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Bug#779707: amide: Missing Recommends/Suggests on (x)medcon
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Axel Beckert
Mar 4, 2015, 5:10:03 AM3/4/15
to
Package: amide
Version: 1.0.5-2+b2
Dear Debian-Med Team,
amide uses multiple external tools for importing data. In the Import
menu, there are multiple entries labeled "via (X)MedCon", but there's
neither a package relation with medcon nor with xmedcon.
-- System Information:
Debian Release: 8.0
APT prefers testing
APT policy: (909, 'testing'), (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 amide depends on:
ii gconf-service 3.2.6-3
ii libart-2.0-2 2.3.21-2
ii libatk1.0-0 2.14.0-1
ii libavcodec56 6:11.2-1
ii libavutil54 6:11.2-1
ii libc6 2.19-15
ii libcairo2 1.14.0-2.1
ii libdcmtk2 3.6.0-15+b1
ii libfontconfig1 2.11.0-6.3
ii libfreetype6 2.5.2-2
ii libgcc1 1:4.9.1-19
ii libgconf-2-4 3.2.6-3
ii libgdk-pixbuf2.0-0 2.31.1-2+b1
ii libglib2.0-0 2.42.1-1
ii libgnomecanvas2-0 2.30.3-2
ii libgnomevfs2-0 1:2.24.4-6+b1
ii libgsl0ldbl 1.16+dfsg-2
ii libgtk2.0-0 2.24.25-1
ii libmdc2 0.13.0-2
ii libpango-1.0-0 1.36.8-3
ii libpangocairo-1.0-0 1.36.8-3
ii libpangoft2-1.0-0 1.36.8-3
ii libpng12-0 1.2.50-2+b2
ii libstdc++6 4.9.1-19
ii libvolpack1 1.0b3-5
ii libxml2 2.9.1+dfsg1-5
ii zlib1g 1:1.2.8.dfsg-2+b1
amide recommends no packages.
amide suggests no packages.
-- no debconf information
--
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with a subject of "unsubscribe". Trouble? Contact listm...@lists.debian.org
Version: 1.0.5-2+b2
Dear Debian-Med Team,
amide uses multiple external tools for importing data. In the Import
menu, there are multiple entries labeled "via (X)MedCon", but there's
neither a package relation with medcon nor with xmedcon.
-- System Information:
Debian Release: 8.0
APT prefers testing
APT policy: (909, 'testing'), (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 amide depends on:
ii gconf-service 3.2.6-3
ii libart-2.0-2 2.3.21-2
ii libatk1.0-0 2.14.0-1
ii libavcodec56 6:11.2-1
ii libavutil54 6:11.2-1
ii libc6 2.19-15
ii libcairo2 1.14.0-2.1
ii libdcmtk2 3.6.0-15+b1
ii libfontconfig1 2.11.0-6.3
ii libfreetype6 2.5.2-2
ii libgcc1 1:4.9.1-19
ii libgconf-2-4 3.2.6-3
ii libgdk-pixbuf2.0-0 2.31.1-2+b1
ii libglib2.0-0 2.42.1-1
ii libgnomecanvas2-0 2.30.3-2
ii libgnomevfs2-0 1:2.24.4-6+b1
ii libgsl0ldbl 1.16+dfsg-2
ii libgtk2.0-0 2.24.25-1
ii libmdc2 0.13.0-2
ii libpango-1.0-0 1.36.8-3
ii libpangocairo-1.0-0 1.36.8-3
ii libpangoft2-1.0-0 1.36.8-3
ii libpng12-0 1.2.50-2+b2
ii libstdc++6 4.9.1-19
ii libvolpack1 1.0b3-5
ii libxml2 2.9.1+dfsg1-5
ii zlib1g 1:1.2.8.dfsg-2+b1
amide recommends no packages.
amide suggests no packages.
-- no debconf information
--
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Gert Wollny
Mar 4, 2015, 5:50:04 AM3/4/15
to
The package requires libmdc2, which is the library provided by the
xmedcon project, so there is a relation.
Considering the suggestion of (x)medcon one might add that amide does
also not suggest dcmtk (another set of command line tools for
manipulating DICOM files) even though it also has dicom import by using
dcmtk.
