Save R workspace with antsImage wont work at reload. about antsr HOT 3 CLOSED

This is because the images are internally represented as pointers. Once
you close R and restart it, there's no way to recover where the pointer
points to. You will need to actually save the image as a Nifti (or
similar) and re-read from R.

On Fri, Dec 5, 2014 at 3:54 PM, dorianps [email protected] wrote:

I am having this issue all the time. AntsImages are unusuable if saved in
.R files and then reloaded.

For example, I load antsImages in workspace, save the workspace, and
reload it again later. What happens is that antsImages seem to be there,
but are compromised. If I try to use them R goes in segmentaiton fault.
There are two examples below, first I load an .R file, use mask from
within it and R crashes. Second I remove mask and reload it again, and all
works.
Is this a bug or antsImages S4 objects simply cannot be saved?

######################################
Welcome! Loading ANTsR...
ANTsR is loaded.

load(file="subjectdata.R")
mask
An object of class "antsImage"
Slot "pixeltype":
[1] "float"

Slot "dimension":
[1] 3

Slot "pointer":

ls()
[1] "imageList" "mask" "mydata" "thick" "workfolder"
mat<-imagesToMatrix(imageList, mask)

*** caught segfault ***
address (nil), cause 'memory not mapped'

Traceback:
1: .Call("antsImage_RelationalOperators", e1, e2, region, operator,
PACKAGE = "ANTsR")
2: mask > 0
3: mask > 0
4: which(mask > 0)
5: imagesToMatrix(imageList, mask)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection: q()
Selection: 3
#########################################
working example

Welcome! Loading ANTsR...
ANTsR is loaded.

load(file="subjectdata.R")
rm(mask)
mask<-antsImageRead('processing/smo_4_NormCortThick/mask.nii.gz', 3)
mat<-imagesToMatrix(imageList, mask)

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#7.

from antsr.

yes - ben is correct ... there is a way around this. if you convert the
image to an array, you can save ... but would have to reconvert back to an
image to use it as an image. there is probably a way to automate this
process and prevent this issue from happening: basically (optionally)
store the array within the ants image class. if the pointer is null then
reload the image from the array. maybe there is a better way, though.

brian

On Fri, Dec 5, 2014 at 3:59 PM, bkandel [email protected] wrote:

This is because the images are internally represented as pointers. Once
you close R and restart it, there's no way to recover where the pointer
points to. You will need to actually save the image as a Nifti (or
similar) and re-read from R.

On Fri, Dec 5, 2014 at 3:54 PM, dorianps [email protected]
wrote:

I am having this issue all the time. AntsImages are unusuable if saved
in
.R files and then reloaded.

For example, I load antsImages in workspace, save the workspace, and
reload it again later. What happens is that antsImages seem to be there,
but are compromised. If I try to use them R goes in segmentaiton fault.
There are two examples below, first I load an .R file, use mask from
within it and R crashes. Second I remove mask and reload it again, and
all
works.
Is this a bug or antsImages S4 objects simply cannot be saved?

######################################
Welcome! Loading ANTsR...
ANTsR is loaded.

load(file="subjectdata.R")
mask
An object of class "antsImage"
Slot "pixeltype":
[1] "float"

Slot "dimension":
[1] 3

Slot "pointer":

ls()
[1] "imageList" "mask" "mydata" "thick" "workfolder"
mat<-imagesToMatrix(imageList, mask)

*** caught segfault ***
address (nil), cause 'memory not mapped'

Traceback:
1: .Call("antsImage_RelationalOperators", e1, e2, region, operator,
PACKAGE = "ANTsR")
2: mask > 0
3: mask > 0
4: which(mask > 0)
5: imagesToMatrix(imageList, mask)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection: q()
Selection: 3
#########################################
working example

Welcome! Loading ANTsR...
ANTsR is loaded.

load(file="subjectdata.R")
rm(mask)
mask<-antsImageRead('processing/smo_4_NormCortThick/mask.nii.gz', 3)
mat<-imagesToMatrix(imageList, mask)

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#7.

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#7 (comment).

from antsr.

Thank you. I had the feeling this was the case.
This might confuse users. It would be great if there is a way to skip the saving of antsImages, or convert automatically to array, or perhaps show a notice that antsImages cannot be saved/loaded from data files. By the way, from what I understand these are regular S4 objects, it's weird that R itself is allowing to save pointers like any other data class.

Dorian

from antsr.