Add green normalized difference vegetative index (GNDVI)

docs/spectral_index.md

@@ -201,21 +201,45 @@ Index range: -1, 1
 Calculates the Green Difference Vegetation Index using reflectance values ([Sripada et al., 2006](#references)):
 
 ```
-GDVI = (NIR - GREEN) / (NIR + GREEN)
+GDVI = (NIR - GREEN)
 ```
 
 Here, we use ~R800 for NIR and ~R550 for GREEN:
 
 ```
-GDVI = (R800 - R550) / (R800 + R550)
+GDVI = (R800 - R550)
 ```
 
-Index range: -2.0, 2.0
+Index range: -1.0, 1.0
 
 **plantcv.spectral_index.gdvi**(*hsi, distance=20*)
 
 **returns** calculated index array (instance of the `Spectral_data` class)
 
+- **Parameters:**
+    - hsi         - Hyperspectral image object, an instance of the `Spectral_data` class in plantcv (read in using [pcv.readimage](read_image.md) with `mode='envi'`)
+    - distance    - Amount of flexibility (in nanometers) regarding the bands used to calculate an index.
+
+### GNDVI
+
+Calculates the Green Normalized Difference Vegetation Index using reflectance values ([Gitelson et al., 1996](#references)):
+
+```
+GNDVI = (NIR - GREEN) / (NIR + GREEN)
+```
+
+Here, we use ~R800 for NIR and ~R550 for GREEN:
+
+```
+GNDVI = (R800 - R550) / (R800 + R550)
+```
+
+Index range: -1.0, 1.0
+
+**plantcv.spectral_index.gndvi**(*hsi, distance=20*)
+
+**returns** calculated index array (instance of the `Spectral_data` class)
+
 - **Parameters:**
     - hsi         - Hyperspectral image object, an instance of the `Spectral_data` class in plantcv (read in using [pcv.readimage](read_image.md) with `mode='envi'`)
     - distance    - Amount of flexibility (in nanometers) regarding the bands used to calculate an index.
@@ -721,6 +745,9 @@ ndvi_array = pcv.spectral_index.ndvi(hsi=spectral_data, distance=20)
 # Extract GDVI index from the datacube
 gdvi_array = pcv.spectral_index.gdvi(hsi=spectral_data, distance=20)
 
+# Extract GNDVI index from the datacube
+gndvi_array = pcv.spectral_index.gndvi(hsi=spectral_data, distance=20)
+
 # Extract SAVI index from the datacube
 savi_array = pcv.spectral_index.savi(hsi=spectral_data, distance=20)
 
@@ -859,6 +886,8 @@ DOI: [10.1080/0143116042000274015](https://doi.org/10.1080/0143116042000274015).
 Gamon JA, Surfus JS. 1999. Assessing leaf pigment content and activity with a reflectometer. The New Phytologist 
 143:105–117. DOI: [10.1046/j.1469-8137.1999.00424.x](https://doi.org/10.1046/j.1469-8137.1999.00424.x).
 
+Gitelson AA, Kaufman YJ, & Merzlyak MN. (1996). Use of a green channel in remote sensing of global vegetation from EOS-MODIS. Remote sensing of Environment, 58(3), 289-298. DOI: [10.1016/S0034-4257(96)00072-7](https://doi.org/10.1016/S0034-4257(96)00072-7)
+
 Gitelson AA, Zur Y, Chivkunova OB, Merzlyak MN. 2002. Assessing carotenoid content in plant leaves with reflectance 
 spectroscopy. Photochemistry and Photobiology 75:272–281. DOI: 
 [10.1562/0031-8655(2002)0750272ACCIPL2.0.CO2](https://doi.org/10.1562/0031-8655(2002)0750272ACCIPL2.0.CO2).

docs/updating.md

@@ -1239,6 +1239,10 @@ pages for more details on the input and output variable types.
 
