errors using patLanW

[janisuser]

Hi Steve!

As the subject says, I am getting errors when using patLanW. This happens with my own photos as well as when reproducing your salamanders example, so I am wondering now if it is me selecting wrong points in the images? In the salamanders example, I am first choosing a point of the yellow area, then a point of the black area. After choosing the black point, I am always getting the following message:

> # extract the patterns using watershed
> rasterList_SalW <- patLanW(imageListSal, landmarkListSal, transformRef = REF, resampleFactor = 5, plotTransformed = TRUE, 
+                            correct = TRUE, plotCorrect = FALSE, blur = FALSE, sigma = 2, bucketfill = FALSE, cleanP = 3, adjustCoords = TRUE,
+                            splitC = 10, plotPriority = TRUE, plotWS = TRUE, plotBF = TRUE, plotFinal = TRUE, maskOutline = REF)
[1] "sample 1 4031 added to array"
[1] "sample 2 3864 added to array"
[1] "sample 3 3875 added to array"
[1] "sample 4 3959 added to array"
[1] "sample 5 4118 added to array"
[1] "sample 6 4706 added to array"
[1] "sample 7 4758 added to array"
[1] "sample 8 5574 added to array"
[1] "sample 9 5580 added to array"
[1] "sample 10 5596 added to array"
[1] "Choose points to identify patterns. Click outside image area to stop."
[1] "Choose at leat one point to identify background. Click outside image area to stop."
Error in imager::split_connected(ws) : Pixset is empty, can't split

Also: When [1] "Choose points to identify patterns. Click outside image area to stop." pops up, I am choosing one point of the yellow area, then the next message automatically pops up [1] "Choose at leat one point to identify background. Click outside image area to stop." so that I next choose the black area. Instead of 'choosing points' I only get the chance to choose a single point.

I have downloaded the latest version of patternize from github and downloaded the salamander example a couple of days ago.

Can you help?

Thank you & best wishes,

Janis

[StevenVB12]

Hi Janis,

I just ran the salamander example with the latest code and it’s working fine for me.

Your output should be looking like this:

[1] "Choose points to identify patterns. Click outside image area to stop." [1] "x: 11.7501067919692 y: 9.25288338316956" [1] "x: 14.7402819307988 y: 20.3165313968389" [1] "Choose at leat one point to identify background. Click outside image area to stop." [1] "x: 15.3383169585647 y: 44.2379325074754" [1] "x: 11.7501067919692 y: 78.6249466040153"

Seeing that when you click on your pattern, you are not getting x and y coordinates, I’m wondering if this could be an R or Rstudio related thing of the plotting window.

When you run this code and click on your pattern in the image, do you get any sensible output:

xy <- locator(n=1)

Best,

Steven From: janisuser @.> Sent: Friday, February 4, 2022 8:20 AM To: StevenVB12/patternize @.> Cc: Subscribed @.***> Subject: [StevenVB12/patternize] errors using patLanW (Issue #29)

Hi Steve!

As the subject says, I am getting errors when using patLanW. This happens with my own photos as well as when reproducing your salamanders example, so I am wondering now if it is me selecting wrong points in the images? In the salamanders example, I am first choosing a point of the yellow area, then a point of the black area. After choosing the black point, I am always getting the following message:

extract the patterns using watershed

rasterList_SalW <- patLanW(imageListSal, landmarkListSal, transformRef = REF, resampleFactor = 5, plotTransformed = TRUE,

•                        correct = TRUE, plotCorrect = FALSE, blur = FALSE, sigma = 2, bucketfill = FALSE, cleanP = 3, adjustCoords = TRUE,
  

•                        splitC = 10, plotPriority = TRUE, plotWS = TRUE, plotBF = TRUE, plotFinal = TRUE, maskOutline = REF)
  

[1] "sample 1 4031 added to array"

[1] "sample 2 3864 added to array"

[1] "sample 3 3875 added to array"

[1] "sample 4 3959 added to array"

[1] "sample 5 4118 added to array"

[1] "sample 6 4706 added to array"

[1] "sample 7 4758 added to array"

[1] "sample 8 5574 added to array"

[1] "sample 9 5580 added to array"

[1] "sample 10 5596 added to array"

[1] "Choose points to identify patterns. Click outside image area to stop."

[1] "Choose at leat one point to identify background. Click outside image area to stop."