Note that (x)medcon is amongst the packages that are pulled in by the
Debian med the task package "med-imaging".
Best,
Gert
xmedcon project, so there is a relation.
Considering the suggestion of (x)medcon one might add that amide does
also not suggest dcmtk (another set of command line tools for
manipulating DICOM files) even though it also has dicom import by using
dcmtk.
Note that (x)medcon is amongst the packages that are pulled in by the
Debian med the task package "med-imaging".
Best,
Gert
Axel Beckert
Mar 4, 2015, 7:00:04 AM3/4/15
to
Control: reassign -1 libmdc2 0.13.0-2
Control: retitle -1 Errors when reading dicomdir file: "No images found" / "Loading: DICM Error reading file"
Hi Gerd,
thanks for the prompt feedback.
Gert Wollny wrote:
> The package requires libmdc2, which is the library provided by the
> xmedcon project, so there is a relation.
Ok, so I may have been a little bit quick with my conclusion.
I tried to import a file named "dicomdir" which I can view with other
DICOM viewers (namely invesalius and dicomimageviewer) by using File
-> Import File (specify) -> via "DICOM 3.0 via (X)MedCon" without
medcon or xmedcon installed. So I expected that the commandline tools
are required but missing.
The error message in the popup is:
AMIDE WARNING
Can't read file .../dicomdir with libmdc/(X)MedCon
The popup actually popped up twice. (BTW, it is very annoying that I
can not copy and paste from that error message. Especially if they're
longer as in the case with using the dcmtk backend, which throws
errors, but seems to work somehow in the end.)
On the commandline where I started amide, it shows the following messages,
but only once:
Mar 04 12:29:49 log[31810]: error: No images found
(amide:31810): (X)MedCon-WARNING **: Loading: DICM Error reading file
So I've installed xmedcon, opened that file with it and it gave me the
same error messages on the commandline:
Mar 04 12:41:43 log[5807]: error: No images found
(xmedcon:5807): (X)MedCon-WARNING **: Reading: DICM Error reading file
So it's either an issue with the medcon library or PEBKAC. I'm
reassiging this to the according library package.
Please feel free to close this bug report if libmdc2 is not expected
to handle dicomdir files (mine contains/references data from two
examinations).
amide as well as xmedcon seems to work well on single frames from an
X-Ray video in DICOM format, but I haven't found a way to view the
whole video with either of these tools.
> Considering the suggestion of (x)medcon one might add that amide does
> also not suggest dcmtk (another set of command line tools for
> manipulating DICOM files) even though it also has dicom import by using
> dcmtk.
Yes, I noticed that, too, but that worked (more or less) without dmctk
being installed. There's also a hard dependency on some dmctk library.
(I did recognize that one but not the medcon library, sorry.) So I
expected that the library suffices in that case.
> Note that (x)medcon is amongst the packages that are pulled in by the
> Debian med the task package "med-imaging".
Yeah, but IMHO that's irrelevant here. That task package pulls in tons
of packages I don't need. I just need an DICOM viewer.
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
Control: retitle -1 Errors when reading dicomdir file: "No images found" / "Loading: DICM Error reading file"
Hi Gerd,
thanks for the prompt feedback.
Gert Wollny wrote:
> The package requires libmdc2, which is the library provided by the
> xmedcon project, so there is a relation.
I tried to import a file named "dicomdir" which I can view with other
DICOM viewers (namely invesalius and dicomimageviewer) by using File
-> Import File (specify) -> via "DICOM 3.0 via (X)MedCon" without
medcon or xmedcon installed. So I expected that the commandline tools
are required but missing.
The error message in the popup is:
AMIDE WARNING
Can't read file .../dicomdir with libmdc/(X)MedCon
The popup actually popped up twice. (BTW, it is very annoying that I
can not copy and paste from that error message. Especially if they're
longer as in the case with using the dcmtk backend, which throws
errors, but seems to work somehow in the end.)
