http://imagej.273.s1.nabble.com/run-Bio-Formats-importer-from-command-line-tp5007445p5007739.html
GUI, then it seems you cannot turn it on with command line. Am I right?
On Thu, May 8, 2014 at 5:00 PM, Nick X. Tsui <
> 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>>
>
>