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AVI, Virtual Stack, >1GB boundery?

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Robert Dougherty

Re: removing out-of-focus objects

Frank,

My favorite technique is to apply a small blur and subtract the
blurred image from the original. Areas that show a big change are
likely to be in focus. (Or maybe not, depending on the details of
the optics.)

Bob

On Feb 2, 2009, at 11:42 AM, Franklin Shaffer wrote:

> I am taking high speed videos of 3D object (particle) flow fields
> with a 2D high speed camera. I have the classic problem in that
> particles are in-focus in a plane and particles outside the plane
> are out-of-focus.
>
> I am testing FFT bandpass and other filters to remove the out-of-
> focus particles.
>
> If anyone has experience with filters or ImageJ plugins that work
> will for removing out-of-focus objects, please advise.
>
> Thank you,
> Frank Shaffer
>
> DOE National Energy Technology Laboratory

Robert Dougherty, Ph.D.
President, OptiNav, Inc.
4176 148th Ave. NE
Redmond, WA 98052
Tel. (425)891-4883
FAX (425)467-1119
www.optinav.com
[hidden email]

Deborah Cole

ARF conversion into IDL?

I have never worked with ARF files before, but apparently they're some
type of movie files stacked on top of each other. I received files I
ordered from a company in ARF files. I've been trying to hunt down any
information I can to help me convert them over so I can view it into
ENVI via IDL programming language. My boss loves IDL, so I have to
figure this out for him and I have no idea. I'm beginning to think ARF
files were created specifically for the ImageJ program.

Has anyone used IDL or ENVI to view ARF files?

Thank you,

Deb

Philip Ershler

Re: ARF conversion into IDL?

Just Google for ARF file format. You will find many hits..

Remember, Google is really your friend ; > )

Phil

On Feb 2, 2009, at 3:10 PM, Deborah Cole wrote:

> I have never worked with ARF files before, but apparently they're some
> type of movie files stacked on top of each other. I received files I
> ordered from a company in ARF files. I've been trying to hunt down
> any
> information I can to help me convert them over so I can view it into
> ENVI via IDL programming language. My boss loves IDL, so I have to
> figure this out for him and I have no idea. I'm beginning to think ARF
> files were created specifically for the ImageJ program.
>
> Has anyone used IDL or ENVI to view ARF files?
>
> Thank you,
>
> Deb

David Webster

Re: ARF conversion into IDL?

In reply to this post by Deborah Cole

Deb,,

For what its worth, the ARF file format I am familiar with was developed by
the Army's Center for Night Vision and Electro-Optics.

David

On Mon, Feb 2, 2009 at 2:10 PM, Deborah Cole <[hidden email]> wrote:

> I have never worked with ARF files before, but apparently they're some
> type of movie files stacked on top of each other. I received files I
> ordered from a company in ARF files. I've been trying to hunt down any
> information I can to help me convert them over so I can view it into
> ENVI via IDL programming language. My boss loves IDL, so I have to
> figure this out for him and I have no idea. I'm beginning to think ARF
> files were created specifically for the ImageJ program.
>
> Has anyone used IDL or ENVI to view ARF files?
>
> Thank you,
>
> Deb
>

Deborah Cole

Re: ARF conversion into IDL?

In reply to this post by Philip Ershler

Thank you, but I wouldn't have posted the question had I not already
done extensive searches online with multiple search engines.

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Philip Ershler
Sent: Monday, February 02, 2009 5:29 PM
To: [hidden email]
Subject: Re: ARF conversion into IDL?

Just Google for ARF file format. You will find many hits..

Remember, Google is really your friend ; > )

Phil

On Feb 2, 2009, at 3:10 PM, Deborah Cole wrote:

Philip Ershler

Re: ARF conversion into IDL?

