Merge pull request #10 from danforthcenter/add_transform_points

Add transform points

docs/changelog.md

@@ -5,3 +5,7 @@ All notable changes to this project will be documented below.
 #### geospatial.read_geotif
 
 * v0.1dev: spectral = **geospatial.read_geotif**(*filename, bands="B,G,R"*)
+
+#### geospatial.transform_points
+
+* v0.1dev: coord = **geospatial.transform_points**(*img, geojson*)

docs/transform_points.md

@@ -0,0 +1,29 @@
+## Transform Points
+
+Transform the points from a georeferenced shapefile/GeoJSON based on an image size. 
+
+**plantcv.geospatial.transform_points**(*img, geojson*)
+
+**returns** list of transformed coordinates
+
+- **Parameters:**
+    - img - Spectral image object, likely read in with [`geo.read_geotif`](read_geotif.md)
+    - geojson - Path to the shapefile/GeoJSON containing the points. Can be Point or MultiPoint geometry.
+
+- **Context:**
+    - Transformed points can be used downstream for Python analysis, such as defining ROIs. 
+- **Example use:**
+    - below to define plot boundaries
+
+
+```python
+import plantcv.geospatial as geo
+
+# Read geotif in
+spectral = geo.read_geotif(filename="./data/example_img.tif", bands="b,g,r,RE,NIR")
+coords = geo.transform_points(img=spectral, geojson="./experimental_bounds_2024.shp")
+roi_objects = pcv.roi.custom(img=spectral.pseudo_rgb, vertices=coords)
+
+```
+
+**Source Code:** [Here](https://github.com/danforthcenter/plantcv-geospatial/blob/main/plantcv/geospatial/transform_points.py)

mkdocs.yml

@@ -18,6 +18,7 @@ nav:
   - 'PlantCV Namespace':
     - 'Geopspatial Tools':
         - Read Geo-tif Data: read_geotif.md
+        - Transform coordinate points: transform_points.md
 markdown_extensions:
   - toc:
       permalink: True

plantcv/geospatial/__init__.py

@@ -1,9 +1,11 @@
 from importlib.metadata import version
 from plantcv.geospatial.read_geotif import read_geotif
+from plantcv.geospatial.transform_points import transform_points
 
 # Auto versioning
 __version__ = version("plantcv-geospatial")
 
 __all__ = [
-    "read_geotif"
+    "read_geotif",
+    "transform_points"
     ]

plantcv/geospatial/transform_points.py

@@ -0,0 +1,30 @@
+# Transform georeferenced GeoJSON/shapefile points into python coordinates
+import fiona
+
+
+def transform_points(img, geojson):
+    """Takes a points-type shapefile/GeoJSON and transforms to numpy coordinates
+    Inputs:
+    img:        A spectral object from read_geotif.
+    geojson:    Path to the shape file containing the points.
+
+    Returns:
+    coord:      Transformed points as a list of numpy coordinates
+
+    :param img: [spectral object]
+    :param geojson: str
+    :return coord: list
+    """
+    geo_transform = img.geo_transform
+
+    coord = []
+    with fiona.open(geojson, 'r') as shapefile:
+        for i, _ in enumerate(shapefile):
+            if type((shapefile[i].geometry["coordinates"])) is list:
+                pixel_point = ~(geo_transform) * (shapefile[i].geometry["coordinates"][0])
+            if type((shapefile[i].geometry["coordinates"])) is tuple:
+                pixel_point = ~(geo_transform) * (shapefile[i].geometry["coordinates"])
+            rounded = (int(pixel_point[0]), int(pixel_point[1]))
+            coord.append(rounded)
+
+    return coord

pyproject.toml

@@ -14,7 +14,6 @@ dependencies = [
     "rasterio",
     "fiona",
     "shapely",
-
 ]
 requires-python = ">=3.6"
 authors = [

