Merge remote-tracking branch 'origin/mednist_ddpm' into xray_classifi…

…er_port

models/mednist_ddpm/LICENSE

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+MIT License
+
+Copyright (c) 2023 MONAI Consortium
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

models/mednist_ddpm/configs/common.yaml

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+# This file defines common definitions used in training and inference, most importantly the network definition
+
+imports:
+- $import os
+- $import datetime
+- $import torch
+- $import scripts
+- $import monai
+- $import torch.distributed as dist
+
+image: $monai.utils.CommonKeys.IMAGE
+label: $monai.utils.CommonKeys.LABEL
+pred: $monai.utils.CommonKeys.PRED
+
+is_dist: '$dist.is_initialized()'
+rank: '$dist.get_rank() if @is_dist else 0'
+is_not_rank0: '$@rank > 0'
+device: '$torch.device(f"cuda:{@rank}" if torch.cuda.is_available() else "cpu")'
+
+network_def:
+  _target_: monai.networks.nets.DiffusionModelUNet
+  spatial_dims: 2
+  in_channels: 1
+  out_channels: 1
+  channels: [64, 128, 128]
+  attention_levels: [false, true, true]
+  num_res_blocks: 1
+  num_head_channels: 128
+
+network: $@network_def.to(@device)
+
+bundle_root: .
+ckpt_path: $@bundle_root + '/models/model.pt'
+use_amp: true
+image_dim: 64
+image_size: [1, '@image_dim', '@image_dim']
+num_train_timesteps: 1000
+
+base_transforms:
+- _target_: LoadImaged
+  keys: '@image'
+  image_only: true
+- _target_: EnsureChannelFirstd
+  keys: '@image'
+- _target_: ScaleIntensityRanged
+  keys: '@image'
+  a_min: 0.0
+  a_max: 255.0
+  b_min: 0.0
+  b_max: 1.0
+  clip: true
+
+scheduler:
+  _target_: monai.networks.schedulers.DDPMScheduler
+  num_train_timesteps: '@num_train_timesteps'
+
+inferer:
+  _target_: monai.inferers.DiffusionInferer
+  scheduler: '@scheduler'

models/mednist_ddpm/configs/infer.yaml

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+# This defines an inference script for generating a random image to a Pytorch file
+
+batch_size: 1
+num_workers: 0
+
+noise: $torch.rand(1,1,@image_dim,@image_dim)  # create a random image every time this program is run
+
+out_file: ""  # where to save the tensor to
+
+# using a lambda this defines a simple sampling function used below
+sample: '$lambda x: @inferer.sample(input_noise=x, diffusion_model=@network, scheduler=@scheduler)'
+
+load_state: '$@network.load_state_dict(torch.load(@ckpt_path, weights_only = True))'  # command to load the saved model weights
+
+save_trans:
+  _target_: Compose
+  transforms:
+  - _target_: ScaleIntensity
+    minv: 0.0
+    maxv: 255.0
+  - _target_: ToTensor
+    track_meta: false
+  - _target_: SaveImage
+    output_ext: "jpg"
+    resample: false
+    output_dtype: '$torch.uint8'
+    separate_folder: false
+    output_postfix: '@out_file'
+
+# program to load the model weights, run `sample`, and store results to `out_file`
+testing:
+- '@load_state'
+- '$torch.save(@sample(@noise.to(@device)), @out_file)'
+
+#alternative version which saves to a jpg file
+testing_jpg:
+- '@load_state'
+- '$@save_trans(@sample(@noise.to(@device))[0])'

models/mednist_ddpm/configs/logging.conf

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+[loggers]
+keys=root
+
+[handlers]
+keys=consoleHandler
+
+[formatters]
+keys=fullFormatter
+
+[logger_root]
+level=INFO
+handlers=consoleHandler
+
+[handler_consoleHandler]
+class=StreamHandler
+level=INFO
+formatter=fullFormatter
+args=(sys.stdout,)
+
+[formatter_fullFormatter]
+format=%(asctime)s - %(name)s - %(levelname)s - %(message)s

models/mednist_ddpm/configs/metadata.json

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+{
+    "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220729.json",
+    "version": "1.0.0",
+    "changelog": {
+        "1.0.0": "Initial release"
+    },
+    "monai_version": "1.4.0",
+    "pytorch_version": "2.5.1",
+    "numpy_version": "1.26.4",
+    "optional_packages_version": {},
+    "task": "MedNIST Hand Generation",
+    "description": "",
+    "authors": "Walter Hugo Lopez Pinaya, Mark Graham, and Eric Kerfoot",
+    "copyright": "Copyright (c) KCL",
+    "references": [],
+    "intended_use": "This is suitable for research purposes only.",
+    "image_classes": "Single channel magnitude data.",
+    "data_source": "MedNIST",
+    "network_data_format": {
+        "inputs": {
+            "image": {
+                "type": "image",
+                "format": "magnitude",
+                "modality": "xray",
+                "num_channels": 1,
+                "spatial_shape": [
+                    1,
+                    64,
+                    64
+                ],
+                "dtype": "float32",
+                "value_range": [],
+                "is_patch_data": false,
+                "channel_def": {
+                    "0": "image"
+                }
+            }
+        },
+        "outputs": {
+            "pred": {
+                "type": "image",
+                "format": "magnitude",
+                "modality": "xray",
+                "num_channels": 1,
+                "spatial_shape": [
+                    1,
+                    64,
+                    64
+                ],
+                "dtype": "float32",
+                "value_range": [],
+                "is_patch_data": false,
+                "channel_def": {
+                    "0": "image"
+                }
+            }
+        }
+    }
+}

