StevenVB12
Error in transformRef == "meanshape" : comparison (==) is possible only for atomic and list type
Good morning, Steven!
Thank you very much for your package and for having this website to solve the problems that arise with patternize.
I'm a fairly novice R user, and I'm trying to use your package to compare colour patterns in wings of different species of neuroptera. I have encountered a problem when applying the alignLan function. I get the following error when trying to apply the function:
Error in transformRef == "meanshape" : comparison (==) is possible only for atomic and list types.
My script is as follows:
imageList_aligned <- alignLan(imageList= imageList, landList = landmarkList, transformRef = target, adjustCoords = TRUE, plotTransformed = T, resampleFactor = 5, cartoonID = "asc09_Hd-0", maskOutline = outline_asc09_Hd, inverse = FALSE)
The images I'm working with are in png and each of them has different extent, I don't know if that could give any problem. I have tried to do the same process but transforming them into jpg, but I get the same error.
Thank you very much!
Julene.
HI Julene,
It sounds like something may be wrong with the ‘target’ (maybe it is empty?).
If you struggle resolving it, feel free to send me some of your images, landmarks and script and I’ll help setting up a working example.
Best,
Steven
From: Julenetxu1 @.> Sent: Monday, 24 April 2023 12:36 To: StevenVB12/patternize @.> Cc: Subscribed @.***> Subject: [StevenVB12/patternize] Error in transformRef == "meanshape" : comparison (==) is possible only for atomic and list type (Issue #39)
Good morning, Steven!
Thank you very much for your package and for having this website to solve the problems that arise with patternize.
I'm a fairly novice R user, and I'm trying to use your package to compare colour patterns in wings of different species of neuroptera. I have encountered a problem when applying the alignLan function. I get the following error when trying to apply the function:
Error in transformRef == "meanshape" : comparison (==) is possible only for atomic and list types.
My script is as follows:
imageList_aligned <- alignLan(imageList= imageList, landList = landmarkList, transformRef = target, adjustCoords = TRUE, plotTransformed = T, resampleFactor = 5, cartoonID = "asc09_Hd-0", maskOutline = outline_asc09_Hd, inverse = FALSE)
The images I'm working with are in png and each of them has different extent, I don't know if that could give any problem. I have tried to do the same process but transforming them into jpg, but I get the same error.
Thank you very much!
Julene.
— Reply to this email directly, view it on GitHubhttps://github.com/StevenVB12/patternize/issues/39, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABQOC43GWG7SNRO5PNDXYOLXCZJP7ANCNFSM6AAAAAAXJMFJFM. You are receiving this because you are subscribed to this thread.Message ID: @.@.>>
Hello, Steven!
I have checked the target object and apparently there is no problem with it. I don't know if it could be a formatting problem or something similar. I'll send you the script, the images and the landmarks:
https://drive.google.com/drive/folders/1N6XDXY5K6t60uJH8opCgR3z-aaUfuUpZ?usp=sharing
Thanks again for your help!
Best regards, Julene.
El lun, 24 abr 2023 a las 17:35, Steven M. Van Belleghem (< @.***>) escribió:
HI Julene,
It sounds like something may be wrong with the ‘target’ (maybe it is empty?).
If you struggle resolving it, feel free to send me some of your images, landmarks and script and I’ll help setting up a working example.
Best,
Steven
From: Julenetxu1 @.> Sent: Monday, 24 April 2023 12:36 To: StevenVB12/patternize @.> Cc: Subscribed @.***> Subject: [StevenVB12/patternize] Error in transformRef == "meanshape" : comparison (==) is possible only for atomic and list type (Issue #39)
Good morning, Steven!
Thank you very much for your package and for having this website to solve the problems that arise with patternize.
I'm a fairly novice R user, and I'm trying to use your package to compare colour patterns in wings of different species of neuroptera. I have encountered a problem when applying the alignLan function. I get the following error when trying to apply the function:
Error in transformRef == "meanshape" : comparison (==) is possible only for atomic and list types.
My script is as follows:
imageList_aligned <- alignLan(imageList= imageList, landList = landmarkList, transformRef = target, adjustCoords = TRUE, plotTransformed = T, resampleFactor = 5, cartoonID = "asc09_Hd-0", maskOutline = outline_asc09_Hd, inverse = FALSE)
The images I'm working with are in png and each of them has different extent, I don't know if that could give any problem. I have tried to do the same process but transforming them into jpg, but I get the same error.
Thank you very much!
Julene.
— Reply to this email directly, view it on GitHub< https://github.com/StevenVB12/patternize/issues/39>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/ABQOC43GWG7SNRO5PNDXYOLXCZJP7ANCNFSM6AAAAAAXJMFJFM>.
You are receiving this because you are subscribed to this thread.Message ID: @.@.>>
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Hi Julene,
I think like this it should work (the target has to be the landmarks):
imageList_aligned <- alignLan(imageList = imageList, landList = landmarkList, IDlist = IDlist, transformRef = target, adjustCoords = TRUE, plotTransformed = T, resampleFactor = 5, cartoonID = "asc09_Hd-0", maskOutline = outline_asc09_Hd, inverse = FALSE)
Please let me know how it goes!
