Local and Central DP with Fed-BioMed: MONAI 2d image registration¶
Introduction¶
This tutorial shows how to deploy in Fed-BioMed the 2d image registration example provided in the project MONAI (https://monai.io/), trained with Differential Privacy (DP). We are going to compare results of:
- non private training
- train with Local Differential Privacy (LDP)
- train with Central Differential Privacy (CDP)
In order to enforce differential privacy during training (both local and central) we will rely on the Opacus library (https://opacus.ai/).
Image Registration¶
Image registration is the process of transforming and recalibrating different images into one coordinate system. It makes possible to compare several images captured with the same modality.
In this tutorial, we are using a UNet-like registration network ( https://arxiv.org/abs/1711.01666 ). Goal of the notebook is to train a model given moving images and fixed images (recalibrated images).
Creating MedNIST nodes¶
MedNIST provides an artificial 2d classification dataset created by gathering different medical imaging datasets from TCIA, the RSNA Bone Age Challenge, and the NIH Chest X-ray dataset. The dataset is kindly made available by Dr. Bradley J. Erickson M.D., Ph.D. (Department of Radiology, Mayo Clinic) under the Creative Commons CC BY-SA 4.0 license.
To proceed with the tutorial, we created an iid partitioning of the MedNIST dataset between 3 clients. Each client has 3000 image samples for each class. The training partitions are availables at the following link:
https://drive.google.com/file/d/1vLIcBdtdAhh6K-vrgCFy_0Y55dxOWZwf/view
The dataset owned by each client has structure:
└── client_*/
├── AbdomenCT/
└── BreastMRI/
└── CXR/
└── ChestCT/
└── Hand/
└── HeadCT/ To create the federated dataset, we follow the standard procedure for node creation/population of Fed-BioMed.
we use the environment where Fed-BioMed node is installed
we create a first node by using the commands
fedbiomed node start
We then poulate the node with the data of first client:
fedbiomed node dataset add
We select option 3 (images) to add MedNIST partition of client 1, by just picking the folder of client 1. Assign tag mednist to the data when asked.
We can further check that the data has been added by executing fedbiomed node dataset list
Following the same procedure, we create the other two nodes with the datasets of client 2 and client 3 respectively.
Running Fed-BioMed Researcher¶
We are now ready to start the researcher by using the environment where Fed-BioMed researcher is installed, and open the Jupyter notebook with fedbiomed researcher start.
We can first quesry the network for the mednist dataset. In this case, the nodes are sharing the respective partitions unsing the same tag mednist:
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from fedbiomed.researcher.requests import Requests
from fedbiomed.researcher.config import config
req = Requests(config)
req.list(verbose=True)
from fedbiomed.researcher.requests import Requests from fedbiomed.researcher.config import config req = Requests(config) req.list(verbose=True)
Create an experiment to train a model on the data found¶
The code for network and data loader of the MONAI tutorial can now be deployed in Fed-BioMed. We first import the necessary modules from fedbiomed and monai libraries:
We can now define the training plan. Note that we use the standard TorchTrainingPlan natively provided in Fed-BioMed. We reuse the MedNISTDataset data loader defined in the original MONAI tutorial, which is returned by the method training_data, which also implements the data parsing from the nodes dataset_path. We should also properly define the training_routine, following the MONAI tutorial. According to the MONAI tutorial, the model is the GlobalNet and the loss is MSELoss.
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import numpy as np
import torch
from torch.nn import MSELoss
from fedbiomed.common.training_plans import TorchTrainingPlan
from fedbiomed.common.data import DataManager
#from torch.utils.data import Dataset, DataLoader
import monai
from monai.utils import set_determinism, first
from monai.transforms import (
EnsureChannelFirstD,
Compose,
LoadImageD,
RandRotateD,
RandZoomD,
ScaleIntensityRanged,
EnsureTypeD,
)
