Configuration file

The config folder presents a few examples of configuration files for NiftyNet applications.

This page describes commands and configurations supported by NiftyNet.

Overview

In general, a NiftyNet workflow can be fully specified by a NiftyNet application and a configuration file. The command to run the workflow is:

# command to run from git-cloned NiftyNet source code folder
python net_run.py [train|inference|evaluation] -c <path_to/config.ini> -a <application>

or:

# command to run using pip-installed NiftyNet
net_run [train|inference|evaluation] -c <path_to/config.ini> -a <application>

net_run is the entry point of NiftyNet, followed by an action argument of either train or inference:

  • train indicates updating the underlying network model using provided data.
  • inference indicates loading existing network model and generating responses according to data provided.

The <application> argument

<application> should be specified in the form of user.path.python.module.MyApplication, NiftyNet will try to import the class named MyApplication implemented in user/path/python/module.py.

A few applications are already included in NiftyNet, and can be passed as an argument of -a. Aliases are also created for these application (full specification can be found here: SUPPORTED_APP): The commands include:

# command
net_run -a niftynet.application.segmentation_application.SegmentationApplication -c ...
# alias:
net_segment -c ...
# command
net_run -a niftynet.application.regression_application.RegressionApplication -c ...
# alias:
net_regress -c ...
# command
net_run -a niftynet.application.autoencoder_application.AutoencoderApplication -c ...
# alias:
net_autoencoder -c ...
# command
net_run -a niftynet.application.gan_application.GANApplication -c ...
# alias:
net_gan -c ...

Overriding the arguments

In the case of quickly adjusting only a few options in the configuration file, creating a separate file is sometimes tedious.

To make it more accessible, net_run command also accepts parameters specification in the form of --<name> <value> or --<name>=<value>. When these are used, value will override the corresponding value of name defined both by system default and configuration file.

The following sections describes content of a configuration file <path_to/config.ini>.

Configuration sections

The configuration file currently adopts the INI file format, and is parsed by configparser. The file consists of multiple sections of name=value elements.

All files should have at least these two sections:

If train action is specified, then a [TRAINING] section is required.

If inference action is specified, then an [INFERENCE] section is required.

Additionally, an application specific section is required for each application (please find further comments on creating customised parsers here):

  • [GAN] for generative adversarial networks
  • [SEGMENTATION] for segmentation networks
  • [REGRESSION] for regression networks
  • [AUTOENCODER] for autoencoder networks

The user parameter parser tries to match the section names listed above. All other section names will be treated as input data source specifications.

The following sections specify parameters (<name> = <value> pairs) available within each section.

Input data source section

This section will be used by ImageReader to generate a list of input images objects. For example, the section

[T1Image]
path_to_search = ./example_volumes/image_folder
filename_contains = T1, subject
filename_not_contains = T1c, T2
spatial_window_size = 128, 128, 1
pixdim = 1.0, 1.0, 1.0
axcodes = A, R, S
interp_order = 3

specifies a set of images (currently supports NIfTI format via NiBabel library) from ./example_volumes/image_folder, with filenames containing both T1 and subject, but not T1c and T2. These images will be read into memory and transformed into “A, R, S” orientation (using NiBabel). The images will also be transformed to have voxel size (1.0, 1.0, 1.0) with an interpolation order of 3.

A CSV file with the matched filenames and extracted subject names will be generated to T1Image.csv in model_dir (by default; the CSV file location can be specified by setting csv_file). To exclude particular images, the csv_file can be edited manually.

This input source can be used alone, as a monomodal input to an application. Additional modalities can be used, as shown in this example.

The input filename matching guide is useful to understand how files are matched.

