monailabel.datastore.local module¶

class monailabel.datastore.local.DataModel(**data)[source]¶

Bases: pydantic.main.BaseModel

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

ext: str¶

info: Dict[str, Any]¶

model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}¶: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

model_config: ClassVar[ConfigDict] = {}¶: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'ext': FieldInfo(annotation=str, required=False, default=''), 'info': FieldInfo(annotation=Dict[str, Any], required=False, default={})}¶

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

class monailabel.datastore.local.ImageLabelModel(**data)[source]¶

Bases: pydantic.main.BaseModel

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

image: monailabel.datastore.local.DataModel¶

labels: Dict[str, monailabel.datastore.local.DataModel]¶

model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}¶: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

model_config: ClassVar[ConfigDict] = {}¶: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'image': FieldInfo(annotation=DataModel, required=True), 'labels': FieldInfo(annotation=Dict[str, monailabel.datastore.local.DataModel], required=False, default={})}¶

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

tags()[source]¶

class monailabel.datastore.local.LocalDatastore(datastore_path, images_dir='.', labels_dir='labels', datastore_config='datastore_v2.json', extensions=('*.nii.gz', '*.nii'), auto_reload=False, read_only=False)[source]¶

Bases: monailabel.interfaces.datastore.Datastore

Class to represent a datastore local to the MONAI-Label Server

`name

The name of the datastore

Type: str`

`description

The description of the datastore

Type: str`

Creates a LocalDataset object

Parameters:

datastore_path: str: a string to the directory tree of the desired dataset
datastore_config: str: optional file name of the dataset configuration file (by default dataset.json)

__init__(datastore_path, images_dir='.', labels_dir='labels', datastore_config='datastore_v2.json', extensions=('*.nii.gz', '*.nii'), auto_reload=False, read_only=False)[source]¶

Creates a LocalDataset object

Parameters:

datastore_path: str: a string to the directory tree of the desired dataset
datastore_config: str: optional file name of the dataset configuration file (by default dataset.json)

add_image(image_id, image_filename, image_info)[source]¶

Save a image for the given image id and return the newly saved image’s id

Parameters

image_id (str) – the image id for the image; If None then base filename will be used
image_filename (str) – the path to the image file
image_info (Dict[str, Any]) – additional info for the image

Return type

str

Returns

the image id for the saved image filename

datalist(full_path=True)[source]¶

Return a dictionary of image and label pairs corresponding to the ‘image’ and ‘label’ keys respectively

Return type: List[Dict[str, Any]]
Returns: the {‘label’: image, ‘label’: label} pairs for training

description()[source]¶

Gets the description field for the dataset

Return description: str
Return type: str

get_dataset_archive(limit_cases)[source]¶

Retrieve ZIP archive of the full dataset containing images, labels and metadata

Parameters: limit_cases (Optional[int]) – limit the included cases to this number
Return type: str
Returns: path to ZIP archive of the full dataset

get_image(image_id, params=None)[source]¶

Retrieve image object based on image id

Parameters

image_id (str) – the desired image’s id
params – any optional params

Return type

Any

Returns

return the “image”

get_image_info(image_id)[source]¶

Get the image information for the given image id

Parameters: image_id (str) – the desired image id
Return type: Dict[str, Any]
Returns: image info as a list of dictionaries Dict[str, Any]

get_image_uri(image_id)[source]¶

Retrieve image uri based on image id

Parameters: image_id (str) – the desired image’s id
Return type: str
Returns: return the image uri

get_label(label_id, label_tag, params=None)[source]¶

Retrieve image object based on label id

Parameters

label_id (str) – the desired label’s id
label_tag (str) – the matching label’s tag
params – any optional params

Return type

Any

Returns

return the “label”

get_label_by_image_id(image_id, tag)[source]¶

Retrieve label id for the given image id and tag

Parameters

image_id (str) – the desired image’s id
tag (str) – matching tag name

Return type

str

Returns

label id

get_label_info(label_id, label_tag)[source]¶

Get the label information for the given label id

Parameters

label_id (str) – the desired label id
label_tag (str) – the matching label tag

Return type

Dict[str, Any]

Returns

label info as a list of dictionaries Dict[str, Any]

get_label_uri(label_id, label_tag)[source]¶

Retrieve label uri based on image id

Parameters

label_id (str) – the desired label’s id
label_tag (str) – the matching label’s tag

