run Bio-Formats importer from command line?

[nickxtsui]

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

[ctrueden]

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

[nickxtsui]

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

[ctrueden]

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

[nickxtsui]

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

[ctrueden]

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

[nickxtsui]

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

[ctrueden]

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

[nickxtsui]

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

[ctrueden]

Hi Nick,

> Basically, how can I open an image without the image actually showing?

What does it mean to "open" the image, if a window doesn't show?

Do you want to write a script/macro/plugin that has a variable referencing
that image?

In other words: what state do you want the software to be in after opening
your image?

A common workflow is to write a macro with setBatchMode(true) at the top,
which opens an image, does some processing, saves some results somewhere
(either images or textual or both) and then completes. If that is not what
you want to do, please describe in detail what you *do* want to do.

-Curtis


On Wed, Apr 30, 2014 at 1:05 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

[nickxtsui]

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

[nickxtsui]

Hi Curtis:
Sorry for the confusion. I simply want to using command line to open an
image with its OME-XML displaying, but I don't want to write a macro, just
the command line, and it should be one click for all, assuming the path of
the file is already know.

I can use something like
run("Bio-Formats Importer","open=[myimage.tif] display_metadata=True
display_ome-xml_metadata=True");
to open an image, but no OME-XMl is showing. That is the closest I can get.

Conceptually as long as he file path is know, one click should be doable I
suppose? If I know what file I want to open, and I know I want to open it
with OME-XML, why do I have to click so many times navigating among folders
and choosing options?

Best,
Nick


On Wed, Apr 30, 2014 at 2:14 PM, Curtis Rueden <[hidden email]> wrote:

> Hi Nick,
>
> > Basically, how can I open an image without the image actually showing?
>
> What does it mean to "open" the image, if a window doesn't show?
>
> Do you want to write a script/macro/plugin that has a variable referencing
> that image?
>
> In other words: what state do you want the software to be in after opening
> your image?
>
> A common workflow is to write a macro with setBatchMode(true) at the top,
> which opens an image, does some processing, saves some results somewhere
> (either images or textual or both) and then completes. If that is not what
> you want to do, please describe in detail what you *do* want to do.
>
> -Curtis
>
>
> On Wed, Apr 30, 2014 at 1:05 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
>

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

[ctrueden]

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

[ctrueden]

Hi Nick,

> If I know what file I want to open, and I know I want to open it with
> OME-XML, why do I have to click so many times navigating among folders
> and choosing options?

You can use the Bio-Formats Windowless Importer to skip the big options
dialog that Bio-Formats normally presents.

You can enable "Windowless" mode per file format using the Bio-Formats
Plugins Configuration dialog, or use it globally by executing the
"Bio-Formats Windowless Importer" plugin.

> display_ome-xml_metadata=True");
> to open an image, but no OME-XMl is showing.

You need to remove the "=True" from your "display_ome-xml" if you want the
OME-XML to show.

-Curtis


On Wed, Apr 30, 2014 at 1:34 PM, Nick X. Tsui <[hidden email]> wrote:

> Hi Curtis:
> Sorry for the confusion. I simply want to using command line to open an
> image with its OME-XML displaying, but I don't want to write a macro, just
> the command line, and it should be one click for all, assuming the path of
> the file is already know.
>
> I can use something like
> run("Bio-Formats Importer","open=[myimage.tif] display_metadata=True
> display_ome-xml_metadata=True");
> to open an image, but no OME-XMl is showing. That is the closest I can get.
>
> Conceptually as long as he file path is know, one click should be doable I
> suppose? If I know what file I want to open, and I know I want to open it
> with OME-XML, why do I have to click so many times navigating among folders
> and choosing options?
>
> Best,
> Nick
>
>
> On Wed, Apr 30, 2014 at 2:14 PM, Curtis Rueden <[hidden email]> wrote:
>
> > Hi Nick,
> >
> > > Basically, how can I open an image without the image actually showing?
> >
> > What does it mean to "open" the image, if a window doesn't show?
> >
> > Do you want to write a script/macro/plugin that has a variable
> referencing
> > that image?
> >
> > In other words: what state do you want the software to be in after
> opening
> > your image?
> >
> > A common workflow is to write a macro with setBatchMode(true) at the top,
> > which opens an image, does some processing, saves some results somewhere
> > (either images or textual or both) and then completes. If that is not
> what
> > you want to do, please describe in detail what you *do* want to do.
> >
> > -Curtis
> >
> >
> > On Wed, Apr 30, 2014 at 1:05 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
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[nickxtsui]

