Imagej.cfg file missing, not created

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Imagej.cfg file missing, not created

Menelaos Symeonides
Hello,

I am trying to increase the available memory in Fiji (ImageJ
2.0.0-rc-65/1.51w, on Windows 10 64-bit) and am getting an error saying
that imagej.cfg could not be edited. There is no imagej.cfg file in the
Fiji root folder, and none is ever created. The Fiji location is
C:\Fiji.app\.

I have tried running ImageJ-win64.exe as administrator, and have also
tried deleting the java folder and setting my environment variables so
that it can use my own java version. I also tried creating a dummy
imagej.cfg file. I even tried deleting my Fiji installation entirely and
re-downloading a fresh one, same thing happens. This is also happening
on two different Windows 10 machines. Otherwise, ImageJ is working fine,
I just can't change my memory availability.

Help would be appreciated!

Mel


--
Menelaos Symeonides
Post-Doctoral Associate, Thali Lab
Department of Microbiology and Molecular Genetics
University of Vermont
318 Stafford Hall
95 Carrigan Dr
Burlington, VT 05405
[hidden email]
Phone: 802-656-1161

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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Re: Imagej.cfg file missing, not created

ctrueden
Hi Mel,

Have you tried putting your Fiji installation into
C:\Users\<YourUserName>\Fiji.app, as recommended by the installation
instructions [1]?

There are often permissions issues placing the Fiji.app installation
outside of folders the current user controls.

If that also does not work for you, let us know, and I can try to reproduce
the issue on my Windows 10 system.

Regards,
Curtis

[1] http://imagej.net/Fiji/Downloads#Installation

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Wed, Apr 11, 2018 at 10:45 PM, Menelaos Symeonides <[hidden email]>
wrote:

> Hello,
>
> I am trying to increase the available memory in Fiji (ImageJ
> 2.0.0-rc-65/1.51w, on Windows 10 64-bit) and am getting an error saying
> that imagej.cfg could not be edited. There is no imagej.cfg file in the
> Fiji root folder, and none is ever created. The Fiji location is
> C:\Fiji.app\.
>
> I have tried running ImageJ-win64.exe as administrator, and have also
> tried deleting the java folder and setting my environment variables so that
> it can use my own java version. I also tried creating a dummy imagej.cfg
> file. I even tried deleting my Fiji installation entirely and
> re-downloading a fresh one, same thing happens. This is also happening on
> two different Windows 10 machines. Otherwise, ImageJ is working fine, I
> just can't change my memory availability.
>
> Help would be appreciated!
>
> Mel
>
>
> --
> Menelaos Symeonides
> Post-Doctoral Associate, Thali Lab
> Department of Microbiology and Molecular Genetics
> University of Vermont
> 318 Stafford Hall
> 95 Carrigan Dr
> Burlington, VT 05405
> [hidden email]
> Phone: 802-656-1161
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
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Re: Imagej.cfg file missing, not created

Menelaos Symeonides
Hi Curtis,

No, that doesn't fix it (thank you for alerting me to the recommended
installation location, though). I also tried placing it under
C:\Users\<MyUserName>\Documents\Fiji.app, but it behaves the same, with
or without admin rights.

I was able to replicate this issue on 3 different Windows 10 64-bit
systems and one Windows 7 32-bit computer.

Thanks,
Mel


On 4/12/2018 1:30 PM, Curtis Rueden wrote:

> Hi Mel,
>
> Have you tried putting your Fiji installation into
> C:\Users\<YourUserName>\Fiji.app, as recommended by the installation
> instructions [1]?
>
> There are often permissions issues placing the Fiji.app installation
> outside of folders the current user controls.
>
> If that also does not work for you, let us know, and I can try to reproduce
> the issue on my Windows 10 system.
>
> Regards,
> Curtis
>
> [1] http://imagej.net/Fiji/Downloads#Installation
>
> --
> Curtis Rueden
> LOCI software architect - https://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
> Did you know ImageJ has a forum? http://forum.imagej.net/
>
>
> On Wed, Apr 11, 2018 at 10:45 PM, Menelaos Symeonides <[hidden email]>
> wrote:
>
>> Hello,
>>
>> I am trying to increase the available memory in Fiji (ImageJ
>> 2.0.0-rc-65/1.51w, on Windows 10 64-bit) and am getting an error saying
>> that imagej.cfg could not be edited. There is no imagej.cfg file in the
>> Fiji root folder, and none is ever created. The Fiji location is
>> C:\Fiji.app\.
>>
>> I have tried running ImageJ-win64.exe as administrator, and have also
>> tried deleting the java folder and setting my environment variables so that
>> it can use my own java version. I also tried creating a dummy imagej.cfg
>> file. I even tried deleting my Fiji installation entirely and
>> re-downloading a fresh one, same thing happens. This is also happening on
>> two different Windows 10 machines. Otherwise, ImageJ is working fine, I
>> just can't change my memory availability.
>>
>> Help would be appreciated!
>>
>> Mel
>>
>>
>> --
>> Menelaos Symeonides
>> Post-Doctoral Associate, Thali Lab
>> Department of Microbiology and Molecular Genetics
>> University of Vermont
>> 318 Stafford Hall
>> 95 Carrigan Dr
>> Burlington, VT 05405
>> [hidden email]
>> Phone: 802-656-1161
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
Menelaos Symeonides
Post-Doctoral Associate, Thali Lab
Department of Microbiology and Molecular Genetics
University of Vermont
318 Stafford Hall
95 Carrigan Dr
Burlington, VT 05405
[hidden email]
Phone: 802-656-1161

