Material doesn't show when loaded in MIB 2.01
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#8 Material doesn't show when loaded in MIB 2.01
Hi Ilya,
I'm having a frustrating and confusing issue with the current version of MIB (2.01).
I created a material in MIB, saved it as .model and tried to open it again in a new MIB window, but once it "loads", the material is blank. It is listed in the Material panel, but no overlay shows up in the viewer. It's not an issue with the transparency, I don't have the material hidden, and regardless of the file type, it won't appear (I saved .model, .am, .tif and tried to open all of them...nothing). Doing model statistics also shows that nothing is in the model.
I can open the file in FIJI and after doing an auto-contrast can see it, so the data is there...I tried opening on previous versions of MIB as well but it won't open there either. Have you experienced this bug since the update?? I'm a bit worried since I have about 3 weeks of data that I can't open. Thanks!
P.S. MIB is awesome, I work with it every day and reccomend it to everyone I talk to, particularly love the watershed/graphcut function, it's genius.
Cheers,
Connon Thomas
Hi,
Do you have this problem only with some particular model file?
is it large .model file? Could you send it to me, so that I can check?
Indeed MIB1 can't read the models from MIB2. The other direction MIB1
models in MIB2 is working fine. I probably have to implement saving of
models in MIB1 format from MIB2.
Ilya
Wow, you're fast.
It's not one particular file, I am doing 5 other chunks of data that are also not working. They're all similar in size, maybe a bit large? I've worked with larger though (in previous versions). The stack I'm working with is 79 images at 3584 x 3333 pixels (~9 MB). I'll send it to you. Thanks!
Connon
Last edit: Connon Thomas 2017-04-25
Hi,
Do you have this problem only with some particular model file?
is it large .model file? Could you send it to me, so that I can check?
Indeed MIB1 can't read the models from MIB2. The other direction MIB1
models in MIB2 is working fine. I probably have to implement saving of
models in MIB1 format from MIB2.
Ilya
On Tue, Apr 25, 2017 at 11:25 PM, Connon Thomas connont@users.sf.net wrote:
Related
Tickets: #8
Hi,
thank you for the file, I've checked it.
I found one bug during import of it from Matlab and fixed it. But I don't think that this bug is causing problems for you. Do you use compiled or matlab version of MIB?
I can suggest 2 things:
If you are using the Matlab version I can send you the current beta, where I fixed that bug with the import for testing
Otherwise, we can have a Skype meeting where you can shere the screen and I will check what might be wrong.
Ilya
Ilya,
I use the compiled version; I'm on a computer that doesn't have Matlab. There is another computer I can use that does have the Matlab version, if you want to send me that and see if it works. If not, I think we can try Skype.
Thanks!
ok, so it seems that the issue was due to singleton limitation of MIB version 2.00-2.01 (only one instance of MIB allowed at the time).
In the next update this limitation should be fixed and multiple instances will be allowed.
Ilya
Hi,
I have the exact same problem. I have a .model .nrrd and .mask file. Neither show up, statistics are empty, Exterior seems to occupy the whole volume. I can still render the model in 3D slicer. I attached a picture of the files that I am using. Are the file sizes what you would expect? The .mrc fiel is 6.6GB the .nrrd model 3.3GB and the .model 21MB?
Has this been resolved yet?
Best wishes,
Timm
Hi Timm,
which version of mib do you use, is it matlab or compiled? wundows or mac?
So your dataset is in Mrc and 6.6 gb. The model in nrrd file is 3gb, which
indicates that uou are working with 16 bit images. I suggest to load mrc
dataset, convert it to 8bit and save in amiramesh or nrrd format.This will
improve general performance.
Next, the .mask and the .model files are 70 and 20 Mb. When those files are
saved Matlab compresses them, and since they are quite big the model and
the mask should contain some data.
Have you been able to render this .nrrd file in Slicer, but in mib it looks
empty? Try to load the model again, highlight material that you have drawn
in the segmentation table, press the right mouse button and select Get
statistics. In the get statistics window press the Run button to find
whether you have any objects in this material.
