patternize icon indicating copy to clipboard operation
patternize copied to clipboard
verified publisher icon StevenVB12

question about colorChecker and issue with makeOutline

Open kaspardelhey opened this issue 5 months ago • 5 comments

Hi Steven,

I have been trying to use patternize to calibrate images (using colorChecker) and apply a mask on the image using maskOutline. I have two questions:

  1. When using colorChecker on a set of images, is there a way to skip the stage when you have to press enter to save the calibrated image each time? I would like to run the script on a set of images without having to press enter multiple times.

  2. When trying to apply a mask (which will define my ROI in the image to be analysed) I seem to have run into an issue. I have saved the coordinates of a polygon in ImageJ which defines the outlines of the mask I want to apply in the file 'XY_Coordinates1010s.txt'. But then when I try to run the code I get the

outline <- read.table('XY_Coordinates1010s.txt', header = FALSE)

ii <- makeList('1D3A1010s.jpg_calibrated', type='image') [1] "sample 1 1D3A1010s.jpg_calibrated added to list" >

img2 <- maskOutline(RasterStack=ii[[1]], outline=outline) Error: unable to find an inherited method for function ‘extent’ for signature ‘x = "NULL"’

I would be thankful for any suggestions.

Thanks in advance and thanks for the great package!

Kaspar

kaspardelhey avatar Aug 13 '25 05:08 kaspardelhey

Dear Kasper,

If your colorChecker is in the same position in each picture, you can use 'fixedCorners = TRUE'

Could you send me the picture and outline? I could haev a quick look.

Best,

Steven

Van Belleghem Steven

Van: kaspardelhey @.> Verzonden: woensdag 13 augustus 2025 7:59 Aan: StevenVB12/patternize @.> CC: Subscribed @.***> Onderwerp: [StevenVB12/patternize] question about colorChecker and issue with makeOutline (Issue #46)

[https://avatars.githubusercontent.com/u/226236686?s=20&v=4]kaspardelhey created an issue (StevenVB12/patternize#46)https://github.com/StevenVB12/patternize/issues/46

Hi Steven,

I have been trying to use patternize to calibrate images (using colorChecker) and apply a mask on the image using maskOutline. I have two questions:

  1. When using colorChecker on a set of images, is there a way to skip the stage when you have to press enter to save the calibrated image each time? I would like to run the script on a set of images without having to press enter multiple times.

  2. When trying to apply a mask (which will define my ROI in the image to be analysed) I seem to have run into an issue. I have saved the coordinates of a polygon in ImageJ which defines the outlines of the mask I want to apply in the file 'XY_Coordinates1010s.txt'. But then when I try to run the code I get the

outline <- read.table('XY_Coordinates1010s.txt', header = FALSE)

ii <- makeList('1D3A1010s.jpg_calibrated', type='image') [1] "sample 1 1D3A1010s.jpg_calibrated added to list" >

img2 <- maskOutline(RasterStack=ii[[1]], outline=outline) Error: unable to find an inherited method for function ‘extent’ for signature ‘x = "NULL"’

I would be thankful for any suggestions.

Thanks in advance and thanks for the great package!

Kaspar

— Reply to this email directly, view it on GitHubhttps://github.com/StevenVB12/patternize/issues/46, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABQOC46AK6UXCLV3VJNCT6L3NLH2JAVCNFSM6AAAAACDYQZCDCVHI2DSMVQWIX3LMV43ASLTON2WKOZTGMYTOMBRGM3TQMA. You are receiving this because you are subscribed to this thread.Message ID: @.***>

StevenVB12 avatar Aug 13 '25 07:08 StevenVB12

Hi Steven, Thanks for the quick reply!

  1. Unfortunately the chart is in different positions in different pictures, so I guess the only way to change that will be to see if the function can be changed to avoid the prompt, I will have a look.

