import tensorflow as tf
[docs]def get_pretrained_network(file_id=None,
target_file_name=None,
antsxnet_cache_directory=None):
"""
Download pretrained network/weights.
Arguments
---------
file_id string
One of the permitted file ids or pass "show" to list all
valid possibilities. Note that most require internet access
to download.
target_file_name string
Optional target filename.
antsxnet_cache_directory string
Optional target output. If not specified these data will be downloaded
to the subdirectory ~/.keras/ANTsXNet/.
Returns
-------
A filename string
Example
-------
>>> model_file = get_pretrained_network('dbpn4x')
"""
def switch_networks(argument):
switcher = {
"arterialLesionWeibinShi": "https://figshare.com/ndownloader/files/30761716",
"brainAgeGender": "https://ndownloader.figshare.com/files/22179948",
"brainAgeDeepBrainNet": "https://ndownloader.figshare.com/files/23573402",
"brainExtraction": "https://ndownloader.figshare.com/files/22944632",
"brainExtractionT1": "https://ndownloader.figshare.com/files/27334370",
"brainExtractionT1v1": "https://ndownloader.figshare.com/files/28057626",
"brainExtractionT2": "https://ndownloader.figshare.com/files/23066153",
"brainExtractionFLAIR": "https://ndownloader.figshare.com/files/23562194",
"brainExtractionBOLD": "https://ndownloader.figshare.com/files/22761977",
"brainExtractionFA": "https://ndownloader.figshare.com/files/22761926",
"brainExtractionNoBrainer": "https://ndownloader.figshare.com/files/22598039",
"brainExtractionInfantT1T2": "https://ndownloader.figshare.com/files/22968833",
"brainExtractionInfantT1": "https://ndownloader.figshare.com/files/22968836",
"brainExtractionInfantT2": "https://ndownloader.figshare.com/files/22968830",
"brainSegmentation": "https://ndownloader.figshare.com/files/13900010",
"brainSegmentationPatchBased": "https://ndownloader.figshare.com/files/14249717",
"claustrum_axial_0": "https://ndownloader.figshare.com/files/27844068",
"claustrum_axial_1": "https://ndownloader.figshare.com/files/27844059",
"claustrum_axial_2": "https://ndownloader.figshare.com/files/27844062",
"claustrum_coronal_0": "https://ndownloader.figshare.com/files/27844074",
"claustrum_coronal_1": "https://ndownloader.figshare.com/files/27844071",
"claustrum_coronal_2": "https://ndownloader.figshare.com/files/27844065",
"ctHumanLung": "https://ndownloader.figshare.com/files/20005217",
"dbpn4x": "https://ndownloader.figshare.com/files/13347617",
"deepFlashLeftT1": "https://ndownloader.figshare.com/files/28966269",
"deepFlashRightT1": "https://ndownloader.figshare.com/files/28966266",
"deepFlashLeftBoth": "https://ndownloader.figshare.com/files/28966275",
"deepFlashRightBoth": "https://ndownloader.figshare.com/files/28966272",
"deepFlashLeftT1Hierarchical": "",
"deepFlashRightT1Hierarchical": "",
"deepFlashLeftBothHierarchical": "",
"deepFlashRightBothHierarchical": "",
"deepFlash": "https://ndownloader.figshare.com/files/22933757",
"deepFlashLeft8": "https://ndownloader.figshare.com/files/25441007",
"deepFlashRight8": "https://ndownloader.figshare.com/files/25441004",
"deepFlashLeft16": "https://ndownloader.figshare.com/files/25465844",
"deepFlashRight16": "https://ndownloader.figshare.com/files/25465847",
"deepFlashLeft16new": "https://ndownloader.figshare.com/files/25991681",
"deepFlashRight16new": "https://ndownloader.figshare.com/files/25991678",
"denoising": "https://ndownloader.figshare.com/files/14235296",
"dktInner": "https://ndownloader.figshare.com/files/23266943",
"dktOuter": "https://ndownloader.figshare.com/files/23765132",
"dktOuterWithSpatialPriors": "https://ndownloader.figshare.com/files/24230768",
"elBicho": "https://ndownloader.figshare.com/files/26736779",