from monai.data import DataLoader, Dataset, CacheDataset
from monai.config import print_config, USE_COMPILED
from monai.networks.nets import GlobalNet
from monai.networks.blocks import Warp
from monai.apps import MedNISTDataset
# Here we define the training plan to be used.
class MyTrainingPlan(TorchTrainingPlan):
# Dependencies for training plan
def init_dependencies(self):
deps = ["import numpy as np",
"import monai",
"from torch.nn import MSELoss",
"from monai.utils import set_determinism, first",
"from monai.transforms import (EnsureChannelFirstD,Compose,LoadImageD,RandRotateD,RandZoomD,ScaleIntensityRanged,EnsureTypeD,)",
"from monai.data import DataLoader, Dataset, CacheDataset",
"from monai.networks.nets import GlobalNet",
"from monai.config import USE_COMPILED",
"from monai.networks.blocks import Warp",
"from monai.apps import MedNISTDataset" ]
return deps
# Model for training
def init_model(self):
# Define model related attributes
self.image_loss = MSELoss()
if USE_COMPILED:
self.warp_layer = Warp(3, "border")
else:
self.warp_layer = Warp("bilinear", "border")
# Define model
model = GlobalNet(image_size=(64, 64),
spatial_dims=2,
in_channels=2, # moving and fixed
num_channel_initial=16,
depth=3)
return model
# Optimizer for training
def init_optimizer(self, optimizer_args):
optimizer = torch.optim.Adam(self.model().parameters(), lr=optimizer_args["lr"])
return optimizer
def training_data(self):
# Custom torch Dataloader for MedNIST data
data_path = self.dataset_path
# The following line is needed if client structure does not contain the "/MedNIST" folder
MedNISTDataset.dataset_folder_name = ""
train_data = MedNISTDataset(root_dir=data_path, section="training", download=False, transform=None)
training_datadict = [
{"fixed_hand": item["image"], "moving_hand": item["image"]}
for item in train_data.data if item["label"] == 4 # label 4 is for xray hands
]
train_transforms = Compose(
[
LoadImageD(keys=["fixed_hand", "moving_hand"]),
EnsureChannelFirstD(keys=["fixed_hand", "moving_hand"]),
ScaleIntensityRanged(keys=["fixed_hand", "moving_hand"],
a_min=0., a_max=255., b_min=0.0, b_max=1.0, clip=True,),
RandRotateD(keys=["moving_hand"], range_x=np.pi/4, prob=1.0, keep_size=True, mode="bicubic"),
RandZoomD(keys=["moving_hand"], min_zoom=0.9, max_zoom=1.1,
monaiprob=1.0, mode="bicubic", align_corners=False),
EnsureTypeD(keys=["fixed_hand", "moving_hand"]),
]
)
train_ds = CacheDataset(data=training_datadict, transform=train_transforms,
cache_rate=1.0, num_workers=0)
dl = self.MednistDataLoader(train_ds)
return DataManager(dl, shuffle=True, num_workers=0)
def training_step(self, moving, fixed):
ddf = self.model().forward(torch.cat((moving, fixed), dim=1))
pred_image = self.warp_layer(moving, ddf)
loss = self.image_loss(pred_image, fixed)
return loss
class MednistDataLoader(monai.data.Dataset):
# Custom DataLoader that inherits from monai's Dataset object
def __init__(self, dataset):
self.dataset = dataset
def __len__(self):
return len(self.dataset)
def __getitem__(self, idx):
return (self.dataset[idx]["moving_hand"],
self.dataset[idx]["fixed_hand"])
import numpy as np import torch from torch.nn import MSELoss from fedbiomed.common.training_plans import TorchTrainingPlan from fedbiomed.common.data import DataManager #from torch.utils.data import Dataset, DataLoader import monai from monai.utils import set_determinism, first from monai.transforms import ( EnsureChannelFirstD, Compose, LoadImageD, RandRotateD, RandZoomD, ScaleIntensityRanged, EnsureTypeD, ) from monai.data import DataLoader, Dataset, CacheDataset from monai.config import print_config, USE_COMPILED from monai.networks.nets import GlobalNet from monai.networks.blocks import Warp from monai.apps import MedNISTDataset # Here we define the training plan to be used. class MyTrainingPlan(TorchTrainingPlan): # Dependencies for training plan def init_dependencies(self): deps = ["import numpy as np", "import monai", "from torch.nn import MSELoss", "from monai.utils import set_determinism, first", "from monai.transforms import (EnsureChannelFirstD,Compose,LoadImageD,RandRotateD,RandZoomD,ScaleIntensityRanged,EnsureTypeD,)", "from monai.data import DataLoader, Dataset, CacheDataset", "from monai.networks.nets import GlobalNet", "from monai.config import USE_COMPILED", "from monai.networks.blocks import Warp", "from monai.apps import MedNISTDataset" ] return deps # Model for training def init_model(self): # Define model related attributes self.image_loss = MSELoss() if USE_COMPILED: self.warp_layer = Warp(3, "border") else: self.warp_layer = Warp("bilinear", "border") # Define model model = GlobalNet(image_size=(64, 64), spatial_dims=2, in_channels=2, # moving and fixed num_channel_initial=16, depth=3) return model # Optimizer for training def