Bug#1027215: How much do we lose if we remove theano (+keras, deepnano, invesalius)?

[Thiago Franco Moraes]

Hi Andreas,

Done! I removed both python3-theano and python3-keras.

Best regards.

Em seg., 16 de jan. de 2023 às 09:54, Andreas Tille 
escreveu:

> Hi Thiago,
>
> Am Sat, Jan 14, 2023 at 07:50:27PM -0300 schrieb Thiago Franco Moraes:
> > Hi Rebecca,
> >
> > InVesalius can work without Theano (and Keras). It will use Pytorch.
>
> Would you mind updating the packaging without Theano?  Currently its in
> its Build-Depends.  Would it be sufficient to drop this Build-Depends?
> If yes, I would upload a fixed package.
>
> Kind regards
>Andreas.
>
> --
> http://fam-tille.de
>

Bug#1027215: How much do we lose if we remove theano (+keras, deepnano, invesalius)?

[Thiago Franco Moraes]

Hi Rebecca,

InVesalius can work without Theano (and Keras). It will use Pytorch.

Best regards.

Em sáb., 14 de jan. de 2023 às 08:12, Rebecca N. Palmer <
rebecca_pal...@zoho.com> escreveu:

> theano has been mostly abandoned upstream since 2018.  (The Aesara fork
> is not abandoned, but includes interface changes including the import
> name, so would break reverse dependencies not specifically altered for it.)
>
> Its reverse dependencies are keras, deepnano and invesalius.
>
> It is currently broken, probably by numpy 1.24 (#1027215), and the
> immediately obvious fixes weren't enough
> (https://salsa.debian.org/science-team/theano/-/pipelines).
>
> Is this worth spending more effort on fixing, or should we just remove it?
>
>
>

Bug#927387: invesalius: crashes after splash screen

[Thiago Franco Moraes]

Hi David,

I think I've found the problem. Devuan is using Python3.7 and
InVesalius-bin was compiled using Python3.6. I tried to rename .so from
*-36m*.so to *-37m*.so it work but with warnings. It's necessary to compile
invesalius-bin to Python3.7. I don't know to proceed in this case.

On Sun, Apr 21, 2019 at 9:52 PM David Paul  wrote:

> > What is the content of the folder /usr/lib/invesalius/invesalius_cy/ ?
>
> ```
> $ ls -AlF /usr/lib/invesalius/invesalius_cy/
> total 1380
> -rw-r--r-- 1 root root 246352 Sep 12  2018
> cy_mesh.cpython-36m-x86_64-linux-gnu.so
> -rw-r--r-- 1 root root 339928 Sep 12  2018
> floodfill.cpython-36m-x86_64-linux-gnu.so
> -rw-r--r-- 1 root root  0 Sep 12  2018 __init__.py
> -rw-r--r-- 1 root root 370080 Sep 12  2018
> interpolation.cpython-36m-x86_64-linux-gnu.so
> -rw-r--r-- 1 root root 200128 Sep 12  2018
> mips.cpython-36m-x86_64-linux-gnu.so
> -rw-r--r-- 1 root root 247424 Sep 12  2018
> transforms.cpython-36m-x86_64-linux-gnu.so
> ```
>

Bug#927387: invesalius: crashes after splash screen

[Thiago Franco Moraes]

Thanks for the bug report.

What is the content of the folder /usr/lib/invesalius/invesalius_cy/ ?
Em 18 de abr de 2019 17:03 -0300, David Paul  escreveu:
> Package: invesalius
> Version: 3.1.2-2
> Severity: grave
>
> Dear Maintainer,
>
> When attempting to run InVesalius for the first time, I am presented
> with the first-run language selector followed by the splash screen,
> but no window ever appears and the invesalius3 process remains active
> until manually terminated. Subsequent run attempts differ only in that
> the language selector is not presented and the invesalius3 process
> terminates on its own.
>
> The following is the console output:
> ```
> $ invesalius3 -d
> /usr/lib/python3/dist-packages/wx/lib/pubsub/__init__.py:25: 
> wxPyDeprecationWarning: wx.lib.pubsub has been deprecated, plese migrate your 
> code to use pypubsub, available on PyPI.
> wx.wxPyDeprecationWarning)
> app.py:234: DeprecationWarning: Yield() is deprecated
> wx.Yield()
> Could not import dl
> /usr/share/invesalius/invesalius/data/transformations.py:1899: UserWarning: 
> failed to import module _transformations
> warnings.warn("failed to import module %s" % name)
> Traceback (most recent call last):
> File "/usr/lib/python3/dist-packages/wx/core.py", line 2228, in Notify
> self.notify()
> File "/usr/lib/python3/dist-packages/wx/core.py", line 3384, in Notify
> self.result = self.callable(*self.args, **self.kwargs)
> File "app.py", line 240, in Startup
> from invesalius.gui.frame import Frame
> File "/usr/share/invesalius/invesalius/gui/frame.py", line 41, in 
> import invesalius.gui.default_tasks as tasks
> File "/usr/share/invesalius/invesalius/gui/default_tasks.py", line 28, in 
> 
> import invesalius.gui.data_notebook as nb
> File "/usr/share/invesalius/invesalius/gui/data_notebook.py", line 40, in 
> 
> import invesalius.data.slice_ as slice_
> File "/usr/share/invesalius/invesalius/data/slice_.py", line 34, in 
> from invesalius.data.mask import Mask
> File "/usr/share/invesalius/invesalius/data/mask.py", line 33, in 
> from invesalius_cy import floodfill
> ImportError: cannot import name 'floodfill' from 'invesalius_cy' 
> (/usr/lib/invesalius/invesalius_cy/__init__.py)
> Traceback (most recent call last):
> File "/usr/lib/python3/dist-packages/wx/core.py", line 2228, in Notify
> self.notify()
> File "/usr/lib/python3/dist-packages/wx/core.py", line 3384, in Notify
> self.result = self.callable(*self.args, **self.kwargs)
> File "app.py", line 123, in Startup2
> self.control = self.splash.control
> AttributeError: 'Inv3SplashScreen' object has no attribute 'control'
> Traceback (most recent call last):
> File "app.py", line 264, in OnClose
> if self.fc.IsRunning():
> AttributeError: 'Inv3SplashScreen' object has no attribute 'fc'
> ```
>
> -- System Information:
> Distributor ID: Devuan
> Description: Devuan GNU/Linux 3.0 (Beowulf)
> Release: 3.0
> Codename: beowulf
> Architecture: x86_64
>
> Kernel: Linux 4.19.29-gnu (SMP w/16 CPU cores)
> Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), 
> LANGUAGE=en_US.UTF-8 (charmap=UTF-8)
> Shell: /bin/sh linked to /bin/dash
> Init: sysvinit (via /sbin/init)
>
> Versions of packages invesalius depends on:
> ii invesalius-bin 3.1.2-2
> ii python3 3.7.2-1
> ii python3-gdcm 2.8.8-6
> ii python3-nibabel 2.3.2-1
> ii python3-numpy 1:1.16.2-1
> ii python3-pil 5.4.1-2
> ii python3-psutil 5.5.1-1
> ii python3-scipy 1.1.0-3
> ii python3-serial 3.4-4
> ii python3-skimage 0.14.2-2
> ii python3-vtk7 7.1.1+dfsg1-12+b1
> ii python3-vtkgdcm 2.8.8-6
> ii python3-wxgtk4.0 4.0.4+dfsg-2
>
> invesalius recommends no packages.
>
> invesalius suggests no packages.
>
> -- no debconf information
>

