Bad Magic Number #5
Comments
|
Il giorno lun 29 lug 2019 alle ore 17:36 JeffreyStirman <
notifications@github.com> ha scritto:
Hi, I am trying to run the paraconverter to convert from 2D TIFF series to
IMS file. When running I get a "Bad Magic Number" error. I am using Python
3.7 (Anaconda download) for other reasons. Could it be that it was compiled
in 2.7 and this causes the error? If so could I get the .py file and
compile it in 3.7 and use this?
Jeffrey, there is something I am not sure to understand.
You say that you are using "paraconverter" to convert to IMS format. Are
you launching multiple instances of TeraStitcher using the python script?
In this case consider that IMS format is a single HDF5 file which cannot be
generated by multiple processes, so if you try to do that it is normal that
something goes wrong.
Unfortunately, to convert to IMS format you have to use a single instance
of TeraConverter.
If this is not the problem (i.e. you are using a single instance of
TeraConverter or you have specified -np 2 as an mpirun option) let me
understand if the error is raised by the TIFF libary (i.e. an error window
appears with a message like "not a TIFF or MDI file bad magic number XXXXX
(0xhhhhh)". In this case it is possible that in your folder there is a non
TIFF file that should be deleted before running TeraConverter (e.g. a
Thumb.db file on mac os x).
If the problem is none of these let me know more details.
Best.
…-- Giulio
____________________________________________________________________
Giulio Iannello
Preside della Facolta' Dipartimentale di Ingegneria
Universita' Campus Bio-Medico di Roma
v. Alvaro del Portillo, 21
00128 Roma, Italy
Tel: +39-06-22541-9602 E-mail:
g.iannello@unicampus.it
Fax: +39-06-22541-9609 URL:
https://scholar.google.it/citations?user=L-UJxIgAAAAJ
____________________________________________________________________
|
|
It is possible that is a problem of Python version.
Attached there is the last script. I tested it with Python 3, but I do not
remember the version.
Let me know if you solve the problem.
…-- Giulio
Il giorno mar 30 lug 2019 alle ore 19:09 JeffreyStirman <
notifications@github.com> ha scritto:
OK, so let's forget about that issue since I cannot convert to IMS.
But I am now running the parallel processes for the alignment and merge.
When I run the parastitcher I also get the 'bad magic number' error.
I run:
mpiexec -np 40 python C:\terastitcher\Parastitcher3.2.0.pyc -2
--projin=.\xml_import.xml --projout=.\xml_displcomp_par2.xml
And get RuntimeError: Bad magic number in .pyc file
Again I am using Python 3.7. Could it be that the .pyc was compiled in the
earlier version? If so could I get the .py file and compile it in 3.7?
Thanks
Jeff
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____________________________________________________________________
Giulio Iannello
Preside della Facolta' Dipartimentale di Ingegneria
Universita' Campus Bio-Medico di Roma
v. Alvaro del Portillo, 21
00128 Roma, Italy
Tel: +39-06-22541-9602 E-mail:
g.iannello@unicampus.it
Fax: +39-06-22541-9609 URL:
https://scholar.google.it/citations?user=L-UJxIgAAAAJ
____________________________________________________________________
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OK, let's leave that alone since I cannot convert to Imaris. And the issue was totally the Python version. Got 2.7 and it 'works'. I say works because of this issue: When running the Align step using parasitcher, it rund for about 20 min on my data set (~480GB) and it outputs a xml_displcomp.xml file, but that file contains no information: Here is a text file of the input and the output when I run that step. From what I can tell it runs fine as in it takes about the right amount of time, uses almost all 256GB of RAM, and uses quite a few processors. Just no output of use Any ideas what is going on? Thanks! |
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Oh, and it doesnt show any outputs until its done. When using terstitcher I always remember seeing updates/outputs as it was progressing. Basically what is in the text file, but as it is doing it. |
|
Jeffrey,
it is possible ther is a bug in the distributed termination algorithm. I
have to think a bit about that.