On the commandline where I started amide, it shows the following messages,
but only once:
Mar 04 12:29:49 log[31810]: error: No images found
(amide:31810): (X)MedCon-WARNING **: Loading: DICM Error reading file
So I've installed xmedcon, opened that file with it and it gave me the
same error messages on the commandline:
Mar 04 12:41:43 log[5807]: error: No images found
(xmedcon:5807): (X)MedCon-WARNING **: Reading: DICM Error reading file
So it's either an issue with the medcon library or PEBKAC. I'm
reassiging this to the according library package.
Please feel free to close this bug report if libmdc2 is not expected
to handle dicomdir files (mine contains/references data from two
examinations).
amide as well as xmedcon seems to work well on single frames from an
X-Ray video in DICOM format, but I haven't found a way to view the
whole video with either of these tools.
> Considering the suggestion of (x)medcon one might add that amide does
> also not suggest dcmtk (another set of command line tools for
> manipulating DICOM files) even though it also has dicom import by using
> dcmtk.
being installed. There's also a hard dependency on some dmctk library.
(I did recognize that one but not the medcon library, sorry.) So I
expected that the library suffices in that case.
> Note that (x)medcon is amongst the packages that are pulled in by the
> Debian med the task package "med-imaging".
of packages I don't need. I just need an DICOM viewer.
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
Andreas Tille
May 7, 2015, 3:20:03 AM5/7/15
to
Hi,
I admit I do not fully understand all this but do you think that libmdc2
should depend from xmedcon to finally solve this issue?
On Wed, Mar 04, 2015 at 12:51:35PM +0100, Axel Beckert wrote:
>
> > Note that (x)medcon is amongst the packages that are pulled in by the
> > Debian med the task package "med-imaging".
>
> Yeah, but IMHO that's irrelevant here.
Yes.
> That task package pulls in tons
> of packages I don't need. I just need an DICOM viewer.
I'd love if some medical imaging expert would consider splitting up the
task into more sensible parts - but I'm no such expert ...
Kind regards
Andreas.
--
http://fam-tille.de
I admit I do not fully understand all this but do you think that libmdc2
should depend from xmedcon to finally solve this issue?
On Wed, Mar 04, 2015 at 12:51:35PM +0100, Axel Beckert wrote:
>
> > Note that (x)medcon is amongst the packages that are pulled in by the
> > Debian med the task package "med-imaging".
>
> Yeah, but IMHO that's irrelevant here.
> That task package pulls in tons
> of packages I don't need. I just need an DICOM viewer.
task into more sensible parts - but I'm no such expert ...
Kind regards
Andreas.
--
http://fam-tille.de
Axel Beckert
Dec 4, 2022, 10:50:03 AM12/4/22
to
Control: reopen 779707
Control: found 779707 1.0.6-1
Hi Andreas,
On Sun, Dec 04, 2022 at 11:23:35AM +0100, Andreas Tille wrote:
> I tried to do something to solve the issue in 2015 and asked the reporter
> whether this was helpful.
JFTR: Well, yes, you asked, but that mail
(https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=779707#33)
never reached me as I'm not subscribed to the bug report and you did
neither Cc me directly nor 79707-s...@bugs.debian.org:
> From: Andreas Tille <and...@fam-tille.de>
> To: 671...@bugs.debian.org, 779...@bugs.debian.org
> Subject: Could you please verify the bug with latest upstream
So that's the reason why you never got an answer. So I try to answer
this now.
Took a moment to remember, which file I tried to open with Amide back
in 2015, but my reply to Gert
(https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=779707#15) helped
to remember it.
If I now try to open that "dicomdir" file directly on the command
line, it just crashes:
$ amide dicomdir
[1] 11595 IOT instruction (core dumped) amide dicomdir
If I try to import it via the menues "Import File (specify)" → "DICOM
3.0 via (X)MedCon" I still get a similar error message, although a
tiny bit more informative as it now also mentions "libmdc":
First "AMIDE WARNING" popup:
Can't read file […]/dicomdir with libmdc/(X)MedCon.