Bug#901562: invesalius is marked for autoremoval from testing

[Thiago Franco Moraes]

Hi Andreas,

Thanks, I can push to repository now. I've pushed both the master and
upstream/3.1.1

Best regards

On Sat, Aug 18, 2018 at 2:32 AM Andreas Tille  wrote:
>
> Hi Thiago,
>
> On Fri, Aug 17, 2018 at 09:12:46PM -0300, Thiago Franco Moraes wrote:
> > I' ve created a merge request in the Debian Salsa with a new version
> > tag (3.1.9991) of InVesalius. This new version fixes the bug #901562.
>
> I've added you to the Debian Med team now.  Please check whether you
> can push directly to the repository.
> > This package is not using Python3 because there is not a
> > pyhton3-vtkgdcm package in Debian Testing. But InVesalius is already
> > running with Python3.
>
> I've just opened a bug against gdcm to ask for Python3 support.  As
> I understood Gerd in #895900 this is planed and was just delayed due
> to Invesalius.  So I think we can expect pyhton3-vtkgdcm soon.
>
> Thanks for your work on this
>
>   Andreas.
>
> --
> http://fam-tille.de

Bug#901562: invesalius is marked for autoremoval from testing

[Thiago Franco Moraes]

Hi Andreas,

I' ve created a merge request in the Debian Salsa with a new version
tag (3.1.9991) of InVesalius. This new version fixes the bug #901562.
This package is not using Python3 because there is not a
pyhton3-vtkgdcm package in Debian Testing. But InVesalius is already
running with Python3.

Best regards
On Wed, Jul 11, 2018 at 12:35 PM Andreas Tille  wrote:
>
> On Wed, Jul 11, 2018 at 12:18:28PM -0300, Thiago Franco Moraes wrote:
> >
> > I was thinking the second option. I'll create a new version tag,
> > something like 3.1.9997, then I'll have a tarball with this version.
> > Also, I'll package it using Python3.
>
> Perfect.
>
> Kind regards
>
>Andreas.
>
> --
> http://fam-tille.de

Bug#901562: invesalius is marked for autoremoval from testing

[Thiago Franco Moraes]

Hi Andreas,

On Wed, Jul 11, 2018 at 3:30 AM Andreas Tille  wrote:
>
> Hi Thiago,
>
> On Tue, Jul 10, 2018 at 09:39:12PM -0300, Thiago Franco Moraes wrote:
> > I think the easiest way to fix this bug is to package the git version.
> > Also, the git version is already working with Python3. What do you
> > think?
>
> I have no opinion about what code works better - that's perfectly your
> decision as upstream and probably active user.  While we could even turn
> the debian/watch file to git mode which fetches the lastet Git commit
> I'm afraid that this is always in flux.  What do you think about an
> early beta release and we use this tarball until there is a stable
> version of the next release?  The thing is that also non-Debian users
> might stumble upon the issues.  If you can refer those users to such a
> release that might have some users that have tested exactly this code
> and not a random Git commit this could have some advantages.
>
> What do you think about this suggestion?

I was thinking the second option. I'll create a new version tag,
something like 3.1.9997, then I'll have a tarball with this version.
Also, I'll package it using Python3.

Kind regards.

> Kind regards
>
>Andreas.
>
> --
> http://fam-tille.de
>

Bug#901562: invesalius is marked for autoremoval from testing

[Thiago Franco Moraes]

Hi Andreas,

I think the easiest way to fix this bug is to package the git version.
Also, the git version is already working with Python3. What do you
think?

Best regards.
On Tue, Jul 10, 2018 at 3:27 AM Andreas Tille  wrote:
>
> Hi Thiago,
>
> any news about this?  Note that bug #901377 is fixed so we need to
> concentrate only on #901562.  Are you able to reproduce the issue or do
> you need more information from the bug reporter?
>
> Kind regards
>
>Andreas.
>
>
> On Tue, Jul 10, 2018 at 04:39:04AM +, Debian testing autoremoval watch 
> wrote:
> > invesalius 3.1.1-3 is marked for autoremoval from testing on 2018-07-26
> >
> > It is affected by these RC bugs:
> > 901562: invesalius: Segmentation fault at startup
> >
> > It (build-)depends on packages with these RC bugs:
> > 901377: skimage: FTBFS and Debci failure with NumPy 1.14
>
> --
> http://fam-tille.de

Bug#901562: invesalius: Segmentation fault at startup

[Thiago Franco Moraes]

Hi Andreas,

I reported the bug to the python-vtk6 package. Here the link
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=902125

This bug will continue to open or do I have to do something to close it?

Best regards,
Thiago Franco de Moraes

Bug#902125: Segmentation fault at wxVTKRenderWindowInteractor

[Thiago Franco Moraes]

Package: python-vtk6
Version: 6.3.0+dfsg2-2+b2

When I run a python software that uses wxVTKRenderWindowInteractor a
segmentation fault happens. This segmentation fault doesn't happen
when the window manager is KDE. This segmentation fault happens when
run in Gnome-shell and XFCE4. I haven' t tested with other window
managers. If used wxpython4, this segmentation fault doesn't happen,
in any window manager, it just happens if used wxpython3.

A simple code to test this is:


from vtk.wx.wxVTKRenderWindowInteractor import
wxVTKRenderWindowInteractorConeExample
wxVTKRenderWindowInteractorConeExample()


Please, see this bug for more informations
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=901562

Best regards.

