_names = sorted(
list(self.products.loc[self.products.species == "Mouse"]
["name"].values))
else:
raise ConnectionError(
"It seems that you are not connected to the internet, you won't be able to download stuff."
)
def __init__(self):
SvgApi.__init__(
self
) # https://github.com/AllenInstitute/AllenSDK/blob/master/allensdk/api/queries/svg_api.py
ImageDownloadApi.__init__(
self
) # https://github.com/AllenInstitute/AllenSDK/blob/master/allensdk/api/queries/image_download_api.py
self.annsetsapi = (
AnnotatedSectionDataSetsApi()
) # https://github.com/AllenInstitute/AllenSDK/blob/master/allensdk/api/queries/annotated_section_data_sets_api.py
self.oapi = (
OntologiesApi()
) # https://github.com/AllenInstitute/AllenSDK/blob/master/allensdk/api/queries/ontologies_api.py
# Get metadata about atlases
self.atlases = pd.DataFrame(self.oapi.get_atlases_table())
self.atlases_names = sorted(list(self.atlases["name"].values))
self.mouse_coronal_atlas_id = int(self.atlases.loc[
self.atlases["name"] == self.mouse_coronal].id.values[0])
self.mouse_sagittal_atlas_id = int(self.atlases.loc[
self.atlases["name"] == self.mouse_sagittal].id.values[0])
self.mouse_3D_atlas_id = int(self.atlases.loc[
self.atlases["name"] == self.mouse3d].id.values[0])
# Get metadata about products
self.products = pd.DataFrame(
send_query(
"http://api.brain-map.org/api/v2/data/query.json?criteria=model::Product"
))
self.mouse_brain_reference_product_id = 12
self.mouse_brain_ish_data_product_id = 1
self.products_names = sorted(list(self.products["name"].values))
self.mouse_products_names = sorted(
list(self.products.loc[self.products.species == "Mouse"]
["name"].values))
def verify_svg(file_path, width_scale, height_scale):
# we're using this function to display scaled svg in the rendered notebook.
# we suggest that in your own work you use a tool such as inkscape or illustrator to view svg
with open(file_path, 'rb') as svg_file:
svg = svg_file.read()
encoded_svg = b64encode(svg)
decoded_svg = encoded_svg.decode('ascii')
st = r'<img class="figure" src="data:image/svg+xml;base64,{}" width={}% height={}%></img>'.format(decoded_svg, width_scale, height_scale)
display(HTML(st))
image_api = ImageDownloadApi()
svg_api = SvgApi()
#Downloading all of the images from a section data set
section_data_set_id = 71724696
downsample = 4
expression = 1
section_image_directory = str(section_data_set_id) + '_section_images'
format_str = '.jpg'
section_images = image_api.section_image_query(section_data_set_id)
section_image_ids = [si['id'] for si in section_images]
print(len(section_image_ids))
def svg():
sa = SvgApi()
return sa