Second "AMIDE WARNING" popup:
Could not import data sets from file […]/dicomdir
I then tried "Import File (guess)" with the "dicomdir" file. This did
something else and got me this "AMIDE WARNING" which shows that it at
least got a bit farther:
Couldn't find ImageOrientationPatient in file […]/86617/86625/866663
The path "[…]" is the same as above, i.e. the directory the "dicomdir"
file is. Maybe this bit of information helps:
$ file -L 86617/86625/866663
86617/86625/866663: DICOM medical imaging data
A second such popup says:
Couldn't find ImagePositionPatient nor SliceLocation in file
[…]/86617/86625/866663
It though did something. An empty (and focus grabbing) popup "Progress
Dialog" appeared 6 times and the whole application seems to be rather
unresponsive during that time (which is kinda ok-ish).
It also threw tons of GTK errors in terminal where I started it.
Didn't capture the output and it was far more than the terminal's
history. But it seems to be a repitition of these few messages:
(amide:11820): GLib-GObject-WARNING **: 15:47:26.266: invalid uninstantiatable type '(null)' in cast to 'GtkProgressBar'
(amide:11820): Gtk-CRITICAL **: 15:47:26.266: IA__gtk_progress_bar_set_fraction: assertion 'GTK_IS_PROGRESS_BAR (pbar)' failed
(amide:11820): GLib-GObject-WARNING **: 15:47:26.267: invalid uninstantiatable type '(null)' in cast to 'GtkProgressBar'
(amide:11820): Gtk-CRITICAL **: 15:47:26.267: IA__gtk_progress_bar_set_fraction: assertion 'GTK_IS_PROGRESS_BAR (pbar)' failed
(amide:11820): GLib-GObject-WARNING **: 15:47:27.239: invalid unclassed pointer in cast to 'GtkLabel'
(amide:11820): Gtk-CRITICAL **: 15:47:27.239: IA__gtk_label_set_text: assertion 'GTK_IS_LABEL (label)' failed
(amide:11820): Gtk-CRITICAL **: 15:47:27.239: IA__gtk_container_foreach: assertion 'GTK_IS_CONTAINER (container)' failed
(amide:11820): GLib-GObject-WARNING **: 15:47:27.239: invalid uninstantiatable type '(null)' in cast to 'GtkProgressBar'
(amide:11820): Gtk-CRITICAL **: 15:47:27.239: IA__gtk_progress_bar_set_fraction: assertion 'GTK_IS_PROGRESS_BAR (pbar)' failed
(amide:11820): GLib-GObject-WARNING **: 15:47:27.239: invalid uninstantiatable type '(null)' in cast to 'GtkProgressBar'
(amide:11820): Gtk-CRITICAL **: 15:47:27.239: IA__gtk_progress_bar_set_fraction: assertion 'GTK_IS_PROGRESS_BAR (pbar)' failed
(The blank lines were output as well. So citing them as well. These
errors are likely related to the empty, i.e. non-working "Progress
Dialog".)
Then another "AMIDE WARNING" popup appeared saying:
Couldn't find ImageOrientationPatient in file […]/8651/8652/8659
And immediately after closing that one another one:
Couldn't find ImagePositionPatient nor SliceLocation in file
[…]/8651/8652/8659
And immediately after closing that one another one:
Couldn't find ImageOrientationPatient in file […]/8651/8652/86516
And immediately after closing that one another one:
Couldn't find ImagePositionPatient nor SliceLocation in file
[…]/8651/8652/86516
The last empty Progress Dialog window closes and another empty
Progress Dialog appears. Then I get the popup pair:
Couldn't find ImageOrientationPatient in file […]/8651/8654/86511
Couldn't find ImagePositionPatient nor SliceLocation in file
[…]/8651/8654/86511
etc. pp. Then, after a while of more such popups with always other
file names, a different "AMIDE WARNING" popup shows up (and now I
really curse that widget library for not being able to copy and paste
this error message *grrrr* — even a screenshot would not have worked
as the popup is fixed size and just has a four-line scroll window in
it):
Could not find the slice thickness, setting to 1mm for File
[…]/86617/86618/86626
Could not find the pixel size, setting to 1mm for File
[…]/86617/86625/866663
Could not find the slice thickness, setting to 1mm for File
[…]/86617/86625/866663
Slice thickness (2.000 mm) not equal to slice spacing (1.500 mm) in
data set Lu[censored] 2mm - will use slice spacing for thickness
Slice thickness (7.000 mm) not equal to slice spacing (5.000 mm) in
data set Lu[censored] MIP cor - will use slice spacing for thickness
Slice thickness (2.000 mm) not equal to slice spacing (2.001 mm) in
