Bitmasks

import cv2
import numpy as np
from encord import EncordUserClient

# Instantiate Encord client by substituting the path to your private key
user_client = EncordUserClient.create_with_ssh_private_key(
    ssh_private_key_path="<private_key_path>"
)

# Specify a project using project hash
project = user_client.get_project("<project_hash>")

# Obtain labels for the media of interest
label_row = project.list_label_rows_v2()[0]
label_row.initialise_labels()

# Find annotation
# In this example, it is just a first object on a first frame
object_with_bitmask_annotation = label_row.get_frame_views()[
    0
].get_object_instances()[0]

# Get a bitmask annotation
# In this example, it is a first annotation on the object
bitmask_annotation = object_with_bitmask_annotation.get_annotations()[0]

# Convert bitmask to a numpy array
# Obtained array is a binary mask, so to work with it as an image,
# it is necessary to convert it to a different datatype and scale
bitmask = bitmask_annotation.coordinates.to_numpy_array().astype(np.uint8)

bitmask[bitmask == 1] = 255

# And now we can save the mask as a grayscale image
cv2.imwrite("./mask_as_an_image.png", bitmask)

import numpy as np
from encord import EncordUserClient
from encord.objects import Object, OntologyStructure
from encord.objects.coordinates import BitmaskCoordinates

# Firstly, we need to prepare the mask itself.
# For simplicity, we can just mask the whole image
# Note, that the size of the mask must be identical to the size of the image
numpy_coordinates = np.ones((512, 512))

# we also need to make sure that the image is in boolean format
numpy_coordinates = numpy_coordinates.astype(bool)

# Now we can upload it with the following steps

# Instantiate Encord client and get a project using project hash
user_client = EncordUserClient.create_with_ssh_private_key("<your_private_key>")
project = user_client.get_project("<project_hash>")

# Obtain labels for the media of interest
# In this case, just a first image of the project
label_row = project.list_label_rows_v2()[0]
label_row.initialise_labels()

# Find a bitmask annotation object in the project ontology
ontology_structure: OntologyStructure = label_row.ontology_structure
bitmask_ontology_object: Object = ontology_structure.get_child_by_title(
    title="My bitmask feature", type_=Object
)

# Create the instance of this object - actual annotation
bitmask_ontology_object_instance = bitmask_ontology_object.create_instance()

# Set the bitmask as coordinates for the annotation
bitmask_ontology_object_instance.set_for_frames(
    # Create coordinates from provided numpy bitmask
    coordinates=BitmaskCoordinates(numpy_coordinates),
    # Add the bounding box to the first frame
    frames=0,
    # There are multiple additional fields that can be set optionally:
    manual_annotation=True,
)

# And assign the object instance to the label row
label_row.add_object_instance(bitmask_ontology_object_instance)

label_row.save()

# Import dependencies
import json
from pathlib import Path
import numpy as np
from encord.objects.coordinates import BitmaskCoordinates
from PIL import Image

# Read the JSON file.
# Replace labels.json with the path to the JSON file containing your Bitmask
labels = json.loads(Path("labels.json").read_text())
output_folder = Path("output")
output_folder.mkdir(parents=True, exist_ok=True)

# Finds the rleString and saves it to a .png image
found_any = False
for label_row in labels:
    for du in label_row["data_units"].values():
        slice_nums = list(du["labels"].keys())
        for slice_num in slice_nums:
            for obj in du["labels"][slice_num]["objects"]:
                bmc = BitmaskCoordinates.from_dict(obj)
                nparr = np.array(bmc)
                img = Image.fromarray(nparr)
                # img.show()
                # Replace example.png with the name of the output file
                img.save(output_folder / f"mask_{int(slice_num):05d}_{obj['objectHash']}.png")
print("Decoding complete.")

from encord.objects.coordinates import BitmaskCoordinates

# Create a numpy array
np_mask = BitmaskCoordinates.from_dict(obj).to_numpy_array() 
print(np_mask.astype(int))

from pycocotools.coco import COCO
import numpy as np
from pycocotools import mask as maskUtils
from PIL import Image
import json


# Read the COCO file. Replace 'labels.json' with the path to your COCO format annotations file
coco_annotations_path = 'labels.json'
coco = COCO(coco_annotations_path)

# Get all annotation IDs (you might want to filter or select specific ones)
annIds = coco.getAnnIds()
anns = coco.loadAnns(annIds)

# Decode each rleString and save as a .png image
for i, ann in enumerate(anns):
    if 'segmentation' in ann and isinstance(ann['segmentation'], dict):

        rle = ann['segmentation']
        
        mask = maskUtils.decode(rle)

        img = Image.fromarray(mask * 255).convert('L')  # Convert to grayscale

# Replace example.png with the name of the output file
        img.save("example.png")

print("Decoding complete.")