order of file names
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This is really frustrating - but I have 3 folders
cy2 cy3 cy5 and in each folder there are 40 files in the form of NAME_#_CHANNEL where "channel" is either cy2, cy3, or cy5 and # goes from 1 to 40. So I drag the folder onto imageJ and it asks me if I want to open all the files in a stack. That is exactly what I want to do. I do this for all three folders - and the file order is not the same between the stacks. What aspects of a filename dictate the file order? Considering that hte file names are exact and only differ by the tag on the end - is there anything I can do? The only solution I have found is to open the folder and highlight all the files and drag them all onto imageJ. Then run Convert Images to Stack I repeat this with the 3 folders and then I have 3 stacks with the same file order. But it would be far more convenient to not have to do this. Any suggestions? Thanks, John PS - I am running Suse linus 10.2 with ImageJ 1.39J and java 1.6.0 This problem has been occurring with all previous ImageJ versions and previous Java versions. |
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I have had a similar problem. I had to choose 5 files for a bunch of files
in a folder (say the filenames were - 1.tif, 2.tif, 3.tif, 4.tif, 5.tif) and when I drag to image j, and use a stack concatenate function, I assumed it would make it in order od 1-2-3-4-5. But, it seems something else dictates this order. Can someone throw some light ? Sagar On Jan 18, 2008 2:54 PM, John Alexander <[hidden email]> wrote: > This is really frustrating - but I have 3 folders > cy2 > cy3 > cy5 > and in each folder there are 40 files in the form of NAME_#_CHANNEL > where "channel" is either cy2, cy3, or cy5 and # goes from 1 to 40. > > So I drag the folder onto imageJ and it asks me if I want to open all > the files in a stack. > > That is exactly what I want to do. > > I do this for all three folders - and the file order is not the same > between the stacks. > > What aspects of a filename dictate the file order? Considering that hte > file names are exact and only differ by the tag on the end - is there > anything I can do? > > The only solution I have found is to open the folder and highlight all > the files and drag them all onto imageJ. Then run Convert Images to Stack > I repeat this with the 3 folders and then I have 3 stacks with the same > file order. > But it would be far more convenient to not have to do this. > > Any suggestions? > > Thanks, > > John > > > PS - I am running Suse linus 10.2 with ImageJ 1.39J and java 1.6.0 > > This problem has been occurring with all previous ImageJ versions and > previous Java versions. > |
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In reply to this post by John Alexander-7
use teh File/Import Image Seq routine where it will sort the files
correctly if you stick to the default of 'sort numerically'. I have had similar bad luck with drap/drop stacks but the import routine works John Alexander wrote: > This is really frustrating - but I have 3 folders > cy2 > cy3 > cy5 > and in each folder there are 40 files in the form of NAME_#_CHANNEL > where "channel" is either cy2, cy3, or cy5 and # goes from 1 to 40. > > So I drag the folder onto imageJ and it asks me if I want to open all > the files in a stack. > > That is exactly what I want to do. > > I do this for all three folders - and the file order is not the same > between the stacks. > > What aspects of a filename dictate the file order? Considering that hte > file names are exact and only differ by the tag on the end - is there > anything I can do? > > The only solution I have found is to open the folder and highlight all > the files and drag them all onto imageJ. Then run Convert Images to Stack > I repeat this with the 3 folders and then I have 3 stacks with the same > file order. > But it would be far more convenient to not have to do this. > > Any suggestions? > > Thanks, > > John > > > PS - I am running Suse linus 10.2 with ImageJ 1.39J and java 1.6.0 > > This problem has been occurring with all previous ImageJ versions and > previous Java versions. > -- __ Vytas Bindokas, Ph.D. Research Assoc. / Assoc. Prof., Director, BSD Light Microscopy Core Facility Dept Neurobiol Pharmacol Physiol MC0926 947 E 58th Street The University of Chicago Chicago IL 60637 Room Abbott 120 773-702-4875 email [hidden email] web site for LMCF: http://digital.bsd.uchicago.edu/index.html This email is intended only for the use of the individual or entity to which it is addressed and may contain information that is privileged and confidential. If the reader of this email message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication is prohibited. If you have received this email in error, please notify the sender and destroy/delete all copies of the transmittal. Thank you. |
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My experience has also been good with Import Image Seq.
