How do you open files that have brackets in the filename in a macro?

[jchanson]

                I'm stumped.  I have a batch of files that I want to analyze with a macro.  When the macro tries to open the files, it cuts the filename off at the close bracket (]).  I tried throwing in a \ to escape the embedded brackets, but, it didn't help.
                Is there a way to open the files in a way that doesn't treat the brackets as a special character?  Or, is there a way to get it to ignore the brackets in the middle of the filename?

Thanks,
Jeff

ps - Here's an example of what I was trying to do...

file = "awkward_filename_[39254,8006]_component_data.tif";
bracketPattern = "([\\[\\]])";
addBackslashPattern = "\\\\$1";
escapedFile = replace(file, bracketPattern, addBackslashPattern);

// This throws an exception, because it cuts the filename off at the "]" -- and says the file does not exist
//run("Bio-Formats", "open=["+file+"] color_mode=Default open_all_series view=Hyperstack stack_order=XYCZT");
// This didn't fix it.  :-(
run("Bio-Formats", "open=["+escapedFile+"] color_mode=Default open_all_series view=Hyperstack stack_order=XYCZT");

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[Cammer, Michael]

I think I had this problem with files from a Zeiss lightsheet two years ago and I renamed the files in a cmd window (Win7) with something like:
ren ??????[??]*.tif ??????x??x*.tif

=*===========================================================*=
 Michael Cammer, DART Microscopy Laboratory, NYU Langone Medical Center
    Cell:  914-309-3270 (this is for calling, not texting)    Office: Skirball 2nd Floor main office, back right
      http://ocs.med.nyu.edu/microscopy & http://microscopynotes.com/
http://nyusackler.university-tour.com/15/34/core-laboratories-and-shared-resources/microscopy-core
http://nyusackler.university-tour.com/15/32/core-laboratories-and-shared-resources/introduction



-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Jeff C Hanson
Sent: Thursday, April 20, 2017 2:52 PM
To: [hidden email]
Subject: How do you open files that have brackets in the filename in a macro?

                I'm stumped.  I have a batch of files that I want to analyze with a macro.  When the macro tries to open the files, it cuts the filename off at the close bracket (]).  I tried throwing in a \ to escape the embedded brackets, but, it didn't help.
                Is there a way to open the files in a way that doesn't treat the brackets as a special character?  Or, is there a way to get it to ignore the brackets in the middle of the filename?

Thanks,
Jeff

ps - Here's an example of what I was trying to do...

file = "awkward_filename_[39254,8006]_component_data.tif";
bracketPattern = "([\\[\\]])";
addBackslashPattern = "\\\\$1";
escapedFile = replace(file, bracketPattern, addBackslashPattern);

// This throws an exception, because it cuts the filename off at the "]" -- and says the file does not exist //run("Bio-Formats", "open=["+file+"] color_mode=Default open_all_series view=Hyperstack stack_order=XYCZT"); // This didn't fix it.  :-( run("Bio-Formats", "open=["+escapedFile+"] color_mode=Default open_all_series view=Hyperstack stack_order=XYCZT");

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[Krs5]

Dear Jeff

You could replace them using

file = "awkward_filename_[39254,8006]_component_data.tif";
bracketPattern = "(\\[)";
bracketPattern2 = "(\\])";
addBackslashPattern = "\\\\";
escapedFile = replace(file, bracketPattern, addBackslashPattern);
escapedFile = replace(escapedFile, bracketPattern2, addBackslashPattern);

results in: awkward_filename_\39254,8006\_component_data.tif

However, I would not even insert a \ but just replace it with "" so that you end up with: awkward_filename_39254,8006_component_data.tif as an \ also will introduce problems.

However, I am also able to open the file when using:
open("C:\\TEMP\\awkward_filename_\[39254,8006\]_component_data.tif");
although the text between "" has the wrong colour in the Fiji editor, green/greyish instead of magenta.

Best wishes

Kees

Dr Ir K.R. Straatman
Senior Experimental Officer
Advanced Imaging Facility
Centre for Core Biotechnology Services
University of Leicester
http://www2.le.ac.uk/colleges/medbiopsych/facilities-and-services/cbs/lite/aif

ImageJ workshops 1 and 2 June: http://www2.le.ac.uk/colleges/medbiopsych/facilities-and-services/cbs/AIF/workshops/imagej-workshops-June-2017


-----Original Message-----
From: Jeff C Hanson [mailto:[hidden email]]
Sent: 20 April 2017 19:52
To: [hidden email]
Subject: How do you open files that have brackets in the filename in a macro?

