Visualizations¶
Tensorboard visuals¶
- monai.visualize.img2tensorboard.add_animated_gif(writer, tag, image_tensor, max_out=3, frame_dim=- 3, scale_factor=1.0, global_step=None)[source]¶
Creates an animated gif out of an image tensor in ‘CHWD’ format and writes it with SummaryWriter.
- Parameters
writer (
SummaryWriter
) – Tensorboard SummaryWriter to write totag (
str
) – Data identifierimage_tensor (
Union
[ndarray
,Tensor
]) – tensor for the image to add, expected to be in CHWD formatmax_out (
int
) – maximum number of image channels to animate throughframe_dim (
int
) – the dimension used as frames for GIF image, expect input data shape as CHWD, default to -3 (the first spatial dim)scale_factor (
float
) – amount to multiply values by. If the image data is between 0 and 1, using 255 for this value will scale it to displayable rangeglobal_step (
Optional
[int
]) – Global step value to record
- Return type
None
- monai.visualize.img2tensorboard.make_animated_gif_summary(tag, image, writer=None, max_out=3, frame_dim=- 3, scale_factor=1.0)[source]¶
Creates an animated gif out of an image tensor in ‘CHWD’ format and returns Summary.
- Parameters
tag (
str
) – Data identifierimage (
Union
[ndarray
,Tensor
]) – The image, expected to be in CHWD formatwriter – the tensorboard writer to plot image
max_out (
int
) – maximum number of image channels to animate throughframe_dim (
int
) – the dimension used as frames for GIF image, expect input data shape as CHWD, default to -3 (the first spatial dim)scale_factor (
float
) – amount to multiply values by. if the image data is between 0 and 1, using 255 for this value will scale it to displayable range
- Return type
Summary
- monai.visualize.img2tensorboard.plot_2d_or_3d_image(data, step, writer, index=0, max_channels=1, frame_dim=- 3, max_frames=24, tag='output')[source]¶
Plot 2D or 3D image on the TensorBoard, 3D image will be converted to GIF image.
Note
Plot 3D or 2D image(with more than 3 channels) as separate images. And if writer is from TensorBoardX, data has 3 channels and max_channels=3, will plot as RGB video.
- Parameters
data (
Union
[~NdarrayTensor,List
[~NdarrayTensor]]) – target data to be plotted as image on the TensorBoard. The data is expected to have ‘NCHW[D]’ dimensions or a list of data with CHW[D] dimensions, and only plot the first in the batch.step (
int
) – current step to plot in a chart.writer (
SummaryWriter
) – specify TensorBoard or TensorBoardX SummaryWriter to plot the image.index (
int
) – plot which element in the input data batch, default is the first element.max_channels (
int
) – number of channels to plot.frame_dim (
int
) – if plotting 3D image as GIF, specify the dimension used as frames, expect input data shape as NCHWD, default to -3 (the first spatial dim)max_frames (
int
) – if plot 3D RGB image as video in TensorBoardX, set the FPS to max_frames.tag (
str
) – tag of the plotted image on TensorBoard.
- Return type
None
Class activation map¶
- class monai.visualize.class_activation_maps.CAM(nn_module, target_layers, fc_layers='fc', upsampler=<function default_upsampler>, postprocessing=<function default_normalizer>)[source]¶
Compute class activation map from the last fully-connected layers before the spatial pooling. This implementation is based on:
Zhou et al., Learning Deep Features for Discriminative Localization. CVPR ‘16, https://arxiv.org/abs/1512.04150
Examples
import torch # densenet 2d from monai.networks.nets import DenseNet121 from monai.visualize import CAM model_2d = DenseNet121(spatial_dims=2, in_channels=1, out_channels=3) cam = CAM(nn_module=model_2d, target_layers="class_layers.relu", fc_layers="class_layers.out") result = cam(x=torch.rand((1, 1, 48, 64))) # resnet 2d from monai.networks.nets import se_resnet50 from monai.visualize import CAM model_2d = se_resnet50(spatial_dims=2, in_channels=3, num_classes=4) cam = CAM(nn_module=model_2d, target_layers="layer4", fc_layers="last_linear") result = cam(x=torch.rand((2, 3, 48, 64)))
N.B.: To help select the target layer, it may be useful to list all layers:
for name, _ in model.named_modules(): print(name)
- Parameters
nn_module (
Module
) – the model to be visualizedtarget_layers (
str
) – name of the model layer to generate the feature map.fc_layers (
Union
[str
,Callable
]) – a string or a callable used to get fully-connected weights to compute activation map from the target_layers (without pooling). and evaluate it at every spatial location.upsampler (
Callable
) – An upsampling method to upsample the output image. Default is N dimensional linear (bilinear, trilinear, etc.) depending on num spatial dimensions of input.postprocessing (
Callable
) – a callable that applies on the upsampled output image. Default is normalizing between min=1 and max=0 (i.e., largest input will become 0 and smallest input will become 1).