Best regards,
Ilya
On Jul 19, 2017 17:35, "Timm Mohr" timmmmmm@users.sf.net wrote:
Hi,
I have the exact same problem. I have a .model .nrrd and .mask file.
Neither show up, statistics are empty, Exterior seems to occupy the whole
volume. I can still render the model in 3D slicer. I attached a picture of
the files that I am using. Are the file sizes what you would expect? The
.mrc fiel is 6.6GB the .nrrd model 3.3GB and the .model 21MB?
Has this been resolved yet?
Best wishes,
Timm
Attachments:
https://sourceforge.net/p/im-browser/tickets/_discuss/thread/b6305f4b/ecdf/attachment/Capture.PNG
(12.4 kB; image/png)
doesn't show when loaded in MIB 2.01*
Status: New
Created: Tue Apr 25, 2017 08:25 PM UTC by Connon Thomas
Last Updated: Wed Apr 26, 2017 04:43 PM UTC
Owner: nobody
Hi Ilya,
I'm having a frustrating and confusing issue with the current version of
MIB (2.01).
I created a material in MIB, saved it as .model and tried to open it again
in a new MIB window, but once it "loads", the material is blank. It is
listed in the Material panel, but no overlay shows up in the viewer. It's
not an issue with the transparency, I don't have the material hidden, and
regardless of the file type, it won't appear (I saved .model, .am, .tif and
tried to open all of them...nothing). Doing model statistics also shows
that nothing is in the model.
I can open the file in FIJI and after doing an auto-contrast can see it, so
the data is there...I tried opening on previous versions of MIB as well but
it won't open there either. Have you experienced this bug since the
update?? I'm a bit worried since I have about 3 weeks of data that I can't
open. Thanks!
P.S. MIB is awesome, I work with it every day and reccomend it to everyone
I talk to, particularly love the watershed/graphcut function, it's genius.
Cheers,
Connon Thomas
Sent from sourceforge.net because you indicated interest in
https://sourceforge.net/p/im-browser/tickets/8/
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Sry I didn't see your next message. I am running the standalone 2.1 version
on Windows. I thought I was running in 8 bit but I might be wrong, I did a
lot of experimenting. It's really good to know that other formats increase
performance.
The material statistics are unfortunately empty in both the .model and
.nrrd files.
On 20 July 2017 at 08:35, Ilya Belevich ajaxel@users.sf.net wrote:
Hi Timm,
well, it is a bit difficult to comment.
Could you share those model files? I can take a look. However, I am on
holidays and will be able to check it only when I am back after about days.
But it is strange, because you definitely have something in the model files.
Best regards,
Ilya
On Jul 20, 2017 9:57 AM, "Timm Mohr" timmmmmm@users.sf.net wrote:
Sry I didn't see your next message. I am running the standalone 2.1 version
on Windows. I thought I was running in 8 bit but I might be wrong, I did a
lot of experimenting. It's really good to know that other formats increase
performance.
The material statistics are unfortunately empty in both the .model and
.nrrd files.
On 20 July 2017 at 08:35, Ilya Belevich ajaxel@users.sf.net wrote:
Hi Timm,
which version of mib do you use, is it matlab or compiled? wundows or mac?
So your dataset is in Mrc and 6.6 gb. The model in nrrd file is 3gb, which
indicates that uou are working with 16 bit images. I suggest to load mrc
dataset, convert it to 8bit and save in amiramesh or nrrd format.This will
improve general performance.
Next, the .mask and the .model files are 70 and 20 Mb. When those files are
saved Matlab compresses them, and since they are quite big the model and
the mask should contain some data.
Have you been able to render this .nrrd file in Slicer, but in mib it looks
empty? Try to load the model again, highlight material that you have drawn
in the segmentation table, press the right mouse button and select Get
statistics. In the get statistics window press the Run button to find
whether you have any objects in this material.
Best regards,
Ilya
On Jul 19, 2017 17:35, "Timm Mohr" timmmmmm@users.sf.net wrote:
Hi,
I have the exact same problem. I have a .model .nrrd and .mask file.
