run Bio-Formats importer from command line?

[nickxtsui]

I see. Thanks!


On Wed, May 14, 2014 at 4:19 PM, Curtis Rueden <[hidden email]> wrote:

> 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
>

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