Best,
Steven
From: Julenetxu1 @.> Sent: Tuesday, 25 April 2023 16:06 To: StevenVB12/patternize @.> Cc: Steven M. Van Belleghem @.>; Comment @.> Subject: Re: [StevenVB12/patternize] Error in transformRef == "meanshape" : comparison (==) is possible only for atomic and list type (Issue #39)
Hello, Steven!
I have checked the target object and apparently there is no problem with it. I don't know if it could be a formatting problem or something similar. I'll send you the script, the images and the landmarks:
https://drive.google.com/drive/folders/1N6XDXY5K6t60uJH8opCgR3z-aaUfuUpZ?usp=sharing
Thanks again for your help!
Best regards, Julene.
El lun, 24 abr 2023 a las 17:35, Steven M. Van Belleghem (< @.***mailto:***@***.***>) escribió:
HI Julene,
It sounds like something may be wrong with the ‘target’ (maybe it is empty?).
If you struggle resolving it, feel free to send me some of your images, landmarks and script and I’ll help setting up a working example.
Best,
Steven
From: Julenetxu1 @.mailto:***@***.***> Sent: Monday, 24 April 2023 12:36 To: StevenVB12/patternize @.mailto:***@***.***> Cc: Subscribed @.***mailto:***@***.***> Subject: [StevenVB12/patternize] Error in transformRef == "meanshape" : comparison (==) is possible only for atomic and list type (Issue #39)
Good morning, Steven!
Thank you very much for your package and for having this website to solve the problems that arise with patternize.
I'm a fairly novice R user, and I'm trying to use your package to compare colour patterns in wings of different species of neuroptera. I have encountered a problem when applying the alignLan function. I get the following error when trying to apply the function:
Error in transformRef == "meanshape" : comparison (==) is possible only for atomic and list types.
My script is as follows:
imageList_aligned <- alignLan(imageList= imageList, landList = landmarkList, transformRef = target, adjustCoords = TRUE, plotTransformed = T, resampleFactor = 5, cartoonID = "asc09_Hd-0", maskOutline = outline_asc09_Hd, inverse = FALSE)
The images I'm working with are in png and each of them has different extent, I don't know if that could give any problem. I have tried to do the same process but transforming them into jpg, but I get the same error.
Thank you very much!
Julene.
— Reply to this email directly, view it on GitHub< https://github.com/StevenVB12/patternize/issues/39>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/ABQOC43GWG7SNRO5PNDXYOLXCZJP7ANCNFSM6AAAAAAXJMFJFM>.
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Hello, Steven!
I still haven't managed to solve the problem.
I didn't realise that I had defined the target wrong. I got it right with the following function:
target <- landmarkList[['asc09_Hd-0']]
It still doesn't work after running your script. I get the following error:
Error in !is.null(maskOutline) && transformRef == "meanshape" : 'length = 16' in coercion to 'logical(1)'
I don't know what could be the problem.
Thanks again for your help.
Best regards, Julene.
El mié, 26 abr 2023 a las 9:58, Steven M. Van Belleghem (< @.***>) escribió:
Hi Julene,
I think like this it should work (the target has to be the landmarks):
imageList_aligned <- alignLan(imageList = imageList, landList = landmarkList, IDlist = IDlist, transformRef = target, adjustCoords = TRUE, plotTransformed = T, resampleFactor = 5, cartoonID = "asc09_Hd-0", maskOutline = outline_asc09_Hd, inverse = FALSE)
Please let me know how it goes!
Best,
Steven
From: Julenetxu1 @.> Sent: Tuesday, 25 April 2023 16:06 To: StevenVB12/patternize @.> Cc: Steven M. Van Belleghem @.>; Comment @.> Subject: Re: [StevenVB12/patternize] Error in transformRef == "meanshape" : comparison (==) is possible only for atomic and list type (Issue #39)
Hello, Steven!
I have checked the target object and apparently there is no problem with it. I don't know if it could be a formatting problem or something similar. I'll send you the script, the images and the landmarks:
https://drive.google.com/drive/folders/1N6XDXY5K6t60uJH8opCgR3z-aaUfuUpZ?usp=sharing
Thanks again for your help!
Best regards, Julene.
El lun, 24 abr 2023 a las 17:35, Steven M. Van Belleghem (< @.***mailto:***@***.***>) escribió:
HI Julene,
It sounds like something may be wrong with the ‘target’ (maybe it is empty?).
If you struggle resolving it, feel free to send me some of your images, landmarks and script and I’ll help setting up a working example.
Best,
Steven
From: Julenetxu1 @.mailto:***@***.***> Sent: Monday, 24 April 2023 12:36 To: StevenVB12/patternize @.mailto:***@***.***> Cc: Subscribed @.***mailto:***@***.***> Subject: [StevenVB12/patternize] Error in transformRef == "meanshape" : comparison (==) is possible only for atomic and list type (Issue #39)
Good morning, Steven!
Thank you very much for your package and for having this website to solve the problems that arise with patternize.
