def create_feed_dict(data_index):
# create feed dict
current_image_RGB = cv2.imread(imageNames_RGB[data_index])
current_image_Red = cv2.imread(imageNames_Red[data_index])
current_image_NIR = cv2.imread(imageNames_NIR[data_index])
current_image_Red_Edge = cv2.imread(imageNames_Red_Edge[data_index])
current_image_Green = cv2.imread(imageNames_Green[data_index])
current_image_green, _, _ = cv2.split(current_image_Green)
current_image_red, _, _ = cv2.split(current_image_Red)
current_image_nir, _, _ = cv2.split(current_image_NIR)
current_image_red_edge,_, _ = cv2.split(current_image_Red_Edge)
channel_marge = cv2.merge([current_image_red, current_image_nir, current_image_red_edge])
channel_6 = np.concatenate((channel_marge, current_image_RGB), axis=2)
ndvi = (current_image_nir - current_image_red) / (current_image_nir + current_image_red)
VIgreen = (current_image_green - current_image_red) / (current_image_green + current_image_red)
gndvi = (current_image_nir - current_image_green) / (current_image_nir + current_image_green)
ndre = (current_image_nir - current_image_red_edge) / (current_image_nir + current_image_red_edge)
savi = ((current_image_nir - current_image_red) / (current_image_nir + current_image_red) + 0.5) * 1.5
data_index = str(data_index)
masked_ndvi = np.ma.masked_outside(ndvi, 0.45, 1.2)
fig, axis = plotutils.plotwithcolorbar(masked_ndvi, 'ndvi', figsize=figsize)
plt.draw()
fig.savefig(Training_path + data_index + '_ndvi.png')
plt.close(fig)
masked_vigreen = np.ma.masked_outside(VIgreen, 0.0, 0.2)
fig, axis = plotutils.plotwithcolorbar(masked_vigreen, 'vi_green', figsize=figsize)
plt.draw()
fig.savefig(Training_path + data_index + '_vigreen.png')
plt.close(fig)
masked_gndvi = np.ma.masked_outside(gndvi, -1, 1)
fig, axis = plotutils.plotwithcolorbar(masked_gndvi, 'gndvi', figsize=figsize)
plt.draw()
fig.savefig(Training_path + data_index + '_gndvi.png')
plt.close(fig)
masked_ndre = np.ma.masked_outside(ndre, -1, 1)
fig, axis = plotutils.plotwithcolorbar(masked_ndre, 'ndre', figsize=figsize)
plt.draw()
fig.savefig(Training_path + data_index + '_ndre.png')
plt.close(fig)
masked_savi = np.ma.masked_outside(savi, -1, 1)
fig, axis = plotutils.plotwithcolorbar(masked_savi, 'savi', figsize=figsize)
plt.draw()
fig.savefig(Training_path + data_index + '_savi.png')
plt.close(fig)
def plot_raw(self, title=None, figsize=None):
''' Create a single plot of the raw image '''
if title is None:
title = '{} Band {} Raw DN'.format(self.band_name, self.band_index)
return plotutils.plotwithcolorbar(self.raw(),
title=title,
figsize=figsize)
def plot_undistorted_radiance(self, title=None, figsize=None):
''' Create a single plot of the undistorted radiance '''
if title is None:
title = '{} Band {} Undistorted Radiance'.format(
self.band_name, self.band_index)
return plotutils.plotwithcolorbar(self.undistorted(self.radiance()),
title=title,
figsize=figsize)
def plot_vignette(self, title=None, figsize=None):
''' Create a single plot of the vignette '''
if title is None:
title = '{} Band {} Vignette'.format(self.band_name,
self.band_index)
return plotutils.plotwithcolorbar(self.plottable_vignette(),
title=title,
figsize=figsize)
def plot_radiance(self, title=None, figsize=None):
''' Create a single plot of the image converted to radiance '''
if title is None:
title = '{} Band {} Radiance'.format(self.band_name,
self.band_index)
return plotutils.plotwithcolorbar(self.radiance(),
