search

SciViews / zooimage

Plankton images analysis system
http://www.sciviews.org/zooimage
GNU General Public License v2.0
1 stars 0 forks source link

creation of zidb files and other functions: #2

Open TeresaSilva opened 6 years ago

TeresaSilva commented 6 years ago

Issue 6# Unable to create zidb files while using the most recent version of zooimage (vs 5.4-11): It worked fine in the older version (vs. 5.4-8)

zidbMake("./data/Samples/MTPS.2004-10-20.V5")
Error in charToDate(x) : 
  character string is not in a standard unambiguous format
In addition: Warning message:
In if (zisData$Label == "<<<SMP>>>") zisData$Label <- basename(zidir) :
  the condition has length > 1 and only the first element will be used
Error during wrapup: character string is not in a standard unambiguous format

Issue 7#

Unable to read compress ZI1 files into .zidb.

makeZidb()
Warning message:
In zidbMake(smpdir, type = "ZI3", check = TRUE, check.vignettes = TRUE,  :
  only 'ZI5' is currently supported for 'type'

I haven't found anymore "bugs" in the zooimage package. :) Great effort Philippe and others

phgrosjean commented 6 years ago

Issue #6: the error message says it cannot create a valid date (from the corresponding part extracted from the sample filename). Your file name probably does not respect the convention imposed by ZooImage, that is: .YYYY-MM-DD.X.tif with a small string identifying the series without dot in it, YYYY = the year, MM = the month, DD = the day of sampling, is one letter identifying the way the sample was collected (we typically use 'H' for horizontal, and 'V' for vertical, but could be any convention you like and X is a number in case several samples were done for that series). If the sample name is OK, then, there should be a bug indeed. Could you check, please?

Issue #7: Correct. The ZI5 process is completely different, and thus incompatible with previous versions. However, we have to make it backward compatible. Working on this one...

phgrosjean commented 6 years ago

Sorry, I got issue #6 which should be fine now in version 5.5.0. Still working on issue #7.

TeresaSilva commented 6 years ago

Great dear Philippe, We always have our images labeled the same way…as we did in the past Like e.g. „af032000_14.2000-5-10.WA1+A.if“ so I though that the code had some mistake when I inspected it … I am glad you were able to find the problem. Cheers Teresa

From: Philippe Grosjean notifications@github.com Sent: 30 April 2018 08:46 To: SciViews/zooimage zooimage@noreply.github.com Cc: Teresa Sofia Giesta da Silva teresa.silva@hafogvatn.is; Author author@noreply.github.com Subject: Re: [SciViews/zooimage] creation of zidb files and other functions: (#2)

Sorry, I got issue #6 which should be fine now in version 5.5.0. Still working on issue #7.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FSciViews%2Fzooimage%2Fissues%2F2%23issuecomment-385341695&data=02%7C01%7C%7C92068ec40e5c4dcf79a508d5ae76c3da%7C8e105b94435e4303a61063620dbe162b%7C0%7C0%7C636606747470467496&sdata=%2BGIKnDuD4DbSSExL%2F%2FYrbYHj3KVp5YcB2nJWWyL55eo%3D&reserved=0, or mute the threadhttps://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FADdWff1BP9NavVnaEUC9BppqzF_MUpVTks5tts8xgaJpZM4SPa46&data=02%7C01%7C%7C92068ec40e5c4dcf79a508d5ae76c3da%7C8e105b94435e4303a61063620dbe162b%7C0%7C0%7C636606747470467496&sdata=4%2FGYY4qWjc9PRhnKesO6DgOGrD5datnCdokHSMhKW%2Fs%3D&reserved=0.

phgrosjean commented 6 years ago

Deat Teresa,

On 30 Apr 2018, at 11:10, TeresaSilva notifications@github.com wrote:

Great dear Philippe, We always have our images labeled the same way…as we did in the past Like e.g. „af032000_14.2000-5-10.WA1+A.if“ so I though that the code had some mistake when I inspected it … I am glad you were able to find the problem.

Yes, sorry, it takes a little bit of time to dive into the code again. All these issues come from the new ZI5 format incompatible with ZI1-3 for image processing (but series are still inter-compatibles ZI1-5). I work on smoothing this.