Neither show up, statistics are empty, Exterior seems to occupy the whole
volume. I can still render the model in 3D slicer. I attached a picture of
the files that I am using. Are the file sizes what you would expect? The
.mrc fiel is 6.6GB the .nrrd model 3.3GB and the .model 21MB?
Has this been resolved yet?
Best wishes,
Timm
Attachments:
https://sourceforge.net/p/im-browser/tickets/_discuss/
thread/b6305f4b/ecdf/attachment/Capture.PNG
https://sourceforge.net/p/im-browser/tickets/_discuss/
thread/b6305f4b/ecdf/attachment/Capture.PNG
https://sourceforge.net/p/im-browser/tickets/_discuss/thread/b6305f4b/ecdf/attachment/Capture.PNG
(12.4 kB; image/png)
https://sourceforge.net/p/im-browser/tickets/8/
https://sourceforge.net/p/im-browser/tickets/8/
https://sourceforge.net/p/im-browser/tickets/8/
https://sourceforge.net/p/im-browser/tickets/8/ Material
doesn't show when loaded in MIB 2.01*
Status: New
Created: Tue Apr 25, 2017 08:25 PM UTC by Connon Thomas
Last Updated: Wed Apr 26, 2017 04:43 PM UTC
Owner: nobody
Hi Ilya,
I'm having a frustrating and confusing issue with the current version of
MIB (2.01).
I created a material in MIB, saved it as .model and tried to open it again
in a new MIB window, but once it "loads", the material is blank. It is
listed in the Material panel, but no overlay shows up in the viewer. It's
not an issue with the transparency, I don't have the material hidden, and
regardless of the file type, it won't appear (I saved .model, .am, .tif and
tried to open all of them...nothing). Doing model statistics also shows
that nothing is in the model.
I can open the file in FIJI and after doing an auto-contrast can see it, so
the data is there...I tried opening on previous versions of MIB as well but
it won't open there either. Have you experienced this bug since the
update?? I'm a bit worried since I have about 3 weeks of data that I can't
open. Thanks!
P.S. MIB is awesome, I work with it every day and reccomend it to everyone
I talk to, particularly love the watershed/graphcut function, it's genius.
Cheers,
Connon Thomas
Sent from sourceforge.net because you indicated interest in
https://sourceforge.net/p/im-browser/tickets/8/
To unsubscribe from further messages, please visit
https://sourceforge.net/auth/subscriptions/
https://sourceforge.net/p/im-browser/tickets/8/
https://sourceforge.net/p/im-browser/tickets/8/ Material
doesn't show when loaded in MIB 2.01*
Status: New
Created: Tue Apr 25, 2017 08:25 PM UTC by Connon Thomas
Last Updated: Wed Jul 19, 2017 03:50 PM UTC
Owner: nobody
Hi Ilya,
I'm having a frustrating and confusing issue with the current version of
MIB (2.01).
I created a material in MIB, saved it as .model and tried to open it again
in a new MIB window, but once it "loads", the material is blank. It is
listed in the Material panel, but no overlay shows up in the viewer. It's
not an issue with the transparency, I don't have the material hidden, and
regardless of the file type, it won't appear (I saved .model, .am, .tif and
tried to open all of them...nothing). Doing model statistics also shows
that nothing is in the model.
I can open the file in FIJI and after doing an auto-contrast can see it,
so the data is there...I tried opening on previous versions of MIB as well
but it won't open there either. Have you experienced this bug since the
update?? I'm a bit worried since I have about 3 weeks of data that I can't
open. Thanks!
P.S. MIB is awesome, I work with it every day and reccomend it to everyone
I talk to, particularly love the watershed/graphcut function, it's genius.
Cheers,
Connon Thomas
Sent from sourceforge.net because you indicated interest in
https://sourceforge.net/p/im-browser/tickets/8/
To unsubscribe from further messages, please visit
https://sourceforge.net/auth/subscriptions/
doesn't show when loaded in MIB 2.01*
Status: New
Created: Tue Apr 25, 2017 08:25 PM UTC by Connon Thomas
Last Updated: Wed Jul 19, 2017 03:50 PM UTC
Owner: nobody
Hi Ilya,
I'm having a frustrating and confusing issue with the current version of
MIB (2.01).
