mask2bbox 0.0.20

Gets the bounding boxes from a mask file.

mask2bbox

For a given mask, gets the coordinates of bounding box of each element of the mask. It will also allow for more operations in the future.

Installation

pip install mask2bbox

CLI

python isolate-cells -h

Usage

import numpy as np
from mask2bbox import BBoxes

# Create a BBoxes object
all_boxes = BBoxes.from_mask("path/to/mask.png")

# Expand the bounding boxes
all_boxes = all_boxes.expand(n=10)

# Remove the bounding boxes that are located on the edge of the image
all_boxes = all_boxes.remove_from_edge()

# Get the sides of all the bounding boxes
sides = all_boxes.get("sides")

# Filter the bounding boxes by the sides
filtered_boxes = all_boxes.filter("sides", np.greater_equal, (35, 35))

# Get the IoU matrix of all the bounding boxes
iou = filtered_boxes.iou_matrix()

# Save the overlapping pairs to
filtered_boxes.save_overlapping_pairs("path/to/save/overlapping_pairs.csv")

# Save the IOU matrix to a csv file
filtered_boxes.save_iou_matrix("path/to/save/iou_matrix.csv")   

# Plot the bounding boxes on the mask image
filtered_boxes.draw(to="image", method="matplotlib", show="False", save="path/to/save/image.png")

# Save your bounding boxes
filtered_boxes.save_csv("path/to/bounding_boxes.csv")

# Get resize factors to resize the bounding boxes to a given size
resize_factors = filtered_boxes.de(desired_ratio=0.7, size=(256, 256))

# Extract the bounding boxes as images
filtered_boxes.extract(resize_factors, size=(256, 256), output="path/to/save/images")