Merge pull request #1532 from danforthcenter/read-images-http

Read images over HTTP

Author: nfahlgren

docs/io_open_url.md

@@ -0,0 +1,31 @@
+## Open an image from a URL
+
+Opens an image file stored at a URL.
+
+**plantcv.io.open_url**(*url*)
+
+**returns** img
+
+- **Parameters:**
+    - url - URL of the image file to be opened
+- **Context:**
+    - Used to open an image file stored at a URL
+- **Example use:**
+
+```python
+from plantcv import plantcv as pcv
+
+# Set global debug behavior to None (default), "print" (to file), 
+# or "plot" (Jupyter Notebooks or X11)
+pcv.params.debug = "plot"
+
+# Open image from URL
+img = pcv.io.open_url(url="https://plantcv.org/s/plantcv-hyperspectral.png")
+
+```
+
+**Image**
+
+<img title="PlantCV logo" alt="PlantCV logo" src="https://plantcv.org/s/plantcv-hyperspectral.png" width="300px">
+
+**Source Code:** [Here](https://github.com/danforthcenter/plantcv/blob/main/plantcv/plantcv/io/open_url.py)

docs/updating.md

@@ -565,6 +565,11 @@ pages for more details on the input and output variable types.
 * pre v3.0dev2: device, img_inv = **plantcv.invert**(*img, device, debug=None*)
 * post v3.0dev2: img_inv = **plantcv.invert**(*gray_img*)
 
+#### plantcv.io.open_url
+
+* pre v4.2.1: NA
+* post v4.2.1: img = **plantcv.io.open_url**(*url*)
+
 #### plantcv.io.random_subset
 
 * pre v3.14.0: NA

mkdocs.yml

@@ -88,6 +88,7 @@ nav:
       - 'Image Fusion': image_fusion.md
       - 'Invert': invert.md
       - 'I/O Functions':
+          - 'Open Image from URL': io_open_url.md
           - 'Random Subset': io_random_subset.md
           - 'Read Dataset': io_read_dataset.md
       - 'Kmeans Clustering Classifier': kmeans_classifier.md

plantcv/plantcv/io/__init__.py

@@ -1,5 +1,6 @@
 from plantcv.plantcv.io.read_dataset import read_dataset
 from plantcv.plantcv.io.random_subset import random_subset
+from plantcv.plantcv.io.open_url import open_url
 
 # add new functions to end of lists
-__all__ = ["read_dataset", "random_subset"]
+__all__ = ["read_dataset", "random_subset", "open_url"]

plantcv/plantcv/io/open_url.py

@@ -0,0 +1,35 @@
+"""Open an image from a URL."""
+import imageio.v3 as iio
+import cv2
+from plantcv.plantcv import fatal_error
+from plantcv.plantcv._debug import _debug
+
+
+def open_url(url):
+    """Open an image from a URL and return it as a numpy array.
+
+    Parameters
+    ----------
+    url : str
+        URL of the image to be opened.
+
+    Returns
+    -------
+    numpy.ndarray
+        Image data as a numpy array.
+    """
+    # Read the image from the URL using imageio
+    image = iio.imread(url)
+
+    # Check if the image is grayscale or RGB
+    if len(image.shape) not in [2, 3]:
+        fatal_error("Image is not RGB or grayscale.")
+
+    if image.shape[-1] == 3:
+        # Convert the image to RGB format
+        image = cv2.cvtColor(image, cv2.COLOR_RGB2BGR)
+
+    # Debugging visualization
+    _debug(visual=image, filename="url_image.png")
+
+    return image

tests/plantcv/io/test_open_url.py

@@ -0,0 +1,18 @@
+"""Tests for the open_url function."""
+import pytest
+from plantcv.plantcv.io import open_url
+
+
+def test_open_url():
+    """PlantCV Test"""
+    url = ("https://github.com/danforthcenter/plantcv-tutorial-simple-rgb-workflow/blob/" +
+           "af312af00e21c84efe942132a1910359faadd49a/img/1_B73_sand_C_2023-04-14_10_19_07.jpg?raw=true")
+    rgb_img = open_url(url=url)
+    assert rgb_img.shape == (3456, 4608, 3)
+
+
+def test_open_url_unsupported():
+    """PlantCV Test"""
+    url = "https://upload.wikimedia.org/wikipedia/commons/2/2c/Rotating_earth_%28large%29.gif"
+    with pytest.raises(RuntimeError):
+        _ = open_url(url=url)