General purpose TIFF file I/O for R users. Currently the only such package with read and write support for TIFF files with floating point (real-numbered) pixels, and the only package that can correctly import TIFF files that were saved from 'ImageJ' and write TIFF files than can be correctly read by 'ImageJ' < https://imagej.nih.gov/ij/>. Also supports text image I/O.
This is a general purpose TIFF I/O utility for R. The
package already exists for
this purpose but
ijtiff adds some functionality and overcomes some
ijtiffcan write TIFF files whose pixel values are real (floating-point) numbers;
ijtiffcan read and write text images;
tiffstruggles to interpret channel information and gives cryptic errors when reading TIFF files written by the ImageJ software;
ijtiffworks smoothly with these images.
To learn about
ijtiff and how to use it, visit the package website at
ijtiff requires you to have the
libtiff C library installed. To
sudo apt-get install libtiff5-dev, or if that fails, try
sudo apt-get install libtiff4-dev.
sudo yum install libtiff5-dev, or if that doesn’t work, try
sudo yum install libtiff4-dev.
brew install libtiff.
You can install
ijtiff from CRAN (recommended) with:
You can install the development version from GitHub with:
This package uses a lot of code from the original
tiff package by
If you’re authoring a package which is to depend on
ijtiff and you’re
using AppVeyor, be sure to force AppVeyor to use 64-bit architecture.
This avoids some peculiarities of 32-bit AppVeyor which cause
installations to fail. You can see how to do this in the
appveyor.yml file in this repository.
Contributions to this package are welcome. The preferred method of contribution is through a github pull request. Feel free to contact me by creating an issue. Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.
write_txt_img()was using decimal points for integers (e.g. 3.000 instead of just 3).
configurescript to deal with lack of
stack_to_linescan()useful for FCS data.
write_tif()is now slightly (<10%) faster.
write_tif()messages are now more informative.
count_imgs()counts the number of images in a TIFF file without reading the images themselves.
read_tags()reads the tags from TIFF images without reading the images themselves.
display()is more flexible, accepting 3 and 4-dimensional arrays, just displaying the first frame from the first channel.
libtiffissues (thanks to Jeroen Ooms).
protection stack overflowerror for TIFFs with many images.