update read_data to transform uint8 data

plantcv/plantcv/hyperspectral/read_data.py

@@ -320,6 +320,11 @@ def read_data(filename, mode="ENVI"):
     pseudo_rgb = _make_pseudo_rgb(spectral_array)
     spectral_array.pseudo_rgb = pseudo_rgb
 
+    if spectral_array.d_type == np.uint8:
+        spectral_array.array_data = spectral_array.array_data.astype("float32")  # required for further calculations
+        spectral_array.array_data = spectral_array.array_data / 255  # convert 0-255 (orig.) to 0-1 range
+        spectral_array.d_type = np.float32
+
     _debug(visual=pseudo_rgb, filename=os.path.join(params.debug_outdir, str(params.device) + "_pseudo_rgb.png"))
 
     return spectral_array

tests/plantcv/hyperspectral/conftest.py

@@ -24,6 +24,8 @@ def __init__(self):
         self.hsi_whiteref_file = os.path.join(self.datadir, "hsi_whiteref.pkl")
         self.hsi_darkref_file = os.path.join(self.datadir, "hsi_darkref.pkl")
         self.savi_file = os.path.join(self.datadir, "savi.pkl")
+        self.hsi_uint8 = os.path.join(self.datadir, "test-hyperpectral-uint8.raw")
+        self.hsi_uint8_hdr = os.path.join(self.datadir, "test-hyperpectral-uint8.hdr")
 
     @staticmethod
     def load_hsi(pkl_file):

tests/plantcv/hyperspectral/test_read_data.py

@@ -37,3 +37,8 @@ def test_read_data_parse_arcgis(hyperspectral_test_data):
     """Test for PlantCV."""
     array_data = read_data(filename=hyperspectral_test_data.arcgis, mode="arcgis")
     assert np.shape(array_data.array_data) == (1, 1600, 978)
+
+def test_read_data_uint8(hyperspectral_test_data):
+    """Test for PlantCV."""
+    array_data = read_data(filename=hyperspectral_test_data.hsi_uint8)
+    assert np.shape(array_data.array_data) == (1, 2, 978)

tests/testdata/test-hyperspectral-uint8.hdr

@@ -0,0 +1,21 @@
+ENVI
+; this file was created using PlantCV version 3.6.dev124+gf033097d
+; original file: ./RC5-9B3D54_000000_20240603_010000
+interleave = bil
+samples = 2
+lines = 1
+bands = 10
+data type = 1
+wavelength units = nm
+wavelength = {
+0.0,
+475.0,
+500.0,
+526.0,
+595.0,
+630.0,
+665.0,
+740.0,
+850.0,
+940.0
+}