class ImageDownloadApiTests(unittest.TestCase):
def __init__(self, *args, **kwargs):
super(ImageDownloadApiTests, self).__init__(*args, **kwargs)
self.ida = None
def setUp(self):
self.ida = ImageDownloadApi()
def tearDown(self):
self.ida = None
def test_api_doc_url_download_image_downsampled(self):
'''
Notes
-----
See: `Experimental Overview and Metadata `<http://help.brain-map.org/display/mouseconnectivity/API#API-ExperimentalOverviewandMetadata>_
, link labeled 'Download image downsampled by factor of 6 using default thresholds'.
'''
expected = 'http://api.brain-map.org/api/v2/section_image_download/126862575?downsample=6&range=0,932,0,1279,0,4095'
path = '126862575.jpg'
self.ida.retrieve_file_over_http = \
MagicMock(name='retrieve_file_over_http')
section_image_id = 126862575
self.ida.download_section_image(section_image_id,
downsample=6,
range=[0,932, 0,1279, 0,4095])
self.ida.retrieve_file_over_http.assert_called_once_with(expected, path)
def test_api_doc_url_download_image_full_resolution(self):
'''
Notes
-----
See: `Experimental Overview and Metadata `<http://help.brain-map.org/display/mouseconnectivity/API#API-ExperimentalOverviewandMetadata>_
, link labeled 'Download a region of interest at full resolution using default thresholds'.
'''
expected = 'http://api.brain-map.org/api/v2/section_image_download/126862575?left=19045&top=11684&width=1000&height=1000&range=0,932,0,1279,0,4095'
path = '126862575.jpg'
self.ida.retrieve_file_over_http = \
MagicMock(name='retrieve_file_over_http')
section_image_id = 126862575
self.ida.download_section_image(section_image_id,
left=19045,
top=11684,
width=1000,
height=1000,
range=[0,932, 0,1279, 0,4095])
self.ida.retrieve_file_over_http.assert_called_once_with(expected, path)
def download_section(savepath, section_id, downsample):
# Downloading all of the images from a section data set
image_api = ImageDownloadApi()
input_directory = str(section_id) + '_input'
output_directory = str(section_id) + '_output'
format_str = '.jpg'
section_images = image_api.section_image_query(section_id)
section_image_ids = [si['id'] for si in section_images]
# You have probably noticed that the AllenSDK has a logger which notifies you of file downloads.
# Since we are downloading ~300 images, we don't want to see messages for each one.
# The following line will temporarily disable the download logger.(optional)
logging.getLogger(
'allensdk.api.api.retrieve_file_over_http').disabled = True
for section_image_id in section_image_ids:
file_name = str(section_image_id) + format_str
input_file_path = os.path.join(savepath, input_directory, file_name)
output_file_path = os.path.join(savepath, output_directory, file_name)
Manifest.safe_make_parent_dirs(input_file_path)
image_api.download_section_image(section_image_id,
file_path=input_file_path,
downsample=downsample,
expression=0)
Manifest.safe_make_parent_dirs(output_file_path)
image_api.download_section_image(section_image_id,
file_path=output_file_path,
downsample=downsample,
expression=1)
# re-enable the logger (optional)
logging.getLogger(
'allensdk.api.api.retrieve_file_over_http').disabled = False
file_names = os.listdir(os.path.join(savepath, input_directory))
print(len(file_names))
def download_brain_slice(df):
# create an image download API
image_api = ImageDownloadApi()
format_str = ".jpg"
# You have probably noticed that the AllenSDK has a logger which notifies you of file downloads.
# Since we are downloading ~300 images, we don't want to see messages for each one.
# The following line will temporarily disable the download logger.
logging.getLogger("allensdk.api.api.retrieve_file_over_http").disabled = True
# get parameters
path, downsample, indices = ask_parameters_for_downloading(df)
print(
"Downloads initiated", end="...", file=sys.stderr, flush=True,
)
for index in indices:
# from indices, get experiment id and gene symbol from df
exp_id = df["Experiment"][index]
# set the dirname as the gene symbol
dirname = df["Gene Symbol"][index]
plane = df["Plane"][index]
section_data_set_id = exp_id
section_image_directory = os.path.join(path, dirname)
# get the image ids for all of the images in this data set
section_images = image_api.section_image_query(
section_data_set_id
) # Should be a dicionary of the features of section images
section_image_ids = [
si["id"] for si in section_images
] # Take value of 'id' from the dictionary
# Create a progress bar
pbar_image = tqdm(total=len(section_image_ids), desc=dirname + " " + plane)
for section_image_id in section_image_ids:
file_name = str(section_image_id) + format_str
file_path = os.path.join(section_image_directory, file_name)
Manifest.safe_make_parent_dirs(file_path)
# Check if the file is already downloaded, which happens if the downloads have been interrupted.
saved_file_names = os.listdir(section_image_directory)
if file_name in saved_file_names:
pass
else:
image_api.download_section_image(
section_image_id, file_path=file_path, downsample=downsample
)
pbar_image.update()
pbar_image.close()
# re-enable the logger
logging.getLogger("allensdk.api.api.retrieve_file_over_http").disabled = False
print(
"Downloads completed.", file=sys.stderr, flush=True,
)
section_image_ids = [si['id'] for si in section_images]
print(len(section_image_ids))
# You have probably noticed that the AllenSDK has a logger which notifies you of file downloads.
# Since we are downloading ~300 images, we don't want to see messages for each one.
# The following line will temporarily disable the download logger.(optional)
logging.getLogger('allensdk.api.api.retrieve_file_over_http').disabled = True
for section_image_id in section_image_ids:
file_name = str(section_image_id) + format_str
file_path = os.path.join(section_image_directory, file_name)
Manifest.safe_make_parent_dirs(file_path)
image_api.download_section_image(section_image_id, file_path=file_path, downsample=downsample,expression = expression, view='expression', colormap='expression')
# re-enable the logger (optional)
logging.getLogger('allensdk.api.api.retrieve_file_over_http').disabled = False
file_names = os.listdir(section_image_directory)
print(len(file_names))