Fiji - compressed .mhd file not working

[robert atwood]

Hi,

In FIJI, I find the capability to use .mhd files, which is useful for me. However I tried saving an (8-bt binary thresholded) image in compressed form , and subsequently opening the file only gives noise or else nothing at all.

However, the file that is written is properly read by other application (using ITK in c++) , and the compressed .mhd file that was created by the ITK application can be read in the Fiji .


In trying to replicated at a smaller scale (original file is 250 Mb -> compressed 9 Mb) I found that sometimes it just silently fails to read the file.

I updated Fiji this morning and it is running on Linux (centOs) platform .

Here is a macro that creates an image to replicate two behaviour modes:
 
__________________________________

newImage("Untitled", "8-bit white", 150, 150, 100);
makeOval(28, 27, 33, 45);
setBackgroundColor(0, 0, 0);
run("Clear", "stack");
run("MHD/MHA compressed ...", "save=blob_compressed.mhd");

run("Add Specified Noise...", "stack standard=25");
run("MHD/MHA compressed ...", "save=blob_noise_compressed.mhd");
run("Close All");


open("blob_compressed.mhd");
getBoolean("Did any file get opened?");
open("blob_noise_compressed.mhd");
getBoolean("Does this look like the original image?");
_______________________________





Dr. Robert C. Atwood
Diamond Light Source
and
Manchester X-ray Imaging Facility (University of Manchester)
Rm G15, Research Complex at Harwell
Harwell Science and Innovation Campous, Didcot,  OX11 0FA
Tel: [phone]
www.diamond.ac.uk
www.rc-harwell.ac.uk 
www.mxif.manchester.ac.uk


--
This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd.
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[ctrueden]

Hi Robert,

Thanks for the bug report. I filed an issue in the relevant component on
GitHub:

https://github.com/fiji/IO/issues/12

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Thu, May 25, 2017 at 7:20 AM, Robert Atwood <[hidden email]>
wrote:

> Hi,
>
> In FIJI, I find the capability to use .mhd files, which is useful for me.
> However I tried saving an (8-bt binary thresholded) image in compressed
> form , and subsequently opening the file only gives noise or else nothing
> at all.
>
> However, the file that is written is properly read by other application
> (using ITK in c++) , and the compressed .mhd file that was created by the
> ITK application can be read in the Fiji .
>
>
> In trying to replicated at a smaller scale (original file is 250 Mb ->
> compressed 9 Mb) I found that sometimes it just silently fails to read the
> file.
>
> I updated Fiji this morning and it is running on Linux (centOs) platform .
>
> Here is a macro that creates an image to replicate two behaviour modes:
>
> __________________________________
>
> newImage("Untitled", "8-bit white", 150, 150, 100);
> makeOval(28, 27, 33, 45);
> setBackgroundColor(0, 0, 0);
> run("Clear", "stack");
> run("MHD/MHA compressed ...", "save=blob_compressed.mhd");
>
> run("Add Specified Noise...", "stack standard=25");
> run("MHD/MHA compressed ...", "save=blob_noise_compressed.mhd");
> run("Close All");
>
>
> open("blob_compressed.mhd");
> getBoolean("Did any file get opened?");
> open("blob_noise_compressed.mhd");
> getBoolean("Does this look like the original image?");
> _______________________________
>
>
>
>
>
> Dr. Robert C. Atwood
> Diamond Light Source
> and
> Manchester X-ray Imaging Facility (University of Manchester)
> Rm G15, Research Complex at Harwell
> Harwell Science and Innovation Campous, Didcot,  OX11 0FA
> Tel: [phone]
> www.diamond.ac.uk
> www.rc-harwell.ac.uk
> www.mxif.manchester.ac.uk
>
>
> --
> This e-mail and any attachments may contain confidential, copyright and or
> privileged material, and are for the use of the intended addressee only. If
> you are not the intended addressee or an authorised recipient of the
> addressee please notify us of receipt by returning the e-mail and do not
> use, copy, retain, distribute or disclose the information in or attached to
> the e-mail.
> Any opinions expressed within this e-mail are those of the individual and
> not necessarily of Diamond Light Source Ltd.
> Diamond Light Source Ltd. cannot guarantee that this e-mail or any
> attachments are free from viruses and we cannot accept liability for any
> damage which you may sustain as a result of software viruses which may be
> transmitted in or with the message.
> Diamond Light Source Limited (company no. 4375679). Registered in England
> and Wales with its registered office at Diamond House, Harwell Science and
> Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[robert atwood]

Thanks for creating a ticket. Is anyone likely to pick up the ticket?