I created a material in MIB, saved it as .model and tried to open it again
in a new MIB window, but once it "loads", the material is blank. It is
listed in the Material panel, but no overlay shows up in the viewer. It's
not an issue with the transparency, I don't have the material hidden, and
regardless of the file type, it won't appear (I saved .model, .am, .tif and
tried to open all of them...nothing). Doing model statistics also shows
that nothing is in the model.
I can open the file in FIJI and after doing an auto-contrast can see it, so
the data is there...I tried opening on previous versions of MIB as well but
it won't open there either. Have you experienced this bug since the
update?? I'm a bit worried since I have about 3 weeks of data that I can't
open. Thanks!
P.S. MIB is awesome, I work with it every day and reccomend it to everyone
I talk to, particularly love the watershed/graphcut function, it's genius.
Cheers,
Connon Thomas
Sent from sourceforge.net because you indicated interest in
https://sourceforge.net/p/im-browser/tickets/8/
To unsubscribe from further messages, please visit
https://sourceforge.net/auth/subscriptions/
Oh, of course. Please don't respond anymore :) Maybe once you are back you
can let me know what way you want me to share the files?
So sorry to have disturbed your holiday.
On 20 July 2017 at 09:21, Ilya Belevich ajaxel@users.sf.net wrote:
Hi Timm,
could you send me to ilya.belevich -at- helsinki.fi the .model file?
It is big for the attachment, so better to use google drive or dropbox
for sharing it.
Thanks!
Ilya
On Thu, Jul 20, 2017 at 12:01 PM, Timm Mohr timmmmmm@users.sf.net wrote:
An odd thing I just noticed. I made a test model with just some squiggles added to a material. I saved it and it loads up again. When I then try to load my model again(currently 15 materials) it still shows the squiggles but in a different colour (I deleted the first material on my model). The .model files also take quite a while to load.
Best regards,
Ilya
On Jul 19, 2017 17:50, "Timm Mohr" timmmmmm@users.sf.net wrote:
An odd thing I just noticed. I made a test model with just some squiggles
added to a material. I saved it and it loads up again. When I then try to
load my model again(currently 15 materials) it still shows the squiggles
but in a different colour (I deleted the first material on my model). The
.model files also take quite a while to load.
doesn't show when loaded in MIB 2.01*
Status: New
Created: Tue Apr 25, 2017 08:25 PM UTC by Connon Thomas
Last Updated: Wed Jul 19, 2017 03:35 PM UTC
Owner: nobody
Hi Ilya,
I'm having a frustrating and confusing issue with the current version of
MIB (2.01).
I created a material in MIB, saved it as .model and tried to open it again
in a new MIB window, but once it "loads", the material is blank. It is
listed in the Material panel, but no overlay shows up in the viewer. It's
not an issue with the transparency, I don't have the material hidden, and
regardless of the file type, it won't appear (I saved .model, .am, .tif and
tried to open all of them...nothing). Doing model statistics also shows
that nothing is in the model.
I can open the file in FIJI and after doing an auto-contrast can see it, so
the data is there...I tried opening on previous versions of MIB as well but
it won't open there either. Have you experienced this bug since the
update?? I'm a bit worried since I have about 3 weeks of data that I can't
open. Thanks!
P.S. MIB is awesome, I work with it every day and reccomend it to everyone
I talk to, particularly love the watershed/graphcut function, it's genius.
Cheers,
Connon Thomas
Sent from sourceforge.net because you indicated interest in
https://sourceforge.net/p/im-browser/tickets/8/
To unsubscribe from further messages, please visit
https://sourceforge.net/auth/subscriptions/
Hi Ilya,
did you see my first message? My main problem at the moment is that the
model is not showing up and appears to be empty although the data seem to
be there still.
Timm
On 20 July 2017 at 08:28, Ilya Belevich ajaxel@users.sf.net wrote:
Related
Tickets: #8