class ImageDownload(SvgApi, ImageDownloadApi):
# useful tutorial: https://allensdk.readthedocs.io/en/latest/_static/examples/nb/image_download.html
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."
)
# UTILS
def get_atlas_by_name(self, atlas_name):
if not atlas_name in self.atlases_names:
raise ValueError("Available atlases: {}".format(
self.atlases_names))
return self.atlases.loc[self.atlases['name'] ==
atlas_name].id.values[0]
def get_products_by_species(self, species):
return self.products.loc[self.products.species == species]
def get_experimentsid_by_productid(self, productid, **kwargs):
# for more details: https://github.com/AllenInstitute/AllenSDK/blob/master/allensdk/api/queries/image_download_api.py
return pd.DataFrame(
self.get_section_data_sets_by_product([productid], **kwargs))
def get_experimentimages_by_expid(self, expid):
# expid should be a section dataset id
return pd.DataFrame(self.section_image_query(expid))
def get_atlasimages_by_atlasid(self, atlasid):
if not isinstance(atlasid, int):
raise ValueError(
"Atlas id should be an integer not: {}".format(atlasid))
return pd.DataFrame(self.atlas_image_query(atlasid))
def download_images_by_imagesid(self,
savedir,
imagesids,
downsample=0,
annotated=True,
snames=None,
atlas_svg=True):
if not os.path.isdir(savedir):
os.mkdir(savedir)
curdir = os.getcwd()
os.chdir(savedir)
for i, imgid in tqdm(enumerate(imagesids)):
if not atlas_svg and not annotated:
savename = str(imgid) + ".jpg"
elif not atlas_svg and annotated:
savename = str(imgid) + "_annotated.jpg"
else:
savename = str(imgid) + ".svg"
if snames is not None:
sname, ext = savename.split(".")
savename = sname + "_sect{}_img{}.".format(snames[i],
i + 1) + ext
if os.path.isfile(savename): continue
if not atlas_svg and not annotated:
self.download_section_image(imgid,
file_path=savename,
downsample=downsample)
elif not atlas_svg and annotated:
self.download_atlas_image(imgid,
file_path=savename,
annotation=True,
downsample=downsample)
else:
self.download_svg(imgid, file_path=savename)
file_names = os.listdir(savedir)
print("Downloaded {} images".format(len(file_names)))
os.chdir(curdir)
def download_images_by_atlasid(self, savedir, atlasid, **kwargs):
imgsids = self.get_atlasimages_by_atlasid(atlasid)['id']
imgs_secs_n = self.get_atlasimages_by_atlasid(
atlasid)['section_number']
self.download_images_by_imagesid(savedir,
imgsids,
snames=imgs_secs_n,
**kwargs)
class ImageDownload(SvgApi, ImageDownloadApi):
"""
Handles query to the Allen ImageDownloadApi and saves the data
"""
# useful tutorial: https://allensdk.readthedocs.io/en/latest/_static/examples/nb/image_download.html
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."
)
# UTILS
def get_atlas_by_name(self, atlas_name):
"""
Get a brain atlas in the Allen's database given it's name
:param atlas_name: str with atlas name
"""
if not atlas_name in self.atlases_names:
raise ValueError("Available atlases: {}".format(
self.atlases_names))
return self.atlases.loc[self.atlases['name'] ==
atlas_name].id.values[0]
def get_products_by_species(self, species):
"""
Get all 'products' in the Allen Database for a given species
:param species: str
"""
return self.products.loc[self.products.species == species]
def get_experimentsid_by_productid(self, productid, **kwargs):
"""
Get the experiment's ID that belong to the same project (product).
:param productid: int with product ID number
:param **kwargs:
"""
# for more details: https://github.com/AllenInstitute/AllenSDK/blob/master/allensdk/api/queries/image_download_api.py
return pd.DataFrame(
self.get_section_data_sets_by_product([productid], **kwargs))
def get_experimentimages_by_expid(self, expid):
"""
Get's images that belong to an experiment
:param expid: int with experiment name.
"""
# expid should be a section dataset id
return pd.DataFrame(self.section_image_query(expid))
def get_atlasimages_by_atlasid(self, atlasid):
"""
Get the metadata of images that belong to an atlas.
:param atlasid: int with atlas number
"""
if not isinstance(atlasid, int):
raise ValueError(
"Atlas id should be an integer not: {}".format(atlasid))
return pd.DataFrame(self.atlas_image_query(atlasid))
def download_images_by_imagesid(self,
savedir,
imagesids,
downsample=0,
annotated=True,
snames=None,
atlas_svg=True):
"""
Downloads and saves images given a list of images IDs.