Great! it works! It was the display_ome-xml that makes the difference.
Thanks Curtis for your support. Really appreciate it.
Best,
Nick


On Wed, Apr 30, 2014 at 2:35 PM, Curtis Rueden <[hidden email]> wrote:

> 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
>

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

[nickxtsui]

Hi Curtis and ImageJ Users:
I am wondering can I run Bio-Formats Windowless Importer using command line
to open multiple files at one time?
I have done the single-file case, thanks for your help, as something like
this

imagej-win64.exe -eval Bio-Formats Windowless Importer open=[D:\image1.tif]
display_ome-xml

but when I do
imagej-win64.exe -eval Bio-Formats Windowless Importer open=[D:\image1.tif
D:\image2.tif D:\image3.tif] display_ome-xml

it seems not working. Any suggestions?

Thanks  a lot.

Best,
Nick


On Wed, Apr 30, 2014 at 2:40 PM, Curtis Rueden <[hidden email]> wrote:

> Hi Nick,
>
> > If I know what file I want to open, and I know I want to open it with
> > OME-XML, why do I have to click so many times navigating among folders
> > and choosing options?
>
> You can use the Bio-Formats Windowless Importer to skip the big options
> dialog that Bio-Formats normally presents.
>
> You can enable "Windowless" mode per file format using the Bio-Formats
> Plugins Configuration dialog, or use it globally by executing the
> "Bio-Formats Windowless Importer" plugin.
>
> > display_ome-xml_metadata=True");
> > to open an image, but no OME-XMl is showing.
>
> You need to remove the "=True" from your "display_ome-xml" if you want the
> OME-XML to show.
>
> -Curtis
>
>
> On Wed, Apr 30, 2014 at 1:34 PM, Nick X. Tsui <[hidden email]> wrote:
>
> > Hi Curtis:
> > Sorry for the confusion. I simply want to using command line to open an
> > image with its OME-XML displaying, but I don't want to write a macro,
> just
> > the command line, and it should be one click for all, assuming the path
> of
> > the file is already know.
> >
> > I can use something like
> > run("Bio-Formats Importer","open=[myimage.tif] display_metadata=True
> > display_ome-xml_metadata=True");
> > to open an image, but no OME-XMl is showing. That is the closest I can
> get.
> >
> > Conceptually as long as he file path is know, one click should be doable
> I
> > suppose? If I know what file I want to open, and I know I want to open it
> > with OME-XML, why do I have to click so many times navigating among
> folders
> > and choosing options?
> >
> > Best,
> > Nick
> >
> >
> > On Wed, Apr 30, 2014 at 2:14 PM, Curtis Rueden <[hidden email]>
> wrote:
> >
> > > Hi Nick,
> > >
> > > > Basically, how can I open an image without the image actually
> showing?
> > >
> > > What does it mean to "open" the image, if a window doesn't show?
> > >
> > > Do you want to write a script/macro/plugin that has a variable
> > referencing
> > > that image?
> > >
> > > In other words: what state do you want the software to be in after
> > opening
> > > your image?
> > >
> > > A common workflow is to write a macro with setBatchMode(true) at the
> top,
> > > which opens an image, does some processing, saves some results
> somewhere
> > > (either images or textual or both) and then completes. If that is not
> > what
> > > you want to do, please describe in detail what you *do* want to do.
> > >
> > > -Curtis
> > >
> > >
> > > On Wed, Apr 30, 2014 at 1:05 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
> > >
> >
> > --
> > 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

[ctrueden]

Hi Nick,

> I am wondering can I run Bio-Formats Windowless Importer using command
> line to open multiple files at one time?