Here's a freeware program that claims it can convert ARF files. It two
clicks past the main page when I googled for ARF file format.

http://pagesperso-orange.fr/pierre.g/xnview/enxnview.html

HTH,

Phil

On Feb 3, 2009, at 7:16 AM, Deborah Cole wrote:

> Thank you, but I wouldn't have posted the question had I not already
> done extensive searches online with multiple search engines.
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Philip Ershler
> Sent: Monday, February 02, 2009 5:29 PM
> To: [hidden email]
> Subject: Re: ARF conversion into IDL?
>
> Just Google for ARF file format. You will find many hits..
>
> Remember, Google is really your friend ; > )
>
> Phil
>
> On Feb 2, 2009, at 3:10 PM, Deborah Cole wrote:
>
>> I have never worked with ARF files before, but apparently they're
>> some
>> type of movie files stacked on top of each other. I received files I
>> ordered from a company in ARF files. I've been trying to hunt down
>> any
>> information I can to help me convert them over so I can view it into
>> ENVI via IDL programming language. My boss loves IDL, so I have to
>> figure this out for him and I have no idea. I'm beginning to think
>> ARF
>> files were created specifically for the ImageJ program.
>>
>> Has anyone used IDL or ENVI to view ARF files?
>>
>> Thank you,
>>
>> Deb

Deborah Cole

Re: ARF conversion into IDL?

If someone looks up 'da bomb' in the dictionary, I'll bet your picture
is there! You're a real life-saver. This is exactly what I needed.
You rock. Thank you so very much! :)

Debbie

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Philip Ershler
Sent: Tuesday, February 03, 2009 2:10 PM
To: [hidden email]
Subject: Re: ARF conversion into IDL?

Here's a freeware program that claims it can convert ARF files. It two
clicks past the main page when I googled for ARF file format.

http://pagesperso-orange.fr/pierre.g/xnview/enxnview.html

HTH,

Phil

On Feb 3, 2009, at 7:16 AM, Deborah Cole wrote:

Deborah Cole

Re: ARF conversion into IDL?

In reply to this post by Philip Ershler

Whoops. Spoke too soon. The program says ARF files are not supported,
even though it does say in the website that they are. Oh well. I'll
keep on truckin'....

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Philip Ershler
Sent: Tuesday, February 03, 2009 2:10 PM
To: [hidden email]
Subject: Re: ARF conversion into IDL?

Here's a freeware program that claims it can convert ARF files. It two
clicks past the main page when I googled for ARF file format.

http://pagesperso-orange.fr/pierre.g/xnview/enxnview.html

HTH,

Phil

On Feb 3, 2009, at 7:16 AM, Deborah Cole wrote:

Philip Ershler

Re: ARF conversion into IDL?

OK, we need to know a bit more about where these files came from. It
turns out that .arf is not a unique file format. It could be one of
the following.

.arf - Automatic Response file
.arf - ARF image format
.arf - Active Tutor data file
.arf - AOL Instant Messenger (AIM) resource file
.arf - Flexible image transport system bitmap

Do you have any information about which of these dogs you have to deal
with? (arf, arf). ; > )

Phil

On Feb 4, 2009, at 2:16 PM, Deborah Cole wrote:

> Whoops. Spoke too soon. The program says ARF files are not supported,
> even though it does say in the website that they are. Oh well. I'll
> keep on truckin'....
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Philip Ershler
> Sent: Tuesday, February 03, 2009 2:10 PM
> To: [hidden email]
> Subject: Re: ARF conversion into IDL?
>
> Here's a freeware program that claims it can convert ARF files. It two
> clicks past the main page when I googled for ARF file format.
>
> http://pagesperso-orange.fr/pierre.g/xnview/enxnview.html
>
> HTH,
>
> Phil
>
> On Feb 3, 2009, at 7:16 AM, Deborah Cole wrote:
>
>> Thank you, but I wouldn't have posted the question had I not already
>> done extensive searches online with multiple search engines.
>>
>>
>> -----Original Message-----
>> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
>> Philip Ershler
>> Sent: Monday, February 02, 2009 5:29 PM
>> To: [hidden email]
>> Subject: Re: ARF conversion into IDL?
>>
>> Just Google for ARF file format. You will find many hits..
>>
>> Remember, Google is really your friend ; > )
>>
>> Phil
>>
>> On Feb 2, 2009, at 3:10 PM, Deborah Cole wrote:
>>
>>> I have never worked with ARF files before, but apparently they're
>>> some
>>> type of movie files stacked on top of each other. I received files I
>>> ordered from a company in ARF files. I've been trying to hunt down
>>> any
>>> information I can to help me convert them over so I can view it into
>>> ENVI via IDL programming language. My boss loves IDL, so I have to
>>> figure this out for him and I have no idea. I'm beginning to think
>>> ARF
>>> files were created specifically for the ImageJ program.
>>>
>>> Has anyone used IDL or ENVI to view ARF files?
>>>
>>> Thank you,
>>>
>>> Deb

