Trouble opening tif files from a macro

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Trouble opening tif files from a macro

Stoyan Pavlov
Hi everyone,
I stumbled upon something that seems very trivial. It is obvious that I am
doing something wrong but can't find out what. I have the following problem:
When I try to execute the following macro:

//subtract dir1 from dir2
inputDir1 = getDirectory("Choose minuend image directory! ");
inputDir2 = getDirectory("Choose subtrahend image directory! ");
outputDir = getDirectory("Choose Output image directory! ");
fileList1 = getFileList(inputDir1);
fileList2 = getFileList(inputDir2);
if (fileList1.length != fileList2.length) {
  exit("Input directories must have same number of files.");
}
for (i = 0; i < fileList1.length; i++) {
  file1 = fileList1[i];
  file2 = fileList2[i];
  open(file1);
  id1 = getImageID();
  open(file2);
  id2 = getImageID();
  imageCalculator("Subtract ", id1, id2);
  outName = File.getName(file1) + "-" + File.getName(file2);
  saveAs("Tiff", outputDir + "/" + outName);
}
//

 the opener returns this message:
"File is not in a supported format, a reader plugin is not available or it
was not found."
The thing is that when I try to open it from the file menu it opens just
fine (these are simple tif files generated by imagej). Even more other
macros that I use (like the batch folder process macro) also open the files
in these directories. I traced the problem to the following (although i am
not sure that this is the problem): When i use the File>Open command the
Macro recorder shows the path to the file with double backslashes (D:\\My
Documents\\Processing\\All-red\\2256_1.tif")
When I used the print command it turned out that the getDirectory command
writes the path with single backslashes. I do not know what to do. Please
help I've got too many files to load and subtract separately.
Thanks in advance!

Stoyan
--
Dr. Stoyan P. Pavlov, MD, PhD
Departament of Anatomy, Histology and Embryology
Medical University "Prof. Dr. Paraskev Stoyanov", Varna
Prof. Marin Drinov Str.55
9002 Varna
 Bulgaria
Tel: +359 (0) 52 - 677 - 086
e-mail: [hidden email]

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Re: Trouble opening tif files from a macro

Jerome Mutterer-3
Dear Stoyan,
file1 is only the filename, without the path.
You should use open(inputDir1+file1)  instead of open (file1).
Same for file2.
Sincerely,

Jerome


On 7 April 2013 17:49, Stoyan Pavlov <[hidden email]> wrote:

> Hi everyone,
> I stumbled upon something that seems very trivial. It is obvious that I am
> doing something wrong but can't find out what. I have the following
> problem:
> When I try to execute the following macro:
>
> //subtract dir1 from dir2
> inputDir1 = getDirectory("Choose minuend image directory! ");
> inputDir2 = getDirectory("Choose subtrahend image directory! ");
> outputDir = getDirectory("Choose Output image directory! ");
> fileList1 = getFileList(inputDir1);
> fileList2 = getFileList(inputDir2);
> if (fileList1.length != fileList2.length) {
>   exit("Input directories must have same number of files.");
> }
> for (i = 0; i < fileList1.length; i++) {
>   file1 = fileList1[i];
>   file2 = fileList2[i];
>   open(file1);
>   id1 = getImageID();
>   open(file2);
>   id2 = getImageID();
>   imageCalculator("Subtract ", id1, id2);
>   outName = File.getName(file1) + "-" + File.getName(file2);
>   saveAs("Tiff", outputDir + "/" + outName);
> }
> //
>
>  the opener returns this message:
> "File is not in a supported format, a reader plugin is not available or it
> was not found."
> The thing is that when I try to open it from the file menu it opens just
> fine (these are simple tif files generated by imagej). Even more other
> macros that I use (like the batch folder process macro) also open the files
> in these directories. I traced the problem to the following (although i am
> not sure that this is the problem): When i use the File>Open command the
> Macro recorder shows the path to the file with double backslashes (D:\\My
> Documents\\Processing\\All-red\\2256_1.tif")
> When I used the print command it turned out that the getDirectory command
> writes the path with single backslashes. I do not know what to do. Please
> help I've got too many files to load and subtract separately.
> Thanks in advance!
>
> Stoyan
> --
> Dr. Stoyan P. Pavlov, MD, PhD
> Departament of Anatomy, Histology and Embryology
> Medical University "Prof. Dr. Paraskev Stoyanov", Varna
> Prof. Marin Drinov Str.55
> 9002 Varna
>  Bulgaria
> Tel: +359 (0) 52 - 677 - 086
> e-mail: [hidden email]
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Re: Trouble opening tif files from a macro

