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creation of zidb files and other functions: #2

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TeresaSilva opened this issue Feb 22, 2018 · 8 comments
Open

creation of zidb files and other functions: #2

TeresaSilva opened this issue Feb 22, 2018 · 8 comments

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

@TeresaSilva
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TeresaSilva commented Apr 30, 2018 via email

@phgrosjean
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phgrosjean commented Apr 30, 2018 via email

@TeresaSilva
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TeresaSilva commented May 4, 2018 via email

@phgrosjean
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phgrosjean commented May 7, 2018 via email

@TeresaSilva
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TeresaSilva commented May 7, 2018 via email

@TeresaSilva
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Hi Philippe,
I am revisiting zooimage. I found some bugs when creating the zidb files.
Before, you mentioned that we only needed to have ZI1 or ZI5 in the zim files, but now, after running the makeZidb() function, the data are transformed into the ZI1 version every time, no matter what I add into the first line in the zim files, and description file.
I also tried to specify the type of version I want to use with the function zidbMakeAll, and I got a lot of error messages:

 zidbMakeAll(".",type = "ZI5", delete.source = FALSE, replace = TRUE)
Creation Progress: 1 on 1  Warning in checkFileExists(zimfile, extension = "zim", force.file = TRUE) :
  file not found: ./done_ZI1.zim
Warning in zidDatMake(zidir, type = type, replace = replace) :
  no '_dat1.zim', '_dat3.zim', or '_dat5.zim' file!
Warning in zidbMake(samples[item], zisfile = zisfiles[item], type = type,  :
  problem when creating the RData file

Warning message:
In zidbMakeAll(".", type = "ZI5", delete.source = FALSE, replace = TRUE) :
  0/1 items were correctly processed (see .last.batch)

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@phgrosjean @TeresaSilva