amide-users — general discussion and announcement list

Re: [amide-users] volumetric measurement

[Andy L. <lo...@st...>]

Hi Andy,

There's currently no function in AMIDE for doing free hand ROI drawing... 
So I don't think this program will work for what you want to do.

Could anyone on the list comment on other programs that are out there that 
can do free hand ROI drawing?

Andy

On Mon, 25 Oct 2004, AK wrote:

> Dear Sirs:
>
> I ran across your site and found it very interesting. I am a doctor and 
> am interested in being able to take a ct scan [ie of the thorax -lungs] 
> and be able to trace out only the lung fields from one image of the ct 
> scan and be able to get this volume and then do the same in all the 
> other sections of the ct scan until I get the entire lung volume 
> completely.  is this possible? how do I go about doing this? or this 
> there any other free software that can do this for me . thank you in 
> advance for you help.
>
>   sincerely ,
>
> Andy Kalides MD

[amide-users] volumetric measurement

[AK <and...@ot...>]

Dear Sirs:=20

I ran across your site and found it very interesting. I am a doctor and =
am interested in being able to take a ct scan [ie of the thorax -lungs] =
and be able to trace out only the lung fields from one image of the ct =
scan and be able to get this volume and then do the same in all the =
other sections of the ct scan until I get the entire lung volume =
completely.  is this possible? how do I go about doing this? or this =
there any other free software that can do this for me . =20
thank you in advance for you help. =20

   sincerely ,=20

Andy Kalides MD

[amide-users] OS X Installation - Server Problem?

[Tien-chi P. <tc...@ma...>]

Hi,

I was trying to install AMIDE on a PowerBook with Mac OS 10.3.5. The step "sudo apt-get update" failed because http://ricebox.mednet.ucla.edu didn't seem to be alive. Is it a temporary problem? Is there another server I can try?

Many thanks,

Tien-chi

-- 
Tien-chi Pan
Department of Cancer Biology
Abramson Family Cancer Research Institute
613 BRB II/III, 421 Curie Boulevard
University of Pennsylvania School of Medicine
Philadelphia, PA  19104-6160
Phone: (215) 898-1156  Fax: (215) 573-6725

[amide-users] Re: Amide on a mac

[Andy L. <lo...@st...>]

Sorry for the slow reply, I've been out of town for a good portion of the
last couple of weeks.

I have not been able to replicate the problems you're experiencing under 
Mac OS X.  Are you using a third party mouse by any chance?  

Is anyone else on the list experiencing problems under Mac OS X?

In related news for all those on the list, I've just fixed the Mac OS X
packages for the latest version of fink.  The install instructions have
been modified slightly too.

Andy

On Thu, 9 Sep 2004, Sharon Sudarshan wrote:

> Andy--
> Hope this e-mail finds you well.  I use Amide to analyze PET data on small animals.  I am having some problems when I run the program on a G5 mac.  
> 
> 1) I find that I have to "click" the mouse buttons multiple times for
> certain functions in working with ROIs.  On a PC this does not happen.
> 
> 2) When erasing voxels using the middle click button, the Mac freezes as
> if the button were continuously pressed.  This wouldn't be so bad as it
> gets tedious to erase numerous voxels.  however, I can't get it out of
> that function to do something else.  I have to quit the program.
> 
> Any ideas?  I am switching over to a mac for my work, and I want to make
> sure that I can still work with Amide.  Any help would be much
> appreciated.
> 
> Thanks, 
> 
> Sharon

[amide-users] read center location

[Kai-Hsiang C. <ch...@ni...>]

Hi,

I tried to get the "center location" of a realigned image from the saved XIF
directory files. I tried reading the "coordinate_space_offset", but the
values are different from those I saw in Amide. Is there scaling factors or
additional offsets I should use?
Thank you!

--
 Kai-Hsiang Chuang, Ph.D.
Laboratory of Functional and Molecular Imaging
National Institutes of Health
Building 10, B1D109
Bethesda, MD 20892-1065, USA
Phone: +1-301-594-7314
Fax: +1-301-480-2558

RE: [amide-users] Re: Elliptical ROI

[Kris T. <kri...@cs...>]

Hi

I do a similar thing in STIR: in the 1st pass, I check if the centres of
the voxels are in. The 2nd pass then checks border voxels. That also can
miss small objects of course. However, an ROI which is small than the
voxel size (in at least 1 dimension) does not make a lot of sense I
guess.
I also don't know of a fast but accurate way. 

Kris Thielemans
(kri...@im...)
Hammersmith Imanet
Du Cane Road
London W12 0NN
UK
http://www.HammersmithImanet.com/~kris
 

