Implementation in R a pipeline that uses AROSICS to perform a global or local co-registration on a file or a group of files located inside a folder
Usage
align_Mosa(
path_in,
ref_filepath,
out_dir_path,
corr_type = "global",
max_shift = 250L,
max_iter = 100L,
min_reliability = 60,
grid_res = 1000L,
window_size = NULL,
window_pos = list(NULL, NULL),
mp = NULL,
save_data = TRUE,
save_vector_plot = FALSE,
apply_matrix = FALSE,
suffix = ""
)Arguments
- path_in
character. Path to the target images, or to a folder containing multiple target images. Images must be of Geotiff format.
- ref_filepath
character. Path to the reference image.
- out_dir_path
character. Directory where the outputs are saved.
- corr_type
character. Type of co-registration. Either 'global' (default) or 'local'.
- max_shift
integer. Maximum shift distance in reference image pixel units
- max_iter
integer. Maximum number of iterations for matching (default: 5).
- min_reliability
integer. Minimum reliability threshold (in percents), below which tie points are marked as false-positives. Only applies to local co-registration.
- grid_res
integer. Tie point grid resolution in pixels of the target image (x-direction). Only applies to local co-registration. By default, generates a 25*25 points grid
- window_size
integer. Custom matching window size (in pixels) as (X, Y) tuple (default: (1000, 1000)).
- window_pos
list. Custom matching window position as (X, Y) map coordinate in the same projection as the reference image (default: central position of image overlap). Only used when performing global co-registration.
- mp
integer or NULL. Number of CPUs to use. If None (default), all available CPUs are used. If mp=1, no multiprocessing is done.
- save_data
logical. Saves the transformation metadata in a .pkl file, and the tie points data in a csv file. The latter only happens when performing local co-registration.
- save_vector_plot
logical. saves the a map of the calculated tie point grid in a JPEG file. Has an effect only when performing local co-registration.
- apply_matrix
logical. When correcting multiple images, applies the shifts computed for the first image to all the remaining ones, instead of computing the shifts independently. Allows for better alignement and faster computing time. WARNING : Currently, if inputs images don't all have the same extent, temporary padded images need to be created. We hope to change that soon ; until then, apply_matrix is disabled by default)
- suffix
character. Text to add at the end of the output filenames.
Examples
if (FALSE) { # \dontrun{
align_Mosa(path_in = "path_to_ortho.tif",
ref_filepath = "ref_image.tif",
out_dir_path = "my_output_dir",
corr_type = "local",
grid_res = 500,
save_data = TRUE,
save_vector_plot = TRUE
)
align_Mosa(path_in = "path_to_input_folder",
ref_filepath = "ref_image.tif",
out_dir_path = "my_output_dir",
corr_type = "local",
grid_res = 500,
save_data = FALSE,
mp = 5,
)
align_Mosa(path_in = "path_to_input_folder",
ref_filepath = "ref_image.tif",
out_dir_path = "my_output_dir",
corr_type = "global",
max_shift = 200,
save_data = TRUE,
apply_matrix = TRUE,
mp = 1
)
} # }