http://imagej.273.s1.nabble.com/Help-Save-output-files-to-a-created-directory-tp5006211p5006214.html
File.makeDirectory makes the diretory but does not return a string with the path name.
and perhaps you can replace the \\ with +File.separator+"405" ... (so
trying to create it. Here is an example:
> Hello all,
>
> So I am having a little problem with trying to save output files to a
> created directory and was wondering if anyone might have any ideas as to
> what the problem may be.
>
> My problem is thus,
>
> I have created an automated process for collecting tiled images of a slide
> of Drosophila embryos stained for various markers. The process collects a
> grid of defined size (6x6) for each embryo and then moves on to the next.
> The complete output is saved to folder. So, at the end of collection, I am
> left with a directory of files which is a multiple of 36. With each set of
> 36 files being one channel for one complete embryo. I am trying to create a
> macro which will:
>
> 1. Choose this directory
> 2. Run grid/collection stitching plugin for each set of 36 files
> 3. Save the resulting outputs into distinct folders for each embryo/channel
>
> I have gotten pretty far in this process (macro code below), but am running
> into troubles with File.makeDirectory("path"). In the "for" loop, I have a
> directory for each channel created and saved as a variable which is called
> as the output directory required by the Grid/Collection stitching plugin.
> However, when I go to run the code below, it initiates the plugin, loads the
> files and then gives me the following error:
>
> <
http://imagej.1557.x6.nabble.com/file/n5006211/macroerror.png>
>
> I am completely baffled by why this is occurring. From what I can see,
> ImageJ is replacing my defined dir488 variable with a nonexistant path
> "Fiji.app\0.0\". I checked and ImageJ IS creating the directory that I asked
> it too, so that is not the problem. It just doesn't seem to want to specify
> it as a path.
>
> In case anyone needs, or wants, to know, the directory with sample images
> for a test run was placed on my desktop on a Windows 7 PC.
>
> Any ideas?
>
> I am relatively new to macro programming and have not yet tried anything
> with directory manipulation, so any advice or help would be greatly
> appreciated. Sorry in advance for the length and thanks to anyone who reads
> this through!
>
> =====================
> Macro code
> =====================
> dir1 = getDirectory("Choose Source Directory ");
> list = getFileList(dir1);
> n=list.length;
>
> Dialog.create("Parameters");
> Dialog.addNumber("Grid Size x:", 6);
> Dialog.addNumber("Grid Size y:", 6);
> Dialog.addNumber("File Overlap [%]:", 10);
> Dialog.show();
> xpanels = Dialog.getNumber();
> ypanels = Dialog.getNumber();
> overlap = Dialog.getNumber();
>
> f = xpanels * ypanels;
> j = n/f;
> if ((n%f)!=0)
> exit("The number of files must be a multiple of "+f+"!");
>
> setBatchMode(true);
>
> c=1;
>
> for (i=1; i<j; i+=f) {
>
> dir488=File.makeDirectory(dir1 + "Embryo_"+c+"\\488\\");
>
> run("Grid/Collection stitching", "type=[Grid: row-by-row] order=[Right &
> Down ] grid_size_x=&xpanels grid_size_y=&ypanels
> tile_overlap=&overlap first_file_index_i=&i directory=[&dir1]
> file_names=[embryo{iii}_w1Confocal 488.tif]
> output_textfile_name=TileConfiguration.txt fusion_method=[Linear Blending]
> regression_threshold=0.30 max/avg_displacement_threshold=2.50
> absolute_displacement_threshold=3.50 computation_parameters=[Save
> computation time (but use more RAM)] image_output=[Write to disk]
> output_directory=[&dir488]");
>
> dir647=File.makeDirectory(dir1 + "Embryo_"+c+"\\647\\");
>
> run("Grid/Collection stitching", "type=[Grid: row-by-row] order=[Right &
> Down ] grid_size_x=&xpanels grid_size_y=&ypanels
> tile_overlap=&overlap first_file_index_i=&i directory=[&dir1]
> file_names=[embryo{iii}_w3Confocal 640.tif]
> output_textfile_name=TileConfiguration.txt fusion_method=[Linear Blending]
> regression_threshold=0.30 max/avg_displacement_threshold=2.50
> absolute_displacement_threshold=3.50 computation_parameters=[Save
> computation time (but use more RAM)] image_output=[Write to disk]
> output_directory=[&dir647]");
>
> dir405=File.makeDirectory(dir1 + "Embryo_"+c+"\\405\\");
>
> run("Grid/Collection stitching", "type=[Grid: row-by-row] order=[Right &
> Down ] grid_size_x=&xpanels grid_size_y=&ypanels
> tile_overlap=&overlap first_file_index_i=&i directory=[&dir1]
> file_names=[embryo{iii}_w4Confocal 405.tif]
> output_textfile_name=TileConfiguration.txt fusion_method=[Linear Blending]
> regression_threshold=0.30 max/avg_displacement_threshold=2.50
> absolute_displacement_threshold=3.50 computation_parameters=[Save
> computation time (but use more RAM)] image_output=[Write to disk]
> output_directory=[&dir405]");
>
> c++;
>
> }
> =====================
>
> Thanks again!
>
>
>
> --
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>
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