> -----Original Message-----
> From: ami...@li... 
> [mailto:ami...@li...] On Behalf Of 
> Andy Loening
> Sent: Thursday, August 19, 2004 6:47 AM
> To: Peter Bloomfield
> Cc: ami...@li...
> Subject: [amide-users] Re: Elliptical ROI
> 
> 
> Hi Peter,
> 
> Thanks for the file.  I pinned down the problem, it's a 
> side-effect of the 
> method I'm using to calculate ROI's.  Instead of dividing 
> every voxel up 
> into 4x4x4 subvoxels, the algorithm looks at the 8 corners of 
> the ROI.  If 
> all 8 are in, the algorithm assumes the ROI is completely in. 
>  If all 8 
> corners are out of the ROI, the algorithm assumes the ROI is 
> completely 
> out.  If some of the corners are in, then the algorithm 
> divides the voxel 
> up into subvoxels.
> 
> The problem is, that an ROI can pass through a voxel without 
> touching any of the corners.  Conversely, in the case of an 
> irregular ROI (3D isocontour), just because all 8 corners are 
> in doesn't mean the whole ROI is necessarily in.  So the 
> algorithm occasionally ignores voxels that technically should 
> be in the ROI.  In your case of an ellipsoid, the ellipsoid 
> width is small enough that it never crosses a voxel's corner, 
> so the algorith doesn't see it.
> 
> I don't know of a more satisfactory way to write the 
> algorithm without making it much more computationally 
> expensive.  What I've done instead, is to add a check box to 
> the little pop-up dialog that comes up before the ROI stats; 
> "more accurate (slow)".  When this is checked, the ROI 
> analysis algorithm divides all voxels up into subvoxels.  
> It's much slower, but it always gives the right answer.
> 
> Thanks again for the bug report,
> 	Andy
> 
> On Thu, 12 Aug 2004, Peter Bloomfield wrote:
> 
> > It is coming across now. The file is called Test.xif
> > 
> > Peter
> > 
> > On Thursday 12 August 2004 14:34, you wrote:
> > > You can anon ftp into my workstation and drop it
> > > into the incoming folder.
> > >
> > > Andy
> > >
> > > On Thu, 12 Aug 2004, Peter Bloomfield wrote:
> > > > I can do that, a single image and a roi. I tend to save 
> them in a 
> > > > directory structure, but I can change that to a single file.
> > > >
> > > > Let me know where I can put it. We don't have an anonymous ftp 
> > > > server here.
> > > >
> > > > Cheers
> > > >
> > > > Peter
> > > >
> > > > On Thursday 12 August 2004 13:44, you wrote:
> > > > > Okay, now things are just getting strange.  That the problem 
> > > > > goes away when you draw another ROI makes me think 
> its either a 
> > > > > compiler error in gcc, or a memory error in AMIDE (and it may 
> > > > > not even be an error in the ROI analysis code).
> > > > >
> > > > > Since I still haven't been able to replicate the problem, I 
> > > > > think things would be easiest if you could put a test 
> case .xif 
> > > > > file together that gives you the error, and get that to me.
> > > > >
> > > > > Andy
> > > > >
> > > > > On Wed, 11 Aug 2004, Peter Bloomfield wrote:
> > > > > > Now I am getting confused.
> > > > > >
> > > > > > I changed the constant "AMITK_ROI_GRANULARITY"  to 8, but 
> > > > > > still no joy.
> > > > > >
> > > > > > But, I then drew a ellipsoid region on a coronal plane and 
> > > > > > then the original region on the transverse plane was 
> > > > > > calculated 'correctly', as well as the coronal region.
> > > > > >
> > > > > > There is something else I just noticed. If I move 
> to another 
> > > > > > part of the volume using the cross hairs and 
> clicking a mouse 
> > > > > > button, I can longer see my original ROI on the transverse 
> > > > > > slice, even stepping through the transverse planes 
> give me no 
> > > > > > region. I can see it on the coronal but not on the 
> transverse. 
> > > > > > I can try pointing to it and clicking the mouse to move the 
> > > > > > display to that part of the image, but still no region. Is 
> > > > > > this a diversion?
> > > > > >
> > > > > > Peter
> > > > > >
> > > > > > On Tuesday 10 August 2004 17:16, you wrote:
> > > > > > > If you have super thin ROI's, you can run into problems 
> > > > > > > because the ROI calculation algorithm does an 
> approximation 
> > > > > > > (it divides voxels into 4x4x4 subvoxels).
> > > > > > >
> > > > > > > Your ROI doesn't sound like it's thin enough to 
> be running 
> > > > > > > into that problem, but try this anyway.  Try changing the 
> > > > > > > constant "AMITK_ROI_GRANULARITY" in amitk_roi.h 
> to 8 (it's 
> > > > > > > currently 4), recompiling, and see if that fixes your 
> > > > > > > problem.
> > > > > > >
> > > > > > > Andy
> > > > > > >
> > > > > > > On Tue, 10 Aug 2004, Peter Bloomfield wrote:
> > > > > > > > Andy
> > > > > > > >
> > > > > > > > I may have misled you, the regions I am having 
> difficulty 
> > > > > > > > with are ellipsoid, ie the first option in the 
> ROI list; 
> > > > > > > > sorry for my mistake.
> > > > > > > >
> > > > > > > > 	The images are isotropic volumes, of 
> > > > > > > > 1.21875x1.21875x1.21875 (or close to).
> > > > > > > >
> > > > > > > > 	If I describe an ellipsoid region with 
> depth 1.21875 mm, 
> > > > > > > > then I get zero in the ROI stats. If I describe 
> a region 
> > > > > > > > with depth 2.4375 mm, then I get values in the 
> ROI stats.
> > > > > > > >
> > > > > > > > Sorry for the naming mistake in the regions, does this 
> > > > > > > > point you any further on?
> > > > > > > >
> > > > > > > > Peter
> > > > > > > >
> > > > > > > > On Tuesday 10 August 2004 14:42, you wrote:
> > > > > > > > > And the mystery continues...
> > > > > > > > >
> > > > > > > > > I'm using gcc 3.3.3 (on Fedora Core 2), and I just 
> > > > > > > > > haven't been able to replicate the problem you're 
> > > > > > > > > encountering...
> > > > > > > > >
> > > > > > > > > If you want, you can try emailing me the .xif file 
> > > > > > > > > (probably don't want to spam the whole list), or 
> > > > > > > > > alternatively, I can give you an account on 
> one of our 
> > > > > > > > > boxes.  This would help us pin down if it's a problem 
> > > > > > > > > with Suse.
> > > > > > > > >
> > > > > > > > > Thanks,
> > > > > > > > > 	Andy
> > > > > > > > >
> > > > > > > > > On Tue, 10 Aug 2004, Peter Bloomfield wrote:
> > > > > > > > > > Andy,
> > > > > > > > > >
> > > > > > > > > > I have just done the following
> > > > > > > > > >
> > > > > > > > > > 	Drawn a large elliptical ROI and a large box ROI
> > > > > > > > > >
> > > > > > > > > > 	Applied the two ROI to two different 
> data sets, and 
> > > > > > > > > > the elliptical statistics are all zero, whereas the 
> > > > > > > > > > box is calculated
> > > > > > > > > >
> > > > > > > > > > I have attached ROI placement and region 
> calculation 
> > > > > > > > > > output. Also, elliptic cylinders work fine.
> > > > > > > > > >
> > > > > > > > > > Here is the version of gcc:
> > > > > > > > > > gcc --ver
> > > > > > > > > > Reading specs from 
> > > > > > > > > > /usr/lib/gcc-lib/i586-suse-linux/3.3.3/specs 
> > > > > > > > > > Configured with: ../configure 
> --enable-threads=posix 
> > > > > > > > > > --prefix=/usr --with-local-prefix=/usr/local 
> > > > > > > > > > --infodir=/usr/share/info --mandir=/usr/share/man 
> > > > > > > > > > --enable-languages=c,c++,f77,objc,java,ada 
> > > > > > > > > > --disable-checking --libdir=/usr/lib 
> --enable-libgcj 
> > > > > > > > > > --with-gxx-include-dir=/usr/include/g++ 
> > > > > > > > > > --with-slibdir=/lib --with-system-zlib 
> --enable-shared 
> > > > > > > > > > --enable-__cxa_atexit i586-suse-linux Thread model: 
> > > > > > > > > > posix gcc version 3.3.3 (SuSE Linux)
> > > > > > > > > >
> > > > > > > > > > Peter
> > > > > > > > > >
> > > > > > > > > > On Monday 09 August 2004 17:40, Andy Loening wrote:
> > > > > > > > > > > Whoa, that doesn't sound right.
> > > > > > > > > > >
> > > > > > > > > > > Does this occur only for ellipitical 
> ROI's?  Are you 
> > > > > > > > > > > sure that the ROI is located in space 
> over a portion 
> > > > > > > > > > > of the data set?  Is there anything unusual about 
> > > > > > > > > > > your data set or ROI dimensions that might be 
> > > > > > > > > > > hitting a bug in the algorithm? Which 
> version of gcc 
> > > > > > > > > > > are you using?
> > > > > > > > > > >
> > > > > > > > > > > Andy
> > > > > > > > > > >
> > > > > > > > > > > On Mon, 9 Aug 2004, Peter Bloomfield wrote:
> > > > > > > > > > > > Has anyone else seen this?
> > > > > > > > > > > >
> > > > > > > > > > > > The results from the ROI calculation for an 
> > > > > > > > > > > > elliptical region are zero, irrespective of the 
> > > > > > > > > > > > region size? Have I made an error in 
> compilation?
> > > > > > > > > > > >
> > > > > > > > > > > > I am running Amide v 0.8.6 under SuSE 9.1
> > > > > > > > > > > >
> > > > > > > > > > > > Cheers
> > > > > > > > > > > >
> > > > > > > > > > > > Peter
> > > > > > > > > > > >
> > > > > > > > > > > > --
> > > > > > > > > > > > Peter M. Bloomfield
> > > > > > > > > > > > Physicist,
> > > > > > > > > > > > PET Centre,
> > > > > > > > > > > > Centre for Addiction and Mental Health, 250 
> > > > > > > > > > > > College St., Toronto, Ontario,
> > > > > > > > > > > > Canada M5T 1R8
> > > > > > > > > > > > Tel: 416 535 8501 Ext. 4243
> > > > > > > > > > > >
> > > > > > > > > > > > Registered Linux User #360164 at Linux Counter, 
> > > > > > > > > > > > http://counter.li.org
> > > > > > > > > > > >
> > > > > > > > > > > >
> > > > > > > > > > > > 
> --------------------------------------------------
> > > > > > > > > > > > -----
> > > > > > > > > > > > This SF.Net email is sponsored by OSTG. 
> Have you noticed
> > > > > > > > > > > > the changes on Linux.com, 
> ITManagersJournal and NewsForge
> > > > > > > > > > > > in the past few weeks? Now, one more 
> big change to
> > > > > > > > > > > > announce. We are now OSTG- Open Source 
> Technology Group.
> > > > > > > > > > > > Come see the changes on the new OSTG 
> site. www.ostg.com
> > > > > > > > > > > > _______________________________________________
> > > > > > > > > > > > amide-users mailing list
> > > > > > > > > > > > ami...@li...
> > > > > > > > > > > > 
> https://lists.sourceforge.net/lists/listinfo/amide-users
> > > > > > > > > >
> > > > > > > > > > --
> > > > > > > > > > Peter M. Bloomfield
> > > > > > > > > > Physicist,
> > > > > > > > > > PET Centre,
> > > > > > > > > > Centre for Addiction and Mental Health,
> > > > > > > > > > 250 College St.,
> > > > > > > > > > Toronto, Ontario,
> > > > > > > > > > Canada M5T 1R8
> > > > > > > > > > Tel: 416 535 8501 Ext. 4243
> > > > > > > > > >
> > > > > > > > > > Registered Linux User #360164 at Linux Counter, 
> > > > > > > > > > http://counter.li.org
> > > > > > > >
> > > > > > > > --
> > > > > > > > Peter M. Bloomfield
> > > > > > > > Physicist,
> > > > > > > > PET Centre,
> > > > > > > > Centre for Addiction and Mental Health,
> > > > > > > > 250 College St.,
> > > > > > > > Toronto, Ontario,
> > > > > > > > Canada M5T 1R8
> > > > > > > > Tel: 416 535 8501 Ext. 4243
> > > > > > > >
> > > > > > > > Registered Linux User #360164 at Linux Counter, 
> > > > > > > > http://counter.li.org
> > > > > >
> > > > > > --
> > > > > > Peter M. Bloomfield
> > > > > > Physicist,
> > > > > > PET Centre,
> > > > > > Centre for Addiction and Mental Health,
> > > > > > 250 College St.,
> > > > > > Toronto, Ontario,
> > > > > > Canada M5T 1R8
> > > > > > Tel: 416 535 8501 Ext. 4243
> > > > > >
> > > > > > Registered Linux User #360164 at Linux Counter, 
> > > > > > http://counter.li.org
> > > >
> > > > --
> > > > Peter M. Bloomfield
> > > > Physicist,
> > > > PET Centre,
> > > > Centre for Addiction and Mental Health,
> > > > 250 College St.,
> > > > Toronto, Ontario,
> > > > Canada M5T 1R8
> > > > Tel: 416 535 8501 Ext. 4243
> > > >
> > > > Registered Linux User #360164 at Linux Counter, 
> > > > http://counter.li.org
> > 
> > --
> > Peter M. Bloomfield
> > Physicist,
> > PET Centre,
> > Centre for Addiction and Mental Health,
> > 250 College St.,
> > Toronto, Ontario,
> > Canada M5T 1R8
> > Tel: 416 535 8501 Ext. 4243
> > 
> > Registered Linux User #360164 at Linux Counter, 
http://counter.li.org
> 