data set BW[censored] - will use slice spacing for thickness
Could not find the pixel size, setting to 1mm for File
[…]/8651/8652/8659
Could not find the slice thickness, setting to 1mm for File
[…]/8651/8652/8659
Could not find the pixel size, setting to 1mm for File
[…]/8651/8652/86516
Could not find the slice thickness, setting to 1mm for File
[…]/8651/8652/86516
Could not find the pixel size, setting to 1mm for File
[…]/8651/8654/86511
Could not find the slice thickness, setting to 1mm for File
[…]/8651/8654/86511
Could not find the pixel size, setting to 1mm for File
[…]/8651/8655/86512
Could not find the slice thickness, setting to 1mm for File
[…]/8651/8655/86512
Could not find the pixel size, setting to 1mm for File
[…]/8651/8656/86513
Could not find the slice thickness, setting to 1mm for File
[…]/8651/8656/86513
Could not find the pixel size, setting to 1mm for File
[…]/8651/8657/86514
Could not find the slice thickness, setting to 1mm for File
[…]/8651/8657/86514
Could not find the pixel size, setting to 1mm for File
[…]/8651/8658/86515
Could not find the slice thickness, setting to 1mm for File
[…]/8651/8658/86515
Could not find the pixel size, setting to 1mm for File
[…]/8651/8653/86510
Could not find the slice thickness, setting to 1mm for File
[…]/8651/8653/86510
And then the main window resizes to 4507x1646 spawning all my four
screens (which are together maximum 4992 pixels wide and 2048 pixels
high, but not on all screens) and because my screens together don't
make a rectangular shape together and the window is not resizable, it
is impossible to see all if its content.
In the end it though shows three subwindows inside the window, named
"transverse 1", "coronal 1" and "sagittal 1". And if I check some
checkboxes in the tree hierachy shown on the left side, I indeed get
some pictures. Some checkboxes though only show grey rectangles in one
of the subwindows. This probably relates to the import errors.
I hope this gives a bit more insight in what might have caused the
issue with my original try to import stuff into Amide via
libmdc/(X)MedCon. As mentioned, the whole thing is a DICOM CD with two
data sets of which one is an x-ray video. The other data set is a
computer tomography and in the end, Amide seems to display only that
one (after the "Import File (Guess)").
Not sure if some of the issues I ran into with the other paths I tried
today (crash on "amide dicomdir" and "Import File (Guess)") should be
a separate issue or not. At least usability is horrible in many ways:
popups to acknowledge, fixed window size, broken progress windows,
etc. But then again it still just doesn't seem to cope with videos in
DICOM data sets and I'm not sure which issues are just follow up
issues and which are separate issues.
Regards, Axel
--
,''`. | Axel Beckert <a...@debian.org>, https://people.debian.org/~abe/
Control: found 779707 1.0.6-1
Hi Andreas,
On Sun, Dec 04, 2022 at 11:23:35AM +0100, Andreas Tille wrote:
> I tried to do something to solve the issue in 2015 and asked the reporter
> whether this was helpful.
JFTR: Well, yes, you asked, but that mail
(https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=779707#33)
never reached me as I'm not subscribed to the bug report and you did
neither Cc me directly nor 79707-s...@bugs.debian.org:
> From: Andreas Tille <and...@fam-tille.de>
> To: 671...@bugs.debian.org, 779...@bugs.debian.org
> Subject: Could you please verify the bug with latest upstream
So that's the reason why you never got an answer. So I try to answer
this now.
Took a moment to remember, which file I tried to open with Amide back
in 2015, but my reply to Gert
(https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=779707#15) helped
to remember it.
If I now try to open that "dicomdir" file directly on the command
line, it just crashes:
$ amide dicomdir
[1] 11595 IOT instruction (core dumped) amide dicomdir
If I try to import it via the menues "Import File (specify)" → "DICOM
3.0 via (X)MedCon" I still get a similar error message, although a
tiny bit more informative as it now also mentions "libmdc":
First "AMIDE WARNING" popup:
Can't read file […]/dicomdir with libmdc/(X)MedCon.