Is it a difficulty with cross-platform OSs that makes it impossible to make drag/drop stack building work the same as Import Image Seq. It would be mighty convenient if it worked the same! Bill >use teh File/Import Image Seq routine where it will sort the files >correctly if you stick to the default of 'sort numerically'. I have >had similar bad luck with drap/drop stacks but the import routine >works > > >John Alexander wrote: >>This is really frustrating - but I have 3 folders >>cy2 >>cy3 >>cy5 >>and in each folder there are 40 files in the form of NAME_#_CHANNEL >>where "channel" is either cy2, cy3, or cy5 and # goes from 1 to 40. >> >>So I drag the folder onto imageJ and it asks me if I want to open all >>the files in a stack. >> >>That is exactly what I want to do. >> >>I do this for all three folders - and the file order is not the same >>between the stacks. >> >>What aspects of a filename dictate the file order? Considering that hte >>file names are exact and only differ by the tag on the end - is there >>anything I can do? >> >>The only solution I have found is to open the folder and highlight all >>the files and drag them all onto imageJ. Then run Convert Images to Stack >>I repeat this with the 3 folders and then I have 3 stacks with the same >>file order. >>But it would be far more convenient to not have to do this. >> >>Any suggestions? >> >>Thanks, >> >>John >> >> >>PS - I am running Suse linus 10.2 with ImageJ 1.39J and java 1.6.0 >> >>This problem has been occurring with all previous ImageJ versions and >>previous Java versions. >> > >-- >__ > >Vytas Bindokas, Ph.D. >Research Assoc. / Assoc. Prof., >Director, BSD Light Microscopy Core Facility >Dept Neurobiol Pharmacol Physiol MC0926 >947 E 58th Street >The University of Chicago >Chicago IL 60637 >Room Abbott 120 >773-702-4875 > >email [hidden email] >web site for LMCF: >http://digital.bsd.uchicago.edu/index.html > > >This email is intended only for the use of the individual or entity >to which it is addressed and may contain information that is >privileged and confidential. If the reader of this email message is >not the intended recipient, you are hereby notified that any >dissemination, distribution, or copying of this communication is >prohibited. If you have received this email in error, please notify >the sender and destroy/delete all copies of the transmittal. Thank >you. |
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In reply to this post by John Alexander-7
John,
Until the real solution turns up, you might be able to use Sort by Label on Stack Sorter. http://www.optinav.com/Stack-Sorter.htm Bob Robert P. Dougherty, Ph.D. President, OptiNav, Inc. Phone (425) 990-5912 Fax (425) 467-1119 www.optinav.com > -----Original Message----- > From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of John > Alexander > Sent: Friday, January 18, 2008 11:55 AM > To: [hidden email] > Subject: order of file names > > This is really frustrating - but I have 3 folders > cy2 > cy3 > cy5 > and in each folder there are 40 files in the form of NAME_#_CHANNEL > where "channel" is either cy2, cy3, or cy5 and # goes from 1 to 40. > > So I drag the folder onto imageJ and it asks me if I want to open all > the files in a stack. > > That is exactly what I want to do. > > I do this for all three folders - and the file order is not the same > between the stacks. > > What aspects of a filename dictate the file order? Considering that hte > file names are exact and only differ by the tag on the end - is there > anything I can do? > > The only solution I have found is to open the folder and highlight all > the files and drag them all onto imageJ. Then run Convert Images to Stack > I repeat this with the 3 folders and then I have 3 stacks with the same > file order. > But it would be far more convenient to not have to do this. > > Any suggestions? > > Thanks, > > John > > > PS - I am running Suse linus 10.2 with ImageJ 1.39J and java 1.6.0 > > This problem has been occurring with all previous ImageJ versions and > previous Java versions. |
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In reply to this post by vbindokas
Vytas,
Sorry, I missed your post. That probably is the real solution. Bob > -----Original Message----- > From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of > vbindoka > Sent: Friday, January 18, 2008 1:18 PM > To: [hidden email] > Subject: Re: order of file names > > use teh File/Import Image Seq routine where it will sort the files > correctly if you stick to the default of 'sort numerically'. I have had > similar bad luck with drap/drop stacks but the import routine works > > > John Alexander wrote: > > This is really frustrating - but I have 3 folders > > cy2 > > cy3 > > cy5 > > and in each folder there are 40 files in the form of NAME_#_CHANNEL > > where "channel" is either cy2, cy3, or cy5 and # goes from 1 to 40. > > > > So I drag the folder onto imageJ and it asks me if I want to open all > > the files in a stack. > > > > That is exactly what I want to do. > > > > I do this for all three folders - and the file order is not the same > > between the stacks. > > > > What aspects of a filename dictate the file order? Considering that hte > > file names are exact and only differ by the tag on the end - is there > > anything I can do? > > > > The only solution I have found is to open the folder and highlight all > > the files and drag them all onto imageJ. Then run Convert Images to > Stack > > I repeat this with the 3 folders and then I have 3 stacks with the same > > file order. > > But it would be far more convenient to not have to do this. > > > > Any