Name Type Example Default
csv_file string csv_file=file_list.csv ''
path_to_search string path_to_search=my_data/fold_1 NiftyNet home folder
filename_contains string or string array filename_contains=foo, bar ''
filename_not_contains string or string array filename_not_contains=foo ''
filename_removefromid string filename_removefromid=bar ''
interp_order integer interp_order=0 3
pixdim float array pixdim=1.2, 1.2, 1.2 ''
axcodes string array axcodes=L, P, S ''
spatial_window_size integer array spatial_window_size=64, 64, 64 ''
loader string loader=simpleitk None

csv_file

Path to a CSV file containing a list of input images:

image_id_0,/path/to/image_0.nii.gz
image_id_4,/path/to/image_4.nii.gz
image_id_9,/path/to/image_9.nii.gz

If the CSV file exists, the input image name list will be loaded from the file. The filename-based image search will be disabled and the parameters path_to_search, filename_contains, filename_not_contains, and filename_removefromid will be ignored. If this parameter is left blank or the file does not exist, input image search will be enabled, and the matched filenames will be written to this file path.

filename_contains

Keywords used to match filenames. The matched keywords will be removed, and the remaining part is used as subject name (for loading corresponding images across modalities). Note that if the type pf filename_contains is a string array, then a filename has to contain every string in the array to be a match.

See also: input filename matching guide

filename_not_contains

Keywords used to exclude filenames. The filenames with these keywords will not be used as input. Note that if the type of filename_not_contains is a string array, then a filename must not contain any of the strings in the array to be a match.

See also: input filename matching guide

filename_removefromid

Regular expression for extracting subject id from filename, matched pattern will be removed from the file names to form the subject id.

See also: input filename matching guide

interp_order

Interpolation order of the input data. Note that only the following values are supported.

  • 0: nearest neighbour with sitk.sitkNearestNeighbor
  • 1: linear interpolation with sitk.sitkLinear
  • 2 and above: B-spline interpolation with sitk.sitkBSpline
  • negative values: returns original image

B-spline interpolation produces the best results, but it’s slower than linear or nearest neighbour. Linear interpolation is usually a good compromise between speed and quality.

This SimpleITK notebook shows some interpolation examples.

pixdim

If specified, the input volume will be resampled to the voxel sizes before fed into the network.

axcodes

If specified, the input volume will be reoriented to the axes codes before fed into the network. This is useful if the input images have different orientations.

The impact on performance is minimal, so it’s a good idea to set this parameter in order to force the reorientation to, for example, R, A, S. More information about NIfTI orientation can be found on 3D Slicer or NiBabel docs.

spatial_window_size

Array of three integers specifying the input window size. Setting it to single slice, e.g., spatial_window_size=64, 64, 1, yields a 2-D slice window.

See also: Patch-based analysis guide and U-Net window shape tutorial

loader

Specify the loader to be used to load the files in the input section. Some loaders require additional Python packages. Supported loaders: nibabel, opencv, skimage, pillow, simpleitk, dummy in priority order. Default value None indicates trying all available loaders, in the above priority order.

SYSTEM

Name Type Example Default
cuda_devices integer or integer array cuda_devices=0,1,2 ''
num_threads positive integer num_threads=1 2
num_gpus integer num_gpus=4 1
model_dir string model_dir=/User/test_dir The directory of the config file
dataset_split_file string dataset_split_file=/User/my_test ./dataset_split_file.csv
event_handler string or a list of strings event_handler=model_restorer model_saver, model_restorer, sampler_threading, apply_gradients, output_interpreter, console_logger, tensorboard_logger

cuda_devices

Sets the environment variable CUDA_VISIBLE_DEVICES, e.g. 0,2,3 uses devices 0, 2, 3 and device 1 is masked.

num_threads

Sets number of preprocessing threads for training.

num_gpus

Sets number of training GPUs. The value should be the number of available GPUs at most. This option is ignored if there’s no GPU device.

model_dir

Directory to save/load intermediate training models and logs. NiftyNet tries to interpret this parameter as an absolute system path or a path relative to the current command. It defaults to the directory of the current configuration file if left blank.

If running inference, it is assumed that model_dir contains two folders named models and logs.

dataset_split_file

Path to a CSV file assigning subjects to training/validation/inference subsets:

subject_001,training
subject_021,training
subject_027,training
subject_029,validation
subject_429,validation
subject_002,inference

If the string is a relative path, NiftyNet interprets this as relative to model_dir.

event_handler

Event handler functions registered to these signals will be called by the engine, along with NiftyNet application properties and iteration messages as function parameters. See Signals and event handlers for more details.