title=title,
figsize=figsize)
def plot_intensity(self, title=None, figsize=None):
''' Create a single plot of the image converted to uncalibrated intensity '''
if title is None:
title = '{} Band {} Intensity (DN*sec)'.format(
self.band_name, self.band_index)
return plotutils.plotwithcolorbar(self.intensity(),
title=title,
figsize=figsize)
def align(pair):
""" Determine an alignment matrix between two images
@input:
Dictionary of the following form:
{
'warp_mode': cv2.MOTION_* (MOTION_AFFINE, MOTION_HOMOGRAPHY)
'max_iterations': Maximum number of solver iterations
'epsilon_threshold': Solver stopping threshold
'ref_index': index of reference image
'match_index': index of image to match to reference
}
@returns:
Dictionary of the following form:
{
'ref_index': index of reference image
'match_index': index of image to match to reference
'warp_matrix': transformation matrix to use to map match image to reference image frame
}
Major props to Alexander Reynolds ( https://stackoverflow.com/users/5087436/alexander-reynolds ) for his
insight into the pyramided matching process found at
https://stackoverflow.com/questions/45997891/cv2-motion-euclidean-for-the-warp-mode-in-ecc-image-alignment-method
"""
warp_mode = pair['warp_mode']
max_iterations = pair['max_iterations']
epsilon_threshold = pair['epsilon_threshold']
ref_index = pair['ref_index']
match_index = pair['match_index']
translations = pair['translations']
# Initialize the matrix to identity
if warp_mode == cv2.MOTION_HOMOGRAPHY:
warp_matrix = np.array(
[[1, 0, translations[1]], [0, 1, translations[0]], [0, 0, 1]],
dtype=np.float32)
else:
# warp_matrix = np.array([[1,0,0],[0,1,0]], dtype=np.float32)
warp_matrix = np.array(
[[1, 0, translations[1]], [0, 1, translations[0]]],
dtype=np.float32)
w = pair['ref_image'].shape[1]
nol = int(w / (1280 / 3)) - 1
print("number of pyramid levels: {}".format(nol))
warp_matrix[0][2] /= (2**nol)
warp_matrix[1][2] /= (2**nol)
if ref_index != match_index:
show_debug_images = pair['debug']
# construct grayscale pyramid
gray1 = pair['ref_image']
gray2 = pair['match_image']
if gray2.shape[0] < gray1.shape[0]:
cv2.resize(gray2,
None,
fx=gray1.shape[0] / gray2.shape[0],
fy=gray1.shape[0] / gray2.shape[0],
interpolation=cv2.INTER_AREA)
gray1_pyr = [gray1]
gray2_pyr = [gray2]
for level in range(nol):
gray1_pyr[0] = gaussian(normalize(gray1_pyr[0]))
gray1_pyr.insert(
0,
cv2.resize(gray1_pyr[0],
None,
fx=1 / 2,
fy=1 / 2,
interpolation=cv2.INTER_AREA))
gray2_pyr[0] = gaussian(normalize(gray2_pyr[0]))
gray2_pyr.insert(
0,
cv2.resize(gray2_pyr[0],
None,
fx=1 / 2,
fy=1 / 2,
interpolation=cv2.INTER_AREA))
# Terminate the optimizer if either the max iterations or the threshold are reached
criteria = (cv2.TERM_CRITERIA_EPS | cv2.TERM_CRITERIA_COUNT,
max_iterations, epsilon_threshold)
# run pyramid ECC
for level in range(nol + 1):
grad1 = gradient(gray1_pyr[level])
grad2 = gradient(gray2_pyr[level])
if show_debug_images:
import micasense.plotutils as plotutils
plotutils.plotwithcolorbar(gray1_pyr[level],
"ref level {}".format(level))
plotutils.plotwithcolorbar(gray2_pyr[level],
"match level {}".format(level))
plotutils.plotwithcolorbar(grad1,
"ref grad level {}".format(level))
plotutils.plotwithcolorbar(grad2,
"match grad level {}".format(level))
print("Starting warp for level {} is:\n {}".format(
level, warp_matrix))
cc, warp_matrix = cv2.findTransformECC(grad1,
