batch conversion of images?

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batch conversion of images?

Kenneth Sloan-3
I write Java plugins.  I'm a complete novice at writing macros,
or even "shortcuts".  So, I thought I would ask here to see
if what I need has already been done 100 times, or if it's
so trivial that an experienced developer can just type it
off the top of their head.

Failing that, I'll probably write a Java plugin to do this.

The good news is that I don't need it NOW.  I just performed this
task manually...because it had to be done IMMEDIATELY and
I calculated that I could do it manually about as fast, if not faster,
than building a tool.  But...this task will return, so it's time
to build the tool.

The task: given a directory full of images of type A (say, .tif files)
convert them all to type B (say, .png files).  Keep the same names,
probably deposit the results in the same directory (although that looks
like the first "bell & whistle" to add).

In the past (probably using plain ImageJ) I build a shortcut which saved the
current image as PNG and closed it.  Then, I would load a directory full of images
into ImageJ and pound on that shortcut key.  Worked great.

Until last week - when:

a) the shortcut disappeared (there has been turmoil...)
b) when I tried to recreate it, I found that "Save As PNG" defaulted
to a directory OTHER THAN the one from which the current image had
been loaded.

At that point, I gave up, and did a manual sequence of "Save As...", "PNG",
..."close window".   And moved on to the next task.

What I'd like to have is a macro which itself calls a second macro.
The second macro should have a reserved name (such as "CustomConvertImage"),
which I can edit separately.  The first macro would be responsible
for loading a directory full of images (is it possible to filter on extension?),
and sequentially apply "CustomConvertImage" to each image.  I suspect that it's
best to let "CustomConvertImage" actually SAVE the image file, because that's where
the format conversion actually gets done. (or....is it?  Is it possible to specify
that an existing image *should be later* saved as (say) "PNG", and then later
call a neutral "save Image".  I just thought of that, but don't recall seeing it anywhere.
Anyway..."CustomConvertImage" would need to be told, somehow, what directory to write to.

This has gone on far too long - I hope that what I'm asking for is clear.

As I say, I'm confident that this is something I can do easily in Java, but a full-on
Java plugin seems like overkill for this task.

All help gratefully accepted.  

--
Kenneth Sloan
[hidden email]
Vision is the art of seeing what is invisible to others.

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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Re: batch conversion of images?

Curtis Rueden
Hi Kenneth,

* File > New > Script...
* Templates > ImageJ 1.x > Examples > Process Folder (Groovy)

There is also Process Folder (Macro) and Process Folder (Python). Take your
pick. I suggest Groovy because it is the closest of the three to Java.

See also https://imagej.net/Batch

Regards,
Curtis

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


On Wed, Jun 6, 2018 at 12:19 AM, Kenneth Sloan <[hidden email]>
wrote:

> I write Java plugins.  I'm a complete novice at writing macros,
> or even "shortcuts".  So, I thought I would ask here to see
> if what I need has already been done 100 times, or if it's
> so trivial that an experienced developer can just type it
> off the top of their head.
>
> Failing that, I'll probably write a Java plugin to do this.
>
> The good news is that I don't need it NOW.  I just performed this
> task manually...because it had to be done IMMEDIATELY and
> I calculated that I could do it manually about as fast, if not faster,
> than building a tool.  But...this task will return, so it's time
> to build the tool.
>
> The task: given a directory full of images of type A (say, .tif files)
> convert them all to type B (say, .png files).  Keep the same names,
> probably deposit the results in the same directory (although that looks
> like the first "bell & whistle" to add).
>
> In the past (probably using plain ImageJ) I build a shortcut which saved
> the
> current image as PNG and closed it.  Then, I would load a directory full
> of images
> into ImageJ and pound on that shortcut key.  Worked great.
>
> Until last week - when:
>
> a) the shortcut disappeared (there has been turmoil...)
> b) when I tried to recreate it, I found that "Save As PNG" defaulted
> to a directory OTHER THAN the one from which the current image had
> been loaded.
>
> At that point, I gave up, and did a manual sequence of "Save As...", "PNG",
> ..."close window".   And moved on to the next task.
>
> What I'd like to have is a macro which itself calls a second macro.
> The second macro should have a reserved name (such as
> "CustomConvertImage"),
> which I can edit separately.  The first macro would be responsible
> for loading a directory full of images (is it possible to filter on
> extension?),
> and sequentially apply "CustomConvertImage" to each image.  I suspect that
> it's
> best to let "CustomConvertImage" actually SAVE the image file, because
> that's where
> the format conversion actually gets done. (or....is it?  Is it possible to
> specify
> that an existing image *should be later* saved as (say) "PNG", and then
> later
> call a neutral "save Image".  I just thought of that, but don't recall
> seeing it anywhere.
> Anyway..."CustomConvertImage" would need to be told, somehow, what
> directory to write to.
>
> This has gone on far too long - I hope that what I'm asking for is clear.
>
> As I say, I'm confident that this is something I can do easily in Java,
> but a full-on
> Java plugin seems like overkill for this task.
>
> All help gratefully accepted.
>
> --
> Kenneth Sloan
> [hidden email]
> Vision is the art of seeing what is invisible to others.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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Re: batch conversion of images?

Gabriel Landini
In reply to this post by Kenneth Sloan-3
Hi Kenneth,
I think that what  you are looking for can be done with:

Process>Batch>Convert...

Cheers

Gabriel



On Tuesday, 5 June 2018 23:19:29 BST you wrote:

> I write Java plugins.  I'm a complete novice at writing macros,
> or even "shortcuts".  So, I thought I would ask here to see
> if what I need has already been done 100 times, or if it's
> so trivial that an experienced developer can just type it
> off the top of their head.
>
> Failing that, I'll probably write a Java plugin to do this.
>
> The good news is that I don't need it NOW.  I just performed this
> task manually...because it had to be done IMMEDIATELY and
> I calculated that I could do it manually about as fast, if not faster,
> than building a tool.  But...this task will return, so it's time
> to build the tool.
>
> The task: given a directory full of images of type A (say, .tif files)
> convert them all to type B (say, .png files).  Keep the same names,
> probably deposit the results in the same directory (although that looks
> like the first "bell & whistle" to add).
>
> In the past (probably using plain ImageJ) I build a shortcut which saved the
> current image as PNG and closed it.  Then, I would load a directory full of
> images into ImageJ and pound on that shortcut key.  Worked great.
>
> Until last week - when:
>
> a) the shortcut disappeared (there has been turmoil...)
> b) when I tried to recreate it, I found that "Save As PNG" defaulted
> to a directory OTHER THAN the one from which the current image had
> been loaded.
>
> At that point, I gave up, and did a manual sequence of "Save As...", "PNG",
> ..."close window".   And moved on to the next task.
>
> What I'd like to have is a macro which itself calls a second macro.
> The second macro should have a reserved name (such as "CustomConvertImage"),
> which I can edit separately.  The first macro would be responsible for
> loading a directory full of images (is it possible to filter on
> extension?), and sequentially apply "CustomConvertImage" to each image.  I
> suspect that it's best to let "CustomConvertImage" actually SAVE the image
> file, because that's where the format conversion actually gets done.
> (or....is it?  Is it possible to specify that an existing image *should be
> later* saved as (say) "PNG", and then later call a neutral "save Image".  I
> just thought of that, but don't recall seeing it anywhere.
> Anyway..."CustomConvertImage" would need to be told, somehow, what
> directory to write to.
>
> This has gone on far too long - I hope that what I'm asking for is clear.
>
> As I say, I'm confident that this is something I can do easily in Java, but
> a full-on Java plugin seems like overkill for this task.
>
> All help gratefully accepted.
>
> --
> Kenneth Sloan
> [hidden email]
> Vision is the art of seeing what is invisible to others.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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