NETWORK

Name Type Example Default
name string name=niftynet.network.toynet.ToyNet ''
activation_function string activation_function=prelu relu
batch_size integer batch_size=10 2
smaller_final_batch_mode string pad
decay non-negative float decay=1e-5 0.0
reg_type string reg_type=L1 L2
volume_padding_size integer array volume_padding_size=4, 4, 4 0,0,0
volume_padding_mode string volume_padding_mode=symmetric minimum
window_sampling string window_sampling=uniform uniform
force_output_identity_resizing boolean force_output_identity_resizing=True False
queue_length integer queue_length=10 5
keep_prob non-negative float keep_prob=0.2 1.0

name

A network class from niftynet/network or from a user-specified module string. NiftyNet tries to import this string as a module specification. For example, setting it to niftynet.network.toynet.ToyNet will import the ToyNet class defined in niftynet/network/toynet.py (the relevant module path must be a valid Python path). There are also some shortcuts for NiftyNet’s default network modules defined in [SUPPORTED_NETWORK].

activation_function

Sets the type of activation function of the network layers. Available choices are listed in SUPPORTED_OP in activation layer. Depending on the implementation, the network might ignore this option.

batch_size

Number of image windows to be processed at each iteration. When num_gpus is greater than 1, batch_size is used for each GPU. That is, the effective inputs at each iteration become batch_size x num_gpus.

See the interactive buffer animation to simulate the effect of modifying this parameter.

smaller_final_batch_mode

When the total number of window samples is not divisible by batch_size the class supports different modes for the final batch:

  • drop: drop the remainder batch
  • pad: padding the final smaller batch with -1
  • dynamic: output the remainder directly (in this case the batch_size is undetermined at “compile time”)

reg_type

Type of regularisation for trainable parameters. Currently the available choices are L1 (Lasso regression) and L2 (ridge regression or weight decay). The regularisation looks like this:

J' = J + λ * 1/2 * sum(w ** n)

where J is the loss, J' is the regularised loss, λ is the decay parameter, w is an array containing all the trainable parameters and n defines the regularisation type (1 for L1, 2 for L2).

This option will be ignored if decay is 0.

The loss will be added to the tf.GraphKeys.REGULARIZATION_LOSSES collection.

decay

Weight decay factor λ, see reg_type. A largest value means stronger regularisation, used to prevent overfitting.

volume_padding_size

Number of voxels padded at image volume level (before window sampling). The padding effect is equivalent to numpy.pad with:

i, j, k = volume_padding_size
numpy.pad(
    input_volume,
    (i, j, k, 0, 0),
    mode='minimum',
)

For 2D inputs, the third dimension of volume_padding_size should be set to 0, e.g. volume_padding_size=M,N,0.

For 3D inputs, setting volume_padding_size=M is equivalent to volume_padding_size=M,M,M. The same amount of padding will be removed before writing the output volume.

See also: Patch-based analysis guide

volume_padding_mode

Set which type of numpy padding to do, see numpy.pad for details.

window_sampling

Type of sampler used to generate image windows from each image volume:

  • uniform: fixed size uniformly distributed,
  • weighted: fixed size where the likelihood of sampling a voxel is proportional to the cumulative intensity histogram on the sampling prior,
  • balanced: fixed size where each label in the sampling prior has the same probability of being sampled,
  • resize: resize image to the window size.

For weighted and balanced, an input section is required to load sampling priors. In the sampling demo the sampler parameter is set to label, indicating that the sampler uses the label section as the sampling prior.

See also: Patch-based analysis guide

force_output_identity_resizing

Boolean to prevent the inferred output from being resized up to input image shape during regression tasks when the resize sampler is used. An example use case is regression of a single value from an input image, where the inferred output should not be resized to image shape.

queue_length

Size of the buffer used when sampling image windows from image volumes. Image window samplers fill the buffer and networks read the buffer. Because the network reads batch_size windows at each iteration, this value is set to at least 5 * batch_size to allow for a possible randomised buffer, i.e.

queue_length = max(queue_length, batch_size * 5)

A longer queue increases the probability of windows in a batch coming from different input volumes, but it will take longer to fill and consume more memory.

