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Functions339 in github.com/ImprintLab/MedSegDiff

↓ 27 callersMethodlog
(self, *args, level=INFO)
guided_diffusion/logger.py:376
↓ 25 callersFunction_extract_into_tensor
Extract values from a 1-D numpy array for a batch of indices. :param arr: the 1-D numpy array. :param timesteps: a tensor of indices into
guided_diffusion/gaussian_diffusion.py:1126
↓ 19 callersFunctionconv_nd
Create a 1D, 2D, or 3D convolution module.
guided_diffusion/nn.py:22
↓ 19 callersMethodmarginal_lambda
Compute lambda_t = log(alpha_t) - log(sigma_t) of a given continuous-time label t in [0, T].
guided_diffusion/dpm_solver.py:128
↓ 19 callersMethodmarginal_std
Compute sigma_t of a given continuous-time label t in [0, T].
guided_diffusion/dpm_solver.py:122
↓ 18 callersMethod__init__
(self, channels, use_conv, dims=2, out_channels=None)
guided_diffusion/unet.py:100
↓ 16 callersMethodget_device
(self)
guided_diffusion/unet.py:1354
↓ 16 callersMethodmarginal_log_mean_coeff
Compute log(alpha_t) of a given continuous-time label t in [0, T].
guided_diffusion/dpm_solver.py:103
↓ 15 callersMethodmodel_fn
Convert the model to the noise prediction model or the data prediction model.
guided_diffusion/dpm_solver.py:414
↓ 13 callersFunctionconv_dw
(inp, oup, stride)
guided_diffusion/unet.py:158
↓ 9 callersFunctionget_current
()
guided_diffusion/logger.py:325
↓ 8 callersMethodlogkv_mean
(self, key, val)
guided_diffusion/logger.py:350
↓ 8 callersFunctionnormalization
Make a standard normalization layer. :param channels: number of input channels. :return: an nn.Module for normalization.
guided_diffusion/nn.py:96
↓ 7 callersMethodclose
(self)
guided_diffusion/logger.py:391
↓ 7 callersFunctionlinear
Create a linear module.
guided_diffusion/nn.py:38
↓ 7 callersFunctionmean_flat
Take the mean over all non-batch dimensions.
guided_diffusion/nn.py:89
↓ 6 callersFunctionlog
Write the sequence of args, with no separators, to the console and output files (if you've configured an output file).
guided_diffusion/logger.py:247
↓ 5 callersMethodget_time_steps
Compute the intermediate time steps for sampling. Args: skip_type: A `str`. The type for the spacing of the time steps. We support
guided_diffusion/dpm_solver.py:423
↓ 5 callersMethodinverse_lambda
Compute the continuous-time label t in [0, T] of a given half-logSNR lambda_t.
guided_diffusion/dpm_solver.py:136
↓ 5 callersFunctionmodel_and_diffusion_defaults
Defaults for image training.
guided_diffusion/script_util.py:43
↓ 5 callersFunctionzero_module
Zero out the parameters of a module and return it.
guided_diffusion/nn.py:71
↓ 4 callersFunctionlayer_norm
(shape, *args, **kwargs)
guided_diffusion/nn.py:34
↓ 4 callersMethodmarginal_alpha
Compute alpha_t of a given continuous-time label t in [0, T].
guided_diffusion/dpm_solver.py:116
↓ 4 callersFunctionmaybe_to_torch
(d)
guided_diffusion/utils.py:22
↓ 4 callersFunctionnoise_pred_fn
(x, t_continuous, cond=None)
guided_diffusion/dpm_solver.py:251
↓ 4 callersMethodp_mean_variance
Apply the model to get p(x_{t-1} | x_t), as well as a prediction of the initial x, x_0. :param model: the model, which takes
guided_diffusion/gaussian_diffusion.py:244
↓ 4 callersMethodq_posterior_mean_variance
Compute the mean and variance of the diffusion posterior: q(x_{t-1} | x_t, x_0)
guided_diffusion/gaussian_diffusion.py:221
↓ 4 callersMethodq_sample
Diffuse the data for a given number of diffusion steps. In other words, sample from q(x_t | x_0). :param x_start: the initial
guided_diffusion/gaussian_diffusion.py:203
↓ 4 callersFunctionto_cuda
(data, non_blocking=True, gpu_id=0)
guided_diffusion/utils.py:30
↓ 3 callersMethod_internal_predict_2D_2Dconv
This one does fully convolutional inference. No sliding window
guided_diffusion/unet.py:1690
↓ 3 callersMethod_predict_eps_from_xstart
(self, x_t, t, pred_xstart)
guided_diffusion/gaussian_diffusion.py:362
↓ 3 callersMethod_scale_timesteps
(self, t)
guided_diffusion/gaussian_diffusion.py:368
↓ 3 callersMethod_wrap_model
(self, model)
guided_diffusion/respace.py:103
↓ 3 callersFunctioncreate_gaussian_diffusion
( *, steps=1000, learn_sigma=False, sigma_small=False, noise_schedule="linear", use_kl
guided_diffusion/script_util.py:414
↓ 3 callersMethodddim_sample_loop_progressive
Use DDIM to sample from the model and yield intermediate samples from each timestep of DDIM. Same usage as p_sample_loop_prog
guided_diffusion/gaussian_diffusion.py:885
↓ 3 callersFunctiondice_coeff
Dice coeff for batches
scripts/segmentation_env.py:75
↓ 3 callersMethoddpm_solver_first_update
DPM-Solver-1 (equivalent to DDIM) from time `s` to time `t`. Args: x: A pytorch tensor. The initial value at time `s`.