  2. I attach the dropbox link to a folder with the script, uncalibrated and calibrated images, xrite coordinates and polygon coordinates, because mail bounced due to its size. https://www.dropbox.com/scl/fo/ew5n64d0u495my7346uzk/AHozhm-DIAmB7H2GHFMaAKE?rlkey=3rsarh1kogcqomnfafgyzc63k&dl=0

Thanks for checking this out and let me know if you can't access the files

Cheers,

Kaspar

kaspardelhey avatar Aug 13 '25 10:08 kaspardelhey

Hi Kasper,

You would only need to remove line 778-780 here https://github.com/StevenVB12/patternize/blob/master/R/colorChecker.R

if(all(c(fixedCorners == FALSE, is.null(fixedModel)))){ todo <- readline(prompt="Press [enter] to continue and save image >>> ") }

    2. It took me some effort too as the code has seemed to be getting more buggy... Sorry! This works for me:

xy_coords <- makeList( IDlist=c('xrite_coords.txt'), type='landmark', prepath = NULL, extension = NULL, format = "imageJ", tpsFile = NULL, skipLandmark = NULL )

img <- colorChecker( IDlist=c('1D3A1010s'), prepath = NULL, extension = '.jpg', colorCheckerType = "X-Rite", fixedCorners = FALSE, patchSize = 0.6, colorCheckerXY = xy_coords, fixedModel = NULL, resampleFactor = NULL, adjustCoords = TRUE )

outline <- read.table('XY_Coordinates1010s.txt', header = FALSE)

#this step is not needed if we run the script from the start #img <- makeList('1D3A1010s.jpg_calibrated', type='image')

IDlist=c('1D3A1010s') prepath <- NULL extension <- '_calibrated.jpg' imageList <- makeList(IDlist, 'image', prepath, extension)

img2 <- maskOutline(imageList[[1]], outline, 'target', imageList = imageList, adjustCoords = TRUE, flipOutline = 'y')

raster::plot(img2)

Van Belleghem Steven

Van: kaspardelhey @.> Verzonden: woensdag 13 augustus 2025 12:02 Aan: StevenVB12/patternize @.> CC: Steven M. Van Belleghem @.>; Comment @.> Onderwerp: Re: [StevenVB12/patternize] question about colorChecker and issue with makeOutline (Issue #46)

[https://avatars.githubusercontent.com/u/226236686?s=20&v=4]kaspardelhey left a comment (StevenVB12/patternize#46)https://github.com/StevenVB12/patternize/issues/46#issuecomment-3183100301

Hi Steven, Thanks for the quick reply!

  1. Unfortunately the chart is in different positions in different pictures, so I guess the only way to change that will be to see if the function can be changed to avoid the prompt, I will have a look.

  2. I attach the dropbox link to a folder with the script, uncalibrated and calibrated images, xrite coordinates and polygon coordinates, because mail bounced due to its size. https://www.dropbox.com/scl/fo/ew5n64d0u495my7346uzk/AHozhm-DIAmB7H2GHFMaAKE?rlkey=3rsarh1kogcqomnfafgyzc63k&dl=0

Thanks for checking this out and let me know if you can't access the files

Cheers,

Kaspar

— Reply to this email directly, view it on GitHubhttps://github.com/StevenVB12/patternize/issues/46#issuecomment-3183100301, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABQOC434ZLPVPN7R3SREZ3D3NMEKFAVCNFSM6AAAAACDYQZCDCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTCOBTGEYDAMZQGE. You are receiving this because you commented.Message ID: @.***>

StevenVB12 avatar Aug 13 '25 16:08 StevenVB12

Hi Steven,

Thanks for the quick fix! It seems to work now. I will let you know how I go about it. The only further issue is that I wanted to continue with some functions from the package recolorize, but when I try to use function:

img3 <- brick_to_array(img2)

I get the following error message:

Error in .local(x, ...) : invalid layer names

Not sure what causes that, but I may contact Hannah Weller about it, since she is the first author of that package.

Cheers!

