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Functions153 in github.com/Pulkit-Khandelwal/medical-mldg-seg

⨍ Functions 153◇ Types & classes 27
↓ 17 callersFunctioncompute_accuracy
(predictions, labels)
mldg-seg/utils.py:96
↓ 14 callersFunctionconv3d
(inputs, weight, bias, meta_step_size=0.001, stride=1, padding=1, dilation=1, groups=1, meta_loss=None,
mldg-seg/ops.py:133
↓ 10 callersFunctionrelu
(inputs)
mldg-seg/ops.py:113
↓ 8 callersMethodload_state_dict
(self, state_dict='')
mldg-seg/meta_learning_spine.py:137
↓ 6 callersMethod__init__
(self, epsilon=1e-5, weight=None, ignore_index=None, sigmoid_normalization=True, skip_last_ta
mldg-seg/dice_loss.py:66
↓ 6 callersFunctionfix_seed
()
mldg-seg/utils.py:83
↓ 6 callersFunctionnormalization
(planes, norm='gn')
mldg-seg/Unet3D_meta_learning_orig.py:13
↓ 6 callersFunctionnormalization
(planes, norm='gn')
mldg-seg/Unet3D_meta_learning.py:13
↓ 5 callersFunctionflatten
Flattens a given tensor such that the channel axis is first. The shapes are transformed as follows: (N, C, D, H, W) -> (C, N * D * H * W)
mldg-seg/dice_loss.py:317
↓ 3 callersMethodforward
(self, input, target)
mldg-seg/dice_loss.py:84
↓ 3 callersFunctionsave_nifti
Save image as nifti images
mldg-seg/data_reader_unet_spine.py:100
↓ 2 callersMethod__init__
(self, inplanes, planes, dropout=0.3, norm='gn', first=False)
mldg-seg/Unet3D_meta_learning_orig.py:26
↓ 2 callersMethod__init__
(self, inplanes, planes, meta_loss, meta_step_size, stop_gradient, dropout=0.3, norm='gn', first=False)
mldg-seg/Unet3D_meta_learning.py:26
↓ 2 callersFunctionmaxpool3D
(inputs, kernel_size, stride=None, padding=0)
mldg-seg/ops.py:179
↓ 2 callersFunctionread_nifti
(filepath_image, filepath_label=False)
postprocess/EvaluationMetrics.py:23
↓ 2 callersFunctionsave_nifti
(image, filepath_name, img_obj=False)
postprocess/EvaluationMetrics.py:36
↓ 2 callersMethodtrain
(self)
mldg-seg/meta_learning_spine.py:159
↓ 2 callersMethodtrain
(self)
mldg-seg/fewshot_meta_learning.py:163
↓ 2 callersMethodtrain
(self)
mldg-seg/fewshot_baseline.py:163
↓ 2 callersMethodtrain
(self)
mldg-seg/baseline_spine.py:146
↓ 2 callersMethodtrain
(self)
mldg-seg/upper_bound_spine.py:170
↓ 2 callersFunctionupsample
(input)
mldg-seg/ops.py:182
↓ 1 callersFunctionNormalize
chnage the intensity range
mldg-seg/data_reader_unet_spine.py:227
↓ 1 callersFunctionRandomFlip
Randomly flips the image across the given axes. Note from original repo: When creating make sure that the provided RandomStates are consisten
mldg-seg/data_reader_unet_spine.py:195
↓ 1 callersFunctionRandomRotate90
Randomly rotate an image
mldg-seg/data_reader_unet_spine.py:208
↓ 1 callersFunctionStandardize
zero-mean, unit standard deviation
mldg-seg/data_reader_unet_spine.py:219
↓ 1 callersMethod_class_weights
(input)
mldg-seg/dice_loss.py:181
↓ 1 callersFunctioncompute_per_channel_dice
(input, target, epsilon=1e-5, ignore_index=None, weight=None)
mldg-seg/dice_loss.py:34
↓ 1 callersMethodconfigure
(self)
mldg-seg/meta_learning_spine.py:152
↓ 1 callersMethodconfigure
(self)
mldg-seg/fewshot_meta_learning.py:137
↓ 1 callersMethodconfigure
(self)
mldg-seg/fewshot_baseline.py:139
↓ 1 callersMethodconfigure
(self)
mldg-seg/baseline_spine.py:139
↓ 1 callersMethodconfigure
(self)
mldg-seg/upper_bound_spine.py:160
↓ 1 callersMethodconfigure
(self)
postprocess/tsne.py:99
↓ 1 callersMethodconfigure
(self)
postprocess/inference.py:127
↓ 1 callersFunctiondice
(output, target)
mldg-seg/utils3D.py:12
↓ 1 callersFunctiondice_coeff
(input, target)
mldg-seg/dice_loss.py:25
↓ 1 callersFunctiondice_per_im
(output, target)
mldg-seg/utils3D.py:109
↓ 1 callersFunctiongenerate_patch_locations
(patches, patch_size, im_size)
mldg-seg/data_reader_unet_spine.py:36
↓ 1 callersFunctiongenerate_patch_probs
(patch_locations, patch_size, im_size, label_cropped)
mldg-seg/data_reader_unet_spine.py:45
↓ 1 callersFunctiongetLargestCC
(segmentation)
postprocess/EvaluationMetrics.py:46
↓ 1 callersFunctiongetLargestCC
(segmentation)
postprocess/ConnectedComponent.py:16
↓ 1 callersFunctionget_patches
get image, and label patches Default: returns one randomly selected patch of the given size, else returns a list of all the patches.
