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)
Ejemplo n.º 2
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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))
Ejemplo n.º 3
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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,
    )
Ejemplo n.º 4
0
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))