                I'm stumped.  I have a batch of files that I want to analyze with a macro.  When the macro tries to open the files, it cuts the filename off at the close bracket (]).  I tried throwing in a \ to escape the embedded brackets, but, it didn't help.
                Is there a way to open the files in a way that doesn't treat the brackets as a special character?  Or, is there a way to get it to ignore the brackets in the middle of the filename?

Thanks,
Jeff

ps - Here's an example of what I was trying to do...

file = "awkward_filename_[39254,8006]_component_data.tif";
bracketPattern = "([\\[\\]])";
addBackslashPattern = "\\\\$1";
escapedFile = replace(file, bracketPattern, addBackslashPattern);

// This throws an exception, because it cuts the filename off at the "]" -- and says the file does not exist //run("Bio-Formats", "open=["+file+"] color_mode=Default open_all_series view=Hyperstack stack_order=XYCZT"); // This didn't fix it.  :-( run("Bio-Formats", "open=["+escapedFile+"] color_mode=Default open_all_series view=Hyperstack stack_order=XYCZT");

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[jchanson]

Thanks for the tips on dealing with filenames with brackets in them.  Renaming the files so they didn't have brackets would be the easiest thing to do -- thanks, Michael for the simple windows command for stripping them out.  However, just using the plain "open" command worked, too (thanks, Kees for showing that it worked).  With some googling, I was able to find the macro extension command equivalent of the open command to use BioFormats.  The following was able to open my file with brackets in the filename:

// Load Bio-Formats extensions so that the "Ext." bioformats commands are available.
run("Bio-Formats Macro Extensions");
file = "awkward_filename_[39254,8006]_component_data.tif";
Ext.openImagePlus(file);


Thanks again everyone,
Jeff

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[Stoyan Pavlov]

Or you could simply use a file renaming tool like AntRenamer ?(
http://www.antp.be/software/renamer/features)

На 21.04.2017 г. 5:41 сл.об. "Jeff C Hanson" <[hidden email]>
написа:

> Thanks for the tips on dealing with filenames with brackets in them.
> Renaming the files so they didn't have brackets would be the easiest thing
> to do -- thanks, Michael for the simple windows command for stripping them
> out.  However, just using the plain "open" command worked, too (thanks,
> Kees for showing that it worked).  With some googling, I was able to find
> the macro extension command equivalent of the open command to use
> BioFormats.  The following was able to open my file with brackets in the
> filename:
>
> // Load Bio-Formats extensions so that the "Ext." bioformats commands are
> available.
> run("Bio-Formats Macro Extensions");
> file = "awkward_filename_[39254,8006]_component_data.tif";
> Ext.openImagePlus(file);
>
>
> Thanks again everyone,
> Jeff
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[CARL Philippe (LBP)]

Dear написа:,
In the case you want to go into this direction, you can indeed dowload an ad hoc tool for each needed application (files renaming, files comparison, FTP,...).
Or rather use a kind of "Swiss knife" tool as Total Commander:
https://www.ghisler.com/index.htm
which will allow you to do all this in one:
https://www.ghisler.com/screenshots/en/06.html
https://www.ghisler.com/screenshots/en/07.html
https://www.ghisler.com/screenshots/en/04.html
...
Have  nice week-end,
Philippe

Le Samedi 29 Avril 2017 23:07 CEST, Stoyan Pavlov <[hidden email]> a écrit:

> Or you could simply use a file renaming tool like AntRenamer ?(
> http://www.antp.be/software/renamer/features)
>
> На 21.04.2017 г. 5:41 сл.об. "Jeff C Hanson" <[hidden email]>
> написа:
>
> > Thanks for the tips on dealing with filenames with brackets in them.
> > Renaming the files so they didn't have brackets would be the easiest thing
> > to do -- thanks, Michael for the simple windows command for stripping them
> > out.  However, just using the plain "open" command worked, too (thanks,
> > Kees for showing that it worked).  With some googling, I was able to find
> > the macro extension command equivalent of the open command to use
> > BioFormats.  The following was able to open my file with brackets in the
> > filename:
> >
> > // Load Bio-Formats extensions so that the "Ext." bioformats commands are
> > available.
> > run("Bio-Formats Macro Extensions");
> > file = "awkward_filename_[39254,8006]_component_data.tif";
> > Ext.openImagePlus(file);
> >
> >
> > Thanks again everyone,
> > Jeff
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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