About the FIELDimageR category

[pierotofy]

This discussion group provides an online source of information about the FIELDimageR package.

The pipeline scripts and further information, as well as links to the original publication, can be found at the FIELDimageR Github page

FIELDimageR is a R package to analyze orthomosaic images from agricultural field trials. This package is a compilation of functions to analyze pos-mosaicking images from research fields, and allows to: crop the image; remove soil effect; build vegetation indices; rotate the image; build the plot shapefile; extract information for each plot; and evaluate stand count, canopy percentage, and plant height. It is a complete pipeline developed primarily to support curation, data extraction, research, and breeding programs wishing to utilize images for the cost-effective phenome-wide characterization of plant resources.

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• For bug reports please include as much information as possible including any error messages.

Thank you !!!

[amithaldar87]

Thank you for sharing, it looks very promising. I am trying to install the package in my RStudio with R version 3.6.1, unfortunately, its saying the FIELDimageR is not available for R version 3.6.1

Here is what I have followed

1. Installed Rtools35 (as compatible with R3.6.1)

   library(devtools)
   install_github(“filipematias23/FIELDimageR”)

#error
Failed to install ‘unknown package’ from GitHub:
Timeout was reached: [api.github.com] Operation timed out after 10001 milliseconds with 0 out of 0 bytes received

#alternatively
library(remotes)
remotes::install_github(“filipematias23/FIELDimageR”)

#error
Failed to install ‘unknown package’ from GitHub:
Timeout was reached: [api.github.com] Operation timed out after 10000 milliseconds with 0 out of 0 bytes received

#if through conventional way
install.packages("FIELDimageR")

#error
Warning in install.packages :
package ‘FIELDimageR’ is not available (for R version 3.6.1)

Can anyone help me to resolve this issue?

[filipematias]

Hi @amithaldar87, thanks for asking.

This error is new to me. I am using R version 3.6.1 and it is working fine.
Try it first:

library(devtools)
install_github(“OpenDroneMap/FIELDimageR”)

If not, try:

Open a new R window:

remove.packages(“devtools”)

Close this R window.

Open again a new R window:

install.packages(“devtools”)
library(devtools)
install_github(“filipematias23/FIELDimageR”)
library(FIELDimageR)

Close this R window.

If it doesn’t work, try reinstalling R ( https://brieger.esalq.usp.br/CRAN/ ) and RStudio ( Download RStudio | The Popular Open-Source IDE from Posit ). With this, you will have to reinstall all packages that you normally use. Something that I always like to do, when installing a new version I use “install R for the first time” to keep all the versions that I normally use in my scripts.

See if this works and let me know the errors.

[filipematias]

FIELDimageR is working well for R version 3.6.1 and earlier. R version 3.6.3 works for some systems and not for others, I do not know yet and I am looking for answers. But, one solution that worked for some users is to install the newest R version 4.0.0 (https://brieger.esalq.usp.br/CRAN/) and use the following code:

install.packages(“devtools”)
devtools::install_github(“filipematias23/FIELDimageR”, type = “source”)

If it doesn’t work, try to use:

devtools::install_github(“filipematias23/FIELDimageR”, type = “source”, dependencies = F)
install.packages(“raster”)
install.packages(“doParallel”)
install.packages(“grDevices”)
install.packages(“plyr”)
install.packages(“BiocManager”)
BiocManager::install(“EBImage”)

Please, let me know if one of these two solutions worked for you.

[amithaldar87]

Hi @filipematias,

As per your instructions, I have re-installed the updated versions of R-4.0.0 and RStudio-1.2.5042.

Followed all the methods to install.

install.packages(“FIELDimageR”)

Error is same as before

Warning in install.packages :
package ‘FIELDimageR’ is not available (for R version 4.0.0)

Through devtools

devtools::install_github(“filipematias23/FIELDimageR”, type = “source”)
devtools::install_github(“filipematias23/FIELDimageR”, type = “source”, dependencies = F)

install_github(“filipematias23/FIELDimageR”)
install_github(“OpenDroneMap/FIELDimageR”)

Error from all aforesaid codes are same

Error: Failed to install ‘unknown package’ from GitHub:
Timeout was reached: [api.github.com] Operation timed out after 10000 milliseconds with 0 out of 0 bytes received

I hope I am the only one who is facing this issue and you may recommend some alternative ways to resolve the issues. I also would like to convey you that I am working from a restrictive environment (Company IT Policy); however; I have a local admin account. Which means I should not face any issue to access any third party urls. But if this an issue, then I should be able to explain it to our IT. Your thoughts please.

[filipematias]

I am sorry, I have no idea.
I tried on other computers and 4.0.0 is working perfectly.

Could you try the following code again:

install.packages(“raster”)
install.packages(“doParallel”)
install.packages(“grDevices”)
install.packages(“plyr”)
install.packages(“BiocManager”)
BiocManager::install(“EBImage”)
devtools::install_github(“filipematias23/FIELDimageR”)

I will keep searching.
Best

[amithaldar87]

No issues. I did follow all the steps, still not resolved the issue. Thank you so much for your attention and time to respond. I really appreciate it. Meanwhile, I will also try to find some solution.