I will write you as soon as I have identified the problem.
Sorry :-(
…-- Giulio
Il giorno mer 31 lug 2019 alle ore 01:28 JeffreyStirman <
notifications@github.com> ha scritto:
OK, let's leave that alone since I cannot convert to Imaris.
And the issue was totally the Python version. Got 2.7 and it 'works'. I
say works because of this issue:
When running the Align step using parasitcher, it rund for about 20 min on
my data set (~480GB) and it outputs a xml_displcomp.xml file, but that file
contains no information:
xml_displcomp
<https://user-images.githubusercontent.com/3090732/62172325-de731780-b2ff-11e9-8fc7-9b2899f27170.jpeg>
Here is a text file of the input and the output when I run that step. From
what I can tell it runs fine as in it takes about the right amount of time,
uses almost all 256GB of RAM, and uses quite a few processors. Just no
output of use
Input_output.txt
<https://github.com/Vaa3D/Vaa3D_Wiki/files/3449189/Input_output.txt>
Any ideas what is going on?
Thanks!
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____________________________________________________________________
Giulio Iannello
Preside della Facolta' Dipartimentale di Ingegneria
Universita' Campus Bio-Medico di Roma
v. Alvaro del Portillo, 21
00128 Roma, Italy
Tel: +39-06-22541-9602 E-mail:
g.iannello@unicampus.it
Fax: +39-06-22541-9609 URL:
https://scholar.google.it/citations?user=L-UJxIgAAAAJ
____________________________________________________________________
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Ok. If there is anything I can do to help, let me know. This software is
extremely useful and this is one of the last hurdles.
Skipping this step and just merging from the nominal stage coordinates is
great and works well and fast (with parastitcher). The only downside I can
find is there is no progress bar...
Thanks!
…On Thu, Aug 1, 2019, 11:21 AM Giulio Iannello ***@***.***> wrote:
Jeffrey,
it is possible ther is a bug in the distributed termination algorithm. I
have to think a bit about that.
I will write you as soon as I have identified the problem.
Sorry :-(
-- Giulio
Il giorno mer 31 lug 2019 alle ore 01:28 JeffreyStirman <
***@***.***> ha scritto:
> OK, let's leave that alone since I cannot convert to Imaris.
>
> And the issue was totally the Python version. Got 2.7 and it 'works'. I
> say works because of this issue:
>
> When running the Align step using parasitcher, it rund for about 20 min
on
> my data set (~480GB) and it outputs a xml_displcomp.xml file, but that
file
> contains no information:
>
> xml_displcomp
> <
https://user-images.githubusercontent.com/3090732/62172325-de731780-b2ff-11e9-8fc7-9b2899f27170.jpeg
>
>
> Here is a text file of the input and the output when I run that step.
From
> what I can tell it runs fine as in it takes about the right amount of
time,
> uses almost all 256GB of RAM, and uses quite a few processors. Just no
> output of use
>
> Input_output.txt
> <https://github.com/Vaa3D/Vaa3D_Wiki/files/3449189/Input_output.txt>
>
> Any ideas what is going on?
>
> Thanks!
>
> —
> You are receiving this because you commented.
> Reply to this email directly, view it on GitHub
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>,
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>
--
____________________________________________________________________
Giulio Iannello
Preside della Facolta' Dipartimentale di Ingegneria
Universita' Campus Bio-Medico di Roma
v. Alvaro del Portillo, 21
00128 Roma, Italy
Tel: +39-06-22541-9602 E-mail:
***@***.***
Fax: +39-06-22541-9609 URL:
https://scholar.google.it/citations?user=L-UJxIgAAAAJ
____________________________________________________________________
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Please try this version. I did only one test, but it is likely that the bug
is fixed.
Let me know what happens.
…-- Giulio
Il giorno gio 1 ago 2019 alle ore 18:19 JeffreyStirman <
notifications@github.com> ha scritto:
Ok. If there is anything I can do to help, let me know. This software is
extremely useful and this is one of the last hurdles.
