Merge pull request #23 from danforthcenter/22-clicks-to-shapefile

Clicked points to shape file

docs/changelog.md

@@ -2,6 +2,10 @@
 
 All notable changes to this project will be documented below.
 
+#### geospatial.points_to_geojson
+
+* v0.1dev: **geosptial.points_to_geojson**(*img, viewer, out_path*)
+
 #### geospatial.read_geotif
 
 * v0.1dev: spectral = **geospatial.read_geotif**(*filename, bands="B,G,R", cropto=None*)

docs/points_to_geojson.md

@@ -0,0 +1,36 @@
+## Output clicked points as a geojson shapefile
+
+Using a Napari or PlantCV-annotate viewer object with clicked points, output a shapefile.  
+
+**geospatial.points_to_geojson**(*img, viewer, out_path*)
+
+- **Parameters:**
+    - img - Spectral image object, likely read in with [`geo.read_geotif`](read_geotif.md)
+    - viewer - Napari viewer class object, possible created with PlantCV-Annotate.
+    - out_path - Path to save the geojson shapefile. Must be ".geojson" file type. 
+
+- **Context:**
+    - Saved points can be used downstream for generating circular ROIs or circles for use with rasterstats. 
+- **Example use:**
+    - below to click plant locations
+
+
+```python
+import plantcv.geospatial as geo
+import plantcv.annotate as an
+
+# Read geotif in
+img = geo.read_geotif("../read_geotif/rgb.tif", bands="R,G,B")
+viewer = an.napari_open(img=img.pseudo_rgb)
+viewer.add_points()
+
+# A napari viewer window will pop up, use the points function to add clicks
+```
+```python
+# In a separate cell, save the output after clicking:
+geo.points_to_geojson(img, viewer, out_path="./points_example.geojson")
+```
+
+![Screenshot](documentation_images/napari_clicks.png)
+
+**Source Code:** [Here](https://github.com/danforthcenter/plantcv-geospatial/blob/main/plantcv/geospatial/points_to_geojson.py)

mkdocs.yml

@@ -20,6 +20,7 @@ nav:
         - Read Geo-tif Data: read_geotif.md
         - Transform coordinate points: transform_points.md
         - Transform coordinate polygons: transform_polygons.md
+        - Save clicked points as geojson: points_to_geojson.md
 markdown_extensions:
   - toc:
       permalink: True

plantcv/geospatial/__init__.py

@@ -2,12 +2,14 @@
 from plantcv.geospatial.read_geotif import read_geotif
 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
 
 # Auto versioning
 __version__ = version("plantcv-geospatial")
 
 __all__ = [
     "read_geotif",
     "transform_points",
-    "transform_polygons"
+    "transform_polygons",
+    "points_to_geojson"
     ]

plantcv/geospatial/points_to_geojson.py

@@ -0,0 +1,41 @@
+# Save clicked points from Napari or PlantCV-annotate as a geojson points file.
+
+import geojson
+import rasterio
+from plantcv.plantcv import fatal_error
+
+
+def points_to_geojson(img, viewer, out_path):
+    """Use clicks from a Napari or plantcv-annotate viewer to output a geojson shapefile.
+
+    Parameters
+    ----------
+    img : PlantCV spectral_data class object
+        The image used for clicking on points, should be from read_geotif.
+    viewer: Napari viewer class object or plantcv-annotate Points class object.
+        The viewer used to make the clicks.
+    out_path : str
+        Path to save to shapefile. Must have "geojson" file extension
+    """
+    # Napari output, points must be reversed
+    if hasattr(viewer, 'layers'):
+        points = [(img.metadata["transform"]*reversed(i)) for i in viewer.layers["Points"].data]
+    # Annotate output
+    elif hasattr(viewer, 'coords'):
+        points = [(img.metadata["transform"]*i) for i in viewer.coords['default']]
+    else:
+        fatal_error("Viewer class type not recognized. Currently, Napari and PlantCV-annotate viewers supported.")
+    features = [geojson.Feature(geometry=geojson.Point((lon, lat))) for lon, lat in points]
+    feature_collection = geojson.FeatureCollection(features)
+    # Make sure the coordinate system is the same as the original image
+    feature_collection['crs'] = {
+        "type": "name",
+        "properties": {
+            "name": rasterio.crs.CRS.to_string(img.metadata["crs"])
+        }
+    }
+    if ".geojson" in out_path:
+        with open(out_path, 'w') as f:
+            geojson.dump(feature_collection, f)
+    else:
+        fatal_error("File type not supported.")

pyproject.toml

@@ -14,6 +14,8 @@ dependencies = [
     "rasterio",
     "fiona",
     "shapely",
+    "geojson",
+    "napari",
 ]
 requires-python = ">=3.6"
 authors = [

tests/test_geospatial_points_to_geojson.py

@@ -0,0 +1,54 @@
+"""Tests for geospatial.points_to_geojson"""
+
+import pytest
+import os
+import napari
+from plantcv.geospatial import read_geotif
+from plantcv.geospatial import points_to_geojson
+
+# Set up fake class just for testing the annotate output
+# Don't want to have to have annotate as a dependency
+
+class FakePoints:
+    def __init__(self):
+        self.coords = {}
+
+def test_geospatial_points_to_geojson_napari(test_data, tmpdir):
+    """Test for plantcv-geospatial."""
+    cache_dir = tmpdir.mkdir("cache")
+    img = read_geotif(filename=test_data.rgb_tif, bands="R,G,B")
+    viewer = napari.Viewer(show=False)
+    viewer.add_image(img.pseudo_rgb)
+    viewer.add_points()
+    filename = os.path.join(cache_dir, 'test_out.geojson')
+    points_to_geojson(img, viewer, out_path=filename)
+    assert os.path.exists(filename)
+
+def test_geospatial_points_to_geojson_an(test_data, tmpdir):
+    """Test for plantcv-geospatial."""
+    cache_dir = tmpdir.mkdir("cache")
+    img = read_geotif(filename=test_data.rgb_tif, bands="R,G,B")
+    viewer = FakePoints()
+    viewer.coords["default"] = []
+    filename = os.path.join(cache_dir, 'test_out.geojson')
+    points_to_geojson(img, viewer, out_path=filename)
+    assert os.path.exists(filename)
+
+def test_geospatial_points_to_geojson_badviewer(test_data, tmpdir):
+    """Test for plantcv-geospatial."""
+    cache_dir = tmpdir.mkdir("cache")
+    img = read_geotif(filename=test_data.rgb_tif, bands="R,G,B")
+    viewer = []
+    filename = os.path.join(cache_dir, 'test_out.geojson')
+    with pytest.raises(RuntimeError):
+        points_to_geojson(img, viewer, out_path=filename)
+
+def test_geospatial_points_to_geojson_badfilename(test_data, tmpdir):
+    """Test for plantcv-geospatial."""
+    cache_dir = tmpdir.mkdir("cache")
+    img = read_geotif(filename=test_data.rgb_tif, bands="R,G,B")
+    viewer = FakePoints()
+    viewer.coords["default"] = []
+    filename = os.path.join(cache_dir, 'test_out.txt')
+    with pytest.raises(RuntimeError):
+        points_to_geojson(img, viewer, out_path=filename)