ng_data_config
Data configuration.
CoordFilterConfig = Union[MaskFilterConfig] module-attribute #
Coordinate filter type.
Float = Annotated[float, PlainSerializer(np_float_to_scientific_str, return_type=str)] module-attribute #
Annotated float type, used to serialize floats to strings.
PatchFilterConfig = Union[MaxFilterConfig, MeanSTDFilterConfig, ShannonFilterConfig] module-attribute #
Patch filter type.
PatchingConfig = Union[FixedRandomPatchingConfig, RandomPatchingConfig, TiledPatchingConfig, WholePatchingConfig] module-attribute #
Patching strategy type.
Mode #
NGDataConfig #
Bases: BaseModel
Next-Generation Dataset configuration.
NGDataConfig are used for both training and prediction, with the patching strategy determining how the data is processed. Note that random is the only patching strategy compatible with training, while tiled and whole are only used for prediction.
If std is specified, mean must be specified as well. Note that setting the std first and then the mean (if they were both None before) will raise a validation error. Prefer instead set_means_and_stds to set both at once. Means and stds are expected to be lists of floats, one for each channel. For supervised tasks, the mean and std of the target could be different from the input data.
All supported transforms are defined in the SupportedTransform enum.
Source code in src/careamics/config/data/ng_data_config.py
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axes instance-attribute #
Axes of the data, as defined in SupportedAxes.
batch_size = Field(default=1, ge=1, validate_default=True) class-attribute instance-attribute #
Batch size for training.
channels = Field(default=None) class-attribute instance-attribute #
Channels to use from the data. If None, all channels are used.
coord_filter = Field(default=None, discriminator='name') class-attribute instance-attribute #
Coordinate filter to apply when using random patching. Only available if mode is training.
data_type instance-attribute #
Type of input data.
image_means = Field(default=None, min_length=0, max_length=32) class-attribute instance-attribute #
Means of the data across channels, used for normalization.
image_stds = Field(default=None, min_length=0, max_length=32) class-attribute instance-attribute #
Standard deviations of the data across channels, used for normalization.
in_memory = Field(default_factory=default_in_memory, validate_default=True) class-attribute instance-attribute #
Whether to load all data into memory. This is only supported for 'array', 'tiff' and 'custom' data types. Must be True for array. If None, defaults to True for 'array', 'tiff' and custom, and False for 'zarr' and 'czi' data types.
mode instance-attribute #
Dataset mode, either training, validating or predicting.
patch_filter = Field(default=None, discriminator='name') class-attribute instance-attribute #
Patch filter to apply when using random patching. Only available if mode is training.
patch_filter_patience = Field(default=5, ge=1) class-attribute instance-attribute #
Number of consecutive patches not passing the filter before accepting the next patch.
patching = Field(..., discriminator='name') class-attribute instance-attribute #
Patching strategy to use. Note that random is the only supported strategy for training, while tiled and whole are only used for prediction.
pred_dataloader_params = Field(default={}) class-attribute instance-attribute #
Dictionary of PyTorch prediction dataloader parameters.
seed = Field(default_factory=generate_random_seed, gt=0) class-attribute instance-attribute #
Random seed for reproducibility. If not specified, a random seed is generated.
target_means = Field(default=None, min_length=0, max_length=32) class-attribute instance-attribute #
Means of the target data across channels, used for normalization.
target_stds = Field(default=None, min_length=0, max_length=32) class-attribute instance-attribute #
Standard deviations of the target data across channels, used for normalization.
train_dataloader_params = Field(default={'shuffle': True}, validate_default=True) class-attribute instance-attribute #
Dictionary of PyTorch training dataloader parameters. The dataloader parameters, should include the shuffle key, which is set to True by default. We strongly recommend to keep it as True to ensure the best training results.
transforms = Field(default=(XYFlipConfig(), XYRandomRotate90Config()), validate_default=True) class-attribute instance-attribute #
List of transformations to apply to the data, available transforms are defined in SupportedTransform.
val_dataloader_params = Field(default={}) class-attribute instance-attribute #
Dictionary of PyTorch validation dataloader parameters.
__str__() #
Pretty string reprensenting the configuration.
Returns:
| Type | Description |
|---|---|
str | Pretty string. |
axes_valid(axes, info) classmethod #
Validate axes.