I'm a fairly novice R user, and I'm trying to use your package to compare colour patterns in wings of different species of neuroptera. I have encountered a problem when applying the alignLan function. I get the following error when trying to apply the function:
Error in transformRef == "meanshape" : comparison (==) is possible only for atomic and list types.
My script is as follows:
imageList_aligned <- alignLan(imageList= imageList, landList = landmarkList, transformRef = target, adjustCoords = TRUE, plotTransformed = T, resampleFactor = 5, cartoonID = "asc09_Hd-0", maskOutline = outline_asc09_Hd, inverse = FALSE)
The images I'm working with are in png and each of them has different extent, I don't know if that could give any problem. I have tried to do the same process but transforming them into jpg, but I get the same error.
Thank you very much!
Julene.
— Reply to this email directly, view it on GitHub< https://github.com/StevenVB12/patternize/issues/39>, or unsubscribe<
https://github.com/notifications/unsubscribe-auth/ABQOC43GWG7SNRO5PNDXYOLXCZJP7ANCNFSM6AAAAAAXJMFJFM>.
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Hi Julene,
Did you install patternize through github (with the latest updates). Something is deprecated with the raster package that should be partly resolved now (I only get the warning instead of an error).
Steven
From: Julenetxu1 @.> Sent: Wednesday, 26 April 2023 13:47 To: StevenVB12/patternize @.> Cc: Steven M. Van Belleghem @.>; Comment @.> Subject: Re: [StevenVB12/patternize] Error in transformRef == "meanshape" : comparison (==) is possible only for atomic and list type (Issue #39)
Hello, Steven!
I still haven't managed to solve the problem.
I didn't realise that I had defined the target wrong. I got it right with the following function:
target <- landmarkList[['asc09_Hd-0']]
It still doesn't work after running your script. I get the following error:
Error in !is.null(maskOutline) && transformRef == "meanshape" : 'length = 16' in coercion to 'logical(1)'
I don't know what could be the problem.
Thanks again for your help.
Best regards, Julene.
El mié, 26 abr 2023 a las 9:58, Steven M. Van Belleghem (< @.***mailto:***@***.***>) escribió:
Hi Julene,
I think like this it should work (the target has to be the landmarks):
imageList_aligned <- alignLan(imageList = imageList, landList = landmarkList, IDlist = IDlist, transformRef = target, adjustCoords = TRUE, plotTransformed = T, resampleFactor = 5, cartoonID = "asc09_Hd-0", maskOutline = outline_asc09_Hd, inverse = FALSE)
Please let me know how it goes!
Best,
Steven
From: Julenetxu1 @.mailto:***@***.***> Sent: Tuesday, 25 April 2023 16:06 To: StevenVB12/patternize @.mailto:***@***.***> Cc: Steven M. Van Belleghem @.mailto:***@***.***>; Comment @.mailto:***@***.***> Subject: Re: [StevenVB12/patternize] Error in transformRef == "meanshape" : comparison (==) is possible only for atomic and list type (Issue #39)
Hello, Steven!
I have checked the target object and apparently there is no problem with it. I don't know if it could be a formatting problem or something similar. I'll send you the script, the images and the landmarks:
https://drive.google.com/drive/folders/1N6XDXY5K6t60uJH8opCgR3z-aaUfuUpZ?usp=sharing
Thanks again for your help!
Best regards, Julene.
El lun, 24 abr 2023 a las 17:35, Steven M. Van Belleghem (< @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>>) escribió:
HI Julene,
It sounds like something may be wrong with the ‘target’ (maybe it is empty?).
If you struggle resolving it, feel free to send me some of your images, landmarks and script and I’ll help setting up a working example.
Best,
Steven
From: Julenetxu1 @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>> Sent: Monday, 24 April 2023 12:36 To: StevenVB12/patternize @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>> Cc: Subscribed @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>> Subject: [StevenVB12/patternize] Error in transformRef == "meanshape" : comparison (==) is possible only for atomic and list type (Issue #39)
Good morning, Steven!
Thank you very much for your package and for having this website to solve the problems that arise with patternize.
I'm a fairly novice R user, and I'm trying to use your package to compare colour patterns in wings of different species of neuroptera. I have encountered a problem when applying the alignLan function. I get the following error when trying to apply the function:
Error in transformRef == "meanshape" : comparison (==) is possible only for atomic and list types.
My script is as follows:
imageList_aligned <- alignLan(imageList= imageList, landList = landmarkList, transformRef = target, adjustCoords = TRUE, plotTransformed = T, resampleFactor = 5, cartoonID = "asc09_Hd-0", maskOutline = outline_asc09_Hd, inverse = FALSE)
The images I'm working with are in png and each of them has different extent, I don't know if that could give any problem. I have tried to do the same process but transforming them into jpg, but I get the same error.
Thank you very much!
Julene.
— Reply to this email directly, view it on GitHub< https://github.com/StevenVB12/patternize/issues/39>, or unsubscribe<
https://github.com/notifications/unsubscribe-auth/ABQOC43GWG7SNRO5PNDXYOLXCZJP7ANCNFSM6AAAAAAXJMFJFM>.
