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Jessica Davis

Simple Macro

Hello everyone,

I am looking for help to write a simple macro to open different single
images in the same folder, combine them into a stack, and save the stack
under a different name in a different folder.

The images I want to combine have similar titles. For example:
"w000_t000_tt000" , "w000_t000_tt001" , "w000_t000_tt002"... and
"w001_t000_tt000" , "w001_t000_tt0001" , "w001_t000_tt002" ...

Can this be done?

Many thanks.

Kind Regards,

Jessica

--

Jessica Davis MSc.

Conway Institute of Biomolecular and Biomedical Research,
University College Dublin,
Belfield, Dublin 4.

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Василий Попков

Re: Simple Macro

Hey. Well, I have the opposite macros for unstacking and saving images
under different names. So maybe you can use it as an example

n=nSlices();
n=20;
run("Stack to Images");
dir = getDirectory("Choose a source directory ");
for (i=1; i<=n; i++)
{
a=i+100;
showProgress(i, n);
//setSlice(i);
saveAs("Tiff", dir+a+".tif");
close();
g=dir+a;
}

Your macros should be something like (havent checked it, just I think so)

n=20;
dir = getDirectory("Choose a source directory ");
for (i=1; i<=n; i++)
{ open("w000_t000_tt00"+a+".tif");
}
run("Images to stack");

2016-01-26 16:40 GMT+03:00 Jessica Davis <[hidden email]>:

> Hello everyone,
>
> I am looking for help to write a simple macro to open different single
> images in the same folder, combine them into a stack, and save the stack
> under a different name in a different folder.
>
> The images I want to combine have similar titles. For example:
> "w000_t000_tt000" , "w000_t000_tt001" , "w000_t000_tt002"... and
> "w001_t000_tt000" , "w001_t000_tt0001" , "w001_t000_tt002" ...
>
> Can this be done?
>
> Many thanks.
>
> Kind Regards,
>
> Jessica
>
> --
>
> Jessica Davis MSc.
>
> Conway Institute of Biomolecular and Biomedical Research,
> University College Dublin,
> Belfield, Dublin 4.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
Vasily A Popkov
Lab.Structure and function of mitochondria
A.N.Belozersky Institute of Physico-Chemical Biology
Moscow State University

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

ctrueden

Re: Simple Macro

In reply to this post by Jessica Davis

Hi Jessica,

> I am looking for help to write a simple macro to open different single
> images in the same folder, combine them into a stack, and save the
> stack under a different name in a different folder.

Try this:

* Press L for Command Finder
* Check the "Close window after running command" option
* Type "Record." and press enter to run the Plugins>Macros>Record...
function
* Press L again
* Type "Bio-Formats", down arrow, enter to run the File > Import >
Bio-Formats command
* Choose one of your files and press OK.
* Check the "Group files with similar names" option of the Bio-Formats
Importer Options dialog box.
* All your files should open as a single stack
* Use the File > Save As menu to save the stack to the desired output format
* Now look at your Recorder window. It contains your macro to repeat the
process. (You can prune out the "Command Finder" lines; they are
unnecessary for the macro to work.)

Regards,
Curtis

On Tue, Jan 26, 2016 at 7:40 AM, Jessica Davis <[hidden email]>
wrote:

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Aryeh Weiss

Re: Simple Macro

In reply to this post by Jessica Davis

On 26/01/2016 3:40 PM, Jessica Davis wrote:

This macro may help you (you may need to repair line breaks). It was
deigned to take a directory with x###_y###_z### and create
x###_y### stacks which contain all of the z### images. I have a more
developed python version, which does all sorts of other things.
If you want that, or need clarification for this, feel free to ask:

// beginning of macro------------------------------------------------------

inputPath = File.openDialog("choose an image file");

if (inputPath == "") {
exit("User canceled the dialog");
}

inputName = File.getName(inputPath);
inputDir = File.getParent(inputPath);
dirName = substring(inputDir, lastIndexOf(inputDir,"/")+1);
print("input path: ", inputPath);
print("input directory path: ", inputDir);
print("input durectory name: ", dirName);
// print(inputName);

inputPrefix = substring(inputName, 0, lastIndexOf(inputName, "."));
// nprint(inputPrefix);
fileList = getFileList(inputDir);

