import argparse

import os

import time

from pathlib import Path

import numpy as np

import pandas as pd

from mapboxgl.utils import df_to_geojson

from skimage.transform import ProjectiveTransform

import micasense.capture as capture

import micasense.imageset as imageset

parser = argparse.ArgumentParser(

)

parser.add_argument('--imagepath', required=True, type=Path)

parser.add_argument('--outputpath', required=True, type=Path)

parser.add_argument('--panelpath', required=True, nargs='*')

parser.add_argument('--alignmentimage')

args = parser.parse_args()

print(args.imagepath)

print(args.panelpath)

pan_sharpen = True

use_dls = True

image_path = args.imagepath

panel_names = args.panelpath

panelCap = capture.Capture.from_filelist(panel_names)

outputPath = args.outputpath.resolve().as_posix()

print(outputPath)

thumbnailPath = args.outputpath / 'thumbnails'

thumbnailPath = thumbnailPath.resolve().as_posix()

print(thumbnailPath)

cam_model = panelCap.camera_model

cam_serial = panelCap.camera_serial

if cam_model == 'RedEdge-P' or cam_model == 'Altum-PT':

panchro_cam = True

else:

panchro_cam = False

pan_sharpen = False

if len(panelCap.camera_serials) > 1:

cam_serial = "_".join(panelCap.camera_serials)

print("Serial number:", cam_serial)

else:

cam_serial = panelCap.camera_serial

print("Serial number:", cam_serial)

overwrite = False # can be set to False to continue interrupted processing

generateThumbnails = True

if panel_names is not None:

panelCap = capture.Capture.from_filelist(panel_names)

else:

panelCap = None

if panelCap is not None:

if panelCap.panel_albedo() is not None and not any(v is None for v in panelCap.panel_albedo()):

panel_reflectance_by_band = panelCap.panel_albedo()

else:

panel_reflectance_by_band = [0.49] * len(panelCap.eo_band_names()) # RedEdge band_index order

panel_irradiance = panelCap.panel_irradiance(panel_reflectance_by_band)

img_type = "reflectance"

else:

if use_dls:

img_type = 'reflectance'

else:

img_type = "radiance"

imgset = imageset.ImageSet.from_directory(image_path)

data, columns = imgset.as_nested_lists()

df = pd.DataFrame.from_records(data, index='timestamp', columns=columns)

geojson_data = df_to_geojson(df, columns[3:], lat='latitude', lon='longitude')

if panchro_cam:

warp_matrices_filename = cam_serial + "_warp_matrices_SIFT.npy"

else:

warp_matrices_filename = cam_serial + "_warp_matrices_opencv.npy"

if Path('./' + warp_matrices_filename).is_file():

print("Found existing warp matrices for camera", cam_serial)

load_warp_matrices = np.load(warp_matrices_filename, allow_pickle=True)

loaded_warp_matrices = []

for matrix in load_warp_matrices:

if panchro_cam:

transform = ProjectiveTransform(matrix=matrix.astype('float64'))

loaded_warp_matrices.append(transform)

else:

loaded_warp_matrices.append(matrix.astype('float32'))

if panchro_cam:

warp_matrices_SIFT = loaded_warp_matrices

else:

warp_matrices = loaded_warp_matrices

print("Loaded warp matrices from", Path('./' + warp_matrices_filename).resolve())

else:

print("No warp matrices found at expected location:", warp_matrices_filename)

if not os.path.exists(outputPath):

os.makedirs(outputPath)

if generateThumbnails and not os.path.exists(thumbnailPath):

os.makedirs(thumbnailPath)

with open(os.path.join(outputPath, 'imageSet.json'), 'w') as f:

f.write(str(geojson_data))

try:

irradiance = panel_irradiance + [0]

except NameError:

irradiance = None

start = time.time()

for i, capture in enumerate(imgset.captures):

outputFilename = capture.uuid + '.tif'

thumbnailFilename = capture.uuid + '.jpg'

fullOutputPath = os.path.join(outputPath, outputFilename)

fullThumbnailPath = os.path.join(thumbnailPath, thumbnailFilename)

if (not os.path.exists(fullOutputPath)) or overwrite:

if (len(capture.images) == len(imgset.captures[0].images)):

if panchro_cam:

capture.radiometric_pan_sharpened_aligned_capture(warp_matrices=warp_matrices_SIFT,

irradiance_list=irradiance)

else:

capture.create_aligned_capture(irradiance_list=irradiance, warp_matrices=warp_matrices)

capture.save_capture_as_stack(fullOutputPath, pansharpen=pan_sharpen, sort_by_wavelength=False)

if generateThumbnails:

capture.save_capture_as_rgb(fullThumbnailPath)

current = time.time()

diff = current - start

print("Saved stack", str(i), "of", str(len(imgset.captures)), "in", str(int(diff)), "seconds", end="\r")

capture.clear_image_data()

end = time.time()

print("Saving time:", end - start)