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Good morning, Steven.
Yes, I have updated patternize from github. I also made sure to delete its dependencies beforehand, to make sure I installed the latest versions (raster, cluster R, s2 and units). However, I'm still getting the same error. Could there be a problem with the version of R I'm using? I'm currently using version 4.3.0.
If I apply the same function, but using transformRef = "meanshape" I get the following error: Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'extent': attempt to select less than one element in get1index.
When I try to run the function, but removing the maskOutline argument, the function runs, but the resulting images are completely black (although with a small coloured part at the top left). [image: image.png] [image: image.png]
I think there might be some error defining the extension of the images. I think this is because when I try to run the function... rasterList_lanK_tps_K <- patLanK(imageList, landmarkList, k=3, adjustCoords = FALSE, plot=T, resampleFactor = 3) is able to perform the analysis, but I constantly get the following warning: performing Procrustes Fit in... 0.456033 secs
Operation completed in 0.4966139793396 secs
Warning: [rast] unknown extent Warning: [rast] unknown extent Warning: [rast] unknown extent [1] "sample asc09_Hd-0 processed". Warning: [rast] unknown extent Warning: [rast] unknown extent Warning: [rast] unknown extent ...
I don't know if there might be some error in my images or if I need to update some more packages.
Thank you very much again.
Best regards, Julene.
El mié, 26 abr 2023 a las 14:20, Steven M. Van Belleghem (< @.***>) escribió:
Hi Julene,
Did you install patternize through github (with the latest updates). Something is deprecated with the raster package that should be partly resolved now (I only get the warning instead of an error).
Steven
From: Julenetxu1 @.> Sent: Wednesday, 26 April 2023 13:47 To: StevenVB12/patternize @.> Cc: Steven M. Van Belleghem @.>; Comment @.> Subject: Re: [StevenVB12/patternize] Error in transformRef == "meanshape" : comparison (==) is possible only for atomic and list type (Issue #39)
Hello, Steven!
I still haven't managed to solve the problem.
I didn't realise that I had defined the target wrong. I got it right with the following function:
target <- landmarkList[['asc09_Hd-0']]
It still doesn't work after running your script. I get the following error:
Error in !is.null(maskOutline) && transformRef == "meanshape" : 'length = 16' in coercion to 'logical(1)'
I don't know what could be the problem.
Thanks again for your help.
Best regards, Julene.
El mié, 26 abr 2023 a las 9:58, Steven M. Van Belleghem (< @.***mailto:***@***.***>) escribió:
Hi Julene,
I think like this it should work (the target has to be the landmarks):
imageList_aligned <- alignLan(imageList = imageList, landList = landmarkList, IDlist = IDlist, transformRef = target, adjustCoords = TRUE, plotTransformed = T, resampleFactor = 5, cartoonID = "asc09_Hd-0", maskOutline = outline_asc09_Hd, inverse = FALSE)
Please let me know how it goes!
Best,
Steven
From: Julenetxu1 @.mailto:***@***.***> Sent: Tuesday, 25 April 2023 16:06 To: StevenVB12/patternize @.mailto:***@***.***> Cc: Steven M. Van Belleghem @.mailto:***@***.***>; Comment @.mailto:***@***.***> Subject: Re: [StevenVB12/patternize] Error in transformRef == "meanshape" : comparison (==) is possible only for atomic and list type (Issue #39)
Hello, Steven!
I have checked the target object and apparently there is no problem with it. I don't know if it could be a formatting problem or something similar. I'll send you the script, the images and the landmarks:
https://drive.google.com/drive/folders/1N6XDXY5K6t60uJH8opCgR3z-aaUfuUpZ?usp=sharing
Thanks again for your help!
Best regards, Julene.
El lun, 24 abr 2023 a las 17:35, Steven M. Van Belleghem (< @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>>) escribió:
HI Julene,
It sounds like something may be wrong with the ‘target’ (maybe it is empty?).
If you struggle resolving it, feel free to send me some of your images, landmarks and script and I’ll help setting up a working example.
Best,
Steven
From: Julenetxu1 @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>>
Sent: Monday, 24 April 2023 12:36 To: StevenVB12/patternize @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>>
Cc: Subscribed @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>>
Subject: [StevenVB12/patternize] Error in transformRef == "meanshape" : comparison (==) is possible only for atomic and list type (Issue #39)
Good morning, Steven!
Thank you very much for your package and for having this website to solve the problems that arise with patternize.
I'm a fairly novice R user, and I'm trying to use your package to compare colour patterns in wings of different species of neuroptera. I have encountered a problem when applying the alignLan function. I get the following error when trying to apply the function:
Error in transformRef == "meanshape" : comparison (==) is possible only for atomic and list types.
My script is as follows:
imageList_aligned <- alignLan(imageList= imageList, landList = landmarkList, transformRef = target, adjustCoords = TRUE, plotTransformed = T, resampleFactor = 5, cartoonID = "asc09_Hd-0", maskOutline = outline_asc09_Hd, inverse = FALSE)
The images I'm working with are in png and each of them has different extent, I don't know if that could give any problem. I have tried to do the same process but transforming them into jpg, but I get the same error.
