Text archives Help
- From: "Jim Kress" <jimkress_58@kressworks.org>
- To: <iv3d-users@sci.utah.edu>
- Subject: [IV3D-USERS] RE: Re: RE: Re: Help on data input and Axis Display
- Date: Tue, 19 Jan 2010 17:19:17 -0500
BTW, after using the information you provided, I had no problem importing
the data (at least on another windows machine - I'll try the 1st one again
as soon as I can).
Can I assume the X axis is identified by the red arrow in the coordinate
cross, the Y axis is identified by the green arrow in the coordinate cross
and the Z axis is identified by the blue arrow in the coordinate cross?
Thanks.
Jim
-----Original Message-----
From: tom fogal [
mailto:tfogal@alumni.unh.edu]
Sent: Tuesday, January 19, 2010 3:57 PM
To: iv3d-users@sci.utah.edu
Subject: [IV3D-USERS] Re: RE: Re: Help on data input and Axis Display
"Jim Kress" <jimkress_58@kressworks.org> writes:
>
> After selecting that file and then a UVF to save to, you should get
>
> a dialog where IV3D complains it cannot recognize the file, and it
>
> should ask if you want to specify the data set parameters manually.
>
> That is, page 13 and 14 of the manual. Is that not popping up for
>
> you? Please "Report an Issue" and send me (personally) a ping if
>
> so.
>
>
Using the data set I sent you previously, and following the process
>
shown in the attached file ImageVis3D crashes as the last image
>
shows.
>
>
What did I do wrong in image 2?
You need to set the "Encoding" to "Text", and I think I've been saying
the data are "32 bit (float)" because your data are FP, even if your
indices are not.
That said, ImageVis3D should never crash, of course. I can't reproduce
the crash on my workstation, but I will give this a try on a Windows
box and see if the issue is platform-specific. Thanks for the report!
-tom
>
> -----Original Message-----
>
> From: tom fogal [mailto:tfogal@alumni.unh.edu]
>
> Sent: Tuesday, January 19, 2010 2:41 PM
>
> To: iv3d-users@sci.utah.edu
>
> Subject: [IV3D-USERS] Re: Help on data input and Axis Display
>
>
>
> "Jim Kress" <jimkress_58@kressworks.org> writes:
>
> > Tom,
>
> >
>
> > What file extension did you use to enable the text reader?
>
>
>
> What you sent it as -- a .txt.
>
>
>
> I did have to change "Files of type" to "All Files", because otherwise
>
> ImaegVis3D's file selection dialog would filter it out, thinking it was
>
> something that could be opened.
>
>
>
> > Did you make any changes to the input file?
>
>
>
> Nope.
>
>
>
>
>
> After selecting that file and then a UVF to save to, you should get a
>
> dialog where IV3D complains it cannot recognize the file, and it should
>
> ask if you want to specify the data set parameters manually. That is,
>
> page 13 and 14 of the manual. Is that not popping up for you? Please
>
> "Report an Issue" and send me (personally) a ping if so.
>
>
>
> -tom
>
>
>
> > > -----Original Message-----
>
> > > From: tom fogal [mailto:tfogal@alumni.unh.edu]
>
> > > Sent: Saturday, January 16, 2010 5:40 PM
>
> > > To: iv3d-users@sci.utah.edu
>
> > > Subject: [IV3D-USERS] Re: Help on data input and Axis Display
>
> > >
>
> > > "jimkress_58" <jimkress_58@kressworks.org> writes:
>
> > > > > Unfortunately the raw reader is generally based around an
implicit
>
> > > > > data layout, i.e. data start at (0,0,0) and change in X slowly
and
>
> > > > > in Z quickly. There's a radio button for "text" input, but
>
looking
>
> > > > > through the code, all our IO is unformatted so I'm a little wary
>
> > > > > that the text path is relatively untested.
>
> > >
>
> > > Side note: we actually do parse text using the right kind of IO
>
> > > routines, I just didn't notice the code before my earlier mail.
>
> > >
>
> > > > Yeah. I tried the "text" option and my computer hung.
>
> > >
>
> > > Hrm. It loaded up fine on my workstation...
>
> > >
>
> > > Could you use the report an issue dialog && create a bug report for
>
> > > this, so I don't forget about it?
