[MINC-users] miset_dimension_apparent_voxel_order - should it not affect miget_voxel_value_hyperslab?

[Soren Christensen]

Hi Leila,
 I pulled the branches but not sure how to determine if your changes
are there - which branch is it in and is there any identifying feature
in the code.
I was using minc from the minc-toolkit installed just a couple of
weeks ago, but perhaps an older commit in the submodule.

Cheers
Soren

On Mon, Sep 17, 2012 at 11:40 PM, Leila Baghdadi
<baghdadi at phenogenomics.ca> wrote:
> Soren,
>
> a while ago, I checked in some changes to the minc2 git code which address the issue you are talking about! I suspect you are using a version of the code which does not have these changes.
>
> you should be able to check your micn directory (libsrc2/hyper.c --> check mitranslate_hyperslab_origin --> mine is around line 280) and see the changes
>
> if not please update your minc2 source and rebuild
>
> HTH
>
> Leila
>
> ----- Original Message -----
> From: Soren Christensen <sorench at gmail.com>
> Sent: Sat, 9/15/2012 9:23am
> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
> Subject: [MINC-users] miset_dimension_apparent_voxel_order - should it not affect miget_voxel_value_hyperslab?
>
> Hi,
>  Sorry for the multiple questions - this is a separate issue so I am
> posting separately.
> I am trying to use miset_dimension_apparent_voxel_order hoping it
> could give my data with a fixed relationship between array direction
> and spatial direction.
> When I use it though, there seems to be no difference to the voxel
> output. I had expected a "flip".
> Where am I going wrong here?
>
> This is what I do:
> give my all y of xrow 16 in native ordering:
> -2048 -2048 -2048 -1918 -1789 -1659 -1528 -1405 -1251 -1191 -996 -1168
> -1237 -1025 -954 -1156 -1498 -1631 -2048 -2048 -2048 -2048 -2048 -2048
> -2048 -2048 -2048 -2048 -2048 -2048 -2048 -2048
> dimname is yspace
> step is -1.844
>
> now attempt to reverse y by req y to come out positive by using
> miset_dimension_apparent_voxel_order.  Output is now:
> -2048 -2048 -2048 -1918 -1789 -1659 -1528 -1405 -1251 -1191 -996 -1168
> -1237 -1025 -954 -1156 -1498 -1631 -2048 -2048 -2048 -2048 -2048 -2048
> -2048 -2048 -2048 -2048 -2048 -2048 -2048 -2048   (identical)
> step is -1.844  (also not changed)
>
>
> (I had thought the second array would come out flipped)
>
>
> mincinfo:
> image dimensions: time zspace yspace xspace
>     dimension name         length         step        start
>     --------------         ------         ----        -----
>     time                       12            1            0
>     zspace                     80            2         -539
>     yspace                     32       -1.844      18.6907
>     xspace                     32       -1.844      28.6905
>
>
>
>  Code:
>  mihandle_t minc_volume;
>  int result = miopen_volume(fname.toStdString().c_str(),
> MI2_OPEN_READ, &minc_volume);
>
>
>     mitype_t volume_data_type[1];
>     miget_data_type(minc_volume,volume_data_type );
>
>
>     size_t start[4]={0,0,0,16};
>     size_t end[4]={1,1,32,1};
>
>     //get y row
>     signed short data[32]={0};
>
>     result=miget_voxel_value_hyperslab(minc_volume,volume_data_type[0],start,end,static_cast<void*>(data));
>
>      for (int k=0; k<32; k++)
>      {
>          std::cout << data[k] << " ";
>
>      }
>      std::cout <<  std::endl;
>
>      //what is the y step?
>      midimhandle_t dimensions[4];
>      result=miget_volume_dimensions(minc_volume,
> MI_DIMCLASS_SPATIAL,MI_DIMATTR_ALL,MI_DIMORDER_FILE, 4, dimensions);
>
>      char *name_ptr[1];
>      miget_dimension_name(dimensions[2], name_ptr );
>      std::cout << "dimname is " << *name_ptr;
>      std::cout  << std::endl;
>      double step[1];
>      miget_dimension_separation(dimensions[2],MI_ORDER_FILE,step);
>
>      std::cout << "step is " << step[0] << std::endl;
>
>      std::cout << "now attempt to reverse y by req y to come out positive ";
>      result=miset_dimension_apparent_voxel_order(dimensions[2],MI_POSITIVE);
>
>      result=miget_voxel_value_hyperslab(minc_volume,volume_data_type[0],start,end,static_cast<void*>(data));
>
>       for (int k=0; k<32; k++)
>       {
>           std::cout << data[k] << " ";
>
>       }
>       std::cout <<  std::endl;
>
>      miget_dimension_separation(dimensions[2],MI_ORDER_FILE,step);
>
>      std::cout << "step is " << step[0] << std::endl;
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