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[amide-users] Version 0.8.7 Released

[Andy L. <lo...@st...>]

Hi All,

A new release of AMIDE is out for Linux, Windows, and Mac OS X.  The
change log is below.  

Note that both Windows and Mac OS X versions also contain a patched
(X)MedCon version to fix an error in reading Concorde attenuation files.  
For any Linux users who care, this patch will be incorporated into the
next release of (X)MedCon.

Take care,
	Andy

-------------------------------------------

Version 0.8.7
        * spin buttons on roi initial popup didn't take decimal places [1]
	* ui_series panel size can now be adjusted [2]
	* new isocontour, wasn't showing image value on help window [3]
	* fixed isocontour erasing [3]
        * fixed error in profile tool, incorrect values for view_duration < frame_duration [4]
        * users now have the option of a more accurate roi quantitation algorithm [5]
        * increased accuracy of the fast roi quantitation algorithm
        [1] Found by Keon Kang
        [2] Requested by Freimut Juengling
        [3] Found by Steve Jones
        [4] Found by Patrick Chow
        [5] Found by Peter Bloomfield
 

[amide-users] Re: Elliptical ROI

[Andy L. <lo...@st...>]

Hi Peter,

Thanks for the file.  I pinned down the problem, it's a side-effect of the 
method I'm using to calculate ROI's.  Instead of dividing every voxel up 
into 4x4x4 subvoxels, the algorithm looks at the 8 corners of the ROI.  If 
all 8 are in, the algorithm assumes the ROI is completely in.  If all 8 
corners are out of the ROI, the algorithm assumes the ROI is completely 
out.  If some of the corners are in, then the algorithm divides the voxel 
up into subvoxels.

The problem is, that an ROI can pass through a voxel without touching any
of the corners.  Conversely, in the case of an irregular ROI (3D
isocontour), just because all 8 corners are in doesn't mean the whole ROI
is necessarily in.  So the algorithm occasionally ignores voxels that
technically should be in the ROI.  In your case of an ellipsoid, the
ellipsoid width is small enough that it never crosses a voxel's corner, so
the algorith doesn't see it.

I don't know of a more satisfactory way to write the algorithm without
making it much more computationally expensive.  What I've done instead, is
to add a check box to the little pop-up dialog that comes up before the
ROI stats; "more accurate (slow)".  When this is checked, the ROI analysis
algorithm divides all voxels up into subvoxels.  It's much slower, but it
always gives the right answer.

Thanks again for the bug report,
	Andy

On Thu, 12 Aug 2004, Peter Bloomfield wrote:

> It is coming across now. The file is called Test.xif
> 
> Peter
> 
> On Thursday 12 August 2004 14:34, you wrote:
> > You can anon ftp into my workstation and drop it
> > into the incoming folder.
> >
> > Andy
> >
> > On Thu, 12 Aug 2004, Peter Bloomfield wrote:
> > > I can do that, a single image and a roi. I tend to save them in a
> > > directory structure, but I can change that to a single file.
> > >
> > > Let me know where I can put it. We don't have an anonymous ftp server
> > > here.
> > >
> > > Cheers
> > >
> > > Peter
> > >
> > > On Thursday 12 August 2004 13:44, you wrote:
> > > > Okay, now things are just getting strange.  That the problem goes away
> > > > when you draw another ROI makes me think its either a compiler error in
> > > > gcc, or a memory error in AMIDE (and it may not even be an error in the
> > > > ROI analysis code).
> > > >
> > > > Since I still haven't been able to replicate the problem, I think
> > > > things would be easiest if you could put a test case .xif file together
> > > > that gives you the error, and get that to me.
> > > >
> > > > Andy
> > > >
> > > > On Wed, 11 Aug 2004, Peter Bloomfield wrote:
> > > > > Now I am getting confused.
> > > > >
> > > > > I changed the constant "AMITK_ROI_GRANULARITY"  to 8, but still no
> > > > > joy.
> > > > >
> > > > > But, I then drew a ellipsoid region on a coronal plane and then the
> > > > > original region on the transverse plane was calculated 'correctly',
> > > > > as well as the coronal region.
> > > > >
> > > > > There is something else I just noticed. If I move to another part of
> > > > > the volume using the cross hairs and clicking a mouse button, I can
> > > > > longer see my original ROI on the transverse slice, even stepping
> > > > > through the transverse planes give me no region. I can see it on the
> > > > > coronal but not on the transverse. I can try pointing to it and
> > > > > clicking the mouse to move the display to that part of the image, but
> > > > > still no region. Is this a diversion?
> > > > >
> > > > > Peter
> > > > >
> > > > > On Tuesday 10 August 2004 17:16, you wrote:
> > > > > > If you have super thin ROI's, you can run into problems because the
> > > > > > ROI calculation algorithm does an approximation (it divides voxels
> > > > > > into 4x4x4 subvoxels).
> > > > > >
> > > > > > Your ROI doesn't sound like it's thin enough to be running into
> > > > > > that problem, but try this anyway.  Try changing the constant
> > > > > > "AMITK_ROI_GRANULARITY" in amitk_roi.h to 8 (it's currently 4),
> > > > > > recompiling, and see if that fixes your problem.
> > > > > >
> > > > > > Andy
> > > > > >
> > > > > > On Tue, 10 Aug 2004, Peter Bloomfield wrote:
> > > > > > > Andy
> > > > > > >
> > > > > > > I may have misled you, the regions I am having difficulty with
> > > > > > > are ellipsoid, ie the first option in the ROI list; sorry for my
> > > > > > > mistake.
> > > > > > >
> > > > > > > 	The images are isotropic volumes, of 1.21875x1.21875x1.21875 (or
> > > > > > > close to).
> > > > > > >
> > > > > > > 	If I describe an ellipsoid region with depth 1.21875 mm, then I
> > > > > > > get zero in the ROI stats. If I describe a region with depth
> > > > > > > 2.4375 mm, then I get values in the ROI stats.
> > > > > > >
> > > > > > > Sorry for the naming mistake in the regions, does this point you
> > > > > > > any further on?
> > > > > > >
> > > > > > > Peter
> > > > > > >
> > > > > > > On Tuesday 10 August 2004 14:42, you wrote:
> > > > > > > > And the mystery continues...
> > > > > > > >
> > > > > > > > I'm using gcc 3.3.3 (on Fedora Core 2), and I just haven't been
> > > > > > > > able to replicate the problem you're encountering...
> > > > > > > >
> > > > > > > > If you want, you can try emailing me the .xif file (probably
> > > > > > > > don't want to spam the whole list), or alternatively, I can
> > > > > > > > give you an account on one of our boxes.  This would help us
> > > > > > > > pin down if it's a problem with Suse.
> > > > > > > >
> > > > > > > > Thanks,
> > > > > > > > 	Andy
> > > > > > > >
> > > > > > > > On Tue, 10 Aug 2004, Peter Bloomfield wrote:
> > > > > > > > > Andy,
> > > > > > > > >
> > > > > > > > > I have just done the following
> > > > > > > > >
> > > > > > > > > 	Drawn a large elliptical ROI and a large box ROI
> > > > > > > > >
> > > > > > > > > 	Applied the two ROI to two different data sets, and the
> > > > > > > > > elliptical statistics are all zero, whereas the box is
> > > > > > > > > calculated
> > > > > > > > >
> > > > > > > > > I have attached ROI placement and region calculation output.
> > > > > > > > > Also, elliptic cylinders work fine.
> > > > > > > > >
> > > > > > > > > Here is the version of gcc:
> > > > > > > > > gcc --ver
> > > > > > > > > Reading specs from
> > > > > > > > > /usr/lib/gcc-lib/i586-suse-linux/3.3.3/specs Configured with:
> > > > > > > > > ../configure --enable-threads=posix --prefix=/usr
> > > > > > > > > --with-local-prefix=/usr/local
> > > > > > > > > --infodir=/usr/share/info --mandir=/usr/share/man
> > > > > > > > > --enable-languages=c,c++,f77,objc,java,ada --disable-checking
> > > > > > > > > --libdir=/usr/lib --enable-libgcj
> > > > > > > > > --with-gxx-include-dir=/usr/include/g++ --with-slibdir=/lib
> > > > > > > > > --with-system-zlib --enable-shared --enable-__cxa_atexit
> > > > > > > > > i586-suse-linux Thread model: posix
> > > > > > > > > gcc version 3.3.3 (SuSE Linux)
> > > > > > > > >
> > > > > > > > > Peter
> > > > > > > > >
> > > > > > > > > On Monday 09 August 2004 17:40, Andy Loening wrote:
> > > > > > > > > > Whoa, that doesn't sound right.
> > > > > > > > > >
> > > > > > > > > > Does this occur only for ellipitical ROI's?  Are you sure
> > > > > > > > > > that the ROI is located in space over a portion of the data
> > > > > > > > > > set?  Is there anything unusual about your data set or ROI
> > > > > > > > > > dimensions that might be hitting a bug in the algorithm? 
> > > > > > > > > > Which version of gcc are you using?
> > > > > > > > > >
> > > > > > > > > > Andy
> > > > > > > > > >
> > > > > > > > > > On Mon, 9 Aug 2004, Peter Bloomfield wrote:
> > > > > > > > > > > Has anyone else seen this?
> > > > > > > > > > >
> > > > > > > > > > > The results from the ROI calculation for an elliptical
> > > > > > > > > > > region are zero, irrespective of the region size? Have I
> > > > > > > > > > > made an error in compilation?
> > > > > > > > > > >
> > > > > > > > > > > I am running Amide v 0.8.6 under SuSE 9.1
> > > > > > > > > > >
> > > > > > > > > > > Cheers
> > > > > > > > > > >
> > > > > > > > > > > Peter
> > > > > > > > > > >
> > > > > > > > > > > --
> > > > > > > > > > > Peter M. Bloomfield
> > > > > > > > > > > Physicist,
> > > > > > > > > > > PET Centre,
> > > > > > > > > > > Centre for Addiction and Mental Health,
> > > > > > > > > > > 250 College St.,
> > > > > > > > > > > Toronto, Ontario,
> > > > > > > > > > > Canada M5T 1R8
> > > > > > > > > > > Tel: 416 535 8501 Ext. 4243
> > > > > > > > > > >
> > > > > > > > > > > Registered Linux User #360164 at Linux Counter,
> > > > > > > > > > > http://counter.li.org
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > > -------------------------------------------------------
> > > > > > > > > > > This SF.Net email is sponsored by OSTG. Have you noticed
> > > > > > > > > > > the changes on Linux.com, ITManagersJournal and NewsForge
> > > > > > > > > > > in the past few weeks? Now, one more big change to
> > > > > > > > > > > announce. We are now OSTG- Open Source Technology Group.
> > > > > > > > > > > Come see the changes on the new OSTG site. www.ostg.com
> > > > > > > > > > > _______________________________________________
> > > > > > > > > > > amide-users mailing list
> > > > > > > > > > > ami...@li...
> > > > > > > > > > > https://lists.sourceforge.net/lists/listinfo/amide-users
> > > > > > > > >
> > > > > > > > > --
> > > > > > > > > Peter M. Bloomfield
> > > > > > > > > Physicist,
> > > > > > > > > PET Centre,
> > > > > > > > > Centre for Addiction and Mental Health,
> > > > > > > > > 250 College St.,
> > > > > > > > > Toronto, Ontario,
> > > > > > > > > Canada M5T 1R8
> > > > > > > > > Tel: 416 535 8501 Ext. 4243
> > > > > > > > >
> > > > > > > > > Registered Linux User #360164 at Linux Counter,
> > > > > > > > > http://counter.li.org
> > > > > > >
> > > > > > > --
> > > > > > > Peter M. Bloomfield
> > > > > > > Physicist,
> > > > > > > PET Centre,
> > > > > > > Centre for Addiction and Mental Health,
> > > > > > > 250 College St.,
> > > > > > > Toronto, Ontario,
> > > > > > > Canada M5T 1R8
> > > > > > > Tel: 416 535 8501 Ext. 4243
> > > > > > >
> > > > > > > Registered Linux User #360164 at Linux Counter,
> > > > > > > http://counter.li.org
> > > > >
> > > > > --
> > > > > Peter M. Bloomfield
> > > > > Physicist,
> > > > > PET Centre,
> > > > > Centre for Addiction and Mental Health,
> > > > > 250 College St.,
> > > > > Toronto, Ontario,
> > > > > Canada M5T 1R8
> > > > > Tel: 416 535 8501 Ext. 4243
> > > > >
> > > > > Registered Linux User #360164 at Linux Counter, http://counter.li.org
> > >
> > > --
> > > Peter M. Bloomfield
> > > Physicist,
> > > PET Centre,
> > > Centre for Addiction and Mental Health,
> > > 250 College St.,
> > > Toronto, Ontario,
> > > Canada M5T 1R8
> > > Tel: 416 535 8501 Ext. 4243
> > >
> > > Registered Linux User #360164 at Linux Counter, http://counter.li.org
> 
> -- 
> Peter M. Bloomfield
> Physicist,
> PET Centre,
> Centre for Addiction and Mental Health,
> 250 College St.,
> Toronto, Ontario,
> Canada M5T 1R8
> Tel: 416 535 8501 Ext. 4243
> 
> Registered Linux User #360164 at Linux Counter, http://counter.li.org
> 

Re: [amide-users] Elliptical ROI

[Andy L. <lo...@st...>]

And the mystery continues...

I'm using gcc 3.3.3 (on Fedora Core 2), and I just haven't been able to
replicate the problem you're encountering...

If you want, you can try emailing me the .xif file (probably don't want to
spam the whole list), or alternatively, I can give you an account on one
of our boxes.  This would help us pin down if it's a problem with Suse.