init_optimizer(self, optimizer_args): optimizer = torch.optim.Adam(self.model().parameters(), lr=optimizer_args["lr"]) return optimizer def training_data(self): # Custom torch Dataloader for MedNIST data data_path = self.dataset_path # The following line is needed if client structure does not contain the "/MedNIST" folder MedNISTDataset.dataset_folder_name = "" train_data = MedNISTDataset(root_dir=data_path, section="training", download=False, transform=None) training_datadict = [ {"fixed_hand": item["image"], "moving_hand": item["image"]} for item in train_data.data if item["label"] == 4 # label 4 is for xray hands ] train_transforms = Compose( [ LoadImageD(keys=["fixed_hand", "moving_hand"]), EnsureChannelFirstD(keys=["fixed_hand", "moving_hand"]), ScaleIntensityRanged(keys=["fixed_hand", "moving_hand"], a_min=0., a_max=255., b_min=0.0, b_max=1.0, clip=True,), RandRotateD(keys=["moving_hand"], range_x=np.pi/4, prob=1.0, keep_size=True, mode="bicubic"), RandZoomD(keys=["moving_hand"], min_zoom=0.9, max_zoom=1.1, monaiprob=1.0, mode="bicubic", align_corners=False), EnsureTypeD(keys=["fixed_hand", "moving_hand"]), ] ) train_ds = CacheDataset(data=training_datadict, transform=train_transforms, cache_rate=1.0, num_workers=0) dl = self.MednistDataLoader(train_ds) return DataManager(dl, shuffle=True, num_workers=0) def training_step(self, moving, fixed): ddf = self.model().forward(torch.cat((moving, fixed), dim=1)) pred_image = self.warp_layer(moving, ddf) loss = self.image_loss(pred_image, fixed) return loss class MednistDataLoader(monai.data.Dataset): # Custom DataLoader that inherits from monai's Dataset object def __init__(self, dataset): self.dataset = dataset def __len__(self): return len(self.dataset) def __getitem__(self, idx): return (self.dataset[idx]["moving_hand"], self.dataset[idx]["fixed_hand"])
Finally we import the required modules for running any experiment
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from fedbiomed.researcher.federated_workflows import Experiment
from fedbiomed.researcher.aggregators.fedavg import FedAverage
from fedbiomed.researcher.federated_workflows import Experiment from fedbiomed.researcher.aggregators.fedavg import FedAverage
Non-private training¶
We first train our model in a non-private way. We set the model and training parameters. In particular, we are going to perform 2 epochs over 3 rounds for this experiment. Moreover the training is performed on ~26% of the locally available training data. We are also trying to use GPU if available.
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model_args = {}
training_args = {
'loader_args': { 'batch_size': 16, },
'optimizer_args': {
'lr': 1e-5
},
'use_gpu': True,
'epochs': 4,
'dry_run': False
# 'batch_maxnum': 2, # can be used to debugging to limit the number of batches per epoch
# 'log_interval': 1, # output a logging message every log_interval batches
}
tags = ['#MEDNIST', '#dataset']
rounds = 5
model_args = {} training_args = { 'loader_args': { 'batch_size': 16, }, 'optimizer_args': { 'lr': 1e-5 }, 'use_gpu': True, 'epochs': 4, 'dry_run': False # 'batch_maxnum': 2, # can be used to debugging to limit the number of batches per epoch # 'log_interval': 1, # output a logging message every log_interval batches } tags = ['#MEDNIST', '#dataset'] rounds = 5
The experiment can be now defined, by providing the mednist tag, and running the local training on nodes with training plan defined in training_plan_path, standard aggregator (FedAvg) and client_selection_strategy (all nodes used). Federated learning is going to be perfomed through 3 optimization rounds.
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exp = Experiment(tags=tags,
training_plan_class=MyTrainingPlan,
model_args=model_args,
training_args=training_args,
round_limit=rounds,
aggregator=FedAverage(),
node_selection_strategy=None
)
exp = Experiment(tags=tags, training_plan_class=MyTrainingPlan, model_args=model_args, training_args=training_args, round_limit=rounds, aggregator=FedAverage(), node_selection_strategy=None )
Let's start the experiment.
By default, this function doesn't stop until all the round_limit rounds are done for all the clients
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exp.run()
exp.run()
Save trained model to file
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exp.training_plan().export_model('./trained_model')
exp.training_plan().export_model('./trained_model')
Training with DP¶
Download and execute RDP Accountant Module¶
Following actions will download RDP module to calculate privacy budget and create a function called get_iterations which is going to be used for calculating the number training iterations that respects the privacy budget. The result of the function will be used for finding max number of rounds for the experiment.