"ewDavidSysu": "https://ndownloader.figshare.com/files/28757622", # "https://ndownloader.figshare.com/files/28403973",
"ewDavidSysuRankedIntensity": "https://ndownloader.figshare.com/files/28403937",
"ewDavidSysuT1Only": "https://ndownloader.figshare.com/files/28757628", #"https://ndownloader.figshare.com/files/28403934",
"ewDavidSysuFlairOnly": "https://ndownloader.figshare.com/files/28757625", # "https://ndownloader.figshare.com/files/28403931",
"ewDavidSysuWithAttention": "https://ndownloader.figshare.com/files/28757631", # "https://ndownloader.figshare.com/files/28431312",
"ewDavidSysuWithAttentionT1Only": "https://ndownloader.figshare.com/files/28757646", # "https://ndownloader.figshare.com/files/28403970",
"ewDavidSysuWithAttentionFlairOnly": "https://ndownloader.figshare.com/files/28757643", # "https://ndownloader.figshare.com/files/28403943",
"ewDavidSysuWithAttentionAndSite": "https://ndownloader.figshare.com/files/28757634",
"ewDavidSysuWithAttentionAndSiteT1Only": "https://ndownloader.figshare.com/files/28757640",
"ewDavidSysuWithAttentionAndSiteFlairOnly": "https://ndownloader.figshare.com/files/28757637",
"ewDavidSysuPlus": "https://ndownloader.figshare.com/files/28403976",
"ewDavidSysuPlusT1Only": "https://ndownloader.figshare.com/files/28403958",
"ewDavidSysuPlusFlairOnly": "https://ndownloader.figshare.com/files/28403946",
"ewDavidSysuPlusSeg": "https://ndownloader.figshare.com/files/28403940",
"ewDavidSysuPlusSegT1Only": "https://ndownloader.figshare.com/files/28403955",
"ewDavidSysuPlusSegWithSite": "https://ndownloader.figshare.com/files/28431375",
"ewDavidSysuPlusSegWithSiteT1Only": "https://ndownloader.figshare.com/files/28431372",
"ewDavidSysuWithSite": "https://ndownloader.figshare.com/files/28403964",
"ewDavidSysuWithSiteT1Only": "https://ndownloader.figshare.com/files/28403952",
"ewDavidSysuWithSiteFlairOnly": "https://ndownloader.figshare.com/files/28403979",
"functionalLungMri": "https://ndownloader.figshare.com/files/13824167",
"hippMapp3rInitial": "https://ndownloader.figshare.com/files/18068408",
"hippMapp3rRefine": "https://ndownloader.figshare.com/files/18068411",
"hypothalamus": "https://ndownloader.figshare.com/files/28344378",
"koniqMBCS": "https://ndownloader.figshare.com/files/24967376",
"koniqMS": "https://ndownloader.figshare.com/files/25461887",
"koniqMS2": "https://ndownloader.figshare.com/files/25474850",
"koniqMS3": "https://ndownloader.figshare.com/files/25474847",
"lungCtWithPriorsSegmentationWeights": "https://ndownloader.figshare.com/files/28357818",
"maskLobes": "https://figshare.com/ndownloader/files/30678458",
"mriSuperResolution": "https://ndownloader.figshare.com/files/24128618",
"protonLungMri": "https://ndownloader.figshare.com/files/13606799",
"protonLobes": "https://figshare.com/ndownloader/files/30678455",
"sixTissueOctantBrainSegmentation": "https://ndownloader.figshare.com/files/23776025",
"sixTissueOctantBrainSegmentationWithPriors1": "https://ndownloader.figshare.com/files/28159869",
"sysuMediaWmhFlairOnlyModel0": "https://ndownloader.figshare.com/files/22898441",
"sysuMediaWmhFlairOnlyModel1": "https://ndownloader.figshare.com/files/22898570",
"sysuMediaWmhFlairOnlyModel2": "https://ndownloader.figshare.com/files/22898438",
"sysuMediaWmhFlairT1Model0": "https://ndownloader.figshare.com/files/22898450",
"sysuMediaWmhFlairT1Model1": "https://ndownloader.figshare.com/files/22898453",
"sysuMediaWmhFlairT1Model2": "https://ndownloader.figshare.com/files/22898459",
"tidsQualityAssessment": "https://ndownloader.figshare.com/files/24292895",
"wholeTumorSegmentationT2Flair": "https://ndownloader.figshare.com/files/14087045",
"wholeLungMaskFromVentilation": "https://ndownloader.figshare.com/files/28914441"
}
return(switcher.get(argument, "Invalid argument."))
