Modified boxes_to_shapefile function

deepforest/utilities.py

@@ -382,13 +382,13 @@ def check_image(image):
                          "found image with shape {}".format(image.shape))
 
 
-def boxes_to_shapefile(df, root_dir, projected=True, flip_y_axis=False):
+def boxes_to_shapefile(df, rgb, projected=True, flip_y_axis=False):
     """
     Convert from image coordinates to geographic coordinates
     Note that this assumes df is just a single plot being passed to this function
     Args:
        df: a pandas type dataframe with columns: name, xmin, ymin, xmax, ymax. Name is the relative path to the root_dir arg.
-       root_dir: directory of images to lookup image_path column
+       rgb: path for the image file
        projected: If True, convert from image to geographic coordinates, if False, keep in image coordinate system
        flip_y_axis: If True, reflect predictions over y axis to align with raster data in QGIS, which uses a negative y origin compared to numpy. See https://gis.stackexchange.com/questions/306684/why-does-qgis-use-negative-y-spacing-in-the-default-raster-geotransform
     Returns:
@@ -401,15 +401,7 @@ def boxes_to_shapefile(df, root_dir, projected=True, flip_y_axis=False):
             .format(flip_y_axis, projected), UserWarning)
         projected = False
 
-    plot_names = df.image_path.unique()
-    if len(plot_names) > 1:
-        raise ValueError("This function projects a single plots worth of data. "
-                         "Multiple plot names found {}".format(plot_names))
-    else:
-        plot_name = plot_names[0]
-
-    rgb_path = "{}/{}".format(root_dir, plot_name)
-    with rasterio.open(rgb_path) as dataset:
+    with rasterio.open(rgb) as dataset:
         bounds = dataset.bounds
         pixelSizeX, pixelSizeY = dataset.res
         crs = dataset.crs

docs/annotation.md

@@ -83,7 +83,7 @@ for path in files:
     plt.imshow(fig)
 
     #Create a shapefile, in this case img data was unprojected
-    shp = boxes_to_shapefile(boxes, root_dir=PATH_TO_DIR, projected=False)
+    shp = boxes_to_shapefile(boxes, rgb=path, projected=False)
 
     #Get name of image and save a .shp in the same folder
     basename = os.path.splitext(os.path.basename(path))[0]

tests/test_utilities.py

@@ -88,28 +88,28 @@ def test_boxes_to_shapefile_projected(m):
     img = get_data("OSBS_029.tif")
     r = rio.open(img)
     df = m.predict_image(path=img)
-    gdf = utilities.boxes_to_shapefile(df, root_dir=os.path.dirname(img), projected=True)
+    gdf = utilities.boxes_to_shapefile(df, rgb=img, projected=True)
 
     #Confirm that each boxes within image bounds
     geom = geometry.box(*r.bounds)
     assert all(gdf.geometry.apply(lambda x: geom.intersects(geom)).values)
 
     #Edge case, only one row in predictions
-    gdf = utilities.boxes_to_shapefile(df.iloc[:1,], root_dir=os.path.dirname(img), projected=True)
+    gdf = utilities.boxes_to_shapefile(df.iloc[:1,], rgb=img, projected=True)
     assert gdf.shape[0] == 1
 
 def test_boxes_to_shapefile_projected_from_predict_tile(m):
     img = get_data("OSBS_029.tif")
     r = rio.open(img)
     df = m.predict_tile(raster_path=img)
-    gdf = utilities.boxes_to_shapefile(df, root_dir=os.path.dirname(img), projected=True)
+    gdf = utilities.boxes_to_shapefile(df, rgb=img, projected=True)
 
     #Confirm that each boxes within image bounds
     geom = geometry.box(*r.bounds)
     assert all(gdf.geometry.apply(lambda x: geom.intersects(geom)).values)
 
     #Edge case, only one row in predictions
-    gdf = utilities.boxes_to_shapefile(df.iloc[:1,], root_dir=os.path.dirname(img), projected=True)
+    gdf = utilities.boxes_to_shapefile(df.iloc[:1,], rgb=img, projected=True)
     assert gdf.shape[0] == 1
 
 # Test unprojected data, including warning if flip_y_axis is set to True, but projected is False
@@ -123,7 +123,7 @@ def test_boxes_to_shapefile_unprojected(m, flip_y_axis, projected):
     with pytest.warns(UserWarning):
         gdf = utilities.boxes_to_shapefile(
             df,
-            root_dir=os.path.dirname(img),
+            rgb=img,
             projected=projected,
             flip_y_axis=flip_y_axis)