guided_diffusion/dpm_solver.py:514
↓ 3 callersFunctionexpand_dims
Expand the tensor `v` to the dim `dims`. Args: `v`: a PyTorch tensor with shape [N]. `dim`: a `int`. Returns: a P
guided_diffusion/dpm_solver.py:1248
↓ 3 callersFunctionfind_resume_checkpoint
()
guided_diffusion/train_util.py:325
↓ 3 callersFunctioniou
(outputs: np.array, labels: np.array)
scripts/segmentation_env.py:37
↓ 3 callersMethodlogkv
(self, key, val)
guided_diffusion/logger.py:347
↓ 3 callersMethodsample
Compute the sample at time `t_end` by DPM-Solver, given the initial `x` at time `t_start`. ==========================================
guided_diffusion/dpm_solver.py:1004
↓ 3 callersMethodsave
(self)
guided_diffusion/train_util.py:278
↓ 3 callersMethodsinglestep_dpm_solver_second_update
Singlestep solver DPM-Solver-2 from time `s` to time `t`. Args: x: A pytorch tensor. The initial value at time `s`.
guided_diffusion/dpm_solver.py:560
↓ 3 callersFunctiontimestep_embedding
Create sinusoidal timestep embeddings. :param timesteps: a 1-D Tensor of N indices, one per batch element. These may b
guided_diffusion/nn.py:106
↓ 2 callersMethod_compute_norms
(self, grad_scale=1.0)
guided_diffusion/fp16_util.py:216
↓ 2 callersMethod_compute_steps_for_sliding_window
(patch_size: Tuple[int, ...], image_size: Tuple[int, ...], step_size: float)
guided_diffusion/unet.py:1523
↓ 2 callersMethod_get_gaussian
(patch_size, sigma_scale=1. / 8)
guided_diffusion/unet.py:1507
↓ 2 callersMethod_internal_maybe_mirror_and_pred_2D
(self, x: Union[np.ndarray, torch.tensor], mirror_axes: tuple, do_m
guided_diffusion/unet.py:1829
↓ 2 callersMethod_internal_maybe_mirror_and_pred_3D
(self, x: Union[np.ndarray, torch.tensor], mirror_axes: tuple, do_m
guided_diffusion/unet.py:1762
↓ 2 callersMethod_internal_predict_2D_2Dconv_tiled
(self, x: np.ndarray, step_size: float, do_mirroring: bool, mirror_axes: tuple,
guided_diffusion/unet.py:1879
↓ 2 callersMethod_predict_xstart_from_eps
(self, x_t, t, eps)
guided_diffusion/gaussian_diffusion.py:345
↓ 2 callersMethod_truncate
(self, s)
guided_diffusion/logger.py:80
↓ 2 callersFunctionadd_dict_to_argparser
(parser, default_dict)
guided_diffusion/script_util.py:457
↓ 2 callersFunctionapprox_standard_normal_cdf
A fast approximation of the cumulative distribution function of the standard normal.
guided_diffusion/losses.py:42
↓ 2 callersFunctionargs_to_dict
(args, keys)
guided_diffusion/script_util.py:467
↓ 2 callersFunctioncheckpoint
Evaluate a function without caching intermediate activations, allowing for reduced memory at the expense of extra compute in the backward pas
guided_diffusion/nn.py:127
↓ 2 callersFunctionconfigure
If comm is provided, average all numerical stats across that comm
guided_diffusion/logger.py:442
↓ 2 callersMethodconvert_to_fp16
Convert the torso of the model to float16.
guided_diffusion/unet.py:1303
↓ 2 callersFunctioncount_flops_attn
A counter for the `thop` package to count the operations in an attention operation. Meant to be used like: macs, params = thop.pr
guided_diffusion/unet.py:373
↓ 2 callersFunctioncreate_model_and_diffusion
( image_size, class_cond, learn_sigma, num_channels, num_res_blocks, channel_mult,
guided_diffusion/script_util.py:77
↓ 2 callersMethoddata_prediction_fn
Return the data prediction model (with corrector).
guided_diffusion/dpm_solver.py:403
↓ 2 callersFunctiondiffusion_defaults
Defaults for image and classifier training.
guided_diffusion/script_util.py:11
↓ 2 callersMethoddumpkvs
(self)
guided_diffusion/logger.py:355
↓ 2 callersFunctionget_blob_logdir
()
guided_diffusion/train_util.py:319
↓ 2 callersMethodget_dir
(self)
guided_diffusion/logger.py:388
↓ 2 callersFunctionget_model_input_time
Convert the continuous-time `t_continuous` (in [epsilon, T]) to the model input time. For discrete-time DPMs, we convert `t_continuou
guided_diffusion/dpm_solver.py:240
↓ 2 callersFunctionget_param_groups_and_shapes
(named_model_params)
guided_diffusion/fp16_util.py:82
↓ 2 callersFunctioninterpolate_fn
A piecewise linear function y = f(x), using xp and yp as keypoints. We implement f(x) in a differentiable way (i.e. applicable for autograd).
