image_classifier_3d.models package

Submodules

image_classifier_3d.models.build_classifier module

PyTorch Lightning model class for mitotic classifier

class image_classifier_3d.models.build_classifier.mitotic_classifier(hparams)[source]

Bases: pytorch_lightning.core.lightning.LightningModule

define a project class, consistent with project_name in config file

configure_optimizers()[source]

Choose what optimizers and learning-rate schedulers to use in your optimization. Normally you’d need one. But in the case of GANs or similar you might have multiple.

Return:

Any of these 6 options.

  • Single optimizer.

  • List or Tuple of optimizers.

  • Two lists - The first list has multiple optimizers, and the second has multiple LR schedulers (or multiple lr_dict).

  • Dictionary, with an "optimizer" key, and (optionally) a "lr_scheduler" key whose value is a single LR scheduler or lr_dict.

  • Tuple of dictionaries as described above, with an optional "frequency" key.

  • None - Fit will run without any optimizer.

The lr_dict is a dictionary which contains the scheduler and its associated configuration. The default configuration is shown below.

lr_dict = {
    # REQUIRED: The scheduler instance
    'scheduler': lr_scheduler,
    # The unit of the scheduler's step size, could also be 'step'.
    # 'epoch' updates the scheduler on epoch end whereas 'step'
    # updates it after a optimizer update.
    'interval': 'epoch',
    # How many epochs/steps should pass between calls to
    # `scheduler.step()`. 1 corresponds to updating the learning
    # rate after every epoch/step.
    'frequency': 1,
    # Metric to to monitor for schedulers like `ReduceLROnPlateau`
    'monitor': 'val_loss',
    # If set to `True`, will enforce that the value specified 'monitor'
    # is available when the scheduler is updated, thus stopping
    # training if not found. If set to `False`, it will only produce a warning
    'strict': True,
    # If using the `LearningRateMonitor` callback to monitor the
    # learning rate progress, this keyword can be used to specify
    # a custom logged name
    'name': None,
}

When there are schedulers in which the .step() method is conditioned on a value, such as the torch.optim.lr_scheduler.ReduceLROnPlateau scheduler, Lightning requires that the lr_dict contains the keyword "monitor" set to the metric name that the scheduler should be conditioned on.

Metrics can be made available to monitor by simply logging it using self.log('metric_to_track', metric_val) in your LightningModule.

Note:

The frequency value specified in a dict along with the optimizer key is an int corresponding to the number of sequential batches optimized with the specific optimizer. It should be given to none or to all of the optimizers. There is a difference between passing multiple optimizers in a list, and passing multiple optimizers in dictionaries with a frequency of 1:

  • In the former case, all optimizers will operate on the given batch in each optimization step.

  • In the latter, only one optimizer will operate on the given batch at every step.

This is different from the frequency value specified in the lr_dict mentioned above.

def configure_optimizers(self):
    optimizer_one = torch.optim.SGD(self.model.parameters(), lr=0.01)
    optimizer_two = torch.optim.SGD(self.model.parameters(), lr=0.01)
    return [
        {'optimizer': optimizer_one, 'frequency': 5},
        {'optimizer': optimizer_two, 'frequency': 10},
    ]

In this example, the first optimizer will be used for the first 5 steps, the second optimizer for the next 10 steps and that cycle will continue. If an LR scheduler is specified for an optimizer using the lr_scheduler key in the above dict, the scheduler will only be updated when its optimizer is being used.

Examples:

# most cases. no learning rate scheduler
def configure_optimizers(self):
    return Adam(self.parameters(), lr=1e-3)

# multiple optimizer case (e.g.: GAN)
def configure_optimizers(self):
    gen_opt = Adam(self.model_gen.parameters(), lr=0.01)
    dis_opt = Adam(self.model_dis.parameters(), lr=0.02)
    return gen_opt, dis_opt

# example with learning rate schedulers
def configure_optimizers(self):
    gen_opt = Adam(self.model_gen.parameters(), lr=0.01)
    dis_opt = Adam(self.model_dis.parameters(), lr=0.02)
    dis_sch = CosineAnnealing(dis_opt, T_max=10)
    return [gen_opt, dis_opt], [dis_sch]