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Curtis Rueden
Sent: Friday, May 26, 2017 19:40
To: [hidden email]
Subject: Re: Fiji - compressed .mhd file not working

Hi Robert,

Thanks for the bug report. I filed an issue in the relevant component on
GitHub:

https://github.com/fiji/IO/issues/12

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden Did you know ImageJ has a forum? http://forum.imagej.net/


On Thu, May 25, 2017 at 7:20 AM, Robert Atwood <[hidden email]>
wrote:

> Hi,
>
> In FIJI, I find the capability to use .mhd files, which is useful for me.
> However I tried saving an (8-bt binary thresholded) image in
> compressed form , and subsequently opening the file only gives noise
> or else nothing at all.
>
> However, the file that is written is properly read by other
> application (using ITK in c++) , and the compressed .mhd file that was
> created by the ITK application can be read in the Fiji .
>
>
> In trying to replicated at a smaller scale (original file is 250 Mb ->
> compressed 9 Mb) I found that sometimes it just silently fails to read
> the file.
>
> I updated Fiji this morning and it is running on Linux (centOs) platform .
>
> Here is a macro that creates an image to replicate two behaviour modes:
>
> __________________________________
>
> newImage("Untitled", "8-bit white", 150, 150, 100); makeOval(28, 27,
> 33, 45); setBackgroundColor(0, 0, 0); run("Clear", "stack");
> run("MHD/MHA compressed ...", "save=blob_compressed.mhd");
>
> run("Add Specified Noise...", "stack standard=25"); run("MHD/MHA
> compressed ...", "save=blob_noise_compressed.mhd");
> run("Close All");
>
>
> open("blob_compressed.mhd");
> getBoolean("Did any file get opened?");
> open("blob_noise_compressed.mhd");
> getBoolean("Does this look like the original image?");
> _______________________________
>
>
>
>
>
> Dr. Robert C. Atwood
> Diamond Light Source
> and
> Manchester X-ray Imaging Facility (University of Manchester) Rm G15,
> Research Complex at Harwell Harwell Science and Innovation Campous,
> Didcot,  OX11 0FA
> Tel: [phone]
> www.diamond.ac.uk
> www.rc-harwell.ac.uk
> www.mxif.manchester.ac.uk
>
>
> --
> This e-mail and any attachments may contain confidential, copyright
> and or privileged material, and are for the use of the intended
> addressee only. If you are not the intended addressee or an authorised
> recipient of the addressee please notify us of receipt by returning
> the e-mail and do not use, copy, retain, distribute or disclose the
> information in or attached to the e-mail.
> Any opinions expressed within this e-mail are those of the individual
> and not necessarily of Diamond Light Source Ltd.
> Diamond Light Source Ltd. cannot guarantee that this e-mail or any
> attachments are free from viruses and we cannot accept liability for
> any damage which you may sustain as a result of software viruses which
> may be transmitted in or with the message.
> Diamond Light Source Limited (company no. 4375679). Registered in
> England and Wales with its registered office at Diamond House, Harwell
> Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United
> Kingdom
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd.
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[ctrueden]

Hi Robert,

> Is anyone likely to pick up the ticket?

I am not sure. The official maintainer of the fiji/IO component right now
is Greg Jefferis, but he has been mostly inactive (with respect to ImageJ)
in recent years. The ticket could be addressed in one of the following
scenarios:

- Greg becomes active again.
- Someone else steps in to maintain fiji/IO (see https://imagej.net/Team)
- I find time to look at the issue in the latter half of this year.