Error in imager::split_connected(ws) : Pixset is empty, can't split

Also: When [1] "Choose points to identify patterns. Click outside image area to stop." pops up, I am choosing one point of the yellow area, then the next message automatically pops up [1] "Choose at leat one point to identify background. Click outside image area to stop." so that I next choose the black area. Instead of 'choosing points' I only get the chance to choose a single point.

I have downloaded the latest version of patternize from github and downloaded the salamander example a couple of days ago.

Can you help?

Thank you & best wishes,

Janis

— Reply to this email directly, view it on GitHubhttps://github.com/StevenVB12/patternize/issues/29, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABQOC42C3KMYTBISHUPZCDDUZO763ANCNFSM5NRUEJ3Q. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you are subscribed to this thread.Message ID: @.@.>>

[janisuser]

Hi Steven,

Thanks for your quick reply! I have tried it on three different laptops, reinstalled R, RStudio, Rtools and patternize, but I keep getting the same error message. I also redownloaded your example folder but this does not help either.

Are there any other issues that could play a role?

Edit: No, I am not getting x and y coordinates when I click on the image.

Thank you and best regards,

Janis

[StevenVB12]

Hi Janis,

After your code failing, is an image plotted?

Can you then try locator(n=1) and tell me what the output looks like?

Steven

From: janisuser @.> Sent: Friday, February 4, 2022 7:02 PM To: StevenVB12/patternize @.> Cc: Steven M. Van Belleghem @.>; Comment @.> Subject: Re: [StevenVB12/patternize] errors using patLanW (Issue #29)

Hi Steven,

Thanks for your quick reply! I have tried it on three different laptops, reinstalled R, RStudio, Rtools and patternize, but I keep getting the same error message. I also redownloaded your example folder but this does not help either.

Are there any other issues that could play a role?

Thank you and best regards,

Janis

— Reply to this email directly, view it on GitHubhttps://github.com/StevenVB12/patternize/issues/29#issuecomment-1030416116, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABQOC45HFQM4UK3UNAJJ5U3UZRLGXANCNFSM5NRUEJ3Q. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you commented.Message ID: @.@.>>

[janisuser]

Hi Steven,

The plot remains the same, exept that the area where the salamander pattern was turns black.

locator(n=1) works as it should; prints a set of coordinates when I choose a point of the image.

> locator(n=1)
$x
[1] -17.4926

$y
[1] 52.92488

Don't know if this info is of help, but I just found that in very few cases, the patLanW function prints one or two sets of coordinates, but then crashes with the same error message as before. I have been running the code many times now and would say I am getting one or two coordinates in 10 % of trials.

Best wishes,

Janis

[StevenVB12]

I'm scratching my head. Are you working on a Mac? I'm wondering if it's a X11 device problem. The error where it says there's no pixels sound like it's not getting good x y coordinates.

Have you installed the Morpho depency through github? That one may fail at times otherwise.

Steven

-------- Original message -------- From: janisuser @.> Date: 2/6/22 11:56 AM (GMT-04:00) To: StevenVB12/patternize @.> Cc: "Steven M. Van Belleghem" @.>, Comment @.> Subject: Re: [StevenVB12/patternize] errors using patLanW (Issue #29)

Hi Steven,

The plot remains the same, exept that the area where the salamander pattern was turns black.

locator(n=1) works as it should; prints a set of coordinates when I choose a point of the image.

Don't know if this info is of help, but I just found that in very few cases, the patLanW function prints one or two sets of coordinates, but then crashes with the same error message as before. I have been running the code many times now and would say I am getting one or two coordinates in 10 % of trials.

Best wishes,

Janis

— Reply to this email directly, view it on GitHubhttps://github.com/StevenVB12/patternize/issues/29#issuecomment-1030860644, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABQOC45MKXUSSSROEHQXXI3UZ2K3VANCNFSM5NRUEJ3Q. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you commented.Message ID: @.***>

[janisuser]

No I have only tried it with Windows10, and yes, I have installed both patternize and Morpho through github.

Thanks for your help, I know this is a weird problem. I will try it with patLanRGB now, this could also work for my photos and has not led to any error messages so far :-)

Thanks again and best wishes!

Janis

[RJGrayEcology]

I am having this same issue. I resolved the previous issues I posted before by rolling back to R 4.1.1. but now that the function is "working" it is doing exactly what is explained here. I choose points within the image, it creates some coordinates, then fails.