Skipping this step and just merging from the nominal stage coordinates is
great and works well and fast (with parastitcher). The only downside I can
find is there is no progress bar...
Thanks!
On Thu, Aug 1, 2019, 11:21 AM Giulio Iannello ***@***.***>
wrote:
> Jeffrey,
> it is possible ther is a bug in the distributed termination algorithm. I
> have to think a bit about that.
> I will write you as soon as I have identified the problem.
> Sorry :-(
>
> -- Giulio
>
>
>
> Il giorno mer 31 lug 2019 alle ore 01:28 JeffreyStirman <
> ***@***.***> ha scritto:
>
> > OK, let's leave that alone since I cannot convert to Imaris.
> >
> > And the issue was totally the Python version. Got 2.7 and it 'works'. I
> > say works because of this issue:
> >
> > When running the Align step using parasitcher, it rund for about 20 min
> on
> > my data set (~480GB) and it outputs a xml_displcomp.xml file, but that
> file
> > contains no information:
> >
> > xml_displcomp
> > <
>
https://user-images.githubusercontent.com/3090732/62172325-de731780-b2ff-11e9-8fc7-9b2899f27170.jpeg
> >
> >
> > Here is a text file of the input and the output when I run that step.
> From
> > what I can tell it runs fine as in it takes about the right amount of
> time,
> > uses almost all 256GB of RAM, and uses quite a few processors. Just no
> > output of use
> >
> > Input_output.txt
> > <https://github.com/Vaa3D/Vaa3D_Wiki/files/3449189/Input_output.txt>
> >
> > Any ideas what is going on?
> >
> > Thanks!
> >
> > —
> > You are receiving this because you commented.
> > Reply to this email directly, view it on GitHub
> > <
>
#5?email_source=notifications&email_token=ACDW7VQPQWTIZDQZ2JQEZ2DQCDFCPA5CNFSM4IHTV442YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3FTJCY#issuecomment-516633739
> >,
> > or mute the thread
> > <
>
https://github.com/notifications/unsubscribe-auth/ACDW7VXZ3EJWXVJYNPKFUNLQCDFCPANCNFSM4IHTV44Q
> >
> > .
> >
>
>
> --
> ____________________________________________________________________
>
> Giulio Iannello
> Preside della Facolta' Dipartimentale di Ingegneria
> Universita' Campus Bio-Medico di Roma
> v. Alvaro del Portillo, 21
> 00128 Roma, Italy
>
> Tel: +39-06-22541-9602 E-mail:
> ***@***.***
> Fax: +39-06-22541-9609 URL:
> https://scholar.google.it/citations?user=L-UJxIgAAAAJ
> ____________________________________________________________________
>
> —
> You are receiving this because you authored the thread.
> Reply to this email directly, view it on GitHub
> <
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>,
> or mute the thread
> <
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> .
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____________________________________________________________________
Giulio Iannello
Preside della Facolta' Dipartimentale di Ingegneria
Universita' Campus Bio-Medico di Roma
v. Alvaro del Portillo, 21
00128 Roma, Italy
Tel: +39-06-22541-9602 E-mail:
g.iannello@unicampus.it
Fax: +39-06-22541-9609 URL:
https://scholar.google.it/citations?user=L-UJxIgAAAAJ
____________________________________________________________________
|
|
I will try this Sunday when I return. Thanks so much.
On Thu, Aug 1, 2019, 1:18 PM Giulio Iannello <notifications@github.com>
wrote:
… Please try this version. I did only one test, but it is likely that the bug
is fixed.
Let me know what happens.
-- Giulio
Il giorno gio 1 ago 2019 alle ore 18:19 JeffreyStirman <
***@***.***> ha scritto:
> Ok. If there is anything I can do to help, let me know. This software is
> extremely useful and this is one of the last hurdles.
>
> Skipping this step and just merging from the nominal stage coordinates is
> great and works well and fast (with parastitcher). The only downside I
can
> find is there is no progress bar...