suggestions? > > > > Thanks, > > > > John > > > > > > PS - I am running Suse linus 10.2 with ImageJ 1.39J and java 1.6.0 > > > > This problem has been occurring with all previous ImageJ versions and > > previous Java versions. > > > > -- > __ > > Vytas Bindokas, Ph.D. > Research Assoc. / Assoc. Prof., > Director, BSD Light Microscopy Core Facility > Dept Neurobiol Pharmacol Physiol MC0926 > 947 E 58th Street > The University of Chicago > Chicago IL 60637 > Room Abbott 120 > 773-702-4875 > > email [hidden email] > web site for LMCF: > http://digital.bsd.uchicago.edu/index.html > > > > This email is intended only for the use of the individual or entity to > which it is addressed and may contain information that is privileged and > confidential. If the reader of this email message is not the intended > recipient, you are hereby notified that any dissemination, distribution, > or copying of this communication is prohibited. If you have received this > email in error, please notify the sender and destroy/delete all copies of > the transmittal. Thank you. |
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It appears that version 1.39q has fixed the problem. At least on the
few folders I have tested. Thanks to everyone for the suggestions! John Robert Dougherty wrote: > Vytas, > > Sorry, I missed your post. That probably is the real solution. > > Bob > >> -----Original Message----- >> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of >> vbindoka >> Sent: Friday, January 18, 2008 1:18 PM >> To: [hidden email] >> Subject: Re: order of file names >> >> use teh File/Import Image Seq routine where it will sort the files >> correctly if you stick to the default of 'sort numerically'. I have had >> similar bad luck with drap/drop stacks but the import routine works >> >> >> John Alexander wrote: >>> This is really frustrating - but I have 3 folders >>> cy2 >>> cy3 >>> cy5 >>> and in each folder there are 40 files in the form of NAME_#_CHANNEL >>> where "channel" is either cy2, cy3, or cy5 and # goes from 1 to 40. >>> >>> So I drag the folder onto imageJ and it asks me if I want to open all >>> the files in a stack. >>> >>> That is exactly what I want to do. >>> >>> I do this for all three folders - and the file order is not the same >>> between the stacks. >>> >>> What aspects of a filename dictate the file order? Considering that hte >>> file names are exact and only differ by the tag on the end - is there >>> anything I can do? >>> >>> The only solution I have found is to open the folder and highlight all >>> the files and drag them all onto imageJ. Then run Convert Images to >> Stack >>> I repeat this with the 3 folders and then I have 3 stacks with the same >>> file order. >>> But it would be far more convenient to not have to do this. >>> >>> Any suggestions? >>> >>> Thanks, >>> >>> John >>> >>> >>> PS - I am running Suse linus 10.2 with ImageJ 1.39J and java 1.6.0 >>> >>> This problem has been occurring with all previous ImageJ versions and >>> previous Java versions. >>> >> -- >> __ >> >> Vytas Bindokas, Ph.D. >> Research Assoc. / Assoc. Prof., >> Director, BSD Light Microscopy Core Facility >> Dept Neurobiol Pharmacol Physiol MC0926 >> 947 E 58th Street >> The University of Chicago >> Chicago IL 60637 >> Room Abbott 120 >> 773-702-4875 >> >> email [hidden email] >> web site for LMCF: >> http://digital.bsd.uchicago.edu/index.html >> >> >> >> This email is intended only for the use of the individual or entity to >> which it is addressed and may contain information that is privileged and >> confidential. If the reader of this email message is not the intended >> recipient, you are hereby notified that any dissemination, distribution, >> or copying of this communication is prohibited. If you have received this >> email in error, please notify the sender and destroy/delete all copies of >> the transmittal. Thank you. > -- John K. Alexander, Ph.D. Post-Doctoral Fellow William Green Laboratory University of Chicago Dept. Neurobiology, Pharmacology, and Physiology 947 East 58th Street Abott Hall 402 Chicago, IL 60637 (off) 773-702-9386 (fax) 773-702-3774 [hidden email] |
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In reply to this post by Robert Dougherty
This bug is fixed in ImageJ 1.39q, due next week. ImageJ opens
dragged and dropped folders using File>Import>Image Sequence, but, in earlier versions of ImageJ, the "Sort Names Numerically" option was not enabled. -wayne > This is really frustrating - but I have 3 folders > cy2 > cy3 > cy5 > and in each folder there are 40 files in the form of NAME_#_CHANNEL > where "channel" is either cy2, cy3, or cy5 and # goes from 1 to 40. > > So I drag the folder onto imageJ and it asks me if I want to open all > the files in a stack. > > That is exactly what I want to do. > > I do this for all three folders - and the file order is not the same > between the stacks. > > What aspects of a filename dictate the file order? Considering > that hte > file names are exact and only differ by the tag on the end - is there > anything I can do? > > The only solution I have found is to open the folder and highlight all > the files and drag them all onto imageJ. Then run Convert Images > to Stack > I repeat this with the 3 folders and then I have 3 stacks with the > same > file order. > But it would be far more convenient to not have to do this. > > Any suggestions? > > Thanks, > > John > > > PS - I am running Suse linus 10.2 with ImageJ 1.39J and java 1.6.0 > > This problem has been occurring with all previous ImageJ versions and > previous Java versions. > |
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