// print(indexOf(fileList[fileList.length-1],"_x")+2);

/* determine the number of fields in the x and y directions
* The naming convention is: name_x###_y###_z###
* total number of fields (numFields) = total number of files/number
of z planes.
* number of x fields is found by parsing x### in the last file of the
input directory
* number of y fields is (total fields)/(x fields)
*
*/

// determine number of z-planes each xy field
zPlanesStr = substring(fileList[fileList.length-1],
indexOf(fileList[fileList.length-1],"_z")+2,
indexOf(fileList[fileList.length-1],"_z")+5);
zPlanes = parseInt(zPlanesStr);
print("number of z planes: ",zPlanes);
numFields = fileList.length/zPlanes;
print("total number of fields: ",numFields);

// Find total number of x### values
xFieldsStr = substring(fileList[fileList.length-1],
indexOf(fileList[fileList.length-1],"_x")+2,
indexOf(fileList[fileList.length-1],"_x")+5);
xFields = parseInt(xFieldsStr);

// number in y direction must equal total/x-dimension. This can be
verified to make it more robust.
yFields = numFields/xFields;
print("number of x fields: ",xFields, " number of y fields: ",yFields);

sliceIndex = 1;
// loop through all of the XY locations
for (yLoc = 1; yLoc <= yFields; yLoc++) {
for (xLoc = 1; xLoc <= xFields; xLoc++) {
// open an image sequence fro all images which have the current XY
location. This will be our z-stack
run("Image Sequence...", "open="+inputDir+"
file=x"+IJ.pad(d2s(xLoc,0),3)+"_y"+IJ.pad(d2s(yLoc,0),3)+" sort");
selectWindow(dirName);
rename(dirName+"_"+IJ.pad(xLoc,3)+"_"+IJ.pad(yLoc,3));

}
}

// end of macro------------------------------------------------------

hope this helps
--aryeh

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph: 972-3-5317638
FAX: 972-3-7384051

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Jessica Davis

Re: Simple Macro

In reply to this post by ctrueden

Hi Curtis,

Thank you for your response. When I follow your instructions, and I check
the "Group files with similar names" option and press OK, I receive the
following error:

java.io.FileNotFoundException: E:\File and Library
Storage\Desktop\USERS\Jessica
Davis\Marina\pIL+Psfl-test4_20160126_120201\pIL+Psfl-test4_t0000_w0000_tt0000.tif
(The system cannot find the file specified)
at java.io.RandomAccessFile.open(Native Method)
at java.io.RandomAccessFile.<init>(RandomAccessFile.java:212)
at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:123)
at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:139)
at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:148)
at loci.common.Location.getHandle(Location.java:324)
at loci.common.Location.getHandle(Location.java:294)
at loci.common.Location.getHandle(Location.java:284)
at loci.common.Location.getHandle(Location.java:274)
at loci.common.Location.checkValidId(Location.java:349)
at loci.formats.ImageReader.getReader(ImageReader.java:173)
at loci.formats.ImageReader.setId(ImageReader.java:832)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
at loci.formats.DimensionSwapper.setId(DimensionSwapper.java:293)
at loci.formats.FileStitcher$ExternalSeries.<init>(FileStitcher.java:1264)
at loci.formats.FileStitcher.initFile(FileStitcher.java:921)
at loci.formats.FileStitcher.setId(FileStitcher.java:872)
at loci.plugins.in.ImportProcess.initializeStack(ImportProcess.java:520)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:147)
at loci.plugins.in.Importer.showDialogs(Importer.java:140)
at loci.plugins.in.Importer.run(Importer.java:76)
at loci.plugins.LociImporter.run(LociImporter.java:78)
at ij.IJ.runUserPlugIn(IJ.java:212)
at ij.IJ.runPlugIn(IJ.java:176)
at ij.Executer.runCommand(Executer.java:136)
at ij.Executer.run(Executer.java:65)
at java.lang.Thread.run(Thread.java:662)

I am not familiar with computer programming language, so I am unsure what
this error means. Each one of my files have similar names but would I need
to change them to a more simple name for this to work?