You can use this interactive animation to simulate the effect of modifying the parameters related to the buffer:

keep_prob

The probability that each unit is kept if dropout is supported by the network. The default value is 0.5, meaning randomly dropout at the ratio of 0.5. This is also used as a default value at inference stage.

To achieve a deterministic inference, set keep_prob=1; to draw stochastic samples at inferece, set keep_prob to a value between 0 and 1.

In the case of drawing multiple Monte Carlo samples, the user can run the inference command mutiple times, with each time a different save_seg_dir, for example:

python net_segment.py inference ... --save_seg_dir run_2 --keep_prob 0.5.

Volume-normalisation

Intensity based volume normalisation can be configured using a combination of parameters described below:

(1) Setting normalisation=True enables the histogram-based standardisation as described by Nyúl et al., 2000. The relevant configuration parameters are:

histogram_ref_file, norm_type, cutoff, normalise_foreground_only, foreground_type, multimod_foreground_type.

If normalisation=False, these parameters are ignored and histogram-based normalisation is disabled.

(2) Setting whitening=True enables the volume level normalisation computed by (I - mean(I))/std(I), i.e. the volume is set to have zero-mean and unit variance. The relevant configuration parameters are:

normalise_foreground_only, foreground_type, multimod_foreground_type.

If whitening=False, these parameters are ignored and whitening is disabled.

(3) Setting rgb_normalisation=True enables RGB histogram equalisation. It requires OpenCV (opencv-python) and only supports 2D images. Unlike normalisation, it does not use histogram landmarks or files.

More specifically:

Name Type Example Default
normalisation boolean normalisation=True False
whitening boolean whitening=True False
rgb_normalisation boolean rgb_normalisation=True False
histogram_ref_file string histogram_ref_file=./hist_ref.txt ''
norm_type string norm_type=percentile percentile
cutoff float array (two elements) cutoff=0.1, 0.9 0.01, 0.99
normalise_foreground_only boolean normalise_foreground_only=True False
foreground_type string foreground_type=otsu_plus otsu_plus
multimod_foreground_type string multimod_foreground_type=and and
normalisation

Boolean indicates if histogram standardisation (as described in Nyúl et al., 2000) should be applied to the data.

whitening

Boolean to indicate if the loaded image should be whitened, that is, given input image I, returns (I - mean(I))/std(I).

rgb_normalisation

Boolean to indicate if an RGB histogram equalisation should be applied to the data.

histogram_ref_file

Name of the file that contains the standardisation parameters if it has been trained before or where to save it.

norm_type

Type of histogram landmarks used in histogram-based standardisation (percentile or quartile).

cutoff

Inferior and superior cutoff in histogram-based standardisation.

normalise_foreground_only

Boolean to indicate if a mask should be computed based on foreground_type and multimod_foreground_type. If this parameter is set to True, all normalisation steps will be applied to the generated foreground regions only.

foreground_type

To generate a foreground mask and the normalisation will be applied to foreground only. Available choices:

otsu_plus, otsu_minus, thresh_plus, thresh_minus, mean_plus.
multimod_foreground_type

Strategies applied to combine foreground masks of multiple modalities, can take one of the following:

  • or union of the available masks,
  • and intersection of the available masks,
  • all masks computed from each modality independently.

TRAINING

Name Type Example Default
optimiser string optimiser=momentum adam
sample_per_volume positive integer sample_per_volume=5 1
lr float lr=0.001 0.1
loss_type string loss_type=CrossEntropy Dice
starting_iter integer starting_iter=0 0
save_every_n integer save_every_n=5 500
tensorboard_every_n integer tensorboard_every_n=5 20
max_iter integer max_iter=1000 10000
max_checkpoints integer max_checkpoints=5 100
vars_to_restore string vars_to_restore=^.*(conv_1|conv_2).*$ ''
vars_to_freeze string vars_to_freeze=^.*(conv_3|conv_4).*$ value of vars_to_restore

optimiser

Type of optimiser for computing graph gradients. Current available options are defined here in SUPPORTED_OPTIMIZERS.

sample_per_volume

Number of samples to take from each image volume when filling the queue.