>
> > >
>
> > > > > I would doubt it is meaningful, because I don't think the
>
> > > > > conversion step did something intelligent. Then again, you know
>
> > > > > your data better than I do :). Do the generated images "look"
like
>
> > > > > your data?
>
> > > >
>
> > > > Hard to tell if I cannot determine their x,y,z spatial location.
>
> > > > Maybe I'll try slicing the data and see if the contoured intensity
>
> > > > for each slice corresponds to the volumetric information
presented.
>
> > >
>
> > > Now that I've found what code reads this, I can see it's not
>
> > > understanding the data correctly. Nonetheless I've attached an
image.
>
> > >
>
> > > > > C++. Adding a new reader is pretty easy/self-contained, so
really
>
> > > > > if you've got someone that knows any ALGOL-derived language &&
is
>
> > > > > willing to google some terms, that will be enough that we could
>
> > > > > walk them through what's needed.
>
> > > >
>
> > > > ARGH! You've hit the chink in my armor. However, I can try to
>
> > > > struggle through it (I have 30 years of FORTRAN experience but am
>
> > > > just starting to learn C++). What's the best existing reader to
use
>
> > > > as a starting template?
>
> > >
>
> > > I get this/similar questions a lot. I *finally* wrote up some
>
> > > documentation for it; a PDF is attached.
>
> > >
>
> > > -tom
>
> > >
>
> > > > > -----Original Message-----
>
> > > > > From: tom fogal [mailto:tfogal@alumni.unh.edu]
>
> > > > > Sent: Saturday, January 16, 2010 1:48 PM
>
> > > > > To: iv3d-users@sci.utah.edu
>
> > > > > Subject: [IV3D-USERS] Re: RE: Re: RE: Re: Help on data input and
>
Axis
>
> > > > > Display
>
> > > > >
>
> > > > > "jimkress_58" <jimkress_58@kressworks.org> writes:
>
> > > > > > > From a (very) quick read, I'd say this isn't a point cloud.
>
It
>
> > > > > > > looks as if your data's ranges are [1:16],[2:9],[7:15], and
>
> > further
>
> > > > > > > there are no `holes' in the data (i.e. no combination of
those
>
> > > > > > > three indices which is not represented). If this is true,
>
you've
>
> > > > > > > got regular, gridded data, which is exactly what we need for
>
> > > > > > > ImageVis3D.
>
> > > > > >
>
> > > > > > OK.
>
> > > > > >
>
> > > > > > However, when asked, ImageVis3D appears to import the file.
It
>
> > > > > > just asks for the extent (number of points?) in each
direction,
>
> > > > > > i.e. 16,8,9.
>
> > > > >
>
> > > > > Yeah, you're getting the raw conversion dialog, which (if you
say
>
> > > > > `yes') comes up when we can't figure out any metadata that would
>
help
>
> > > > > us read the file.
>
> > > > >
>
> > > > > Unfortunately the raw reader is generally based around an
implicit
>
> > data
>
> > > > > layout, i.e. data start at (0,0,0) and change in X slowly and in
Z
>
> > > > > quickly. There's a radio button for "text" input, but looking
>
through
>
> > > > > the code, all our IO is unformatted so I'm a little wary that
the
>
text
>
> > > > > path is relatively untested.
>
> > > > >
>
> > > > > Worse, detecting errors at that stage is essentially impossible,
>
> > > > > because we don't know anything about the file. So, ImageVis3D
>
will
>
> > > > > happily do whatever conversion you've asked for, without regard
to
>
> > > > > whether that conversion makes any sense.
>
> > > > >
>
> > > > > > Is this imported volumetric image I observe meaningful?
>
> > > > >
>
> > > > > I would doubt it is meaningful, because I don't think the
>
conversion
>
> > > > > step did something intelligent. Then again, you know your data
>
better
>
> > > > > than I do :). Do the generated images "look" like your data?
>
> > > > >
>
> > > > >
>
> > > > > As a side note, these data are pretty low res. If they're low
>
> > > > > resolution for visualization reasons, and you can obtain higher
>
res,
>
> > > > > do so. People don't tend to believe me until they've done it a
>
couple
>
> > > > > times, but (seriously!) the size of the data is irrelevant to
>
IV3D.