You will need to write a script or plugin that does this, and then invoke
that script or plugin from the command line.

Regards,
Curtis


On Thu, May 8, 2014 at 2:02 PM, Nick X. Tsui <[hidden email]> wrote:

> Hi Curtis and ImageJ Users:
> I am wondering can I run Bio-Formats Windowless Importer using command line
> to open multiple files at one time?
> I have done the single-file case, thanks for your help, as something like
> this
>
> imagej-win64.exe -eval Bio-Formats Windowless Importer open=[D:\image1.tif]
> display_ome-xml
>
> but when I do
> imagej-win64.exe -eval Bio-Formats Windowless Importer open=[D:\image1.tif
> D:\image2.tif D:\image3.tif] display_ome-xml
>
> it seems not working. Any suggestions?
>
> Thanks  a lot.
>
> Best,
> Nick
>
>
> On Wed, Apr 30, 2014 at 2:40 PM, Curtis Rueden <[hidden email]> wrote:
>
> > Hi Nick,
> >
> > > If I know what file I want to open, and I know I want to open it with
> > > OME-XML, why do I have to click so many times navigating among folders
> > > and choosing options?
> >
> > You can use the Bio-Formats Windowless Importer to skip the big options
> > dialog that Bio-Formats normally presents.
> >
> > You can enable "Windowless" mode per file format using the Bio-Formats
> > Plugins Configuration dialog, or use it globally by executing the
> > "Bio-Formats Windowless Importer" plugin.
> >
> > > display_ome-xml_metadata=True");
> > > to open an image, but no OME-XMl is showing.
> >
> > You need to remove the "=True" from your "display_ome-xml" if you want
> the
> > OME-XML to show.
> >
> > -Curtis
> >
> >
> > On Wed, Apr 30, 2014 at 1:34 PM, Nick X. Tsui <[hidden email]>
> wrote:
> >
> > > Hi Curtis:
> > > Sorry for the confusion. I simply want to using command line to open an
> > > image with its OME-XML displaying, but I don't want to write a macro,
> > just
> > > the command line, and it should be one click for all, assuming the path
> > of
> > > the file is already know.
> > >
> > > I can use something like
> > > run("Bio-Formats Importer","open=[myimage.tif] display_metadata=True
> > > display_ome-xml_metadata=True");
> > > to open an image, but no OME-XMl is showing. That is the closest I can
> > get.
> > >
> > > Conceptually as long as he file path is know, one click should be
> doable
> > I
> > > suppose? If I know what file I want to open, and I know I want to open
> it
> > > with OME-XML, why do I have to click so many times navigating among
> > folders
> > > and choosing options?
> > >
> > > Best,
> > > Nick
> > >
> > >
> > > On Wed, Apr 30, 2014 at 2:14 PM, Curtis Rueden <[hidden email]>
> > wrote:
> > >
> > > > Hi Nick,
> > > >
> > > > > Basically, how can I open an image without the image actually
> > showing?
> > > >
> > > > What does it mean to "open" the image, if a window doesn't show?
> > > >
> > > > Do you want to write a script/macro/plugin that has a variable
> > > referencing
> > > > that image?
> > > >
> > > > In other words: what state do you want the software to be in after
> > > opening
> > > > your image?
> > > >
> > > > A common workflow is to write a macro with setBatchMode(true) at the
> > top,
> > > > which opens an image, does some processing, saves some results
> > somewhere
> > > > (either images or textual or both) and then completes. If that is not
> > > what
> > > > you want to do, please describe in detail what you *do* want to do.
> > > >
> > > > -Curtis
> > > >
> > > >
> > > > On Wed, Apr 30, 2014 at 1:05 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
> > > >
> > >
> > > --
> > > 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

[nickxtsui]

