Personal Update Sites for Fiji/ImageJ

[dscho]

Dear Fiji/ImageJ users,

probably the most popular feature of Fiji is the updater which lets users
and developers alike keep up-to-date without hassles. Developers upload
their macros, scripts or plugins, and users are notified whenever there
are new versions available that can be downloaded with a couple of mouse
clicks.

The feature is so popular that we worked hard to allow for 3rd-party
update sites. The only problem with such sites was that you needed to have
your own server to set up your own update site.

But this just changed.

For a couple of weeks, the updater has had support for personal update
sites, the perfect way for every Fiji/ImageJ user to share their macros,
scripts and plugins. Thanks to LOCI at UW-Madison who host the personal
update sites, everybody who wants to distribute their macros, scripts
and/or plugins can do so within five minutes.

From now on, there is no excuse anymore for articles demonstrating or
using ImageJ macros or plugins... it is too easy to set up an update site
and upload those macros and plugins...

Curious? Find out how... http://fiji.sc/Personal_Update_Sites

Ciao,
Johannes

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[dscho]

Dear Fiji/ImageJ users,

On Fri, 27 Sep 2013, Johannes Schindelin wrote:

> From now on, there is no excuse anymore for articles demonstrating or
> using ImageJ macros or plugins... it is too easy to set up an update site
> and upload those macros and plugins...

It has been brought to my attention that my wording was not quite clear,
and it did not come over as funny despite all my good intentions. So,
please, let me try again to describe what I believe to be the importance
of personal update sites being available to every Fiji/ImageJ user:

From now on ImageJ plugins or macros can be shared with the scientific
community regardless of their publication status through a personal update
site that ensures unambiguous crediting of the work.

Personal update sites are not only a very convenient way to increase the
impact of your work (by making not only the results but also the tools of
your research available to other scientists -- and therefore increase the
citability of your publications), but they make it easy to update the
macros and plugins with new and improved versions, too.

> Curious? Find out how... http://fiji.sc/Personal_Update_Sites

Ciao,
Johannes

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[Jarek Sacha-3]

Hello Johannes,

Do you/can you provide some king of statistics to plugin publishers how
many times their plugins were downloaded, what type of systems (Windows,
Linux, Mac), etc?

Jarek

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[dscho]

Hi Jarek,

On Thu, 3 Oct 2013, Jarek Sacha wrote:

> Do you/can you provide some king of statistics to plugin publishers how
> many times their plugins were downloaded, what type of systems (Windows,
> Linux, Mac), etc?

What kind of king did you have in mind? :-)

Seriously again, I just verified that the logging is turned on on
http://sites.imagej.net/. So data about the accesses is available.

As to the statistics, I would appreciate any help with that. Do you have a
preferred access.log frontend? Or are you willing to contribute a
.php-based one so we can integrate it into the Fiji Wiki?

Ciao,
Dscho

P.S.: After hearing a lot of privacy concerns, I am a little bit hesitant
to publish the raw access.log... That's the reason why we do not publish
it for the Fiji wiki either, providing only the condensed
http://fiji.sc/Fiji_Usage instead.

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[Jarek Sacha-3]

On Sun, Oct 6, 2013 at 12:20 PM, Johannes Schindelin <
[hidden email]> wrote:

> Hi Jarek,
>
> On Thu, 3 Oct 2013, Jarek Sacha wrote:
>
> > Do you/can you provide some king of statistics to plugin publishers how
> > many times their plugins were downloaded, what type of systems (Windows,
> > Linux, Mac), etc?
>
> What kind of king did you have in mind? :-)
>

I meant king Spellchecker the Infallible. His Majesty approved that
message.


> Seriously again, I just verified that the logging is turned on on
> http://sites.imagej.net/. So data about the accesses is available.
>
> As to the statistics, I would appreciate any help with that. Do you have a
> preferred access.log frontend? Or are you willing to contribute a
> .php-based one so we can integrate it into the Fiji Wiki?
>
I have absolutely no experience in this area, though it is no excuse not to
try to figure it out :) If somebody has suggestions they are very welcomed.

P.S.: After hearing a lot of privacy concerns, I am a little bit hesitant
> to publish the raw access.log... That's the reason why we do not publish
> it for the Fiji wiki either, providing only the condensed
> http://fiji.sc/Fiji_Usage instead.
>
I definitely agree that no personally identifiable information from the
logs should be published; no IP addresses, IDs or anything similar.
My interest was a combined number of download for a plugin, to have some
idea about popularity. Having some info about number of downloads in a day,
week, or month will be nice too. If I publish a plugin it will be nice to
see if people are downloading it.
Operating system is probably less important. It may be of interest for
certain plugins that have some hardware/OS dependencies (graphics, native
code …). Though this type of stats maybe difficult to correctly interpret.

Jarek

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[dscho]

Hi Jarek,

On Sun, 6 Oct 2013, Jarek Sacha wrote:

> On Sun, Oct 6, 2013 at 12:20 PM, Johannes Schindelin <
> [hidden email]> wrote:
>
> > On Thu, 3 Oct 2013, Jarek Sacha wrote:
> >
> > > Do you/can you provide some king of statistics to plugin publishers
> > > how many times their plugins were downloaded, what type of systems
> > > (Windows, Linux, Mac), etc?
> >
> > What kind of king did you have in mind? :-)
> >
> I meant king Spellchecker the Infallible. His Majesty approved that
> message.

*grins* Nice one!

