http://imagej.273.s1.nabble.com/run-Bio-Formats-importer-from-command-line-tp5007445p5007525.html
Thanks Curtis for your support. Really appreciate it.
> Hi Nick,
>
> > The image does show up, but no metadata information displaying.
>
> The following macro opens and displays an image as well as the OME-XML
> window:
>
> fiji -eval 'run("Bio-Formats", "open=/Users/curtis/data/toucan.png
> autoscale color_mode=Default display_ome-xml view=Hyperstack
> stack_order=XYCZT");'
>
> Notice that there is no "=1" or "=True". I generated the above using the
> Macro Recorder: Plugins > Macros > Record. I advise always using this to
> generate Bio-Formats macro commands.
>
> Alternately, if what you want is to dump the OME-XML to the console, you
> can use the "showinf" Bio-Formats command line tool (
>
>
https://www.openmicroscopy.org/site/support/bio-formats5/users/comlinetools/> )
> with the "-omexml-only" flag.
>
> Regards,
> Curtis
>
>
> On Wed, Apr 30, 2014 at 1:27 PM, Nick X. Tsui <
[hidden email]> wrote:
>
> > I am also wondering can I display OME-XML using macro like this?
> >
> > run("Bio-Formats Importer","open=[myimage.tif] display_metadata=1
> > display_ome-xml_metadata=1");
> >
> > which is not working. The image does show up, but no metadata information
> > displaying.
> >
> > I also tried
> >
> > run("Bio-Formats Importer","open=[myimage.tif] display_metadata=True
> > display_ome-xml_metadata=True");
> >
> > no luck either.
> >
> > Can I open image with its OME-XML displaying just using a macro? Or can I
> > not?
> > Thanks.
> > Nick
> >
> >
> >
> > On Wed, Apr 30, 2014 at 2:05 PM, Nick X. Tsui <
[hidden email]>
> wrote:
> >
> > > Sorry.
> > > Basically, how can I open an image without the image actually showing?
> > > Thanks.
> > > Nick
> > >
> > >
> > > On Wed, Apr 30, 2014 at 1:49 PM, Curtis Rueden <
[hidden email]>
> > wrote:
> > >
> > >> Hi Nick,
> > >>
> > >> > OK. So is there any chance using command line to open an image
> without
> > >> > showing the image window? Not headless motion, but ImageJ launches,
> > >> > image selected, opened, but now really its window is showing. Can
> this
> > >> > be done using something like in a C++ script?
> > >>
> > >> My apologies, but I do not understand the question. Can you please
> > >> elaborate?
> > >>
> > >> Thanks,
> > >> Curtis
> > >>
> > >>
> > >> On Wed, Apr 30, 2014 at 11:58 AM, Nick X. Tsui <
[hidden email]>
> > >> wrote:
> > >>
> > >> > OK. So is there any chance using command line to open an image
> without
> > >> > showing the image window?
> > >> > Not headless motion, but ImageJ launches, image selected, opened,
> but
> > >> now
> > >> > really its window is showing.
> > >> > Can this be done using something like in a C++ script?
> > >> >
> > >> > imagej.exe - run "run(open...)"
> > >> >
> > >> > Thanks.
> > >> > Nick
> > >> >
> > >> >
> > >> > On Wed, Apr 30, 2014 at 12:36 PM, Curtis Rueden <
[hidden email]>
> > >> wrote:
> > >> >
> > >> > > Hi Nick,
> > >> > >
> > >> > > > It seems to me in this way if there are escaping characters, it
> > >> cannot
> > >> > > > handle it?
> > >> > >
> > >> > > You will need to learn about how the Windows command shell handles
> > >> > escaped
> > >> > > quotes:
> > >> > >
http://stackoverflow.com/q/7760545> > >> > >
> > >> > > The increased complexity is one reason to consider writing the
> macro
> > >> to a
> > >> > > file and executing it that way.
> > >> > >
> > >> > > Regards,
> > >> > > Curtis
> > >> > >
> > >> > >
> > >> > > On Wed, Apr 30, 2014 at 11:28 AM, Nick X. Tsui <
>
[hidden email]
> > >
> > >> > > wrote:
> > >> > >
> > >> > > > Hi Curtis:
> > >> > > > Thanks. What if I have more than 1 parameters, for example I
> want
> > to
> > >> > > open a
> > >> > > > file using bio-format importer, like this if in macro:
> > >> > > >
> > >> > > > "run("Bio-Formats Importer",
> > >> > > >
> > >> > > >
> > >> > >
> > >> >
> > >>
> >
> 'open=['C:\\Users\\nickt\\Documents\\Untitled013\\ChanA_0001_0001_0001_0001.tif']')";
> > >> > > >
> > >> > > > It seems to me in this way if there are escaping characters, it
> > >> cannot
> > >> > > > handle it?
> > >> > > >
> > >> > > > Thanks a lot.
> > >> > > >
> > >> > > > Nick
> > >> > > >
> > >> > > >
> > >> > > >
> > >> > > >
> > >> > > > On Wed, Apr 30, 2014 at 10:45 AM, Curtis Rueden <
> >
[hidden email]>
> > >> > > wrote:
> > >> > > >
> > >> > > > > Hi Nick,
> > >> > > > >
> > >> > > > > > Any chance I can run with command line, but without any
> macro
> > >> file
> > >> > > > > > involved?
> > >> > > > >
> > >> > > > > Yes, you can use the "-eval" option to pass a macro string
> > >> directly.
