batch conversion of a folder

[Younes Leysi]

Hello ImageJ Lovers,

I would like to convert 12-bit tiff images to 8-bit tiff images in a
main folder which has already several sub-folders. the sub-folders
have thousands of images which can be easily converted one-by-one,
using the "batch converter" plugin  from the following link. the
problem is that I have to use this plugin for all sub-folders one by
one and the number of the sub-folders are too much. I am wondering if
there is a way to run this plugin for the main folder; i.e. ask a
macro to do the conversion job for all other sub-folders. any
suggestions are highly appreciated.
http://rsb.info.nih.gov/ij/plugins/batch-converter.html

Truly yours,
Younes
--
Younes Leysi
"Life is a song, sing it."

[ctrueden]

Hi Younes,

Take a look at the "list files recursively" macro:
http://rsb.info.nih.gov/ij/macros/ListFilesRecursively.txt

-Curtis

On Wed, Mar 12, 2008 at 12:43 PM, Younes Leysi Derilou <
[hidden email]> wrote:

> Hello ImageJ Lovers,
>
> I would like to convert 12-bit tiff images to 8-bit tiff images in a
> main folder which has already several sub-folders. the sub-folders
> have thousands of images which can be easily converted one-by-one,
> using the "batch converter" plugin  from the following link. the
> problem is that I have to use this plugin for all sub-folders one by
> one and the number of the sub-folders are too much. I am wondering if
> there is a way to run this plugin for the main folder; i.e. ask a
> macro to do the conversion job for all other sub-folders. any
> suggestions are highly appreciated.
> http://rsb.info.nih.gov/ij/plugins/batch-converter.html
>
> Truly yours,
> Younes
> --
> Younes Leysi
> "Life is a song, sing it."
>

[Younes Leysi]

Hello Curtis,

Thank you for the link. i saved that file as "directory_call.txt" in
"imageJ/macros/" folder. i run the macro first through
"Menu/plugins/macro/run", which asked me to select the directory, i
chose one (for example F:\test_conversion\day5c which had 49
subfolders), then i run the batch converter plugin. that plugin just
converted the images inside the subfolder that i had chosen, nothing
else. i did not see any benefits of running that macro. i have also
tried to run macro after that plugin, but nothing happened. is there
other procedure that i should follow to joint the macro and plugin
together?

Thanks and Regards,
Younes

On Wed, Mar 12, 2008 at 2:06 PM, Curtis Rueden <[hidden email]> wrote:

> Hi Younes,
>
> Take a look at the "list files recursively" macro:
> http://rsb.info.nih.gov/ij/macros/ListFilesRecursively.txt
>
> -Curtis
>
>
> On Wed, Mar 12, 2008 at 12:43 PM, Younes Leysi Derilou <
> [hidden email]> wrote:
>
> > Hello ImageJ Lovers,
> >
> > I would like to convert 12-bit tiff images to 8-bit tiff images in a
> > main folder which has already several sub-folders. the sub-folders
> > have thousands of images which can be easily converted one-by-one,
> > using the "batch converter" plugin  from the following link. the
> > problem is that I have to use this plugin for all sub-folders one by
> > one and the number of the sub-folders are too much. I am wondering if
> > there is a way to run this plugin for the main folder; i.e. ask a
> > macro to do the conversion job for all other sub-folders. any
> > suggestions are highly appreciated.
> > http://rsb.info.nih.gov/ij/plugins/batch-converter.html
> >
> > Truly yours,
> > Younes
> > --
> > Younes Leysi
> > "Life is a song, sing it."
> >
>

--
Younes Leysi
"Life is a song, sing it."

[ctrueden]

Hi Younes,

You need to modify the macro to perform the tasks you want. To get you
started, here is a version that recursively converts files to TIFF format:

------
// Recursively converts files to TIFF starting in a user-specified directory

requires("1.32f");
dir = getDirectory("Choose a Directory ");
count = 1;
prefix = "converted-";
listFiles(dir);

function listFiles(dir) {
    list = getFileList(dir);
    for (i=0; i<list.length; i++) {
        if (endsWith(list[i], "/"))
            listFiles(""+dir+list[i]);
        else {
            print((count++) + ": " + dir + list[i]);
            open(dir + list[i]);
            // convert all open images to TIFF
            c = 1;
            while (nImages > 0) {
                saveAs("Tiff", dir + prefix + list[i] + "-" + c + ".tif");
                close();
                c++;
            }
        }
    }
}
------

