[ome-users] ND2 loci name confusion

[Melissa Linkert]

Hi David,

> I found the problem. I do not know how to solve it but I can work with it
> now. Basically my file were like this "28jun2012-mcc640-AND t cells-TCR
> green-32ms2-exp2-1.nd2" With space or "-" and for some reason the command
> Ext.setId(id) catch the file name well but then the command
> Ext.getImageCreationDate(creationDate) does not make difference between
> the file starting in this example by 28jun2012, if I remove all spaces and
> "-" or any other of these characters the macro is working very well!!!

Thank you for the update.  Upon re-reading your initial mail, it now
makes sense.  The 'Ext.setId(id)' command currently operates as though
you are opening the file with the "Group files with similar names"
option checked.  So these files:

> >>> 28jun2012-mcc640-AND t cells-TCR green-32ms2-exp2-1.nd2
> >>> 28jun2012-mcc640-AND t cells-TCR green-32ms2-exp2-2.nd2
> >>> 28jun2012-mcc640-AND t cells-TCR green-32ms2-exp2-3.nd2

would all be treated as a single dataset.

There is now a ticket on our issue tracking system to make this
behavior configurable:

http://trac.openmicroscopy.org.uk/ome/ticket/9778

Regards,
-Melissa

On Fri, Oct 19, 2012 at 07:46:21PM +0000, Depoil, David wrote:
> Hi,
> 
> I found the problem. I do not know how to solve it but I can work with it
> now. Basically my file were like this "28jun2012-mcc640-AND t cells-TCR
> green-32ms2-exp2-1.nd2" With space or "-" and for some reason the command
> Ext.setId(id) catch the file name well but then the command
> Ext.getImageCreationDate(creationDate) does not make difference between
> the file starting in this example by 28jun2012, if I remove all spaces and
> "-" or any other of these characters the macro is working very well!!!
> 
> Best,
> 
> David
> 
> 
> 
> On 10/19/12 11:35 AM, "Depoil, David" <David.Depoil at nyumc.org> wrote:
> 
> >Dear Melissa,
> >
> >When I open the file in Element I can have access to a creation time that
> >is the same than the one called "textinfoItem_9" in the Metadata file.
> >This one is (for my file) 20 seconds earlier (my acquisition time is
> >20sec) than the one Acquisition time in the OME data file. I tried to get
> >this one (textinfoItem 9) with the macro with the command
> >Ext.getMetadataValue(field, value) but unfortunately it is giving me the
> >same error ( working with name starting differently and confusing the name
> >if they are too similar..). I then try to get any other metadata info like
> >dTimeAbsolute, and I have the same problem so it seems to be a problem
> >with the command it self.
> >
> >Best,
> >
> >David
> >
> >
> >
> >
> >On 10/18/12 6:22 PM, "Melissa Linkert" <melissa at glencoesoftware.com>
> >wrote:
> >
> >>Hi David,
> >>
> >>> I am truing to get the acquisition date from ND2 file using the command
> >>>Ext.getImageCreationDate(creationDate); I did a macro to batch process
> >>>it. It is working great when all the file in the folder have name
> >>>starting differently but if the name are too similar (only the last bit
> >>>is different) the command is taking only the date from the first file
> >>>and use it for all the files of the folder.
> >>
> >>I assume that this is the same problem as was reported by Michael Cammer:
> >>
> >>http://lists.openmicroscopy.org.uk/pipermail/ome-users/2012-October/00334
> >>8
> >>.html
> >>
> >>This is likely not an issue with the macro or the file names, and almost
> >>certainly a result of the fact that Bio-Formats does not find the
> >>acquisition
> >>date in the file, and so uses the file's modification time instead.  This
> >>time
> >>can vary depending upon the file system and operating system; you can
> >>verify
> >>that this is indeed the problem by comparing the timestamp in Finder or
> >>the
> >>output of 'ls -l' with the output of the macro.
> >>
> >>Unfortunately, the absolute acquisition time does not appear to be
> >>recorded in .nd2 files - at least, I don't see it in any of the files
> >>that I have here.  Nikon's NIS-Elements Viewer software also only shows
> >>the file modification time as far as I can tell.  When you open these
> >>files in Elements, do you see the correct acquisition time?
> >>
> >>Regards,
> >>-Melissa
> >>
> >>On Thu, Oct 18, 2012 at 03:08:21PM +0000, Depoil, David wrote:
> >>> Dear all,
> >>> 
> >>> I am truing to get the acquisition date from ND2 file using the command
> >>>Ext.getImageCreationDate(creationDate); I did a macro to batch process
> >>>it. It is working great when all the file in the folder have name
> >>>starting differently but if the name are too similar (only the last bit
> >>>is different) the command is taking only the date from the first file
> >>>and use it for all the files of the folder.
> >>> 
> >>> Here is the macro :
> >>> --------
> >>> requires("1.44c");
> >>> 
> >>> setBatchMode(true);
> >>> 
> >>> dir = getDirectory("Choose a Directory");
> >>> getTimeacquisition(dir);
> >>> 
> >>> setBatchMode(false);
> >>> 
> >>> function getTimeacquisition(dir){
> >>> list=getFileList(dir);
> >>> for (i=0; i<(list.length); i++){
> >>> print(list[i]);
> >>> if (endsWith(list[i], ".nd2")) {
> >>> title1 = "time";
> >>> title2 = "["+title1+"]";
> >>> f = title2;
> >>> run("Text Window...", "name="+title2+" width=70 height=8");
> >>> run("Bio-Formats Macro Extensions");
> >>> id = dir+list[i];
> >>> Ext.setId(id);
> >>> creationDate = "";
> >>> Ext.getImageCreationDate(creationDate);
> >>> print(f,id + ";AcquisitionDate; " + creationDate);
> >>> selectWindow("time");
> >>> Path=id+(".txt");
> >>> saveAs("Text", Path);
> >>> run ("Close");
> >>> 
> >>> }
> >>> }
> >>> }
> >>> -----
> >>> If the name in the folder are  :
> >>> !!!!!!!!!!!28jun2012-mcc640-AND t cells-TCR green-32ms2-exp2-1.nd2
> >>> !!!!!!!!!!28jun2012-mcc640-AND t cells-TCR green-32ms2-exp2-2.nd2
> >>> !!!!!!!!!28jun2012-mcc640-AND t cells-TCR green-32ms2-exp2-3.nd2
> >>> 
> >>> This is working
> >>> 
> >>> But if the name are
> >>> 28jun2012-mcc640-AND t cells-TCR green-32ms2-exp2-1.nd2
> >>> 28jun2012-mcc640-AND t cells-TCR green-32ms2-exp2-2.nd2
> >>> 28jun2012-mcc640-AND t cells-TCR green-32ms2-exp2-3.nd2
> >>> 
> >>> Only the date from the file one is used and aply to the other
> >>> -----
> >>> 
> >>> I am using the LOCI oct 17th daily version with latest ImageJ or Fidji.
> >>>It seems to happen only on mac computers.
> >>> 
> >>> Best,
> >>> 
> >>> David D
> >>> 
> >>> 
> >>
> >>> _______________________________________________
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> >>> ome-users at lists.openmicroscopy.org.uk
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> >>
> >
>