Add napari assisted warp

docs/changelog.md

@@ -2,9 +2,13 @@
 
 All notable changes to this project will be documented below.
 
+#### geospatial.napari_save_points
+
+* v0.1dev: **geospatial.napari_save_points**(*images, num_points, outdir="./", bands="R,G,B", block=True, show=True*)
+
 #### geospatial.points_to_geojson
 
-* v0.1dev: **geosptial.points_to_geojson**(*img, viewer, out_path*)
+* v0.1dev: **geospatial.points_to_geojson**(*img, viewer, out_path*)
 
 #### geospatial.read_geotif
 

docs/napari_save_points.md

@@ -0,0 +1,41 @@
+## Save Napari clicked points
+
+Uses Napari to open a list of images one at a time. The user then clicks a defined number of points on each image, which are then saved to a text file with the same name as the image. To be used upstream of warp for geospatial images that are not georeferenced. 
+
+**geospatial.napari_save_points**(*images, num_points, outdir="./", bands="R,G,B", block=True, show=True*)
+
+- **Parameters:**
+    - images - Either a list of image paths or a directory where images are stored. Each image will be opened in sequence.
+    - num_points - Integer of expected number of clicked points. For warping downstream, this should be minimally 4.
+    - outdir - Directory to save output text files with saved points for each image. Defaults to "./".
+    - bands - If input images are geotifs, this is the required band order for `plantcv.geospatial.read_geotif`. Not required if image type is not geotif. 
+    - block - True/False whether to stop function from advancing before user closes the viewer window.
+    - show - True/False whether to show the Napari viewer. Necessary for tests.
+
+- **Outputs:**
+    - redo_list - list of images to redo because the number of clicks did not match num_points. Useful if the user makes a mistake and would like to retry for a subset of images.
+
+- **Context:**
+    - Saved files can be used to warp all images to a specified reference image to bring all images to the same frame. This is useful for geospatial images that have not been georeferenced, as this approximates a version of what using ground control points achieves. 
+
+- **Example use:**
+    - below to click field corners
+
+
+```python
+import plantcv.geospatial as geo
+
+# Make a list of images, can also be a directory
+img_list = ["./image1.jpg", "./image2.jpg", "./image3.jpg", "./image4.jpg"]
+
+# Opens a Napari window with a points layer for each image
+# User should click reference points equal to num_points and then close the window, prompting the next one to open
+
+redo_list = geo.napari_save_points(img_list, num_points=4, outdir="./")
+
+# Text files with points are saved to outdir
+# Output is a list of any images the user should redo
+
+```
+
+**Source Code:** [Here](https://github.com/danforthcenter/plantcv-geospatial/blob/main/plantcv/geospatial/napari_save_points.py)

mkdocs.yml

@@ -21,6 +21,7 @@ nav:
         - Transform coordinate points: transform_points.md
         - Transform coordinate polygons: transform_polygons.md
         - Save clicked points as geojson: points_to_geojson.md
+        - Save Napari points to text file: napari_save_points.md
 markdown_extensions:
   - toc:
       permalink: True

plantcv/geospatial/__init__.py

@@ -3,6 +3,7 @@
 from plantcv.geospatial.transform_points import transform_points
 from plantcv.geospatial.transform_polygons import transform_polygons
 from plantcv.geospatial.points_to_geojson import points_to_geojson
+from plantcv.geospatial.napari_save_points import napari_save_points
 
 # Auto versioning
 __version__ = version("plantcv-geospatial")
@@ -11,5 +12,6 @@
     "read_geotif",
     "transform_points",
     "transform_polygons",
-    "points_to_geojson"
+    "points_to_geojson",
+    "napari_save_points"
     ]

plantcv/geospatial/napari_save_points.py

@@ -0,0 +1,71 @@
+# Function to save out clicked points collected in napari
+
+import plantcv.plantcv as pcv
+from plantcv.plantcv import warn
+from plantcv.geospatial import read_geotif
+import napari
+import os
+
+
+def napari_save_points(images, num_points, outdir="./", bands="R,G,B", show_window=True):
+    """Opens a set of images one at a time in a Napari window, waits for users
+    to click points and then saves those points to a file with the same name as the image.
+
+    Args:
+        images (list or str): Either a list of image paths or a directory name.
+        num_points (int): Number of points expected. If number of clicks received is different,
+                        the image path is added to redo_list and returned.
+        outdir (str, optional): Directory to save text files with points. Defaults to "./".
+        bands (str, optional): Band list if input images are geotifs. Defaults to "R,G,B".
+        block (boolean): Whether to stop the function from advancing before user closes the viewer window.
+        show (boolean): Whether to show the Napari viewer. Necessary for tests.
+
+    Returns:
+        list: List of images to be redone due to a different number of clicked points than expected.
+    """
+    # store debug
+    debug = pcv.params.debug
+
+    pcv.params.debug = None
+    # Store images with mistakes to a new list
+    redo_list = []
+
+    image_paths = images
+    if not isinstance(images, list):
+        image_paths = [os.path.join(images, i) for i in os.listdir(images)]
+    # Loop over each image
+    for image_path in image_paths:
+        # Load the current image
+        img_type = (image_path.split("/")[-1]).split(".")[-1]
+        if img_type == "tif":
+            geo_image = read_geotif(image_path, bands=bands)
+            image = geo_image.pseudo_rgb
+        else:
+            image, _, _ = pcv.readimage(image_path)
+        # Save image name for output file
+        img_name = (image_path.split("/")[-1]).split(".")[:-1]
+
+        viewer = napari.Viewer(show=show_window)
+
+        # Add the image and points layer
+        viewer.add_image(image)
+        viewer.add_points(name="points")
+        if show_window:
+            viewer.show(block=True)
+
+        # Save file if correct number of points
+        if len(viewer.layers["points"].data) == num_points:
+            with open(os.path.join(outdir, img_name[0]+"_warp.txt"), "w") as output:
+                for i in viewer.layers["points"].data:
+                    point = [i[1], i[0]]
+                    output.write(str(point) + '\t')
+        else:
+            redo_list.append(image_path)
+            warn('Image ' + str(image_path) + ' collected incorrect number of points. ' +
+                 'Added to redo list.')
+        # Close the viewer in case it wasn't shown
+        if not show_window:
+            viewer.close()
+    # Reset debug
+    pcv.params.debug = debug
+    return redo_list

tests/test_geospatial_napari_save_points.py

@@ -0,0 +1,24 @@
+"""Tests for geospatial.napari_save_points"""
+
+import os
+from plantcv.geospatial import napari_save_points, read_geotif
+from plantcv.plantcv import print_image
+
+
+def test_geospatial_napari_save_points(test_data, tmpdir):
+    """Test for plantcv-geospatial."""
+    cache_dir = tmpdir.mkdir("cache")
+    images = [test_data.rgb_tif]
+    redo_list = napari_save_points(images, num_points=4, outdir=cache_dir, show_window=False) 
+    assert len(redo_list) == 1
+
+
+def test_geospatial_napari_save_points_output(test_data, tmpdir):
+    """Test for plantcv-geospatial."""
+    cache_dir = tmpdir.mkdir("cache")
+    # test with a png by creating a temp version of the rgb tif in cache_dir
+    img = read_geotif(filename=test_data.rgb_tif, bands="R,G,B")
+    print_image(img.pseudo_rgb, os.path.join(cache_dir, "rgb.png"))
+    images = [os.path.join(cache_dir, "rgb.png")]
+    _ = napari_save_points(images, num_points=0, outdir=cache_dir, show_window=False) 
+    assert os.path.exists(os.path.join(cache_dir, "rgb_warp.txt"))