ctrueden

Re: ARF conversion into IDL?

Hi Phil & Deb,

OK, we need to know a bit more about where these files came from. It turns
> out that .arf is not a unique file format. It could be one of the following.
>

Dscho & I believe it may be the Axon Raw Format produced by Imaging
Workbench (http://www.imagingworkbench.com/support_ent.asp), and we are
creating a preliminary ARF reader for Bio-Formats. We'll reply again when we
have something to try.

Deb, do you think Imaging Workbench might be what this company used?

-Curtis

On Wed, Feb 4, 2009 at 4:53 PM, Philip Ershler <[hidden email]>wrote:

> OK, we need to know a bit more about where these files came from. It turns
> out that .arf is not a unique file format. It could be one of the following.
>
> .arf - Automatic Response file
> .arf - ARF image format
> .arf - Active Tutor data file
> .arf - AOL Instant Messenger (AIM) resource file
> .arf - Flexible image transport system bitmap
>
> Do you have any information about which of these dogs you have to deal
> with? (arf, arf). ; > )
>
> Phil
>
>
> On Feb 4, 2009, at 2:16 PM, Deborah Cole wrote:
>
> Whoops. Spoke too soon. The program says ARF files are not supported,
>> even though it does say in the website that they are. Oh well. I'll
>> keep on truckin'....
>>
>>
>> -----Original Message-----
>> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
>> Philip Ershler
>> Sent: Tuesday, February 03, 2009 2:10 PM
>> To: [hidden email]
>> Subject: Re: ARF conversion into IDL?
>>
>> Here's a freeware program that claims it can convert ARF files. It two
>> clicks past the main page when I googled for ARF file format.
>>
>> http://pagesperso-orange.fr/pierre.g/xnview/enxnview.html
>>
>> HTH,
>>
>> Phil
>>
>> On Feb 3, 2009, at 7:16 AM, Deborah Cole wrote:
>>
>> Thank you, but I wouldn't have posted the question had I not already
>>> done extensive searches online with multiple search engines.
>>>
>>>
>>> -----Original Message-----
>>> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
>>> Philip Ershler
>>> Sent: Monday, February 02, 2009 5:29 PM
>>> To: [hidden email]
>>> Subject: Re: ARF conversion into IDL?
>>>
>>> Just Google for ARF file format. You will find many hits..
>>>
>>> Remember, Google is really your friend ; > )
>>>
>>> Phil
>>>
>>> On Feb 2, 2009, at 3:10 PM, Deborah Cole wrote:
>>>
>>> I have never worked with ARF files before, but apparently they're
>>>> some
>>>> type of movie files stacked on top of each other. I received files I
>>>> ordered from a company in ARF files. I've been trying to hunt down
>>>> any
>>>> information I can to help me convert them over so I can view it into
>>>> ENVI via IDL programming language. My boss loves IDL, so I have to
>>>> figure this out for him and I have no idea. I'm beginning to think
>>>> ARF
>>>> files were created specifically for the ImageJ program.
>>>>
>>>> Has anyone used IDL or ENVI to view ARF files?
>>>>
>>>> Thank you,
>>>>
>>>> Deb
>>>>
>>>

ctrueden

Re: ARF conversion into IDL?

