normalization_config
Pydantic models for normalization strategies.
MeanStdConfig #
Bases: BaseModel
Mean and standard deviation normalization configuration.
Holds mean and standard deviation statistics for input and target, used to normalize data. Each statistic can be a single float (applied globally to all channels) or a list of floats (one per channel). If not provided, statistics can be computed automatically.
Attributes:
| Name | Type | Description |
|---|---|---|
name | Literal['mean_std'] | Identifier for the mean-std normalization scheme. |
input_means | float | list[float] | None | Means for input normalization. None for automatic computation. |
input_stds | float | list[float] | None | Standard deviations for input normalization. None for automatic computation. |
target_means | float | list[float] | None | Means for target normalization. None for automatic computation. |
target_stds | float | list[float] | None | Standard deviations for target normalization. None for automatic computation. |
per_channel | bool | When True (default), statistics are computed independently for each channel. When False, a single statistic is computed across all channels. |
Source code in src/careamics/config/data/normalization_config.py
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needs_computation() #
Check if statistics need to be computed.
Returns:
| Type | Description |
|---|---|
bool | True if input statistics are missing, False otherwise. |
Source code in src/careamics/config/data/normalization_config.py
set_input_stats(means, stds) #
Set input means and stds together to avoid validation errors.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
means | list[float] | Mean values per channel. | required |
stds | list[float] | Standard deviation values per channel. | required |
Source code in src/careamics/config/data/normalization_config.py
set_target_stats(means, stds) #
Set target means and stds together to avoid validation errors.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
means | list[float] | Mean values per channel. | required |
stds | list[float] | Standard deviation values per channel. | required |
Source code in src/careamics/config/data/normalization_config.py
validate_global_stats_single_element(v, info) classmethod #
Validate stats length against the per_channel parameter.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
v | OptionalFloatStats | Value to validate. | required |
info | ValidationInfo | Validated values. | required |
Returns:
| Type | Description |
|---|---|
OptionalFloatStats | Validate value. |
Source code in src/careamics/config/data/normalization_config.py
validate_means_stds() #
Validate that means and stds are provided in pairs or set to None.
Returns:
| Type | Description |
|---|---|
Self | The validated model instance. |
Raises:
| Type | Description |
|---|---|
ValueError | If only one of means or stds is provided for input or target, or if paired lists have mismatched lengths. |
Source code in src/careamics/config/data/normalization_config.py
validate_size(n_input_channels, n_output_channels) #
Validate that statistics sizes match the number of channels.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
n_input_channels | int | The number of input channels to validate against. | required |
n_output_channels | int | The number of output channels to validate against. | required |
Raises:
| Type | Description |
|---|---|
ValueError | If any provided statistics list does not match the expected size. |
Source code in src/careamics/config/data/normalization_config.py
MinMaxConfig #
Bases: BaseModel
Min-max normalization configuration.
Stores minimum and maximum statistics for scaling data into a desired range. Each statistic can be a single float (applied globally to all channels) or a list of floats (one per channel). If not provided, statistics can be computed automatically.
Attributes:
| Name | Type | Description |
|---|---|---|
name | Literal['min_max'] | Identifier for min-max normalization. |
input_mins | float | list[float] | None | Minimum values for input normalization. None for automatic computation. |
input_maxes | float | list[float] | None | Maximum values for input normalization. None for automatic computation. |
target_mins | float | list[float] | None | Minimum values for target normalization. None for automatic computation. |
target_maxes | float | list[float] | None | Maximum values for target normalization. None for automatic computation. |
per_channel | bool | When True (default), statistics are computed independently for each channel. When False, a single statistic is computed across all channels. |
Source code in src/careamics/config/data/normalization_config.py
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needs_computation() #
Check if min/max values need to be computed.
Returns:
| Type | Description |
|---|---|
bool | True if input statistics are missing, False otherwise. |
Source code in src/careamics/config/data/normalization_config.py
set_input_range(mins, maxes) #
Set input mins and maxes together to avoid validation errors.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
mins | list[float] | Minimum values per channel. | required |
maxes | list[float] | Maximum values per channel. | required |
Source code in src/careamics/config/data/normalization_config.py
set_target_range(mins, maxes) #
Set target mins and maxes together to avoid validation errors.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
mins | list[float] | Minimum values per channel. | required |
maxes | list[float] | Maximum values per channel. | required |
Source code in src/careamics/config/data/normalization_config.py
validate_global_stats_single_element(v, info) classmethod #
Validate stats length against the per_channel parameter.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
v | OptionalFloatStats | Value to validate. | required |
info | ValidationInfo | Validated values. | required |
Returns:
| Type | Description |
|---|---|
OptionalFloatStats | Validate value. |
Source code in src/careamics/config/data/normalization_config.py
validate_mins_maxes() #
Validate that mins and maxes are provided in pairs or both None.