HTH,
Curtis

On Wed, Mar 12, 2008 at 2:18 PM, Younes Leysi Derilou <
[hidden email]> wrote:

> Hello Curtis,
>
> Thank you for the link. i saved that file as "directory_call.txt" in
> "imageJ/macros/" folder. i run the macro first through
> "Menu/plugins/macro/run", which asked me to select the directory, i
> chose one (for example F:\test_conversion\day5c which had 49
> subfolders), then i run the batch converter plugin. that plugin just
> converted the images inside the subfolder that i had chosen, nothing
> else. i did not see any benefits of running that macro. i have also
> tried to run macro after that plugin, but nothing happened. is there
> other procedure that i should follow to joint the macro and plugin
> together?
>
> Thanks and Regards,
> Younes
>
> On Wed, Mar 12, 2008 at 2:06 PM, Curtis Rueden <[hidden email]> wrote:
> > Hi Younes,
> >
> > Take a look at the "list files recursively" macro:
> > http://rsb.info.nih.gov/ij/macros/ListFilesRecursively.txt
> >
> > -Curtis
> >
> >
> > On Wed, Mar 12, 2008 at 12:43 PM, Younes Leysi Derilou <
> > [hidden email]> wrote:
> >
> > > Hello ImageJ Lovers,
> > >
> > > I would like to convert 12-bit tiff images to 8-bit tiff images in a
> > > main folder which has already several sub-folders. the sub-folders
> > > have thousands of images which can be easily converted one-by-one,
> > > using the "batch converter" plugin  from the following link. the
> > > problem is that I have to use this plugin for all sub-folders one by
> > > one and the number of the sub-folders are too much. I am wondering if
> > > there is a way to run this plugin for the main folder; i.e. ask a
> > > macro to do the conversion job for all other sub-folders. any
> > > suggestions are highly appreciated.
> > > http://rsb.info.nih.gov/ij/plugins/batch-converter.html
> > >
> > > Truly yours,
> > > Younes
> > > --
> > > Younes Leysi
> > > "Life is a song, sing it."
> > >
> >
>
>
>
> --
> Younes Leysi
> "Life is a song, sing it."
>

[Younes Leysi]

Dear Curtis,

Thank you for your time to write the macro. i saved your text as
"directory_convert_tiff.txt" in ij/macros folder and then run it. it
asked me again to choose a directory which i selected the main folder.
but then it showed an error like this "File is not in tiff, jpeg,
giff, bmp .... format, a plugin for this format is not installed, or
it was not found.". I have the batch converter plugin ( saved in
ij/plugins) which works properly. I had also put the plugin into that
main folder, but the same error came up. all of my images (in the
subfloders) are in 12-bit tiff format and need to be converted to
8-bit tiff. is there something else i am missing to joint this plugin
and macro together?

thanks a lot for your kind collaboration,

Best regards,
Younes

On Wed, Mar 12, 2008 at 4:40 PM, Curtis Rueden <[hidden email]> wrote:

> Hi Younes,
>
> You need to modify the macro to perform the tasks you want. To get you
> started, here is a version that recursively converts files to TIFF format:
>
> ------
> // Recursively converts files to TIFF starting in a user-specified directory
>
> requires("1.32f");
> dir = getDirectory("Choose a Directory ");
> count = 1;
> prefix = "converted-";
> listFiles(dir);
>
> function listFiles(dir) {
>    list = getFileList(dir);
>    for (i=0; i<list.length; i++) {
>        if (endsWith(list[i], "/"))
>            listFiles(""+dir+list[i]);
>        else {
>            print((count++) + ": " + dir + list[i]);
>            open(dir + list[i]);
>            // convert all open images to TIFF
>            c = 1;
>            while (nImages > 0) {
>                saveAs("Tiff", dir + prefix + list[i] + "-" + c + ".tif");
>                close();
>                c++;
>            }
>        }
>    }
> }
> ------
>
> HTH,
> Curtis
>
> On Wed, Mar 12, 2008 at 2:18 PM, Younes Leysi Derilou <
>
> [hidden email]> wrote:
>
> > Hello Curtis,
> >
> > Thank you for the link. i saved that file as "directory_call.txt" in
> > "imageJ/macros/" folder. i run the macro first through
> > "Menu/plugins/macro/run", which asked me to select the directory, i
> > chose one (for example F:\test_conversion\day5c which had 49
> > subfolders), then i run the batch converter plugin. that plugin just
> > converted the images inside the subfolder that i had chosen, nothing
> > else. i did not see any benefits of running that macro. i have also
> > tried to run macro after that plugin, but nothing happened. is there
> > other procedure that i should follow to joint the macro and plugin
> > together?
> >
> > Thanks and Regards,
> > Younes
> >
> > On Wed, Mar 12, 2008 at 2:06 PM, Curtis Rueden <[hidden email]> wrote:
> > > Hi Younes,
> > >
> > > Take a look at the "list files recursively" macro:
> > > http://rsb.info.nih.gov/ij/macros/ListFilesRecursively.txt
> > >
> > > -Curtis
> > >
> > >
> > > On Wed, Mar 12, 2008 at 12:43 PM, Younes Leysi Derilou <
> > > [hidden email]> wrote:
> > >
> > > > Hello ImageJ Lovers,
> > > >
> > > > I would like to convert 12-bit tiff images to 8-bit tiff images in a
> > > > main folder which has already several sub-folders. the sub-folders
> > > > have thousands of images which can be easily converted one-by-one,
> > > > using the "batch converter" plugin  from the following link. the
> > > > problem is that I have to use this plugin for all sub-folders one by
> > > > one and the number of the sub-folders are too much. I am wondering if
> > > > there is a way to run this plugin for the main folder; i.e. ask a
> > > > macro to do the conversion job for all other sub-folders. any
> > > > suggestions are highly appreciated.
> > > > http://rsb.info.nih.gov/ij/plugins/batch-converter.html
> > > >
> > > > Truly yours,
> > > > Younes
> > > > --
> > > > Younes Leysi
> > > > "Life is a song, sing it."
> > > >
> > >
> >
> >
> >
> > --
> > Younes Leysi
> > "Life is a song, sing it."
> >
>

--
Younes Leysi
"Life is a song, sing it."

[ctrueden]

Hi Younes,

You do not need the batch converter plugin to use the macro I sent. My guess
is that some of the files in the subfolders are in a format that ImageJ does
not recognize. You could either move them, or change the macro to ignore
files unless they end with a particular extension.

Below is a version that only converts files originally in TIFF format. I
noticed you also said you want to convert from 12-bit to 8-bit, so I put an
extra line in to do that as well.

You can add more statements in the same place, immediately following the
"while (nImages > 0)" command. You can easily discover what a statement to
perform a particular action looks like by using the Macro Recorder (Plugins
> Macros > Record) feature. Just perform an action using the menus, then
copy and paste the resulting command from the macro recorder window into
your macro.

------
// Recursively converts files to TIFF starting in a user-specified directory

requires("1.32f");
dir = getDirectory("Choose a Directory ");
count = 1;
prefix = "converted-";
listFiles(dir);

function listFiles(dir) {
    list = getFileList(dir);
    for (i=0; i<list.length; i++) {
        if (endsWith(list[i], "/"))
            listFiles(""+dir+list[i]);
        else if (endsWith(toLowerCase(list[i]), ".tif") ||
            endsWith(toLowerCase(list[i]), ".tiff"))
        {
            print((count++) + ": " + dir + list[i]);
            open(dir + list[i]);
            // convert all open images to TIFF
            c = 1;
            while (nImages > 0) {
                run("8-bit");
                // place additional commands here
                saveAs("Tiff", dir + prefix + list[i] + "-" + c + ".tif");
                close();
                c++;
            }
        }
    }
}
------

-Curtis

On Thu, Mar 13, 2008 at 8:33 AM, Younes Leysi Derilou <
[hidden email]> wrote:

> Dear Curtis,
>
> Thank you for your time to write the macro. i saved your text as
> "directory_convert_tiff.txt" in ij/macros folder and then run it. it
> asked me again to choose a directory which i selected the main folder.
> but then it showed an error like this "File is not in tiff, jpeg,
> giff, bmp .... format, a plugin for this format is not installed, or
> it was not found.". I have the batch converter plugin ( saved in
> ij/plugins) which works properly. I had also put the plugin into that
> main folder, but the same error came up. all of my images (in the
> subfloders) are in 12-bit tiff format and need to be converted to
> 8-bit tiff. is there something else i am missing to joint this plugin
> and macro together?
>
> thanks a lot for your kind collaboration,
>
> Best regards,
> Younes
>
> On Wed, Mar 12, 2008 at 4:40 PM, Curtis Rueden <[hidden email]> wrote:
> > Hi Younes,
> >
> > You need to modify the macro to perform the tasks you want. To get you
> > started, here is a version that recursively converts files to TIFF
> format:
> >
> > ------
> > // Recursively converts files to TIFF starting in a user-specified
> directory
> >
> > requires("1.32f");
> > dir = getDirectory("Choose a Directory ");
> > count = 1;
> > prefix = "converted-";
> > listFiles(dir);
> >
> > function listFiles(dir) {
> >    list = getFileList(dir);
> >    for (i=0; i<list.length; i++) {
> >        if (endsWith(list[i], "/"))
> >            listFiles(""+dir+list[i]);
> >        else {
> >            print((count++) + ": " + dir + list[i]);
> >            open(dir + list[i]);
> >            // convert all open images to TIFF
> >            c = 1;
> >            while (nImages > 0) {
> >                saveAs("Tiff", dir + prefix + list[i] + "-" + c +
> ".tif");
> >                close();
> >                c++;
> >            }
> >        }
> >    }
> > }
> > ------
> >
> > HTH,
> > Curtis
> >
> > On Wed, Mar 12, 2008 at 2:18 PM, Younes Leysi Derilou <
> >
> > [hidden email]> wrote:
> >
> > > Hello Curtis,
> > >
> > > Thank you for the link. i saved that file as "directory_call.txt" in
> > > "imageJ/macros/" folder. i run the macro first through
> > > "Menu/plugins/macro/run", which asked me to select the directory, i
> > > chose one (for example F:\test_conversion\day5c which had 49
> > > subfolders), then i run the batch converter plugin. that plugin just
> > > converted the images inside the subfolder that i had chosen, nothing
> > > else. i did not see any benefits of running that macro. i have also
> > > tried to run macro after that plugin, but nothing happened. is there
> > > other procedure that i should follow to joint the macro and plugin
> > > together?
> > >
> > > Thanks and Regards,
> > > Younes
> > >
> > > On Wed, Mar 12, 2008 at 2:06 PM, Curtis Rueden <[hidden email]>
> wrote:
> > > > Hi Younes,
> > > >
> > > > Take a look at the "list files recursively" macro:
> > > > http://rsb.info.nih.gov/ij/macros/ListFilesRecursively.txt
> > > >
> > > > -Curtis
> > > >
> > > >
> > > > On Wed, Mar 12, 2008 at 12:43 PM, Younes Leysi Derilou <
> > > > [hidden email]> wrote:
> > > >
> > > > > Hello ImageJ Lovers,
> > > > >
> > > > > I would like to convert 12-bit tiff images to 8-bit tiff images in
> a
> > > > > main folder which has already several sub-folders. the sub-folders
> > > > > have thousands of images which can be easily converted one-by-one,
> > > > > using the "batch converter" plugin  from the following link. the
> > > > > problem is that I have to use this plugin for all sub-folders one
> by
> > > > > one and the number of the sub-folders are too much. I am wondering
> if
> > > > > there is a way to run this plugin for the main folder; i.e. ask a
> > > > > macro to do the conversion job for all other sub-folders. any
> > > > > suggestions are highly appreciated.
> > > > > http://rsb.info.nih.gov/ij/plugins/batch-converter.html
> > > > >
> > > > > Truly yours,
> > > > > Younes
> > > > > --
> > > > > Younes Leysi
> > > > > "Life is a song, sing it."
> > > > >
> > > >
> > >
> > >
> > >
> > > --
> > > Younes Leysi
> > > "Life is a song, sing it."
> > >
> >
>
>
>
> --
> Younes Leysi
> "Life is a song, sing it."
>

[Younes Leysi]

Hello Curtis,

Thanks so much for your time to edit the macro. it works fine. I had
to change the macro to overwrite the files (to save the hard drive
memory), as following. I understood that why and how you asked macro
to save with different prefix and extension. the small tiny problem is
that the macro opens the images that converts and then closes. this
results in a flashing windows in the working environment that bothers
a user. is there a way to block displaying the conversion process?