>
> Thanks!
>
> On Thu, Aug 1, 2019, 11:21 AM Giulio Iannello ***@***.***>
> wrote:
>
> > Jeffrey,
> > it is possible ther is a bug in the distributed termination algorithm.
I
> > have to think a bit about that.
> > I will write you as soon as I have identified the problem.
> > Sorry :-(
> >
> > -- Giulio
> >
> >
> >
> > Il giorno mer 31 lug 2019 alle ore 01:28 JeffreyStirman <
> > ***@***.***> ha scritto:
> >
> > > OK, let's leave that alone since I cannot convert to Imaris.
> > >
> > > And the issue was totally the Python version. Got 2.7 and it
'works'. I
> > > say works because of this issue:
> > >
> > > When running the Align step using parasitcher, it rund for about 20
min
> > on
> > > my data set (~480GB) and it outputs a xml_displcomp.xml file, but
that
> > file
> > > contains no information:
> > >
> > > xml_displcomp
> > > <
> >
>
https://user-images.githubusercontent.com/3090732/62172325-de731780-b2ff-11e9-8fc7-9b2899f27170.jpeg
> > >
> > >
> > > Here is a text file of the input and the output when I run that step.
> > From
> > > what I can tell it runs fine as in it takes about the right amount of
> > time,
> > > uses almost all 256GB of RAM, and uses quite a few processors. Just
no
> > > output of use
> > >
> > > Input_output.txt
> > > <https://github.com/Vaa3D/Vaa3D_Wiki/files/3449189/Input_output.txt>
> > >
> > > Any ideas what is going on?
> > >
> > > Thanks!
> > >
> > > —
> > > You are receiving this because you commented.
> > > Reply to this email directly, view it on GitHub
> > > <
> >
>
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> > >,
> > > or mute the thread
> > > <
> >
>
https://github.com/notifications/unsubscribe-auth/ACDW7VXZ3EJWXVJYNPKFUNLQCDFCPANCNFSM4IHTV44Q
> > >
> > > .
> > >
> >
> >
> > --
> > ____________________________________________________________________
> >
> > Giulio Iannello
> > Preside della Facolta' Dipartimentale di Ingegneria
> > Universita' Campus Bio-Medico di Roma
> > v. Alvaro del Portillo, 21
> > 00128 Roma, Italy
> >
> > Tel: +39-06-22541-9602 E-mail:
> > ***@***.***
> > Fax: +39-06-22541-9609 URL:
> > https://scholar.google.it/citations?user=L-UJxIgAAAAJ
> > ____________________________________________________________________
> >
> > —
> > You are receiving this because you authored the thread.
> > Reply to this email directly, view it on GitHub
> > <
>
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> >,
> > or mute the thread
> > <
>
https://github.com/notifications/unsubscribe-auth/AAXSSLCTUJJIUZU7GW4RVITQCL5PLANCNFSM4IHTV44Q
> >
> > .
> >
>
> —
> You are receiving this because you commented.
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> <
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>,
> or mute the thread
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> .
>
--
____________________________________________________________________
Giulio Iannello
Preside della Facolta' Dipartimentale di Ingegneria
Universita' Campus Bio-Medico di Roma
v. Alvaro del Portillo, 21
00128 Roma, Italy
Tel: +39-06-22541-9602 E-mail:
***@***.***
Fax: +39-06-22541-9609 URL:
https://scholar.google.it/citations?user=L-UJxIgAAAAJ
____________________________________________________________________
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Was there a file attached or a link? im not seeing one... |
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You can also email me directly at
jeffrey.stirman@gmail.com
On Thu, Aug 1, 2019, 1:19 PM Jeffrey Stirman <jeffrey.stirman@gmail.com>
wrote:
… I will try this Sunday when I return. Thanks so much.
On Thu, Aug 1, 2019, 1:18 PM Giulio Iannello ***@***.***>
wrote:
> Please try this version. I did only one test, but it is likely that the
> bug
> is fixed.