Best,

Philippe

Cheers Teresa

From: Philippe Grosjean notifications@github.com Sent: 30 April 2018 08:46 To: SciViews/zooimage zooimage@noreply.github.com Cc: Teresa Sofia Giesta da Silva teresa.silva@hafogvatn.is; Author author@noreply.github.com Subject: Re: [SciViews/zooimage] creation of zidb files and other functions: (#2)

Sorry, I got issue #6 which should be fine now in version 5.5.0. Still working on issue #7.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FSciViews%2Fzooimage%2Fissues%2F2%23issuecomment-385341695&data=02%7C01%7C%7C92068ec40e5c4dcf79a508d5ae76c3da%7C8e105b94435e4303a61063620dbe162b%7C0%7C0%7C636606747470467496&sdata=%2BGIKnDuD4DbSSExL%2F%2FYrbYHj3KVp5YcB2nJWWyL55eo%3D&reserved=0, or mute the threadhttps://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FADdWff1BP9NavVnaEUC9BppqzF_MUpVTks5tts8xgaJpZM4SPa46&data=02%7C01%7C%7C92068ec40e5c4dcf79a508d5ae76c3da%7C8e105b94435e4303a61063620dbe162b%7C0%7C0%7C636606747470467496&sdata=4%2FGYY4qWjc9PRhnKesO6DgOGrD5datnCdokHSMhKW%2Fs%3D&reserved=0. — You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/SciViews/zooimage/issues/2#issuecomment-385346632, or mute the thread https://github.com/notifications/unsubscribe-auth/ADIncTcakIC8r9Iq90SJ52zLG1ApuU78ks5tttUTgaJpZM4SPa46.

TeresaSilva commented 6 years ago

Dear Philippe, I was trying to check what you did and I see that the newsest version of zooimage (vs 5.5.0) is not upploed yet on Github. Cheers, Teresa

From: Philippe Grosjean notifications@github.com Sent: 30 April 2018 08:46 To: SciViews/zooimage zooimage@noreply.github.com Cc: Teresa Sofia Giesta da Silva teresa.silva@hafogvatn.is; Author author@noreply.github.com Subject: Re: [SciViews/zooimage] creation of zidb files and other functions: (#2)

Sorry, I got issue #6 which should be fine now in version 5.5.0. Still working on issue #7.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FSciViews%2Fzooimage%2Fissues%2F2%23issuecomment-385341695&data=02%7C01%7C%7C92068ec40e5c4dcf79a508d5ae76c3da%7C8e105b94435e4303a61063620dbe162b%7C0%7C0%7C636606747470467496&sdata=%2BGIKnDuD4DbSSExL%2F%2FYrbYHj3KVp5YcB2nJWWyL55eo%3D&reserved=0, or mute the threadhttps://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FADdWff1BP9NavVnaEUC9BppqzF_MUpVTks5tts8xgaJpZM4SPa46&data=02%7C01%7C%7C92068ec40e5c4dcf79a508d5ae76c3da%7C8e105b94435e4303a61063620dbe162b%7C0%7C0%7C636606747470467496&sdata=4%2FGYY4qWjc9PRhnKesO6DgOGrD5datnCdokHSMhKW%2Fs%3D&reserved=0.

phgrosjean commented 6 years ago

Dear Teresa,

My fault: I forgot to commint changes. That said, not all problems are solved yet.

I see that you had to split some pictures into several pieces. Is that a memory limitation? I ask because the ZI5 process with a recent version of ImageJ can now process larger pictures at once, providing you have enough RAM.

Best,

Philippe

On 4 May 2018, at 17:26, TeresaSilva notifications@github.com wrote:

Dear Philippe, I was trying to check what you did and I see that the newsest version of zooimage (vs 5.5.0) is not upploed yet on Github. Cheers, Teresa

From: Philippe Grosjean notifications@github.com Sent: 30 April 2018 08:46 To: SciViews/zooimage zooimage@noreply.github.com Cc: Teresa Sofia Giesta da Silva teresa.silva@hafogvatn.is; Author author@noreply.github.com Subject: Re: [SciViews/zooimage] creation of zidb files and other functions: (#2)

Sorry, I got issue #6 which should be fine now in version 5.5.0. Still working on issue #7.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FSciViews%2Fzooimage%2Fissues%2F2%23issuecomment-385341695&data=02%7C01%7C%7C92068ec40e5c4dcf79a508d5ae76c3da%7C8e105b94435e4303a61063620dbe162b%7C0%7C0%7C636606747470467496&sdata=%2BGIKnDuD4DbSSExL%2F%2FYrbYHj3KVp5YcB2nJWWyL55eo%3D&reserved=0, or mute the threadhttps://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FADdWff1BP9NavVnaEUC9BppqzF_MUpVTks5tts8xgaJpZM4SPa46&data=02%7C01%7C%7C92068ec40e5c4dcf79a508d5ae76c3da%7C8e105b94435e4303a61063620dbe162b%7C0%7C0%7C636606747470467496&sdata=4%2FGYY4qWjc9PRhnKesO6DgOGrD5datnCdokHSMhKW%2Fs%3D&reserved=0. — You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/SciViews/zooimage/issues/2#issuecomment-386636538, or mute the thread https://github.com/notifications/unsubscribe-auth/ADIncTf0Sq_gWdFhvbRoK0o7XRtf9FI1ks5tvHNAgaJpZM4SPa46.