Hi again,

Dscho created an initial (totally untested) version of the ARF reader, which
you can try out using the latest Bio-Formats daily build:

http://www.loci.wisc.edu/software/daily/loci_tools.jar

Deb, you can try it out by dropping loci_tools.jar into your ImageJ plugins
folder, choosing Plugins > LOCI > Bio-Formats Importer from the menu, and
checking the "Virtual stack" box on the options dialog that pops up. This
procedure should allow you to read very large ARF files with limited RAM.
You could then convert to a format more friendly for IDL (using File > Save
as...), or try Karsten Rodenacker's Bio-Formats IDL bindings (
http://www.loci.wisc.edu/ome/formats-idl.html).

Please let us know whether the reader works. If it fails, and you are
willing to send a sample dataset, it would be very helpful for diagnosing
the problem.

-Curtis

On Wed, Feb 4, 2009 at 5:09 PM, Curtis Rueden <[hidden email]> wrote:

> Hi Phil & Deb,
>
> OK, we need to know a bit more about where these files came from. It turns
>> out that .arf is not a unique file format. It could be one of the following.
>>
>
> Dscho & I believe it may be the Axon Raw Format produced by Imaging
> Workbench (http://www.imagingworkbench.com/support_ent.asp), and we are
> creating a preliminary ARF reader for Bio-Formats. We'll reply again when we
> have something to try.
>
> Deb, do you think Imaging Workbench might be what this company used?
>
> -Curtis
>
>
> On Wed, Feb 4, 2009 at 4:53 PM, Philip Ershler <[hidden email]>wrote:
>
>> OK, we need to know a bit more about where these files came from. It turns
>> out that .arf is not a unique file format. It could be one of the following.
>>
>> .arf - Automatic Response file
>> .arf - ARF image format
>> .arf - Active Tutor data file
>> .arf - AOL Instant Messenger (AIM) resource file
>> .arf - Flexible image transport system bitmap
>>
>> Do you have any information about which of these dogs you have to deal
>> with? (arf, arf). ; > )
>>
>> Phil
>>
>>
>> On Feb 4, 2009, at 2:16 PM, Deborah Cole wrote:
>>
>> Whoops. Spoke too soon. The program says ARF files are not supported,
>>> even though it does say in the website that they are. Oh well. I'll
>>> keep on truckin'....
>>>
>>>
>>> -----Original Message-----
>>> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
>>> Philip Ershler
>>> Sent: Tuesday, February 03, 2009 2:10 PM
>>> To: [hidden email]
>>> Subject: Re: ARF conversion into IDL?
>>>
>>> Here's a freeware program that claims it can convert ARF files. It two
>>> clicks past the main page when I googled for ARF file format.
>>>
>>> http://pagesperso-orange.fr/pierre.g/xnview/enxnview.html
>>>
>>> HTH,
>>>
>>> Phil
>>>
>>> On Feb 3, 2009, at 7:16 AM, Deborah Cole wrote:
>>>
>>> Thank you, but I wouldn't have posted the question had I not already
>>>> done extensive searches online with multiple search engines.
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
>>>> Philip Ershler
>>>> Sent: Monday, February 02, 2009 5:29 PM
>>>> To: [hidden email]
>>>> Subject: Re: ARF conversion into IDL?
>>>>
>>>> Just Google for ARF file format. You will find many hits..
>>>>
>>>> Remember, Google is really your friend ; > )
>>>>
>>>> Phil
>>>>
>>>> On Feb 2, 2009, at 3:10 PM, Deborah Cole wrote:
>>>>
>>>> I have never worked with ARF files before, but apparently they're
>>>>> some
>>>>> type of movie files stacked on top of each other. I received files I
>>>>> ordered from a company in ARF files. I've been trying to hunt down
>>>>> any
>>>>> information I can to help me convert them over so I can view it into
>>>>> ENVI via IDL programming language. My boss loves IDL, so I have to
>>>>> figure this out for him and I have no idea. I'm beginning to think
>>>>> ARF
>>>>> files were created specifically for the ImageJ program.
>>>>>
>>>>> Has anyone used IDL or ENVI to view ARF files?
>>>>>
>>>>> Thank you,
>>>>>
>>>>> Deb
>>>>>
>>>>
>

JesperSP

Re: AVI, Virtual Stack, >1GB boundery?