# example with step-based learning rate schedulers
# each optimizer has its own scheduler
def configure_optimizers(self):
    gen_opt = Adam(self.model_gen.parameters(), lr=0.01)
    dis_opt = Adam(self.model_dis.parameters(), lr=0.02)
    gen_sch = {
        'scheduler': ExponentialLR(gen_opt, 0.99),
        'interval': 'step'  # called after each training step
    }
    dis_sch = CosineAnnealing(dis_opt, T_max=10) # called every epoch
    return [gen_opt, dis_opt], [gen_sch, dis_sch]

# example with optimizer frequencies
# see training procedure in `Improved Training of Wasserstein GANs`, Algorithm 1
# https://arxiv.org/abs/1704.00028
def configure_optimizers(self):
    gen_opt = Adam(self.model_gen.parameters(), lr=0.01)
    dis_opt = Adam(self.model_dis.parameters(), lr=0.02)
    n_critic = 5
    return (
        {'optimizer': dis_opt, 'frequency': n_critic},
        {'optimizer': gen_opt, 'frequency': 1}
    )
Note:

Some things to know:

  • Lightning calls .backward() and .step() on each optimizer and learning rate scheduler as needed.

  • If you use 16-bit precision (precision=16), Lightning will automatically handle the optimizers.

  • If you use multiple optimizers, training_step() will have an additional optimizer_idx parameter.

  • If you use torch.optim.LBFGS, Lightning handles the closure function automatically for you.

  • If you use multiple optimizers, gradients will be calculated only for the parameters of current optimizer at each training step.

  • If you need to control how often those optimizers step or override the default .step() schedule, override the optimizer_step() hook.

forward(x, **kwargs)[source]

forward pass

static get_dataloader(data_m: Dict, filenames: List, flag: str)[source]
test_dataloader()[source]

Implement one or multiple PyTorch DataLoaders for testing.

The dataloader you return will not be reloaded unless you set :paramref:`~pytorch_lightning.trainer.Trainer.reload_dataloaders_every_n_epochs` to a postive integer.

For data processing use the following pattern:

  • download in prepare_data()

  • process and split in setup()

However, the above are only necessary for distributed processing.

Warning

do not assign state in prepare_data

Note:

Lightning adds the correct sampler for distributed and arbitrary hardware. There is no need to set it yourself.

Return:

A torch.utils.data.DataLoader or a sequence of them specifying testing samples.

Example:

def test_dataloader(self):
    transform = transforms.Compose([transforms.ToTensor(),
                                    transforms.Normalize((0.5,), (1.0,))])
    dataset = MNIST(root='/path/to/mnist/', train=False, transform=transform,
                    download=True)
    loader = torch.utils.data.DataLoader(
        dataset=dataset,
        batch_size=self.batch_size,
        shuffle=False
    )

    return loader

# can also return multiple dataloaders
def test_dataloader(self):
    return [loader_a, loader_b, ..., loader_n]
Note:

If you don’t need a test dataset and a test_step(), you don’t need to implement this method.

Note:

In the case where you return multiple test dataloaders, the test_step() will have an argument dataloader_idx which matches the order here.

test_epoch_end(outputs)[source]

Called at the end of a test epoch with the output of all test steps.

# the pseudocode for these calls
test_outs = []
for test_batch in test_data:
    out = test_step(test_batch)
    test_outs.append(out)
test_epoch_end(test_outs)
Args:
outputs: List of outputs you defined in test_step_end(), or if there

are multiple dataloaders, a list containing a list of outputs for each dataloader

Return:

None

Note:

If you didn’t define a test_step(), this won’t be called.

Examples:

With a single dataloader:

def test_epoch_end(self, outputs):
    # do something with the outputs of all test batches
    all_test_preds = test_step_outputs.predictions

    some_result = calc_all_results(all_test_preds)
    self.log(some_result)

With multiple dataloaders, outputs will be a list of lists. The outer list contains one entry per dataloader, while the inner list contains the individual outputs of each test step for that dataloader.

def test_epoch_end(self, outputs):
    final_value = 0
    for dataloader_outputs in outputs:
        for test_step_out in dataloader_outputs:
            # do something
            final_value += test_step_out

    self.log('final_metric', final_value)
test_step(batch, batch_idx, optimizer_idx=0)[source]

Operates on a single batch of data from the test set. In this step you’d normally generate examples or calculate anything of interest such as accuracy.

