From 5790b22cb18d319c36313f21bfdd78981efa03f5 Mon Sep 17 00:00:00 2001
From: HaleySchuhl <haleyschuhl@gmail.com>
Date: Mon, 15 Apr 2024 16:58:06 -0500
Subject: [PATCH] remove pseudo rgb code

---
 plantcv/geospatial/read_geotif.py | 100 +-----------------------------
 1 file changed, 1 insertion(+), 99 deletions(-)

diff --git a/plantcv/geospatial/read_geotif.py b/plantcv/geospatial/read_geotif.py
index c18aac3..d71f218 100644
--- a/plantcv/geospatial/read_geotif.py
+++ b/plantcv/geospatial/read_geotif.py
@@ -1,100 +1,3 @@
-# Read TIF File
-import os
-import re
-import cv2
-import numpy as np
-from plantcv.plantcv import params
-from plantcv.plantcv._debug import _debug
-from plantcv.plantcv import Spectral_data
-from plantcv.plantcv import fatal_error
-
-
-def _find_closest(spectral_array, target):
-    """Find index of a target wavelength band in a hyperspectral data instance.
-
-    Inputs:
-        spectral_array = Hyperspectral data instance
-        target         = Target wavelength value
-
-    Returns:
-        idx            = Index
-
-    :param spectral_array: __main__.Spectral_data
-    :param target: float
-    :return spectral_array: __main__.Spectral_data
-    """
-    # Array must be sorted
-    idx = spectral_array.searchsorted(target)
-    idx = np.clip(idx, 1, len(spectral_array) - 1)
-    left = spectral_array[idx - 1]
-    right = spectral_array[idx]
-    idx -= target - left < right - target
-    return idx
-
-
-def _make_pseudo_rgb(spectral_array):
-    """Create the best pseudo-rgb image possible from a hyperspectral datacube
-
-    Inputs:
-        spectral_array = Hyperspectral data instance
-
-    Returns:
-        pseudo_rgb     = Pseudo-rgb image
-
-    :param spectral_array: __main__.Spectral_data
-    :return pseudo_rgb: numpy.ndarray
-    """
-    # Make shorter variable names for data from the spectral class instance object
-    array_data = spectral_array.array_data
-    default_bands = spectral_array.default_bands
-    wl_keys = spectral_array.wavelength_dict.keys()
-
-    if default_bands is not None:
-        pseudo_rgb = cv2.merge((array_data[:, :, int(default_bands[0])],
-                                array_data[:, :, int(default_bands[1])],
-                                array_data[:, :, int(default_bands[2])]))
-
-    else:
-        max_wavelength = max(float(i) for i in wl_keys)
-        min_wavelength = min(float(i) for i in wl_keys)
-        # Check range of available wavelength
-        if max_wavelength >= 635 and min_wavelength <= 490:
-            print("combining bands to make false color image")
-            id_red = _find_closest(spectral_array=np.array([float(i) for i in wl_keys]), target=710)
-            id_green = _find_closest(spectral_array=np.array([float(i) for i in wl_keys]), target=540)
-            id_blue = _find_closest(spectral_array=np.array([float(i) for i in wl_keys]), target=480)
-
-            pseudo_rgb = cv2.merge((array_data[:, :, [id_blue]],
-                                    array_data[:, :, [id_green]],
-                                    array_data[:, :, [id_red]]))
-            print("Red ID: " + str(id_red))
-            print("Green ID: " + str(id_green))
-            print("Blue ID: " + str(id_blue))
-
-        else:
-            # Otherwise take 3 wavelengths, first, middle and last available wavelength
-            id_red = int(len(spectral_array.wavelength_dict)) - 1
-            id_green = int(id_red / 2)
-            pseudo_rgb = cv2.merge((array_data[:, :, [0]],
-                                    array_data[:, :, [id_green]],
-                                    array_data[:, :, [id_red]]))
-
-    # Gamma correct pseudo_rgb image
-    pseudo_rgb = pseudo_rgb ** (1 / 2.2)
-    print("gamma correction complete")
-    # Scale each of the channels up to 255
-    debug = params.debug
-    params.debug = None
-    # pseudo_rgb = cv2.merge((rescale(pseudo_rgb[:, :, 0]),
-    #                         rescale(pseudo_rgb[:, :, 1]),
-    #                         rescale(pseudo_rgb[:, :, 2])))
-
-    # Reset debugging mode
-    params.debug = debug
-
-    return pseudo_rgb
-
-
 import rasterio
 import numpy as np
 from plantcv.plantcv import fatal_error
@@ -155,12 +58,11 @@ def read_geotif(filename, bands="R,G,B"):
                                    wavelength_units="nm", array_type="datacube",
                                    pseudo_rgb=None, filename=filename, default_bands=None)
 
-    # Make 
+    # Make pseudo RGB image for visualization 
     pseudo_rgb = spectral_array.array_data[:, :, :3]
     pseudo_rgb = pseudo_rgb ** (1 / 2.2)
     spectral_array.pseudo_rgb = pseudo_rgb
 
-
     pseudo_rgb = _make_pseudo_rgb(spectral_array)
     pseudo_rgb = pseudo_rgb.astype('float32')
     plot_image(img=pseudo_rgb)  # Replace with _debug