Re: batch importing files - double backslashes?

Posted by gankaku on
URL: http://imagej.273.s1.nabble.com/batch-importing-files-double-backslashes-tp5011545p5011546.html

Hi Djoere,

The error occurs because you are missing the connecting "+"-signs:

your code:
run("Bio-Formats Importer", "open=["input + file"] autoscale
color_mode=Default display_metadata view=Hyperstack stack_order=XYCZT");

corrected code:
run("Bio-Formats Importer", "open=[" + input + file + "] autoscale
color_mode=Default display_metadata view=Hyperstack stack_order=XYCZT");

This should solve the problem.

If you want to have the file and folder separators it might be better to
use the following command

variable1 + file.separator + variable2

The command "file.separator" gives you the correct separators no matter in
which system you are running the macro. Otherwise, it will be running only
on Windows or only on Mac since the file separators used in IJ are
different in the two systems.

cheers,
Jan

2015-02-10 10:53 GMT+01:00 Djoere Gaublomme <[hidden email]>:

> Hello,
>
> I have run into a problem which might be quite trivial.
>
> I am trying to batch process a folder, for which I used the 'Process
> Folder' template macro code (I have copy pasted it at the bottom of this
> message).
> The first command is to import the file with Bioformats Importer, however
> I get an error:  ")" expected  .
>
> The command is:
> run("Bio-Formats Importer", "open=["input + file"] autoscale
> color_mode=Default display_metadata view=Hyperstack stack_order=XYCZT");
>
> Where input is the path from getDirectory, and file is the filename.
> I assume I am making a basic mistake here somewhere.
>
> I thought the problem might be due to a case of single or double
> backslashes, as when you ' print(input + file) ', in the log there are only
> single backslashes visible in the path name (but perhaps internally the
> string does contain 2 backslashes?)
>
>
>
> I looked at some suggestions online and tried replacing the input string
> as follows:
>
> inputReal = replace(input,"\\" , "\\\\")
> This gave the error:  //java.util.regex.PatternSyntaxException:
> Unexpected internal error
> near index 1
>
> or
>
> inputReal = replace(input,"\\" , "/")
> This gave the error: ' ";" expected '  , when trying to '
> print(inputReal); '
>
>
> Any suggestions?
>
> Thanks
>
> Djoere
>
>
>
>
>
> 'Process Folder' template macro code :
>
> input = getDirectory("Input directory");
> output = getDirectory("Output directory");
>
> Dialog.create("File type");
> Dialog.addString("File suffix: ", ".lsm", 5);
> Dialog.show();
> suffix = Dialog.getString();
>
> processFolder(input);
>
> function processFolder(input) {
>         list = getFileList(input);
>         for (i = 0; i < list.length; i++) {
>                 if(endsWith(list[i], "/"))
>                         processFolder("" + input + list[i]);
>                 if(endsWith(list[i], suffix))
>                         processFile(input, output, list[i]);
>         }
> }
>
> function processFile(input, output, file) {
>         // do the processing here by replacing
>         // the following two lines by your own code
>         print("Processing: " + input + file);
>         print("Saving to: " + output);
>         print(output);
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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