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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Re: Imagej.cfg file missing, not created

Menelaos Symeonides
Can anyone else out there please try to replicate this issue and report
back? I just need to do something that requires a lot of memory and
right now it is impossible without a .cfg file.

Mel


On 4/12/2018 4:08 PM, Menelaos Symeonides wrote:

> Hi Curtis,
>
> No, that doesn't fix it (thank you for alerting me to the recommended
> installation location, though). I also tried placing it under
> C:\Users\<MyUserName>\Documents\Fiji.app, but it behaves the same,
> with or without admin rights.
>
> I was able to replicate this issue on 3 different Windows 10 64-bit
> systems and one Windows 7 32-bit computer.
>
> Thanks,
> Mel
>
>
> On 4/12/2018 1:30 PM, Curtis Rueden wrote:
>> Hi Mel,
>>
>> Have you tried putting your Fiji installation into
>> C:\Users\<YourUserName>\Fiji.app, as recommended by the installation
>> instructions [1]?
>>
>> There are often permissions issues placing the Fiji.app installation
>> outside of folders the current user controls.
>>
>> If that also does not work for you, let us know, and I can try to
>> reproduce
>> the issue on my Windows 10 system.
>>
>> Regards,
>> Curtis
>>
>> [1] http://imagej.net/Fiji/Downloads#Installation
>>
>> --
>> Curtis Rueden
>> LOCI software architect - https://loci.wisc.edu/software
>> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
>> Did you know ImageJ has a forum? http://forum.imagej.net/
>>
>>
>> On Wed, Apr 11, 2018 at 10:45 PM, Menelaos Symeonides <[hidden email]>
>> wrote:
>>
>>> Hello,
>>>
>>> I am trying to increase the available memory in Fiji (ImageJ
>>> 2.0.0-rc-65/1.51w, on Windows 10 64-bit) and am getting an error saying
>>> that imagej.cfg could not be edited. There is no imagej.cfg file in the
>>> Fiji root folder, and none is ever created. The Fiji location is
>>> C:\Fiji.app\.
>>>
>>> I have tried running ImageJ-win64.exe as administrator, and have also
>>> tried deleting the java folder and setting my environment variables
>>> so that
>>> it can use my own java version. I also tried creating a dummy
>>> imagej.cfg
>>> file. I even tried deleting my Fiji installation entirely and
>>> re-downloading a fresh one, same thing happens. This is also
>>> happening on
>>> two different Windows 10 machines. Otherwise, ImageJ is working fine, I
>>> just can't change my memory availability.
>>>
>>> Help would be appreciated!
>>>
>>> Mel
>>>
>>>
>>> --
>>> Menelaos Symeonides
>>> Post-Doctoral Associate, Thali Lab
>>> Department of Microbiology and Molecular Genetics
>>> University of Vermont
>>> 318 Stafford Hall
>>> 95 Carrigan Dr
>>> Burlington, VT 05405
>>> [hidden email]
>>> Phone: 802-656-1161
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
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Re: Imagej.cfg file missing, not created

ctrueden
In reply to this post by Menelaos Symeonides
Hi Mel,

> Allow me to possibly blow your mind:
>
> Do the same procedure you just described (with no cfg file in your
> folder), change only one thing: Launch Memory & Threads by searching
> for it in the search box and then starting it from there. No cfg file
> created. Then try launching it from Edit > Options, it creates a cfg
> file.

Wow, that does blow my mind! O_O

I did some digging. The cause is that Fiji overrides the Memory & Threads
command to behave differently.

I filed an issue detailing all the consequences here:

    https://github.com/fiji/fiji/issues/185

I would like to fix it, so that other users do not stumble into this issue.
But unfortunately, I am not sure of the best approach. Developers with
ideas are welcome to chime in on the GitHub thread.