# the pseudocode for these calls
test_outs = []
for test_batch in test_data:
    out = test_step(test_batch)
    test_outs.append(out)
test_epoch_end(test_outs)
Args:
batch (Tensor | (Tensor, …) | [Tensor, …]):

The output of your DataLoader. A tensor, tuple or list.

batch_idx (int): The index of this batch. dataloader_idx (int): The index of the dataloader that produced this batch

(only if multiple test dataloaders used).

Return:

Any of.

  • Any object or value

  • None - Testing will skip to the next batch

# if you have one test dataloader:
def test_step(self, batch, batch_idx)

# if you have multiple test dataloaders:
def test_step(self, batch, batch_idx, dataloader_idx)

Examples:

# CASE 1: A single test dataset
def test_step(self, batch, batch_idx):
    x, y = batch

    # implement your own
    out = self(x)
    loss = self.loss(out, y)

    # log 6 example images
    # or generated text... or whatever
    sample_imgs = x[:6]
    grid = torchvision.utils.make_grid(sample_imgs)
    self.logger.experiment.add_image('example_images', grid, 0)

    # calculate acc
    labels_hat = torch.argmax(out, dim=1)
    test_acc = torch.sum(y == labels_hat).item() / (len(y) * 1.0)

    # log the outputs!
    self.log_dict({'test_loss': loss, 'test_acc': test_acc})

If you pass in multiple test dataloaders, test_step() will have an additional argument.

# CASE 2: multiple test dataloaders
def test_step(self, batch, batch_idx, dataloader_idx):
    # dataloader_idx tells you which dataset this is.
Note:

If you don’t need to test you don’t need to implement this method.

Note:

When the test_step() is called, the model has been put in eval mode and PyTorch gradients have been disabled. At the end of the test epoch, the model goes back to training mode and gradients are enabled.

train_dataloader()[source]

Implement one or more PyTorch DataLoaders for training.

Return:

A collection of torch.utils.data.DataLoader specifying training samples. In the case of multiple dataloaders, please see this page.

The dataloader you return will not be reloaded unless you set :paramref:`~pytorch_lightning.trainer.Trainer.reload_dataloaders_every_n_epochs` to a positive integer.

For data processing use the following pattern:

  • download in prepare_data()

  • process and split in setup()

However, the above are only necessary for distributed processing.

Warning

do not assign state in prepare_data

Note:

Lightning adds the correct sampler for distributed and arbitrary hardware. There is no need to set it yourself.

Example:

# single dataloader
def train_dataloader(self):
    transform = transforms.Compose([transforms.ToTensor(),
                                    transforms.Normalize((0.5,), (1.0,))])
    dataset = MNIST(root='/path/to/mnist/', train=True, transform=transform,
                    download=True)
    loader = torch.utils.data.DataLoader(
        dataset=dataset,
        batch_size=self.batch_size,
        shuffle=True
    )
    return loader

# multiple dataloaders, return as list
def train_dataloader(self):
    mnist = MNIST(...)
    cifar = CIFAR(...)
    mnist_loader = torch.utils.data.DataLoader(
        dataset=mnist, batch_size=self.batch_size, shuffle=True
    )
    cifar_loader = torch.utils.data.DataLoader(
        dataset=cifar, batch_size=self.batch_size, shuffle=True
    )
    # each batch will be a list of tensors: [batch_mnist, batch_cifar]
    return [mnist_loader, cifar_loader]

# multiple dataloader, return as dict
def train_dataloader(self):
    mnist = MNIST(...)
    cifar = CIFAR(...)
    mnist_loader = torch.utils.data.DataLoader(
        dataset=mnist, batch_size=self.batch_size, shuffle=True
    )
    cifar_loader = torch.utils.data.DataLoader(
        dataset=cifar, batch_size=self.batch_size, shuffle=True
    )
    # each batch will be a dict of tensors: {'mnist': batch_mnist, 'cifar': batch_cifar}
    return {'mnist': mnist_loader, 'cifar': cifar_loader}
training = None
training_epoch_end(outputs)[source]

Called at the end of the training epoch with the outputs of all training steps. Use this in case you need to do something with all the outputs returned by training_step().