Thanks,
	Andy

On Tue, 10 Aug 2004, Peter Bloomfield wrote:

> 
> Andy,
> 
> I have just done the following
> 
> 	Drawn a large elliptical ROI and a large box ROI
> 
> 	Applied the two ROI to two different data sets, and the elliptical statistics are all zero,
> 	whereas the box is calculated
> 
> I have attached ROI placement and region calculation output. Also, elliptic cylinders work fine.
> 
> Here is the version of gcc:
> gcc --ver
> Reading specs from /usr/lib/gcc-lib/i586-suse-linux/3.3.3/specs
> Configured with: ../configure --enable-threads=posix --prefix=/usr --with-local-prefix=/usr/local
> 	--infodir=/usr/share/info --mandir=/usr/share/man --enable-languages=c,c++,f77,objc,java,ada
> 		--disable-checking --libdir=/usr/lib --enable-libgcj --with-gxx-include-dir=/usr/include/g++
> 			--with-slibdir=/lib --with-system-zlib --enable-shared --enable-__cxa_atexit i586-suse-linux
> Thread model: posix
> gcc version 3.3.3 (SuSE Linux)
> 
> Peter
> 
> 
> 
> On Monday 09 August 2004 17:40, Andy Loening wrote:
> > Whoa, that doesn't sound right.
> >
> > Does this occur only for ellipitical ROI's?  Are you sure that the ROI is
> > located in space over a portion of the data set?  Is there anything
> > unusual about your data set or ROI dimensions that might be hitting a bug
> > in the algorithm?  Which version of gcc are you using?
> >
> > Andy
> >
> > On Mon, 9 Aug 2004, Peter Bloomfield wrote:
> > > Has anyone else seen this?
> > >
> > > The results from the ROI calculation for an elliptical region are zero,
> > > irrespective of the region size? Have I made an error in compilation?
> > >
> > > I am running Amide v 0.8.6 under SuSE 9.1
> > >
> > > Cheers
> > >
> > > Peter
> > >
> > > --
> > > Peter M. Bloomfield
> > > Physicist,
> > > PET Centre,
> > > Centre for Addiction and Mental Health,
> > > 250 College St.,
> > > Toronto, Ontario,
> > > Canada M5T 1R8
> > > Tel: 416 535 8501 Ext. 4243
> > >
> > > Registered Linux User #360164 at Linux Counter, http://counter.li.org
> > >
> > >
> > > -------------------------------------------------------
> > > This SF.Net email is sponsored by OSTG. Have you noticed the changes on
> > > Linux.com, ITManagersJournal and NewsForge in the past few weeks? Now,
> > > one more big change to announce. We are now OSTG- Open Source Technology
> > > Group. Come see the changes on the new OSTG site. www.ostg.com
> > > _______________________________________________
> > > amide-users mailing list
> > > ami...@li...
> > > https://lists.sourceforge.net/lists/listinfo/amide-users
> 
> -- 
> Peter M. Bloomfield
> Physicist,
> PET Centre,
> Centre for Addiction and Mental Health,
> 250 College St.,
> Toronto, Ontario,
> Canada M5T 1R8
> Tel: 416 535 8501 Ext. 4243
> 
> Registered Linux User #360164 at Linux Counter, http://counter.li.org
> 

Re: [amide-users] Elliptical ROI

[Peter B. <pet...@ca...>]

Andy,

I have just done the following

	Drawn a large elliptical ROI and a large box ROI

	Applied the two ROI to two different data sets, and the elliptical statistics are all zero,
	whereas the box is calculated

I have attached ROI placement and region calculation output. Also, elliptic cylinders work fine.

Here is the version of gcc:
gcc --ver
Reading specs from /usr/lib/gcc-lib/i586-suse-linux/3.3.3/specs
Configured with: ../configure --enable-threads=posix --prefix=/usr --with-local-prefix=/usr/local
	--infodir=/usr/share/info --mandir=/usr/share/man --enable-languages=c,c++,f77,objc,java,ada
		--disable-checking --libdir=/usr/lib --enable-libgcj --with-gxx-include-dir=/usr/include/g++
			--with-slibdir=/lib --with-system-zlib --enable-shared --enable-__cxa_atexit i586-suse-linux
Thread model: posix
gcc version 3.3.3 (SuSE Linux)

Peter



On Monday 09 August 2004 17:40, Andy Loening wrote:
> Whoa, that doesn't sound right.
>
> Does this occur only for ellipitical ROI's?  Are you sure that the ROI is
> located in space over a portion of the data set?  Is there anything
> unusual about your data set or ROI dimensions that might be hitting a bug
> in the algorithm?  Which version of gcc are you using?
>
> Andy
>
> On Mon, 9 Aug 2004, Peter Bloomfield wrote:
> > Has anyone else seen this?
> >
> > The results from the ROI calculation for an elliptical region are zero,
> > irrespective of the region size? Have I made an error in compilation?
> >
> > I am running Amide v 0.8.6 under SuSE 9.1
> >
> > Cheers
> >
> > Peter
> >
> > --
> > Peter M. Bloomfield
> > Physicist,
> > PET Centre,
> > Centre for Addiction and Mental Health,
> > 250 College St.,
> > Toronto, Ontario,
> > Canada M5T 1R8
> > Tel: 416 535 8501 Ext. 4243
> >
> > Registered Linux User #360164 at Linux Counter, http://counter.li.org
> >
> >
> > -------------------------------------------------------
> > This SF.Net email is sponsored by OSTG. Have you noticed the changes on
> > Linux.com, ITManagersJournal and NewsForge in the past few weeks? Now,
> > one more big change to announce. We are now OSTG- Open Source Technology
> > Group. Come see the changes on the new OSTG site. www.ostg.com
> > _______________________________________________
> > amide-users mailing list
> > ami...@li...
> > https://lists.sourceforge.net/lists/listinfo/amide-users

-- 
Peter M. Bloomfield
Physicist,
PET Centre,
Centre for Addiction and Mental Health,
250 College St.,
Toronto, Ontario,
Canada M5T 1R8
Tel: 416 535 8501 Ext. 4243

Registered Linux User #360164 at Linux Counter, http://counter.li.org

Re: [amide-users] Elliptical ROI

[Andy L. <lo...@st...>]

Whoa, that doesn't sound right.

Does this occur only for ellipitical ROI's?  Are you sure that the ROI is
located in space over a portion of the data set?  Is there anything
unusual about your data set or ROI dimensions that might be hitting a bug
in the algorithm?  Which version of gcc are you using?

Andy

On Mon, 9 Aug 2004, Peter Bloomfield wrote:

> 
> Has anyone else seen this?
> 
> The results from the ROI calculation for an elliptical region are zero, 
> irrespective of the region size? Have I made an error in compilation?
> 
> I am running Amide v 0.8.6 under SuSE 9.1
> 
> Cheers
> 
> Peter
> 
> -- 
> Peter M. Bloomfield
> Physicist,
> PET Centre,
> Centre for Addiction and Mental Health,
> 250 College St.,
> Toronto, Ontario,
> Canada M5T 1R8
> Tel: 416 535 8501 Ext. 4243
> 
> Registered Linux User #360164 at Linux Counter, http://counter.li.org
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by OSTG. Have you noticed the changes on
> Linux.com, ITManagersJournal and NewsForge in the past few weeks? Now,
> one more big change to announce. We are now OSTG- Open Source Technology
> Group. Come see the changes on the new OSTG site. www.ostg.com
> _______________________________________________
> amide-users mailing list
> ami...@li...
> https://lists.sourceforge.net/lists/listinfo/amide-users
> 

[amide-users] Elliptical ROI

[Peter B. <pet...@ca...>]

Has anyone else seen this?

The results from the ROI calculation for an elliptical region are zero, 
irrespective of the region size? Have I made an error in compilation?

I am running Amide v 0.8.6 under SuSE 9.1

Cheers

Peter

-- 
Peter M. Bloomfield
Physicist,
PET Centre,
Centre for Addiction and Mental Health,
250 College St.,
Toronto, Ontario,
Canada M5T 1R8
Tel: 416 535 8501 Ext. 4243

Registered Linux User #360164 at Linux Counter, http://counter.li.org

RE: [amide-users] Import File (Specify) Options

[Rutao Y. Ph.D. <RutaoYao@Buffalo.Edu>]

Thanks Andy, It worked!

