http://imagej.273.s1.nabble.com/run-Bio-Formats-importer-from-command-line-tp5007445p5007520.html
which is not working. The image does show up, but no metadata information
On Wed, Apr 30, 2014 at 2:05 PM, Nick X. Tsui <
> 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>>
>
>