Re: run Bio-Formats importer from command line?

Posted by nickxtsui on Apr 30, 2014; 4:28pm
URL: http://imagej.273.s1.nabble.com/run-Bio-Formats-importer-from-command-line-tp5007445p5007513.html

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
>

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