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Update README.md #10

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robinsv Apr 19, 2024
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36 changes: 30 additions & 6 deletions README.md
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Expand Up @@ -57,6 +57,8 @@ All diamorse programs use the NetCDF3 file format for input and output of image

Once you have a greyscale image in NetCDF3 format you can generate the persistence pairs, Morse skeleton and basins using the following.

CAUTION: Python scripts are out of date.

* diamorse/python/persistence.py

Python2.7 wrapper for the vector field and persistence computations
Expand Down Expand Up @@ -94,18 +96,40 @@ Once you have a greyscale image in NetCDF3 format you can generate the persisten
USAGE: `diamorse $ ./python/plot_basins -h` will display the full list of options.


The following commandline executable programs provide lower level functionality for 3d images. These compute the Morse vector field from a NetCDF image, simplify it to a desired threshold, compute persistence pairs, output the Morse Skeleton and pore labels as NetCDF files for visualisation.

NOTE: 3D visualisation is not currently provided as part of diamorse.

* `diamorse $ ./bin/VectorField tomo_float_input.nc [OUTPUT]`

OUTPUT defaults to vector_field_input_GVF.nc

* `diamorse $ ./bin/Simplify tomo_float_input.nc vector_field_input_GVF.nc [OUTPUT]`

OUTPUT defaults to vector_field_input_GVF_SMP.nc

* diamorse/bin/VectorField
OPTION: -p <float> (default = 1.0) persistence limit for feature cancellation

OPTION: -s <float> size limit for feature cancellation

OPTION: -t <float> value of a level threshold to preserve

* `diamorse $ ./bin/PersistencePairs tomo_float_input.nc vector_field_input_GVF_SMP.nc [OUTPUT]`

* diamorse/bin/Simplify
OUTPUT defaults to persistence_input_GVF_SMP_PP.txt

* diamorse/bin/Skeleton
* `diamorse $ ./bin/Skeleton tomo_float_input.nc vector_field_input_GVF_SMP.nc [OUTPUT]`

* diamorse/bin/Pores
OUTPUT defaults to segmented_input_GVF_SMP_SKL.nc

The above programs provide lower level functionality for 3d images. These compute the Morse vector field from a NetCDF image, simplify it to a desired threshold, output the Morse Skeleton and pore labels as NetCDF files for visualisation.
OPTION: -t <float> (default = 0.0) level set threshold

3D visualisation is not currently provided as part of diamorse.
* `diamorse $ ./bin/Pores tomo_float_input.nc vector_field_input_GVF_SMP.nc [OUTPUT]`

OUTPUT defaults to labels_input_GVF_SMP_POR.nc

OPTION: -t <float> (default = 0.0) level set threshold



# License
Expand Down