I actually a for loop, and that solves the problem. No additional
script/macro needed.
Thanks a lot.
Best,
Nick


On Thu, May 8, 2014 at 3:23 PM, Curtis Rueden <[hidden email]> wrote:

> Hi Nick,
>
> > I am wondering can I run Bio-Formats Windowless Importer using command
> > line to open multiple files at one time?
>
> You will need to write a script or plugin that does this, and then invoke
> that script or plugin from the command line.
>
> Regards,
> Curtis
>
>
> On Thu, May 8, 2014 at 2:02 PM, Nick X. Tsui <[hidden email]> wrote:
>
> > Hi Curtis and ImageJ Users:
> > I am wondering can I run Bio-Formats Windowless Importer using command
> line
> > to open multiple files at one time?
> > I have done the single-file case, thanks for your help, as something like
> > this
> >
> > imagej-win64.exe -eval Bio-Formats Windowless Importer
> open=[D:\image1.tif]
> > display_ome-xml
> >
> > but when I do
> > imagej-win64.exe -eval Bio-Formats Windowless Importer
> open=[D:\image1.tif
> > D:\image2.tif D:\image3.tif] display_ome-xml
> >
> > it seems not working. Any suggestions?
> >
> > Thanks  a lot.
> >
> > Best,
> > Nick
> >
> >
> > On Wed, Apr 30, 2014 at 2:40 PM, Curtis Rueden <[hidden email]>
> wrote:
> >
> > > Hi Nick,
> > >
> > > > If I know what file I want to open, and I know I want to open it with
> > > > OME-XML, why do I have to click so many times navigating among
> folders
> > > > and choosing options?
> > >
> > > You can use the Bio-Formats Windowless Importer to skip the big options
> > > dialog that Bio-Formats normally presents.
> > >
> > > You can enable "Windowless" mode per file format using the Bio-Formats
> > > Plugins Configuration dialog, or use it globally by executing the
> > > "Bio-Formats Windowless Importer" plugin.
> > >
> > > > display_ome-xml_metadata=True");
> > > > to open an image, but no OME-XMl is showing.
> > >
> > > You need to remove the "=True" from your "display_ome-xml" if you want
> > the
> > > OME-XML to show.
> > >
> > > -Curtis
> > >
> > >
> > > On Wed, Apr 30, 2014 at 1:34 PM, Nick X. Tsui <[hidden email]>
> > wrote:
> > >
> > > > Hi Curtis:
> > > > Sorry for the confusion. I simply want to using command line to open
> an
> > > > image with its OME-XML displaying, but I don't want to write a macro,
> > > just
> > > > the command line, and it should be one click for all, assuming the
> path
> > > of
> > > > the file is already know.
> > > >
> > > > I can use something like
> > > > run("Bio-Formats Importer","open=[myimage.tif] display_metadata=True
> > > > display_ome-xml_metadata=True");
> > > > to open an image, but no OME-XMl is showing. That is the closest I
> can
> > > get.
> > > >
> > > > Conceptually as long as he file path is know, one click should be
> > doable
> > > I
> > > > suppose? If I know what file I want to open, and I know I want to
> open
> > it
> > > > with OME-XML, why do I have to click so many times navigating among
> > > folders
> > > > and choosing options?
> > > >
> > > > Best,
> > > > Nick
> > > >
> > > >
> > > > On Wed, Apr 30, 2014 at 2:14 PM, Curtis Rueden <[hidden email]>
> > > wrote:
> > > >
> > > > > Hi Nick,
> > > > >
> > > > > > Basically, how can I open an image without the image actually
> > > showing?
> > > > >
> > > > > What does it mean to "open" the image, if a window doesn't show?
> > > > >
> > > > > Do you want to write a script/macro/plugin that has a variable
> > > > referencing
> > > > > that image?
> > > > >
> > > > > In other words: what state do you want the software to be in after
> > > > opening
> > > > > your image?
> > > > >
> > > > > A common workflow is to write a macro with setBatchMode(true) at
> the
> > > top,
> > > > > which opens an image, does some processing, saves some results
> > > somewhere
> > > > > (either images or textual or both) and then completes. If that is
> not
> > > > what
> > > > > you want to do, please describe in detail what you *do* want to do.
> > > > >
> > > > > -Curtis
> > > > >
> > > > >
> > > > > On Wed, Apr 30, 2014 at 1:05 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
> > > > >
> > > >
> > > > --
> > > > 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

[nickxtsui]

Hi ImageJ Users and Curtis:

Is there anyway to force the image to open with hyperstack option turned on
using command line?

