atlas_images

Contents

ImageDownload

Handles query to the Allen ImageDownloadApi and saves the data

__init__ [#34]

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def __init__(self):
  docstring:
no docstring

get_atlas_by_name [#89]

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def get_atlas_by_name(self, atlas_name):
  docstring:
Get a brain atlas in the Allen's database given it's name
:param atlas_name: str with atlas name

get_products_by_species [#104]

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def get_products_by_species(self, species):
  docstring:
Get all 'products' in the Allen Database for a given species
:param species: str

get_experimentsid_by_productid [#113]

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def get_experimentsid_by_productid(self, productid, **kwargs):
  docstring:
Get the experiment's ID that belong to the same project (product).
:param productid: int with product ID number
:param **kwargs:

get_experimentimages_by_expid [#126]

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def get_experimentimages_by_expid(self, expid):
  docstring:
Get's images that belong to an experiment
:param expid: int with experiment name.

get_atlasimages_by_atlasid [#136]

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def get_atlasimages_by_atlasid(self, atlasid):
  docstring:
Get the metadata of images that belong to an atlas.
:param atlasid: int with atlas number

download_images_by_imagesid [#149]

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def download_images_by_imagesid(self, savedir, imagesids,
downsample=0, annotated=True, snames=None, atlas_svg=True):
  docstring:
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)

download_images_by_atlasid [#216]

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def download_images_by_atlasid(self, savedir, atlasid, debug=False,
**kwargs):
  docstring:
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