[Swift-devel] Re: arrays of structures and building them in SWIFT

[Ben Clifford]

The v3 code probably has a very similar problem to that expressed in 
bug123, which I think is that mapper parameters don't interact in well 
with runtime constructed datasets.

Perhaps this would be doable with a custom mapper that mapped an array inp 
declared as:

type t { file head; file brik; }
t inp[][];

such that:

  inputs/Snnnn.runbyrun.reg_TS_run-.rrrrrr+orig.sssss

is mapped to:

 inp[nnn][rrrr].sssss

That is, rather than feeding list of nnn and rrr and then attempting to 
construct filenames, do it the other way round - use the presence of files 
in the input/ directory to cause a data structure to be constructed.

That would be straightforward, I think, if you want to process all files 
that look like:

  inputs/S*.runbyrun.reg_TS_run-*+orig.*

rather than some subset of those.

So one question is: do you want to process all files that look like:
  inputs/S*.runbyrun.reg_TS_run-*+orig.*
or do you want to process only a subset? And if so, what is the longer 
term goal for selecting the subset (you have "05" and 1 hard-coded at the 
moment, but I guess there's some intention to do otherwise eventually)

On Sun, 4 May 2008, Mihael Hategan wrote:

> Right. The problem here is that you can't reasonably "assign" file names
> to data on the fly.
> 
> How do your files look like? In other words, what are your input files?
> (I get the ones in the graph, but you mention an array, so I figured
> there's more).
> 
> Mihael
> 
> On Sun, 2008-05-04 at 11:54 -0500, Uri Hasson wrote:
> > Hi Mihael,
> > 
> > I'm trying to write an MRAC and so am finalizing up some swift
> > routines...
> > 
> > One thing I can't seem to manage is to declare a complex type that
> > will contain two types (both of which are files), assign data to that
> > type, and then pass that type to a call. I think my problem is that I
> > don't know how to setup an array of structures and assign it values
> > that are file locations.
> > 
> > If you have a sec, could you advise on this?
> > For starters, a graph of my current, nonelegant workflow can be seen
> > in 
> > /disks/gpfs/fmri/cnari/swift/projects/uhasson/AFNIflows/SNR/snrgraph1.png
> > 
> > and the script that generates it is:
> > /disks/gpfs/fmri/cnari/swift/projects/uhasson/AFNIflows/SNR/AFNIsnrV2.swift
> > 
> > All the procedures I write are very simple: they take *.HEAD and
> > *.BRIK file pairs as input (a pair defines  a brain dataset), and
> > output a *.HEAD and *.BRIK file as output. 
> > 
> > Now, Currently, I am stating each HEAD and BRIK file seperately as
> > arguments, e.g., AFNI_mean (string baseName, file headFile, file
> > brikFile ...)
> > 
> > What I want to do is create a type like
> > type AFNI_obj{
> > file head;
> > file brik;
> > };
> > 
> > assign the *.HEAD and *.BRIK file to that type and then pass that
> > complex type like this: AFNI_mean (string baseName, AFNI_obj t, ...)
> > 
> > I've tried doing this with Sarah, but we couldn't get it to work.
> > If I do the csv mapper way, I can do it (AFNIsnrV4.swift in same dir)
> > but if I try constructing the filenames on the fly within the script
> > (feeble attempts in AFNIsnrV3.swift), it doesn't work. 
> > 
> > I think what I don't understand is how to manully set up an array of
> > structures similarly to what the csv mapper does.
> > If meeting in person is faster, would be very glad to meet.
> > 
> > Any advice,
> > Much appreciated.
> > 
> > Uri
> > 
> 
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