search

tractatus / wholebrain

R package for segmentation, registration and generating web-based brain atlases from microscope images
GNU General Public License v3.0
83 stars 42 forks source link

Error in createfilter(filename) : could not find function "createfilter" #27

Closed arashnh11 closed 4 years ago

arashnh11 commented 4 years ago

Hi Daniel,

First of all, thanks for sharing your great work and for being responsive to the issues. I am working on a containerized version of your code to run it on a high-performance computing cluster and I almost got there. In fact, I could get the screenshot below at some point. But later on, R couldn't find the "createfilter" function library from the Namespace? Could you please have a look?

Screen Shot 2019-12-19 at 4 36 12 PM

library(wholebrain) Loading required package: Rcpp Loading required package: png Loading required package: MASS Loading required package: grImport Loading required package: grid Loading required package: XML Loading required package: sp Loading required package: rgl Loading required package: misc3d Loading required package: plyr WholeBrain (version 0.1.35) "Thurstone" by Daniel Fürth, 2018, by using this software you agree to the EULA filename<-system.file('sample_tiles/rabiesEGFP.tif', package='wholebrain') filter<-createfilter(filename) Error in createfilter(filename) : could not find function "createfilter"

arashnh11 commented 4 years ago

Maybe should I explicitly point to those library function definitions? If so how can I get the path?

tractatus commented 4 years ago

@arashnh11 Dont think I ever included a createfilter function. I can see it is on my to do list. Probably my idea was for people to have a quick qay to initialize such an object.

A filter is just a list object with something like this:

myfilter<-list(alim = c(40, 999),
threshold.range = c(0, 1463),
eccentricity = 360L,
Max = 1500, Min = 0,
brain.threshold = 30,
resize = 0.03,
blur = 3,
downsample = 0.25)
arashnh11 commented 4 years ago

Oh, shoot... I was testing with the Archlinux verification that had that function call instead of the ubuntu/Debian one which indeed had a different function call with segment. This is resolved. library(wholebrain) filename<-system.file('sample_tiles/rabiesEGFP.tif', package='wholebrain') seg<-segment(filename)

arashnh11 commented 4 years ago

Also, I am working with our researchers to verify this container. Once stable, I would be happy to share that with you and I am sure that would make a lot of researchers who are struggling to install this on their Linux systems happy.

The solution is a singularity/docker container from ubuntu 14.04 that is running on CentOS 7.6 Any operating system that has singularity installed should be able to execute the container.

tractatus commented 4 years ago

@arashnh11 sounds good. Let me know how it goes.