tests/conftest.py

@@ -18,6 +18,10 @@ def __init__(self):
         self.empty_tif = os.path.join(self.datadir, "cropped_empty.tif")
         # rgb image
         self.rgb_tif = os.path.join(self.datadir, "rgb.tif")
+        # multiPoints shapefilex
+        self.pts_geojson = os.path.join(self.datadir, "test_pts.geojson")
+        # points shapefilex
+        self.single_pts_geojson = os.path.join(self.datadir, "single_test_pts.geojson")
         # polygon shapefile
         self.square_crop = os.path.join(self.datadir, "square_crop.geojson")
         # points shapefile

tests/test_geospatial_transform_points.py

@@ -0,0 +1,19 @@
+"""Tests for geospatial.readd_geotif."""
+
+from plantcv.geospatial import read_geotif, transform_points
+
+
+def test_geospatial_transform_points(test_data):
+    """Test for plantcv-geospatial."""
+    # read in small 5-band tif image
+    img = read_geotif(filename=test_data.rgb_tif, bands="B,G,R")
+    coords = transform_points(img=img, geojson=test_data.pts_geojson)
+    assert len(coords) == 4
+
+
+def test_geospatial_transform_single_points(test_data):
+    """Test for plantcv-geospatial."""
+    # read in small 5-band tif image
+    img = read_geotif(filename=test_data.rgb_tif, bands="B,G,R")
+    coords = transform_points(img=img, geojson=test_data.single_pts_geojson)
+    assert len(coords) == 8

tests/testdata/single_test_pts.geojson

@@ -0,0 +1,15 @@
+{
+"type": "FeatureCollection",
+"name": "single_test_pts",
+"crs": { "type": "name", "properties": { "name": "urn:ogc:def:crs:EPSG::32615" } },
+"features": [
+{ "type": "Feature", "properties": { "id": null }, "geometry": { "type": "Point", "coordinates": [ 720201.455548222991638, 4302929.009466916322708 ] } },
+{ "type": "Feature", "properties": { "id": null }, "geometry": { "type": "Point", "coordinates": [ 720200.939437506720424, 4302928.515762113966048 ] } },
+{ "type": "Feature", "properties": { "id": null }, "geometry": { "type": "Point", "coordinates": [ 720200.359096014057286, 4302927.93337285425514 ] } },
+{ "type": "Feature", "properties": { "id": null }, "geometry": { "type": "Point", "coordinates": [ 720199.889628155739047, 4302927.349608448334038 ] } },
+{ "type": "Feature", "properties": { "id": null }, "geometry": { "type": "Point", "coordinates": [ 720199.406284277676605, 4302926.797856044024229 ] } },
+{ "type": "Feature", "properties": { "id": null }, "geometry": { "type": "Point", "coordinates": [ 720198.922733629238792, 4302926.185171222314239 ] } },
+{ "type": "Feature", "properties": { "id": null }, "geometry": { "type": "Point", "coordinates": [ 720198.442067798110656, 4302925.539512793533504 ] } },
+{ "type": "Feature", "properties": { "id": null }, "geometry": { "type": "Point", "coordinates": [ 720197.996919097611681, 4302925.057554029859602 ] } }
+]
+}

tests/testdata/test_pts.geojson

@@ -0,0 +1,11 @@
+{
+"type": "FeatureCollection",
+"name": "test_pts",
+"crs": { "type": "name", "properties": { "name": "urn:ogc:def:crs:EPSG::32615" } },
+"features": [
+{ "type": "Feature", "properties": { "id": null }, "geometry": { "type": "MultiPoint", "coordinates": [ [ 720198.48000389453955, 4302927.004775654524565 ] ] } },
+{ "type": "Feature", "properties": { "id": null }, "geometry": { "type": "MultiPoint", "coordinates": [ [ 720199.890186188276857, 4302928.102779876440763 ] ] } },
+{ "type": "Feature", "properties": { "id": null }, "geometry": { "type": "MultiPoint", "coordinates": [ [ 720200.501309029874392, 4302929.21947811357677 ] ] } },
+{ "type": "Feature", "properties": { "id": null }, "geometry": { "type": "MultiPoint", "coordinates": [ [ 720197.757872894289903, 4302926.144173440523446 ] ] } }
+]
+}