Bug#901562: invesalius: Segmentation fault at startup

[Thiago Franco Moraes]

 wxEvtHandler::SafelyProcessEvent(wxEvent&) ()
> from /usr/lib/x86_64-linux-gnu/libwx_baseu-3.0.so.0
> #33 0x74dd4557 in wxWindow::DoSetSize(int, int, int, int, int)
> () from /usr/lib/x86_64-linux-gnu/libwx_gtk3u_core-3.0.so.0
> #34 0x74dd661d in wxWindow::DoSetClientSize(int, int) () from
> /usr/lib/x86_64-linux-gnu/libwx_gtk3u_core-3.0.so.0
> #35 0x74f649a7 in wxSizer::Fit(wxWindow*) () from
> /usr/lib/x86_64-linux-gnu/libwx_gtk3u_core-3.0.so.0
> #36 0x76043941 in ?? () from
> /usr/lib/python2.7/dist-packages/wx-3.0-gtk3/wx/_core_.x86_64-linux-gnu.so
> #37 0x5564f874 in PyEval_EvalFrameEx ()
> #38 0x55646c7a in PyEval_EvalCodeEx ()
> #39 0x5564edb4 in PyEval_EvalFrameEx ()
> #40 0x5564e3e2 in PyEval_EvalFrameEx ()
> #41 0x55646c7a in PyEval_EvalCodeEx ()
> #42 0x55662b09 in ?? ()
> #43 0x5567b2be in ?? ()
> #44 0x5567aeca in ?? ()
> #45 0x55637afb in ?? ()
> #46 0x5564e5d0 in PyEval_EvalFrameEx ()
> #47 0x5564e3e2 in PyEval_EvalFrameEx ()
> #48 0x55646c7a in PyEval_EvalCodeEx ()
> #49 0x55662b09 in ?? ()
> #50 0x5567b2be in ?? ()
> #51 0x5567aeca in ?? ()
> #52 0x55637afb in ?? ()
> #53 0x5564e5d0 in PyEval_EvalFrameEx ()
> #54 0x5564e3e2 in PyEval_EvalFrameEx ()
> #55 0x55646c7a in PyEval_EvalCodeEx ()
> #56 0x55662b09 in ?? ()
> #57 0x5567b2be in ?? ()
> #58 0x5567aeca in ?? ()
> #59 0x55637afb in ?? ()
> #60 0x5564e5d0 in PyEval_EvalFrameEx ()
> #61 0x55646c7a in PyEval_EvalCodeEx ()
> #62 0x55662d9d in ?? ()
> #63 0x5563290e in PyObject_Call ()
> #64 0x5564b6d3 in PyEval_EvalFrameEx ()
> #65 0x5564e3e2 in PyEval_EvalFrameEx ()
> #66 0x55646c7a in PyEval_EvalCodeEx ()
> #67 0x55662b09 in ?? ()
> #68 0x5567b2be in ?? ()
> #69 0x5563290e in PyObject_Call ()
> #70 0x556529f0 in PyEval_CallObjectWithKeywords ()
> #71 0x75fa915e in wxPyCallbackHelper::callCallbackObj(_object*)
> const () from
> /usr/lib/python2.7/dist-packages/wx-3.0-gtk3/wx/_core_.x86_64-linux-gnu.so
> #72 0x75fa91cd in wxPyCallbackHelper::callCallback(_object*)
> const () from
> /usr/lib/python2.7/dist-packages/wx-3.0-gtk3/wx/_core_.x86_64-linux-gnu.so
> #73 0x7fffe8a05f03 in wxPyTimer::Notify() () from
> /usr/lib/python2.7/dist-packages/wx-3.0-gtk3/wx/_misc_.x86_64-linux-gnu.so
> #74 0x74dcc2c1 in ?? () from
> /usr/lib/x86_64-linux-gnu/libwx_gtk3u_core-3.0.so.0
> #75 0x7241bb73 in ?? () from
> /usr/lib/x86_64-linux-gnu/libglib-2.0.so.0
> #76 0x7241b0f5 in g_main_context_dispatch () from
> /usr/lib/x86_64-linux-gnu/libglib-2.0.so.0
> #77 0x7241b4c0 in ?? () from
> /usr/lib/x86_64-linux-gnu/libglib-2.0.so.0
> #78 0x7241b7d2 in g_main_loop_run () from
> /usr/lib/x86_64-linux-gnu/libglib-2.0.so.0
> #79 0x735e3e85 in gtk_main () from
> /usr/lib/x86_64-linux-gnu/libgtk-3.so.0
> #80 0x74db9cc5 in wxGUIEventLoop::DoRun() () from
> /usr/lib/x86_64-linux-gnu/libwx_gtk3u_core-3.0.so.0
> #81 0x742ffea3 in wxEventLoopBase::Run() () from
> /usr/lib/x86_64-linux-gnu/libwx_baseu-3.0.so.0
> #82 0x742c74b6 in wxAppConsoleBase::MainLoop() () from
> /usr/lib/x86_64-linux-gnu/libwx_baseu-3.0.so.0
> #83 0x75faf027 in wxPyApp::MainLoop() () from
> /usr/lib/python2.7/dist-packages/wx-3.0-gtk3/wx/_core_.x86_64-linux-gnu.so
> #84 0x7600ad45 in ?? () from
> /usr/lib/python2.7/dist-packages/wx-3.0-gtk3/wx/_core_.x86_64-linux-gnu.so
> #85 0x5564f874 in PyEval_EvalFrameEx ()
> #86 0x55646c7a in PyEval_EvalCodeEx ()
> #87 0x55662b09 in ?? ()
> #88 0x5567b2be in ?? ()
> #89 0x5564e5d0 in PyEval_EvalFrameEx ()
> #90 0x5564e3e2 in PyEval_EvalFrameEx ()
> #91 0x5564e3e2 in PyEval_EvalFrameEx ()
> #92 0x55646c7a in PyEval_EvalCodeEx ()
> #93 0x55646709 in PyEval_EvalCode ()
> #94 0x5567771f in ?? ()
> #95 0x55672472 in PyRun_FileExFlags ()
> #96 0x556718ed in PyRun_SimpleFileExFlags ()
> #97 0x55620a2b in Py_Main ()
> #98 0x76e69a87 in __libc_start_main () from
> /lib/x86_64-linux-gnu/libc.so.6
> #99 0x556202aa in _start ()
> (gdb) quit
>
> if this is useful...
>
> Best regards,
> Torquil Sørensen
>
> On 15/06/18 23:19, Thiago Franco Moraes wrote:
> > Hi,
> >
> > What window manager are your using? I don't why yet, but this error
> > doesn't happen if you use KDE as window manager. It's happening also
> > with the git version (ht

Bug#901562: invesalius: Segmentation fault at startup

[Thiago Franco Moraes]

Hi,

What window manager are your using? I don't why yet, but this error
doesn't happen if you use KDE as window manager. It's happening also
with the git version (https://github.com/invesalius/invesalius3). If
you use the WXPython4 this doesn't happen, but you need to use the git
version.