Axes must: - be a combination of 'STCZYX' - not contain duplicates - contain at least 2 contiguous axes: X and Y - contain at most 4 axes - not contain both S and T axes
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
axes | str | Axes to validate. | required |
info | ValidationInfo | Validation information. | required |
Returns:
| Type | Description |
|---|---|
str | Validated axes. |
Raises:
| Type | Description |
|---|---|
ValueError | If axes are not valid. |
Source code in src/careamics/config/data/ng_data_config.py
convert_mode(new_mode, new_patch_size=None, overlap_size=None, new_batch_size=None, new_data_type=None, new_axes=None, new_channels=None, new_in_memory=None, new_dataloader_params=None) #
Convert a training dataset configuration to a different mode.
This method is intended to facilitate creating validation or prediction configurations from a training configuration.
Switching mode to predicting without specifying new_patch_size and overlap_size will apply the default patching strategy, namely whole image strategy. overlap_size is only used when switching to predicting.
channels=None will retain the same channels as in the current configuration. To select all channels, please specify all channels explicitly or pass channels='all'.
New dataloader parameters will be placed in the appropriate dataloader params field depending on the new mode.
To create a new training configuration, please use careamics.config.create_ng_data_configuration.
This method compares the new parameters with the current ones and raises errors if incompatible changes are requested, such as switching between 2D and 3D axes, or changing the number of channels. Incompatibility across parameters may be delegated to Pydantic validation.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
new_mode | Literal['validating', 'predicting'] | The new dataset mode, one of | required |
new_patch_size | Sequence of int | New patch size. If None for | None |
overlap_size | Sequence of int | New overlap size. Necessary when switching to | None |
new_batch_size | int | New batch size. | None |
new_data_type | Literal['array', 'tiff', 'zarr', 'czi', 'custom'] | New data type. | None |
new_axes | str | New axes. | None |
new_channels | Sequence of int or "all" | New channels. | None |
new_in_memory | bool | New in_memory value. | None |
new_dataloader_params | dict of {str: Any} | New dataloader parameters. These will be placed in the appropriate dataloader params field depending on the new mode. | None |
Returns:
| Type | Description |
|---|---|
NGDataConfig | New NGDataConfig with the updated mode and parameters. |
Raises:
| Type | Description |
|---|---|
ValueError | If conversion to training mode is requested, or if incompatible changes are requested. |
Source code in src/careamics/config/data/ng_data_config.py
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propagate_seed_to_filters() #
Propagate the main seed to patch and coordinate filters that support seeds.
This ensures that all filters use the same seed for reproducibility, unless they already have a seed explicitly set.
Returns:
| Type | Description |
|---|---|
Self | Data model with propagated seeds. |
Source code in src/careamics/config/data/ng_data_config.py
propagate_seed_to_patching() #
Propagate the main seed to the patching strategy if it supports seeds.
This ensures that the patching strategy uses the same seed for reproducibility, unless it already has a seed explicitly set.
Returns:
| Type | Description |
|---|---|
Self | Data model with propagated seed. |
Source code in src/careamics/config/data/ng_data_config.py
propagate_seed_to_transforms() #
Propagate the main seed to all transforms that support seeds.
This ensures that all transforms use the same seed for reproducibility, unless they already have a seed explicitly set.
Returns:
| Type | Description |
|---|---|
Self | Data model with propagated seeds. |
Source code in src/careamics/config/data/ng_data_config.py
set_default_pin_memory(dataloader_params) classmethod #
Set default pin_memory for dataloader parameters if not provided.
- If 'pin_memory' is not set, it defaults to True if CUDA is available.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
dataloader_params | dict of {str: Any} | The dataloader parameters. | required |
Returns:
| Type | Description |
|---|---|
dict of {str: Any} | The dataloader parameters with pin_memory default applied. |
Source code in src/careamics/config/data/ng_data_config.py
set_default_train_workers(dataloader_params) classmethod #
Set default num_workers for training dataloader if not provided.
- If 'num_workers' is not set, it defaults to the number of available CPU cores.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
dataloader_params | dict of {str: Any} | The training dataloader parameters. | required |
Returns:
| Type | Description |
|---|---|
dict of {str: Any} | The dataloader parameters with num_workers default applied. |
Source code in src/careamics/config/data/ng_data_config.py
set_means_and_stds(image_means, image_stds, target_means=None, target_stds=None) #
Set mean and standard deviation of the data across channels.
This method should be used instead setting the fields directly, as it would otherwise trigger a validation error.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
image_means | (ndarray, tuple or list) | Mean values for normalization. | required |
image_stds | (ndarray, tuple or list) | Standard deviation values for normalization. | required |
target_means | (ndarray, tuple or list) | Target mean values for normalization, by default (). | None |
target_stds | (ndarray, tuple or list) | Target standard deviation values for normalization, by default (). | None |
Source code in src/careamics/config/data/ng_data_config.py
set_val_workers_to_match_train() #
Set validation dataloader num_workers to match training dataloader.