As the "blanket" maintainer of ImageJ2 and Fiji, I try to address the most
"high-impact" issues as time allows, but there are too many bug reports for
me to cover everything, and I also have active development work I need to
achieve.

Soon, I will send an email to the ImageJ community with a comprehensive
update regarding who is maintaining each component of Fiji. I am hoping
this starts a dialogue which not only improves the accuracy of that
information, but also yields new recruits to step in and help cover
additional components. The reality right now is that most Fiji components
do not have dedicated maintainers besides myself.

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Thu, Jun 1, 2017 at 3:43 AM, Robert Atwood <[hidden email]>
wrote:

> Thanks for creating a ticket. Is anyone likely to pick up the ticket?
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Curtis Rueden
> Sent: Friday, May 26, 2017 19:40
> To: [hidden email]
> Subject: Re: Fiji - compressed .mhd file not working
>
> Hi Robert,
>
> Thanks for the bug report. I filed an issue in the relevant component on
> GitHub:
>
> https://github.com/fiji/IO/issues/12
>
> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect - https://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden Did you
> know ImageJ has a forum? http://forum.imagej.net/
>
>
> On Thu, May 25, 2017 at 7:20 AM, Robert Atwood <
> [hidden email]>
> wrote:
>
> > Hi,
> >
> > In FIJI, I find the capability to use .mhd files, which is useful for me.
> > However I tried saving an (8-bt binary thresholded) image in
> > compressed form , and subsequently opening the file only gives noise
> > or else nothing at all.
> >
> > However, the file that is written is properly read by other
> > application (using ITK in c++) , and the compressed .mhd file that was
> > created by the ITK application can be read in the Fiji .
> >
> >
> > In trying to replicated at a smaller scale (original file is 250 Mb ->
> > compressed 9 Mb) I found that sometimes it just silently fails to read
> > the file.
> >
> > I updated Fiji this morning and it is running on Linux (centOs) platform
> .
> >
> > Here is a macro that creates an image to replicate two behaviour modes:
> >
> > __________________________________
> >
> > newImage("Untitled", "8-bit white", 150, 150, 100); makeOval(28, 27,
> > 33, 45); setBackgroundColor(0, 0, 0); run("Clear", "stack");
> > run("MHD/MHA compressed ...", "save=blob_compressed.mhd");
> >
> > run("Add Specified Noise...", "stack standard=25"); run("MHD/MHA
> > compressed ...", "save=blob_noise_compressed.mhd");
> > run("Close All");
> >
> >
> > open("blob_compressed.mhd");
> > getBoolean("Did any file get opened?");
> > open("blob_noise_compressed.mhd");
> > getBoolean("Does this look like the original image?");
> > _______________________________
> >
> >
> >
> >
> >
> > Dr. Robert C. Atwood
> > Diamond Light Source
> > and
> > Manchester X-ray Imaging Facility (University of Manchester) Rm G15,
> > Research Complex at Harwell Harwell Science and Innovation Campous,
> > Didcot,  OX11 0FA
> > Tel: [phone] <+44%201235%20778670>
> > www.diamond.ac.uk
> > www.rc-harwell.ac.uk
> > www.mxif.manchester.ac.uk
> >
> >
> > --
> > This e-mail and any attachments may contain confidential, copyright
> > and or privileged material, and are for the use of the intended
> > addressee only. If you are not the intended addressee or an authorised
> > recipient of the addressee please notify us of receipt by returning
> > the e-mail and do not use, copy, retain, distribute or disclose the
> > information in or attached to the e-mail.
> > Any opinions expressed within this e-mail are those of the individual
> > and not necessarily of Diamond Light Source Ltd.
> > Diamond Light Source Ltd. cannot guarantee that this e-mail or any
> > attachments are free from viruses and we cannot accept liability for
> > any damage which you may sustain as a result of software viruses which
> > may be transmitted in or with the message.
> > Diamond Light Source Limited (company no. 4375679). Registered in
> > England and Wales with its registered office at Diamond House, Harwell
> > Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United
> > Kingdom
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> This e-mail and any attachments may contain confidential, copyright and or
> privileged material, and are for the use of the intended addressee only. If
> you are not the intended addressee or an authorised recipient of the
> addressee please notify us of receipt by returning the e-mail and do not
> use, copy, retain, distribute or disclose the information in or attached to
> the e-mail.
> Any opinions expressed within this e-mail are those of the individual and
> not necessarily of Diamond Light Source Ltd.
> Diamond Light Source Ltd. cannot guarantee that this e-mail or any
> attachments are free from viruses and we cannot accept liability for any
> damage which you may sustain as a result of software viruses which may be
> transmitted in or with the message.
> Diamond Light Source Limited (company no. 4375679). Registered in England
> and Wales with its registered office at Diamond House, Harwell Science and
> Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[ctrueden]