I set the hyperstack option on like following in command line:

display_ome-xml view=Hyperstack stack_order=XYCZT

but as long as the hyperstack option was not checked from last time in FIJI
GUI, then it seems you cannot turn it on with command line. Am I right?
Thanks a lot.

Nick


On Thu, May 8, 2014 at 5:00 PM, Nick X. Tsui <[hidden email]> wrote:

> I actually a for loop, and that solves the problem. No additional
> script/macro needed.
> Thanks a lot.
> Best,
> Nick
>
>
> On Thu, May 8, 2014 at 3:23 PM, Curtis Rueden <[hidden email]> wrote:
>
>> Hi Nick,
>>
>> > I am wondering can I run Bio-Formats Windowless Importer using command
>> > line to open multiple files at one time?
>>
>> You will need to write a script or plugin that does this, and then invoke
>> that script or plugin from the command line.
>>
>> Regards,
>> Curtis
>>
>>
>> On Thu, May 8, 2014 at 2:02 PM, Nick X. Tsui <[hidden email]> wrote:
>>
>> > Hi Curtis and ImageJ Users:
>> > I am wondering can I run Bio-Formats Windowless Importer using command
>> line
>> > to open multiple files at one time?
>> > I have done the single-file case, thanks for your help, as something
>> like
>> > this
>> >
>> > imagej-win64.exe -eval Bio-Formats Windowless Importer
>> open=[D:\image1.tif]
>> > display_ome-xml
>> >
>> > but when I do
>> > imagej-win64.exe -eval Bio-Formats Windowless Importer
>> open=[D:\image1.tif
>> > D:\image2.tif D:\image3.tif] display_ome-xml
>> >
>> > it seems not working. Any suggestions?
>> >
>> > Thanks  a lot.
>> >
>> > Best,
>> > Nick
>> >
>> >
>> > On Wed, Apr 30, 2014 at 2:40 PM, Curtis Rueden <[hidden email]>
>> wrote:
>> >
>> > > Hi Nick,
>> > >
>> > > > If I know what file I want to open, and I know I want to open it
>> with
>> > > > OME-XML, why do I have to click so many times navigating among
>> folders
>> > > > and choosing options?
>> > >
>> > > You can use the Bio-Formats Windowless Importer to skip the big
>> options
>> > > dialog that Bio-Formats normally presents.
>> > >
>> > > You can enable "Windowless" mode per file format using the Bio-Formats
>> > > Plugins Configuration dialog, or use it globally by executing the
>> > > "Bio-Formats Windowless Importer" plugin.
>> > >
>> > > > display_ome-xml_metadata=True");
>> > > > to open an image, but no OME-XMl is showing.
>> > >
>> > > You need to remove the "=True" from your "display_ome-xml" if you want
>> > the
>> > > OME-XML to show.
>> > >
>> > > -Curtis
>> > >
>> > >
>> > > On Wed, Apr 30, 2014 at 1:34 PM, Nick X. Tsui <[hidden email]>
>> > wrote:
>> > >
>> > > > Hi Curtis:
>> > > > Sorry for the confusion. I simply want to using command line to
>> open an
>> > > > image with its OME-XML displaying, but I don't want to write a
>> macro,
>> > > just
>> > > > the command line, and it should be one click for all, assuming the
>> path
>> > > of
>> > > > the file is already know.
>> > > >
>> > > > I can use something like
>> > > > run("Bio-Formats Importer","open=[myimage.tif] display_metadata=True
>> > > > display_ome-xml_metadata=True");
>> > > > to open an image, but no OME-XMl is showing. That is the closest I
>> can
>> > > get.
>> > > >
>> > > > Conceptually as long as he file path is know, one click should be
>> > doable
>> > > I
>> > > > suppose? If I know what file I want to open, and I know I want to
>> open
>> > it
>> > > > with OME-XML, why do I have to click so many times navigating among
>> > > folders
>> > > > and choosing options?
>> > > >
>> > > > Best,
>> > > > Nick
>> > > >
>> > > >
>> > > > On Wed, Apr 30, 2014 at 2:14 PM, Curtis Rueden <[hidden email]>
>> > > wrote:
>> > > >
>> > > > > Hi Nick,
>> > > > >
>> > > > > > Basically, how can I open an image without the image actually
>> > > showing?
>> > > > >
>> > > > > What does it mean to "open" the image, if a window doesn't show?
>> > > > >
>> > > > > Do you want to write a script/macro/plugin that has a variable
>> > > > referencing
>> > > > > that image?
>> > > > >
>> > > > > In other words: what state do you want the software to be in after
>> > > > opening
>> > > > > your image?
>> > > > >
>> > > > > A common workflow is to write a macro with setBatchMode(true) at
>> the
>> > > top,
>> > > > > which opens an image, does some processing, saves some results
>> > > somewhere
>> > > > > (either images or textual or both) and then completes. If that is
>> not
>> > > > what
>> > > > > you want to do, please describe in detail what you *do* want to
>> do.
>> > > > >
>> > > > > -Curtis
>> > > > >
>> > > > >
>> > > > > On Wed, Apr 30, 2014 at 1:05 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
>> > > > >
>> > > >
>> > > > --
>> > > > 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