Return type

str

Returns

return the label uri

get_labeled_images(label_tag=None, labels=None)[source]¶

Get all images that have a corresponding label

Return type: List[str]
Returns: list of image ids List[str]

get_labels_by_image_id(image_id)[source]¶

Retrieve all label ids for the given image id

Parameters: image_id (str) – the desired image’s id
Return type: Dict[str, str]
Returns: label ids mapped to the appropriate LabelTag as Dict[LabelTag, str]

get_unlabeled_images(label_tag=None, labels=None)[source]¶

Get all images that have no corresponding label

Return type: List[str]
Returns: list of image ids List[str]

json()[source]¶: Return json representation of datastore

list_images()[source]¶

Return list of image ids available in the datastore

Return type: List[str]
Returns: list of image ids List[str]

name()[source]¶

Dataset name (if one is assigned)

Returns: Dataset name as string
Return type: name (str)

refresh()[source]¶: Refresh the datastore based on the state of the files on disk

remove_image(image_id)[source]¶

Remove image for the datastore. This will also remove all associated labels.

Parameters: image_id (str) – the image id for the image to be removed from datastore
Return type: None

remove_label(label_id, label_tag)[source]¶

Remove label from the datastore

Parameters

label_id (str) – the label id for the label to be removed from datastore
label_tag (str) – the label tag for the label to be removed from datastore

Return type

None

save_label(image_id, label_filename, label_tag, label_info)[source]¶

Save a label for the given image id and return the newly saved label’s id

Parameters

image_id (str) – the image id for the label
label_filename (str) – the path to the label file
label_tag (str) – the tag for the label
label_info (Dict[str, Any]) – additional info for the label

Return type

str

Returns

the label id for the given label filename

set_description(description)[source]¶

Set a description for the dataset

Parameters: description (str) – str

set_name(name)[source]¶

Sets the dataset name in a standardized format (lowercase, no spaces).

Parameters:
name (str): Desired dataset name

status()[source]¶

Return current statistics of datastore

Return type: Dict[str, Any]

update_image_info(image_id, info)[source]¶

Update (or create a new) info tag for the desired image

Parameters

image_id (str) – the id of the image we want to add/update info
info (Dict[str, Any]) – a dictionary of custom image information Dict[str, Any]

Return type

None

update_label_info(label_id, label_tag, info)[source]¶

Update (or create a new) info tag for the desired label

Parameters

label_id (str) – the id of the label we want to add/update info
label_tag (str) – the matching label tag
info (Dict[str, Any]) – a dictionary of custom label information Dict[str, Any]

Return type

None

class monailabel.datastore.local.LocalDatastoreModel(**data)[source]¶

Bases: pydantic.main.BaseModel

Create a new model by parsing and validating input data from keyword arguments.

Raises [ValidationError][pydantic_core.ValidationError] if the input data cannot be validated to form a valid model.

self is explicitly positional-only to allow self as a field name.

base_path: str¶

description: str¶

filter_by_tag(tag)[source]¶

image_path()[source]¶

images_dir: str¶

label(id, tag)[source]¶

label_path(tag)[source]¶

labels_dir: str¶

labels_path()[source]¶

model_computed_fields: ClassVar[dict[str, ComputedFieldInfo]] = {}¶: A dictionary of computed field names and their corresponding ComputedFieldInfo objects.

model_config: ClassVar[ConfigDict] = {}¶: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].

model_fields: ClassVar[dict[str, FieldInfo]] = {'base_path': FieldInfo(annotation=str, required=False, default=''), 'description': FieldInfo(annotation=str, required=True), 'images_dir': FieldInfo(annotation=str, required=False, default=''), 'labels_dir': FieldInfo(annotation=str, required=False, default='labels'), 'name': FieldInfo(annotation=str, required=True), 'objects': FieldInfo(annotation=Dict[str, monailabel.datastore.local.ImageLabelModel], required=False, default={})}¶

Metadata about the fields defined on the model, mapping of field names to [FieldInfo][pydantic.fields.FieldInfo].

This replaces Model.__fields__ from Pydantic V1.

name: str¶

objects: Dict[str, monailabel.datastore.local.ImageLabelModel]¶

tags()[source]¶

monailabel.datastore.dsa module

monailabel.datastore.xnat module