Hi SeiHien,
> I have been trying to use macro to batch process my .oif images. The macro
> works when both .oif and .oif.files are in the directory that I've selected
> but doesn't work when they are in one of the subfolders. For example:
>
> C:\Users\SeiHien\Desktop\Macros\FV10_2011\Track0001
>
> It works only when I select "Track0001" and both Image0001_01.oif/.oif.files
> are in "Track0001"
> It doesn't work when I select "FV10_2011" where I have Track0001 to
> Track0012. The error message pops up as
>
> "Sorry, there was a problem during input"
>
> and in the log it is stated as
>
> "loci.formats.FormatException: Required directory Image0001_01.oif.files was
> not found."
The problem is that any subdirectories returned by the getFileList(dir)
command will have a "/" appended, regardless of the platform's file
separator character ("/" on Mac/Linux, "\" on Windows). This causes
interesting behavior on Windows, because you will end up with file names
like this:
C:\path\to\file/Image0001.oif
Perhaps the easiest way around this is to modify the "processFile" function:
// -- begin modified function --
function processFile(path, name, dir) {
path = replace(path, "/", File.separator);
run("Bio-Formats Importer", "open="+path+" autoscale color_mode=Default concatenate_series crop open_all_series split_channels view=Hyperstack stack_order=XYCZT x_coordinate_1=0 y_coordinate_1=0 width_1=640 height_1=900");
}
// -- end modified function --
Regards,
-Melissa
On Wed, Feb 29, 2012 at 02:36:24PM -0800, SeiHien wrote:
> Hi
>
> I have been trying to use macro to batch process my .oif images. The macro
> works when both .oif and .oif.files are in the directory that I've selected
> but doesn't work when they are in one of the subfolders. For example:
>
> C:\Users\SeiHien\Desktop\Macros\FV10_2011\Track0001
>
> It works only when I select "Track0001" and both Image0001_01.oif/.oif.files
> are in "Track0001"
> It doesn't work when I select "FV10_2011" where I have Track0001 to
> Track0012. The error message pops up as
>
> "Sorry, there was a problem during input"
>
> and in the log it is stated as
>
> "loci.formats.FormatException: Required directory Image0001_01.oif.files was
> not found."
>
> May I know if there is any way for me to overcome this problem? Below is the
> code I use, I've deleted the image processing part for easy viewing:
>
> Thanks!
>
> -SeiHien
>
> requires("1.33s");
> dir = getDirectory("Choose a Directory ");
> setBatchMode(true);
> count = 0;
> countFiles(dir);
> n = 0;
> processFiles(dir);
> print(count+" files processed");
>
> function countFiles(dir) {
> list = getFileList(dir);
> for (i=0; i<list.length; i++) {
> if (endsWith(list[i], "/"))
> countFiles(""+dir+list[i]);
> else if(endsWith(list[i], ".oif"))
> count++;
> }
> }
>
> function processFiles(dir) {
> list = getFileList(dir);
> for (i=0; i<list.length; i++) {
> if (endsWith(list[i], "/"))
> processFiles(""+dir+list[i]);
> else if(endsWith(list[i], ".oif")){
> showProgress(n++, count);
> path = dir+list[i];
> print(dir);
> processFile(path, list[i], dir);
> }
> }
> }
>
> function processFile(path, name, dir) {
> if (endsWith(name, ".oif")) {
> run("Bio-Formats Importer", "open="+path+" autoscale
> color_mode=Default concatenate_series crop open_all_series split_channels
> view=Hyperstack stack_order=XYCZT x_coordinate_1=0 y_coordinate_1=0
> width_1=640 height_1=900");
>
> --
> View this message in context:
http://imagej.1557.n6.nabble.com/Bio-Formats-Importer-Couldn-t-Read-OIF-in-Subfolders-During-Batch-Processing-tp4533132p4533132.html> Sent from the ImageJ mailing list archive at Nabble.com.
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