Stoyan Pavlov
Thank you very much, Jerome!
That did it!
Stoyan


2013/4/7 Jerome Mutterer <[hidden email]>

> Dear Stoyan,
> file1 is only the filename, without the path.
> You should use open(inputDir1+file1)  instead of open (file1).
> Same for file2.
> Sincerely,
>
> Jerome
>
>
> On 7 April 2013 17:49, Stoyan Pavlov <[hidden email]> wrote:
>
> > Hi everyone,
> > I stumbled upon something that seems very trivial. It is obvious that I
> am
> > doing something wrong but can't find out what. I have the following
> > problem:
> > When I try to execute the following macro:
> >
> > //subtract dir1 from dir2
> > inputDir1 = getDirectory("Choose minuend image directory! ");
> > inputDir2 = getDirectory("Choose subtrahend image directory! ");
> > outputDir = getDirectory("Choose Output image directory! ");
> > fileList1 = getFileList(inputDir1);
> > fileList2 = getFileList(inputDir2);
> > if (fileList1.length != fileList2.length) {
> >   exit("Input directories must have same number of files.");
> > }
> > for (i = 0; i < fileList1.length; i++) {
> >   file1 = fileList1[i];
> >   file2 = fileList2[i];
> >   open(file1);
> >   id1 = getImageID();
> >   open(file2);
> >   id2 = getImageID();
> >   imageCalculator("Subtract ", id1, id2);
> >   outName = File.getName(file1) + "-" + File.getName(file2);
> >   saveAs("Tiff", outputDir + "/" + outName);
> > }
> > //
> >
> >  the opener returns this message:
> > "File is not in a supported format, a reader plugin is not available or
> it
> > was not found."
> > The thing is that when I try to open it from the file menu it opens just
> > fine (these are simple tif files generated by imagej). Even more other
> > macros that I use (like the batch folder process macro) also open the
> files
> > in these directories. I traced the problem to the following (although i
> am
> > not sure that this is the problem): When i use the File>Open command the
> > Macro recorder shows the path to the file with double backslashes (D:\\My
> > Documents\\Processing\\All-red\\2256_1.tif")
> > When I used the print command it turned out that the getDirectory command
> > writes the path with single backslashes. I do not know what to do. Please
> > help I've got too many files to load and subtract separately.
> > Thanks in advance!
> >
> > Stoyan
> > --
> > Dr. Stoyan P. Pavlov, MD, PhD
> > Departament of Anatomy, Histology and Embryology
> > Medical University "Prof. Dr. Paraskev Stoyanov", Varna
> > Prof. Marin Drinov Str.55
> > 9002 Varna
> >  Bulgaria
> > Tel: +359 (0) 52 - 677 - 086
> > e-mail: [hidden email]
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>



--
Dr. Stoyan P. Pavlov, MD, PhD
Departament of Anatomy, Histology and Embryology
Medical University "Prof. Dr. Paraskev Stoyanov", Varna
Prof. Marin Drinov Str.55
9002 Varna
 Bulgaria
Tel: +359 (0) 52 - 677 - 086
e-mail: [hidden email]

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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Re: Trouble opening tif files from a macro

Nadi
In reply to this post by Stoyan Pavlov
Hi!

I got the same problem while running a macro, but it doesn't look like this
case.
That's the beginning of the macro :

if (list1.length != list2.length) {
  exit("Input directories must have same number of files.");
}
for (i = 0; i < list1.length; i++) {
  file1 = list1[i];
  file2 = list2[i];
  open(dir1+file1);
  run("Create Selection");
  run("Make Inverse");
  open(dir2+file2);
  run("Restore Selection");
  run("Measure", "select = Area Mean Min Max" );
etc


I did not copy the paths because they're fine. I also tried to write
inputDir and so on so far, but it does not change anything, it still can't
open any file (and the files are juste simple tif...)

Thanks in advance!





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Re: Trouble opening tif files from a macro

Michael Schmid-3
Hi Nadi,

please specify your problem more clearly.
Is "The same problem" the following error message (as discussed in this
mailing list more than 5 years ago)?
   "File is not in a supported format, a reader plugin is not available
or it was not found."

Then please print the file paths to the log file before opening the files

   print(dir1+file1);
   print(dir2+file2);

and see whether they are correct.
If they are correct, try opening the files manually and see what error
message you get.


Michael
________________________________________________________________
On 07.02.19 11:22, Nadi wrote:

> Hi!
>
> I got the same problem while running a macro, but it doesn't look like this
> case.
> That's the beginning of the macro :
>
> if (list1.length != list2.length) {
>    exit("Input directories must have same number of files.");
> }
> for (i = 0; i < list1.length; i++) {
>    file1 = list1[i];
>    file2 = list2[i];
>    open(dir1+file1);
>    run("Create Selection");
>    run("Make Inverse");
>    open(dir2+file2);
>    run("Restore Selection");
>    run("Measure", "select = Area Mean Min Max" );
> etc
>
>
> I did not copy the paths because they're fine. I also tried to write
> inputDir and so on so far, but it does not change anything, it still can't
> open any file (and the files are juste simple tif...)
>
> Thanks in advance!
>

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Re: Trouble opening tif files from a macro

Nadi
hi Michael,

yes, the message I got was the same of the first user opening this topic,
the macro couldn't open the tif files and gave me this error saying that a
plugin was missing or wasn't found.

Nevertheless, I followed your advices and I tried to print the paths and
there was somehow a problem (i was getting symbols instead of letters). By
creating two other folders and changing Dir1 and Dir2, it works again.

So I guess that there was a problem with the two folders i was using before!

thanks a lot!



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