TeresaSilva commented 6 years ago

Many thanks dear Philippe, Yes we crop the images because of the Image J memory limitation. This is off course samples that we scanned a long time ago. We dont have the most recent version of the zooimage process for Image J can you please sent us, if you have it. All the best, Many thanks once more for spending time on this. Teresa

From: Philippe Grosjean notifications@github.com Sent: 07 May 2018 13:07 To: SciViews/zooimage zooimage@noreply.github.com Cc: Teresa Sofia Giesta da Silva teresa.silva@hafogvatn.is; Author author@noreply.github.com Subject: Re: [SciViews/zooimage] creation of zidb files and other functions: (#2)

Dear Teresa,

My fault: I forgot to commint changes. That said, not all problems are solved yet.

I see that you had to split some pictures into several pieces. Is that a memory limitation? I ask because the ZI5 process with a recent version of ImageJ can now process larger pictures at once, providing you have enough RAM.

Best,

Philippe

On 4 May 2018, at 17:26, TeresaSilva notifications@github.com<mailto:notifications@github.com> wrote:

Dear Philippe, I was trying to check what you did and I see that the newsest version of zooimage (vs 5.5.0) is not upploed yet on Github. Cheers, Teresa

From: Philippe Grosjean notifications@github.com<mailto:notifications@github.com> Sent: 30 April 2018 08:46 To: SciViews/zooimage zooimage@noreply.github.com<mailto:zooimage@noreply.github.com> Cc: Teresa Sofia Giesta da Silva teresa.silva@hafogvatn.is<mailto:teresa.silva@hafogvatn.is>; Author author@noreply.github.com<mailto:author@noreply.github.com> Subject: Re: [SciViews/zooimage] creation of zidb files and other functions: (#2)

Sorry, I got issue #6 which should be fine now in version 5.5.0. Still working on issue #7.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FSciViews%2Fzooimage%2Fissues%2F2%23issuecomment-385341695&data=02%7C01%7C%7C92068ec40e5c4dcf79a508d5ae76c3da%7C8e105b94435e4303a61063620dbe162b%7C0%7C0%7C636606747470467496&sdata=%2BGIKnDuD4DbSSExL%2F%2FYrbYHj3KVp5YcB2nJWWyL55eo%3D&reserved=0, or mute the threadhttps://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FADdWff1BP9NavVnaEUC9BppqzF_MUpVTks5tts8xgaJpZM4SPa46&data=02%7C01%7C%7C92068ec40e5c4dcf79a508d5ae76c3da%7C8e105b94435e4303a61063620dbe162b%7C0%7C0%7C636606747470467496&sdata=4%2FGYY4qWjc9PRhnKesO6DgOGrD5datnCdokHSMhKW%2Fs%3D&reserved=0. — You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/SciViews/zooimage/issues/2#issuecomment-386636538, or mute the thread https://github.com/notifications/unsubscribe-auth/ADIncTf0Sq_gWdFhvbRoK0o7XRtf9FI1ks5tvHNAgaJpZM4SPa46.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FSciViews%2Fzooimage%2Fissues%2F2%23issuecomment-387058472&data=02%7C01%7C%7C1c16907e803f4aaa564008d5b41b79fd%7C8e105b94435e4303a61063620dbe162b%7C0%7C0%7C636612952467117752&sdata=5w4TBkmoKyzhN8Kuu6vD2MqONuF4rSM6Ut58cx2ooms%3D&reserved=0, or mute the threadhttps://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FADdWfdtRXyTllWtp0Q_29cKJ2kCrSO5qks5twEcBgaJpZM4SPa46&data=02%7C01%7C%7C1c16907e803f4aaa564008d5b41b79fd%7C8e105b94435e4303a61063620dbe162b%7C0%7C0%7C636612952467117752&sdata=cT6LybTfqqTr5NHpM5kdCvIJjQhyesMDEqXichV8soI%3D&reserved=0.