Thanks so much for your kind help,
Younes

// Recursively converts files to 8-bit TIFF starting in a
user-specified directory and overwrites
requires("1.32f");
dir = getDirectory("Choose a Directory ");
count = 1;
//prefix = "converted-";
listFiles(dir);
function listFiles(dir) {
   list = getFileList(dir);
   for (i=0; i<list.length; i++) {
       if (endsWith(list[i], "/"))
           listFiles(""+dir+list[i]);
       else if (endsWith(toLowerCase(list[i]), ".tif") ||
           endsWith(toLowerCase(list[i]), ".tiff"))
       {
           print((count++) + ": " + dir + list[i]);
           open(dir + list[i]);
           // convert all open images to TIFF
           c = 1;
           while (nImages > 0) {
               run("8-bit");
               // place additional commands here
               saveAs("Tiff", dir + list[i]);
               close();
               c++;
           }
       }
   }
}

On Thu, Mar 13, 2008 at 10:54 AM, Curtis Rueden <[hidden email]> wrote:

> Hi Younes,
>
> You do not need the batch converter plugin to use the macro I sent. My guess
> is that some of the files in the subfolders are in a format that ImageJ does
> not recognize. You could either move them, or change the macro to ignore
> files unless they end with a particular extension.
>
> Below is a version that only converts files originally in TIFF format. I
> noticed you also said you want to convert from 12-bit to 8-bit, so I put an
> extra line in to do that as well.
>
> You can add more statements in the same place, immediately following the
> "while (nImages > 0)" command. You can easily discover what a statement to
> perform a particular action looks like by using the Macro Recorder (Plugins
> > Macros > Record) feature. Just perform an action using the menus, then
> copy and paste the resulting command from the macro recorder window into
> your macro.
>
> ------
> // Recursively converts files to TIFF starting in a user-specified directory
>
> requires("1.32f");
> dir = getDirectory("Choose a Directory ");
> count = 1;
> prefix = "converted-";
> listFiles(dir);
>
> function listFiles(dir) {
>    list = getFileList(dir);
>    for (i=0; i<list.length; i++) {
>        if (endsWith(list[i], "/"))
>            listFiles(""+dir+list[i]);
>        else if (endsWith(toLowerCase(list[i]), ".tif") ||
>            endsWith(toLowerCase(list[i]), ".tiff"))
>        {
>            print((count++) + ": " + dir + list[i]);
>            open(dir + list[i]);
>            // convert all open images to TIFF
>            c = 1;
>            while (nImages > 0) {
>                run("8-bit");
>                // place additional commands here
>                saveAs("Tiff", dir + prefix + list[i] + "-" + c + ".tif");
>                close();
>                c++;
>            }
>        }
>    }
> }
> ------
>
> -Curtis
>
> On Thu, Mar 13, 2008 at 8:33 AM, Younes Leysi Derilou <
>
> [hidden email]> wrote:
>
> > Dear Curtis,
> >
> > Thank you for your time to write the macro. i saved your text as
> > "directory_convert_tiff.txt" in ij/macros folder and then run it. it
> > asked me again to choose a directory which i selected the main folder.
> > but then it showed an error like this "File is not in tiff, jpeg,
> > giff, bmp .... format, a plugin for this format is not installed, or
> > it was not found.". I have the batch converter plugin ( saved in
> > ij/plugins) which works properly. I had also put the plugin into that
> > main folder, but the same error came up. all of my images (in the
> > subfloders) are in 12-bit tiff format and need to be converted to
> > 8-bit tiff. is there something else i am missing to joint this plugin
> > and macro together?
> >
> > thanks a lot for your kind collaboration,
> >
> > Best regards,