>
> > > > >
>
> > > > > > Is the grey scale presented in the image controlled by the
>
number of
>
> > > > > > bytes allowed by the graphics card?
>
> > > > >
>
> > > > > You're seeing grey because the default renderer is based on 1D
>
> > transfer
>
> > > > > functions, and the default 1D transfer function is a ramp for
all
>
4
>
> > > > > color channels. You can modify the current function with the
"1D
>
> > > > > Transferfunction editor", accessible from the Workspace menu.
>
More
>
> > > > > details are in the manual.
>
> > > > >
>
> > > > > > What would happen if I changed the file so that the intensity
>
for
>
> > > > > > points outside the current data ranges, that is for points
>
[1:16],
>
> > > > > > [1,10:16] [1:6,16], are zero?
>
> > > > >
>
> > > > > I'm not sure I follow that syntax correctly, but it sounds like
>
you
>
> > > > > want to add more points to your domain, outside the original
>
domain,
>
> > > > > initialized to 0? With the default parameters, the only thing
>
that
>
> > > > > will happen is that your domain size will increase. This is
>
because
>
> > > > > the default transfer functions are set to remove / not visualize
>
> > > > > 0-valued data. You could change this in the 1D TF editor by
>
making
>
> > the
>
> > > > > leftmost components non-zero.
>
> > > > >
>
> > > > > > > If there's anybody in your group who can code, have them
>
follow up
>
> > > > > > > on tuvok-developers [1].
>
> > > > > >
>
> > > > > > Code in what language?
>
> > > > >
>
> > > > > C++. Adding a new reader is pretty easy/self-contained, so
really
>
if
>
> > > > > you've got someone that knows any ALGOL-derived language && is
>
willing
>
> > > > > to google some terms, that will be enough that we could walk
them
>
> > > > > through what's needed.
>
> > > > >
>
> > > > > > Also, is the amount of video memory just that which is on the
>
(in
>
> > > > > > my case) embedded controller or does it include the TOTAL
>
Available
>
> > > > > > Graphics Memory = Dedicated Video Memory + Share System
Memory?
>
> > > > >
>
> > > > > To be honest, we ignore the graphics memory setting for now, due
>
to
>
> > > > > limitations of the rendering API. Someday in the distant future
I
>
> > hope
>
> > > > > that will be fixable, at which point the "GPU Memory" slider
would
>
> > want
>
> > > > > to know just your "Dedicated Video Memory".
>
> > > > >
>
> > > > > > Thanks for your help. I hate to be such a nag but the
software
>
has
>
> > > > > > such a huge upside for the work I am doing that could help
many
>
> > > > > > people.
>
> > > > >
>
> > > > > Not a nag at all. We love to get more people using our
software!
>
=)
>
> > > > >
>
> > > > > Cheers,
>
> > > > >
>
> > > > > -tom
>
> > > > >
>
> > > > > > -----Original Message-----
>
> > > > > > From: tom fogal [mailto:tfogal@alumni.unh.edu]
>
> > > > > > Sent: Saturday, January 16, 2010 3:41 AM
>
> > > > > > To: iv3d-users@sci.utah.edu
>
> > > > > > Subject: [IV3D-USERS] Re: RE: Re: Help on data input and Axis
>
> > Display
>
> > > > > >
>
> > > > > > "Jim Kress" <jimkress_58@kressworks.org> writes:
>
> > > > > > > The file is attached. It is ASCII and would meet (I
believe)
>
your
>
> > > > > > > definition as point clouds. Please note: cloud is in the
>
plural.
>
> > > > > >
>
> > > > > > >From a (very) quick read, I'd say this isn't a point cloud.
It
>
> > looks
>
> > > > > > as if your data's ranges are [1:16],[2:9],[7:15], and further
>
there
>
> > > > > > are no `holes' in the data (i.e. no combination of those three
>
> > indices
>
> > > > > > which is not represented). If this is true, you've got
regular,
>
> > > > > > gridded data, which is exactly what we need for ImageVis3D.
>
> > > > > >
>
> > > > > > If there's anybody in your group who can code, have them
follow
>
up
>
> > on
>
> > > > > > tuvok-developers [1]. Otherwise I'll add an ASCII reader to
my
>
todo
>
> > > > > > list...