# the pseudocode for these calls
train_outs = []
for train_batch in train_data:
    out = training_step(train_batch)
    train_outs.append(out)
training_epoch_end(train_outs)
Args:
outputs: List of outputs you defined in training_step(), or if there are

multiple dataloaders, a list containing a list of outputs for each dataloader.

Return:

None

Note:

If this method is not overridden, this won’t be called.

Example:

def training_epoch_end(self, training_step_outputs):
    # do something with all training_step outputs
    return result

With multiple dataloaders, outputs will be a list of lists. The outer list contains one entry per dataloader, while the inner list contains the individual outputs of each training step for that dataloader.

def training_epoch_end(self, training_step_outputs):
    for out in training_step_outputs:
        # do something here
training_step(batch, batch_idx, optimizer_idx=0)[source]

Here you compute and return the training loss and some additional metrics for e.g. the progress bar or logger.

Args:
batch (Tensor | (Tensor, …) | [Tensor, …]):

The output of your DataLoader. A tensor, tuple or list.

batch_idx (int): Integer displaying index of this batch optimizer_idx (int): When using multiple optimizers, this argument will also be present. hiddens(Tensor): Passed in if

Return:

Any of.

  • Tensor - The loss tensor

  • dict - A dictionary. Can include any keys, but must include the key 'loss'

  • None - Training will skip to the next batch

Note:

Returning None is currently not supported for multi-GPU or TPU, or with 16-bit precision enabled.

In this step you’d normally do the forward pass and calculate the loss for a batch. You can also do fancier things like multiple forward passes or something model specific.

Example:

def training_step(self, batch, batch_idx):
    x, y, z = batch
    out = self.encoder(x)
    loss = self.loss(out, x)
    return loss

If you define multiple optimizers, this step will be called with an additional optimizer_idx parameter.

# Multiple optimizers (e.g.: GANs)
def training_step(self, batch, batch_idx, optimizer_idx):
    if optimizer_idx == 0:
        # do training_step with encoder
    if optimizer_idx == 1:
        # do training_step with decoder

If you add truncated back propagation through time you will also get an additional argument with the hidden states of the previous step.

# Truncated back-propagation through time
def training_step(self, batch, batch_idx, hiddens):
    # hiddens are the hidden states from the previous truncated backprop step
    ...
    out, hiddens = self.lstm(data, hiddens)
    ...
    return {'loss': loss, 'hiddens': hiddens}
Note:

The loss value shown in the progress bar is smoothed (averaged) over the last values, so it differs from the actual loss returned in train/validation step.

val_dataloader()[source]

Implement one or multiple PyTorch DataLoaders for validation.

The dataloader you return will not be reloaded unless you set :paramref:`~pytorch_lightning.trainer.Trainer.reload_dataloaders_every_n_epochs` to a positive integer.

It’s recommended that all data downloads and preparation happen in prepare_data().

Note:

Lightning adds the correct sampler for distributed and arbitrary hardware There is no need to set it yourself.

Return:

A torch.utils.data.DataLoader or a sequence of them specifying validation samples.

Examples:

def val_dataloader(self):
    transform = transforms.Compose([transforms.ToTensor(),
                                    transforms.Normalize((0.5,), (1.0,))])
    dataset = MNIST(root='/path/to/mnist/', train=False,
                    transform=transform, download=True)
    loader = torch.utils.data.DataLoader(
        dataset=dataset,
        batch_size=self.batch_size,
        shuffle=False
    )

    return loader

# can also return multiple dataloaders
def val_dataloader(self):
    return [loader_a, loader_b, ..., loader_n]
Note:

If you don’t need a validation dataset and a validation_step(), you don’t need to implement this method.

Note:

In the case where you return multiple validation dataloaders, the validation_step() will have an argument dataloader_idx which matches the order here.

validation_epoch_end(outputs)[source]

Called at the end of the validation epoch with the outputs of all validation steps.

# the pseudocode for these calls
val_outs = []
for val_batch in val_data:
    out = validation_step(val_batch)
    val_outs.append(out)
validation_epoch_end(val_outs)
Args:
outputs: List of outputs you defined in validation_step(), or if there

are multiple dataloaders, a list containing a list of outputs for each dataloader.