> > Younes
> >
> > On Wed, Mar 12, 2008 at 4:40 PM, Curtis Rueden <[hidden email]> wrote:
> > > Hi Younes,
> > >
> > > You need to modify the macro to perform the tasks you want. To get you
> > > started, here is a version that recursively converts files to TIFF
> > format:
> > >
> > > ------
> > > // Recursively converts files to TIFF starting in a user-specified
> > directory
> > >
> > > requires("1.32f");
> > > dir = getDirectory("Choose a Directory ");
> > > count = 1;
> > > prefix = "converted-";
> > > listFiles(dir);
> > >
> > > function listFiles(dir) {
> > >    list = getFileList(dir);
> > >    for (i=0; i<list.length; i++) {
> > >        if (endsWith(list[i], "/"))
> > >            listFiles(""+dir+list[i]);
> > >        else {
> > >            print((count++) + ": " + dir + list[i]);
> > >            open(dir + list[i]);
> > >            // convert all open images to TIFF
> > >            c = 1;
> > >            while (nImages > 0) {
> > >                saveAs("Tiff", dir + prefix + list[i] + "-" + c +
> > ".tif");
> > >                close();
> > >                c++;
> > >            }
> > >        }
> > >    }
> > > }
> > > ------
> > >
> > > HTH,
> > > Curtis
> > >
> > > On Wed, Mar 12, 2008 at 2:18 PM, Younes Leysi Derilou <
> > >
> > > [hidden email]> wrote:
> > >
> > > > Hello Curtis,
> > > >
> > > > Thank you for the link. i saved that file as "directory_call.txt" in
> > > > "imageJ/macros/" folder. i run the macro first through
> > > > "Menu/plugins/macro/run", which asked me to select the directory, i
> > > > chose one (for example F:\test_conversion\day5c which had 49
> > > > subfolders), then i run the batch converter plugin. that plugin just
> > > > converted the images inside the subfolder that i had chosen, nothing
> > > > else. i did not see any benefits of running that macro. i have also
> > > > tried to run macro after that plugin, but nothing happened. is there
> > > > other procedure that i should follow to joint the macro and plugin
> > > > together?
> > > >
> > > > Thanks and Regards,
> > > > Younes
> > > >
> > > > On Wed, Mar 12, 2008 at 2:06 PM, Curtis Rueden <[hidden email]>
> > wrote:
> > > > > Hi Younes,
> > > > >
> > > > > Take a look at the "list files recursively" macro:
> > > > > http://rsb.info.nih.gov/ij/macros/ListFilesRecursively.txt
> > > > >
> > > > > -Curtis
> > > > >
> > > > >
> > > > > On Wed, Mar 12, 2008 at 12:43 PM, Younes Leysi Derilou <
> > > > > [hidden email]> wrote:
> > > > >
> > > > > > Hello ImageJ Lovers,
> > > > > >
> > > > > > I would like to convert 12-bit tiff images to 8-bit tiff images in
> > a
> > > > > > main folder which has already several sub-folders. the sub-folders
> > > > > > have thousands of images which can be easily converted one-by-one,
> > > > > > using the "batch converter" plugin  from the following link. the
> > > > > > problem is that I have to use this plugin for all sub-folders one
> > by
> > > > > > one and the number of the sub-folders are too much. I am wondering
> > if
> > > > > > there is a way to run this plugin for the main folder; i.e. ask a
> > > > > > macro to do the conversion job for all other sub-folders. any
> > > > > > suggestions are highly appreciated.
> > > > > > http://rsb.info.nih.gov/ij/plugins/batch-converter.html
> > > > > >
> > > > > > Truly yours,
> > > > > > Younes
> > > > > > --
> > > > > > Younes Leysi
> > > > > > "Life is a song, sing it."
> > > > > >
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Younes Leysi
> > > > "Life is a song, sing it."
> > > >
> > >
> >
> >
> >
> > --
> > Younes Leysi
> > "Life is a song, sing it."
> >
>

--
Younes Leysi
"Life is a song, sing it."

[ctrueden]

Hi Younes,

Try putting "setBatchMode(true)" at the beginning of the macro.