If num_workers is not specified in val_dataloader_params, it will be set to the same value as train_dataloader_params["num_workers"].
Returns:
| Type | Description |
|---|---|
Self | Validated data model with synchronized num_workers. |
Source code in src/careamics/config/data/ng_data_config.py
shuffle_train_dataloader(train_dataloader_params) classmethod #
Validate that "shuffle" is included in the training dataloader params.
A warning will be raised if shuffle=False.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
train_dataloader_params | dict of {str: Any} | The training dataloader parameters. | required |
Returns:
| Type | Description |
|---|---|
dict of {str: Any} | The validated training dataloader parameters. |
Raises:
| Type | Description |
|---|---|
ValueError | If "shuffle" is not included in the training dataloader params. |
Source code in src/careamics/config/data/ng_data_config.py
std_only_with_mean() #
Check that mean and std are either both None, or both specified.
Returns:
| Type | Description |
|---|---|
Self | Validated data model. |
Raises:
| Type | Description |
|---|---|
ValueError | If std is not None and mean is None. |
Source code in src/careamics/config/data/ng_data_config.py
validate_channels(channels, info) classmethod #
Validate channels.
Channels must be a sequence of non-negative integers without duplicates. If channels are not None, then C must be present in the axes.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
channels | Sequence of int or None | Channels to validate. | required |
info | ValidationInfo | Validation information. | required |
Returns:
| Type | Description |
|---|---|
Sequence of int or None | Validated channels. |
Raises:
| Type | Description |
|---|---|
ValueError | If channels are not valid. |
Source code in src/careamics/config/data/ng_data_config.py
validate_dimensions() #
Validate 2D/3D dimensions between axes and patch size.
Returns:
| Type | Description |
|---|---|
Self | Validated data model. |
Raises:
| Type | Description |
|---|---|
ValueError | If the patch size dimension is not compatible with the axes. |
Source code in src/careamics/config/data/ng_data_config.py
validate_filters_against_mode(filter_obj, info) classmethod #
Validate that the filters are only used during training.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
filter_obj | PatchFilters or CoordFilters or None | Filter to validate. | required |
info | ValidationInfo | Validation information. | required |
Returns:
| Type | Description |
|---|---|
PatchFilters or CoordFilters or None | Validated filter. |
Raises:
| Type | Description |
|---|---|
ValueError | If a filter is used in a mode other than training. |
Source code in src/careamics/config/data/ng_data_config.py
validate_in_memory_with_data_type(in_memory, info) classmethod #
Validate that in_memory is compatible with data_type.
in_memory can only be True for 'array', 'tiff' and 'custom' data types.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
in_memory | bool | Whether to load data into memory. | required |
info | Any | Additional information about the field being validated. | required |
Returns:
| Type | Description |
|---|---|
bool | Validated in_memory value. |
Raises:
| Type | Description |
|---|---|
ValueError | If in_memory is True for unsupported data types. |
Source code in src/careamics/config/data/ng_data_config.py
validate_patching_strategy_against_mode(patching, info) classmethod #
Validate that the patching strategy is compatible with the dataset mode.
- If mode is
training, patching strategy must berandom. - If mode is
validating, patching must befixed_random. - If mode is
predicting, patching strategy must betiledorwhole.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
patching | PatchingStrategies | Patching strategy to validate. | required |
info | ValidationInfo | Validation information. | required |
Returns:
| Type | Description |
|---|---|
PatchingStrategies | Validated patching strategy. |
Raises:
| Type | Description |
|---|---|
ValueError | If the patching strategy is not compatible with the dataset mode. |
Source code in src/careamics/config/data/ng_data_config.py
default_in_memory(validated_params) #
Default factory for the in_memory field.
Based on the value of data_type, set the default for in_memory to True if the data type is 'array', 'tiff', or 'custom', and to False otherwise (zarr or 'czi').
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
validated_params | dict of {str: Any} | Validated parameters. | required |
Returns:
| Type | Description |
|---|---|
bool | Default value for the |
Source code in src/careamics/config/data/ng_data_config.py
generate_random_seed() #
Generate a random seed for reproducibility.
Returns:
| Type | Description |
|---|---|
int | A random integer between 1 and 2^31 - 1. |
np_float_to_scientific_str(x) #
Return a string scientific representation of a float.
In particular, this method is used to serialize floats to strings, allowing numpy.float32 to be passed in the Pydantic model and written to a yaml file as str.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
x | float | Input value. | required |
Returns:
| Type | Description |
|---|---|
str | Scientific string representation of the input value. |