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import urllib.request
response = urllib.request.urlopen('https://raw.githubusercontent.com/tensorflow/privacy/7eea74a6a1cf15e2d2bd890722400edd0e470db8/research/hyperparameters_2022/rdp_accountant.py')
rdp_accountant = response.read()
exec(rdp_accountant)
def get_iterations(target_delta, sigma, q, max_epsilon, max_N):
"""Computes max number of iterations given budget parameters
Args:
target_delta: If not `None`, the delta for which we compute the corresponding epsilon.
sigma: sigma to be used in Gaussian DP mechanism
q: training sample ratio
max_epsilon: Maximum budget allowed
max_N: Maximum number of iterations
Returns:
An integer number of iterations, and the evolution of the budget
Raises:
ValueError: If target_eps and target_delta are messed up.
"""
orders = [1 + x / 10. for x in range(1, 100)] + list(range(12, 64))
rdp = compute_rdp(q=q,
noise_multiplier=sigma,
steps=1,
orders=orders)
epsilon_range = [get_privacy_spent(orders, i * rdp, target_delta=target_delta) for i in range(max_N)]
max_training_steps = int(np.sum(np.array([x[0] for x in epsilon_range]) < max_epsilon))
return max_training_steps, [x[0] for x in epsilon_range][:max_training_steps]
import urllib.request response = urllib.request.urlopen('https://raw.githubusercontent.com/tensorflow/privacy/7eea74a6a1cf15e2d2bd890722400edd0e470db8/research/hyperparameters_2022/rdp_accountant.py') rdp_accountant = response.read() exec(rdp_accountant) def get_iterations(target_delta, sigma, q, max_epsilon, max_N): """Computes max number of iterations given budget parameters Args: target_delta: If not `None`, the delta for which we compute the corresponding epsilon. sigma: sigma to be used in Gaussian DP mechanism q: training sample ratio max_epsilon: Maximum budget allowed max_N: Maximum number of iterations Returns: An integer number of iterations, and the evolution of the budget Raises: ValueError: If target_eps and target_delta are messed up. """ orders = [1 + x / 10. for x in range(1, 100)] + list(range(12, 64)) rdp = compute_rdp(q=q, noise_multiplier=sigma, steps=1, orders=orders) epsilon_range = [get_privacy_spent(orders, i * rdp, target_delta=target_delta) for i in range(max_N)] max_training_steps = int(np.sum(np.array([x[0] for x in epsilon_range]) < max_epsilon)) return max_training_steps, [x[0] for x in epsilon_range][:max_training_steps]
DP parameters¶
In order to perform DP training (both local and central) we need to provide to the model and training schemes:
clip: defining the maximal L2 norm of gradientssigma: defining the strength of Gaussian noise to be added (either to gradients in case of LDP or to the final local model in case of CDP)
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from fedbiomed.researcher.requests import Requests
from fedbiomed.researcher.config import config
req = Requests(config)
query_nodes = req.list()
from fedbiomed.researcher.requests import Requests from fedbiomed.researcher.config import config req = Requests(config) query_nodes = req.list()
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query_nodes
query_nodes
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min_dataset_size = min([dataset['shape'][0] for i in query_nodes for dataset in query_nodes[i] if dataset['tags'] == ['#MEDNIST', '#dataset']]) #see training data in model
tot_dataset_size = sum([dataset['shape'][0] for i in query_nodes for dataset in query_nodes[i] if dataset['tags'] == ['#MEDNIST', '#dataset']]) #see training data in model
min_dataset_size = min([dataset['shape'][0] for i in query_nodes for dataset in query_nodes[i] if dataset['tags'] == ['#MEDNIST', '#dataset']]) #see training data in model tot_dataset_size = sum([dataset['shape'][0] for i in query_nodes for dataset in query_nodes[i] if dataset['tags'] == ['#MEDNIST', '#dataset']]) #see training data in model
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q = training_args['loader_args']['batch_size']/min_dataset_size
sigma = 0.4
clip = 0.005
delta = .1/min_dataset_size
max_epsilon = 10.