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Tue, Apr 17, 2018 at 2:21 PM, Menelaos Symeonides <[hidden email]>
wrote:

> Hi Curtis,
>
> This is really strange, but I can't reproduce the problem anymore (after
> redownloading Fiji). Allow me to possibly blow your mind:
>
> Do the same procedure you just described (with no cfg file in your
> folder), change only one thing: Launch Memory & Threads by searching for it
> in the search box and then starting it from there. No cfg file created.
> Then try launching it from Edit > Options, it creates a cfg file.
>
> What is going on?!
>
> Mel
>
> On 4/17/2018 2:54 PM, Curtis Rueden wrote:
>
> Hi Mel,
>
> > Have you been able to replicate this issue?
>
> I tried just now, but could not reproduce.
>
> * Downloaded a fresh Fiji from https://fiji.sc/#download
> * Unpacked it to C:\Users\Curtis\Programs\Fiji.app.
> * Launched ImageJ-win64.exe.
> * Responded Yes to the Updater prompt; updated the application.
> * Restarted Fiji when it told me to do so.
> * Ran Edit > Options > Memory & Threads...
> * Set the Maximum Memory to 2000 (my default in the VM was ~3300).
> * Restarted Fiji.
> * The ImageJ.cfg was created, and Fiji reported 2000MB when I clicked the
> status bar.
>
> Is your Fiji.app directory on your local file system? You are certain you
> have write access? What happens if you create an ImageJ.cfg yourself with
> the following contents:
>
>   .
>   jre\bin\javaw.exe
>   -Xmx2000m -cp ij.jar ij.ImageJ
>
> Did you try launching from the command line?
> http://imagej.net/Troubleshooting#Launching_ImageJ_from_the_console
>
> You can pass e.g. "-mx1g" to tell ImageJ to use 1 GB of memory.
>
> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect - https://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
> Did you know ImageJ has a forum? http://forum.imagej.net/
>
>
> On Mon, Apr 16, 2018 at 10:55 AM, Menelaos Symeonides <[hidden email]>
> wrote:
>
>> Hi again Curtis,
>>
>> Have you been able to replicate this issue?
>>
>> Mel
>>
>>
>> On 4/12/2018 4:08 PM, Menelaos Symeonides wrote:
>>
>>> Hi Curtis,
>>>
>>> No, that doesn't fix it (thank you for alerting me to the recommended
>>> installation location, though). I also tried placing it under
>>> C:\Users\<MyUserName>\Documents\Fiji.app, but it behaves the same, with
>>> or without admin rights.
>>>
>>> I was able to replicate this issue on 3 different Windows 10 64-bit
>>> systems and one Windows 7 32-bit computer.
>>>
>>> Thanks,
>>> Mel
>>>
>>>
>>> On 4/12/2018 1:30 PM, Curtis Rueden wrote:
>>>
>>>> Hi Mel,
>>>>
>>>> Have you tried putting your Fiji installation into
>>>> C:\Users\<YourUserName>\Fiji.app, as recommended by the installation
>>>> instructions [1]?
>>>>
>>>> There are often permissions issues placing the Fiji.app installation
>>>> outside of folders the current user controls.
>>>>
>>>> If that also does not work for you, let us know, and I can try to
>>>> reproduce
>>>> the issue on my Windows 10 system.
>>>>
>>>> Regards,
>>>> Curtis
>>>>
>>>> [1] http://imagej.net/Fiji/Downloads#Installation
>>>>
>>>> --
>>>> Curtis Rueden
>>>> LOCI software architect - https://loci.wisc.edu/software
>>>> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
>>>> Did you know ImageJ has a forum? http://forum.imagej.net/
>>>>
>>>>
>>>> On Wed, Apr 11, 2018 at 10:45 PM, Menelaos Symeonides <[hidden email]
>>>> >
>>>> wrote:
>>>>
>>>> Hello,
>>>>>
>>>>> I am trying to increase the available memory in Fiji (ImageJ
>>>>> 2.0.0-rc-65/1.51w, on Windows 10 64-bit) and am getting an error saying
>>>>> that imagej.cfg could not be edited. There is no imagej.cfg file in the
>>>>> Fiji root folder, and none is ever created. The Fiji location is
>>>>> C:\Fiji.app\.
>>>>>
>>>>> I have tried running ImageJ-win64.exe as administrator, and have also
>>>>> tried deleting the java folder and setting my environment variables so
>>>>> that
>>>>> it can use my own java version. I also tried creating a dummy
>>>>> imagej.cfg
>>>>> file. I even tried deleting my Fiji installation entirely and
>>>>> re-downloading a fresh one, same thing happens. This is also happening
>>>>> on
>>>>> two different Windows 10 machines. Otherwise, ImageJ is working fine, I
>>>>> just can't change my memory availability.
>>>>>
>>>>> Help would be appreciated!
>>>>>
>>>>> Mel
>>>>>
>>>>>
>>>>> --
>>>>> Menelaos Symeonides
>>>>> Post-Doctoral Associate, Thali Lab
>>>>> Department of Microbiology and Molecular Genetics
>>>>> University of Vermont
>>>>> 318 Stafford Hall
>>>>> 95 Carrigan Dr
>>>>> <https://maps.google.com/?q=95+Carrigan+Dr+%0D%0A++++++++++++++++++++++Burlington,+VT+05405&entry=gmail&source=g>
>>>>> Burlington, VT 05405
>>>>> [hidden email]
>>>>> Phone: 802-656-1161
>>>>>
>>>>> --
>>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>>>
>>>>> --
>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>>
>>>
>>
>
>

--
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