[1] "Choose points to identify patterns. Click outside image area to stop." [1] "Choose at leat one point to identify background. Click outside image area to stop." [1] "x: 651.695722793719 y: 607.343259339469" [1] "x: 606.8229561451 y: 582.102328099621" [1] "x: 550.731997834326 y: 618.561451001624" [1] "x: 612.432051976177 y: 727.938819707634" [1] "x: 570.363833243097 y: 683.066053059015" [1] "x: 511.468327016784 y: 660.629669734705" Error in imager::split_connected(ws) : Pixset is empty, can't split

This occurs both with the example data and my own. I still havent successfully ran the entire sample data and R code yet. Every new version of R and update of packages leads to more errors. Any way to fix this function at least so I can continue with the analysis?

[StevenVB12]

Hi,

Sorry about your errors. I believe it might be an error with R studio itself, failing to give the correct coordinates. Can you try running it in regular R?

Best regards,

Steven

-------- Original message -------- From: RJGrayEcology @.> Date: 5/28/23 12:46 PM (GMT+01:00) To: StevenVB12/patternize @.> Cc: "Steven M. Van Belleghem" @.>, Comment @.> Subject: Re: [StevenVB12/patternize] errors using patLanW (Issue #29)

I am having this same issue. I resolved the previous issues I posted before by rolling back to R 4.1.1. but now that the function is "working" it is doing exactly what is explained here. I choose points within the image, it creates some coordinates, then fails.

[1] "Choose points to identify patterns. Click outside image area to stop." [1] "Choose at leat one point to identify background. Click outside image area to stop." [1] "x: 651.695722793719 y: 607.343259339469" [1] "x: 606.8229561451 y: 582.102328099621" [1] "x: 550.731997834326 y: 618.561451001624" [1] "x: 612.432051976177 y: 727.938819707634" [1] "x: 570.363833243097 y: 683.066053059015" [1] "x: 511.468327016784 y: 660.629669734705" Error in imager::split_connected(ws) : Pixset is empty, can't split

This occurs both with the example data and my own. I still havent successfully ran the entire sample data and R code yet. Every new version of R and update of packages leads to more errors. Any way to fix this function at least so I can continue with the analysis?

— Reply to this email directly, view it on GitHubhttps://github.com/StevenVB12/patternize/issues/29#issuecomment-1566081882, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABQOC46CXKMLK7DU542ZSSDXIMUH7ANCNFSM5NRUEJ3Q. You are receiving this because you commented.Message ID: @.***>

[RJGrayEcology]

Tried it on R rather than R studios, still didn't work. On Monday, May 29, 2023 at 11:00:53 p.m. ICT, Steven M. Van Belleghem @.***> wrote:

Hi,

Sorry about your errors. I believe it might be an error with R studio itself, failing to give the correct coordinates. Can you try running it in regular R?

Best regards,

Steven

-------- Original message -------- From: RJGrayEcology @.> Date: 5/28/23 12:46 PM (GMT+01:00) To: StevenVB12/patternize @.> Cc: "Steven M. Van Belleghem" @.>, Comment @.> Subject: Re: [StevenVB12/patternize] errors using patLanW (Issue #29)

I am having this same issue. I resolved the previous issues I posted before by rolling back to R 4.1.1. but now that the function is "working" it is doing exactly what is explained here. I choose points within the image, it creates some coordinates, then fails.

[1] "Choose points to identify patterns. Click outside image area to stop." [1] "Choose at leat one point to identify background. Click outside image area to stop." [1] "x: 651.695722793719 y: 607.343259339469" [1] "x: 606.8229561451 y: 582.102328099621" [1] "x: 550.731997834326 y: 618.561451001624" [1] "x: 612.432051976177 y: 727.938819707634" [1] "x: 570.363833243097 y: 683.066053059015" [1] "x: 511.468327016784 y: 660.629669734705" Error in imager::split_connected(ws) : Pixset is empty, can't split

This occurs both with the example data and my own. I still havent successfully ran the entire sample data and R code yet. Every new version of R and update of packages leads to more errors. Any way to fix this function at least so I can continue with the analysis?

— Reply to this email directly, view it on GitHubhttps://github.com/StevenVB12/patternize/issues/29#issuecomment-1566081882, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABQOC46CXKMLK7DU542ZSSDXIMUH7ANCNFSM5NRUEJ3Q. You are receiving this because you commented.Message ID: @.***>

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