All your guesses were confirmed. I did a couple of things as you =
suggested:

1) Added /usr/local/xmedcon/lib in file /etc/ld.so.conf, run =
/sbin/ldconfig
2) Added /usr/local/xmedcon/bin to my path
3) "make distclean" and "make clean" to clean up
4) ./configure
5) Added "-I/usr/local/xmedon/include" to the CFLAGS line in Makefile =
and
./src/Makefile (I do not know which is the one)
6) Changed "XMEDCON_LIBS =3D -L/usr/local/lib -lmdc" in one of the =
Makefile to
"XMEDCON_LIBS =3D -L/usr/local/xmedcon/lib -lmdc"

Now I see 11 options for Import File (specify)  :)

Thanks again!

Rutao

> -----Original Message-----
> From: Andy Loening [mailto:lo...@st...]=20
> Sent: Tuesday, July 27, 2004 1:38 AM
> To: Rutao Yao, Ph.D.
> Cc: ami...@li...
> Subject: Re: [amide-users] Import File (Specify) Options
>=20
>=20
> Hi Rutao,
>=20
> Xmedcon is detected at configure time, and whether or not=20
> amide decides to compile itself with xmedcon support will be=20
> noted in the file amide_config.h (generated by configure). =20
> Just changing the Makefile won't do it, you'd also have to=20
> change amide_config.h
>=20
> Now, as to why the configure script isn't detecting=20
> xmedcon... that I'm not sure of.  These are my guesses.
>=20
> 1. /usr/local/lib isn't specified as a library directory in=20
> the file /etc/ld.so.conf.  Add in that line, and then make=20
> sure you run /sbin/ldconfig.
>=20
> 2. /usr/local/bin isn't in your path.  This will prevent the=20
> configure script from running the "xmedcon-config" program.
>=20
> 3. xmedcon is installed somewhere else (like=20
> /usr/local/xmedcon), in which=20
> case you'll have to edit /etc/ld.so.conf appropriately, add=20
> /usr/local/xmedcon/bin to your path, and tell amide where the xmedcon=20
> include files are at configure time, something like:
> 	CFLAGS=3D-I/usr/local/xmedon/include ./configure
> Should do the trick.
>=20
> Get back to me if nothing above works,
> 	Andy
>=20
> On Tue, 27 Jul 2004, Rutao Yao, Ph.D. wrote:
>=20
> > Hello Andy and others,
> >=20
> > I installed the amide 0.8.6 on my system (Linux 8.0 Redhat,=20
> AMD Athlon=20
> > Dual Processor, gcc 3.2), first by compiling the source code. The=20
> > programs run without any error message and displayed the=20
> sample data=20
> > ok. However, I saw only "Raw" and "Ecat 6/7 via libecat"=20
> options under=20
> > "File->Import File (Specify)", which were less than the 7=20
> or 8 options=20
> > that the earlier version
> > (0.7.7) we had on the system.  I then tried rpm approach as=20
> described at the
> > amide web site, the installed amide program showed only=20
> "Raw" option. An
> > attempt of changing ./src/Makefile to make sure the right=20
> include and lib
> > location of xmedcon was also futile. Any suggestions?
> > =20
> > Thanks a lot!
> >=20
> > Rutao    =20
> >=20
> > Rutao Yao, Ph.D.
> > Assistant Professor
> > Dept. of Nuclear Medicine
> > State University of New York at Buffalo
> >=20
> > Tel. 716-838-5889
> > Fax 716-838-4918
> >=20
> >=20
> >=20
> >=20
> > -------------------------------------------------------
> > This SF.Net email is sponsored by BEA Weblogic Workshop
> > FREE Java Enterprise J2EE developer tools!
> > Get your free copy of BEA WebLogic Workshop 8.1 today.=20
> > http://ads.osdn.com/?ad_idG21&alloc_id=10040&op=CCk
> > _______________________________________________
> > amide-users mailing list
> > ami...@li...=20
> > https://lists.sourceforge.net/lists/listinfo/amide-users
> >=20
>=20

Re: [amide-users] Import File (Specify) Options

[Andy L. <lo...@st...>]

Hi Rutao,

Xmedcon is detected at configure time, and whether or not amide decides to
compile itself with xmedcon support will be noted in the file
amide_config.h (generated by configure).  Just changing the Makefile won't
do it, you'd also have to change amide_config.h

Now, as to why the configure script isn't detecting xmedcon... that I'm
not sure of.  These are my guesses.

1. /usr/local/lib isn't specified as a library directory in the file
/etc/ld.so.conf.  Add in that line, and then make sure you run
/sbin/ldconfig.

2. /usr/local/bin isn't in your path.  This will prevent the configure
script from running the "xmedcon-config" program.

3. xmedcon is installed somewhere else (like /usr/local/xmedcon), in which=
=20
case you'll have to edit /etc/ld.so.conf appropriately, add=20
/usr/local/xmedcon/bin to your path, and tell amide where the xmedcon=20
include files are at configure time, something like:
=09CFLAGS=3D-I/usr/local/xmedon/include ./configure
Should do the trick.

Get back to me if nothing above works,
=09Andy

On Tue, 27 Jul 2004, Rutao Yao, Ph.D. wrote:

> Hello Andy and others,
>=20
> I installed the amide 0.8.6 on my system (Linux 8.0 Redhat, AMD Athlon Du=
al
> Processor, gcc 3.2), first by compiling the source code. The programs run
> without any error message and displayed the sample data ok. However, I sa=
w
> only "Raw" and "Ecat 6/7 via libecat" options under "File->Import File
> (Specify)", which were less than the 7 or 8 options that the earlier vers=
ion
> (0.7.7) we had on the system.  I then tried rpm approach as described at =
the
> amide web site, the installed amide program showed only "Raw" option. An
> attempt of changing ./src/Makefile to make sure the right include and lib
> location of xmedcon was also futile. Any suggestions?
> =20
> Thanks a lot!
>=20
> Rutao    =20
>=20
> Rutao Yao, Ph.D.
> Assistant Professor
> Dept. of Nuclear Medicine
> State University of New York at Buffalo
>=20
> Tel. 716-838-5889
> Fax 716-838-4918
>=20
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by BEA Weblogic Workshop
> FREE Java Enterprise J2EE developer tools!
> Get your free copy of BEA WebLogic Workshop 8.1 today.
> http://ads.osdn.com/?ad_idG21&alloc_id=10040&op=CCk
> _______________________________________________
> amide-users mailing list
> ami...@li...
> https://lists.sourceforge.net/lists/listinfo/amide-users
>=20

[amide-users] Import File (Specify) Options

[Rutao Y. Ph.D. <RutaoYao@Buffalo.Edu>]

Hello Andy and others,

I installed the amide 0.8.6 on my system (Linux 8.0 Redhat, AMD Athlon =
Dual
Processor, gcc 3.2), first by compiling the source code. The programs =
run
without any error message and displayed the sample data ok. However, I =
saw
only "Raw" and "Ecat 6/7 via libecat" options under "File->Import File
(Specify)", which were less than the 7 or 8 options that the earlier =
version
(0.7.7) we had on the system.  I then tried rpm approach as described at =
the
amide web site, the installed amide program showed only "Raw" option. An
attempt of changing ./src/Makefile to make sure the right include and =
lib
location of xmedcon was also futile. Any suggestions?
=20
Thanks a lot!

Rutao    =20

Rutao Yao, Ph.D.
Assistant Professor
Dept. of Nuclear Medicine
State University of New York at Buffalo

Tel. 716-838-5889
Fax 716-838-4918

Re: [amide-users] problems running amide 0.8.6 on Linux and WindowsXP

[Andy L. <lo...@st...>]

Hi Emiliano,

Thanks for the bug report.  Sounds like two different problems.

1. The Linux problem is probably a misreading of the data file you're
trying to give it.  What type of file is this?  And can you read it in
correctly with XMedCon?

It might be due to messed up internalization support in AMIDE. We've been
having trouble with the whole "." versus "," as the radix sign thing. Try
changing your locale to english by running AMIDE from the command line as
follows:
	LC_ALL=zh_CN amide

2. I'm not sure what's going wrong with the windows version.  

C:/PROGRA~1/COMMON~1/GTK/2.0/lib
C:/PROGRAM FILES/COMMON FILES/GTK/2.0/lib

These are the same locations in windows land (for compatibility with 
applications that expect the FAT16 filesystem).  So the Gtk runtime 
location was determined correctly by the installation program.  If you 
want to convince yourself that this isn't the issue, you can copy the 
intl.dll file to the bin directory in the AMIDE install (C:/Program 
Files/AMIDE/bin) and see if running AMIDE still gives you the same 
problem.