Second "AMIDE WARNING" popup:
Could not import data sets from file […]/dicomdir
I then tried "Import File (guess)" with the "dicomdir" file. This did
something else and got me this "AMIDE WARNING" which shows that it at
least got a bit farther:
Couldn't find ImageOrientationPatient in file […]/86617/86625/866663
The path "[…]" is the same as above, i.e. the directory the "dicomdir"
file is. Maybe this bit of information helps:
$ file -L 86617/86625/866663
86617/86625/866663: DICOM medical imaging data
A second such popup says:
Couldn't find ImagePositionPatient nor SliceLocation in file
[…]/86617/86625/866663
It though did something. An empty (and focus grabbing) popup "Progress
Dialog" appeared 6 times and the whole application seems to be rather
unresponsive during that time (which is kinda ok-ish).
It also threw tons of GTK errors in terminal where I started it.
Didn't capture the output and it was far more than the terminal's
history. But it seems to be a repitition of these few messages:
(amide:11820): GLib-GObject-WARNING **: 15:47:26.266: invalid uninstantiatable type '(null)' in cast to 'GtkProgressBar'
(amide:11820): Gtk-CRITICAL **: 15:47:26.266: IA__gtk_progress_bar_set_fraction: assertion 'GTK_IS_PROGRESS_BAR (pbar)' failed
(amide:11820): GLib-GObject-WARNING **: 15:47:26.267: invalid uninstantiatable type '(null)' in cast to 'GtkProgressBar'
(amide:11820): Gtk-CRITICAL **: 15:47:26.267: IA__gtk_progress_bar_set_fraction: assertion 'GTK_IS_PROGRESS_BAR (pbar)' failed
(amide:11820): GLib-GObject-WARNING **: 15:47:27.239: invalid unclassed pointer in cast to 'GtkLabel'
(amide:11820): Gtk-CRITICAL **: 15:47:27.239: IA__gtk_label_set_text: assertion 'GTK_IS_LABEL (label)' failed
(amide:11820): Gtk-CRITICAL **: 15:47:27.239: IA__gtk_container_foreach: assertion 'GTK_IS_CONTAINER (container)' failed
(amide:11820): GLib-GObject-WARNING **: 15:47:27.239: invalid uninstantiatable type '(null)' in cast to 'GtkProgressBar'
(amide:11820): Gtk-CRITICAL **: 15:47:27.239: IA__gtk_progress_bar_set_fraction: assertion 'GTK_IS_PROGRESS_BAR (pbar)' failed
(amide:11820): GLib-GObject-WARNING **: 15:47:27.239: invalid uninstantiatable type '(null)' in cast to 'GtkProgressBar'
(amide:11820): Gtk-CRITICAL **: 15:47:27.239: IA__gtk_progress_bar_set_fraction: assertion 'GTK_IS_PROGRESS_BAR (pbar)' failed
(The blank lines were output as well. So citing them as well. These
errors are likely related to the empty, i.e. non-working "Progress
Dialog".)