> > >> > > > E.g.:
> > >> > > > >
> > >> > > > > ImageJ-win32.exe -eval "print('Hello world');"
> > >> > > > >
> > >> > > > > Launches ImageJ and prints "Hello world" to the log.
> > >> > > > >
> > >> > > > > ImageJ-win32.exe -eval "print('Hello world');" -batch
> > >> > > > >
> > >> > > > > Launches ImageJ and prints "Hello world" to the log, then
> > >> immediately
> > >> > > > > exits.
> > >> > > > >
> > >> > > > > ImageJ-win32.exe --headless -eval "print('Hello world');"
> > >> > > > >
> > >> > > > > Launches ImageJ in headless mode and prints "Hello world" to
> the
> > >> > > console.
> > >> > > > >
> > >> > > > > Regards,
> > >> > > > > Curtis
> > >> > > > >
> > >> > > > >
> > >> > > > > On Fri, Apr 25, 2014 at 4:52 PM, Nick X. Tsui <
> > >>
[hidden email]>
> > >> > > > wrote:
> > >> > > > >
> > >> > > > > > Hi Curtis:
> > >> > > > > > Thanks a lot. Any chance I can run with command line, but
> > >> without
> > >> > any
> > >> > > > > macro
> > >> > > > > > file involved? I prefer not to create an additional macro.
> > Just
> > >> > > command
> > >> > > > > > line. Thanks.
> > >> > > > > > Best,
> > >> > > > > > Nick
> > >> > > > > >
> > >> > > > > >
> > >> > > > > > On Fri, Apr 25, 2014 at 5:09 PM, Curtis Rueden <
> > >>
[hidden email]>
> > >> > > > > wrote:
> > >> > > > > >
> > >> > > > > > > Hi Nick,
> > >> > > > > > >
> > >> > > > > > > > I am wondering how I can run Bio-Formats importer from
> > >> command
> > >> > > > line?
> > >> > > > > > >
> > >> > > > > > > 1) Use the Macro Recorder [1] to record the line of macro
> > code
> > >> > that
> > >> > > > > runs
> > >> > > > > > > Bio-Formats that way you want.
> > >> > > > > > >
> > >> > > > > > > 2) Click "Create" to pop up the Script Editor [2], edit as
> > >> > desired,
> > >> > > > > then
> > >> > > > > > > save the macro as a .ijm macro file.
> > >> > > > > > >
> > >> > > > > > > 3) Run the macro from the command line:
> > >> > > > > > >
> > >> > > > > > > ImageJ-win32.exe -macro myMacro.ijm -batch
> > >> > > > > > >
> > >> > > > > > > Leave off the "-batch" flag if you want Fiji to remain
> open
> > >> > > > afterward.
> > >> > > > > > >
> > >> > > > > > > Note that you cannot use the "--headless" option [3]
> because
> > >> > > > > Bio-Formats
> > >> > > > > > > does not work in headless mode, even when running as a
> > macro.
> > >> > (You
> > >> > > > will
> > >> > > > > > see
> > >> > > > > > > "VerifyError" on the console if you try.)
> > >> > > > > > >
> > >> > > > > > > I have added this information to the Bio-Formats wiki
> page:
> > >> > > > > > >
> > >> > >
> >
http://fiji.sc/Bio-Formats#Calling_Bio-Formats_from_the_command_line> > >> > > > > > >
> > >> > > > > > > Regards,
> > >> > > > > > > Curtis
> > >> > > > > > >
> > >> > > > > > > [1]
> > >> > >
http://fiji.sc/Introduction_into_Macro_Programming#The_recorder> > >> > > > > > > [2]
http://fiji.sc/Script_Editor> > >> > > > > > > [3]
>
http://fiji.sc/Headless#Running_macros_in_headless_mode> > >> > > > > > >
> > >> > > > > > >
> > >> > > > > > > On Fri, Apr 25, 2014 at 3:24 PM, Nick X. Tsui <
> > >> >
[hidden email]
> > >> > > >
> > >> > > > > > wrote:
> > >> > > > > > >
> > >> > > > > > > > Dear ImageJ fellows:
> > >> > > > > > > > Thanks for reading my questions.
> > >> > > > > > > > I am wondering how I can run Bio-Formats importer from
> > >> command
> > >> > > > line?
> > >> > > > > > > > Suppose I know what image I want to load, and no need to
> > pop
> > >> > the
> > >> > > > > > > > Bio-Formats importer window.
> > >> > > > > > > > something like this?
> > >> > > > > > > >
> > >> > > > > > > > imagej.exe myImage.tif -run ""Bio-Formats...,
> Bio-Formats
> > >> > > > importer" ?
> > >> > > > > > > >
> > >> > > > > > > > Thanks a lot.
> > >> > > > > > > > Best regards,
> > >> > > > > > > > Nick
> > >> > > > > > > >
> > >> > > > > > > > --
> > >> > > > > > > > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> > >> > > > > > > >
> > >> > > > > > >
> > >> > > > > > > --
> > >> > > > > > > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> > >> > > > > > >
> > >> > > > > >
> > >> > > > > > --
> > >> > > > > > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> > >> > > > > >
> > >> > > > >
> > >> > > > > --
> > >> > > > > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> > >> > > > >
> > >> > > >
> > >> > > > --
> > >> > > > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> > >> > > >
> > >> > >
> > >> > > --
> > >> > > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> > >> > >
> > >> >
> > >> > --
> > >> > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> > >> >
> > >>
> > >> --
> > >> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> > >>
> > >
> > >
> >
> > --
> > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> >
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>