A wrapper around the ImageJ plugin "ImageStabilizer" that enables the jar to be run from command line with conventional flags
https://imagej.net/Image_Stabilizer https://www.cs.cmu.edu/~kangli/code/Image_Stabilizer.html
The original ImageJ plugin above requires images to be open in FIJI/ImageJ and writes them to new windows, or if it's a virtual stack, to disk. It's not possible to execute it directly from command line without writing ImageJ macros and executing those in a headless mode ImageJ instance. Instead, I wrote this simple jar that slightly modifies the original source code to accept files/paths instead of IJ window's ImageProcessor. The "log-applier" functionality is included as well.
from command line, type
java -jar <path to ImageStabilizer.jar> <flags>
Allowed flags are:
-applier,--logApplier <arg> Flag to signify that a log file will be
applied
-i,--input <arg> input file path
-iter,--maxIterations <arg> Maximum num iterations (default 200)
-log,--logEnabled Flag to turn on coordinate logging
-o,--output <arg> output file path
-p,--maxPyramids <arg> Maximum Pyramid Levels: 0, 1, 2, 3, 4
-s,--substring <arg> substring with which to filter the input
files
-t,--transformation <arg> transformation type: Translation or Affine
-tol,--maxTolerance <arg> Error Tolerance (default 1e-7
-update,--updateCoeff <arg> Template Update Coefficient (default 0.9):
0 - 1
-z,--zSlice <arg> Flag to turn on coordinate logging
REQUIRED flags are:
-i,--input <arg> input file path
-o,--output <arg> output file path
-t,--transformation <arg> transformation type: Translation or Affine
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