max_N = int(1e2)
q = training_args['loader_args']['batch_size']/min_dataset_size sigma = 0.4 clip = 0.005 delta = .1/min_dataset_size max_epsilon = 10. max_N = int(1e2)
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N, eps_list = get_iterations(delta, sigma, q, max_epsilon, max_N)
N, eps_list = get_iterations(delta, sigma, q, max_epsilon, max_N)
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max_rounds = N/(training_args['epochs'])
max_rounds = N/(training_args['epochs'])
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assert training_args['epochs']*rounds<=max_rounds, 'Number of rounds not compatible with privacy budget'
print(f'The maximal number of FL rounds for ({max_epsilon},{delta})-LDP training is {max_rounds}')
print('The selected number of FL rounds, '+str(rounds)+
',implies ('+str(eps_list[training_args['epochs']*rounds-1])+','+str(delta)+',)-LDP')
assert training_args['epochs']*rounds<=max_rounds, 'Number of rounds not compatible with privacy budget' print(f'The maximal number of FL rounds for ({max_epsilon},{delta})-LDP training is {max_rounds}') print('The selected number of FL rounds, '+str(rounds)+ ',implies ('+str(eps_list[training_args['epochs']*rounds-1])+','+str(delta)+',)-LDP')
We are now going to repeat the same training but with private SGD: at each epoch gradients are clipped and perturbed according to the provided privacy parameters.
Update training parameters for LDP¶
In order to perform DP-training we should provide an additional argument to training: the dictionalry 'DP_args' containing necessary parameters for DP. If we want to perform LDP, we should specify: 'type' : 'local'.
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model_args = {}
LDP = {'dp_args': {'type' : 'local', 'sigma': sigma, 'clip': clip}}
training_args.update(LDP)
training_args
model_args = {} LDP = {'dp_args': {'type' : 'local', 'sigma': sigma, 'clip': clip}} training_args.update(LDP) training_args
Declare and run the LDP training¶
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exp_LDP = Experiment(tags=tags,
model_args=model_args,
training_plan_class=MyTrainingPlan,
training_args=training_args,
round_limit=rounds,
aggregator=FedAverage(),
node_selection_strategy=None
)
exp_LDP = Experiment(tags=tags, model_args=model_args, training_plan_class=MyTrainingPlan, training_args=training_args, round_limit=rounds, aggregator=FedAverage(), node_selection_strategy=None )
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exp_LDP.run()
exp_LDP.run()
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import numpy as np
num_clients = len([dataset['shape'][0] for i in query_nodes for dataset in query_nodes[i] if dataset['tags'] == tags])
# Here we use the same parameters as LDP to evaluate the number of rounds,
# since we are performing record-level DP
q = training_args['loader_args']['batch_size']/min_dataset_size
sigma = 0.4#/(np.sqrt(num_clients)*training_args['loader_args']['batch_size'])
clip = 0.005
delta = .1/min_dataset_size
max_epsilon = 10.
max_N = int(1e2)
N, eps_list = get_iterations(delta, sigma, q, max_epsilon, max_N)
import numpy as np num_clients = len([dataset['shape'][0] for i in query_nodes for dataset in query_nodes[i] if dataset['tags'] == tags]) # Here we use the same parameters as LDP to evaluate the number of rounds, # since we are performing record-level DP q = training_args['loader_args']['batch_size']/min_dataset_size sigma = 0.4#/(np.sqrt(num_clients)*training_args['loader_args']['batch_size']) clip = 0.005 delta = .1/min_dataset_size max_epsilon = 10. max_N = int(1e2) N, eps_list = get_iterations(delta, sigma, q, max_epsilon, max_N)
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max_rounds = N/(training_args['epochs'])
print(max_rounds)
max_rounds = N/(training_args['epochs']) print(max_rounds)
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assert rounds<=max_rounds, 'Number of rounds not compatible with privacy budget'
print(f'The maximal number of allowed rounds for ({max_epsilon},{delta})-CDP training is {max_rounds}')
print(f'The selected number of training rounds, '+str(rounds)+
',implies ('+str(eps_list[rounds-1])+','+str(delta)+',)-CDP')
assert rounds<=max_rounds, 'Number of rounds not compatible with privacy budget' print(f'The maximal number of allowed rounds for ({max_epsilon},{delta})-CDP training is {max_rounds}') print(f'The selected number of training rounds, '+str(rounds)+ ',implies ('+str(eps_list[rounds-1])+','+str(delta)+',)-CDP')
Update training parameters for CDP¶
If we want to perform CDP, we should update the 'DP_args' dictionary by setting: 'type' : 'central'. Otherwise we are going to keep the same privacy parameters.