Thanks for the bug report.
On Thu, Jun 14, 2018 at 3:27 PM Torquil Macdonald Sørensen
 wrote:
>
> Package: invesalius
> Version: 3.1.1-3
> Severity: grave
> Justification: renders package unusable
>
> When trying to run invesalius, I get this segmentation fault:
>
> torquil@lenovo-p51:~$ invesalius3
> /usr/share/invesalius/invesalius/data/transformations.py:1899: UserWarning: 
> failed to import module _transformations
>   warnings.warn("failed to import module %s" % name)
>   session mode:  0
>   Segmentation fault
> torquil@lenovo-p51:~$
>
> Best regards,
> Torquil Sørensen
>
> -- System Information:
> Debian Release: buster/sid
>   APT prefers unstable
>   APT policy: (500, 'unstable')
> Architecture: amd64 (x86_64)
>
> Kernel: Linux 4.16.0-2-amd64 (SMP w/8 CPU cores)
> Locale: LANG=en_GB.UTF-8, LC_CTYPE=en_GB.UTF-8 (charmap=UTF-8), 
> LANGUAGE=en_GB:en (charmap=UTF-8)
> Shell: /bin/sh linked to /bin/dash
> Init: systemd (via /run/systemd/system)
>
> Versions of packages invesalius depends on:
> ii  invesalius-bin 3.1.1-3
> ii  python 2.7.15-3
> ii  python-concurrent.futures  3.2.0-1
> ii  python-configparser3.5.0-1
> ii  python-gdcm2.8.6-2
> ii  python-nibabel 2.3.0-1
> ii  python-numpy   1:1.14.5-1
> ii  python-pil 5.1.0-1
> ii  python-psutil  5.4.6-1
> ii  python-scipy   0.19.1-2
> ii  python-serial  3.4-3
> ii  python-skimage 0.13.1-3
> ii  python-vtk66.3.0+dfsg2-2+b2
> ii  python-vtkgdcm 2.8.6-2
> ii  python-wxgtk3.03.0.2.0+dfsg-8
> ii  python2.7  2.7.15-1
>
> invesalius recommends no packages.
>
> invesalius suggests no packages.
>
> -- no debconf information

Bug#779655: invesalius: "ZeroDivisionError: float division by zero" upon importing DICOM X-ray videos

[Thiago Franco Moraes]

Thanks for your help, Andreas.

On Fri, Sep 15, 2017 at 1:23 PM Andreas Tille <andr...@fam-tille.de> wrote:

> On Fri, Sep 15, 2017 at 03:03:11PM +0000, Thiago Franco Moraes wrote:
> > Andreas, yes, if it's possible.
>
> Done.  Thank you for your contribution
>
>   Andreas.
>
> --
> http://fam-tille.de
>

Bug#779655: invesalius: "ZeroDivisionError: float division by zero" upon importing DICOM X-ray videos

[Thiago Franco Moraes]

Andreas, yes, if it's possible.

On Fri, Sep 15, 2017 at 12:00 PM Andreas Tille <andr...@fam-tille.de> wrote:

> Hi Thiago,
>
> On Fri, Sep 15, 2017 at 01:52:37PM +, Thiago Franco Moraes wrote:
> > I committed the patch to debian-med git repo of InVesalius. Also, I'll
> > commit it to the upstream.
>
> Since your changes are a bit more than the simple patch by Gert:  Do you
> want me to upload your changes quickly since this all is needed to fix
> the issue?
>
> Thanks a lot for your quick response - its fun to work together with
> responsive upstream developers
>
>   Andreas.
>
> --
> http://fam-tille.de
>

Bug#779655: invesalius: "ZeroDivisionError: float division by zero" upon importing DICOM X-ray videos

[Thiago Franco Moraes]

I committed the patch to debian-med git repo of InVesalius. Also, I'll
commit it to the upstream.

On Fri, Sep 15, 2017 at 9:45 AM Thiago Franco Moraes <totonixs...@gmail.com>
wrote:

> Hi Andreas,
>
> I tested here the patch, it's not working with case it tries to fix. I'm
> hacking here a fix, it almost complete. I'll submit here the patch and I'll
> put it in the upstream.
>
> Thanks!
>
> On Fri, Sep 15, 2017 at 6:09 AM Andreas Tille <andr...@an3as.eu> wrote:
>
>> On Fri, Sep 15, 2017 at 10:38:51AM +0200, Gert Wollny wrote:
>> > Patch pushed to packaging git, but someone should test it on real data.
>>
>> Ahhh, I've first seen the commit message and just uploaded since I was
>> at it.  I think uploading and enabling users to easily test via the
>> package makes sense anyway.  We could reopen if the issue persists.
>>
>> Thanks a lot in any case
>>
>>  Andreas.
>>
>> --
>> http://fam-tille.de
>>
>>

Bug#779655: invesalius: "ZeroDivisionError: float division by zero" upon importing DICOM X-ray videos

[Thiago Franco Moraes]

Hi Andreas,

I tested here the patch, it's not working with case it tries to fix. I'm
hacking here a fix, it almost complete. I'll submit here the patch and I'll
put it in the upstream.

Thanks!

On Fri, Sep 15, 2017 at 6:09 AM Andreas Tille  wrote:

> On Fri, Sep 15, 2017 at 10:38:51AM +0200, Gert Wollny wrote:
> > Patch pushed to packaging git, but someone should test it on real data.
>
> Ahhh, I've first seen the commit message and just uploaded since I was
> at it.  I think uploading and enabling users to easily test via the
> package makes sense anyway.  We could reopen if the issue persists.
>
> Thanks a lot in any case
>
>  Andreas.
>
> --
> http://fam-tille.de
>
>

Bug#779655: invesalius: ZeroDivisionError: float division by zero upon importing DICOM X-ray videos

[Thiago Franco Moraes]

Hi Andreas and Axel,

We've not tested InVesalius with X-ray videos yet. Probably it does not
work, because InVesalius is directed to work with CT, µCT and MRI. Your
error must be because we make some assumptions about the dicom file which
are not appropriate to x-ray videos.

Axel, if possible, could you please send me x-ray dicom file? So I can
investigate if it's possible to open this file in InVesalius.

Thanks!

On Tue, Mar 3, 2015 at 5:21 PM Andreas Tille ti...@debian.org wrote:

 Hi Axel,

 thanks for your bug report.  I hope you are fine and do not need to
 diagnose your own. ;-)  I have put Thiago in  CC (in case he might have
 missed the bug report).  He has close connection to upstream and will
 surely work on fixing the issue.

 As an independant hint you might like to try ginkgocadx, amide and
 aeskulap (in this order) to perhaps see what you want to see.  Any
 reports about these would be welcome as well.