:param savedir: str, folder in which to save the image
:param imagesids: list of int with images IDs
:param downsample: downsample factor, to reduce the image size and resolution (Default value = 0)
:param annotated: if True the images are overlayed with annotations (Default value = True)
:param snames: if True the images are overlayed with the structures names (Default value = None)
:param atlas_svg: if True fetches the images as SVG, otherwise as PNG (Default value = True)
"""
if not os.path.isdir(savedir):
os.mkdir(savedir)
curdir = os.getcwd()
os.chdir(savedir)
for i, imgid in tqdm(enumerate(imagesids)):
if not atlas_svg and not annotated:
savename = str(imgid) + ".jpg"
elif not atlas_svg and annotated:
savename = str(imgid) + "_annotated.jpg"
else:
savename = str(imgid) + ".svg"
if snames is not None:
sname, ext = savename.split(".")
savename = sname + "_sect{}_img{}.".format(snames[i],
i + 1) + ext
if os.path.isfile(savename): continue
if not atlas_svg and not annotated:
self.download_section_image(imgid,
file_path=savename,
downsample=downsample)
elif not atlas_svg and annotated:
self.download_atlas_image(imgid,
file_path=savename,
annotation=True,
downsample=downsample)
else:
self.download_svg(imgid, file_path=savename)
file_names = os.listdir(savedir)
print("Downloaded {} images".format(len(file_names)))
os.chdir(curdir)
def download_images_by_atlasid(self, savedir, atlasid, **kwargs):
"""
Downloads all the images that belong to an altlas
:param savedir: str, folder in which to save the images
:param atlasid: int, ID of the atlas to use
:param **kwargs: keyword arguments for self.download_images_by_imagesid
"""
imgsids = self.get_atlasimages_by_atlasid(atlasid)['id']
imgs_secs_n = self.get_atlasimages_by_atlasid(
atlasid)['section_number']
self.download_images_by_imagesid(savedir,
imgsids,
snames=imgs_secs_n,
**kwargs)
class OntologiesApiTests(unittest.TestCase):
def __init__(self, *args, **kwargs):
super(OntologiesApiTests, self).__init__(*args, **kwargs)
def setUp(self):
self.oa = OntologiesApi()
def tearDown(self):
self.oa = None
def test_get_structure_graph(self):
expected = "http://api.brain-map.org/api/v2/data/query.json?q=model::Structure,rma::criteria,[graph_id$in1],rma::options[num_rows$eq'all'][order$eqstructures.graph_order][count$eqfalse]"
structure_graph_id = 1
self.oa.json_msg_query = \
MagicMock(name='json_msg_query')
self.oa.get_structures(structure_graph_id)
self.oa.json_msg_query.assert_called_once_with(expected)
def test_list_structure_graphs(self):
expected = "http://api.brain-map.org/api/v2/data/query.json?q=model::StructureGraph,rma::options[num_rows$eq'all'][count$eqfalse]"
self.oa.json_msg_query = \
MagicMock(name='json_msg_query')
self.oa.get_structure_graphs()
self.oa.json_msg_query.assert_called_once_with(expected)
def test_list_structure_sets(self):
expected = "http://api.brain-map.org/api/v2/data/query.json?q=model::StructureSet,rma::options[num_rows$eq'all'][count$eqfalse]"
self.oa.json_msg_query = \
MagicMock(name='json_msg_query')
self.oa.get_structure_sets()
self.oa.json_msg_query.assert_called_once_with(expected)
def test_list_atlases(self):
expected = "http://api.brain-map.org/api/v2/data/query.json?q=model::Atlas,rma::options[num_rows$eq'all'][count$eqfalse]"
self.oa.json_msg_query = \
MagicMock(name='json_msg_query')
self.oa.get_atlases()
self.oa.json_msg_query.assert_called_once_with(expected)
def test_structure_graph_by_name(self):
expected = u"http://api.brain-map.org/api/v2/data/query.json?q=model::Structure,rma::criteria,graph[structure_graphs.name$in'Mouse Brain Atlas'],rma::options[num_rows$eq'all'][order$eqstructures.graph_order][count$eqfalse]"
self.oa.json_msg_query = \
MagicMock(name='json_msg_query')
