.. include:: ../global.rst Rearrange voxels in space or time ================================= .. _collate_slice_4dfp: collate_slice_4dfp ------------------ collate interleaved datasets Usage: collate_slice_4dfp <4dfp img1> <4dfp img2> ... <4dfp imgn> <4dfp imgout> Options ======= ================================================ -v verbose mode -@ output big or little endian (default CPU endian) ======= ================================================ .. _paste_4dfp: paste_4dfp ---------- append or average selected frames from multiple files (list directed) Usage: paste_4dfp :code:`inlist` is a file containing rows of 1 to 3 columns: filename, starting frame (counting from 1), number of frames. .. note:: * If a starting frame (column 2) is not specified, the first frame will be used. * Column 3 is only applied during append mode (-a). The period value (-p) will be used otherwise. * In append mode, column 3 has priority over the -p flag. The period value (-p) will only be used for rows that do not specify column 3. Options ======= ========================================================== -a append successive epochs (default average) -p specify period in frames (default=1) -@ output big or little endian (default initial input endian) ======= ========================================================== .. _extract_frame_4dfp: extract_frame_4dfp ------------------ extract single frame from stack (:ref:`paste_4dfp` wrapper) Usage: extract_frame_4dfp <(4dfp) stack> <(int) frame> Examples:: extract_frame_4dfp CDR.5to1+ 3 Options ======= ============================================================== -o specifiy output 4dfp fileroot (default = _frame) ======= ============================================================== chop_4dfp --------- extract contiguous frames from stack (:ref:`paste_4dfp` wrapper) usage: chop_4dfp <(4dfp) stack> <(int) frame0> <(int) frame1> Examples:: chop_4dfp vb12345_b5_dbnd_xr3d[.4dfp[.img]] 4 68 Options ======= ========================================================================= -o specify output 4dfp fileroot (default = _framesto) ======= ========================================================================= crop_4dfp --------- crop or roll (correct image wrap) Usage: crop_4dfp <(4dfp) inroot> [(4dfp) outroot] Options ======================= ============================================================================== -[to[] specify x y z crop/expand limits (1-indexed) -s scroll specified axis by specified number of pixels (after cropping/expanding) -f interpret specifications under 4dfp<->analyze flips -Z zero voxels instead of physically cropping -@ output big or little endian (default input endian) ======================= ============================================================================== N.B.: if upper crop limit exceeds input dimension undefined voxels will be set to 1.e-37 |br| N.B.: default (4dfp) output root is <(4dfp) inroot>"_crop" reindex_4dfp ------------ .. FIXME: figure out what these symbols are supposed to be xy, slicevolume Usage: reindex_4dfp <(4dfp> input> [options] Examples:: reindex_4dfp my4Dstack 3 4 Options ======= ============================================================== -v verbose mode -o specify 4dfp output root (default = _r) -@ output big or little endian (default input endian) ======= ============================================================== N.B.: reindex_4dfp swaps specified indices |br| N.B.: and must be unequal integers in the range 1-4 except as follows: |br| == 4 and == 0: right rotate indices (first index <- last index) |br| == 0 and == 4: left rotate indices ( last index <- first index) .. _unpack_4dfp: unpack_4dfp ----------- mosaic :math:`\rightarrow` volume Usage: unpack_4dfp <(4dfp) input> <(4dfp) output> Examples:: unpack_4dfp 030211_EL_b_1 030211_EL_b1 Options ======== ================================================== -V read frame count from input ifh slice count -R multiply output x and y voxsiz by pack factor -z flipz (unpack slices in reverse order) -y flipy -nx specify unpacked nx (default=64) -ny specify unpacked ny (default=64) -sx squeeze unpacked x dimension by specified factor -sy squeeze unpacked y dimension by specified factor -@ output big or little endian (default input endian) ======== ================================================== multipack_4dfp -------------- volume :math:`\rightarrow` mosaic flip_4dfp --------- flip x, y, z Usage: flip_4dfp <(4dfp) image> [(4dfp) output] Examples:: flip_4dfp -yz vc345 vc345_flipyz Options ======= ================================================== -x flip x -y flip y -z flip z -@ output big or little endian (default input endian) ======= ================================================== N.B.: default output fileroot = _flip[xyz] split_4dfp ---------- split assembled volumes T2S_4dfp -------- transverse :math:`\rightarrow` sagittal Usage: T2S_4dfp <(4dfp) imgroot> [(4dfp) outroot] Examples:: T2S_4dfp vm6c_mpr T2S_4dfp vm6c_mpr vm6c_mprS Options ======= ================================================== -@ output big or little endian (default input endian) ======= ================================================== N.B.: default output root = "S" .. _s2t_4dfp: S2T_4dfp -------- sagittal :math:`\rightarrow` transverse Usage: S2T_4dfp <(4dfp) imgroot> [(4dfp) outroot] Examples:: S2T_4dfp vm6c_mpr S2T_4dfp vm6c_mpr vm6c_mprT Options ======= ================================================== -@ output big or little endian (default input endian) ======= ================================================== N.B.: default output root = "T" .. _c2t_4dfp: C2T_4dfp -------- coronal :math:`\rightarrow` transverse Usage: C2T_4dfp <(4dfp) image> [(4dfp) outroot] Examples:: C2T_4dfp vm6c_b1 C2T_4dfp vm6c_b1 vm6c_b1T Options ======= ================================================== -@ output big or little endian (default input endian) ======= ================================================== N.B.: default output root = "T" T2C_4dfp -------- transverse :math:`\rightarrow` coronal Usage: T2C_4dfp <(4dfp) imgroot> [(4dfp) outroot] Examples:: T2C_4dfp vc12345_b1 T2C_4dfp vc12345_b1 vc12345_b1C Options ======= ================================================== -@ output big or little endian (default input endian) ======= ================================================== N.B.: default output root = "C"