models/mednist_ddpm/configs/train.yaml

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+# This defines the training script for the network
+
+imports:
+- $import operator
+
+# choose a new directory for every run
+output_dir: $datetime.datetime.now().strftime('./results/output_%y%m%d_%H%M%S')
+dataset_dir: ./data
+
+train_data:
+  _target_ : MedNISTDataset
+  root_dir: '@dataset_dir'
+  section: training
+  download: true
+  progress: false
+  seed: 0
+
+val_data:
+  _target_ : MedNISTDataset
+  root_dir: '@dataset_dir'
+  section: validation
+  download: true
+  progress: false
+  seed: 0
+
+train_datalist: '$[{"image": item["image"]} for item in @train_data.data if item["class_name"] == "Hand"]'
+val_datalist: '$[{"image": item["image"]} for item in @val_data.data if item["class_name"] == "Hand"]'
+
+batch_size: 8
+num_substeps: 1
+num_workers: 4
+use_thread_workers: false
+
+lr: 0.000025
+rand_prob: 0.5
+num_epochs: 75
+val_interval: 5
+save_interval: 5
+
+train_transforms:
+- _target_: RandAffined
+  keys: '@image'
+  rotate_range:
+  - ['$-np.pi / 36', '$np.pi / 36']
+  - ['$-np.pi / 36', '$np.pi / 36']
+  translate_range:
+  - [-1, 1]
+  - [-1, 1]
+  scale_range:
+  - [-0.05, 0.05]
+  - [-0.05, 0.05]
+  spatial_size: [64, 64]
+  padding_mode: "zeros"
+  prob: '@rand_prob'
+
+train_ds:
+  _target_: Dataset
+  data: $@train_datalist
+  transform:
+    _target_: Compose
+    transforms: '$@base_transforms + @train_transforms'
+
+train_loader:
+  _target_: ThreadDataLoader
+  dataset: '@train_ds'
+  batch_size: '@batch_size'
+  repeats: '@num_substeps'
+  num_workers: '@num_workers'
+  use_thread_workers: '@use_thread_workers'
+  persistent_workers: '$@num_workers > 0'
+  shuffle: true
+
+val_ds:
+  _target_: Dataset
+  data: $@val_datalist
+  transform:
+    _target_: Compose
+    transforms: '@base_transforms'
+
+val_loader:
+  _target_: DataLoader
+  dataset: '@val_ds'
+  batch_size: '@batch_size'
+  num_workers: '@num_workers'
+  persistent_workers: '$@num_workers > 0'
+  shuffle: false
+
+lossfn:
+  _target_: torch.nn.MSELoss
+
+optimizer:
+  _target_: torch.optim.Adam
+  params: $@network.parameters()
+  lr: '@lr'
+
+prepare_batch:
+  _target_: monai.engines.DiffusionPrepareBatch
+  num_train_timesteps: '@num_train_timesteps'
+
+val_handlers:
+- _target_: StatsHandler
+  name: train_log
+  output_transform: '$lambda x: None'
+  _disabled_: '@is_not_rank0'
+
+evaluator:
+  _target_: SupervisedEvaluator
+  device: '@device'
+  val_data_loader: '@val_loader'
+  network: '@network'
+  amp: '@use_amp'
+  inferer: '@inferer'
+  prepare_batch: '@prepare_batch'
+  key_val_metric:
+    val_mean_abs_error:
+      _target_: MeanAbsoluteError
+      output_transform: $monai.handlers.from_engine([@pred, @label])
+  metric_cmp_fn: '$operator.lt'
+  val_handlers: '$list(filter(bool, @val_handlers))'
+
+handlers:
+- _target_: CheckpointLoader
+  _disabled_: $not os.path.exists(@ckpt_path)
+  load_path: '@ckpt_path'
+  load_dict:
+    model: '@network'
+- _target_: ValidationHandler
+  validator: '@evaluator'
+  epoch_level: true
+  interval: '@val_interval'
+- _target_: CheckpointSaver
+  save_dir: '@output_dir'
+  save_dict:
+    model: '@network'
+  save_interval: '@save_interval'
+  save_final: true
+  epoch_level: true
+  _disabled_: '@is_not_rank0'
+
+trainer:
+  _target_: SupervisedTrainer
+  max_epochs: '@num_epochs'
+  device: '@device'
+  train_data_loader: '@train_loader'
+  network: '@network'
+  loss_function: '@lossfn'
+  optimizer: '@optimizer'
+  inferer: '@inferer'
+  prepare_batch: '@prepare_batch'
+  key_train_metric:
+    train_acc:
+      _target_: MeanSquaredError
+      output_transform: $monai.handlers.from_engine([@pred, @label])
+  metric_cmp_fn: '$operator.lt'
+  train_handlers: '$list(filter(bool, @handlers))'
+  amp: '@use_amp'
+
+training:
+- '$monai.utils.set_determinism(0)'
+- '$@trainer.run()'