Kaspar

On Thu, Aug 14, 2025 at 2:33 AM Steven M. Van Belleghem < @.***> wrote:

StevenVB12 left a comment (StevenVB12/patternize#46) https://github.com/StevenVB12/patternize/issues/46#issuecomment-3184621700 Hi Kasper,

You would only need to remove line 778-780 here https://github.com/StevenVB12/patternize/blob/master/R/colorChecker.R

if(all(c(fixedCorners == FALSE, is.null(fixedModel)))){ todo <- readline(prompt="Press [enter] to continue and save image >>> ") }

  1. It took me some effort too as the code has seemed to be getting more buggy... Sorry! This works for me:

xy_coords <- makeList( IDlist=c('xrite_coords.txt'), type='landmark', prepath = NULL, extension = NULL, format = "imageJ", tpsFile = NULL, skipLandmark = NULL )

img <- colorChecker( IDlist=c('1D3A1010s'), prepath = NULL, extension = '.jpg', colorCheckerType = "X-Rite", fixedCorners = FALSE, patchSize = 0.6, colorCheckerXY = xy_coords, fixedModel = NULL, resampleFactor = NULL, adjustCoords = TRUE )

outline <- read.table('XY_Coordinates1010s.txt', header = FALSE)

#this step is not needed if we run the script from the start #img <- makeList('1D3A1010s.jpg_calibrated', type='image')

IDlist=c('1D3A1010s') prepath <- NULL extension <- '_calibrated.jpg' imageList <- makeList(IDlist, 'image', prepath, extension)

img2 <- maskOutline(imageList[[1]], outline, 'target', imageList = imageList, adjustCoords = TRUE, flipOutline = 'y')

raster::plot(img2)

Van Belleghem Steven

Van: kaspardelhey @.> Verzonden: woensdag 13 augustus 2025 12:02 Aan: StevenVB12/patternize @.> CC: Steven M. Van Belleghem @.>; Comment @.> Onderwerp: Re: [StevenVB12/patternize] question about colorChecker and issue with makeOutline (Issue #46)

[https://avatars.githubusercontent.com/u/226236686?s=20&v=4]kaspardelhey left a comment (StevenVB12/patternize#46)< https://github.com/StevenVB12/patternize/issues/46#issuecomment-3183100301>

Hi Steven, Thanks for the quick reply!

  1. Unfortunately the chart is in different positions in different pictures, so I guess the only way to change that will be to see if the function can be changed to avoid the prompt, I will have a look.

  2. I attach the dropbox link to a folder with the script, uncalibrated and calibrated images, xrite coordinates and polygon coordinates, because mail bounced due to its size.

https://www.dropbox.com/scl/fo/ew5n64d0u495my7346uzk/AHozhm-DIAmB7H2GHFMaAKE?rlkey=3rsarh1kogcqomnfafgyzc63k&dl=0

Thanks for checking this out and let me know if you can't access the files

Cheers,

Kaspar

— Reply to this email directly, view it on GitHub< https://github.com/StevenVB12/patternize/issues/46#issuecomment-3183100301>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/ABQOC434ZLPVPN7R3SREZ3D3NMEKFAVCNFSM6AAAAACDYQZCDCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTCOBTGEYDAMZQGE>.

You are receiving this because you commented.Message ID: @.***>

— Reply to this email directly, view it on GitHub https://github.com/StevenVB12/patternize/issues/46#issuecomment-3184621700, or unsubscribe https://github.com/notifications/unsubscribe-auth/BV6BSDQG7JX4QPZAP2WRMUT3NNSFNAVCNFSM6AAAAACDYQZCDCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTCOBUGYZDCNZQGA . You are receiving this because you authored the thread.Message ID: @.***>

kaspardelhey avatar Aug 14 '25 01:08 kaspardelhey

Hmm, I can't reproduce that error. The step seems to work for me...

Steven

Van Belleghem Steven

Van: kaspardelhey @.> Verzonden: donderdag 14 augustus 2025 3:24 Aan: StevenVB12/patternize @.> CC: Steven M. Van Belleghem @.>; Comment @.> Onderwerp: Re: [StevenVB12/patternize] question about colorChecker and issue with makeOutline (Issue #46)

[https://avatars.githubusercontent.com/u/226236686?s=20&v=4]kaspardelhey left a comment (StevenVB12/patternize#46)https://github.com/StevenVB12/patternize/issues/46#issuecomment-3186371330 Hi Steven,

Thanks for the quick fix! It seems to work now. I will let you know how I go about it. The only further issue is that I wanted to continue with some functions from the package recolorize, but when I try to use function:

img3 <- brick_to_array(img2)

I get the following error message:

Error in .local(x, ...) : invalid layer names

Not sure what causes that, but I may contact Hannah Weller about it, since she is the first author of that package.

