NAME

       tff_generate_trx_from_scratch.py - generate a TRX file from CSV, TXT or NPY files

DESCRIPTION

       usage: tff_generate_trx_from_scratch.py [-h] [--positions POSITIONS]

       [--offsets OFFSETS]
              [--positions_csv    POSITIONS]    [--space    {RASMM,VOXMM,VOX}]    [--origin    {NIFTI,TRACKVIS}]
              [--positions_dtype {float16,float32,float64}] [--offsets_dtype {uint32,uint64}] [--dpv FILE DTYPE]
              [--dps FILE DTYPE]  [--groups  FILE  DTYPE]  [--dpg  GROUP  FILE  DTYPE]  [--verify_invalid]  [-f]
              reference OUT_TRACTOGRAM

       Generate  TRX  file  from  a  collection  of  CSV, TXT or NPY files by individually specifying positions,
       offsets, data_per_vertex, data_per_streamlines, groups and data_per_group. Each file must have  its  data
       type specified by the users.

       A reference file must be provided (NIFTI) and the option --verify_invalid will remove invalid streamlines
       (outside of the bounding box in VOX space).

       All  dimensions  (nbr_vertices  and  nbr_streamlines) and groups/dpg must match otherwise the script will
       (likely) crash.

       Each instance of --dps, --dpv, --groups require 2 arguments (FILE, DTYPE).  --dpg  requires  3  arguments
       (GROUP, FILE, DTYPE).  The choice of DTYPE are:

              - (u)int8, (u)int16, (u)int32, (u)int64 - float16, float32, float64 - bool

       Example    command:   tff_generate_trx_from_scratch.py   fa.nii.gz   generated.trx   -f       --positions
       test_npy/positions.npy  --positions_dtype  float16      --offsets  test_npy/offsets.npy   --offsets_dtype
       uint32        --dpv    test_npy/dpv_cx.npy    uint8       --dpv   test_npy/dpv_cy.npy   uint8       --dpv
       test_npy/dpv_cz.npy uint8     --dps test_npy/dps_algo.npy  uint8      --dps  test_npy/dps_cw.npy  float64
       --groups    test_npy/g_AF_L.npy   int32       --groups   test_npy/g_AF_R.npy   int32       --dpg   g_AF_L
       test_npy/dpg_AF_L_mean_fa.npy float32     --dpg g_AF_R  test_npy/dpg_AF_R_mean_fa.npy  float32      --dpg
       g_AF_L test_npy/dpg_AF_L_volume.npy float32

   positional arguments:
       reference
              Reference anatomy for tck/vtk/fib/dpy file support (.nii or .nii.gz).

       OUT_TRACTOGRAM
              Output filename. Format must be one of trk, tck, vtk, fib, dpy, trx.

   options:
       -h, --help
              show this help message and exit

       --verify_invalid
              Verify that the positions are all valid.  None outside of the bounding box in VOX space.  Requires
              Dipy (due to use of SFT).

       -f     Force overwriting of the output files.

   Positions options:
       --positions POSITIONS
              Binary file containing the streamlines coordinates.  Must be Nx3 (.npy)

       --offsets OFFSETS
              Binary file containing the streamlines offsets (.npy)

       --positions_csv POSITIONS
              CSV file containing the streamlines coordinates.  Rows for each streamlines organized as x1,y1,z1,
              x2,y2,z2,...,xN,yN,zN

       --space {RASMM,VOXMM,VOX}
              Space in which the coordinates are declared.[RASMM] Non-default option requires Dipy.

       --origin {NIFTI,TRACKVIS}
              Origin in which the coordinates are declared. [NIFTI] Non-default option requires Dipy.

   Data type options:
       --positions_dtype {float16,float32,float64}
              Specify the datatype for positions for trx. [float32]

       --offsets_dtype {uint32,uint64}
              Specify the datatype for offsets for trx. [uint64]

   Streamlines metadata options:
       --dpv FILE DTYPE
              Binary file containing data_per_vertex.  Must haveNB_VERTICES as first dimension (.npy)

       --dps FILE DTYPE
              Binary file containing data_per_vertex.  Must haveNB_STREAMLINES as first dimension (.npy)

       --groups FILE DTYPE
              Binary  file  containing  a  sparse  group (indices).  Indices should be lower than NB_STREAMLINES
              (.npy)

       --dpg GROUP FILE DTYPE
              Binary file containing data_per_group.

              Must have(1,) as first dimension (.npy)

tff_generate_trx_from_scratch.py 0.3                July 2024                TFF_GENERATE_TRX_FROM_SCRATCH.PY(1)