Hi Robert,

> Wouldn't it make sense to deactivate that feature if nobody's fixing
> it and it doesn't work?

Are you certain that _all_ compressed MHDs read incorrectly? If not, then
disabling it might break some people's workflows.

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Thu, Jun 1, 2017 at 9:26 AM, <[hidden email]> wrote:

> Wouldn't it make sense to deactivate that feature if nobody's fixing it
> and it doesn't work?
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Curtis Rueden
> Sent: Thursday, June 1, 2017 14:57
> To: [hidden email]
> Subject: Re: Fiji - compressed .mhd file not working
>
> Hi Robert,
>
> > Is anyone likely to pick up the ticket?
>
> I am not sure. The official maintainer of the fiji/IO component right now
> is Greg Jefferis, but he has been mostly inactive (with respect to ImageJ)
> in recent years. The ticket could be addressed in one of the following
> scenarios:
>
> - Greg becomes active again.
> - Someone else steps in to maintain fiji/IO (see https://imagej.net/Team)
> - I find time to look at the issue in the latter half of this year.
>
> As the "blanket" maintainer of ImageJ2 and Fiji, I try to address the most
> "high-impact" issues as time allows, but there are too many bug reports for
> me to cover everything, and I also have active development work I need to
> achieve.
>
> Soon, I will send an email to the ImageJ community with a comprehensive
> update regarding who is maintaining each component of Fiji. I am hoping
> this starts a dialogue which not only improves the accuracy of that
> information, but also yields new recruits to step in and help cover
> additional components. The reality right now is that most Fiji components
> do not have dedicated maintainers besides myself.
>
> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect - https://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden Did you
> know ImageJ has a forum? http://forum.imagej.net/
>
>
> On Thu, Jun 1, 2017 at 3:43 AM, Robert Atwood <[hidden email]
> >
> wrote:
>
> > Thanks for creating a ticket. Is anyone likely to pick up the ticket?
> >
> >
> > -----Original Message-----
> > From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> > Curtis Rueden
> > Sent: Friday, May 26, 2017 19:40
> > To: [hidden email]
> > Subject: Re: Fiji - compressed .mhd file not working
> >
> > Hi Robert,
> >
> > Thanks for the bug report. I filed an issue in the relevant component
> > on
> > GitHub:
> >
> > https://github.com/fiji/IO/issues/12
> >
> > Regards,
> > Curtis
> >
> > --
> > Curtis Rueden
> > LOCI software architect - https://loci.wisc.edu/software
> > ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden Did you
> > know ImageJ has a forum? http://forum.imagej.net/
> >
> >
> > On Thu, May 25, 2017 at 7:20 AM, Robert Atwood <
> > [hidden email]>
> > wrote:
> >
> > > Hi,
> > >
> > > In FIJI, I find the capability to use .mhd files, which is useful for
> me.
> > > However I tried saving an (8-bt binary thresholded) image in
> > > compressed form , and subsequently opening the file only gives noise
> > > or else nothing at all.
> > >
> > > However, the file that is written is properly read by other
> > > application (using ITK in c++) , and the compressed .mhd file that
> > > was created by the ITK application can be read in the Fiji .
> > >
> > >
> > > In trying to replicated at a smaller scale (original file is 250 Mb
> > > -> compressed 9 Mb) I found that sometimes it just silently fails to
> > > read the file.
> > >
> > > I updated Fiji this morning and it is running on Linux (centOs)
> > > platform
> > .
> > >
> > > Here is a macro that creates an image to replicate two behaviour modes:
> > >
> > > __________________________________
> > >
> > > newImage("Untitled", "8-bit white", 150, 150, 100); makeOval(28, 27,
> > > 33, 45); setBackgroundColor(0, 0, 0); run("Clear", "stack");
> > > run("MHD/MHA compressed ...", "save=blob_compressed.mhd");
> > >
