Can't load images from remote directory

[Michael Doube]

Hi all,

I've been trying to drag and drop image stacks from a Windows share
(Samba) straight into ImageJ.  This works fine in Win XP, but fails in
Ubuntu.  ImageJ complains:

File not found:
/home/mdoube/smb:/my_shared_computer.ic.ac.uk/mysharename/path/to/imagedirectory/

In Ubuntu, shares are mounted in the user's home directory under .gvfs/
as, for example, ~/.gvfs/mysharename on my_shared_computer.ic.ac.uk/

Is this a bug in IJ, in the JRE or in Ubuntu / GNOME?

Mike

[Gabriel Landini]

On Tuesday 03 March 2009 11:16:21 Michael Doube wrote:

> I've been trying to drag and drop image stacks from a Windows share
> (Samba) straight into ImageJ.  This works fine in Win XP, but fails in
> Ubuntu.  ImageJ complains:
>
> File not found:
> /home/mdoube/smb:/my_shared_computer.ic.ac.uk/mysharename/path/to/imagedire
>ctory/
>
> In Ubuntu, shares are mounted in the user's home directory under .gvfs/
> as, for example, ~/.gvfs/mysharename on my_shared_computer.ic.ac.uk/
>
> Is this a bug in IJ, in the JRE or in Ubuntu / GNOME?
>
> Mike

Hi Mike,
I am pretty sure that this problem is of the same nature as this one:

http://imagejdocu.tudor.lu/doku.php?id=problem:linux:cannot_drop_files_into_the_imagej_window_in_kde_4.x

i.e. the colon in smb: makes it fail.

Cheers

Gabriel

[Albert Cardona]

Michael Doube wrote:

> Hi all,
>
> I've been trying to drag and drop image stacks from a Windows share
> (Samba) straight into ImageJ.  This works fine in Win XP, but fails in
> Ubuntu.  ImageJ complains:
>
> File not found:
> /home/mdoube/smb:/my_shared_computer.ic.ac.uk/mysharename/path/to/imagedirectory/
>
>
> In Ubuntu, shares are mounted in the user's home directory under
> .gvfs/ as, for example, ~/.gvfs/mysharename on
> my_shared_computer.ic.ac.uk/
>
> Is this a bug in IJ, in the JRE or in Ubuntu / GNOME?

To make files work, mount the smb share into the file system directly,
instead of relying on KDE io slaves or on GNOME's virtual file systems.

See for example:
http://albert.rierol.net/ubuntu_tips.html#Mount%20a%20samba%20share%20in%20fstab


If you know of any reliable way in all linux distributions to identify
where the "smb:" share is mounted on, we could code that into the DND
handler.

Cheers.

Albert

--
Albert Cardona
http://albert.rierol.net

[Gerard van Schip]

Hi.

I downloaded imagej as it is the only package that contains the FFT
function on the Mac (very happy with finding it).

Is there a way to export the FFT image, work on it in another program
and then reimport it to do a reverse fft?

Thanks.

Gerard

[Michael Schmid]

Hi Gerard,

if you want to do an inverse FFT you would need the internal FHT data  
that are hidden behind an FFT image, invisible to the user. Probably,  
it won't be very helpful for you since it is a fast Hartley transform  
(FHT), not FFT.

If you simply want to multiply the FFT with some value depending on  
the spatial frequency, use the FFT>Custom Filter. Note that the  
custom filter has 8 bits resolution only (integer values 0-255  
corresponding to factors of 0...1).

Also note that the FFT displayed on the screen as an image is a  
logarithmic version of the power spectrum. If you want to access the  
true power spectrum or the real&imaginary FFT, use FFT>FFT options.  
You can export these in any format you like (e.g. convert to 16 bit  
before saving), analyze them with your custom program and then, e.g.,  
create a filter for FFT>Custom Filter.

Hope this helps,

Michael
________________________________________________________________

On 3 Mar 2009, at 13:55, Gerard van Schip wrote:

> Hi.
>
> I downloaded imagej as it is the only package that contains the FFT
> function on the Mac (very happy with finding it).
>
> Is there a way to export the FFT image, work on it in another program
> and then reimport it to do a reverse fft?
>
> Thanks.
>
> Gerard

[Michael Doube]

> To make files work, mount the smb share into the file system directly,
> instead of relying on KDE io slaves or on GNOME's virtual file systems.
>
> See for example:
> http://albert.rierol.net/ubuntu_tips.html#Mount%20a%20samba%20share%20in%20fstab

Thanks for the suggestion Albert, but your method requires saving a
password in plaintext, and the needed password is my College-wide login...

