Mask3D¶

class Mask3D[source]¶

Bases: supervisely.geometry.geometry.Geometry

Mask 3D geometry for a single Label. Mask3D object is immutable.

Parameters

data : np.ndarray

Mask 3D mask data. Must be a numpy array with only 2 unique values: [0, 1] or [0, 255] or [False, True].

sly_id : int, optional

Mask 3D ID in Supervisely server.

class_id : int, optional

ID of ObjClass to which Mask 3D belongs.

labeler_login : str, optional

Login of the user who created Mask 3D.

updated_at : str, optional

Date and Time when Mask 3D was modified last. Date Format: Year:Month:Day:Hour:Minute:Seconds. Example: ‘2021-01-22T19:37:50.158Z’.

created_at : str, optional

Date and Time when Mask 3D was created. Date Format is the same as in “updated_at” parameter.

Raises

ValueError, if data is not bool or no pixels set to True in data

Usage example

import supervisely as sly

# Create simple Mask 3D
mask3d = np.zeros((3, 3, 3), dtype=np.bool_)
mask3d[0:2, 0:2, 0:2] = True

shape = sly.Mask3D(mask3d)

print(shape.data)
# Output:
#    [[[ True  True False]
#      [ True  True False]
#      [False False False]]

#     [[ True  True False]
#      [ True  True False]
#      [False False False]]

#     [[False False False]
#      [False False False]
#      [False False False]]]

Methods

add_mask_2d	Draw a 2D mask on a 3D Mask.
allowed_transforms
base64_2_data	Convert base64 encoded string to numpy array.
clone	Clone from GEOMETRYYY
config_from_json
config_to_json
convert
create_from_file	Creates Mask3D geometry from file.
crop	param rect Rectangle
data_2_base64	Convert numpy array to base64 encoded string.
draw	param bitmap np.ndarray
draw_contour	Draws the figure contour on a given bitmap canvas :param bitmap: np.ndarray :param color: [R, G, B] :param thickness: (int) :param config: drawing config specific to a concrete subclass, e.g.
fliplr	param img_size (rows, cols)
flipud	param img_size (rows, cols)
from_bytes	Create a Mask3D geometry object from bytes.
from_file	Load figure geometry from file.
from_json	Convert a json dict to Mask 3D.
geometry_name	Return geometry name
get_mask	Returns 2D boolean mask of the geometry.
name	Same as geometry_name(), but shorter.
relative_crop	Crops object like "crop" method, but return results with coordinates relative to rect :param rect: :return: list of Geometry
resize	param in_size (rows, cols)
rotate	Rotates around image center -> New Geometry :param rotator: ImageRotator :return: Geometry
scale	Scales around origin with a given factor.
to_bbox	rtype Rectangle
to_json	Convert the Mask 3D to a json dict.
translate	param drow int rows shift
validate

Attributes

area	return float

add_mask_2d(mask_2d, plane_name, slice_index, origin=None)[source]¶

Draw a 2D mask on a 3D Mask.

Parameters

mask_2d : np.ndarray

2D array with a flat mask.

plane_name : str

Name of the plane: “axial”, “sagittal”, “coronal”.

slice_index : int

Slice index of the volume figure.

origin : Optional[List[int]], NoneType

(row, col) position. The top-left corner of the mask is located on the specified slice (optional).

static base64_2_data(encoded_string)[source]¶

Convert base64 encoded string to numpy array.

Parameters

s : str

Input base64 encoded string.

Returns

Bool numpy array

Return type

np.ndarray

Usage example

import supervisely as sly

encoded_string = 'H4sIAGWoWmQC/zPWMdYxrmFkZAAiIIAz4AAAE56ciyEAAAA='
figure_data = sly.Mask3D.base64_2_data(encoded_string)
print(figure_data)
# [[[1 1 0]
#   [1 1 0]
#   [0 0 0]]
#  [[1 1 0]
#   [1 1 0]
#   [0 0 0]]
#  [[0 0 0]
#   [0 0 0]
#   [0 0 0]]]

clone()¶

Clone from GEOMETRYYY

classmethod create_from_file(file_path)[source]¶

Creates Mask3D geometry from file.

Parameters

file_path : str

Path to nrrd file with data

Return type

Mask3D

crop(rect)¶

Parameters

rect

Rectangle

Returns

list of Geometry

static data_2_base64(data)[source]¶

Convert numpy array to base64 encoded string.

Parameters

mask : np.ndarray

Bool numpy array.