>
> > > > > >
>
> > > > > > -tom
>
> > > > > >
>
> > > > > > [1]
https://lists.sci.utah.edu/sympa/subscribe/tuvok-developers
>
> > > > > >
>
> > > > > > > -----Original Message-----
>
> > > > > > > From: tom fogal [mailto:tfogal@alumni.unh.edu]
>
> > > > > > > Sent: Friday, January 15, 2010 6:38 PM
>
> > > > > > > To: iv3d-users@sci.utah.edu
>
> > > > > > > Subject: [IV3D-USERS] Re: Help on data input and Axis
Display
>
> > > > > > >
>
> > > > > > > <jimkress_58@kressworks.org> writes:
>
> > > > > > > > My dataset consists of one file with many single lines of
>
data,
>
> > each
>
> > > > > > > > of which contains the X, Y, Z, and Intensity measured at
>
that
>
> > X,Y,Z
>
> > > > > > > > point in space. What is the best way to feed this into
>
> > ImageVis3D?
>
> > > > > > >
>
> > > > > > > We'll need a bit more info on this format. Is there any
>
structure
>
> > to
>
> > > > > > > these points, or do they essentially form a `point cloud'?
>
> > Secondly,
>
> > > > > > > are these ASCII or binary files?
>
> > > > > > >
>
> > > > > > > > Also, I need to be able to display X, Y, and Z axes with
>
user
>
> > > > > > > > configurable scaling and tic mark number, value and
location
>
on
>
> > each
>
> > > > > > > > axis.
>
> > > > > > >
>
> > > > > > > There's currently no support for this in ImageVis3D, though
>
the
>
> > > > > request
>
> > > > > > > has been brought up before.
>
> > > > > > >
>
> > > > > > > > I can provide a sample input file if you will tell me how
to
>
get
>
> > it
>
> > > > > > > > to you.
>
> > > > > > >
>
> > > > > > > If you've got a very small example (kilobytes), sending it
to
>
this
>
> > > > > > > mailing list is the best mechanism.
>
> > > > > > >
>
> > > > > > > If it's anything larger, use ImageVis3D's builtin "Report an
>
> > Issue"
>
> > > > > > > dialog, under the help menu. Add a description describe the
>
file
>
> > > > > > > format, and use the "Add files" button to add one or more
>
example
>
> > > > > > > files.
>
> > > > > > >
>
> > > > > > > -tom
- [IV3D-USERS] RE: Re: Help on data input and Axis Display, (continued)
- [IV3D-USERS] RE: Re: Help on data input and Axis Display, Jim Kress, 01/15/2010
- [IV3D-USERS] Re: RE: Re: Help on data input and Axis Display, tom fogal, 01/16/2010
- [IV3D-USERS] RE: Re: RE: Re: Help on data input and Axis Display, jimkress_58, 01/16/2010
- [IV3D-USERS] Re: RE: Re: RE: Re: Help on data input and Axis Display, tom fogal, 01/16/2010
- [IV3D-USERS] RE: Re: RE: Re: RE: Re: Help on data input and Axis Display, jimkress_58, 01/16/2010
- [IV3D-USERS] Re: Help on data input and Axis Display, tom fogal, 01/16/2010
- [IV3D-USERS] RE: Re: Help on data input and Axis Display, Jim Kress, 01/19/2010
- [IV3D-USERS] Re: Help on data input and Axis Display, tom fogal, 01/19/2010
- [IV3D-USERS] RE: Re: Help on data input and Axis Display, Jim Kress, 01/19/2010
- [IV3D-USERS] Re: RE: Re: Help on data input and Axis Display, tom fogal, 01/19/2010
- [IV3D-USERS] RE: Re: RE: Re: Help on data input and Axis Display, Jim Kress, 01/19/2010
- [IV3D-USERS] Re: Help on data input and Axis Display, tom fogal, 01/19/2010
- [IV3D-USERS] RE: Re: Help on data input and Axis Display, jimkress_58, 01/20/2010
- [IV3D-USERS] Re: RE: Re: Help on data input and Axis Display, tom fogal, 01/20/2010
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