Thank you very much!
Julene.
— Reply to this email directly, view it on GitHub< https://github.com/StevenVB12/patternize/issues/39>, or unsubscribe<
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Hi Julene,
Since it works for me, I would try getting the code I gave you to run first (I also would advise against using meanshape, because it will make comparative analyses later on more difficult).
Some dependencies became deprecated recently and I wonder if it has anything to do with that. I am using R 4.2.0.
Steven
From: Julenetxu1 @.> Sent: Monday, 1 May 2023 13:50 To: StevenVB12/patternize @.> Cc: Steven M. Van Belleghem @.>; Comment @.> Subject: Re: [StevenVB12/patternize] Error in transformRef == "meanshape" : comparison (==) is possible only for atomic and list type (Issue #39)
Good morning, Steven.
Yes, I have updated patternize from github. I also made sure to delete its dependencies beforehand, to make sure I installed the latest versions (raster, cluster R, s2 and units). However, I'm still getting the same error. Could there be a problem with the version of R I'm using? I'm currently using version 4.3.0.
If I apply the same function, but using transformRef = "meanshape" I get the following error: Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'extent': attempt to select less than one element in get1index.
When I try to run the function, but removing the maskOutline argument, the function runs, but the resulting images are completely black (although with a small coloured part at the top left). [image: image.png] [image: image.png]
I think there might be some error defining the extension of the images. I think this is because when I try to run the function... rasterList_lanK_tps_K <- patLanK(imageList, landmarkList, k=3, adjustCoords = FALSE, plot=T, resampleFactor = 3) is able to perform the analysis, but I constantly get the following warning: performing Procrustes Fit in... 0.456033 secs
Operation completed in 0.4966139793396 secs
Warning: [rast] unknown extent Warning: [rast] unknown extent Warning: [rast] unknown extent [1] "sample asc09_Hd-0 processed". Warning: [rast] unknown extent Warning: [rast] unknown extent Warning: [rast] unknown extent ...
I don't know if there might be some error in my images or if I need to update some more packages.
Thank you very much again.
Best regards, Julene.
El mié, 26 abr 2023 a las 14:20, Steven M. Van Belleghem (< @.***mailto:***@***.***>) escribió:
Hi Julene,
Did you install patternize through github (with the latest updates). Something is deprecated with the raster package that should be partly resolved now (I only get the warning instead of an error).
Steven
From: Julenetxu1 @.mailto:***@***.***> Sent: Wednesday, 26 April 2023 13:47 To: StevenVB12/patternize @.mailto:***@***.***> Cc: Steven M. Van Belleghem @.mailto:***@***.***>; Comment @.mailto:***@***.***> Subject: Re: [StevenVB12/patternize] Error in transformRef == "meanshape" : comparison (==) is possible only for atomic and list type (Issue #39)
Hello, Steven!
I still haven't managed to solve the problem.
I didn't realise that I had defined the target wrong. I got it right with the following function:
target <- landmarkList[['asc09_Hd-0']]
It still doesn't work after running your script. I get the following error:
Error in !is.null(maskOutline) && transformRef == "meanshape" : 'length = 16' in coercion to 'logical(1)'
I don't know what could be the problem.
Thanks again for your help.
Best regards, Julene.
El mié, 26 abr 2023 a las 9:58, Steven M. Van Belleghem (< @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>>) escribió:
Hi Julene,
I think like this it should work (the target has to be the landmarks):
imageList_aligned <- alignLan(imageList = imageList, landList = landmarkList, IDlist = IDlist, transformRef = target, adjustCoords = TRUE, plotTransformed = T, resampleFactor = 5, cartoonID = "asc09_Hd-0", maskOutline = outline_asc09_Hd, inverse = FALSE)
Please let me know how it goes!
Best,
Steven
From: Julenetxu1 @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>> Sent: Tuesday, 25 April 2023 16:06 To: StevenVB12/patternize @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>> Cc: Steven M. Van Belleghem @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>>; Comment @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>> Subject: Re: [StevenVB12/patternize] Error in transformRef == "meanshape" : comparison (==) is possible only for atomic and list type (Issue #39)
Hello, Steven!
I have checked the target object and apparently there is no problem with it. I don't know if it could be a formatting problem or something similar. I'll send you the script, the images and the landmarks:
https://drive.google.com/drive/folders/1N6XDXY5K6t60uJH8opCgR3z-aaUfuUpZ?usp=sharing
Thanks again for your help!
Best regards, Julene.
El lun, 24 abr 2023 a las 17:35, Steven M. Van Belleghem (< @.<mailto:@.<mailto:@.%3cmailto:@.mailto:***@***.***%3cmailto:***@***.***%3cmailto:***@***.***%3cmailto:***@***.***>>>) escribió:
HI Julene,
It sounds like something may be wrong with the ‘target’ (maybe it is empty?).
If you struggle resolving it, feel free to send me some of your images, landmarks and script and I’ll help setting up a working example.
