Re: Opening files from TIA software (2)

[William Nicolas]

I use a macro that I have written with the help of a colleague to open all the .ser files in a designated folder and another macro that does the same but converts all the desired .ser files into .tiff files.
If any of you wants it…

Have a nice one !

William Nicolas

>
> Date:    Mon, 12 Jan 2015 00:25:00 -0800
> From:    Jeff Stokes <[hidden email]>
> Subject: Re: Opening files from TIA software
>
> Is anyone aware of a macro or plugin for opening NITF files?  Jeff Stokes
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Kenton
> Arkill
> Sent: Sunday, January 11, 2015 7:37 AM
> To: [hidden email]
> Subject: Re: Opening files from TIA software
>
> I don't know how to attach files to the list so it is printed below.
> ----------------
> // Macro to turn .ser's into .tif's
>
> dir = getDirectory("Choose a Directory");
> list = getFileList(dir);
> setBatchMode(true);
>
> showStatus("Running...");
> for (i=0; i<list.length; i++) {
> path = dir+list[i];
>
>
>
> if(endsWith(path, ".ser")){
> //Could be any ending like ".tif" !
> run("TIA Reader", ".ser-reader...=path"); // Uses a plugin to open
> // would be simply "open(path);" for normal image format
> //----------------------------- CAN PUT ANY MANIPULTION BETWEEN HERE!!!!
> dotIndex = lastIndexOf(path, ".");
> //Finds the dot and therefore checks the file ends in .something
> if (dotIndex!=-1){
> path = substring(path, 0, dotIndex-2);
>                }
> // finds 2 characters before dot to remove "_1.ser" extension
> // for yours cut the -2 so it is just the extension so keep both versions
> //---------------------------- AND HERE!!!!
>
> save(path+".tif");// could add any ending like 'manipulation.tiff'
> }
> close();
> }
> }
> showStatus("Done");
> ---------------
>
> On 11 January 2015 at 13:12, Michael Elbaum <[hidden email]>
> wrote:
>
>> Thanks Kenton (but the macro is missing !?!). The emi is a container for
>> both images and spectroscopy, so for example if you take STEM images in
>> bright and dark field you get XX_1.ser and XX_2.ser and the .emi is twice
>> the size. There is no separate file for spectra. After opening with the
>> TIA_Reader plugin, Image > Show info shows a number of parameters so
>> metadata is present, but one never knows if some is missing.
>> regards,
>> Michael
>>
>> ________________________________________
>> From: ImageJ Interest Group [[hidden email]] on behalf of Kenton
>> Arkill [[hidden email]]
>> Sent: Sunday, January 11, 2015 06:23
>> To: [hidden email]
>> Subject: Re: Opening files from TIA software
>>
>> Here is the marco I use.
>> I normally have 2 files for each XX.emi and XX_1.ser. This macro gestured
>> of the _1.ser but a different version of the software might not have the
> _1
>> bit so will need altering. I've as yet not found a reason to keep the .emi
>> file afterwards. If you open the .tif as a text I think (I haven't
> checked)
>> that at the end is a list of microscope parameters which would have been
> in
>> the .emi, I've only used it when the scale became uncalibrated and had to
>> covert from the scope mag to actual scale....
>>
>> Kenton
>>
>>
>>
>>
>> On 11 January 2015 at 04:01, Michael Elbaum <[hidden email]
>>>
>> wrote:
>>
>>> I'm also using the plugin for .ser files, and re my earlier post about
>>> opening multiple files it is in fact macro-compatible. (Thanks to Aryeh
>>> Weiss and Nadav Elad.) It should be possible to have it open
>> drag-and-drop
>>> according to instructions in a comment in the java source file, by
>>> modifying the HandleExtraFileTypes plugin. I didn't manage to make that
>>> work, but it raises the question that maybe there's some other plugin
>>> catching the .ser filetype on your system? Have you succeeded in adding
>>> other plugins or do you get the same error?
>>>
>>> Kenton, any chance you could share the conversion macro? It would be
> very
>>> helpful to many of us using TIA!
>>>
>>> Michael
>>>
>>> ________________________________________
>>> From: ImageJ Interest Group [[hidden email]] on behalf of Kenton
>>> Arkill [[hidden email]]
>>> Sent: Saturday, January 10, 2015 06:50
>>> To: [hidden email]
>>> Subject: Re: Opening files from TIA software
>>>
>>> I don't know about the error. However the pluggin in the plugging folder
>>> appears in the in-out sub folder in the plugins tree. It also opens the
>>> .ser files not the .emi files. Personally I then have a macro that
>> converts
>>> a folder of .ser into tif. No information (headers etc) are lost.
>>> Not the answer but might help...
>>> Kenton
>>> On Jan 10, 2015 11:29 AM, "Søren Roesgaard Nielsen" <
>> [hidden email]
>>>>
>>> wrote:
>>>
>>>> Hi
>>>>
>>>> I am trying to open TEM files acuired using TIA software.
>>>>
>>>> The file is a .emi file.
>>>>
>>>> I have tried to install the following plugin:
>>>> http://imagej.nih.gov/ij/plugins/tia-reader.html
>>>>
>>>> But I cannot get it to show up I Fiji, I gives the following error
>> when I
>>>> try to install it:
>>>> WARNING: The PluginClassLoader cannot be reset
>>>>
>>>> Any suggestions?
>>>>
>>>> Søren Roesgaard Nielsen
>>>> Ph.D. Student
>>>> Tel.: [phone]
>>>> Office: 1590-151
>>>> Email: [hidden email]<mailto:[hidden email]>
>>>>
>>>> iNANO
>>>> Aarhus University
>>>> Gustav Wieds Vej 14
>>>> DK-8000 Aarhus
>>>> Web: www.inano.au.dk<https://mail.au.dk/owa/UrlBlockedError.aspx>
>>>>
>>>> [
>>>>
>>>
>>
> http://t2.gstatic.com/images?q=tbn:ANd9GcSuNO--QyrO9DDzk905MnRZxHFnNvip2292d
> 5KqdHoryiDJgcsH
>>>> ]
>>>>
>>>>
>>>>
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>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>>
>>>
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>>
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> ------------------------------
>
> Date:    Mon, 12 Jan 2015 20:49:43 +0100
> From:    Herbie <[hidden email]>
> Subject: Re: Opening files from TIA software
>
> Jeff,
>
> why not search the web for ImageJ & NITF?
> <https://github.com/hobu/nitro/tree/master/java/nitf.imagej>
>
> HTH
>
> Herbie
>
> :::::::::::::::::::::::::::::::::::::
> On 12.01.15 09:25, Jeff Stokes wrote:
>> Is anyone aware of a macro or plugin for opening NITF files?  Jeff Stokes
>
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>
> ------------------------------
>

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