- __init__(nn_module, target_layers, fc_layers='fc', upsampler=<function default_upsampler>, postprocessing=<function default_normalizer>)[source]¶
- Parameters
nn_module (
Module
) – the model to be visualizedtarget_layers (
str
) – name of the model layer to generate the feature map.fc_layers (
Union
[str
,Callable
]) – a string or a callable used to get fully-connected weights to compute activation map from the target_layers (without pooling). and evaluate it at every spatial location.upsampler (
Callable
) – An upsampling method to upsample the output image. Default is N dimensional linear (bilinear, trilinear, etc.) depending on num spatial dimensions of input.postprocessing (
Callable
) – a callable that applies on the upsampled output image. Default is normalizing between min=1 and max=0 (i.e., largest input will become 0 and smallest input will become 1).
- compute_map(x, class_idx=None, layer_idx=- 1)[source]¶
Compute the actual feature map with input tensor x.
- Parameters
x – input to nn_module.
class_idx – index of the class to be visualized. Default to None (computing class_idx from argmax)
layer_idx – index of the target layer if there are multiple target layers. Defaults to -1.
- Returns
activation maps (raw outputs without upsampling/post-processing.)
- class monai.visualize.class_activation_maps.GradCAM(nn_module, target_layers, upsampler=<function default_upsampler>, postprocessing=<function default_normalizer>, register_backward=True)[source]¶
Computes Gradient-weighted Class Activation Mapping (Grad-CAM). This implementation is based on:
Selvaraju et al., Grad-CAM: Visual Explanations from Deep Networks via Gradient-based Localization, https://arxiv.org/abs/1610.02391
Examples
import torch # densenet 2d from monai.networks.nets import DenseNet121 from monai.visualize import GradCAM model_2d = DenseNet121(spatial_dims=2, in_channels=1, out_channels=3) cam = GradCAM(nn_module=model_2d, target_layers="class_layers.relu") result = cam(x=torch.rand((1, 1, 48, 64))) # resnet 2d from monai.networks.nets import se_resnet50 from monai.visualize import GradCAM model_2d = se_resnet50(spatial_dims=2, in_channels=3, num_classes=4) cam = GradCAM(nn_module=model_2d, target_layers="layer4") result = cam(x=torch.rand((2, 3, 48, 64)))
N.B.: To help select the target layer, it may be useful to list all layers:
for name, _ in model.named_modules(): print(name)
- compute_map(x, class_idx=None, retain_graph=False, layer_idx=- 1)[source]¶
Compute the actual feature map with input tensor x.
- Parameters
x – input to nn_module.
class_idx – index of the class to be visualized. Default to None (computing class_idx from argmax)
layer_idx – index of the target layer if there are multiple target layers. Defaults to -1.
- Returns
activation maps (raw outputs without upsampling/post-processing.)
- class monai.visualize.class_activation_maps.GradCAMpp(nn_module, target_layers, upsampler=<function default_upsampler>, postprocessing=<function default_normalizer>, register_backward=True)[source]¶
Computes Gradient-weighted Class Activation Mapping (Grad-CAM++). This implementation is based on:
Chattopadhyay et al., Grad-CAM++: Improved Visual Explanations for Deep Convolutional Networks, https://arxiv.org/abs/1710.11063
- compute_map(x, class_idx=None, retain_graph=False, layer_idx=- 1)[source]¶
Compute the actual feature map with input tensor x.
- Parameters
x – input to nn_module.
class_idx – index of the class to be visualized. Default to None (computing class_idx from argmax)
layer_idx – index of the target layer if there are multiple target layers. Defaults to -1.
- Returns
activation maps (raw outputs without upsampling/post-processing.)
- class monai.visualize.class_activation_maps.ModelWithHooks(nn_module, target_layer_names, register_forward=False, register_backward=False)[source]¶
A model wrapper to run model forward/backward steps and storing some intermediate feature/gradient information.
- Parameters
nn_module – the model to be wrapped.
target_layer_names (
Union
[str
,Sequence
[str
]]) – the names of the layer to cache.register_forward (
bool
) – whether to cache the forward pass output corresponding to target_layer_names.register_backward (
bool
) – whether to cache the backward pass output corresponding to target_layer_names.
- __init__(nn_module, target_layer_names, register_forward=False, register_backward=False)[source]¶
- Parameters
nn_module – the model to be wrapped.
target_layer_names (
Union
[str
,Sequence
[str
]]) – the names of the layer to cache.register_forward (
bool
) – whether to cache the forward pass output corresponding to target_layer_names.register_backward (
bool
) – whether to cache the backward pass output corresponding to target_layer_names.