> > > run("Add Specified Noise...", "stack standard=25"); run("MHD/MHA
> > > compressed ...", "save=blob_noise_compressed.mhd");
> > > run("Close All");
> > >
> > >
> > > open("blob_compressed.mhd");
> > > getBoolean("Did any file get opened?");
> > > open("blob_noise_compressed.mhd");
> > > getBoolean("Does this look like the original image?");
> > > _______________________________
> > >
> > >
> > >
> > >
> > >
> > > Dr. Robert C. Atwood
> > > Diamond Light Source
> > > and
> > > Manchester X-ray Imaging Facility (University of Manchester) Rm G15,
> > > Research Complex at Harwell Harwell Science and Innovation Campous,
> > > Didcot,  OX11 0FA
> > > Tel: [phone] <+44%201235%20778670> www.diamond.ac.uk
> > > www.rc-harwell.ac.uk www.mxif.manchester.ac.uk
> > >
> > >
> > > --
> > > This e-mail and any attachments may contain confidential, copyright
> > > and or privileged material, and are for the use of the intended
> > > addressee only. If you are not the intended addressee or an
> > > authorised recipient of the addressee please notify us of receipt by
> > > returning the e-mail and do not use, copy, retain, distribute or
> > > disclose the information in or attached to the e-mail.
> > > Any opinions expressed within this e-mail are those of the
> > > individual and not necessarily of Diamond Light Source Ltd.
> > > Diamond Light Source Ltd. cannot guarantee that this e-mail or any
> > > attachments are free from viruses and we cannot accept liability for
> > > any damage which you may sustain as a result of software viruses
> > > which may be transmitted in or with the message.
> > > Diamond Light Source Limited (company no. 4375679). Registered in
> > > England and Wales with its registered office at Diamond House,
> > > Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11
> > > 0DE, United Kingdom
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
> > --
> > This e-mail and any attachments may contain confidential, copyright
> > and or privileged material, and are for the use of the intended
> > addressee only. If you are not the intended addressee or an authorised
> > recipient of the addressee please notify us of receipt by returning
> > the e-mail and do not use, copy, retain, distribute or disclose the
> > information in or attached to the e-mail.
> > Any opinions expressed within this e-mail are those of the individual
> > and not necessarily of Diamond Light Source Ltd.
> > Diamond Light Source Ltd. cannot guarantee that this e-mail or any
> > attachments are free from viruses and we cannot accept liability for
> > any damage which you may sustain as a result of software viruses which
> > may be transmitted in or with the message.
> > Diamond Light Source Limited (company no. 4375679). Registered in
> > England and Wales with its registered office at Diamond House, Harwell
> > Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United
> > Kingdom
> >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> This e-mail and any attachments may contain confidential, copyright and or
> privileged material, and are for the use of the intended addressee only. If
> you are not the intended addressee or an authorised recipient of the
> addressee please notify us of receipt by returning the e-mail and do not
> use, copy, retain, distribute or disclose the information in or attached to
> the e-mail.
> Any opinions expressed within this e-mail are those of the individual and
> not necessarily of Diamond Light Source Ltd.
> Diamond Light Source Ltd. cannot guarantee that this e-mail or any
> attachments are free from viruses and we cannot accept liability for any
> damage which you may sustain as a result of software viruses which may be
> transmitted in or with the message.
> Diamond Light Source Limited (company no. 4375679). Registered in England
> and Wales with its registered office at Diamond House, Harwell Science and
> Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html