Mike

[Albert Cardona]

Michael Doube wrote:

>> To make files work, mount the smb share into the file system
>> directly, instead of relying on KDE io slaves or on GNOME's virtual
>> file systems.
>>
>> See for example:
>> http://albert.rierol.net/ubuntu_tips.html#Mount%20a%20samba%20share%20in%20fstab 
>>
>
> Thanks for the suggestion Albert, but your method requires saving a
> password in plaintext, and the needed password is my College-wide
> login...

The samba share may be mounted from a shell, without the -cifs parameters.

I know it's quite cumbersome. I don't work with samba shares so I never
bothered to support them in the drag and drop for linux. If you can find
documentation on how are they exactly setup on, say, Ubuntu gnome and
kde, at least we could support these.
 From my experience, documentation about desktop setups is very, very
hard to find.

Albert

--
Albert Cardona
http://albert.rierol.net

[m000an ZH]

Hi, just a very easy question.
I return a value x with myread.
how can I use this value in an other method to use it in "run"?
Thanks for your help
Milan




public int myread (String string) throws Exception {

StringTokenizer st = new StringTokenizer (string, "\t");

int count = st.countTokens ();

int xyz[];


int x;

count = (count> 3) ? 3 : count;

for (int l = 0; l < count; l++) {

String token = st.nextToken ().trim ();

xyz [l] = (new Integer (token)).intValue ();

x = xyz [0];

}

return x;

}

public void run (ImageProcessor ip) {
int i = myread ();

tab = col.getNeighborhoodSphere (i, 2, 3, rad, rad, rad);
}
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[Thomas Boudier]

Hi,

Put your x,y,z values as class variables so they can be read everywhere
(an do not forget to supress the declaration in the function myread) :

class mean3DXYZ {

int x,y,z;

public int myread (String string) {

DO NOT WRITE int x ....

}



Thomas




m000an ZH a écrit :

> Hi, just a very easy question.
> I return a value x with myread.
> how can I use this value in an other method to use it in "run"?
> Thanks for your help
> Milan
>
>
>
>
> public int myread (String string) throws Exception {
>
> StringTokenizer st = new StringTokenizer (string, "\t");
>
> int count = st.countTokens ();
>
> int xyz[];
>
>
> int x;
>
> count = (count> 3) ? 3 : count;
>
> for (int l = 0; l < count; l++) {
>
> String token = st.nextToken ().trim ();
>
> xyz [l] = (new Integer (token)).intValue ();
>
> x = xyz [0];
>
> }
>
> return x;
>
> }
>
> public void run (ImageProcessor ip) {
> int i = myread ();
>
> tab = col.getNeighborhoodSphere (i, 2, 3, rad, rad, rad);
> }
> _________________________________________________________________
> Découvrez toutes les possibilités de communication avec vos proches
> http://download.live.com
>

--
   /**********************************************************/
      Thomas Boudier, MCU Université Pierre et Marie Curie,
      IFR 83. Bat B 7ème étage, porte 709, Jussieu.
      Tel : [phone]  Fax : [phone]
/*******************************************************/

[Volker Baecker]

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Hash: SHA1

Hi,
just to avoid confusion for newcomers, the variables you propose to use
are called instance variables. Class variables are static variables. See
for example here:
http://java.sun.com/docs/books/tutorial/java/javaOO/classvars.html
Volker

Thomas Boudier a écrit :

> Hi,
>
> Put your x,y,z values as class variables so they can be read everywhere
> (an do not forget to supress the declaration in the function myread) :
>
> class mean3DXYZ {
>
> int x,y,z;
>
> public int myread (String string) {
>
> DO NOT WRITE int x ....
>
> }
>
>
>
> Thomas
>
>
>
>
> m000an ZH a écrit :
>> Hi, just a very easy question.
>> I return a value x with myread.
>> how can I use this value in an other method to use it in "run"?
>> Thanks for your help
>> Milan
>>
>>
>>
>>
>> public int myread (String string) throws Exception {
>>
>> StringTokenizer st = new StringTokenizer (string, "\t");
>>
>> int count = st.countTokens ();
>>
>> int xyz[];
>>
>>
>> int x;
>>
>> count = (count> 3) ? 3 : count;
>>
>> for (int l = 0; l < count; l++) {
>>
>> String token    = st.nextToken ().trim ();
>>
>> xyz [l] = (new Integer (token)).intValue ();
>>
>> x = xyz [0];
>>
>> }
>>
>> return x;
>>
>> }
>>
>> public void run (ImageProcessor ip) {
>> int i = myread ();
>>
>> tab = col.getNeighborhoodSphere (i, 2, 3, rad, rad, rad);
>> }
>> _________________________________________________________________
>> Découvrez toutes les possibilités de communication avec vos proches
>> http://download.live.com
>>
>

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