[Debian-med-packaging] Bug#779707: Closing due to no response from reporter (Was: Errors when reading dicomdir file: "No images found" / "Loading: DICM Error reading file")
Axel Beckert
abe at debian.org
Sun Dec 4 15:42:16 GMT 2022
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-submitter at bugs.debian.org:
> From: Andreas Tille <andreas at fam-tille.de>
> To: 671828 at bugs.debian.org, 779707 at 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 <abe at debian.org>, https://people.debian.org/~abe/
: :' : | Debian Developer, ftp.ch.debian.org Admin
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