Returns

Base64 encoded string

Return type

str

Usage example

import supervisely as sly
import os
import nrrd

address = 'https://app.supervise.ly/'
token = 'Your Supervisely API Token'
api = sly.Api(address, token)

meta_json = api.project.get_meta(PROJECT_ID)
meta = sly.ProjectMeta.from_json(meta_json)

ann_json = api.volume.annotation.download_bulk(DATASET_ID, [VOLUME_ID])

figure_id = ann_json[0]["spatialFigures"][0]["id"]
path_for_mesh = f"meshes/{figure_id}.nrrd"
api.volume.figure.download_stl_meshes([figure_id], [path_for_mesh])

mask3d_data, _ = nrrd.read(path_for_mesh)
encoded_string = sly.Mask3D.data_2_base64(mask3d_data)

print(encoded_string)
# 'H4sIAGWoWmQC/zPWMdYxrmFkZAAiIIAz4AAAE56ciyEAAAA='

draw(bitmap, color, thickness=1, config=None)¶

Parameters

bitmap

np.ndarray

color

[R, G, B]

thickness

used only in Polyline and Point

config

drawing config specific to a concrete subclass, e.g. per edge colors

draw_contour(bitmap, color, thickness=1, config=None)¶

Draws the figure contour on a given bitmap canvas :param bitmap: np.ndarray :param color: [R, G, B] :param thickness: (int) :param config: drawing config specific to a concrete subclass, e.g. per edge colors

fliplr(img_size)¶

Parameters

img_size

(rows, cols)

Returns

Geometry

flipud(img_size)¶

Parameters

img_size

(rows, cols)

Returns

Geometry

classmethod from_bytes(geometry_bytes)[source]¶

Create a Mask3D geometry object from bytes.

Parameters

geometry_bytes : bytes

NRRD file represented as bytes.

Returns

A Mask3D geometry object.

Return type

Mask3D

static from_file(figure, file_path)[source]¶

Load figure geometry from file.

Parameters

figure : VolumeFigure

Spatial figure

file_path : str

Path to nrrd file with data

classmethod from_json(json_data)[source]¶

Convert a json dict to Mask 3D.

Parameters

data : dict

Mask in json format as a dict.

Returns

Mask3D object

Return type

Mask3D

Usage example

import supervisely as sly

figure_json = {
    "mask_3d": {
        "data": "eJzrDPBz5+WS4mJgYOD19HAJAtLMIMwIInOeqf8BUmwBPiGuQPr///9Lb86/C2QxlgT5BTM4PLuRBuTwebo4hlTMSa44sKHhISMDuxpTYrr03F6gDIOnq5/LOqeEJgDM5ht6",
    },
    "shape": "mask_3d",
    "geometryType": "mask_3d"
}

figure = sly.Mask3D.from_json(figure_json)

static geometry_name()[source]¶

Return geometry name

get_mask(img_size)¶

Returns 2D boolean mask of the geometry. With shape as img_size (height, width) and filled with True values inside the geometry and False values outside. dtype = np.bool shape = img_size

Parameters

img_size : Tuple[int, int]

size of the image (height, width)

Returns

2D boolean mask of the geometry

Return type

np.ndarray

classmethod name()¶

Same as geometry_name(), but shorter. In order to make the code more concise.

Returns

string with name of geometry

relative_crop(rect)¶

Crops object like “crop” method, but return results with coordinates relative to rect :param rect: :return: list of Geometry

resize(in_size, out_size)¶

Parameters

in_size

(rows, cols)

out_size

(128, 256) (128, KEEP_ASPECT_RATIO) (KEEP_ASPECT_RATIO, 256)

Returns

Geometry

rotate(rotator)¶

Rotates around image center -> New Geometry :param rotator: ImageRotator :return: Geometry

scale(factor)¶

Scales around origin with a given factor. :param: factor (float): :return: Geometry

to_bbox()¶

Return type

Rectangle

Returns

Rectangle

to_json()[source]¶

Convert the Mask 3D to a json dict.

Returns

Json format as a dict

Return type

dict

Usage example

import supervisely as sly

mask = np.array([[[1 1 0]
                  [1 1 0]
                  [0 0 0]]
                 [[1 1 0]
                  [1 1 0]
                  [0 0 0]]
                 [[0 0 0]
                  [0 0 0]
                  [0 0 0]]], dtype=np.bool_)

figure = sly.Mask3D(mask)
figure_json = figure.to_json()
print(json.dumps(figure_json, indent=4))
# Output: {
#    "mask_3d": {
#        "data": "eJzrDPBz5+WS4mJgYOD19HAJAtLMIMwIInOeqf8BUmwBPiGuQPr///9Lb86/C2QxlgT5BTM4PLuRBuTwebo4hlTMSa44sKHhISMDuxpTYrr03F6gDIOnq5/LOqeEJgDM5ht6",
#    },
#    "shape": "mask_3d",
#    "geometryType": "mask_3d"
# }

translate(drow, dcol)¶

Parameters

drow

int rows shift

dcol

int cols shift

Returns

Geometry

property area¶

Returns

float