self.oa.get_structures(structure_graph_names="'Mouse Brain Atlas'")
self.oa.json_msg_query.assert_called_once_with(expected)
def test_structure_graphs_by_names(self):
expected = "http://api.brain-map.org/api/v2/data/query.json?q=model::Structure,rma::criteria,graph[structure_graphs.name$in'Mouse Brain Atlas','Human Brain Atlas'],rma::options[num_rows$eq'all'][order$eqstructures.graph_order][count$eqfalse]"
self.oa.json_msg_query = \
MagicMock(name='json_msg_query')
self.oa.get_structures(structure_graph_names=["'Mouse Brain Atlas'",
"'Human Brain Atlas'"])
self.oa.json_msg_query.assert_called_once_with(expected)
def test_structure_set_by_id(self):
expected = "http://api.brain-map.org/api/v2/data/query.json?q=model::Structure,rma::criteria,[structure_set_id$in8],rma::options[num_rows$eq'all'][order$eqstructures.graph_order][count$eqfalse]"
self.oa.json_msg_query = \
MagicMock(name='json_msg_query')
self.oa.get_structures(structure_set_ids=8)
self.oa.json_msg_query.assert_called_once_with(expected)
def test_structure_sets_by_ids(self):
expected = "http://api.brain-map.org/api/v2/data/query.json?q=model::Structure,rma::criteria,[structure_set_id$in7,8],rma::options[num_rows$eq'all'][order$eqstructures.graph_order][count$eqfalse]"
self.oa.json_msg_query = \
MagicMock(name='json_msg_query')
self.oa.get_structures(structure_set_ids=[7,8])
self.oa.json_msg_query.assert_called_once_with(expected)
def test_structure_set_by_name(self):
expected = "http://api.brain-map.org/api/v2/data/query.json?q=model::Structure,rma::criteria,structure_sets[name$in'Mouse Connectivity - Summary'],rma::options[num_rows$eq'all'][order$eqstructures.graph_order][count$eqfalse]"
self.oa.json_msg_query = \
MagicMock(name='json_msg_query')
self.oa.get_structures(structure_set_names="'Mouse Connectivity - Summary'")
self.oa.json_msg_query.assert_called_once_with(expected)
def test_structure_set_by_names(self):
expected = "http://api.brain-map.org/api/v2/data/query.json?q=model::Structure,rma::criteria,structure_sets[name$in'NHP - Coarse','Mouse Connectivity - Summary'],rma::options[num_rows$eq'all'][order$eqstructures.graph_order][count$eqfalse]"
self.oa.json_msg_query = \
MagicMock(name='json_msg_query')
self.oa.get_structures(structure_set_names=["'NHP - Coarse'",
"'Mouse Connectivity - Summary'"])
self.oa.json_msg_query.assert_called_once_with(expected)
def test_structure_set_no_order(self):
expected = "http://api.brain-map.org/api/v2/data/query.json?q=model::Structure,rma::criteria,[graph_id$in1],rma::options[num_rows$eq'all'][count$eqfalse]"
self.oa.json_msg_query = \
MagicMock(name='json_msg_query')
self.oa.get_structures(1, order=None)
self.oa.json_msg_query.assert_called_once_with(expected)
def test_atlas_1(self):
expected = "http://api.brain-map.org/api/v2/data/query.json?q=model::Atlas,rma::criteria,[id$in1],structure_graph(ontology),graphic_group_labels,rma::include,structure_graph(ontology),graphic_group_labels,rma::options[only$eq'atlases.id,atlases.name,atlases.image_type,ontologies.id,ontologies.name,structure_graphs.id,structure_graphs.name,graphic_group_labels.id,graphic_group_labels.name'][num_rows$eq'all'][count$eqfalse]"
atlas_id = 1
self.oa.json_msg_query = \
MagicMock(name='json_msg_query')
self.oa.get_atlases_table(atlas_id)
self.oa.json_msg_query.assert_called_once_with(expected)
def test_atlas_verbose(self):
expected = "http://api.brain-map.org/api/v2/data/query.json?q=model::Atlas,rma::criteria,structure_graph(ontology),graphic_group_labels,rma::include,structure_graph(ontology),graphic_group_labels,rma::options[num_rows$eq'all'][count$eqfalse]"
self.oa.json_msg_query = \
MagicMock(name='json_msg_query')
self.oa.get_atlases_table(brief=False)
self.oa.json_msg_query.assert_called_once_with(expected)