guided_diffusion/dpm_solver.py:1207
↓ 2 callersFunctionmake_master_params
Copy model parameters into a (differently-shaped) list of full-precision parameters.
guided_diffusion/fp16_util.py:35
↓ 2 callersMethodmultistep_dpm_solver_update
Multistep DPM-Solver with the order `order` from time `t_prev_list[-1]` to time `t`. Args: x: A pytorch tensor. The initi
guided_diffusion/dpm_solver.py:893
↓ 2 callersFunctionmv
(a)
guided_diffusion/utils.py:71
↓ 2 callersMethodnoise_prediction_fn
Return the noise prediction model.
guided_diffusion/dpm_solver.py:394
↓ 2 callersFunctionnormal_kl
Compute the KL divergence between two gaussians. Shapes are automatically broadcasted, so batches can be compared to scalars, among othe
guided_diffusion/losses.py:12
↓ 2 callersMethodp_sample_loop_progressive
Generate samples from the model and yield intermediate samples from each timestep of diffusion. Arguments are the same as p_s
guided_diffusion/gaussian_diffusion.py:598
↓ 2 callersMethodsinglestep_dpm_solver_third_update
Singlestep solver DPM-Solver-3 from time `s` to time `t`. Args: x: A pytorch tensor. The initial value at time `s`.
guided_diffusion/dpm_solver.py:640
↓ 2 callersFunctionunflatten_master_params
(param_group, master_param)
guided_diffusion/fp16_util.py:78
↓ 2 callersFunctionzero_master_grads
(master_params)
guided_diffusion/fp16_util.py:128
↓ 1 callersMethod__init__
directory is expected to contain some folder structure: if some subfolder contains only files, all of these
guided_diffusion/bratsloader.py:11
↓ 1 callersMethod__init__
(self, args, data_path, transform=None, mode="Training", plane=False)
guided_diffusion/custom_dataset_loader.py:21
↓ 1 callersMethod__init__
(self, model, timestep_map, rescale_timesteps, original_num_steps)
guided_diffusion/respace.py:122
↓ 1 callersMethod_anneal_lr
(self)
guided_diffusion/train_util.py:266
↓ 1 callersFunction_configure_default_logger
()
guided_diffusion/logger.py:474
↓ 1 callersMethod_do_log
(self, args)
guided_diffusion/logger.py:397
↓ 1 callersMethod_internal_predict_3D_2Dconv
(self, x: np.ndarray, min_size: Tuple[int, int], do_mirroring: bool, mirro
guided_diffusion/unet.py:2013
↓ 1 callersMethod_internal_predict_3D_2Dconv_tiled
(self, x: np.ndarray, patch_size: Tuple[int, int], do_mirroring: bool,
guided_diffusion/unet.py:2063
↓ 1 callersMethod_internal_predict_3D_3Dconv
This one does fully convolutional inference. No sliding window
guided_diffusion/unet.py:1726
↓ 1 callersMethod_internal_predict_3D_3Dconv_tiled
(self, x: np.ndarray, step_size: float, do_mirroring: bool, mirror_axes: tuple,
guided_diffusion/unet.py:1548
↓ 1 callersMethod_load_and_sync_parameters
(self)
guided_diffusion/train_util.py:125
↓ 1 callersMethod_load_ema_parameters
(self, rate)
guided_diffusion/train_util.py:141
↓ 1 callersMethod_load_optimizer_state
(self)
guided_diffusion/train_util.py:157
↓ 1 callersMethod_optimize_fp16
(self, opt: th.optim.Optimizer)
guided_diffusion/fp16_util.py:189
↓ 1 callersMethod_optimize_normal
(self, opt: th.optim.Optimizer)
guided_diffusion/fp16_util.py:209
↓ 1 callersMethod_predict_xstart_from_xprev
(self, x_t, t, xprev)
guided_diffusion/gaussian_diffusion.py:352
↓ 1 callersMethod_prior_bpd
Get the prior KL term for the variational lower-bound, measured in bits-per-dim. This term can't be optimized, as it only dep
guided_diffusion/gaussian_diffusion.py:1053
↓ 1 callersMethod_update_ema
(self)
guided_diffusion/train_util.py:262
↓ 1 callersMethod_vb_terms_bpd
Get a term for the variational lower-bound. The resulting units are bits (rather than nats, as one might expect). This allows
guided_diffusion/gaussian_diffusion.py:940
↓ 1 callersMethod_warmed_up
(self)
guided_diffusion/resample.py:153
↓ 1 callersMethod_wrap_model2
(self, model)
guided_diffusion/respace.py:109
↓ 1 callersFunctionavg_pool_nd
Create a 1D, 2D, or 3D average pooling module.
guided_diffusion/nn.py:45
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