Source: Pak, Lin & Law (2024) Correction of systematic image misalignment in direct georeferencing of UAV imagery (manuscript in preparation)

1. Install conda
2. If the conda default solver is slow, use the libmamba solver (optional but recommended)
   • conda update -n base conda
   • conda install -n base conda-libmamba-solver
   • conda config --set solver libmamba
3. Create a virtual environment, which will create a virtual environment with the name called micasenseGeoreferencing: conda env create --file micasenseGeoreferencing.yml
4. After all the required packages have been installed, conda activate micasenseGeoreferencing

The preprocessing of the Micasense UAV imagery is facilitated with the Micasense's image processing library, with some modifications to it, as included in this repository.

1. Open the preprocessing.ipynb to preprocess the UAV imagery
2. See georeferencing.ipynb for direct georeferencing of UAV imagery
3. See alignmentError.ipynb for aligning the systematic image misalignment in UAV imagery

Check whether the following folders and data are present after running preprocessing.ipynb. See instructions in preprocessing.ipynb

• flight folder (a folder that contains all the images captured from a flight, as well as meta data, and processed data used the micasense's image processing library).
• flight_attributes (a folder that contains the metadata of each capture from the flight).
  • flight_attributes.csv a csv file that is automatically generated from the modified micasense preprocessing library
  • gps_index.txt a text file that contains the selected gps points selected from the GUI in algorithms/select_GPS.py. Run algorithms/select_GPS.py to interactively select the start and end points of the flight swaths.
• RawImg (a folder that contains all the band images captured from a flight e.g. IMG_0000_1.tif to IMG_xxxx_10.tif. One can easily create a folder named "RawImg" and shift all the raw images here).
  • IMG is the prefix for all image captures
  • _0000 is the index of the image (each capture should have a unique index)
  • _1 is the band number of the capture, e.g. for a 10-band image, the band number will range from 1 - 10. So each capture will have 10 images e.g. IMG_0000_1 to IMG_0000_10.
• stacks (a folder that contains the processed band images, where band images are all band-aligned to create a multispectral image). e.g. the postfix (as a default) always ends with _1, but all images in the stacks folder should have a unique image index.
• thumbnails (a folder that contains the thumbnail rgb of each capture, which allows for fast plotting of rgb orthomosaics)

flight folder (imagePath)
|
│
└───flight_attributes
│   │   flight_attributes.csv
│   │   gps_index.txt
│   
└───RawImg
|   │   IMG_0000_1.tif
|   │   IMG_0000_2.tif
|   |   ...
└───stacks
|   │   IMG_0000_1.tif
|   │   IMG_0001_1.tif
|   |   ...
└───thumbnails
    │   IMG_0000_1.jpg
    │   IMG_0001_1.jpg
    |   ...