> Let me know what happens.
>
> -- Giulio
>
>
>
> Il giorno gio 1 ago 2019 alle ore 18:19 JeffreyStirman <
> ***@***.***> ha scritto:
>
> > Ok. If there is anything I can do to help, let me know. This software is
> > extremely useful and this is one of the last hurdles.
> >
> > Skipping this step and just merging from the nominal stage coordinates
> is
> > great and works well and fast (with parastitcher). The only downside I
> can
> > find is there is no progress bar...
> >
> > Thanks!
> >
> > On Thu, Aug 1, 2019, 11:21 AM Giulio Iannello ***@***.***
> >
> > wrote:
> >
> > > Jeffrey,
> > > it is possible ther is a bug in the distributed termination
> algorithm. I
> > > have to think a bit about that.
> > > I will write you as soon as I have identified the problem.
> > > Sorry :-(
> > >
> > > -- Giulio
> > >
> > >
> > >
> > > Il giorno mer 31 lug 2019 alle ore 01:28 JeffreyStirman <
> > > ***@***.***> ha scritto:
> > >
> > > > OK, let's leave that alone since I cannot convert to Imaris.
> > > >
> > > > And the issue was totally the Python version. Got 2.7 and it
> 'works'. I
> > > > say works because of this issue:
> > > >
> > > > When running the Align step using parasitcher, it rund for about 20
> min
> > > on
> > > > my data set (~480GB) and it outputs a xml_displcomp.xml file, but
> that
> > > file
> > > > contains no information:
> > > >
> > > > xml_displcomp
> > > > <
> > >
> >
> https://user-images.githubusercontent.com/3090732/62172325-de731780-b2ff-11e9-8fc7-9b2899f27170.jpeg
> > > >
> > > >
> > > > Here is a text file of the input and the output when I run that
> step.
> > > From
> > > > what I can tell it runs fine as in it takes about the right amount
> of
> > > time,
> > > > uses almost all 256GB of RAM, and uses quite a few processors. Just
> no
> > > > output of use
> > > >
> > > > Input_output.txt
> > > > <https://github.com/Vaa3D/Vaa3D_Wiki/files/3449189/Input_output.txt
> >
> > > >
> > > > Any ideas what is going on?
> > > >
> > > > Thanks!
> > > >
> > > > —
> > > > You are receiving this because you commented.
> > > > Reply to this email directly, view it on GitHub
> > > > <
> > >
> >
> #5?email_source=notifications&email_token=ACDW7VQPQWTIZDQZ2JQEZ2DQCDFCPA5CNFSM4IHTV442YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3FTJCY#issuecomment-516633739
> > > >,
> > > > or mute the thread
> > > > <
> > >
> >
> https://github.com/notifications/unsubscribe-auth/ACDW7VXZ3EJWXVJYNPKFUNLQCDFCPANCNFSM4IHTV44Q
> > > >
> > > > .
> > > >
> > >
> > >
> > > --
> > > ____________________________________________________________________
> > >
> > > Giulio Iannello
> > > Preside della Facolta' Dipartimentale di Ingegneria
> > > Universita' Campus Bio-Medico di Roma
> > > v. Alvaro del Portillo, 21
> > > 00128 Roma, Italy
> > >
> > > Tel: +39-06-22541-9602 E-mail:
> > > ***@***.***
> > > Fax: +39-06-22541-9609 URL:
> > > https://scholar.google.it/citations?user=L-UJxIgAAAAJ
> > > ____________________________________________________________________
> > >
> > > —
> > > You are receiving this because you authored the thread.
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Hi, I am trying to run the paraconverter to convert from 2D TIFF series to IMS file. When running I get a "Bad Magic Number" error. I am using Python 3.7 (Anaconda download) for other reasons. Could it be that it was compiled in 2.7 and this causes the error? If so could I get the .py file and compile it in 3.7 and use this?
Thanks!
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