Returns:
| Type | Description |
|---|---|
Self | The validated model instance. |
Raises:
| Type | Description |
|---|---|
ValueError | If only one of mins or maxes is provided for input or target, or if paired lists have mismatched lengths. |
Source code in src/careamics/config/data/normalization_config.py
validate_size(n_input_channels, n_output_channels) #
Validate that statistics sizes match the number of channels.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
n_input_channels | int | The number of input channels to validate against. | required |
n_output_channels | int | The number of output channels to validate against. | required |
Raises:
| Type | Description |
|---|---|
ValueError | If any provided statistics list does not match the expected size. |
Source code in src/careamics/config/data/normalization_config.py
NoNormConfig #
Bases: BaseModel
No normalization configuration.
Indicates that no normalization should be applied.
Attributes:
| Name | Type | Description |
|---|---|---|
name | Literal['none'] | Identifier for no normalization scheme. |
Source code in src/careamics/config/data/normalization_config.py
needs_computation() #
Check if statistics need to be computed.
Returns:
| Type | Description |
|---|---|
bool | Always False, as no statistics are required. |
validate_size(*args, **kwargs) #
No validation needed.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
*args | Any | Parameters will be ignored. | () |
**kwargs | Any | Parameters will be ignored. | {} |
Source code in src/careamics/config/data/normalization_config.py
QuantileConfig #
Bases: BaseModel
Quantile normalization configuration.
Normalizes data using quantile-based range scaling. Quantile levels can be specified as a single value (applied to all channels) or a list (one per channel). If not provided, quantile values can be computed automatically.
Attributes:
| Name | Type | Description |
|---|---|---|
name | Literal['quantile'] | Identifier for quantile normalization. |
lower_quantiles | float | list[float] | Lower quantile level(s). Values must be in [0, 1). |
upper_quantiles | float | list[float] | Upper quantile level(s). Values must be in (0, 1]. |
input_lower_quantile_values | float | list[float] | None | Computed lower quantile values for input. |
input_upper_quantile_values | float | list[float] | None | Computed upper quantile values for input. |
target_lower_quantile_values | float | list[float] | None | Computed lower quantile values for target. |
target_upper_quantile_values | float | list[float] | None | Computed upper quantile values for target. |
per_channel | bool | When True (default), quantile values are computed independently for each channel. When False, a single quantile is computed across all channels. |
Source code in src/careamics/config/data/normalization_config.py
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needs_computation() #
Check if quantile values need to be computed.
Returns:
| Type | Description |
|---|---|
bool | True if quantile values need to be computed. |
Source code in src/careamics/config/data/normalization_config.py
set_input_quantile_values(lower, upper) #
Set input quantile values together to avoid validation errors.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
lower | list[float] | Lower quantile values per channel. | required |
upper | list[float] | Upper quantile values per channel. | required |
Source code in src/careamics/config/data/normalization_config.py
set_target_quantile_values(lower, upper) #
Set target quantile values together to avoid validation errors.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
lower | list[float] | Lower quantile values per channel. | required |
upper | list[float] | Upper quantile values per channel. | required |
Source code in src/careamics/config/data/normalization_config.py
validate_global_stats_single_element(v, info) classmethod #
Validate stats length against the per_channel parameter.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
v | OptionalFloatStats | Value to validate. | required |
info | ValidationInfo | Validated values. | required |
Returns:
| Type | Description |
|---|---|
OptionalFloatStats | Validate value. |
Source code in src/careamics/config/data/normalization_config.py
validate_quantile_levels() #
Validate quantile levels are in valid range and properly ordered.
Returns:
| Type | Description |
|---|---|
Self | The validated model instance. |
Source code in src/careamics/config/data/normalization_config.py
validate_quantile_values() #
Validate that computed quantile value lists are provided in pairs.
Returns:
| Type | Description |
|---|---|
Self | The validated model instance. |
Source code in src/careamics/config/data/normalization_config.py
validate_size(n_input_channels, n_output_channels) #
Validate that statistics sizes match the number of channels.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
n_input_channels | int | The number of input channels to validate against. | required |
n_output_channels | int | The number of output channels to validate against. | required |
Raises:
| Type | Description |
|---|---|
ValueError | If any provided statistics list does not match the expected size. |