Saving and reloading FFT
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Hi All,
When I take an FFT of an image, it is obviously using reciprocal space coordinates. However, if I save that FFT to a tif and then reload it later, it loses the reciprocal space and reports the units incorrectly as direct space. Is there a way to set an image back into reciprocal space? I tried, for example, Analyze->Set Scale... Unit of length = nm/c, or changing the distance in pixels from 17.6 to 1/17.6. Better yet, it should retain that info when I save the image. Any ideas? Thanks, Zack Gainsforth Space Sciences Laboratory, UC Berkeley 7 Gauss Way Berkeley, CA 94720 cell: 626-437-9186 [hidden email] -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Saving and reloading FFT
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On Friday 12 September 2014 02:35 AM, Zack Gainsforth wrote:
> Hi All, > > When I take an FFT of an image, it is obviously using reciprocal space coordinates. However, if I save that FFT to a tif and then reload it later, it loses the reciprocal space and reports the units incorrectly as direct space. Is there a way to set an image back into reciprocal space? I tried, for example, Analyze->Set Scale... Unit of length = nm/c, or changing the distance in pixels from 17.6 to 1/17.6. Better yet, it should retain that info when I save the image. > > Any ideas? I have been eagerly awaiting a response to this. A few years ago I had asked a related question about how electron diffraction patterns could be scaled in reciprocal units. The response at that time was that it was required to set a property, that was not accessible through the macro language. Is there a solution now? If the info could be retained when saved as TIFF, it would help a lot. Divakar > Thanks, > > Zack Gainsforth > Space Sciences Laboratory, UC Berkeley > 7 Gauss Way > Berkeley, CA 94720 > cell: 626-437-9186 > [hidden email] > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Saving and reloading FFT
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On Sep 22, 2014, at 8:12 PM, Divakar Ramachandran wrote:
> On Friday 12 September 2014 02:35 AM, Zack Gainsforth wrote: >> Hi All, >> >> When I take an FFT of an image, it is obviously using reciprocal space coordinates. However, if I save that FFT to a tif and then reload it later, it loses the reciprocal space and reports the units incorrectly as direct space. Is there a way to set an image back into reciprocal space? I tried, for example, Analyze->Set Scale... Unit of length = nm/c, or changing the distance in pixels from 17.6 to 1/17.6. Better yet, it should retain that info when I save the image. >> >> Any ideas? > I have been eagerly awaiting a response to this. A few years ago I had > asked a related question about how electron diffraction patterns could > be scaled in reciprocal units. The response at that time was that it was > required to set a property, that was not accessible through the macro > language. Is there a solution now? If the info could be retained when > saved as TIFF, it would help a lot. What version of ImageJ are you using? With version 1.48g and later, File>Save As>Tiff and File>Save As>ZIP save the FFT data of FFT windows, except for FFTs of RGB images. -wayne -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Saving and reloading FFT
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On Tuesday 23 September 2014 06:23 AM, Rasband, Wayne (NIH/NIMH) [E] wrote:
> On Sep 22, 2014, at 8:12 PM, Divakar Ramachandran wrote: > >> On Friday 12 September 2014 02:35 AM, Zack Gainsforth wrote: >>> Hi All, >>> >>> When I take an FFT of an image, it is obviously using reciprocal space coordinates. However, if I save that FFT to a tif and then reload it later, it loses the reciprocal space and reports the units incorrectly as direct space. Is there a way to set an image back into reciprocal space? I tried, for example, Analyze->Set Scale... Unit of length = nm/c, or changing the distance in pixels from 17.6 to 1/17.6. Better yet, it should retain that info when I save the image. >>> >>> Any ideas? >> I have been eagerly awaiting a response to this. A few years ago I had >> asked a related question about how electron diffraction patterns could >> be scaled in reciprocal units. The response at that time was that it was >> required to set a property, that was not accessible through the macro >> language. Is there a solution now? If the info could be retained when >> saved as TIFF, it would help a lot. > What version of ImageJ are you using? With version 1.48g and later, File>Save As>Tiff and File>Save As>ZIP save the FFT data of FFT windows, except for FFTs of RGB images. > > -wayne > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html When I open a TIA ser file (HRSTEM image recorded on a Tecnai TEM) with the TIA plug-in, scale info is correctly available. Process -> FFT gives a spectrum in which the correct reciprocal distances are displayed in the status bar in nm units, as the mouse cursor is moved across the image. When I use Save As TIFF, close the FFT spectrum and re-read it in, the info at the top of the image is shown with "26.75x26.75 nm (512x512)" text suggesting that scale info was read from the file; however, only pixel units are displayed in the status bar as I move mouse across the FFT spectrum. Divakar -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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In reply to this post by Zack Gainsforth
Hi All,