Best,
Steven
From: Julenetxu1 @.<mailto:@.<mailto:@.%3cmailto:@.mailto:***@***.***%3cmailto:***@***.***%3cmailto:***@***.***%3cmailto:***@***.***>>>
Sent: Monday, 24 April 2023 12:36 To: StevenVB12/patternize @.<mailto:@.<mailto:@.%3cmailto:@.mailto:***@***.***%3cmailto:***@***.***%3cmailto:***@***.***%3cmailto:***@***.***>>>
Cc: Subscribed @.<mailto:@.<mailto:@.%3cmailto:@.mailto:***@***.***%3cmailto:***@***.***%3cmailto:***@***.***%3cmailto:***@***.***>>>
Subject: [StevenVB12/patternize] Error in transformRef == "meanshape" : comparison (==) is possible only for atomic and list type (Issue #39)
Good morning, Steven!
Thank you very much for your package and for having this website to solve the problems that arise with patternize.
I'm a fairly novice R user, and I'm trying to use your package to compare colour patterns in wings of different species of neuroptera. I have encountered a problem when applying the alignLan function. I get the following error when trying to apply the function:
Error in transformRef == "meanshape" : comparison (==) is possible only for atomic and list types.
My script is as follows:
imageList_aligned <- alignLan(imageList= imageList, landList = landmarkList, transformRef = target, adjustCoords = TRUE, plotTransformed = T, resampleFactor = 5, cartoonID = "asc09_Hd-0", maskOutline = outline_asc09_Hd, inverse = FALSE)
The images I'm working with are in png and each of them has different extent, I don't know if that could give any problem. I have tried to do the same process but transforming them into jpg, but I get the same error.
Thank you very much!
Julene.
— Reply to this email directly, view it on GitHub< https://github.com/StevenVB12/patternize/issues/39>, or unsubscribe<
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Good afternoon, Steven.
I've figured out what the error was! The problem was that I had the computer configured in such a way that it considers the "," as decimals. That's why I wasn't able to process the landmarks properly. When I changed it to "." it worked fine.
Thank you very much for your help!
Best regards, Julene.
El lun, 1 may 2023 a las 13:56, Steven M. Van Belleghem (< @.***>) escribió:
Hi Julene,
Since it works for me, I would try getting the code I gave you to run first (I also would advise against using meanshape, because it will make comparative analyses later on more difficult).
Some dependencies became deprecated recently and I wonder if it has anything to do with that. I am using R 4.2.0.
Steven
From: Julenetxu1 @.> Sent: Monday, 1 May 2023 13:50 To: StevenVB12/patternize @.> Cc: Steven M. Van Belleghem @.>; Comment @.> Subject: Re: [StevenVB12/patternize] Error in transformRef == "meanshape" : comparison (==) is possible only for atomic and list type (Issue #39)
Good morning, Steven.
Yes, I have updated patternize from github. I also made sure to delete its dependencies beforehand, to make sure I installed the latest versions (raster, cluster R, s2 and units). However, I'm still getting the same error. Could there be a problem with the version of R I'm using? I'm currently using version 4.3.0.
If I apply the same function, but using transformRef = "meanshape" I get the following error: Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'extent': attempt to select less than one element in get1index.
When I try to run the function, but removing the maskOutline argument, the function runs, but the resulting images are completely black (although with a small coloured part at the top left). [image: image.png] [image: image.png]
I think there might be some error defining the extension of the images. I think this is because when I try to run the function... rasterList_lanK_tps_K <- patLanK(imageList, landmarkList, k=3, adjustCoords = FALSE, plot=T, resampleFactor = 3) is able to perform the analysis, but I constantly get the following warning: performing Procrustes Fit in... 0.456033 secs
Operation completed in 0.4966139793396 secs
Warning: [rast] unknown extent Warning: [rast] unknown extent Warning: [rast] unknown extent [1] "sample asc09_Hd-0 processed". Warning: [rast] unknown extent Warning: [rast] unknown extent Warning: [rast] unknown extent ...
I don't know if there might be some error in my images or if I need to update some more packages.
Thank you very much again.
Best regards, Julene.
El mié, 26 abr 2023 a las 14:20, Steven M. Van Belleghem (< @.***mailto:***@***.***>) escribió:
Hi Julene,
Did you install patternize through github (with the latest updates). Something is deprecated with the raster package that should be partly resolved now (I only get the warning instead of an error).
Steven
From: Julenetxu1 @.mailto:***@***.***> Sent: Wednesday, 26 April 2023 13:47 To: StevenVB12/patternize @.mailto:***@***.***> Cc: Steven M. Van Belleghem @.mailto:***@***.***>; Comment @.mailto:***@***.***> Subject: Re: [StevenVB12/patternize] Error in transformRef == "meanshape" : comparison (==) is possible only for atomic and list type (Issue #39)
Hello, Steven!
I still haven't managed to solve the problem.
I didn't realise that I had defined the target wrong. I got it right with the following function:
target <- landmarkList[['asc09_Hd-0']]
It still doesn't work after running your script. I get the following error:
Error in !is.null(maskOutline) && transformRef == "meanshape" : 'length = 16' in coercion to 'logical(1)'
I don't know what could be the problem.
Thanks again for your help.