if file_id == None:
raise ValueError("Missing file id.")
valid_list = ("dbpn4x",
"arterialLesionWeibinShi",
"brainAgeGender",
"brainAgeDeepBrainNet",
"brainExtraction",
"brainExtractionT1",
"brainExtractionT1v1",
"brainExtractionT2",
"brainExtractionFLAIR",
"brainExtractionBOLD",
"brainExtractionFA",
"brainExtractionNoBrainer",
"brainExtractionInfantT1T2",
"brainExtractionInfantT1",
"brainExtractionInfantT2",
"brainSegmentation",
"brainSegmentationPatchBased",
"claustrum_axial_0",
"claustrum_axial_1",
"claustrum_axial_2",
"claustrum_coronal_0",
"claustrum_coronal_1",
"claustrum_coronal_2",
"ctHumanLung",
"deepFlash",
"deepFlashLeftT1",
"deepFlashRightT1",
"deepFlashLeftBoth",
"deepFlashRightBoth",
"deepFlashLeftT1Hierarchical",
"deepFlashRightT1Hierarchical",
"deepFlashLeftBothHierarchical",
"deepFlashRightBothHierarchical",
"deepFlashLeft8",
"deepFlashRight8",
"deepFlashLeft16",
"deepFlashRight16",
"deepFlashLeft16new",
"deepFlashRight16new",
"denoising",
"dktInner",
"dktOuter",
"dktOuterWithSpatialPriors",
"elBicho",
"ewDavidSysu",
"ewDavidSysuRankedIntensity",
"ewDavidSysuT1Only",
"ewDavidSysuFlairOnly",
"ewDavidSysuWithAttention",
"ewDavidSysuWithAttentionT1Only",
"ewDavidSysuWithAttentionFlairOnly",
"ewDavidSysuWithAttentionAndSite",
"ewDavidSysuWithAttentionAndSiteT1Only",
"ewDavidSysuWithAttentionAndSiteFlairOnly",
"ewDavidSysuPlus",
"ewDavidSysuPlusT1Only",
"ewDavidSysuPlusFlairOnly",
"ewDavidSysuPlusSeg",
"ewDavidSysuPlusSegT1Only",
"ewDavidSysuPlusSegWithSite",
"ewDavidSysuPlusSegWithSiteT1Only",
"ewDavidSysuWithSite",
"ewDavidSysuWithSiteT1Only",
"ewDavidSysuWithSiteFlairOnly",
"functionalLungMri",
"hippMapp3rInitial",
"hippMapp3rRefine",
"hypothalamus",
"koniqMBCS",
"koniqMS",
"koniqMS2",
"koniqMS3",
"lungCtWithPriorsSegmentationWeights",
"maskLobes",
"mriSuperResolution",
"protonLungMri",
"protonLobes",
"sixTissueOctantBrainSegmentation",
"sixTissueOctantBrainSegmentationWithPriors1",
"sixTissueOctantBrainSegmentationWithPriors2",
"sysuMediaWmhFlairOnlyModel0",
"sysuMediaWmhFlairOnlyModel1",
"sysuMediaWmhFlairOnlyModel2",
"sysuMediaWmhFlairT1Model0",
"sysuMediaWmhFlairT1Model1",
"sysuMediaWmhFlairT1Model2",
"tidsQualityAssessment",
"wholeTumorSegmentationT2Flair",
"wholeLungMaskFromVentilation",
"show")
if not file_id in valid_list:
raise ValueError("No data with the id you passed - try \"show\" to get list of valid ids.")
if file_id == "show":
return(valid_list)
url = switch_networks(file_id)
if target_file_name == None:
target_file_name = file_id + ".h5"
if antsxnet_cache_directory == None:
antsxnet_cache_directory = "ANTsXNet"
target_file_name_path = tf.keras.utils.get_file(target_file_name, url,
cache_subdir = antsxnet_cache_directory)
return(target_file_name_path)