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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
@author : Romain Graux
@date : 2023 April 25, 11:59:06
@last modified : 2023 September 19, 11:18:36
"""
import re
import imageio
import numpy as np
from collections import namedtuple
physical_metadata = namedtuple("physical_metadata", ["width", "height", "pixel_width", "pixel_height", "unit"])
def extract_physical_metadata(image_path : str, strict:bool=True) -> physical_metadata:
"""
Extracts the physical metadata of an image (only tiff for now)
"""
with open(image_path, "rb") as f:
data = f.read()
reader = imageio.get_reader(data, format=".tif")
metadata = reader.get_meta_data()
if strict and not metadata['is_imagej']:
for key, value in metadata.items():
if key.startswith("is_") and value == True: # Force bool to be True, because it can also pass the condition while being an random object
raise ValueError(f"The image is not TIFF image, but it seems to be a {key[3:]} image")
raise ValueError("Impossible to extract metadata from the image (ImageJ)")
h, w = reader.get_next_data().shape
ipw, iph, _ = metadata['resolution']
result = re.search(r"unit=(.+)", metadata['description'])
if strict and not result:
raise ValueError(f"No scale unit found in the image description : {metadata['description']}")
unit = result and result.group(1)
return physical_metadata(w, h, 1. / ipw, 1. / iph, unit)
def tiff_to_png(image, inplace=True):
img = image if inplace else image.copy()
if np.array(img.getdata()).max() <= 1:
img = img.point(lambda p: p * 255)
return img.convert("RGB")
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