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

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

Jeff C Hanson
                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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Re: How do you open files that have brackets in the filename in a macro?

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

=*===========================================================*=
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-----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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Re: How do you open files that have brackets in the filename in a macro?

Straatman, Kees (Dr.)
In reply to this post by Jeff C Hanson
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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Re: How do you open files that have brackets in the filename in a macro?

Jeff C Hanson
In reply to this post by Jeff C Hanson
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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