 Kind regards

  Andreas.

 On Tue, Mar 03, 2015 at 06:00:56PM +0100, Axel Beckert wrote:
  Package: invesalius
  Version: 3.0~b5-4
  Severity: normal
 
  Hi,
 
  thanks for packaging software for Debian which enables me to view my own
  medical data on my own and Debian running computer! :-)
 
  I've tried to view some X-ray videos in DICOM format with Invesalius and
  when I want to import them it shows me that there 8 videos (or images,
  not 100% sure) to import, but as soon as I click on the Import button,
  I get an empty (0%) progress bar popup and the following Python
  stacktrace on the commandline where I started Invesalius:
 
  Traceback (most recent call last):
File /usr/share/invesalius/invesalius/gui/import_panel.py, line
 171, in OnClickOk
  self.LoadDicom(group)
File /usr/share/invesalius/invesalius/gui/import_panel.py, line
 191, in LoadDicom
  [self.first_image_selection, self.last_image_selection]))
File /usr/lib/python2.7/dist-packages/wx-3.0-gtk2/wx/lib/
 pubsub/core/arg1/publisher.py, line 36, in sendMessage
  topicObj.publish(data)
File /usr/lib/python2.7/dist-packages/wx-3.0-gtk2/wx/lib/
 pubsub/core/arg1/publishermixin.py, line 23, in publish
  self._publish(data)
File 
  /usr/lib/python2.7/dist-packages/wx-3.0-gtk2/wx/lib/pubsub/core/topicobj.py,
 line 376, in _publish
  self.__sendMessage(data, self, iterState)
File 
  /usr/lib/python2.7/dist-packages/wx-3.0-gtk2/wx/lib/pubsub/core/topicobj.py,
 line 397, in __sendMessage
  self._mix_callListener(listener, data, iterState)
File /usr/lib/python2.7/dist-packages/wx-3.0-gtk2/wx/lib/
 pubsub/core/arg1/publishermixin.py, line 34, in _mix_callListener
  listener(self, data)
File /usr/lib/python2.7/dist-packages/wx-3.0-gtk2/wx/lib/
 pubsub/core/arg1/listenerimpl.py, line 51, in __call__
  cb(msg, **kwargs)
File /usr/share/invesalius/invesalius/control.py, line 486, in
 OnOpenDicomGroup
  matrix, matrix_filename, dicom = self.OpenDicomGroup(group,
 interval, file_range, gui=True)
File /usr/share/invesalius/invesalius/control.py, line 542, in
 OpenDicomGroup
  orientation, resolution_percentage)
File /usr/share/invesalius/invesalius/data/imagedata_utils.py, line
 425, in dcm2memmap
  update_progress= vtk_utils.ShowProgress(len(files) - 1, dialog_type
 = ProgressDialog)
File /usr/share/invesalius/invesalius/data/vtk_utils.py, line 52,
 in ShowProgress
  ratio = (100.0 / number_of_filters)
  ZeroDivisionError: float division by zero
 
  (I could import and view my computer tomography data without issues into
  Invesalius, so it's not a general issue, maybe just with some specific
  data formats or even with some specific data.)
 
  -- System Information:
  Debian Release: 8.0
APT prefers testing-updates
APT policy: (500, 'testing-updates'), (500,
 'testing-proposed-updates'), (500, 'testing')
  Architecture: amd64 (x86_64)
 
  Kernel: Linux 3.16.0-4-amd64 (SMP w/2 CPU cores)
  Locale: LANG=en_GB.UTF-8, LC_CTYPE=en_GB.UTF-8 (charmap=UTF-8)
  Shell: /bin/sh linked to /bin/dash
  Init: sysvinit (via /sbin/init)
 
  Versions of packages invesalius depends on:
  ii  invesalius-bin  3.0~b5-4
  ii  python-casmoothing  0.1-2
  ii  python-gdcm 2.4.4-3
  ii  python-imaging  2.6.1-1
  ii  python-nibabel  1.3.0-2
  ii  python-numpy1:1.8.2-2
  ii  python-psutil   2.1.1-1+b1
  ii  python-scipy0.14.0-2
  ii  python-serial   2.6-1.1
  ii  python-vtk  5.8.0-17.5
  ii  python-vtkgdcm  2.4.4-3
  ii  python-wxgtk3.0 3.0.1.1+dfsg-2
  pn  python2.7:any   none
  pn  python:any  none
 
  invesalius recommends no packages.
 
  invesalius suggests no packages.
 
  -- no debconf information
 
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  debian-med-packag...@lists.alioth.debian.org
  http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/
 debian-med-packaging
 

 --
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Bug#779655: invesalius: ZeroDivisionError: float division by zero upon importing DICOM X-ray videos

[Thiago Franco Moraes]

Hi Axel,

No, dicomdir is not enough. Well, I'll try to find on the internet some
dicom samples.

Thanks!

On Wed, Mar 4, 2015 at 10:32 AM Axel Beckert a...@debian.org wrote:

 Hi Thiago,

 Thiago Franco Moraes wrote:
  We've not tested InVesalius with X-ray videos yet. Probably it does not
  work, because InVesalius is directed to work with CT, 湣T and MRI. Your
  error must be because we make some assumptions about the dicom file which
  are not appropriate to x-ray videos.

 That explains it well. :-)

  Axel, if possible, could you please send me x-ray dicom file? So I can
  investigate if it's possible to open this file in InVesalius.

 Does that dicomdir file suffice? It's 412kB and seems to be a kind of
 index file for the actual image and data files. The whole set of files
 is about 500 MB and I don't really want to have to put these files
 anywhere online.

 Regards, Axel
 --
  ,''`.  |  Axel Beckert a...@debian.org, http://people.debian.org/~abe/
 : :' :  |  Debian Developer, ftp.ch.debian.org Admin
 `. `'   |  4096R: 2517 B724 C5F6 CA99 5329  6E61 2FF9 CD59 6126 16B5
   `-|  1024D: F067 EA27 26B9 C3FC 1486  202E C09E 1D89 9593 0EDE

Bug#759060: [o...@survex.com: Bug#759060: invesalius: Partial patch for wxPython 3.0]

[Thiago Franco Moraes]

Hi Olly,

I tested it here inside a VM. It's working now! Thanks! There are some
problems with the widgets layouts and placements, but everything seems
to work. I'll try to solve these problems.

If you want to test, here [1] you have some dicom files.