 * post v3.8: array = **plantcv.spectral_index.gdvi**(*hsi, distance=20*)
 
+#### plantcv.spectral_index.gndvi
+
+* post v5.0: array = **plantcv.spectral_index.gndvi**(*hsi, distance=20*)
+
 #### plantcv.spectral_index.gli
 
 * post v4.4: array = **plantcv.spectral_index.gli**(*img, distance=20*)

plantcv/plantcv/spectral_index/__init__.py

@@ -1,5 +1,6 @@
 from plantcv.plantcv.spectral_index.spectral_index import ndvi
 from plantcv.plantcv.spectral_index.spectral_index import gdvi
+from plantcv.plantcv.spectral_index.spectral_index import gndvi
 from plantcv.plantcv.spectral_index.spectral_index import savi
 from plantcv.plantcv.spectral_index.spectral_index import pri
 from plantcv.plantcv.spectral_index.spectral_index import ari
@@ -35,6 +36,8 @@
 
 
 # add new functions to end of lists
-__all__ = ["ndvi", "gdvi", "savi", "pri", "ari", "ci_rededge", "cri550", "cri700", "egi", "evi", "gli", "sci", "bgr", "bgi",
-           "mari", "mcari", "mtci", "ndre", "npci", "psnd_chla", "psnd_chlb", "psnd_car", "psri", "pssr_chla", "pssr_chlb",
-           "pssr_car", "rgri", "rvsi", "sipi", "sr", "vari", "vi_green", "wi", "ndci"]
+__all__ = ["ndvi", "gdvi", "gndvi", "savi", "pri", "ari", "ci_rededge", "cri550",
+           "cri700", "egi", "evi", "gli", "sci", "bgr", "bgi", "mari", "mcari",
+           "mtci", "ndre", "npci", "psnd_chla", "psnd_chlb", "psnd_car", "psri",
+           "pssr_chla", "pssr_chlb", "pssr_car", "rgri", "rvsi", "sipi", "sr", "vari",
+           "vi_green", "wi", "ndci"]

plantcv/plantcv/spectral_index/spectral_index.py

@@ -73,6 +73,36 @@ def gdvi(hsi, distance=20):
     return None
 
 
+def gndvi(hsi, distance=20):
+    """Green Normalized Difference Vegetation Index.
+
+    GNDVI = (R800 - R550) / (R800 + R550)
+
+    The theoretical range for GNDVI is [-1.0, 1.0].
+
+    Inputs:
+    hsi         = hyperspectral image (PlantCV Spectral_data instance)
+    distance    = how lenient to be if the required wavelengths are not available
+
+    Returns:
+    index_array = Index data as a Spectral_data instance
+
+    :param hsi: __main__.Spectral_data
+    :param distance: int
+    :return index_array: __main__.Spectral_data
+    """
+    if (float(hsi.max_wavelength) + distance) >= 800 and (float(hsi.min_wavelength) - distance) <= 550:
+        r800_index = _find_closest(np.array([float(i) for i in hsi.wavelength_dict.keys()]), 800)
+        r550_index = _find_closest(np.array([float(i) for i in hsi.wavelength_dict.keys()]), 550)
+        r800 = (hsi.array_data[:, :, r800_index])
+        r550 = (hsi.array_data[:, :, r550_index])
+        # Naturally ranges from -1 to 1
+        index_array_raw = (r800 - r550) / (r800 + r550)
+        return _package_index(hsi=hsi, raw_index=index_array_raw, method="GNDVI")
+    warn("Available wavelengths are not suitable for calculating GNDVI. Try increasing distance.")
+    return None
+
+
 def savi(hsi, distance=20):
     """Soil Adjusted Vegetation Index.
 

tests/plantcv/spectral_index/test_spectral_index.py

@@ -27,6 +27,18 @@ def test_gdvi_bad_input(spectral_index_test_data):
     assert spectral_index.gdvi(hsi=index_array, distance=20) is None
 
 
+def test_gndvi(spectral_index_test_data):
+    """Test for PlantCV."""
+    index_array = spectral_index.gndvi(spectral_index_test_data.load_hsi(), distance=20)
+    assert np.shape(index_array.array_data) == (1, 1600) and np.nanmax(index_array.pseudo_rgb) == 255
+
+
+def test_gndvi_bad_input(spectral_index_test_data):
+    """Test for PlantCV."""
+    index_array = spectral_index.gndvi(spectral_index_test_data.load_hsi(), distance=20)
+    assert spectral_index.gndvi(hsi=index_array, distance=20) is None
+
+
 def test_savi(spectral_index_test_data):
     """Test for PlantCV."""
     index_array = spectral_index.savi(spectral_index_test_data.load_hsi(), distance=20)