Return:

None

Note:

If you didn’t define a validation_step(), this won’t be called.

Examples:

With a single dataloader:

def validation_epoch_end(self, val_step_outputs):
    for out in val_step_outputs:
        # do something

With multiple dataloaders, outputs will be a list of lists. The outer list contains one entry per dataloader, while the inner list contains the individual outputs of each validation step for that dataloader.

def validation_epoch_end(self, outputs):
    for dataloader_output_result in outputs:
        dataloader_outs = dataloader_output_result.dataloader_i_outputs

    self.log('final_metric', final_value)
validation_step(batch, batch_idx, optimizer_idx=0)[source]

Operates on a single batch of data from the validation set. In this step you’d might generate examples or calculate anything of interest like accuracy.

# the pseudocode for these calls
val_outs = []
for val_batch in val_data:
    out = validation_step(val_batch)
    val_outs.append(out)
validation_epoch_end(val_outs)
Args:
batch (Tensor | (Tensor, …) | [Tensor, …]):

The output of your DataLoader. A tensor, tuple or list.

batch_idx (int): The index of this batch dataloader_idx (int): The index of the dataloader that produced this batch

(only if multiple val dataloaders used)

Return:
  • Any object or value

  • None - Validation will skip to the next batch

# pseudocode of order
val_outs = []
for val_batch in val_data:
    out = validation_step(val_batch)
    if defined('validation_step_end'):
        out = validation_step_end(out)
    val_outs.append(out)
val_outs = validation_epoch_end(val_outs)
# if you have one val dataloader:
def validation_step(self, batch, batch_idx)

# if you have multiple val dataloaders:
def validation_step(self, batch, batch_idx, dataloader_idx)

Examples:

# CASE 1: A single validation dataset
def validation_step(self, batch, batch_idx):
    x, y = batch

    # implement your own
    out = self(x)
    loss = self.loss(out, y)

    # log 6 example images
    # or generated text... or whatever
    sample_imgs = x[:6]
    grid = torchvision.utils.make_grid(sample_imgs)
    self.logger.experiment.add_image('example_images', grid, 0)

    # calculate acc
    labels_hat = torch.argmax(out, dim=1)
    val_acc = torch.sum(y == labels_hat).item() / (len(y) * 1.0)

    # log the outputs!
    self.log_dict({'val_loss': loss, 'val_acc': val_acc})

If you pass in multiple val dataloaders, validation_step() will have an additional argument.

# CASE 2: multiple validation dataloaders
def validation_step(self, batch, batch_idx, dataloader_idx):
    # dataloader_idx tells you which dataset this is.
Note:

If you don’t need to validate you don’t need to implement this method.

Note:

When the validation_step() is called, the model has been put in eval mode and PyTorch gradients have been disabled. At the end of validation, the model goes back to training mode and gradients are enabled.

image_classifier_3d.models.densenet module

class image_classifier_3d.models.densenet.DenseNet(n_input_channels=3, conv1_t_size=7, conv1_t_stride=1, no_max_pool=False, growth_rate=32, block_config=(6, 12, 24, 16), num_init_features=64, bn_size=4, drop_rate=0, num_classes=1000)[source]

Bases: torch.nn.modules.module.Module

Densenet-BC model class Args:

growth_rate (int) - how many filters to add each layer (k in paper) block_config (list of 4 ints) - how many layers in each pooling block num_init_features (int) - the number of filters to learn in the first convolution layer bn_size (int) - multiplicative factor for number of bottle neck layers

(i.e. bn_size * k features in the bottleneck layer)

drop_rate (float) - dropout rate after each dense layer num_classes (int) - number of classification classes

Initializes internal Module state, shared by both nn.Module and ScriptModule.

forward(x)[source]

Defines the computation performed at every call.

Should be overridden by all subclasses.

Note

Although the recipe for forward pass needs to be defined within this function, one should call the Module instance afterwards instead of this since the former takes care of running the registered hooks while the latter silently ignores them.

training = None
image_classifier_3d.models.densenet.generate_model(model_depth, **kwargs)[source]

image_classifier_3d.models.resnet module

class image_classifier_3d.models.resnet.BasicBlock(in_planes, planes, stride=1, downsample=None)[source]

Bases: torch.nn.modules.module.Module

Initializes internal Module state, shared by both nn.Module and ScriptModule.

expansion = 1
forward(x)[source]

Defines the computation performed at every call.