[ctrueden]

Hi Nick,

> Is there anyway to force the image to open with hyperstack option
> turned on using command line?

Putting "view=Hyperstack" as part of the macro argument is supposed to work.

Regards,
Curtis



On Wed, May 14, 2014 at 3:15 PM, Nick X. Tsui <[hidden email]> wrote:

> Hi ImageJ Users and Curtis:
>
> Is there anyway to force the image to open with hyperstack option turned on
> using command line?
>
> I set the hyperstack option on like following in command line:
>
> display_ome-xml view=Hyperstack stack_order=XYCZT
>
> but as long as the hyperstack option was not checked from last time in FIJI
> GUI, then it seems you cannot turn it on with command line. Am I right?
> Thanks a lot.
>
> Nick
>
>
> On Thu, May 8, 2014 at 5:00 PM, Nick X. Tsui <[hidden email]> wrote:
>
> > I actually a for loop, and that solves the problem. No additional
> > script/macro needed.
> > Thanks a lot.
> > Best,
> > Nick
> >
> >
> > On Thu, May 8, 2014 at 3:23 PM, Curtis Rueden <[hidden email]> wrote:
> >
> >> Hi Nick,
> >>
> >> > I am wondering can I run Bio-Formats Windowless Importer using command
> >> > line to open multiple files at one time?
> >>
> >> You will need to write a script or plugin that does this, and then
> invoke
> >> that script or plugin from the command line.
> >>
> >> Regards,
> >> Curtis
> >>
> >>
> >> On Thu, May 8, 2014 at 2:02 PM, Nick X. Tsui <[hidden email]>
> wrote:
> >>
> >> > Hi Curtis and ImageJ Users:
> >> > I am wondering can I run Bio-Formats Windowless Importer using command
> >> line
> >> > to open multiple files at one time?
> >> > I have done the single-file case, thanks for your help, as something
> >> like
> >> > this
> >> >
> >> > imagej-win64.exe -eval Bio-Formats Windowless Importer
> >> open=[D:\image1.tif]
> >> > display_ome-xml
> >> >
> >> > but when I do
> >> > imagej-win64.exe -eval Bio-Formats Windowless Importer
> >> open=[D:\image1.tif
> >> > D:\image2.tif D:\image3.tif] display_ome-xml
> >> >
> >> > it seems not working. Any suggestions?
> >> >
> >> > Thanks  a lot.
> >> >
> >> > Best,
> >> > Nick
> >> >
> >> >
> >> > On Wed, Apr 30, 2014 at 2:40 PM, Curtis Rueden <[hidden email]>
> >> wrote:
> >> >
> >> > > Hi Nick,
> >> > >
> >> > > > If I know what file I want to open, and I know I want to open it
> >> with
> >> > > > OME-XML, why do I have to click so many times navigating among
> >> folders
> >> > > > and choosing options?
> >> > >
> >> > > You can use the Bio-Formats Windowless Importer to skip the big
> >> options
> >> > > dialog that Bio-Formats normally presents.
> >> > >
> >> > > You can enable "Windowless" mode per file format using the
> Bio-Formats
> >> > > Plugins Configuration dialog, or use it globally by executing the