Since this is the internationalization DLL we're talking about... it might 
also have to do with messed up internationalization support.  You can try 
running the program in the english locale and see if that fixes anything 
(I'm not quite sure how to do that on Windows XP, so if anyone else wants 
to chime in, feel free).


Take care,
	Andy

On Mon, 19 Jul 2004, Emiliano Spezi wrote:

> Hi there,
> 
> 
> I downloaded and installed the latest version of Amide and related
> packages (GTK2, xmedcon etc) on both WindowsXP and Linux RH9 boxes.
> 
> In both cases I have problems running the program.
> 
> On Linux amide crashes with the following message:
> 
> (process:18192): GdkPixbuf-CRITICAL (recursed) **: file
> gdk-pixbuf-data.c: line 62 (gdk_pixbuf_new_from_data): assertion `width
> 0' failed aborting...
> 
> On WindowsXP the erorr message is:
> 
> C:/PROGRA~1/COMMON~1/GTK/2.0/lib/intl.dll not found
> 
> In this case I must say that the right version of GTK is installed, the
> registry looks fine and the library is where it should be: C:/PROGRAM
> FILES/COMMON FILES/GTK/2.0/lib/intl.dll
> 
> Incidentally I noticed that Amide for windows apparently looks for
> C:/PROGRA~1/COMMON~1/GTK/2.0/lib/intl.dll even if GTK was installed
> elsewhere. Therefore I am not sure that the registry is actually scanned
> by the program.
> 
> I wonder if somebody else is having the same problems. Any suggestion
> wuold be appreciated.
> 
> Best regards,
> 
> Emiliano
> 
> 
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[amide-users] problems running amide 0.8.6 on Linux and WindowsXP

[Emiliano S. <emi...@ph...>]

Hi there,


I downloaded and installed the latest version of Amide and related packages (GTK2, xmedcon etc) on both WindowsXP and Linux RH9 boxes. 

In both cases I have problems running the program.

On Linux amide crashes with the following message:

(process:18192): GdkPixbuf-CRITICAL (recursed) **: file gdk-pixbuf-data.c: line 62 (gdk_pixbuf_new_from_data): assertion `width > 0' failed
aborting...

On WindowsXP the erorr message is:

C:/PROGRA~1/COMMON~1/GTK/2.0/lib/intl.dll not found

In this case I must say that the right version of GTK is installed, the registry looks fine and the library is where it should be: C:/PROGRAM FILES/COMMON FILES/GTK/2.0/lib/intl.dll

Incidentally I noticed that Amide for windows apparently looks for C:/PROGRA~1/COMMON~1/GTK/2.0/lib/intl.dll even if GTK was installed elsewhere. Therefore I am not sure that the registry is actually scanned by the program.

I wonder if somebody else is having the same problems.
Any suggestion wuold be appreciated.

Best regards,

Emiliano

RE: [amide-users] installation recent AMIDE on windows

[Andy L. <lo...@st...>]

Hey Kris,

You need to install the runtime environment.  The development package just 
has supplemental stuff (like header files) that you'd only need if you 
were trying to compile something.

Hope that clears things up,
	Andy

On Fri, 9 Jul 2004, Kris Thielemans wrote:

> >
> > GTK is suppose to install two registry keys when it installs:
> > 	HKEY_LOCAL_MACHINE\Software\GTK\2.0\Version
> > 	HKEY_LOCAL_MACHINE\Software\GTK\2.0\DllPath
> >
> > The AMIDE install checks the first key to make sure GTK is installed, and
> > it uses the second key to find the GTK DLL's.  Could you make sure that
> > both keys are in the registry?  And you're using the gtk-runtime package
> > from the dropline site, right?
> >
> 
> I've downloaded
> GTK-Development-Environment-2.2.4-3.exe
> from the site (https://sourceforge.net/project/showfiles.php?group_id=71914)
> that's linked on your page. It's home page is indeed dropline.
> 
> the registry key is
> HKEY_LOCAL_MACHINE\Software\GTK+ Development Environment\2.0\Path
> (only that one)
> 

RE: [amide-users] installation recent AMIDE on windows

[Kris T. <kri...@cs...>]

>
> GTK is suppose to install two registry keys when it installs:
> 	HKEY_LOCAL_MACHINE\Software\GTK\2.0\Version
> 	HKEY_LOCAL_MACHINE\Software\GTK\2.0\DllPath
>
> The AMIDE install checks the first key to make sure GTK is installed, and
> it uses the second key to find the GTK DLL's.  Could you make sure that
> both keys are in the registry?  And you're using the gtk-runtime package
> from the dropline site, right?
>

I've downloaded
GTK-Development-Environment-2.2.4-3.exe
from the site (https://sourceforge.net/project/showfiles.php?group_id=71914)
that's linked on your page. It's home page is indeed dropline.

the registry key is
HKEY_LOCAL_MACHINE\Software\GTK+ Development Environment\2.0\Path
(only that one)

Re: [amide-users] installation recent AMIDE on windows

[Andy L. <lo...@st...>]

Hey Kris,

GTK is suppose to install two registry keys when it installs:
	HKEY_LOCAL_MACHINE\Software\GTK\2.0\Version
	HKEY_LOCAL_MACHINE\Software\GTK\2.0\DllPath

The AMIDE install checks the first key to make sure GTK is installed, and
it uses the second key to find the GTK DLL's.  Could you make sure that
both keys are in the registry?  And you're using the gtk-runtime package 
from the dropline site, right?

Thanks,
	Andy

On Wed, 7 Jul 2004, Kris Thielemans wrote:

> Hi Andy
> 
> I'm trying to get amide on my Windows NT PC. I've installed the gtk+ package
> as mentioned on your website, but had to install it in a nonstandard place
> (due to disk space). Now, clicking the AMIDE install says that "Please
> install the GTK 2.0 ...". So, it obviously didn't find it (and how could
> it).
> Any suggestion?
> 
> Thanks!
> 
> Kris Thielemans
> Hammersmith Imanet (formerly IRSL)
> Cyclotron Building
> Hammersmith Hospital
> Du Cane Road
> London W12 ONN, United Kingdom
> 
> Phone on :   +44 (020)8383 3731
> FAX on :     +44 (020)8383 2029
> 
> web site address:
> http://www.hammersmithimanet.com/~kris
> 
> -------------------------------------------
> NOTE: My inbox has a SPAM filter that automatically throws away suspect
> messages. If you expect a reply and don't get one, your message might have
> been wrongly classified.
> 
> 
> 
> -------------------------------------------------------
> This SF.Net email sponsored by Black Hat Briefings & Training.
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> 

[amide-users] installation recent AMIDE on windows

[Kris T. <kri...@cs...>]

Hi Andy

I'm trying to get amide on my Windows NT PC. I've installed the gtk+ package
as mentioned on your website, but had to install it in a nonstandard place
(due to disk space). Now, clicking the AMIDE install says that "Please
install the GTK 2.0 ...". So, it obviously didn't find it (and how could
it).
Any suggestion?

Thanks!

Kris Thielemans
Hammersmith Imanet (formerly IRSL)
Cyclotron Building
Hammersmith Hospital
Du Cane Road
London W12 ONN, United Kingdom

Phone on :   +44 (020)8383 3731
FAX on :     +44 (020)8383 2029

web site address:
http://www.hammersmithimanet.com/~kris

-------------------------------------------
NOTE: My inbox has a SPAM filter that automatically throws away suspect
messages. If you expect a reply and don't get one, your message might have
been wrongly classified.