[1] - http://www.cti.gov.br/invesalius/?page_id=8

On Sat, Sep 13, 2014 at 11:34 PM, Olly Betts o...@survex.com wrote:
 On Sat, Sep 13, 2014 at 02:10:42PM -0300, Olly Betts wrote:
 On Wed, Sep 10, 2014 at 04:25:23PM -0300, Thiago Franco Moraes wrote:
  I don't know if it's my setup here. But I think there is a problem in
  the interaction between VTK5.8 and wxPython3, it was already reported
  here [1], and is the same problem that Olly Betts reported some emails
  ago. I installed Debian Testing inside a VirtualBox VM. The wxPyhon
  version in 3.0, and VTK is 5.8. The error happens even with this
  simple python script:
 
  script
  from vtk.wx.wxVTKRenderWindowInteractor import
  wxVTKRenderWindowInteractorConeExample
  wxVTKRenderWindowInteractorConeExample()
  /script
 
  Please, could you, please run this script in your setup?

 Fails for me.  It seems that python-vtk needs an update for this
 transition.  It however appears to lack any sort of dependency on
 wx at all, which makes this hard to discover.

 I'll file a bug.

 OK, I filed bugs earlier for vtk and vtk6, and started a vtk build with
 a fix for this which finally completed and I've now added a patch to the
 vtk bug.

 With the patched vtk, invesalius-3.0 actually starts up the GUI.

 It seems to take hours to build vtk (at least on my laptop) so to help
 if you want to test further, I've uploaded the rebuilt python-vtk
 package and a detached GPG signature:

 http://survex.com/~olly/python-vtk_5.8.0-17.4_amd64.deb
 http://survex.com/~olly/python-vtk_5.8.0-17.4_amd64.deb.sig

 You should be able to install the .deb with:

 sudo dpkg -i python-vtk_5.8.0-17.4_amd64.deb

 Cheers,
 Olly


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Bug#759060: [o...@survex.com: Bug#759060: invesalius: Partial patch for wxPython 3.0]

[Thiago Franco Moraes]

Hi again Andreas,

I don't know if it's my setup here. But I think there is a problem in
the interaction between VTK5.8 and wxPython3, it was already reported
here [1], and is the same problem that Olly Betts reported some emails
ago. I installed Debian Testing inside a VirtualBox VM. The wxPyhon
version in 3.0, and VTK is 5.8. The error happens even with this
simple python script:

script
from vtk.wx.wxVTKRenderWindowInteractor import
wxVTKRenderWindowInteractorConeExample
wxVTKRenderWindowInteractorConeExample()
/script

Please, could you, please run this script in your setup?

Ah, I've created a branch to port invesalius to wxPython3.

Best regards!

[1] - https://groups.google.com/forum/#!topic/wxpython-users/MxJPxlOS05A

On Wed, Sep 10, 2014 at 9:52 AM, Thiago Franco Moraes
tfmor...@cti.gov.br wrote:
 Hi Andreas,

 Thanks for notify me about this patch. I was a little off, so I
 haven't seen it. I have a branch of invesalius which works with
 wxpython3, at least in MacOSX. I'm going to test it in Debian and see
 if it works, and if works I'll generate a patch and create new debian
 package with this patch applied.

 Best regards!

 On Wed, Sep 10, 2014 at 3:02 AM, Andreas Tille andr...@an3as.eu wrote:
 Hi Thiago,

 in case you missed this partial patch.  Please note that even if there
 are about six weeks the Freeze for Jessie is approaching and we should
 get this straight in the next couple of weeks.

 Kind regards

 Andreas.

 - Forwarded message from Olly Betts o...@survex.com -

 Date: Tue, 9 Sep 2014 21:19:21 -0300
 From: Olly Betts o...@survex.com
 To: 759...@bugs.debian.org
 Subject: Bug#759060: invesalius: Partial patch for wxPython 3.0
 X-Debian-PR-Message: followup 759060
 X-Debian-PR-Package: src:invesalius
 X-Debian-PR-Keywords: jessie sid
 X-Debian-PR-Source: invesalius

 I've had a look at updating invesalius for wxpython3.0, and made some
 progress.

 However, the startup still isn't clean - the splash screen throws up
 several errors - see invesalius.wxpy3.0.log - and once the app fires up,
 there are clearly issues with the sizing of widgets, to the extent that
 it isn't usable.  I'm not sure if these are as a result of the splash
 screen errors or not.

 The logic in the splashscreen code seems hard to follow, relying on
 several different delayed callbacks.  I wonder if it's just inherently
 racy, and a timing difference causes the failures with wxpython 3.0.

 Anyway, I'm giving up on this one for the moment, but thought I should
 at least send the patch I have so far to avoid duplicated effort if you
 were also looking at it.

 Cheers,
 Olly

 diff -Nru invesalius-3.0~b5/debian/changelog 
 invesalius-3.0~b5/debian/changelog
 --- invesalius-3.0~b5/debian/changelog  2014-06-16 09:01:59.0 -0300
 +++ invesalius-3.0~b5/debian/changelog  2014-09-09 21:00:48.0 -0300
 @@ -1,3 +1,11 @@
 +invesalius (3.0~b5-3.1) unstable; urgency=medium
 +
 +  * Non-maintainer upload.
 +  * Update for wxPython 3.0 (Closes: #759060):
 ++ New patch: wxpython3.0.patch
 +
 + -- Olly Betts o...@survex.com  Wed, 10 Sep 2014 00:00:33 +
 +
  invesalius (3.0~b5-3) unstable; urgency=low

[ Thiago Franco de Moraes ]
 diff -Nru invesalius-3.0~b5/debian/control invesalius-3.0~b5/debian/control
 --- invesalius-3.0~b5/debian/control2014-06-16 09:00:44.0 -0300
 +++ invesalius-3.0~b5/debian/control2014-09-09 20:03:09.0 -0300
 @@ -22,7 +22,7 @@
   ${misc:Depends},
   python-numpy,
   python-scipy,
 - python-wxgtk2.8 (= 2.8.12),
 + python-wxgtk3.0,
   python-imaging,
   python-vtk,
   python-gdcm,
 diff -Nru invesalius-3.0~b5/debian/patches/series 
 invesalius-3.0~b5/debian/patches/series
 --- invesalius-3.0~b5/debian/patches/series 2014-04-28 
 13:21:20.0 -0300
 +++ invesalius-3.0~b5/debian/patches/series 2014-09-09 
 20:03:43.0 -0300
 @@ -1,2 +1,3 @@
  10_sample_path.patch
  10_import_mips.patch
 +wxpython3.0.patch
 diff -Nru invesalius-3.0~b5/debian/patches/wxpython3.0.patch 
 invesalius-3.0~b5/debian/patches/wxpython3.0.patch
 --- invesalius-3.0~b5/debian/patches/wxpython3.0.patch  1969-12-31 
 21:00:00.0 -0300
 +++ invesalius-3.0~b5/debian/patches/wxpython3.0.patch  2014-09-09 
 21:00:03.0 -0300
 @@ -0,0 +1,114 @@
 +Description: Update for wxPython 3.0
 + These changes should remain compatible with wxPython 2.8, aside from the
 + wxversion change in the last hunk.
 + .
 + We can't simply drop the wxversion.select() call and use
 + .
 + wxversion.ensureMinimal('2.8-unicode', optionsRequired=True)
 + .
 + because 3.0 is always Unicode, and the -unicode option has been dropped,
 + but wxversion isn't smart enough to know to allow for this when matching
 + options.
 +Bug-Debian: https://bugs.debian.org/759060
 +Forwarded: no
 +Last-Update: 2014-09-09
 +
 +--- invesalius-3.0~b5.orig/invesalius/gui/dialogs.py
  invesalius-3.0~b5/invesalius/gui