Then another "AMIDE WARNING" popup appeared saying:
Couldn't find ImageOrientationPatient in file […]/8651/8652/8659
And immediately after closing that one another one:
Couldn't find ImagePositionPatient nor SliceLocation in file
[…]/8651/8652/8659
And immediately after closing that one another one:
Couldn't find ImageOrientationPatient in file […]/8651/8652/86516
And immediately after closing that one another one:
Couldn't find ImagePositionPatient nor SliceLocation in file
[…]/8651/8652/86516
The last empty Progress Dialog window closes and another empty
Progress Dialog appears. Then I get the popup pair:
Couldn't find ImageOrientationPatient in file […]/8651/8654/86511
Couldn't find ImagePositionPatient nor SliceLocation in file
[…]/8651/8654/86511
etc. pp. Then, after a while of more such popups with always other
file names, a different "AMIDE WARNING" popup shows up (and now I
really curse that widget library for not being able to copy and paste
this error message *grrrr* — even a screenshot would not have worked
as the popup is fixed size and just has a four-line scroll window in
it):
Could not find the slice thickness, setting to 1mm for File
[…]/86617/86618/86626
Could not find the pixel size, setting to 1mm for File
[…]/86617/86625/866663
Could not find the slice thickness, setting to 1mm for File
[…]/86617/86625/866663
Slice thickness (2.000 mm) not equal to slice spacing (1.500 mm) in
data set Lu[censored] 2mm - will use slice spacing for thickness
Slice thickness (7.000 mm) not equal to slice spacing (5.000 mm) in
data set Lu[censored] MIP cor - will use slice spacing for thickness
Slice thickness (2.000 mm) not equal to slice spacing (2.001 mm) in
data set BW[censored] - will use slice spacing for thickness
Could not find the pixel size, setting to 1mm for File
[…]/8651/8652/8659
Could not find the slice thickness, setting to 1mm for File
[…]/8651/8652/8659
Could not find the pixel size, setting to 1mm for File
[…]/8651/8652/86516
Could not find the slice thickness, setting to 1mm for File
[…]/8651/8652/86516
Could not find the pixel size, setting to 1mm for File
[…]/8651/8654/86511
Could not find the slice thickness, setting to 1mm for File
[…]/8651/8654/86511
Could not find the pixel size, setting to 1mm for File
[…]/8651/8655/86512
Could not find the slice thickness, setting to 1mm for File
[…]/8651/8655/86512
Could not find the pixel size, setting to 1mm for File
[…]/8651/8656/86513
Could not find the slice thickness, setting to 1mm for File
[…]/8651/8656/86513
Could not find the pixel size, setting to 1mm for File
[…]/8651/8657/86514
Could not find the slice thickness, setting to 1mm for File
[…]/8651/8657/86514
Could not find the pixel size, setting to 1mm for File
[…]/8651/8658/86515
Could not find the slice thickness, setting to 1mm for File
[…]/8651/8658/86515
Could not find the pixel size, setting to 1mm for File
[…]/8651/8653/86510
Could not find the slice thickness, setting to 1mm for File
[…]/8651/8653/86510
And then the main window resizes to 4507x1646 spawning all my four
screens (which are together maximum 4992 pixels wide and 2048 pixels
high, but not on all screens) and because my screens together don't
make a rectangular shape together and the window is not resizable, it
is impossible to see all if its content.
In the end it though shows three subwindows inside the window, named
"transverse 1", "coronal 1" and "sagittal 1". And if I check some
checkboxes in the tree hierachy shown on the left side, I indeed get
some pictures. Some checkboxes though only show grey rectangles in one
of the subwindows. This probably relates to the import errors.
I hope this gives a bit more insight in what might have caused the
issue with my original try to import stuff into Amide via
libmdc/(X)MedCon. As mentioned, the whole thing is a DICOM CD with two
data sets of which one is an x-ray video. The other data set is a
computer tomography and in the end, Amide seems to display only that
one (after the "Import File (Guess)").
Not sure if some of the issues I ran into with the other paths I tried
today (crash on "amide dicomdir" and "Import File (Guess)") should be
a separate issue or not. At least usability is horrible in many ways:
popups to acknowledge, fixed window size, broken progress windows,
etc. But then again it still just doesn't seem to cope with videos in
DICOM data sets and I'm not sure which issues are just follow up
issues and which are separate issues.
Regards, Axel
--
,''`. | Axel Beckert <a...@debian.org>, https://people.debian.org/~abe/
Andreas Tille
Dec 4, 2022, 11:50:03 AM12/4/22
to
Control: reassign -1 libmdc3
Hi Axel,
Am Sun, Dec 04, 2022 at 04:42:16PM +0100 schrieb Axel Beckert:
> JFTR: Well, yes, you asked, but that mail
> (https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=779707#33)
> never reached me as I'm not subscribed to the bug report and you did
> neither Cc me directly nor 79707-s...@bugs.debian.org:
Sorry about this.
> ...
to libmdc3 since the library has bumped soname meanwhile.
I'll forward the issue to xmedcom upstream.