> > Seriously again, I just verified that the logging is turned on on
> > http://sites.imagej.net/. So data about the accesses is available.
> >
> > As to the statistics, I would appreciate any help with that. Do you
> > have a preferred access.log frontend? Or are you willing to contribute
> > a .php-based one so we can integrate it into the Fiji Wiki?
> >
> I have absolutely no experience in this area, though it is no excuse not
> to try to figure it out :) If somebody has suggestions they are very
> welcomed.

Well, there are always the default access.log aggregators such as awstats
would be always possible, although it would not really take the special
setup into account that we have: only the top-level files are really
interesting, we can identify the updater by its User-Agent string and we
can identify when the updater tested for updates: it sends a HEAD request
(instead of a GET request, to reduce the server load).

> P.S.: After hearing a lot of privacy concerns, I am a little bit
> hesitant
> > to publish the raw access.log... That's the reason why we do not
> > publish it for the Fiji wiki either, providing only the condensed
> > http://fiji.sc/Fiji_Usage instead.
> >
> I definitely agree that no personally identifiable information from the
> logs should be published; no IP addresses, IDs or anything similar.  My
> interest was a combined number of download for a plugin, to have some
> idea about popularity. Having some info about number of downloads in a
> day, week, or month will be nice too. If I publish a plugin it will be
> nice to see if people are downloading it.

Those stats should certainly be easy to aggregate, it is just a matter of
writing the parser (and probably storing the results -- incrementally --
into a database so that the server is not brought to a screeching halt).
Alas, writing that parser (and a nice front-end to look at the stats)
requires time that I do not have right now ;-) I will keep it in mind (but
would still appreciate help, of course).

> Operating system is probably less important. It may be of interest for
> certain plugins that have some hardware/OS dependencies (graphics,
> native code …). Though this type of stats maybe difficult to correctly
> interpret.

Unfortunately, when I changed the User-Agent for the updater, I forgot to
encode the operating system... When I find the time to do so, I will
change that (because I do see the benefit of knowing the ratios of
operating systems from which certain update sites were accessed).

Ciao,
Dscho

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Francis Burton-3]

Hi,

I just tried to re-compile a plugin I wrote a couple of
years ago and now get the error:

cannot find symbol
symbol  : method quicksort(double[],int[])
location: class ij.util.Tools
    Tools.quicksort(asort, index);
         ^

I'm using ImageJ 1.48f & Java 1.6.0_20 (64-bit).

Has the quicksort function been removed? If so, is there
an equivalent call I can substitute?

Cheers,
Francis

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[José María Mateos]

2013/11/7 Francis Burton <[hidden email]>:
> Has the quicksort function been removed? If so, is there
> an equivalent call I can substitute?

I don't know specifically about Tools.quicksort(), but the standard
Java API offers Arrays.sort() and Collections.sort(), which may be
useful for your purposes.

Best,

José.

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Jan Eglinger]

Hi Francis,

On 07.11.2013, 10:57 AM, Francis Burton wrote:

> I just tried to re-compile a plugin I wrote a couple of
> years ago and now get the error:
>
> cannot find symbol
> symbol  : method quicksort(double[],int[])
> location: class ij.util.Tools
>      Tools.quicksort(asort, index);
>           ^
>
> I'm using ImageJ 1.48f & Java 1.6.0_20 (64-bit).
>
> Has the quicksort function been removed? If so, is there
> an equivalent call I can substitute?

As far as I can see from this commit:

http://fiji.sc/git/?p=ImageJA.git;a=commitdiff;h=dcec30f7a01cd703866c61a825476d35a420bc2d

the Tools.quicksort() function has been removed by Wayne with version
1.46p in May 2012. Maybe you can have a look at the source and see how
far the new rank(double[] values) function can replace your functionality.

Here's the javadoc link for Tools.java:
http://jenkins.imagej.net/job/ImageJ1-javadoc/javadoc/index.html?ij/util/Tools.html


Cheers,
Jan

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Francis Burton-3]

Hi Jan (and José),

Thanks to both of you for your speedy reply!

The quicksort function was removed, but Arrays.sort()
does the job just as well (and allows removal of the
index parameter which I didn't use).

Francis

> -----Original Message-----
> From: Jan Eglinger [mailto:[hidden email]]
> Sent: 07 November 2013 10:23
> To: [hidden email]; Francis Burton
> Subject: Re: Tools.quicksort missing
>
> Hi Francis,
>
> On 07.11.2013, 10:57 AM, Francis Burton wrote:
> > I just tried to re-compile a plugin I wrote a couple of
> > years ago and now get the error:
> >
> > cannot find symbol
> > symbol  : method quicksort(double[],int[])
> > location: class ij.util.Tools
> >      Tools.quicksort(asort, index);
> >           ^
> >
> > I'm using ImageJ 1.48f & Java 1.6.0_20 (64-bit).
> >
> > Has the quicksort function been removed? If so, is there
> > an equivalent call I can substitute?
>
> As far as I can see from this commit:
>
> http://fiji.sc/git/?p=ImageJA.git;a=commitdiff;h=dcec30f7a01cd
> 703866c61a825476d35a420bc2d
>
> the Tools.quicksort() function has been removed by Wayne with version
> 1.46p in May 2012. Maybe you can have a look at the source
> and see how
> far the new rank(double[] values) function can replace your
> functionality.
>
> Here's the javadoc link for Tools.java:
> http://jenkins.imagej.net/job/ImageJ1-javadoc/javadoc/index.ht
> ml?ij/util/Tools.html
>
>
> Cheers,
> Jan
>
>

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