Best regards, Julene.
El mié, 26 abr 2023 a las 9:58, Steven M. Van Belleghem (< @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>>) escribió:
Hi Julene,
I think like this it should work (the target has to be the landmarks):
imageList_aligned <- alignLan(imageList = imageList, landList = landmarkList, IDlist = IDlist, transformRef = target, adjustCoords = TRUE, plotTransformed = T, resampleFactor = 5, cartoonID = "asc09_Hd-0", maskOutline = outline_asc09_Hd, inverse = FALSE)
Please let me know how it goes!
Best,
Steven
From: Julenetxu1 @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>>
Sent: Tuesday, 25 April 2023 16:06 To: StevenVB12/patternize @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>>
Cc: Steven M. Van Belleghem @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>>; Comment @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>>
Subject: Re: [StevenVB12/patternize] Error in transformRef == "meanshape" : comparison (==) is possible only for atomic and list type (Issue #39)
Hello, Steven!
I have checked the target object and apparently there is no problem with it. I don't know if it could be a formatting problem or something similar. I'll send you the script, the images and the landmarks:
https://drive.google.com/drive/folders/1N6XDXY5K6t60uJH8opCgR3z-aaUfuUpZ?usp=sharing
Thanks again for your help!
Best regards, Julene.
El lun, 24 abr 2023 a las 17:35, Steven M. Van Belleghem (< @.<mailto:@.<mailto: @.%3cmailto:@.mailto:***@***.***%3cmailto:***@***.***%3cmailto:***@***.***%3cmailto:***@***.***>>>)
escribió:
HI Julene,
It sounds like something may be wrong with the ‘target’ (maybe it is empty?).
If you struggle resolving it, feel free to send me some of your images, landmarks and script and I’ll help setting up a working example.
Best,
Steven
From: Julenetxu1 @.<mailto:@.<mailto: @.%3cmailto:@.mailto:***@***.***%3cmailto:***@***.***%3cmailto:***@***.***%3cmailto:***@***.***>>>
Sent: Monday, 24 April 2023 12:36 To: StevenVB12/patternize @.<mailto:@.<mailto: @.%3cmailto:@.mailto:***@***.***%3cmailto:***@***.***%3cmailto:***@***.***%3cmailto:***@***.***>>>
Cc: Subscribed @.<mailto:@.<mailto: @.%3cmailto:@.mailto:***@***.***%3cmailto:***@***.***%3cmailto:***@***.***%3cmailto:***@***.***>>>
Subject: [StevenVB12/patternize] Error in transformRef == "meanshape" : comparison (==) is possible only for atomic and list type (Issue #39)
Good morning, Steven!
Thank you very much for your package and for having this website to solve the problems that arise with patternize.
I'm a fairly novice R user, and I'm trying to use your package to compare colour patterns in wings of different species of neuroptera. I have encountered a problem when applying the alignLan function. I get the following error when trying to apply the function:
Error in transformRef == "meanshape" : comparison (==) is possible only for atomic and list types.
My script is as follows:
imageList_aligned <- alignLan(imageList= imageList, landList = landmarkList, transformRef = target, adjustCoords = TRUE, plotTransformed = T, resampleFactor = 5, cartoonID = "asc09_Hd-0", maskOutline = outline_asc09_Hd, inverse = FALSE)
The images I'm working with are in png and each of them has different extent, I don't know if that could give any problem. I have tried to do the same process but transforming them into jpg, but I get the same error.
Thank you very much!
Julene.
— Reply to this email directly, view it on GitHub< https://github.com/StevenVB12/patternize/issues/39>, or unsubscribe<
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Awesome!
-------- Original message -------- From: Julenetxu1 @.> Date: 5/1/23 3:33 PM (GMT+01:00) To: StevenVB12/patternize @.> Cc: "Steven M. Van Belleghem" @.>, Comment @.> Subject: Re: [StevenVB12/patternize] Error in transformRef == "meanshape" : comparison (==) is possible only for atomic and list type (Issue #39)
Good afternoon, Steven.
I've figured out what the error was! The problem was that I had the computer configured in such a way that it considers the "," as decimals. That's why I wasn't able to process the landmarks properly. When I changed it to "." it worked fine.
Thank you very much for your help!
Best regards, Julene.
El lun, 1 may 2023 a las 13:56, Steven M. Van Belleghem (< @.***>) escribió:
Hi Julene,
Since it works for me, I would try getting the code I gave you to run first (I also would advise against using meanshape, because it will make comparative analyses later on more difficult).
Some dependencies became deprecated recently and I wonder if it has anything to do with that. I am using R 4.2.0.
Steven
From: Julenetxu1 @.> Sent: Monday, 1 May 2023 13:50 To: StevenVB12/patternize @.> Cc: Steven M. Van Belleghem @.>; Comment @.> Subject: Re: [StevenVB12/patternize] Error in transformRef == "meanshape" : comparison (==) is possible only for atomic and list type (Issue #39)
Good morning, Steven.
Yes, I have updated patternize from github. I also made sure to delete its dependencies beforehand, to make sure I installed the latest versions (raster, cluster R, s2 and units). However, I'm still getting the same error. Could there be a problem with the version of R I'm using? I'm currently using version 4.3.0.