mldg-seg/data_reader_unet_spine.py:108
↓ 1 callersMethodinference
(self, model_path, test_file)
postprocess/inference.py:135
↓ 1 callersMethodload_state_dict
(self, state_dict='')
mldg-seg/upper_bound_spine.py:144
↓ 1 callersFunctionperturb_patch_locations
(patch_locations, radius)
mldg-seg/data_reader_unet_spine.py:29
↓ 1 callersFunctionread_nifti
(filepath)
mldg-seg/data_reader_unet_spine.py:88
↓ 1 callersMethodsetup_path
(self)
mldg-seg/meta_learning_spine.py:83
↓ 1 callersMethodsetup_path
(self)
mldg-seg/fewshot_meta_learning.py:84
↓ 1 callersMethodsetup_path
(self)
mldg-seg/fewshot_baseline.py:88
↓ 1 callersMethodsetup_path
(self)
mldg-seg/baseline_spine.py:83
↓ 1 callersMethodsetup_path
(self)
mldg-seg/upper_bound_spine.py:87
↓ 1 callersMethodsetup_path
(self)
postprocess/tsne.py:64
↓ 1 callersMethodsetup_path
(self)
postprocess/inference.py:65
↓ 1 callersFunctionsquare_angular_loss
Computes square angular loss between input and target directions. Makes sure that the input and target directions are normalized so that torc
mldg-seg/dice_loss.py:294
↓ 1 callersMethodtest
(self, ite)
mldg-seg/meta_learning_spine.py:342
↓ 1 callersMethodtest
(self, ite)
mldg-seg/fewshot_meta_learning.py:257
↓ 1 callersMethodtest
(self, ite)
mldg-seg/fewshot_baseline.py:255
↓ 1 callersMethodtest
(self, ite)
mldg-seg/baseline_spine.py:282
↓ 1 callersMethodtest
(self, ite)
mldg-seg/upper_bound_spine.py:267
↓ 1 callersMethodtsnePlot
(self)
postprocess/tsne.py:106
Method__call__
(self, input, target)
mldg-seg/dice_loss.py:203
Method__getitem__
(self, index)
mldg-seg/data_reader_unet_spine.py:483
Method__init__
(self, data_source)
mldg-seg/meta_learning_spine.py:31
Method__init__
(self)
mldg-seg/meta_learning_spine.py:43
Method__init__
(self, data_source)
mldg-seg/fewshot_meta_learning.py:33
Method__init__
(self)
mldg-seg/fewshot_meta_learning.py:46
Method__init__
(self)
mldg-seg/dice_loss.py:15
Method__init__
(self, epsilon=1e-5, weight=None, ignore_index=None, sigmoid_normalization=False, num_classes=2)
mldg-seg/dice_loss.py:105
Method__init__
(self, weight=None, ignore_index=-1)
mldg-seg/dice_loss.py:168
Method__init__
(self, loss_criterion, ignore_index=-1, skip_last_target=False)
mldg-seg/dice_loss.py:196
Method__init__
(self, class_weights=None, ignore_index=None)
mldg-seg/dice_loss.py:222
Method__init__
(self)
mldg-seg/dice_loss.py:266
Method__init__
(self, tags_coefficients)
mldg-seg/dice_loss.py:275
Method__init__
(self, data_source)
mldg-seg/fewshot_baseline.py:33
Method__init__
(self)
mldg-seg/fewshot_baseline.py:45
Method__init__
(self, data_source)
mldg-seg/baseline_spine.py:32
Method__init__
(self)
mldg-seg/baseline_spine.py:44
Method__init__
(self, planes, norm='gn', first=False)
mldg-seg/Unet3D_meta_learning_orig.py:66
Method__init__
(self, c=1, n=16, dropout=0.3, norm='gn', num_classes=2)
mldg-seg/Unet3D_meta_learning_orig.py:109
Method__init__
(self, planes, meta_loss, meta_step_size, stop_gradient, norm='gn', first=False)
mldg-seg/Unet3D_meta_learning.py:71
Method__init__
(self, c=1, n=16, dropout=0.3, norm='gn', num_classes=2)
mldg-seg/Unet3D_meta_learning.py:116
Method__init__
(self, data_source)
mldg-seg/upper_bound_spine.py:32
Method__init__
(self)
mldg-seg/upper_bound_spine.py:45
Method__init__
(self, image_list, modality, transform=False, patch_size=32, n_patches_transform=30, all_patches=False, is_tes
mldg-seg/data_reader_unet_spine.py:456
Method__init__
(self)
postprocess/tsne.py:26
Method__init__
(self)
postprocess/inference.py:26
Method__iter__
(self)
mldg-seg/meta_learning_spine.py:34
Method__iter__
(self)
mldg-seg/fewshot_meta_learning.py:36
Method__iter__
(self)
mldg-seg/fewshot_baseline.py:36
Method__iter__
(self)
mldg-seg/baseline_spine.py:35
Method__iter__
(self)
mldg-seg/upper_bound_spine.py:35
Method__len__
(self)
mldg-seg/meta_learning_spine.py:38
Method__len__
(self)
mldg-seg/fewshot_meta_learning.py:41
Method__len__
(self)
mldg-seg/fewshot_baseline.py:40
Method__len__
(self)
mldg-seg/baseline_spine.py:39
Method__len__
(self)
mldg-seg/upper_bound_spine.py:40
Method__len__
(self)
mldg-seg/data_reader_unet_spine.py:598
Functionbatchnorm
(inputs, running_mean, running_var)
mldg-seg/ops.py:124
Functionbias_correct
N4BiasFieldCorrection: PICSL UPenn
mldg-seg/data_reader_unet_spine.py:236
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