Thank you

[filipematias]

Hi @amithaldar87

Could you try the manual way to install using tar.gz, please?

I made the following scheme to help you:

1. Access the GitHub page: GitHub - OpenDroneMap/FIELDimageR: FIELDimageR: A R package to analyze orthomosaic images from agricultural field trials. This package is a compilation of functions to analyze pos-mosaicking images from research fields, and allows to: crop the image; remove soil effect; build vegetation indices; rotate the image; build the plot shapefile; extract information for each plot; and evaluate stand count, canopy percentage, and plant height.
2. Download the “FIELDimageR-master.zip”
3. Save this file in one folder from where you will open a R window
4. Open R and type:

unzip(“FIELDimageR-master.zip”)
file.rename(“FIELDimageR-master”, “FIELDimageR”)
shell(“R CMD build FIELDimageR”)
install.packages(“FIELDimageR_0.1.6.tar.gz”, repos = NULL, type=“source”)
library(FIELDimageR)

5. Start use FIELDimageR.

Let me know if it works.
Best,
Filipe Matias

[amithaldar87]

Hi @filipematias,

This worked perfectly. Thank you so much Filipe for resolving the issue.

I was almost given up on it. I tried installing it manually through direct package installer using Zip, though Git, creating repository and many more but none of the hacks worked.

Thank you again for your attention and time. I will now start exploring the tools and will let you know if I am able to optimize it for forestry applications.

Cheers

Amit

[filipematias]

That’s awesome, you got it !!!

I am glad to know.

Let us know about your results and experience, also any suggestion to improve FIELDimageR is super welcome.

Best,
Filipe

[jkairo]

Hi Filipe,

I am very interested into FieldImageR but I am having some difficulties trying to install it in Ubuntu. I installed R and Rstudio, and I followed the steps:

unzip(“FIELDimageR-master.zip”)
file.rename(“FIELDimageR-master”, “FIELDimageR”)
shell(“R CMD build FIELDimageR”) # or system(“R CMD build FIELDimageR”)
install.packages(“FIELDimageR_0.2.0.tar.gz”, repos = NULL, type=“source”) # Make sure to use the right version (e.g. 0.2.0)

Though, the last step send me this error:

install.packages(“FIELDimageR_0.2.0.tar.gz”, repos = NULL, type=“source”)
Installing package into ‘~/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
Warning: invalid package ‘FIELDimageR_0.2.0.tar.gz’
Error: ERROR: no packages specified
Warning in install.packages :
installation of package ‘FIELDimageR_0.2.0.tar.gz’ had non-zero exit status

And I don’t know what to do (I know nothing on code). I wonder if you can help me.

Thanks,

Jairo

[DGRobotik]

Hi Filipe,

I get timed out error while installing through docker on windows.
Below is the message I get:

Have any idea what may cause the issue? Thanks a lot.
Özden

[mbilenky2015]

Thanks for creating this! I started to use this last year and the ‘fieldCrop’ function worked fine. I am trying it again and I am getting an error that R cannot find the function. Any tips?

[tejasri19]

Hi Jkairo,

Im also facing the same problem while installing FieldImageR. Can you please share how you solved?

[jkairo]

Hi tejasri19, sorry can’t help. I had to change my OS and not longer work with Ubuntu.

[blkwht]

Hello, could someone help me installing FIELDimageR with R 4.2.1 I am having issues. Can´t figure out what I am missing.

Thanks!

[syazoo]

Have there been discussions about this being available in the windows installation?

[Ahasanul_Hoque]

Hi,

I am trying to install FIELDimageR package in R 4.3.0. I followed both methods:

install.packages(“devtools”) devtools::install_github(“OpenDroneMap/FIELDimageR”)

If the method above doesn’t work, use the next lines by downloading the FIELDimageR-master.zip file

setwd(“~/FIELDimageR-master.zip”) # ~ is the path from where you saved the file.zip unzip(“FIELDimageR-master.zip”) file.rename(“FIELDimageR-master”, “FIELDimageR”) shell(“R CMD build FIELDimageR”) # or system(“R CMD build FIELDimageR”) install.packages(“FIELDimageR_0.3.2.tar.gz”, repos = NULL, type=“source”)

But in both cases I found the attached error message. I need help to solve this issue.

Error Message:
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: object ‘elide’ is not exported by ‘namespace:maptools’
Execution halted
ERROR: lazy loading failed for package ‘FIELDimageR’

• removing ‘C:/Users/ahasa/AppData/Local/R/win-library/4.3/FIELDimageR’
  Warning message:
  In i.p(…) :
  installation of package ‘C:/Users/ahasa/AppData/Local/Temp/RtmpQFwJcG/file5b0c1e624bc9/FIELDimageR_0.3.3.tar.gz’ had non-zero exit status