i(6dZddlZddlZGddeZdS)a:mod:`mrc` --- the MRC/CCP4 volumetric data format =================================================== .. versionadded:: 0.7.0 Reading of MRC/CCP4 volumetric files (`MRC2014 file format`_) using the mrcfile_ library [Burnley2017]_. .. _mrcfile: https://mrcfile.readthedocs.io/ .. _`MRC2014 file format`: http://www.ccpem.ac.uk/mrc_format/mrc2014.php References ---------- .. [Burnley2017] Burnley T, Palmer C and Winn M (2017) Recent developments in the CCP-EM software suite. *Acta Cryst.* D73:469-477. doi: `10.1107/S2059798317007859`_ .. _`10.1107/S2059798317007859`: https://doi.org/10.1107/S2059798317007859 Classes ------- .. autoclass:: MRC :members: NcZeZdZdZd dZd dZedZedZdZ d Z dS) MRCaRepresent a MRC/CCP4 file. Load `MRC/CCP4 2014 `_ 3D volumetric data with the mrcfile_ library. Parameters ---------- filename : str (optional) input file (or stream), can be compressed assume_volumetric : bool (optional) If ``False`` (default), check the file header to determine whether the data in `grid` is a 3D volume. If ``True``, assume `grid` is volumetric. .. versionadded:: 1.1.0 Raises ------ ValueError If the unit cell is not orthorhombic or if the data are not volumetric. Attributes ---------- header : numpy.recarray Header data from the MRC file as a numpy record array. array : numpy.ndarray Data as a 3-dimensional array where axis 0 corresponds to X, axis 1 to Y, and axis 2 to Z. This order is always enforced, regardless of the order in the mrc file. delta : numpy.ndarray Diagonal matrix with the voxel size in X, Y, and Z direction (taken from the :attr:`mrcfile.mrcfile.voxel_size` attribute) origin : numpy.ndarray numpy array with coordinates of the coordinate system origin (computed from :attr:`header.origin`, the offsets :attr:`header.origin.nxstart`, :attr:`header.origin.nystart`, :attr:`header.origin.nzstart` and the spacing :attr:`delta`) rank : int The integer 3, denoting that only 3D maps are read. Notes ----- * Only volumetric (3D) densities are read. * Only orthorhombic unitcells supported (other raise :exc:`ValueError`) * Reading and writing are supported. .. versionadded:: 0.7.0 NFcJ||_||||dSdS)N)assume_volumetric)filenameread)selfrrs V/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/gridData/mrc.py__init__z MRC.__init__cs4    IIh2CI D D D D D c|||_tj|5}|r'|jduot |jjdk}n|}|s"td||j x|_ }tj |j j|j j|j jggdsBtd|j j|j j|j jtj|j|j|jg}tj|}tj|ddd}tj|j||_tjtj|jj|jj|jjg|_tj|j|j|j g|tj|jz} tj|j!j|j!j|j!jg| z|_!d|_"ddddS#1swxYwYdS)z8Populate the instance from the MRC/CCP4 file *filename*.Nz(MRC file {} is not a volumetric density.)ZrrzWOnly orthorhombic unitcells are currently supported, not alpha={0}, beta={1}, gamma={2}axes)#rmrcfileopendatalenshape is_volume ValueErrorformatheadercopynpallclosecellbalphabetagammahstackmapcmaprmapsargsort transposearraydiag voxel_sizexyzdeltanxstartnystartnzstartoriginrank) r rrmrcrh axes_order axes_c_ordertranspose_orderoffsetss r rzMRC.readhsk  $DM \( # #% s  ,HD0MS5H5HA5M MMOO  Q >EEhOOQQQ!joo// /DK!; qw|QW]K+||-- R "BBH&%&W]AGL!'-CQCQRRRAFAFAF#;<+;S^=Ms~O_*`!a!abbDJiAIqy ABB<PSUSZ[_[eSfSffG)QXZQXZ$HIIGSDKDIK% % % % % % % % % % % % % % % % % % sI I44I8;I8c|jjS)zShape of the :attr:`array`)r)rr s r rz MRC.shapeszr cDfdtjDS)zzEdges of the grid cells, origin at centre of 0,0,0 grid cell. Only works for regular, orthonormal grids. cg|]U}j||ftjj|dzzj|zdj||fzz VS)g?)r/rarangerr3).0dr s r zMRC.edges..st+++ 1a4 29TZ]Q->#?#?? A!$tz!Q$'7!78+++r )ranger4r<s`r edgesz MRC.edgess8++++ty))+++ +r c|j|jfS)z=Return array data as (edges,grid), i.e. a numpy nD histogram.)r)rEr<s r histogramddzMRC.histogramdds DJ''r c |||_t|drj|j}tj|j|j|jg}t|jt|jt|j}}}ntj gd}d\}}}d}tj |ddd}tj |}tj |j |} | tj } tj|d5} | | tj|j tj } t'| | _|| j_|| j_|| j_|t|j} t|j} t|j}tj |jj|jj|jjgtj }t|j| j_t|j| j_t|j| j_t|d rxt?|j j| jj _t?|j j| jj _t?|j j| jj _t|d rxt?|j!j"| jj!_"t?|j!j#| jj!_#t?|j!j$| jj!_$t|d rt|j%| j_%ntj&| d krtOd | tj(dtj }ttj)|jd | d z } ttj)|jd| dz } ttj)|jd| dz }| | j_| | j_|| j_t?|d | jj_t?|d| jj_t?|d| jj_| *ddddS#1swxYwYdS)a8Write grid data to MRC/CCP4 file format. Parameters ---------- filename : str Output filename for the MRC file Notes ----- The data array should be in xyz order (axis 0=X, axis 1=Y, axis 2=Z). If the MRC object was created by reading an existing file, the original header information (including mapc, mapr, maps ordering) is preserved. Otherwise, standard ordering (mapc=1, mapr=2, maps=3) is used. .. versionadded:: 1.1.0 Nr)r?rrrT) overwrite)dtypecellarispgrz!Voxel size must be positive, got rr?rI)+rhasattrrrr#r$r%r&intr)r'r(astypefloat32rnewset_datar*r/tupler+r0r1r2r3r,r-r.mxmymzfloatrLrr r!r"rManyrzerosroundupdate_header_stats)r rr6r7r$r%r&r9inverse_transpose_order data_for_filer5r+r0r1r2header_origin_xyzs r writez MRC.writes{&  $DM 4 " "  AAFAFAF#;<