- monai.visualize.class_activation_maps.default_normalizer(x)[source]¶
A linear intensity scaling by mapping the (min, max) to (1, 0). If the input data is PyTorch Tensor, the output data will be Tensor on the same device, otherwise, output data will be numpy array.
Note: This will flip magnitudes (i.e., smallest will become biggest and vice versa).
- Return type
~NdarrayTensor
Occlusion sensitivity¶
- class monai.visualize.occlusion_sensitivity.OcclusionSensitivity(nn_module, pad_val=None, mask_size=15, n_batch=128, stride=1, upsampler=functools.partial(<function default_upsampler>, align_corners=True), verbose=True)[source]¶
This class computes the occlusion sensitivity for a model’s prediction of a given image. By occlusion sensitivity, we mean how the probability of a given prediction changes as the occluded section of an image changes. This can be useful to understand why a network is making certain decisions.
As important parts of the image are occluded, the probability of classifying the image correctly will decrease. Hence, more negative values imply the corresponding occluded volume was more important in the decision process.
Two
torch.Tensor
will be returned by the__call__
method: an occlusion map and an image of the most probable class. Both images will be cropped if a bounding box used, but voxel sizes will always match the input.The occlusion map shows the inference probabilities when the corresponding part of the image is occluded. Hence, more -ve values imply that region was important in the decision process. The map will have shape
BCHW(D)N
, whereN
is the number of classes to be inferred by the network. Hence, the occlusion for classi
can be seen withmap[...,i]
.The most probable class is an image of the probable class when the corresponding part of the image is occluded (equivalent to
occ_map.argmax(dim=-1)
).See: R. R. Selvaraju et al. Grad-CAM: Visual Explanations from Deep Networks via Gradient-based Localization. https://doi.org/10.1109/ICCV.2017.74.
Examples:
# densenet 2d from monai.networks.nets import DenseNet121 from monai.visualize import OcclusionSensitivity model_2d = DenseNet121(spatial_dims=2, in_channels=1, out_channels=3) occ_sens = OcclusionSensitivity(nn_module=model_2d) occ_map, most_probable_class = occ_sens(x=torch.rand((1, 1, 48, 64)), b_box=[-1, -1, 2, 40, 1, 62]) # densenet 3d from monai.networks.nets import DenseNet from monai.visualize import OcclusionSensitivity model_3d = DenseNet(spatial_dims=3, in_channels=1, out_channels=3, init_features=2, growth_rate=2, block_config=(6,)) occ_sens = OcclusionSensitivity(nn_module=model_3d, n_batch=10, stride=3) occ_map, most_probable_class = occ_sens(torch.rand(1, 1, 6, 6, 6), b_box=[-1, -1, 1, 3, -1, -1, -1, -1])
See also
monai.visualize.occlusion_sensitivity.OcclusionSensitivity.
Occlusion sensitivity constructor.
- Parameters
nn_module (
Module
) – Classification model to use for inferencepad_val (
Optional
[float
]) – When occluding part of the image, which values should we put in the image? IfNone
is used, then the average of the image will be used.mask_size (
Union
[int
,Sequence
]) – Size of box to be occluded, centred on the central voxel. To ensure that the occluded area is correctly centred,mask_size
andstride
should both be odd or even.n_batch (
int
) – Number of images in a batch for inference.stride (
Union
[int
,Sequence
]) – Stride in spatial directions for performing occlusions. Can be single value or sequence (for varying stride in the different directions). Should be >= 1. Striding in the channel direction will always be 1.upsampler (
Optional
[Callable
]) – An upsampling method to upsample the output image. Default is N-dimensional linear (bilinear, trilinear, etc.) depending on num spatial dimensions of input.verbose (
bool
) – Usetqdm.trange
output (if available).
- __init__(nn_module, pad_val=None, mask_size=15, n_batch=128, stride=1, upsampler=functools.partial(<function default_upsampler>, align_corners=True), verbose=True)[source]¶
Occlusion sensitivity constructor.
- Parameters
nn_module (
Module
) – Classification model to use for inferencepad_val (
Optional
[float
]) – When occluding part of the image, which values should we put in the image? IfNone
is used, then the average of the image will be used.mask_size (
Union
[int
,Sequence
]) – Size of box to be occluded, centred on the central voxel. To ensure that the occluded area is correctly centred,mask_size
andstride
should both be odd or even.n_batch (
int
) – Number of images in a batch for inference.stride (
Union
[int
,Sequence
]) – Stride in spatial directions for performing occlusions. Can be single value or sequence (for varying stride in the different directions). Should be >= 1. Striding in the channel direction will always be 1.upsampler (
Optional
[Callable
]) – An upsampling method to upsample the output image. Default is N-dimensional linear (bilinear, trilinear, etc.) depending on num spatial dimensions of input.verbose (
bool
) – Usetqdm.trange
output (if available).