Bug#759060: [o...@survex.com: Bug#759060: invesalius: Partial patch for wxPython 3.0]

[Thiago Franco Moraes]

Hi Andreas,

Thanks for notify me about this patch. I was a little off, so I
haven't seen it. I have a branch of invesalius which works with
wxpython3, at least in MacOSX. I'm going to test it in Debian and see
if it works, and if works I'll generate a patch and create new debian
package with this patch applied.

Best regards!

On Wed, Sep 10, 2014 at 3:02 AM, Andreas Tille andr...@an3as.eu wrote:
 Hi Thiago,

 in case you missed this partial patch.  Please note that even if there
 are about six weeks the Freeze for Jessie is approaching and we should
 get this straight in the next couple of weeks.

 Kind regards

 Andreas.

 - Forwarded message from Olly Betts o...@survex.com -

 Date: Tue, 9 Sep 2014 21:19:21 -0300
 From: Olly Betts o...@survex.com
 To: 759...@bugs.debian.org
 Subject: Bug#759060: invesalius: Partial patch for wxPython 3.0
 X-Debian-PR-Message: followup 759060
 X-Debian-PR-Package: src:invesalius
 X-Debian-PR-Keywords: jessie sid
 X-Debian-PR-Source: invesalius

 I've had a look at updating invesalius for wxpython3.0, and made some
 progress.

 However, the startup still isn't clean - the splash screen throws up
 several errors - see invesalius.wxpy3.0.log - and once the app fires up,
 there are clearly issues with the sizing of widgets, to the extent that
 it isn't usable.  I'm not sure if these are as a result of the splash
 screen errors or not.

 The logic in the splashscreen code seems hard to follow, relying on
 several different delayed callbacks.  I wonder if it's just inherently
 racy, and a timing difference causes the failures with wxpython 3.0.

 Anyway, I'm giving up on this one for the moment, but thought I should
 at least send the patch I have so far to avoid duplicated effort if you
 were also looking at it.

 Cheers,
 Olly

 diff -Nru invesalius-3.0~b5/debian/changelog 
 invesalius-3.0~b5/debian/changelog
 --- invesalius-3.0~b5/debian/changelog  2014-06-16 09:01:59.0 -0300
 +++ invesalius-3.0~b5/debian/changelog  2014-09-09 21:00:48.0 -0300
 @@ -1,3 +1,11 @@
 +invesalius (3.0~b5-3.1) unstable; urgency=medium
 +
 +  * Non-maintainer upload.
 +  * Update for wxPython 3.0 (Closes: #759060):
 ++ New patch: wxpython3.0.patch
 +
 + -- Olly Betts o...@survex.com  Wed, 10 Sep 2014 00:00:33 +
 +
  invesalius (3.0~b5-3) unstable; urgency=low

[ Thiago Franco de Moraes ]
 diff -Nru invesalius-3.0~b5/debian/control invesalius-3.0~b5/debian/control
 --- invesalius-3.0~b5/debian/control2014-06-16 09:00:44.0 -0300
 +++ invesalius-3.0~b5/debian/control2014-09-09 20:03:09.0 -0300
 @@ -22,7 +22,7 @@
   ${misc:Depends},
   python-numpy,
   python-scipy,
 - python-wxgtk2.8 (= 2.8.12),
 + python-wxgtk3.0,
   python-imaging,
   python-vtk,
   python-gdcm,
 diff -Nru invesalius-3.0~b5/debian/patches/series 
 invesalius-3.0~b5/debian/patches/series
 --- invesalius-3.0~b5/debian/patches/series 2014-04-28 13:21:20.0 
 -0300
 +++ invesalius-3.0~b5/debian/patches/series 2014-09-09 20:03:43.0 
 -0300
 @@ -1,2 +1,3 @@
  10_sample_path.patch
  10_import_mips.patch
 +wxpython3.0.patch
 diff -Nru invesalius-3.0~b5/debian/patches/wxpython3.0.patch 
 invesalius-3.0~b5/debian/patches/wxpython3.0.patch
 --- invesalius-3.0~b5/debian/patches/wxpython3.0.patch  1969-12-31 
 21:00:00.0 -0300
 +++ invesalius-3.0~b5/debian/patches/wxpython3.0.patch  2014-09-09 
 21:00:03.0 -0300
 @@ -0,0 +1,114 @@
 +Description: Update for wxPython 3.0
 + These changes should remain compatible with wxPython 2.8, aside from the
 + wxversion change in the last hunk.
 + .
 + We can't simply drop the wxversion.select() call and use
 + .
 + wxversion.ensureMinimal('2.8-unicode', optionsRequired=True)
 + .
 + because 3.0 is always Unicode, and the -unicode option has been dropped,
 + but wxversion isn't smart enough to know to allow for this when matching
 + options.
 +Bug-Debian: https://bugs.debian.org/759060
 +Forwarded: no
 +Last-Update: 2014-09-09
 +
 +--- invesalius-3.0~b5.orig/invesalius/gui/dialogs.py
  invesalius-3.0~b5/invesalius/gui/dialogs.py
 +@@ -214,7 +214,7 @@ def ShowOpenProjectDialog():
 + dlg = wx.FileDialog(None, message=_(Open InVesalius 3 project...),
 + defaultDir=,
 + defaultFile=, wildcard=WILDCARD_OPEN,
 +-style=wx.OPEN|wx.CHANGE_DIR)
 ++style=wx.FD_OPEN|wx.FD_CHANGE_DIR)
 +
 + # inv3 filter is default
 + dlg.SetFilterIndex(0)
 +@@ -242,7 +242,7 @@ def ShowOpenAnalyzeDialog():
 + dlg = wx.FileDialog(None, message=_(Open Analyze file),
 + defaultDir=,
 + defaultFile=, wildcard=WILDCARD_ANALYZE,
 +-style=wx.OPEN|wx.CHANGE_DIR)
 ++style=wx.FD_OPEN|wx.FD_CHANGE_DIR)
 +
 + # inv3 filter is default
 + dlg.SetFilterIndex(0)
 

Bug#746708: missing license in debian/copyright

[Thiago Franco Moraes]

Hi Andreas,


On Mon, May 12, 2014 at 5:05 PM, Andreas Tille andr...@an3as.eu wrote:

 Hi Thiago,

 On Mon, May 12, 2014 at 04:39:31PM -0300, Thiago Franco Moraes wrote:
  Fixed with the help of cme and this link [1]. It was a problem with the
  license short name and a grammar error. I think it's all ok now.

