- Ensure using latest version of
ijtiff. Old version is buggy.
- Fix some poor C++ typing.
- The package now has it’s own S3 class system:
th for thresholds.
threshed_arr for thresholded arrays.
stack_threshed_arr for stack-thresholded arrays.
arr_mask for a mask of an array.
- The package no longer depends on
EBImage package from Bioconductor.
EBImage is a great package but CRAN packages are easier to install if they depend on CRAN packages only. Now
ijtiff is used instead.
can_be_integer() is gone. Use
- Pillar statistics are no longer exported. Should you be looking for them, they are exported in the
rJava (and hence java) dependency has been removed. All functions which used to be in java are now done in
fail arguments of
med_stack_thresh() now work like the
na argument of
auto_thresh_apply_mask() now have the abbreviations
- The functions now have an
ignore_na argument for
- It is now the case that for a threshold x, values greater than or equal to x are deemed to “pass” the thresholding and values less than x are deemed to “fail” the thresholding. Before what was happening was that values greater than x were deemed to have passed and values less than or equal to x were deemed to have failed.
- There’s a new thresholding method
"Huang2" which is very similar to (but not the same as and hence should not be assumed to give the same results as)
"Huang" and is much faster when applied to 16-bit images.
mean_stack_thresh() can now handle thresholds between 0 and 1.
ignore_white instead of
ignore.white to comply with tidyverse style guide.
ignore_white options to
- Fix issues for Mean and Otsu methods concerning 16-bit images.
- Renamed all exported functions to be in
- The skip.consts option in the stack_thresh functions is gone. Now these functions error if you pass them a constant array.
- Add option to manually set threshold.
- Improve OSX installation instructions in README.md.
- The first CRAN-worthy version.