Should be overridden by all subclasses.

Note

Although the recipe for forward pass needs to be defined within this function, one should call the Module instance afterwards instead of this since the former takes care of running the registered hooks while the latter silently ignores them.

training = None
class image_classifier_3d.models.resnet.Bottleneck(in_planes, planes, stride=1, downsample=None)[source]

Bases: torch.nn.modules.module.Module

Initializes internal Module state, shared by both nn.Module and ScriptModule.

expansion = 4
forward(x)[source]

Defines the computation performed at every call.

Should be overridden by all subclasses.

Note

Although the recipe for forward pass needs to be defined within this function, one should call the Module instance afterwards instead of this since the former takes care of running the registered hooks while the latter silently ignores them.

training = None
class image_classifier_3d.models.resnet.ResNet(block, layers, block_inplanes, n_input_channels=1, conv1_t_size=7, conv1_t_stride=1, no_max_pool=True, shortcut_type='B', widen_factor=1.0, n_classes=400)[source]

Bases: torch.nn.modules.module.Module

Initializes internal Module state, shared by both nn.Module and ScriptModule.

forward(x)[source]

Defines the computation performed at every call.

Should be overridden by all subclasses.

Note

Although the recipe for forward pass needs to be defined within this function, one should call the Module instance afterwards instead of this since the former takes care of running the registered hooks while the latter silently ignores them.

training = None
image_classifier_3d.models.resnet.conv1x1x1(in_planes, out_planes, stride=1)[source]
image_classifier_3d.models.resnet.conv3x3x3(in_planes, out_planes, stride=1)[source]
image_classifier_3d.models.resnet.generate_model(model_depth, **kwargs)[source]
image_classifier_3d.models.resnet.get_inplanes()[source]

image_classifier_3d.models.resnet_GN module

3D ResNet replacing batch normalization with group normalization to train on batches of images without padding (thus different sizes)

class image_classifier_3d.models.resnet_GN.BasicBlock(in_planes, planes, stride=1, downsample=None)[source]

Bases: torch.nn.modules.module.Module

Initializes internal Module state, shared by both nn.Module and ScriptModule.

expansion = 1
forward(x)[source]

Defines the computation performed at every call.

Should be overridden by all subclasses.

Note

Although the recipe for forward pass needs to be defined within this function, one should call the Module instance afterwards instead of this since the former takes care of running the registered hooks while the latter silently ignores them.

training = None
class image_classifier_3d.models.resnet_GN.Bottleneck(in_planes, planes, stride=1, downsample=None)[source]

Bases: torch.nn.modules.module.Module

Initializes internal Module state, shared by both nn.Module and ScriptModule.

expansion = 4
forward(x)[source]

Defines the computation performed at every call.

Should be overridden by all subclasses.

Note

Although the recipe for forward pass needs to be defined within this function, one should call the Module instance afterwards instead of this since the former takes care of running the registered hooks while the latter silently ignores them.

training = None
class image_classifier_3d.models.resnet_GN.ResNetGN(block, layers, block_inplanes, n_input_channels=1, conv1_t_size=7, conv1_t_stride=1, no_max_pool=True, shortcut_type='B', widen_factor=1.0, n_classes=400)[source]

Bases: torch.nn.modules.module.Module

Initializes internal Module state, shared by both nn.Module and ScriptModule.

forward(x)[source]

Defines the computation performed at every call.

Should be overridden by all subclasses.

Note

Although the recipe for forward pass needs to be defined within this function, one should call the Module instance afterwards instead of this since the former takes care of running the registered hooks while the latter silently ignores them.

training = None
image_classifier_3d.models.resnet_GN.conv1x1x1(in_planes, out_planes, stride=1)[source]
image_classifier_3d.models.resnet_GN.conv3x3x3(in_planes, out_planes, stride=1)[source]
image_classifier_3d.models.resnet_GN.generate_model(model_depth, **kwargs)[source]
image_classifier_3d.models.resnet_GN.get_inplanes()[source]

Module contents