Cheers!

Kaspar

On Thu, Aug 14, 2025 at 2:33 AM Steven M. Van Belleghem < @.***> wrote:

StevenVB12 left a comment (StevenVB12/patternize#46) https://github.com/StevenVB12/patternize/issues/46#issuecomment-3184621700 Hi Kasper,

You would only need to remove line 778-780 here https://github.com/StevenVB12/patternize/blob/master/R/colorChecker.R

if(all(c(fixedCorners == FALSE, is.null(fixedModel)))){ todo <- readline(prompt="Press [enter] to continue and save image >>> ") }

  1. It took me some effort too as the code has seemed to be getting more buggy... Sorry! This works for me:

xy_coords <- makeList( IDlist=c('xrite_coords.txt'), type='landmark', prepath = NULL, extension = NULL, format = "imageJ", tpsFile = NULL, skipLandmark = NULL )

img <- colorChecker( IDlist=c('1D3A1010s'), prepath = NULL, extension = '.jpg', colorCheckerType = "X-Rite", fixedCorners = FALSE, patchSize = 0.6, colorCheckerXY = xy_coords, fixedModel = NULL, resampleFactor = NULL, adjustCoords = TRUE )

outline <- read.table('XY_Coordinates1010s.txt', header = FALSE)

#this step is not needed if we run the script from the start #img <- makeList('1D3A1010s.jpg_calibrated', type='image')

IDlist=c('1D3A1010s') prepath <- NULL extension <- '_calibrated.jpg' imageList <- makeList(IDlist, 'image', prepath, extension)

img2 <- maskOutline(imageList[[1]], outline, 'target', imageList = imageList, adjustCoords = TRUE, flipOutline = 'y')

raster::plot(img2)

Van Belleghem Steven

Van: kaspardelhey @.> Verzonden: woensdag 13 augustus 2025 12:02 Aan: StevenVB12/patternize @.> CC: Steven M. Van Belleghem @.>; Comment @.> Onderwerp: Re: [StevenVB12/patternize] question about colorChecker and issue with makeOutline (Issue #46)

[https://avatars.githubusercontent.com/u/226236686?s=20&v=4]kaspardelhey left a comment (StevenVB12/patternize#46)< https://github.com/StevenVB12/patternize/issues/46#issuecomment-3183100301>

Hi Steven, Thanks for the quick reply!

  1. Unfortunately the chart is in different positions in different pictures, so I guess the only way to change that will be to see if the function can be changed to avoid the prompt, I will have a look.

  2. I attach the dropbox link to a folder with the script, uncalibrated and calibrated images, xrite coordinates and polygon coordinates, because mail bounced due to its size.

https://www.dropbox.com/scl/fo/ew5n64d0u495my7346uzk/AHozhm-DIAmB7H2GHFMaAKE?rlkey=3rsarh1kogcqomnfafgyzc63k&dl=0

Thanks for checking this out and let me know if you can't access the files

Cheers,

Kaspar

— Reply to this email directly, view it on GitHub< https://github.com/StevenVB12/patternize/issues/46#issuecomment-3183100301>, or unsubscribe< https://github.com/notifications/unsubscribe-auth/ABQOC434ZLPVPN7R3SREZ3D3NMEKFAVCNFSM6AAAAACDYQZCDCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTCOBTGEYDAMZQGE>.

You are receiving this because you commented.Message ID: @.***>

— Reply to this email directly, view it on GitHub https://github.com/StevenVB12/patternize/issues/46#issuecomment-3184621700, or unsubscribe https://github.com/notifications/unsubscribe-auth/BV6BSDQG7JX4QPZAP2WRMUT3NNSFNAVCNFSM6AAAAACDYQZCDCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTCOBUGYZDCNZQGA . You are receiving this because you authored the thread.Message ID: @.***>

— Reply to this email directly, view it on GitHubhttps://github.com/StevenVB12/patternize/issues/46#issuecomment-3186371330, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABQOC435MMLQGTO7BDYYUYL3NPQMZAVCNFSM6AAAAACDYQZCDCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTCOBWGM3TCMZTGA. You are receiving this because you commented.Message ID: @.***>

StevenVB12 avatar Aug 14 '25 09:08 StevenVB12