grad2,
warp_matrix,
warp_mode,
criteria,
inputMask=None,
gaussFiltSize=1)
if show_debug_images:
print("Warp after alignment level {} is \n{}".format(
level, warp_matrix))
if level != nol: # scale up only the offset by a factor of 2 for the next (larger image) pyramid level
if warp_mode == cv2.MOTION_HOMOGRAPHY:
warp_matrix = warp_matrix * np.array(
[[1, 1, 2], [1, 1, 2], [0.5, 0.5, 1]],
dtype=np.float32)
else:
warp_matrix = warp_matrix * np.array(
[[1, 1, 2], [1, 1, 2]], dtype=np.float32)
return {
'ref_index': pair['ref_index'],
'match_index': pair['match_index'],
'warp_matrix': warp_matrix
}
def align(pair):
""" Determine an alignment matrix between two images
@input:
Dictionary of the following form:
{
'warp_mode': cv2.MOTION_* (MOTION_AFFINE, MOTION_HOMOGRAPHY)
'max_iterations': Maximum number of solver iterations
'epsilon_threshold': Solver stopping threshold
'ref_index': index of reference image
'match_index': index of image to match to reference
}
@returns:
Dictionary of the following form:
{
'ref_index': index of reference image
'match_index': index of image to match to reference
'warp_matrix': transformation matrix to use to map match image to reference image frame
}
Major props to Alexander Reynolds ( https://stackoverflow.com/users/5087436/alexander-reynolds ) for his
insight into the pyramided matching process found at
https://stackoverflow.com/questions/45997891/cv2-motion-euclidean-for-the-warp-mode-in-ecc-image-alignment-method
"""
warp_mode = pair['warp_mode']
max_iterations = pair['max_iterations']
epsilon_threshold = pair['epsilon_threshold']
ref_index = pair['ref_index']
match_index = pair['match_index']
translations = pair['translations']
close_range = pair['close_range']
# Initialize the matrix to identity
if warp_mode == cv2.MOTION_HOMOGRAPHY:
# warp_matrix = np.array([[1,0,0],[0,1,0],[0,0,1]], dtype=np.float32)
warp_matrix = pair['warp_matrix_init']
else:
# warp_matrix = np.array([[1,0,0],[0,1,0]], dtype=np.float32)
warp_matrix = np.array(
[[1, 0, translations[1]], [0, 1, translations[0]]],
dtype=np.float32)
w = pair['ref_image'].shape[1]
if pair['pyramid_levels'] is None:
nol = int(w / (1280 / 3)) - 1
else:
nol = pair['pyramid_levels']
if pair['debug']:
print("number of pyramid levels: {}".format(nol))
warp_matrix[0][2] /= (2**nol)
warp_matrix[1][2] /= (2**nol)
if close_range:
matrix_box = np.zeros((3, 3, 5), dtype=np.float32)
matrix_box[:, :, 0] = np.array(
[[1.01990501e+00, 6.60780396e-02, 1.61565981e+01],
[1.02941529e-02, 1.04839095e+00, -5.93324724e+01],
[-2.39299405e-06, 6.57833196e-05, 1.00000000e+00]],
dtype=np.float32)
matrix_box[:, :, 1] = np.array(
[[9.64607505e-01, -5.80503997e-04, -1.90982485e+00],
[-1.75293196e-02, 9.55154457e-01, -2.94900879e+01],
[-4.10977951e-05, -2.78523751e-06, 1.00000000e+00]],
dtype=np.float32)
matrix_box[:, :, 3] = np.array(
[[1.06259853e+00, 7.81775979e-02, 1.45072993e+01],
[1.99893573e-02, 1.10691304e+00, -4.95636256e+01],
[3.31475328e-05, 8.63813674e-05, 1.00000000e+00]],
dtype=np.float32)
matrix_box[:, :, 4] = np.array(
[[1.00576555e+00, 3.10690919e-02, 5.54705923e+00],
[4.39865262e-03, 1.02901756e+00, -2.45425948e+01],
[-1.34695946e-05, 4.22982177e-05, 1.00000000e+00]],
dtype=np.float32)
warp_matrix = matrix_box[:, :, match_index]