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CDP = {'dp_args': {'type' : 'central', 'sigma': sigma/np.sqrt(num_clients), 'clip': clip}}
training_args.update(CDP)
training_args
CDP = {'dp_args': {'type' : 'central', 'sigma': sigma/np.sqrt(num_clients), 'clip': clip}} training_args.update(CDP) training_args
Declare and run the CDP training¶
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exp_CDP = Experiment(tags=tags,
model_args=model_args,
training_plan_class=MyTrainingPlan,
training_args=training_args,
round_limit=rounds,
aggregator=FedAverage(),
node_selection_strategy=None
)
exp_CDP = Experiment(tags=tags, model_args=model_args, training_plan_class=MyTrainingPlan, training_args=training_args, round_limit=rounds, aggregator=FedAverage(), node_selection_strategy=None )
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exp_CDP.run()
exp_CDP.run()
Testing¶
We are now going to test and compare locally the three final federated models on an independent testing partition. The test dataset is available at this link:
https://drive.google.com/file/d/1YbwA0WitMoucoIa_Qao7IC1haPfDp-XD/
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!pip install matplotlib -q
!pip install gdown -q
!pip install matplotlib -q !pip install gdown -q
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import os
import tempfile
import PIL
import torch
import numpy as np
import matplotlib.pyplot as plt
import gdown
import zipfile
import matplotlib.pyplot as plt
print_config()
set_determinism(42)
import os import tempfile import PIL import torch import numpy as np import matplotlib.pyplot as plt import gdown import zipfile import matplotlib.pyplot as plt print_config() set_determinism(42)
Download the testing dataset on the local temporary folder.
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import gdown
import zipfile
import tempfile
import os
from fedbiomed.researcher.config import config
tmp_dir = tempfile.TemporaryDirectory(dir=config.vars['TMP_DIR']+os.sep)
resource = "https://drive.google.com/uc?id=1YbwA0WitMoucoIa_Qao7IC1haPfDp-XD"
base_dir = tmp_dir.name
test_file = os.path.join(base_dir, "MedNIST_testing.zip")
gdown.download(resource, test_file, quiet=False)
zf = zipfile.ZipFile(test_file)
for file in zf.infolist():
zf.extract(file, base_dir)
data_dir = os.path.join(base_dir, "MedNIST_testing")
import gdown import zipfile import tempfile import os from fedbiomed.researcher.config import config tmp_dir = tempfile.TemporaryDirectory(dir=config.vars['TMP_DIR']+os.sep) resource = "https://drive.google.com/uc?id=1YbwA0WitMoucoIa_Qao7IC1haPfDp-XD" base_dir = tmp_dir.name test_file = os.path.join(base_dir, "MedNIST_testing.zip") gdown.download(resource, test_file, quiet=False) zf = zipfile.ZipFile(test_file) for file in zf.infolist(): zf.extract(file, base_dir) data_dir = os.path.join(base_dir, "MedNIST_testing")
We redefine our custom dataloader (defined previously in the TrainingPlan):
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from monai.data import DataLoader, Dataset, CacheDataset
import monai
class MednistDataLoader(monai.data.Dataset):
def __init__(self, dataset):
self.dataset = dataset
def __len__(self):
return len(self.dataset)
def __getitem__(self, idx):
return (self.dataset[idx]["moving_hand"],
self.dataset[idx]["fixed_hand"])
from monai.data import DataLoader, Dataset, CacheDataset import monai class MednistDataLoader(monai.data.Dataset): def __init__(self, dataset): self.dataset = dataset def __len__(self): return len(self.dataset) def __getitem__(self, idx): return (self.dataset[idx]["moving_hand"], self.dataset[idx]["fixed_hand"])
Create the testing data loader and pairs of moving vs fixed hands:
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# Use a GPU if you have one + enough memory available
#
#use_cuda = torch.cuda.is_available()
#device = torch.device("cuda:0" if use_cuda else "cpu")
device = 'cpu'
# recreate model
model = GlobalNet(
image_size=(64, 64),
spatial_dims=2,
in_channels=2, # moving and fixed
num_channel_initial=16,
depth=3).to(device)
if USE_COMPILED:
warp_layer = Warp(3, "border").to(device)
else:
warp_layer = Warp("bilinear", "border").to(device)
MedNISTDataset.dataset_folder_name = ""
test_data = MedNISTDataset(root_dir=data_dir, section="test", download=False, transform=None)
testing_datadict = [
{"fixed_hand": item["image"], "moving_hand": item["image"]}
for item in test_data.data if item["label"] == 4 # label 4 is for xray hands
]
test_transforms = Compose(
[
LoadImageD(keys=["fixed_hand", "moving_hand"]),
EnsureChannelFirstD(keys=["fixed_hand", "moving_hand"]),
ScaleIntensityRanged(keys=["fixed_hand", "moving_hand"],
a_min=0., a_max=255., b_min=0.0, b_max=1.0, clip=True,),
RandRotateD(keys=["moving_hand"], range_x=np.pi/4, prob=1.0, keep_size=True, mode="bicubic"),
RandZoomD(keys=["moving_hand"], min_zoom=0.9, max_zoom=1.1, prob=1.0, mode="bicubic", align_corners=False),
EnsureTypeD(keys=["fixed_hand", "moving_hand"]),
]
)
val_ds = CacheDataset(data=testing_datadict[:1000], transform=test_transforms,
cache_rate=1.0, num_workers=0)
val_dl = MednistDataLoader(val_ds)
val_loader = DataLoader(val_dl, batch_size=16, num_workers=0)
# Use a GPU if you have one + enough memory available # #use_cuda = torch.cuda.is_available() #device = torch.device("cuda:0" if use_cuda else "cpu") device = 'cpu' # recreate model model = GlobalNet( image_size=(64, 64), spatial_dims=2, in_channels=2, # moving and fixed num_channel_initial=16, depth=3).to(device) if USE_COMPILED: warp_layer = Warp(3, "border").to(device) else: warp_layer = Warp("bilinear", "border").to(device) MedNISTDataset.dataset_folder_name = "" test_data = MedNISTDataset(root_dir=data_dir, section="test", download=False, transform=None) testing_datadict = [ {"fixed_hand": item["image"], "moving_hand": item["image"]} for item in test_data.data if item["label"] == 4 # label 4 is for xray hands ] test_transforms = Compose( [ LoadImageD(keys=["fixed_hand", "moving_hand"]), EnsureChannelFirstD(keys=["fixed_hand", "moving_hand"]), ScaleIntensityRanged(keys=["fixed_hand", "moving_hand"], a_min=0., a_max=255., b_min=0.0, b_max=1.0, clip=True,), RandRotateD(keys=["moving_hand"], range_x=np.pi/4, prob=1.0, keep_size=True, mode="bicubic"), RandZoomD(keys=["moving_hand"], min_zoom=0.9, max_zoom=1.1, prob=1.0, mode="bicubic", align_corners=False), EnsureTypeD(keys=["fixed_hand", "moving_hand"]), ] ) val_ds = CacheDataset(data=testing_datadict[:1000], transform=test_transforms, cache_rate=1.0, num_workers=0) val_dl = MednistDataLoader(val_ds) val_loader = DataLoader(val_dl, batch_size=16, num_workers=0)
To test the federated models we need to create model instances and assign to it the models parameters estimated at the last federated optimization rounds. Then, we generate predictions of the transformation between pairs. In addition, we evaluate the structural similarity index for each model.
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!pip install torchmetrics -q
from torchmetrics.functional import structural_similarity_index_measure
# Non private training
model = exp.training_plan().model()
model.load_state_dict(exp.aggregated_params()[rounds - 1]['params'])
# training with LDP
model_LDP = exp_LDP.training_plan().model()
model_LDP.load_state_dict(exp_LDP.aggregated_params()[rounds - 1]['params'])
# training with CDP
model_CDP = exp_CDP.training_plan().model()
model_CDP.load_state_dict(exp_CDP.aggregated_params()[rounds - 1]['params'])
for moving, fixed in val_loader:
# Non private training
ddf = model(torch.cat((moving, fixed), dim=1))
pred_image = warp_layer(moving, ddf)
# training with LDP
ddf_LDP = model_LDP(torch.cat((moving, fixed), dim=1))
pred_image_LDP = warp_layer(moving, ddf_LDP)
# training with CDP
ddf_CDP = model_CDP(torch.cat((moving, fixed), dim=1))
pred_image_CDP = warp_layer(moving, ddf_CDP)
# ssim predicted vs ground truth
# Non private training
SSIM = structural_similarity_index_measure(pred_image, fixed)
# training with LDP
SSIM_LDP = structural_similarity_index_measure(pred_image_LDP, fixed)
# training with CDP
SSIM_CDP = structural_similarity_index_measure(pred_image_CDP, fixed)
