NetCDF plugin
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I am using the NetCDF plugin for ImageJ. Sometimes I receive NetCDF data
in many partial files (about 64 files) and I want to load all of them at once using a macros/script instead than manually. While writing the Macro I notice this issue: When I try to call and run your plugin from inside a macro or plugin it does nothing, it does not complain neither: MACRO: ====== run("Load NetCDF File", "open=C:\\Users\\rswz\\Desktop\\test.nc"); PLUGIN: ====== IJ.run("Load NetCDF File", "open=C:\\Users\\rswz\\Desktop\\test.nc"); Do you have any advice for me? I will really appreciate it. Regards, Rafael Rafael Salazar-Tio Research Petrophysicist Chevron ETC 6001 Bollinger Canyon Rd. San Ramon, CA 94583 USA |
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Have you found a solution to this problem?? I want to use NetCDF files in an imagej macro but the plugin will only open and requires manual file selection instead of the file path I specified in the macro.
I am having the same issue and can't find a solution anywhere!! Please help!! |
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Hi Emily,
Which NetCDF plugin? What is the URL? Is the source available? Regards, Curtis On Thu, Jun 4, 2015 at 7:34 PM, emsaurette <[hidden email]> wrote: > Have you found a solution to this problem?? I want to use NetCDF files in > an > imagej macro but the plugin will only open and requires manual file > selection instead of the file path I specified in the macro. > > I am having the same issue and can't find a solution anywhere!! > > Please help!! > > > > -- > View this message in context: > http://imagej.1557.x6.nabble.com/NetCDF-plugin-tp3686714p5013035.html > Sent from the ImageJ mailing list archive at Nabble.com. > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Curtis, http://lmb.informatik.uni-freiburg.de/lmbsoft/imagej_plugins/index.en.html.backup_2008_03_14 You can get the plugin at the URL above, I am currently using it to open .VOLUME files. Let me know if you come across anything interesting. Cheers, Emily On Mon, Jun 8, 2015 at 1:44 PM, ctrueden [via ImageJ] <[hidden email]> wrote: Hi Emily, |
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Hi Emily,
> http://lmb.informatik.uni-freiburg.de/lmbsoft/imagej_plugins/index.en.html.backup_2008_03_14 Thanks. I tested, and the following macro works for me: file = "/path/to/myFile.nc"; run("Load NetCDF File", "open=[" + file + "]"); Regards, Curtis On Mon, Jun 8, 2015 at 7:48 PM, emsaurette <[hidden email]> wrote: > Hi Curtis, > > > http://lmb.informatik.uni-freiburg.de/lmbsoft/imagej_plugins/index.en.html.backup_2008_03_14 > > You can get the plugin at the URL above, I am currently using it to open > .VOLUME files. > > Let me know if you come across anything interesting. > > Cheers, > > Emily > > On Mon, Jun 8, 2015 at 1:44 PM, ctrueden [via ImageJ] < > [hidden email]> wrote: > > > Hi Emily, > > > > Which NetCDF plugin? What is the URL? Is the source available? > > > > Regards, > > Curtis > > > > On Thu, Jun 4, 2015 at 7:34 PM, emsaurette <[hidden email] > > <http:///user/SendEmail.jtp?type=node&node=5013076&i=0>> wrote: > > > > > Have you found a solution to this problem?? I want to use NetCDF files > > in > > > an > > > imagej macro but the plugin will only open and requires manual file > > > selection instead of the file path I specified in the macro. > > > > > > I am having the same issue and can't find a solution anywhere!! > > > > > > Please help!! > > > > > > > > > > > > -- > > > View this message in context: > > > http://imagej.1557.x6.nabble.com/NetCDF-plugin-tp3686714p5013035.html > > > Sent from the ImageJ mailing list archive at Nabble.com. > > > > > > -- > > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > > > > -- > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > > > ------------------------------ > > If you reply to this email, your message will be added to the discussion > > below: > > http://imagej.1557.x6.nabble.com/NetCDF-plugin-tp3686714p5013076.html > > To unsubscribe from NetCDF plugin, click here > > < > > > > . > > NAML > > < > http://imagej.1557.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml > > > > > > > > > -- > View this message in context: > http://imagej.1557.x6.nabble.com/NetCDF-plugin-tp3686714p5013077.html > Sent from the ImageJ mailing list archive at Nabble.com. > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Curtis, That macro works and it will show that the file is loading in the progress bar, however it will never actually open the file. Do you have a clue as to what is going wrong? Thank you! Emily On Mon, Jun 8, 2015 at 2:14 PM, ctrueden [via ImageJ] <[hidden email]> wrote: Hi Emily, |
Re: NetCDF plugin
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> On Jun 8, 2015, at 4:16 PM, emsaurette <[hidden email]> wrote:
> > Hi Curtis, > > That macro works and it will show that the file is loading in the progress > bar, however it will never actually open the file. Do you have a clue as to > what is going wrong? The NetCDF plugin displays a dialog where you have to select the images to be loaded. When running the plugin from a macro, you have to include strings like “1d”, “2d” in the options argument or no images will be displayed. These strings (“1d”, “2d”, etc.) are from first word of the checkbox labels in the dialog. This example path = "/Users/wayne/net-cdf/sresa1b_ncar_ccsm3-example.nc"; run("Load NetCDF File", "open=&path 1d 2d 3d 4d”); works with the first example NetCDF file at http://www.unidata.ucar.edu/software/netcdf/examples/files.html -wayne > > Thank you! > > Emily > > On Mon, Jun 8, 2015 at 2:14 PM, ctrueden [via ImageJ] < > [hidden email]> wrote: > >> Hi Emily, >> >>> >> >> http://lmb.informatik.uni-freiburg.de/lmbsoft/imagej_plugins/index.en.html.backup_2008_03_14 >> >> Thanks. I tested, and the following macro works for me: >> >> file = "/path/to/myFile.nc"; >> run("Load NetCDF File", "open=[" + file + "]"); >> >> Regards, >> Curtis >> >> On Mon, Jun 8, 2015 at 7:48 PM, emsaurette <[hidden email] >> <http:///user/SendEmail.jtp?type=node&node=5013078&i=0>> wrote: >> >>> Hi Curtis, >>> >>> >>> >> http://lmb.informatik.uni-freiburg.de/lmbsoft/imagej_plugins/index.en.html.backup_2008_03_14 >>> >>> You can get the plugin at the URL above, I am currently using it to open >>> .VOLUME files. >>> >>> Let me know if you come across anything interesting. >>> >>> Cheers, >>> >>> Emily >>> >>> On Mon, Jun 8, 2015 at 1:44 PM, ctrueden [via ImageJ] < >>> [hidden email] <http:///user/SendEmail.jtp?type=node&node=5013078&i=1>> >> wrote: >>> >>>> Hi Emily, >>>> >>>> Which NetCDF plugin? What is the URL? Is the source available? >>>> >>>> Regards, >>>> Curtis >>>> >>>> On Thu, Jun 4, 2015 at 7:34 PM, emsaurette <[hidden email] >>>> <http:///user/SendEmail.jtp?type=node&node=5013076&i=0>> wrote: >>>> >>>>> Have you found a solution to this problem?? I want to use NetCDF >> files >>>> in >>>>> an >>>>> imagej macro but the plugin will only open and requires manual file >>>>> selection instead of the file path I specified in the macro. >>>>> >>>>> I am having the same issue and can't find a solution anywhere!! >>>>> >>>>> Please help!! >>>>> >>>>> >>>>> >>>>> -- >>>>> View this message in context: >>>>> >> http://imagej.1557.x6.nabble.com/NetCDF-plugin-tp3686714p5013035.html >>>>> Sent from the ImageJ mailing list archive at Nabble.com. >>>>> >>>>> -- >>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >>>>> >>>> >>>> -- >>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >>>> >>>> >>>> ------------------------------ >>>> If you reply to this email, your message will be added to the >> discussion >>>> below: >>>> http://imagej.1557.x6.nabble.com/NetCDF-plugin-tp3686714p5013076.html >>>> To unsubscribe from NetCDF plugin, click here >>>> < >>>> >>>> . >>>> NAML >>>> < >>> >> http://imagej.1557.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml >>>> >>>> >>> >>> >>> >>> >>> -- >>> View this message in context: >>> http://imagej.1557.x6.nabble.com/NetCDF-plugin-tp3686714p5013077.html >>> Sent from the ImageJ mailing list archive at Nabble.com. >>> >>> -- >>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >>> >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> >> >> ------------------------------ >> If you reply to this email, your message will be added to the discussion >> below: >> http://imagej.1557.x6.nabble.com/NetCDF-plugin-tp3686714p5013078.html >> To unsubscribe from NetCDF plugin, click here >> < >> . >> NAML >> <http://imagej.1557.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml> >> > > > > > -- > View this message in context: http://imagej.1557.x6.nabble.com/NetCDF-plugin-tp3686714p5013081.html > Sent from the ImageJ mailing list archive at Nabble.com. > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Wayne, Unfortunately for me when I use that example file and this macro: path= "C:\Users\Adam Lentz\Desktop\Emily_Macro_Test\sresa1b_ncar_ccsm3-example.nc"; run("Load NetCDF File", "open=&path 1d 2d 3d 4d”); I get an 'error opening file' in the progress bar. Thank you though! Emily On Mon, Jun 8, 2015 at 5:39 PM, Rasband, Wayne (NIH/NIMH) [E] [via ImageJ] <[hidden email]> wrote: > On Jun 8, 2015, at 4:16 PM, emsaurette <[hidden email]> wrote: |
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In reply to this post by Rasband, Wayne (NIH/NIMH) [E]
Hi Wayne, Thank you so much that helped a lot, because my volume files only have one variable I needed to write path = "/path/to/my/file.volume"; run("Load NetCDF File", "open=&path single variable”); Thank you again! Emily On Mon, Jun 8, 2015 at 5:39 PM, Rasband, Wayne (NIH/NIMH) [E] [via ImageJ] <[hidden email]> wrote: > On Jun 8, 2015, at 4:16 PM, emsaurette <[hidden email]> wrote: |
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