Kind Regards,

Jessica

On 26 January 2016 at 15:24, Curtis Rueden <[hidden email]> wrote:

> Hi Jessica,
>
> > I am looking for help to write a simple macro to open different single
> > images in the same folder, combine them into a stack, and save the
> > stack under a different name in a different folder.
>
> Try this:
>
> * Press L for Command Finder
> * Check the "Close window after running command" option
> * Type "Record." and press enter to run the Plugins>Macros>Record...
> function
> * Press L again
> * Type "Bio-Formats", down arrow, enter to run the File > Import >
> Bio-Formats command
> * Choose one of your files and press OK.
> * Check the "Group files with similar names" option of the Bio-Formats
> Importer Options dialog box.
> * All your files should open as a single stack
> * Use the File > Save As menu to save the stack to the desired output
> format
> * Now look at your Recorder window. It contains your macro to repeat the
> process. (You can prune out the "Command Finder" lines; they are
> unnecessary for the macro to work.)
>
> Regards,
> Curtis
>
> On Tue, Jan 26, 2016 at 7:40 AM, Jessica Davis <
> [hidden email]>
> wrote:
>
> > Hello everyone,
> >
> > I am looking for help to write a simple macro to open different single
> > images in the same folder, combine them into a stack, and save the stack
> > under a different name in a different folder.
> >
> > The images I want to combine have similar titles. For example:
> > "w000_t000_tt000" , "w000_t000_tt001" , "w000_t000_tt002"... and
> > "w001_t000_tt000" , "w001_t000_tt0001" , "w001_t000_tt002" ...
> >
> > Can this be done?
> >
> > Many thanks.
> >
> > Kind Regards,
> >
> > Jessica
> >
> > --
> >
> > Jessica Davis MSc.
> >
> > Conway Institute of Biomolecular and Biomedical Research,
> > University College Dublin,
> > Belfield, Dublin 4.
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--

Jessica Davis MSc.

Conway Institute of Biomolecular and Biomedical Research,
University College Dublin,
Belfield, Dublin 4.

Tel: +353857444220

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

ctrueden

Re: Simple Macro

Hi Jessica,

Apologies for the long delay in reply.

> When I follow your instructions, and I check the "Group files with
> similar names" option and press OK, I receive the following error:
>
> java.io.FileNotFoundException: E:\File and Library
> Storage\Desktop\USERS\Jessica
>
Davis\Marina\pIL+Psfl-test4_20160126_120201\pIL+Psfl-test4_t0000_w0000_tt0000.tif
> (The system cannot find the file specified)

That error suggests that perhaps there are one or more missing files in
your collection? However, regardless of that, I would classify this error
as a bug in Bio-Formats—it should at least emit something a little more
clear about what the problem is.

If you wish, you can report Bio-Formats bugs as described here:
http://www.openmicroscopy.org/site/support/bio-formats/about/bug-reporting.html

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - http://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/

On Wed, Jan 27, 2016 at 5:51 AM, Jessica Davis <[hidden email]>
wrote:

> Hi Curtis,
>
> Thank you for your response. When I follow your instructions, and I check
> the "Group files with similar names" option and press OK, I receive the
> following error:
>
> java.io.FileNotFoundException: E:\File and Library
> Storage\Desktop\USERS\Jessica
>
> Davis\Marina\pIL+Psfl-test4_20160126_120201\pIL+Psfl-test4_t0000_w0000_tt0000.tif
> (The system cannot find the file specified)
> at java.io.RandomAccessFile.open(Native Method)
> at java.io.RandomAccessFile.<init>(RandomAccessFile.java:212)
> at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:123)
> at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:139)
> at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:148)
> at loci.common.Location.getHandle(Location.java:324)
> at loci.common.Location.getHandle(Location.java:294)
> at loci.common.Location.getHandle(Location.java:284)
> at loci.common.Location.getHandle(Location.java:274)
> at loci.common.Location.checkValidId(Location.java:349)
> at loci.formats.ImageReader.getReader(ImageReader.java:173)
> at loci.formats.ImageReader.setId(ImageReader.java:832)
> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
> at loci.formats.DimensionSwapper.setId(DimensionSwapper.java:293)
> at loci.formats.FileStitcher$ExternalSeries.<init>(FileStitcher.java:1264)
> at loci.formats.FileStitcher.initFile(FileStitcher.java:921)
> at loci.formats.FileStitcher.setId(FileStitcher.java:872)
> at loci.plugins.in.ImportProcess.initializeStack(ImportProcess.java:520)
> at loci.plugins.in.ImportProcess.execute(ImportProcess.java:147)
> at loci.plugins.in.Importer.showDialogs(Importer.java:140)
> at loci.plugins.in.Importer.run(Importer.java:76)
> at loci.plugins.LociImporter.run(LociImporter.java:78)
> at ij.IJ.runUserPlugIn(IJ.java:212)
> at ij.IJ.runPlugIn(IJ.java:176)
> at ij.Executer.runCommand(Executer.java:136)
> at ij.Executer.run(Executer.java:65)
> at java.lang.Thread.run(Thread.java:662)
>
> I am not familiar with computer programming language, so I am unsure what
> this error means. Each one of my files have similar names but would I need
> to change them to a more simple name for this to work?
>
> Kind Regards,
>
> Jessica
>
> On 26 January 2016 at 15:24, Curtis Rueden <[hidden email]> wrote:
>
> > Hi Jessica,
> >
> > > I am looking for help to write a simple macro to open different single
> > > images in the same folder, combine them into a stack, and save the
> > > stack under a different name in a different folder.
> >
> > Try this:
> >
> > * Press L for Command Finder
> > * Check the "Close window after running command" option
> > * Type "Record." and press enter to run the Plugins>Macros>Record...
> > function
> > * Press L again
> > * Type "Bio-Formats", down arrow, enter to run the File > Import >
> > Bio-Formats command
> > * Choose one of your files and press OK.
> > * Check the "Group files with similar names" option of the Bio-Formats
> > Importer Options dialog box.
> > * All your files should open as a single stack
> > * Use the File > Save As menu to save the stack to the desired output
> > format
> > * Now look at your Recorder window. It contains your macro to repeat the
> > process. (You can prune out the "Command Finder" lines; they are
> > unnecessary for the macro to work.)
> >
> > Regards,
> > Curtis
> >
> > On Tue, Jan 26, 2016 at 7:40 AM, Jessica Davis <
> > [hidden email]>
> > wrote:
> >
> > > Hello everyone,
> > >
> > > I am looking for help to write a simple macro to open different single
> > > images in the same folder, combine them into a stack, and save the
> stack
> > > under a different name in a different folder.
> > >
> > > The images I want to combine have similar titles. For example:
> > > "w000_t000_tt000" , "w000_t000_tt001" , "w000_t000_tt002"... and
> > > "w001_t000_tt000" , "w001_t000_tt0001" , "w001_t000_tt002" ...
> > >
> > > Can this be done?
> > >
> > > Many thanks.
> > >
> > > Kind Regards,
> > >
> > > Jessica
> > >
> > > --
> > >
> > > Jessica Davis MSc.
> > >
> > > Conway Institute of Biomolecular and Biomedical Research,
> > > University College Dublin,
> > > Belfield, Dublin 4.
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
>
>
> --
>
> Jessica Davis MSc.
>
> Conway Institute of Biomolecular and Biomedical Research,
> University College Dublin,
> Belfield, Dublin 4.
>
> Tel: +353857444220
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html