Hi Axel,
Am Sun, Dec 04, 2022 at 04:42:16PM +0100 schrieb Axel Beckert:
> JFTR: Well, yes, you asked, but that mail
> (https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=779707#33)
> never reached me as I'm not subscribed to the bug report and you did
> neither Cc me directly nor 79707-s...@bugs.debian.org:
> ...
> Not sure if some of the issues I ran into with the other paths I tried
> today (crash on "amide dicomdir" and "Import File (Guess)") should be
> a separate issue or not. At least usability is horrible in many ways:
> popups to acknowledge, fixed window size, broken progress windows,
> etc. But then again it still just doesn't seem to cope with videos in
> DICOM data sets and I'm not sure which issues are just follow up
> issues and which are separate issues.
Thanks a lot for your effort in this issue. I've reassigned the issue
> today (crash on "amide dicomdir" and "Import File (Guess)") should be
> a separate issue or not. At least usability is horrible in many ways:
> popups to acknowledge, fixed window size, broken progress windows,
> etc. But then again it still just doesn't seem to cope with videos in
> DICOM data sets and I'm not sure which issues are just follow up
> issues and which are separate issues.
to libmdc3 since the library has bumped soname meanwhile.
I'll forward the issue to xmedcom upstream.
Andreas Tille
Dec 4, 2022, 12:00:04 PM12/4/22
to
Control: tags -1 upstream
Control: forwarded -1 Erik Nolf <en...@users.sourceforge.net>
Hi Erik,
there is a long standing bug report in the Debian bug tracking system.
I'd like to bring this to your attention in case you see any chance
to enhance xmedcon.
Control: forwarded -1 Erik Nolf <en...@users.sourceforge.net>
Hi Erik,
there is a long standing bug report in the Debian bug tracking system.
I'd like to bring this to your attention in case you see any chance
to enhance xmedcon.
Andreas Tille
Dec 6, 2022, 2:40:04 AM12/6/22
to
Control: tags -1 wontfix
Hi Erik,
Am Tue, Dec 06, 2022 at 12:11:09AM +0100 schrieb Erik Nolf:
> Aah, dicomdir. This is something we leave to AMIDE, which is better suited
> and uses the established dcmtk toolkit.
>
> (X)MedCon is really only capable of reading just one file (although with
> multiple images), like it was usual in nuclear medicine some decades ago.
>
> Most other DICOM modalities are multiple files for multiple instances,
> sometimes referenced in a dicomdir file. My poor amateurish (X)MedCon
> coding decisions won't handle that. Sorry, I am afraid it will stay that
> way.
Thanks a lot for the clarification. So I'm tagging the bug wontfix to
keep it documented that way.
Hi Erik,
Am Tue, Dec 06, 2022 at 12:11:09AM +0100 schrieb Erik Nolf:
> Aah, dicomdir. This is something we leave to AMIDE, which is better suited
> and uses the established dcmtk toolkit.
>
> (X)MedCon is really only capable of reading just one file (although with
> multiple images), like it was usual in nuclear medicine some decades ago.
>
> Most other DICOM modalities are multiple files for multiple instances,
> sometimes referenced in a dicomdir file. My poor amateurish (X)MedCon
> coding decisions won't handle that. Sorry, I am afraid it will stay that
> way.
Thanks a lot for the clarification. So I'm tagging the bug wontfix to
keep it documented that way.
Erik Nolf
Dec 6, 2022, 2:40:05 AM12/6/22
to
Control: tags -1 upstream
Control: forwarded -1 Erik Nolf <en...@users.sourceforge.net>
Hi Erik,
there is a long standing bug report in the Debian bug tracking system.
I'd like to bring this to your attention in case you see any chance
to enhance xmedcon.
Aah, dicomdir. This is something we leave to AMIDE, which is better suited and uses the established dcmtk toolkit.
(X)MedCon is really only capable of reading just one file (although with multiple images), like it was usual in nuclear medicine some decades ago.
Most other DICOM modalities are multiple files for multiple instances, sometimes referenced in a dicomdir file. My poor amateurish (X)MedCon coding decisions won't handle that. Sorry, I am afraid it will stay that way.
Cheers,
Erik
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