break
fixed_image = fixed.detach().cpu().numpy()[:, 0]
moving_image = moving.detach().cpu().numpy()[:, 0]
pred_image = pred_image.detach().cpu().numpy()[:, 0]
pred_image_LDP = pred_image_LDP.detach().cpu().numpy()[:, 0]
pred_image_CDP = pred_image_CDP.detach().cpu().numpy()[:, 0]
!pip install torchmetrics -q from torchmetrics.functional import structural_similarity_index_measure # Non private training model = exp.training_plan().model() model.load_state_dict(exp.aggregated_params()[rounds - 1]['params']) # training with LDP model_LDP = exp_LDP.training_plan().model() model_LDP.load_state_dict(exp_LDP.aggregated_params()[rounds - 1]['params']) # training with CDP model_CDP = exp_CDP.training_plan().model() model_CDP.load_state_dict(exp_CDP.aggregated_params()[rounds - 1]['params']) for moving, fixed in val_loader: # Non private training ddf = model(torch.cat((moving, fixed), dim=1)) pred_image = warp_layer(moving, ddf) # training with LDP ddf_LDP = model_LDP(torch.cat((moving, fixed), dim=1)) pred_image_LDP = warp_layer(moving, ddf_LDP) # training with CDP ddf_CDP = model_CDP(torch.cat((moving, fixed), dim=1)) pred_image_CDP = warp_layer(moving, ddf_CDP) # ssim predicted vs ground truth # Non private training SSIM = structural_similarity_index_measure(pred_image, fixed) # training with LDP SSIM_LDP = structural_similarity_index_measure(pred_image_LDP, fixed) # training with CDP SSIM_CDP = structural_similarity_index_measure(pred_image_CDP, fixed) break fixed_image = fixed.detach().cpu().numpy()[:, 0] moving_image = moving.detach().cpu().numpy()[:, 0] pred_image = pred_image.detach().cpu().numpy()[:, 0] pred_image_LDP = pred_image_LDP.detach().cpu().numpy()[:, 0] pred_image_CDP = pred_image_CDP.detach().cpu().numpy()[:, 0]
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print('---> Results for non-private training')
print(f'SSIM = {SSIM}')
print('---> Results for training with LDP')
print(f'SSIM = {SSIM_LDP})')
print('---> Results for training with CDP')
print(f'SSIM = {SSIM_CDP})')
print('---> Results for non-private training') print(f'SSIM = {SSIM}') print('---> Results for training with LDP') print(f'SSIM = {SSIM_LDP})') print('---> Results for training with CDP') print(f'SSIM = {SSIM_CDP})')
Finally, we can print some example of predictions of all models from the testing dataset.
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%matplotlib inline
batch_size = 10
plt.subplots(batch_size, 5, figsize=(12, 25))
for b in range(batch_size):
# moving image
plt.subplot(batch_size, 5, b * 5 + 1)
plt.axis('off')
plt.title("moving image")
plt.imshow(moving_image[b], cmap="gray")
# fixed image
plt.subplot(batch_size, 5, b * 5 + 2)
plt.axis('off')
plt.title("fixed image")
plt.imshow(fixed_image[b], cmap="gray")
# warped moving
plt.subplot(batch_size, 5, b * 5 + 3)
plt.axis('off')
plt.title("predicted image")
plt.imshow(pred_image[b], cmap="gray")
# warped moving LDP
plt.subplot(batch_size, 5, b * 5 + 4)
plt.axis('off')
plt.title("predicted image (LDP)")
plt.imshow(pred_image_LDP[b], cmap="gray")
# warped moving CDP
plt.subplot(batch_size, 5, b * 5 + 5)
plt.axis('off')
plt.title("predicted image (CDP)")
plt.imshow(pred_image_CDP[b], cmap="gray")
plt.axis('off')
plt.show()
%matplotlib inline batch_size = 10 plt.subplots(batch_size, 5, figsize=(12, 25)) for b in range(batch_size): # moving image plt.subplot(batch_size, 5, b * 5 + 1) plt.axis('off') plt.title("moving image") plt.imshow(moving_image[b], cmap="gray") # fixed image plt.subplot(batch_size, 5, b * 5 + 2) plt.axis('off') plt.title("fixed image") plt.imshow(fixed_image[b], cmap="gray") # warped moving plt.subplot(batch_size, 5, b * 5 + 3) plt.axis('off') plt.title("predicted image") plt.imshow(pred_image[b], cmap="gray") # warped moving LDP plt.subplot(batch_size, 5, b * 5 + 4) plt.axis('off') plt.title("predicted image (LDP)") plt.imshow(pred_image_LDP[b], cmap="gray") # warped moving CDP plt.subplot(batch_size, 5, b * 5 + 5) plt.axis('off') plt.title("predicted image (CDP)") plt.imshow(pred_image_CDP[b], cmap="gray") plt.axis('off') plt.show()