models/mednist_ddpm/configs/train_multigpu.yaml

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+# This can be mixed in with the training script to enable multi-GPU training
+
+network:
+  _target_: torch.nn.parallel.DistributedDataParallel
+  module: $@network_def.to(@device)
+  device_ids: ['@device']
+  find_unused_parameters: true
+
+tsampler:
+  _target_: DistributedSampler
+  dataset: '@train_ds'
+  even_divisible: true
+  shuffle: true
+train_loader#sampler: '@tsampler'
+train_loader#shuffle: false
+
+vsampler:
+  _target_: DistributedSampler
+  dataset: '@val_ds'
+  even_divisible: false
+  shuffle: false
+val_loader#sampler: '@vsampler'
+
+training:
+- $import torch.distributed as dist
+- $dist.init_process_group(backend='nccl')
+- $torch.cuda.set_device(@device)
+- $monai.utils.set_determinism(seed=123),
+- $@trainer.run()
+- $dist.destroy_process_group()

models/mednist_ddpm/docs/README.md

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+
+# MedNIST DDPM Example Bundle
+
+This implements roughly equivalent code to the "Denoising Diffusion Probabilistic Models with MedNIST Dataset"
+example notebook. This includes scripts for training with single or multiple GPUs and a visualisation notebook.
+
+
+The files included here demonstrate how to use the bundle:
+  * [2d_ddpm_bundle_tutorial.ipynb](./2d_ddpm_bundle_tutorial.ipynb) - demonstrates command line and in-code invocation of the bundle's training and inference scripts
+  * [sub_train.sh](sub_train.sh) - SLURM submission script example for training
+  * [sub_train_multigpu.sh](sub_train_multigpu.sh) - SLURM submission script example for training with multiple GPUs

models/mednist_ddpm/docs/sub_train.sh

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+#! /bin/bash
+#SBATCH --nodes=1
+#SBATCH -J mednist_train
+#SBATCH -c 4
+#SBATCH --gres=gpu:1
+#SBATCH --time=2:00:00
+#SBATCH -p small
+
+set -v
+
+# change this if run submitted from a different directory
+export BUNDLE="$(pwd)/.."
+
+# change this to load a checkpoint instead of started from scratch
+CKPT=none
+
+CONFIG="'$BUNDLE/configs/common.yaml', '$BUNDLE/configs/train.yaml'"
+
+# change this to point to where MedNIST is located
+DATASET="$(pwd)"
+
+# it's useful to include the configuration in the log file
+cat "$BUNDLE/configs/common.yaml"
+cat "$BUNDLE/configs/train.yaml"
+
+python -m monai.bundle run training \
+    --meta_file "$BUNDLE/configs/metadata.json" \
+    --config_file "$CONFIG" \
+    --logging_file "$BUNDLE/configs/logging.conf" \
+    --bundle_root "$BUNDLE" \
+    --dataset_dir "$DATASET"

models/mednist_ddpm/docs/sub_train_multigpu.sh

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+#! /bin/bash
+#SBATCH --nodes=1
+#SBATCH -J mednist_train
+#SBATCH -c 4
+#SBATCH --gres=gpu:2
+#SBATCH --time=2:00:00
+#SBATCH -p big
+
+set -v
+
+# change this if run submitted from a different directory
+export BUNDLE="$(pwd)/.."
+
+# change this to load a checkpoint instead of started from scratch
+CKPT=none
+
+CONFIG="'$BUNDLE/configs/common.yaml', '$BUNDLE/configs/train.yaml', '$BUNDLE/configs/train_multigpu.yaml'"
+
+# change this to point to where MedNIST is located
+DATASET="$(pwd)"
+
+# it's useful to include the configuration in the log file
+cat "$BUNDLE/configs/common.yaml"
+cat "$BUNDLE/configs/train.yaml"
+cat "$BUNDLE/configs/train_multigpu.yaml"
+
+# remember to change arguments to match how many nodes and GPUs you have
+torchrun --standalone --nnodes=1 --nproc_per_node=2 -m monai.bundle run training \
+    --meta_file "$BUNDLE/configs/metadata.json" \
+    --config_file "$CONFIG" \
+    --logging_file "$BUNDLE/configs/logging.conf" \
+    --bundle_root "$BUNDLE" \
+    --dataset_dir "$DATASET"

models/mednist_ddpm/scripts/__init__.py

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+from __future__ import annotations
+
+
+def inv_metric_cmp_fn(current_metric: float, prev_best: float) -> bool:
+    """
+    This inverts comparison for those metrics which reduce like loss values, such that the lower one is better.
+
+    Args:
+        current_metric: metric value of current round computation.
+        prev_best: the best metric value of previous rounds to compare with.
+    """
+    return current_metric < prev_best