 Sounds good.  I left the package as UNRELEASED and tagged the bug as
 pending to let others know that we dealt with the problem.  I think we
 can wait with the final upload until there might be some other reason
 for an upload (or some time has passed - without waiting too long to let
 the package migrate to testing).


OK!  No problem.



 Kind regards

 Andreas.

 --
 http://fam-tille.de


Thanks!

Bug#746708: missing license in debian/copyright

[Thiago Franco Moraes]

Hi Andreas,

Fixed with the help of cme and this link [1]. It was a problem with the
license short name and a grammar error. I think it's all ok now.

Thanks!

[1] - http://spdx.org/licenses/WXwindows


On Mon, May 12, 2014 at 4:20 PM, Andreas Tille andr...@an3as.eu wrote:

 Hi Thiago,

 you should probably try

 cme fix dpkg-copyright

 If this does not help I can easily fix it in SVN - but this is probably
 a good learning lession about cme (see Debian Med policy document what
 packages you need to install).

 Kind regards

  Andreas.


 On Mon, May 12, 2014 at 01:57:16PM -0300, Thiago Franco Moraes wrote:
  Hi Andreas,
 
  Sorry! I was out for some time. I added the copyright info about
  invesalius\gui\widgets\platebtn.py. I don't know if its correct, since
 I'm
  getting a lintian warning about the license name
  (field-name-typo-in-dep5-copyright licence).
 
  Thanks!
 
 
  On Mon, May 12, 2014 at 11:32 AM, Andreas Tille andr...@an3as.eu
 wrote:
 
   Hi Thiago,
  
   did you noticed this bug report?
  
   Kind regards
  
   Andreas.
  
   --
   http://fam-tille.de
  

 --
 http://fam-tille.de

Bug#708258: pyversions: missing X(S)-Python-Version in control file

[Thiago Franco Moraes]

Hi Mathie,

I followed the link you indicated [1] and I've made the transition to
dh_python2 (remove d/pyversion, provide X-Python-Version, etc). It
seems to be right now. The changes are available on debian-med svn.

Thanks!

[1] - http://wiki.debian.org/Python/TransitionToDHPython2


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Bug#708259: Depends: is hardcoded

[Thiago Franco Moraes]

I removed libvtk and libgdcm as dependencies to InVesalius. Now, it's
depending on python-vtk, python-vtkgdcm and python-gdcm, which are the
python bindings to vtk and gdcm. The changes are on debian-med svn.


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Bug#708260: ImportError: cannot import name setuparg1

[Thiago Franco Moraes]

I'm not sure about how to proceed in this case. When we updated
wxPython from 2.8.10 to the last version, we had to rewrite some
codes. To support wxPython 2.8.10 I'd have to write some patches, and
it wouldn't be compatible with the last wxPython version. Maybe, the
best thing to do is set the package to depend to at least
wxPython-2.8.12, which seems to be the version available on the
Wheezy. I don't know ...


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Bug#693963: ITP: python-casmoothing -- Context-aware mesh smoothing for biomedical applications

[Thiago Franco Moraes]

Package: wnpp
Owner: Thiago Franco de Moraes tfmor...@cti.gov.br
X-Debbugs-CC: debian-...@lists.debian.org
Severity: wishlist

* Package name: python-casmoothing
  Version : 0.1.0
  Upstream Author : Thiago Franco de Moraes tfmor...@cti.gov.br
* URL : https://github.com/tfmoraes/python-casmoothing
* License : GPL-2.0
  Programming Lang: C++, Python
  Description : Context-aware mesh smoothing for biomedical applications

Smoothing algorithms allow to reduce artifacts from mesh generation, but
often degrade accuracy. The method described in the paper Context-aware
mesh smoothing for biomedical applications identifies staircase
artifacts which result from image inhomogeneities and binary
segmentation in medical image data for subsequent removal by adaptive
mesh smoothing. Thus, context-aware smoothing enables to adaptively
smooth artifact areas, while non-artifact features can be preserved.
This is a implementation of this method in Cpp with Python bindings.


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Bug#575873: ITP: sigar -- A cross-platform API for collecting software inventory data

[Thiago Franco Moraes]

Package: wnpp
Severity: wishlist

It can be downloaded by svn checkout from trunk, the last stable
version doesn't compile:
svn co http://svn.hyperic.org/projects/sigar_mirror/trunk sigar

Here is the site http://www.hyperic.com/products/sigar

Packages I created:
http://svn.softwarepublico.gov.br/trac/invesalius/browser/requirements/invesalius3/ubuntu32/libsigar-1.6.2-i386.deb?format=raw
http://svn.softwarepublico.gov.br/trac/invesalius/browser/requirements/invesalius3/ubuntu64/libsigar-1.6.2-amd64.deb?format=raw

Sigar is licensed under the terms of the GNU General Public License (GPL v2).

A large description, by the site:

One API to access system information regardless of the underlying platform

Hyperic's System Information Gatherer (SIGAR) is a cross-platform API
for collecting software inventory data. SIGAR is core of HQ's
auto-discovery functionality, and you can use it to extend
auto-discovery behavior.

SIGAR includes support for Linux, FreeBSD, Windows, Solaris, AIX,
HP-UX and Mac OSX across a variety of versions and architectures.
Users of the SIGAR API are given portable access to inventory and
monitoring data including:

* System memory, swap, cpu, load average, uptime, logins
* Per-process memory, cpu, credential info, state, arguments,
environment, open files
* File system detection and metrics
* Network interface detection, configuration information and metrics
* Network route and connection tables

This information is available in most operating systems, but each OS
has its own way(s) providing it. SIGAR provides developers with one
API to access this information regardless of the underlying platform.
The core API is implemented in pure C with bindings currently
implemented for Java, Perl and C#.

SIGAR offers both source code and binary distributions including
native libraries for all supported platforms, examples and
documentation. Hyperic SIGAR is licensed under the terms of the GNU
General Public License (GPL v2).



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