In reply to this post by Michael Schmid

Hi Michael,

Thanks for your input - I've modified the AVI_Reader.java file to load my large AVI files into a virtual stack using the indx and ix## tags - it now loads a 56GB avi file of >611600 frames in a few seconds rather than >10 minutes. I've been trying to compile the file so that ImageJ automatically use my AVI_Reader instead of the built in one, but this is where my novice java skills end. My modifications are not perfect - if I set it not to load all frames into the virtual stack it still loads some extra frames. But it works for me.. If you're interested in the code I can mail it to you..

Cheers,
Jesper

Michael Schmid-3 wrote

Hi Jesper,

as far as I know AVI 2 requires use of index tables, though they seem
to have a different (two-level) format than AVI 1 (and different
fourCCs, 'indx' and 'ix##', not 'idx1').
http://www.the-labs.com/Video/odmlff2-avidef.pdf
So one should be able to get the pointers to the individual frames
from these tables, without scanning the full file. Reading the tables
may require some programming effort, but it should make opening a
large file as virtual stack much faster.

There seems to be some confusion in AVI 1 how to interpret the
offsets given in the index tables (what they are relative to); and
programs should probably check the first frame to get the way how the
offset is calculated (hummm - one of these great format
specifications by Microsoft that Microsoft does not adhere to; some
sources say that the reference to the offset was changed once more in
avifil32.dll of Vista). At least in theory, I think that this problem
should not exist for the AVI 2 index.

Best wishes,

Michael
________________________________________________________________

On 9 Dec 2008, at 18:59, JesperSP wrote:

> Hi Johannes,
>
> I think bashing my own ability rapidly develop applications in
> Java, as much
> as my (apparently) faulty belief that Java is slower than native
> Win32 code
> ;-). The plugin that I modified seeks through the 20GB file to
> locate all
> frames before it loads the first frame for the virtual stack. I
> would be
> better if it simply loaded the first frame, and waited to scan for
> further
> frames until these were needed (same as what MovieIO does). I could
> try to
> program this in java, but I'm much more familiar with Delphi, so I
> guess I
> could make faster progress trying to make the same in Delphi (I was
> thinking
> out loud I guess).. Maybe I should take the time familiarize myself
> with
> Eclipse (I guess Delphi is being depreciated), so that I can build
> java
> application/plugins faster..
>
> Cheers,
> Jesper
>
>
> Johannes Schindelin wrote:
>>
>> Hi,
>>
>> On Mon, 8 Dec 2008, JesperSP wrote:
>>
>>> I have read up on the AVI file format, and "hacked the
>>> AVI_reader.java
>>> so it recognizes the extra RIFF->AVIX segments beyond 1GB - it works
>>> great, but it does take a very long time for ImageJ to scan a
>>> 20GB file
>>> for the pointers to all the frames. If anyone want it I can
>>> upload it on
>>> my server, but I cannot guarantee that it'll work for all large AVI
>>> files. For the simple analysis I want to make, I'm considering
>>> making a
>>> low-level analysis program in a faster language like Borland Delphi.
>>
>> I doubt that the speed has anything to do with the speed of the
>> language,
>> as the problem here is seeking on the disk.
>>
>> Regardless, if you use Java 1.5 or newer, I sincerely doubt that
>> the speed
>> difference between Java and Delphi is substantial. Although I do
>> hear the
>> myth that Java is slow all the time.
>>
>> In any case, making your changes public would help a few people, I
>> guess.
>>
>> Ciao,
>> Dscho
>>
>>
>
> --
> View this message in context: http://n2.nabble.com/AVI%2C-Virtual-
> Stack%2C-%3E1GB-boundery--tp1581053p1635055.html
> Sent from the ImageJ mailing list archive at Nabble.com.