-Curtis

On Thu, Mar 13, 2008 at 11:43 AM, Younes Leysi Derilou <
[hidden email]> wrote:

> Hello Curtis,
>
> Thanks so much for your time to edit the macro. it works fine. I had
> to change the macro to overwrite the files (to save the hard drive
> memory), as following. I understood that why and how you asked macro
> to save with different prefix and extension. the small tiny problem is
> that the macro opens the images that converts and then closes. this
> results in a flashing windows in the working environment that bothers
> a user. is there a way to block displaying the conversion process?
>
> Thanks so much for your kind help,
> Younes
>
> // Recursively converts files to 8-bit TIFF starting in a
> user-specified directory and overwrites
> requires("1.32f");
> dir = getDirectory("Choose a Directory ");
> count = 1;
> //prefix = "converted-";
> listFiles(dir);
> function listFiles(dir) {
>   list = getFileList(dir);
>   for (i=0; i<list.length; i++) {
>       if (endsWith(list[i], "/"))
>           listFiles(""+dir+list[i]);
>       else if (endsWith(toLowerCase(list[i]), ".tif") ||
>           endsWith(toLowerCase(list[i]), ".tiff"))
>       {
>           print((count++) + ": " + dir + list[i]);
>           open(dir + list[i]);
>           // convert all open images to TIFF
>           c = 1;
>           while (nImages > 0) {
>               run("8-bit");
>               // place additional commands here
>                saveAs("Tiff", dir + list[i]);
>               close();
>               c++;
>            }
>       }
>   }
> }
>
> On Thu, Mar 13, 2008 at 10:54 AM, Curtis Rueden <[hidden email]> wrote:
> > Hi Younes,
> >
> > You do not need the batch converter plugin to use the macro I sent. My
> guess
> > is that some of the files in the subfolders are in a format that ImageJ
> does
> > not recognize. You could either move them, or change the macro to ignore
> > files unless they end with a particular extension.
> >
> > Below is a version that only converts files originally in TIFF format. I
> > noticed you also said you want to convert from 12-bit to 8-bit, so I put
> an
> > extra line in to do that as well.
> >
> > You can add more statements in the same place, immediately following the
> > "while (nImages > 0)" command. You can easily discover what a statement
> to
> > perform a particular action looks like by using the Macro Recorder
> (Plugins
> > > Macros > Record) feature. Just perform an action using the menus, then
> > copy and paste the resulting command from the macro recorder window into
> > your macro.
> >
> > ------
> > // Recursively converts files to TIFF starting in a user-specified
> directory
> >
> > requires("1.32f");
> > dir = getDirectory("Choose a Directory ");
> > count = 1;
> > prefix = "converted-";
> > listFiles(dir);
> >
> > function listFiles(dir) {
> >    list = getFileList(dir);
> >    for (i=0; i<list.length; i++) {
> >        if (endsWith(list[i], "/"))
> >            listFiles(""+dir+list[i]);
> >        else if (endsWith(toLowerCase(list[i]), ".tif") ||
> >            endsWith(toLowerCase(list[i]), ".tiff"))
> >        {
> >            print((count++) + ": " + dir + list[i]);
> >            open(dir + list[i]);
> >            // convert all open images to TIFF
> >            c = 1;
> >            while (nImages > 0) {
> >                run("8-bit");
> >                // place additional commands here
> >                saveAs("Tiff", dir + prefix + list[i] + "-" + c +
> ".tif");
> >                close();
> >                c++;
> >            }
> >        }
> >    }
> > }
> > ------
> >
> > -Curtis
> >
> > On Thu, Mar 13, 2008 at 8:33 AM, Younes Leysi Derilou <
> >
> > [hidden email]> wrote:
> >
> > > Dear Curtis,
> > >
> > > Thank you for your time to write the macro. i saved your text as
> > > "directory_convert_tiff.txt" in ij/macros folder and then run it. it
> > > asked me again to choose a directory which i selected the main folder.
> > > but then it showed an error like this "File is not in tiff, jpeg,
> > > giff, bmp .... format, a plugin for this format is not installed, or
> > > it was not found.". I have the batch converter plugin ( saved in
> > > ij/plugins) which works properly. I had also put the plugin into that
