http://imagej.273.s1.nabble.com/run-Bio-Formats-importer-from-command-line-tp5007445p5007741.html
On Wed, May 14, 2014 at 3:15 PM, Nick X. Tsui <
> 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>