# if close_range:
# matrix_box = np.zeros((3, 3, 5), dtype=np.float32)
# matrix_box[:,:,0] = np.array([[ 9.85234288e-01, -6.02857058e-02, -1.97861800e+01],
# [-9.13546319e-03, 9.54160086e-01, 5.71365581e+01],
# [ 3.68473019e-06, -6.25908142e-05, 1.00000000e+00]], dtype=np.float32)
# matrix_box[:,:,1] = np.array([[1.03681022e+00, 7.94539658e-04, 1.94929221e+00],
# [2.05548527e-02, 1.04714741e+00, 3.08336762e+01],
# [4.27748983e-05, 3.30673535e-06, 1.00000000e+00]], dtype=np.float32)
# matrix_box[:,:,3] = np.array([[ 9.45799261e-01, -6.47190144e-02, -1.73228004e+01],
# [-1.90123138e-02, 9.04237787e-01, 4.54668636e+01],
# [-3.06740010e-05, -7.49444305e-05, 1.00000000e+00]], dtype=np.float32)
# matrix_box[:,:,4] = np.array([[ 9.95893056e-01, -2.93410233e-02, -6.50957883e+00],
# [-3.86456817e-03, 9.72735207e-01, 2.37574987e+01],
# [ 1.36621685e-05, -4.07031605e-05, 1.00000000e+00]], dtype=np.float32)
# warp_matrix = matrix_box[:,:, match_index]
if ref_index != match_index:
show_debug_images = pair['debug']
# construct grayscale pyramid
gray1 = pair['ref_image']
gray2 = pair['match_image']
if gray2.shape[0] < gray1.shape[0]:
cv2.resize(gray2,
None,
fx=gray1.shape[0] / gray2.shape[0],
fy=gray1.shape[0] / gray2.shape[0],
interpolation=cv2.INTER_AREA)
gray1_pyr = [gray1]
gray2_pyr = [gray2]
for level in range(nol):
gray1_pyr[0] = gaussian(normalize(gray1_pyr[0]))
gray1_pyr.insert(
0,
cv2.resize(gray1_pyr[0],
None,
fx=1 / 2,
fy=1 / 2,
interpolation=cv2.INTER_AREA))
gray2_pyr[0] = gaussian(normalize(gray2_pyr[0]))
gray2_pyr.insert(
0,
cv2.resize(gray2_pyr[0],
None,
fx=1 / 2,
fy=1 / 2,
interpolation=cv2.INTER_AREA))
# Terminate the optimizer if either the max iterations or the threshold are reached
criteria = (cv2.TERM_CRITERIA_EPS | cv2.TERM_CRITERIA_COUNT,
max_iterations, epsilon_threshold)
# run pyramid ECC
for level in range(nol + 1):
grad1 = gradient(gray1_pyr[level])
grad2 = gradient(gray2_pyr[level])
if show_debug_images:
import micasense.plotutils as plotutils
plotutils.plotwithcolorbar(gray1_pyr[level],
"ref level {}".format(level))
plotutils.plotwithcolorbar(gray2_pyr[level],
"match level {}".format(level))
plotutils.plotwithcolorbar(grad1,
"ref grad level {}".format(level))
plotutils.plotwithcolorbar(grad2,
"match grad level {}".format(level))
print("Starting warp for level {} is:\n {}".format(
level, warp_matrix))
# cc, warp_matrix = cv2.findTransformECC(grad1, grad2, warp_matrix, warp_mode, criteria)
# print("image correlation = {:4.2f}".format(cc))
if show_debug_images:
print("Warp after alignment level {} is \n{}".format(
level, warp_matrix))
if level != nol: # scale up only the offset by a factor of 2 for the next (larger image) pyramid level
if warp_mode == cv2.MOTION_HOMOGRAPHY:
warp_matrix = warp_matrix * np.array(
[[1, 1, 2], [1, 1, 2], [0.5, 0.5, 1]],
dtype=np.float32)
else:
warp_matrix = warp_matrix * np.array(
[[1, 1, 2], [1, 1, 2]], dtype=np.float32)
return {
'ref_index': pair['ref_index'],
'match_index': pair['match_index'],
'warp_matrix': warp_matrix
}
##############################################################################
#Calculate Radiance to Reflectance Conversion for Each Band using the Calibration Panel Images
#Need to perform manually for each band because masked panel area shifts
#PREFLIGHT CALIBRATION IMAGES
##############
#Band 1 (Blue)
#Plotting
imageName = os.path.join(CalibrationFolder_preflight, 'IMG_0002_1.tif')
imageRaw = plt.imread(
imageName).T # Read raw image DN values - 16 bit tif only
plt.imshow(imageRaw.T, cmap='gray')
plotutils.colormap('viridis')
