Hi Ed,
I looked at mapflex. with the Creat option. This maps a file on disk
just fine.
$new = mapflex ("map_$name.cfl",[{Dims=>$dims,Type=>'cfloat'}],{Creat=>1}) ;
Later on, $new is destroyed. Apparently, the file remains and accessing
it causes a SEGV.
So, when do those files should get removed? Apparently, they don't.
Ingo
On 15.05.24 4:05 PM, Ed . wrote:
Hi Ingo,
My best answer to your direct question is a non-answer: only you know
what is your easiest workflow. /However/, if bart does everything via
new files for each stage, and you feel (as sounds likely from your
description) that the various transformations can be done quicker but
still correctly using PDL slicing stuff (especially as, with vaffine
transformations like slice and mv, a copy is /not/ made of the data),
then you should run with that. Probably you’d want to have PDL write
out to a file for stuff that bart is best at. I would note that one of
your example bart commands is “nufft”, and PDL has several FFT
implementations available that might be useful to compare that to
(Slatec, FFTW3, the provided PDL::FFT).
PDL::IO::FlexRaw is probably fine for memory-mapping stuff, though
I’ve not really used it. I have dabbled with PDL::IO::FastRaw to help
with Photonic, and that works fine for stuff that’s too big for RAM.
If you find any problems with FlexRaw, please report them here so they
can be fixed. Once you have stuff working, I hope you’ll put it on CPAN!
Best regards,
Ed
------------------------------------------------------------------------
*From:* Ingo Schmid via pdl-general <pdl-general@lists.sourceforge.net>
*Sent:* Wednesday, May 15, 2024 2:04:41 PM
*To:* perldl <pdl-general@lists.sourceforge.net>
*Subject:* [Pdl-general] PDL and bart
Hi,
I both use PDL and recently started using bart
(https://mrirecon.github.io/bart/ <https://mrirecon.github.io/bart/>).
Documentation is somewhere between non-existent and horribly
insufficient, before you ask.
It has implementations of MRI reconstruction algorithms and its file
format is complex float, very very similar to the FlexRaw format. They
come in pairs of binary data cfl and text hdr files.
Here's a sample dump, of which only the #Dimensions lines are essential:
# Dimensions
200 200 200 1 1 1 1 1 1 1 1 1 1 1 1 1
# Command
pics -d 5 -R W:7:0:0.0015 -e -i 100 -S -t traj549 reshData549 sens
reco_l1
# Files
>reco_l1 <sens <reshData549 <traj549
# Creator
BART v0.8.00-196-g5947a32
I intend to wrap readflex/writeflex calls into readcfl/writecfl (there
are matlab and python interfaces).
Every command reads one or more files and the result is stored in a
new one. This, of course, is not always efficient if things are
temporary and fit into memory. The good thing is, you can run these
from any shell/command prompt.
For example
> bart transpose 1 11 _tmp _tmp1
reads _tmp, swaps dimensions 1 and 11 (starts at 0) and writes _tmp1
or
> bart slice 1 $c1 $eof _eof_c1;
creates a slice at position $c1 in dimension 1 and writes that to _eof_c1.
These are things done much more efficiently in PDL, for example.
Others are very useful (nufft, nlinv), though specific to the field
(pics, cc).
Now, here comes my question. Do you see a straight-forward workflow to
use both bart and PDL in its optimal way?
How to best memory map files, possibly directly into a piddle?
I am grateful for your input.
Best wishes
Ingo
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