See the interactive buffer animation to simulate the effect of modifying this parameter.

lr

The learning rate for the optimiser.

loss_type

Type of loss function. Please see the relevant loss function layer for available choices:

The corresponding loss function type names are defined in the ApplicationFactory.

starting_iter

The iteration from which to resume training the model. Setting starting_iter=0 starts the network from random initialisations. Setting starting_iter=-1 starts the network from the latest checkpoint if it exists.

save_every_n

Frequency of saving the current training model saving. Setting it to 0 disables the saving schedule (the last model will always be saved when quitting the training loop).

tensorboard_every_n

Frequency of evaluating graph elements and writing to tensorboard. Setting it to 0 disables the tensorboard writing schedule.

max_iter

Maximum number of training iterations. Setting both starting_iter and max_iter to 0 can be used to save the random model initialisation.

max_checkpoints

Maximum number of checkpoints to save.

vars_to_restore

Regular expression string to match variable names that will be initialised from a checkpoint file.

See also: guide for finetuning pre-trained networks

vars_to_freeze

Regular expression string to match variable names that will be updated during training. Defaults to the value of vars_to_restore.

See also: guide for finetuning pre-trained networks

Validation during training

Setting validation_every_n to a positive integer enables validation loops during training. When validation is enabled, images list (defined by input specifications) will be treated as the whole dataset, and partitioned into subsets of training, validation, and inference according to exclude_fraction_for_validation and exclude_fraction_for_inference.

A CSV table randomly mapping each file name to one of the stages {'Training', 'Validation', 'Inference'} will be generated and written to dataset_split_file. This file will be created at the beginning of training (starting_iter=0) only if the file does not exist.

To exclude specific subjects or adjust the randomly generated partition, the dataset_split_file can be edited manually. Please note duplicated rows are not removed. For example, if the content of dataset_split_file is as follows:

1040,Training
1071,Inference
1071,Inference
1065,Training
1065,Training
1065,Validation

Each row will be treated as an independent subject. This means that:

Subject 1065 will be used in both Training and Validation stages, and it will be sampled more frequently than subject 1040 during training.
Subject 1071 will be used twice in Inference, and the output of the second inference will overwrite the first.

Note that at each validation iteration, input will be sampled from the set of validation data, and the network parameters will remain unchanged.

The is_training parameter of the network is set to True during validation. As a result, layers with different behaviours in training and inference (such as dropout and batch normalisation) use the training behaviour.

During inference, if a dataset_split_file is available, only image files in the Inference phase will be used, otherwise inference will process all image files defined by input specifications.

Name Type Example Default
validation_every_n integer validation_every_n=10 -1
validation_max_iter integer validation_max_iter=5 1
exclude_fraction_for_validation float exclude_fraction_for_validation=0.2 0.0
exclude_fraction_for_inference float exclude_fraction_for_inference=0.1 0.0
validation_every_n

Run validation iterations after every N training iterations. Setting it to 0 disables the validation.

validation_max_iter

Number of validation iterations to run. This parameter is ignored if validation_every_n is not a positive integer.

exclude_fraction_for_validation

Fraction of dataset to use for validation. Value should be in [0, 1].

exclude_fraction_for_inference

Fraction of dataset to use for inference. Value should be in [0, 1].

Data augmentation during training

Name Type Example Default
rotation_angle float array rotation_angle=-10.0,10.0 ''
scaling_percentage float array scaling_percentage=-20.0,20.0 ''
antialiasing boolean antialiasing=True True
isotropic_scaling boolean isotropic_scaling=True False
random_flipping_axes integer array random_flipping_axes=1,2 -1
do_elastic_deformation boolean do_elastic_deformation=True False
num_ctrl_points integer num_ctrl_points=1 4
deformation_sigma float deformation_sigma=1 15
proportion_to_deform float proportion_to_deform=0.7 0.5
bias_field_range float array bias_field_range=-10.0,10.0 ''
bf_order integer bf_order=1 3
rotation_angle

Interval of rotation degrees to apply a random rotation to the volumes. A different random value is compueted for each rotation axis.