# Optional: pick a color map: 'gray, viridis, plasma, inferno, magma, nipy_spectral'
fig = plotutils.plotwithcolorbar(imageRaw.T,
title='Raw image values with colorbar')
#Image metadata
meta = metadata.Metadata(imageName, exiftoolPath=exiftoolPath)
bandName = meta.get_item('XMP:BandName')
#Converting raw images to Radiance
radianceImage, L, V, R = msutils.raw_image_to_radiance(meta, imageRaw.T)
plotutils.plotwithcolorbar(V, 'Vignette Factor')
plotutils.plotwithcolorbar(R, 'Row Gradient Factor')
plotutils.plotwithcolorbar(V * R, 'Combined Corrections')
plotutils.plotwithcolorbar(L, 'Vignette and row gradient corrected raw values')
plotutils.plotwithcolorbar(radianceImage,
'All factors applied and scaled to radiance')
#Mask to panel and calculate radiance
import micasense.metadata as metadata
sys.path.append('C:/Users/Isaac Miller/Documents/GitHub/imageprocessing')
exiftoolPath = None
if os.name == 'nt':
exiftoolPath = 'C:/exiftool/exiftool.exe'
# get calibration
panelPath = os.path.join('.', 'data', '0000SET', '000')
panelName = glob.glob(os.path.join(panelPath, 'IMG_0000_1.tif'))[0]
panelRaw = plt.imread(panelName)
panelMeta = metadata.Metadata(panelName, exiftoolPath=exiftoolPath)
radianceImage, L, V, R = msutils.raw_image_to_radiance(panelMeta, panelRaw)
plotutils.plotwithcolorbar(V, 'Vignette Factor')
plotutils.plotwithcolorbar(R, 'Row Gradient Factor')
plotutils.plotwithcolorbar(V * R, 'Combined Corrections')
plotutils.plotwithcolorbar(L, 'Vignette and row gradient corrected raw values')
plotutils.plotwithcolorbar(radianceImage,
'All factors applied and scaled to radiance')
markedImg = radianceImage.copy()
ulx = 660 # upper left column (x coordinate) of panel area
uly = 490 # upper left row (y coordinate) of panel area
lrx = 840 # lower right column (x coordinate) of panel area
lry = 670 # lower right row (y coordinate) of panel area
cv2.rectangle(markedImg, (ulx, uly), (lrx, lry), (0, 255, 0), 3)
# Our panel calibration by band (from MicaSense for our specific panel)
panelCalibration = {
"Blue": 0.67,
"Blue": 0.66,
"Green": 0.67,
"Red": 0.67,
"Red edge": 0.66,
"NIR": 0.6
}
# Select panel region from radiance image
print(
'Mean Radiance in panel region: {:1.3f} W/m^2/nm/sr'.format(meanRadiance))
panelReflectance = panelCalibration[bandName]
radianceToReflectance = panelReflectance / meanRadiance
print('Radiance to reflectance conversion factor: {:1.5f}'.format(
radianceToReflectance))
reflectanceImage = radianceImage * radianceToReflectance
plotutils.plotwithcolorbar(reflectanceImage, 'Converted Reflectane Image')
# ulx = int(numpy.min([nw_x,sw_x,ne_x,se_x])*1.2)
# lrx = int(numpy.max([nw_x,sw_x,ne_x,se_x])*0.8)
# uly = int(numpy.min([nw_y,sw_y,ne_y,se_y])*1.2)
# lry = int(numpy.max([nw_y,sw_y,ne_y,se_y])*0.8)
# markedImg = reflectanceImage.copy()
# cv2.rectangle(markedImg,(ulx,uly),(lrx,lry),(0,255,0),3)
# panelRegionRefl = reflectanceImage[uly:lry, ulx:lrx]
# panelRegionReflBlur = cv2.GaussianBlur(panelRegionRefl,(55,55),5)
# plotutils.plotwithcolorbar(panelRegionReflBlur, 'Smoothed panel region in reflectance image')
# print('Min Reflectance in panel region: {:1.2f}'.format(panelRegionRefl.min()))
# print('Max Reflectance in panel region: {:1.2f}'.format(panelRegionRefl.max()))
# print('Mean Reflectance in panel region: {:1.2f}'.format(panelRegionRefl.mean()))
# print('Standard deviation in region: {:1.4f}'.format(panelRegionRefl.std()))