> > > main folder, but the same error came up. all of my images (in the
> > > subfloders) are in 12-bit tiff format and need to be converted to
> > > 8-bit tiff. is there something else i am missing to joint this plugin
> > > and macro together?
> > >
> > > thanks a lot for your kind collaboration,
> > >
> > > Best regards,
> > > Younes
> > >
> > > On Wed, Mar 12, 2008 at 4:40 PM, Curtis Rueden <[hidden email]>
> wrote:
> > > > Hi Younes,
> > > >
> > > > You need to modify the macro to perform the tasks you want. To get
> you
> > > > started, here is a version that recursively converts files to TIFF
> > > format:
> > > >
> > > > ------
> > > > // Recursively converts files to TIFF starting in a user-specified
> > > directory
> > > >
> > > > requires("1.32f");
> > > > dir = getDirectory("Choose a Directory ");
> > > > count = 1;
> > > > prefix = "converted-";
> > > > listFiles(dir);
> > > >
> > > > function listFiles(dir) {
> > > >    list = getFileList(dir);
> > > >    for (i=0; i<list.length; i++) {
> > > >        if (endsWith(list[i], "/"))
> > > >            listFiles(""+dir+list[i]);
> > > >        else {
> > > >            print((count++) + ": " + dir + list[i]);
> > > >            open(dir + list[i]);
> > > >            // convert all open images to TIFF
> > > >            c = 1;
> > > >            while (nImages > 0) {
> > > >                saveAs("Tiff", dir + prefix + list[i] + "-" + c +
> > > ".tif");
> > > >                close();
> > > >                c++;
> > > >            }
> > > >        }
> > > >    }
> > > > }
> > > > ------
> > > >
> > > > HTH,
> > > > Curtis
> > > >
> > > > On Wed, Mar 12, 2008 at 2:18 PM, Younes Leysi Derilou <
> > > >
> > > > [hidden email]> wrote:
> > > >
> > > > > Hello Curtis,
> > > > >
> > > > > Thank you for the link. i saved that file as "directory_call.txt"
> in
> > > > > "imageJ/macros/" folder. i run the macro first through
> > > > > "Menu/plugins/macro/run", which asked me to select the directory,
> i
> > > > > chose one (for example F:\test_conversion\day5c which had 49
> > > > > subfolders), then i run the batch converter plugin. that plugin
> just
> > > > > converted the images inside the subfolder that i had chosen,
> nothing
> > > > > else. i did not see any benefits of running that macro. i have
> also
> > > > > tried to run macro after that plugin, but nothing happened. is
> there
> > > > > other procedure that i should follow to joint the macro and plugin
> > > > > together?
> > > > >
> > > > > Thanks and Regards,
> > > > > Younes
> > > > >
> > > > > On Wed, Mar 12, 2008 at 2:06 PM, Curtis Rueden <[hidden email]>
> > > wrote:
> > > > > > Hi Younes,
> > > > > >
> > > > > > Take a look at the "list files recursively" macro:
> > > > > > http://rsb.info.nih.gov/ij/macros/ListFilesRecursively.txt
> > > > > >
> > > > > > -Curtis
> > > > > >
> > > > > >
> > > > > > On Wed, Mar 12, 2008 at 12:43 PM, Younes Leysi Derilou <
> > > > > > [hidden email]> wrote:
> > > > > >
> > > > > > > Hello ImageJ Lovers,
> > > > > > >
> > > > > > > I would like to convert 12-bit tiff images to 8-bit tiff
> images in
> > > a
> > > > > > > main folder which has already several sub-folders. the
> sub-folders
> > > > > > > have thousands of images which can be easily converted
> one-by-one,
> > > > > > > using the "batch converter" plugin  from the following link.
> the
> > > > > > > problem is that I have to use this plugin for all sub-folders
> one
> > > by
> > > > > > > one and the number of the sub-folders are too much. I am
> wondering
> > > if
> > > > > > > there is a way to run this plugin for the main folder; i.e.
> ask a
> > > > > > > macro to do the conversion job for all other sub-folders. any
> > > > > > > suggestions are highly appreciated.
> > > > > > > http://rsb.info.nih.gov/ij/plugins/batch-converter.html
> > > > > > >
> > > > > > > Truly yours,
> > > > > > > Younes
> > > > > > > --
> > > > > > > Younes Leysi
> > > > > > > "Life is a song, sing it."
> > > > > > >
> > > > > >
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > Younes Leysi
> > > > > "Life is a song, sing it."
> > > > >
> > > >
> > >
> > >
> > >
> > > --
> > > Younes Leysi
> > > "Life is a song, sing it."
> > >
> >
>
>
>
> --
> Younes Leysi
> "Life is a song, sing it."
>