This processing can be slow depending on the input volume size and dimensionality.

scaling_percentage

Interval of percentages relative to 100 to apply a random spatial scaling to the volumes. For example, setting this parameter to (-50, 50) might transform a volume with size 100, 100, 100 to 140, 88, 109.

When random scaling is enabled, it is possible to further specify:

  • antialiasing: indicating if Gaussian filtering should be performed when randomly downsampling the input images.
  • isotropic_scaling: indicating if the same amount of scaling should be applied in each dimension. If this option is set to False, a different random value will be computed for each volume axis.

This processing can be slow depending on the input volume size and dimensionality.

random_flipping_axes

Axes which can be flipped to augment the data.

For example, to randomly flip the first and third axes, use random_flipping_axes = 0, 2

do_elastic_deformation

Boolean value to indicate if data augmentation using elastic deformations should be performed.

When do_elastic_deformation=True, it is possible to further specify:

  • num_ctrl_points: number of control points for the elastic deformation,
  • deformation_sigma: the standard deviation for the elastic deformation,
  • proportion_to_deform: what fraction of samples to deform elastically.

See an example of elastic deformations for data augmentation on the U-Net demo.

bias_field_range

Float array indicating whether to perform data augmentation with randomised bias field.

When bias_field_range is not None, it is possible to further specify:

  • bf_order: maximal polynomial order to use for the bias field augmentation.

INFERENCE

Name Type Example Default
spatial_window_size integer array spatial_window_size=64,64,64 ''
border integer array border=5,5,5 0, 0, 0
inference_iter integer inference_iter=1000 -1
save_seg_dir string save_seg_dir=output/test output
output_postfix string output_postfix=_output _niftynet_out
output_interp_order non-negative integer output_interp_order=0 0
dataset_to_infer string dataset_to_infer=training ''
fill_constant float fill_constant=1.0 0.0

spatial_window_size

Array of integers indicating the size of input window. By default, the window size at inference time is the same as the input source specification. If this parameter is specified, it overrides the spatial_window_size parameter in input source sections.

See also: Patch-based analysis guide

border

Tuple of integers specifying a border size used to crop (along both sides of each dimension) the network output image window. E.g., 3, 3, 3 will crop a 64x64x64 window to size 58x58x58.

See also: Patch-based analysis guide

inference_iter

Integer specifies the trained model to be used for inference. If set to -1 or unspecified, the latest available trained model in model_dir will be used.

save_seg_dir

Prediction directory name. If it’s a relative path, it is set to be relative to model_dir.

output_postfix

Postfix appended to every inference output filenames.

output_interp_order

Interpolation order of the network outputs.

dataset_to_infer

String to specify which dataset (all, training, validation or inference) to compute inference for. By default inference dataset is used. If no dataset_split_file is specified, then all data specified in the CSV or search path are used for inference.

fill_constant

Value used to fill borders of output images.

EVALUATION

For evaluation of the output of an application against some available ground truth, an EVALUATION section must be present. Examples of evaluation config files are available in the config folder with the suffix _eval.ini.

The evaluation command is:

# command to run from git-cloned NiftyNet source code folder
python net_run.py evaluation -c <path_to/config.ini> -a <application>

(For example, multimodal segmentation evaluation could be: python net_run.py evaluation -a niftynet.applications.segmentation_application.SegmentationApplication -c config/default_multimodal_segmentation_eval.ini)

In order to run the evaluation, the input sources section must contain the details on

  • The ground truth against which to compare (label in case of the segmentation)
  • The corresponding files to evaluate (inferred)

The final evaluation file is saved in the folder indicated as input of the field model_dir in the section [SYSTEM] under the form of a csv file with indication of subject id (label if relevant) and the calculated metrics as columns.

The evaluation configuration section ([EVALUATION]) must contain:

Note that application specific configuration (such as evaluation_units) are specified in the application configuration section (such as [SEGMENTATION]).