> >> > > "Bio-Formats Windowless Importer" plugin.
> >> > >
> >> > > > display_ome-xml_metadata=True");
> >> > > > to open an image, but no OME-XMl is showing.
> >> > >
> >> > > You need to remove the "=True" from your "display_ome-xml" if you
> want
> >> > the
> >> > > OME-XML to show.
> >> > >
> >> > > -Curtis
> >> > >
> >> > >
> >> > > On Wed, Apr 30, 2014 at 1:34 PM, Nick X. Tsui <[hidden email]>
> >> > wrote:
> >> > >
> >> > > > Hi Curtis:
> >> > > > Sorry for the confusion. I simply want to using command line to
> >> open an
> >> > > > image with its OME-XML displaying, but I don't want to write a
> >> macro,
> >> > > just
> >> > > > the command line, and it should be one click for all, assuming the
> >> path
> >> > > of
> >> > > > the file is already know.
> >> > > >
> >> > > > I can use something like
> >> > > > run("Bio-Formats Importer","open=[myimage.tif]
> display_metadata=True
> >> > > > display_ome-xml_metadata=True");
> >> > > > to open an image, but no OME-XMl is showing. That is the closest I
> >> can
> >> > > get.
> >> > > >
> >> > > > Conceptually as long as he file path is know, one click should be
> >> > doable
> >> > > I
> >> > > > suppose? If I know what file I want to open, and I know I want to
> >> open
> >> > it
> >> > > > with OME-XML, why do I have to click so many times navigating
> among
> >> > > folders
> >> > > > and choosing options?
> >> > > >
> >> > > > Best,
> >> > > > Nick
> >> > > >
> >> > > >
> >> > > > On Wed, Apr 30, 2014 at 2:14 PM, Curtis Rueden <[hidden email]
> >
> >> > > wrote:
> >> > > >
> >> > > > > Hi Nick,
> >> > > > >
> >> > > > > > Basically, how can I open an image without the image actually
> >> > > showing?
> >> > > > >
> >> > > > > What does it mean to "open" the image, if a window doesn't show?
> >> > > > >
> >> > > > > Do you want to write a script/macro/plugin that has a variable
> >> > > > referencing
> >> > > > > that image?
> >> > > > >
> >> > > > > In other words: what state do you want the software to be in
> after
> >> > > > opening
> >> > > > > your image?
> >> > > > >
> >> > > > > A common workflow is to write a macro with setBatchMode(true) at
> >> the
> >> > > top,
> >> > > > > which opens an image, does some processing, saves some results
> >> > > somewhere
> >> > > > > (either images or textual or both) and then completes. If that
> is
> >> not
> >> > > > what
> >> > > > > you want to do, please describe in detail what you *do* want to
> >> do.
> >> > > > >
> >> > > > > -Curtis
> >> > > > >
> >> > > > >
> >> > > > > On Wed, Apr 30, 2014 at 1:05 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
> >> > > > >
> >> > > >
> >> > > > --
> >> > > > 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