RE: [amide-users] font problem

[Kris T. <kri...@cs...>]

> > I have the impression that the libfreetype6 and libpango1.0
> packages we have
> > installed are really not compatible, even though the debian
> package system
> > should prevent this from happening. (There's a large amount of
> stuff on this
> > that google throws up, so much that I get very confused by it).
> > Unfortunately, the next version of libpango is not yet in the stable
> > distribution, so I cannot install that one.
> >
>
> I would suggest nuking what you have installed in /usr/local, and
> rebuilding (but using the new debian provided fontconfig and pango).
>


This is the last email I send about this on this list (sorry for the
distraction), but the above suggestion doesn't work.

trying to configure gtk-2.2.4 I get in my config.log

configure:24733: checking For sufficiently new FreeType (at least 2.0.1)
configure:24755: gcc-3.3 -c -g -O2 -Wall  -I/usr/include/freetype2
conftest.c >&5
In file included from configure:24787:
/usr/include/freetype2/freetype/freetype.h:20:2: #error "`ft2build.h' hasn't
been included yet!"
/usr/include/freetype2/freetype/freetype.h:21:2: #error "Please always use
macros to include FreeType header files."
/usr/include/freetype2/freetype/freetype.h:22:2: #error "Example:"
/usr/include/freetype2/freetype/freetype.h:23:2: #error "  #include
<ft2build.h>"
/usr/include/freetype2/freetype/freetype.h:24:2: #error "  #include
FT_FREETYPE_H"

this error does not occur when using the older freetype. So, I probably
should be using a more recent gtk then and (again) determine all the
required version numbers and compile by hand.

Maybe the backport option is not so bad after all...

aargh.


Kris

RE: [amide-users] font problem

[Andy L. <lo...@st...>]

On Tue, 29 Jun 2004, Kris Thielemans wrote:

> So, we have the following installed packages
> 
> ii  libfreetype6               2.1.7-1.2.ql.w             FreeType 2 font
> engine, shared library files
> ii  libfreetype6-dev           2.1.7-1.2.ql.w             FreeType 2 font
> engine, development files
> ii  libpango1.0-0              1.0.1-3                    Layout and
> rendering of internationalized text
> ii  libpango1.0-common         1.0.1-3                    Modules and
> configuration files for the Pango
> ii  libpango1.0-dev            1.0.1-3                    Development files
> for the Pango
> ii  fontconfig                 2.2.0-0.1.ql.w             generic font
> configuration library
> ii  libfontconfig1             2.2.0-0.1.ql.w             generic font
> configuration library (shared library)
> ii  libfontconfig1-dev         2.2.0-0.1.ql.w             generic font
> configuration library (development headers)
> 
> and the following compiled libraries in /usr/local/
> freetype-2.0.9
> libgnomecanvas-2.4.0
> (and a lot of other GNOME 2 stuff)
> 
> A mess!

I'm running a vanilla Fedora Core 1 install here.  My packages are:
	pango-1.2.5 (libpango-1.0.so.0.200.5)
	fontconfig-2.2.1 (libfontconfig.so.1.0.4)
	freetype-2.1.4-5 (libfreetype.so.6.3.3)
	libgnomecanvas-2.4.0 (libgnomecanvas-2.so.0.400.0)

Which is fairly comparable to what you've got installed.  My guess would
be that there's some sort of a clash between libgnomecanvas (which you
compiled against your old version of pango and freetype)  and the newly
installed freetype.  Note, that if you've got two different versions of a
library installed and they have the same major number, which library will
be used will be determined by the ordering of the directories in
/etc/ld.so.conf.
 
> I have the impression that the libfreetype6 and libpango1.0 packages we have
> installed are really not compatible, even though the debian package system
> should prevent this from happening. (There's a large amount of stuff on this
> that google throws up, so much that I get very confused by it).
> Unfortunately, the next version of libpango is not yet in the stable
> distribution, so I cannot install that one.
> 
> There are some things that I can try:
> - compile libpango1.0-0 (version 1.0.1-3) from source, using the
> freetype-2.0.9 location as first in the path, an dput that in /usr/local.
> - or compile a more recent version of pango, using the more recent freetype6
> package we have installed. (This will probably lead me into a chain reaction
> of other packages I need to compile from source).
> - go into the murky waters of using gnome 2.2 backports.

I would suggest nuking what you have installed in /usr/local, and
rebuilding (but using the new debian provided fontconfig and pango).
 
> horrible.

I guess there's a reason that the majority of Debian users run testing or
unstable...  They really need to release the next version...
 
Andy

RE: [amide-users] font problem

[Kris T. <kri...@cs...>]

Hi Andy

You probably don't want to help with this. It's pretty horrible. Still any
comments will be appreciated.

> Could you tell me the version numbers of the following:
> 	pango
> 	libgnomecanvas
> 	freetype
>
> In this case the "AMIDE WARNING" isn't actually being generated by AMIDE,
> it's being generated by the underlying libraries.

too bad. that means it will be harder to fix.
on the other hand, it does mean it is due to our installation probably.

as you might remember, we have a woody debian release (i.e. in the 'stable'
distribution), where I compiled gnome 2 packages separately and put them in
our equivalent of /usr/local. This worked fine, until we did some upgrades.
I think that we upgraded the freetype6 package, and then AMIDE. This gave me
problems compiling AMIDE (the missing symbols referenced in
libpangoft2-1.0.so). So, we decided to compile a downgraded freetype6 and
put it in /usr/local. This solved the compilation issues, but results
obviously in a flawed executable as it cannot find some/all of the fonts.

So, we have the following installed packages

ii  libfreetype6               2.1.7-1.2.ql.w             FreeType 2 font
engine, shared library files
ii  libfreetype6-dev           2.1.7-1.2.ql.w             FreeType 2 font
engine, development files
ii  libpango1.0-0              1.0.1-3                    Layout and
rendering of internationalized text
ii  libpango1.0-common         1.0.1-3                    Modules and
configuration files for the Pango
ii  libpango1.0-dev            1.0.1-3                    Development files
for the Pango
ii  fontconfig                 2.2.0-0.1.ql.w             generic font
configuration library
ii  libfontconfig1             2.2.0-0.1.ql.w             generic font
configuration library (shared library)
ii  libfontconfig1-dev         2.2.0-0.1.ql.w             generic font
configuration library (development headers)

and the following compiled libraries in /usr/local/
freetype-2.0.9
libgnomecanvas-2.4.0
(and a lot of other GNOME 2 stuff)

A mess!

I have the impression that the libfreetype6 and libpango1.0 packages we have
installed are really not compatible, even though the debian package system
should prevent this from happening. (There's a large amount of stuff on this
that google throws up, so much that I get very confused by it).
Unfortunately, the next version of libpango is not yet in the stable
distribution, so I cannot install that one.

There are some things that I can try:
- compile libpango1.0-0 (version 1.0.1-3) from source, using the
freetype-2.0.9 location as first in the path, an dput that in /usr/local.
- or compile a more recent version of pango, using the more recent freetype6
package we have installed. (This will probably lead me into a chain reaction
of other packages I need to compile from source).
- go into the murky waters of using gnome 2.2 backports.


horrible.

Kris

PS: now you know why STIR doesn't include anything graphical!

Re: [amide-users] font problem

[Andy L. <lo...@st...>]

Hi Kris,

Could you tell me the version numbers of the following:
	pango
	libgnomecanvas
	freetype

In this case the "AMIDE WARNING" isn't actually being generated by AMIDE, 
it's being generated by the underlying libraries.

Andy

On Mon, 28 Jun 2004, Kris Thielemans wrote:

> Hi Andy
> 
> I probably have a problem with my font installation on my debian system.
> However, Amide doesn't handle it all that graceful... I get the following
> warning box
> 
> 
> AMIDE WARNING: Couldn't load font
> "-*-helvetica-medium-r-normal-*-*-120-*-*-*-*-*-* 10" falling back to "Sans
> 10"
> 
> and I get that some 10 times (have to press OK every time). Not so nice :-)
> 
> Then after loading an image, I get that box a few more times, and then a
> crash with the following message
> 
> ** (process:22819): ERROR (recursed) **: file pango-layout.c: line 2854
> (pango_layout_check_lines): assertion failed: (!layout->log_attrs)
> 
> I don't know if the error is because our Xft set-up is broken, or because
> too deep recursion in AMIDE.
> 
> Anyway, you probably don't want to fix this...
> 
> Kris
> 
> PS: using AMIDE 0.8.6
> 
> 
> 
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