Thanks for looking into this! I am currently using Fiji based on ImageJ 1.49g. File>Save As>Tiff does not record that the FFT is in reciprocal space. The units are saved as direct space coordinates since when I measure a distance or move the mouse around, I get direct space distances. I can send a sample Tiff offline. These are not RGB tiffs, they are 16 or 32 bit tiffs. (Occasionally I use 8 bit, but that's rare.) Typically they are an FFT directly produced from an HRTEM dm3 file written by digital micrograph on a Zeiss Libra or an FEI Titan. I would love a solution to this as much as Divakar! Zack On Sep 22, 2014, at 7:02 PM, Divakar Ramachandran <[hidden email]> wrote: On Tuesday 23 September 2014 06:23 AM, Rasband, Wayne (NIH/NIMH) [E] wrote: > On Sep 22, 2014, at 8:12 PM, Divakar Ramachandran wrote: > >> On Friday 12 September 2014 02:35 AM, Zack Gainsforth wrote: >>> Hi All, >>> >>> When I take an FFT of an image, it is obviously using reciprocal space coordinates. However, if I save that FFT to a tif and then reload it later, it loses the reciprocal space and reports the units incorrectly as direct space. Is there a way to set an image back into reciprocal space? I tried, for example, Analyze->Set Scale... Unit of length = nm/c, or changing the distance in pixels from 17.6 to 1/17.6. Better yet, it should retain that info when I save the image. >>> >>> Any ideas? >> I have been eagerly awaiting a response to this. A few years ago I had >> asked a related question about how electron diffraction patterns could >> be scaled in reciprocal units. The response at that time was that it was >> required to set a property, that was not accessible through the macro >> language. Is there a solution now? If the info could be retained when >> saved as TIFF, it would help a lot. > What version of ImageJ are you using? With version 1.48g and later, File>Save As>Tiff and File>Save As>ZIP save the FFT data of FFT windows, except for FFTs of RGB images. > > -wayne > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html When I open a TIA ser file (HRSTEM image recorded on a Tecnai TEM) with the TIA plug-in, scale info is correctly available. Process -> FFT gives a spectrum in which the correct reciprocal distances are displayed in the status bar in nm units, as the mouse cursor is moved across the image. When I use Save As TIFF, close the FFT spectrum and re-read it in, the info at the top of the image is shown with "26.75x26.75 nm (512x512)" text suggesting that scale info was read from the file; however, only pixel units are displayed in the status bar as I move mouse across the FFT spectrum. Divakar -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Saving and reloading FFT
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In reply to this post by Divakar Ramachandran-2
Thanks! This works for me.
I did a fresh install using the platform independent version from ImageJ site into /opt. This gave me 1.48v which could save and read in the TIFF FFT with reciprocal scale and the correct reciprocal distances were displayed in status bar when I moved the mouse to the various peaks. I also did an update using Help>Update and got 1.49h which also works correctly. With Regards, Divakar On Tuesday 23 September 2014 08:16 AM, Rasband, Wayne (NIH/NIMH) [E] wrote: > Dear Divakar, > > Try the current version of ImageJ (1.49h). You can upgrade using the Help>Update ImageJ command. If upgrading does not fix the problem, send me a sample image that I can use to reproduce it. > > Best regards, > > -wayne > > On Sep 22, 2014, at 10:02 PM, Divakar Ramachandran wrote: > >> On Tuesday 23 September 2014 06:23 AM, Rasband, Wayne (NIH/NIMH) [E] wrote: >>> On Sep 22, 2014, at 8:12 PM, Divakar Ramachandran wrote: >>> >>>> On Friday 12 September 2014 02:35 AM, Zack Gainsforth wrote: >>>>> Hi All, >>>>> >>>>> When I take an FFT of an image, it is obviously using reciprocal space coordinates. However, if I save that FFT to a tif and then reload it later, it loses the reciprocal space and reports the units incorrectly as direct space. Is there a way to set an image back into reciprocal space? I tried, for example, Analyze->Set Scale... Unit of length = nm/c, or changing the distance in pixels from 17.6 to 1/17.6. Better yet, it should retain that info when I save the image. >>>>> >>>>> Any ideas? >>>> I have been eagerly awaiting a response to this. A few years ago I had >>>> asked a related question about how electron diffraction patterns could >>>> be scaled in reciprocal units. The response at that time was that it was >>>> required to set a property, that was not accessible through the macro >>>> language. Is there a solution now? If the info could be retained when >>>> saved as TIFF, it would help a lot. >>> What version of ImageJ are you using? With version 1.48g and later, File>Save As>Tiff and File>Save As>ZIP save the FFT data of FFT windows, except for FFTs of RGB images. >>> >>> -wayne >>> -- >>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> I am using 1.48k installed from the Ubuntu 14.04 LTS 64-bit repsitory. >> When I open a TIA ser file (HRSTEM image recorded on a Tecnai TEM) with >> the TIA plug-in, scale info is correctly available. Process -> FFT gives >> a spectrum in which the correct reciprocal distances are displayed in >> the status bar in nm units, as the mouse cursor is moved across the >> image. When I use Save As TIFF, close the FFT spectrum and re-read it >> in, the info at the top of the image is shown with "26.75x26.75 nm >> (512x512)" text suggesting that scale info was read from the file; >> however, only pixel units are displayed in the status bar as I move >> mouse across the FFT spectrum. >> >> Divakar >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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