If I apply the same function, but using transformRef = "meanshape" I get the following error: Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'extent': attempt to select less than one element in get1index.
When I try to run the function, but removing the maskOutline argument, the function runs, but the resulting images are completely black (although with a small coloured part at the top left). [image: image.png] [image: image.png]
I think there might be some error defining the extension of the images. I think this is because when I try to run the function... rasterList_lanK_tps_K <- patLanK(imageList, landmarkList, k=3, adjustCoords = FALSE, plot=T, resampleFactor = 3) is able to perform the analysis, but I constantly get the following warning: performing Procrustes Fit in... 0.456033 secs
Operation completed in 0.4966139793396 secs
Warning: [rast] unknown extent Warning: [rast] unknown extent Warning: [rast] unknown extent [1] "sample asc09_Hd-0 processed". Warning: [rast] unknown extent Warning: [rast] unknown extent Warning: [rast] unknown extent ...
I don't know if there might be some error in my images or if I need to update some more packages.
Thank you very much again.
Best regards, Julene.
El mié, 26 abr 2023 a las 14:20, Steven M. Van Belleghem (< @.***mailto:***@***.***>) escribió:
Hi Julene,
Did you install patternize through github (with the latest updates). Something is deprecated with the raster package that should be partly resolved now (I only get the warning instead of an error).
Steven
From: Julenetxu1 @.mailto:***@***.***> Sent: Wednesday, 26 April 2023 13:47 To: StevenVB12/patternize @.mailto:***@***.***> Cc: Steven M. Van Belleghem @.mailto:***@***.***>; Comment @.mailto:***@***.***> Subject: Re: [StevenVB12/patternize] Error in transformRef == "meanshape" : comparison (==) is possible only for atomic and list type (Issue #39)
Hello, Steven!
I still haven't managed to solve the problem.
I didn't realise that I had defined the target wrong. I got it right with the following function:
target <- landmarkList[['asc09_Hd-0']]
It still doesn't work after running your script. I get the following error:
Error in !is.null(maskOutline) && transformRef == "meanshape" : 'length = 16' in coercion to 'logical(1)'
I don't know what could be the problem.
Thanks again for your help.
Best regards, Julene.
El mié, 26 abr 2023 a las 9:58, Steven M. Van Belleghem (< @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>>) escribió:
Hi Julene,
I think like this it should work (the target has to be the landmarks):
imageList_aligned <- alignLan(imageList = imageList, landList = landmarkList, IDlist = IDlist, transformRef = target, adjustCoords = TRUE, plotTransformed = T, resampleFactor = 5, cartoonID = "asc09_Hd-0", maskOutline = outline_asc09_Hd, inverse = FALSE)
Please let me know how it goes!
Best,
Steven
From: Julenetxu1 @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>>
Sent: Tuesday, 25 April 2023 16:06 To: StevenVB12/patternize @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>>
Cc: Steven M. Van Belleghem @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>>; Comment @.<mailto:@.mailto:***@***.***%3cmailto:***@***.***>>
Subject: Re: [StevenVB12/patternize] Error in transformRef == "meanshape" : comparison (==) is possible only for atomic and list type (Issue #39)
Hello, Steven!
I have checked the target object and apparently there is no problem with it. I don't know if it could be a formatting problem or something similar. I'll send you the script, the images and the landmarks:
https://drive.google.com/drive/folders/1N6XDXY5K6t60uJH8opCgR3z-aaUfuUpZ?usp=sharing
Thanks again for your help!
Best regards, Julene.
El lun, 24 abr 2023 a las 17:35, Steven M. Van Belleghem (< @.<mailto:@.<mailto: @.%3cmailto:@.mailto:***@***.***%3cmailto:***@***.***%3cmailto:***@***.***%3cmailto:***@***.***>>>)
escribió:
HI Julene,
It sounds like something may be wrong with the ‘target’ (maybe it is empty?).
If you struggle resolving it, feel free to send me some of your images, landmarks and script and I’ll help setting up a working example.
Best,
Steven
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Subject: [StevenVB12/patternize] Error in transformRef == "meanshape" : comparison (==) is possible only for atomic and list type (Issue #39)
Good morning, Steven!
Thank you very much for your package and for having this website to solve the problems that arise with patternize.
I'm a fairly novice R user, and I'm trying to use your package to compare colour patterns in wings of different species of neuroptera. I have encountered a problem when applying the alignLan function. I get the following error when trying to apply the function:
Error in transformRef == "meanshape" : comparison (==) is possible only for atomic and list types.
My script is as follows:
imageList_aligned <- alignLan(imageList= imageList, landList = landmarkList, transformRef = target, adjustCoords = TRUE, plotTransformed = T, resampleFactor = 5, cartoonID = "asc09_Hd-0", maskOutline = outline_asc09_Hd, inverse = FALSE)
The images I'm working with are in png and each of them has different extent, I don't know if that could give any problem. I have tried to do the same process but transforming them into jpg, but I get the same error.
Thank you very much!
Julene.
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