i (ZdZddlmZmZmZmZddlZddlZddlm Z Gdde Z dS)z mrcfile ------- Module which exports the :class:`MrcFile` class. Classes: :class:`MrcFile`: An object which represents an MRC file. )absolute_importdivisionprint_functionunicode_literalsN)MrcInterpretercleZdZdZ dfd ZdZdZdfd ZfdZd Z fd Z d Z dfd Z xZ S)MrcFilea An object which represents an MRC file. The header and data are handled as numpy arrays - see :class:`~mrcfile.mrcobject.MrcObject` for details. :class:`MrcFile` supports a permissive read mode for attempting to open corrupt or invalid files. See :class:`mrcfile.mrcinterpreter.MrcInterpreter` or the :doc:`usage guide <../usage_guide>` for more information. Usage: To create a new MrcFile object, pass a file name and optional mode. To ensure the file is written to disk and closed correctly, it's best to use the :keyword:`with` statement: >>> with MrcFile('tmp.mrc', 'w+') as mrc: ... mrc.set_data(np.zeros((10, 10), dtype=np.int8)) In mode ``r`` or ``r+``, the named file is opened from disk and read. In mode ``w+`` a new empty file is created and will be written to disk at the end of the :keyword:`with` block (or when :meth:`~.MrcInterpreter.flush` or :meth:`close` is called). rFc Btt|jdd|i||dvr"td|t |}d|vrCt j|r$|s"td|||_ |j dk|_ | | d|vr| dS| |dS#t$r|wxYw) aInitialise a new :class:`MrcFile` object. The given file name is opened in the given mode. For mode ``r`` or ``r+`` the header, extended header and data are read from the file. For mode ``w+`` a new file is created with a default header and empty extended header and data arrays. Args: name: The file name to open, as a string or pathlib Path. mode: The file mode to use. This should be one of the following: ``r`` for read-only, ``r+`` for read and write, or ``w+`` for a new empty file. The default is ``r``. overwrite: Flag to force overwriting of an existing file if the mode is ``w+``. If :data:`False` and a file of the same name already exists, the file is not overwritten and an exception is raised. The default is :data:`False`. permissive: Read the file in permissive mode. (See :class:`mrcfile.mrcinterpreter.MrcInterpreter` for details.) The default is :data:`False`. header_only: Only read the header (and extended header) from the file. The default is :data:`False`. Raises: :exc:`ValueError`: If the mode is not one of ``r``, ``r+`` or ``w+``. :exc:`ValueError`: If the file is not a valid MRC file and ``permissive`` is :data:`False`. :exc:`ValueError`: If the mode is ``w+``, the file already exists and overwrite is :data:`False`. :exc:`OSError`: If the mode is ``r`` or ``r+`` and the file does not exist. Warns: RuntimeWarning: If the file appears to be a valid MRC file but the data block is longer than expected from the dimensions in the header. RuntimeWarning: If the file is not a valid MRC file and ``permissive`` is :data:`True`. RuntimeWarning: If the header's ``exttyp`` field is set to a known value but the extended header's size is not a multiple of the number of bytes in the corresponding dtype. permissive)r zr+zw+zMode '{0}' not supportedwz=File '{0}' already exists; set overwrite=True to overwrite itr N)superr __init__ ValueErrorformatstrospathexists_mode _read_only _open_file_create_default_attributes_read Exception _close_file)selfnamemode overwriter header_onlykwargs __class__s Y/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/mrcfile/mrcfile.pyrzMrcFile.__init__4s:X &gt%FFFvFFF ( ( (7>>tDDEE E4yy 4KKBGNN400KK//5vd||== = :,  d{{//11111 ;'''''           s C>'C>> DcLd|jj|jS)NzMrcFile('{0}', mode='{1}'))r _iostreamr rrs r&__repr__zMrcFile.__repr__xs&+224>3F37:?? ?c@t||jdz|_dS)z,Open a file object to use as the I/O stream.bN)openrr()rr s r&rzMrcFile._open_file|sdDJ$455r+c|jdtt||dS)z5Override _read() to move back to start of file first.rN)r(seekrr r)rr#r%s r&rz MrcFile._reads= A gt"";/////r+cv|}|jjt|jjz}||z }t t |||jF|jj}||kr6d ||z }tj |tdSdSdS)zAOverride _read_data() to check file size matches data block size.) max_bytesNz*MRC file is {0} bytes larger than expected) _get_file_sizeheadernbytesintnsymbtrr _read_datadatarwarningswarnRuntimeWarning)r file_size header_sizeremaining_file_size data_sizemsgr%s r&r8zMrcFile._read_datas'')) k(3t{/A+B+BB '+5 gt''2E'FFF 9  (I...C2Y>?? c>22222 ! ..r+c|j}|jdtj|j}|j|tj|S)z8Return the size of the underlying file object, in bytes.r)r(tellr0rSEEK_ENDSEEK_SET)rpossizes r&r3zMrcFile._get_file_sizesan!!## Ar{+++~""$$ C--- r+c~tt||dS)zFlush any changes to disk and close the file. This override calls :meth:`.MrcInterpreter.close` to ensure the stream is flushed and closed, then closes the file object. N)rr closer)rr%s r&rIz MrcFile.closes9 gt""$$$ r+c8|jdS)zClose the file object.N)r(rIr)s r&rzMrcFile._close_files r+Nc^tt||}|jh|}|jj|jjz|jjz}||kr'td |||d}ntd|d}|S)a Validate this MRC file. The tests are: #. MRC format ID string: The ``map`` field in the header should contain "MAP ". #. Machine stamp: The machine stamp should contain one of ``0x44 0x44 0x00 0x00``, ``0x44 0x41 0x00 0x00`` or ``0x11 0x11 0x00 0x00``. #. MRC mode: the ``mode`` field should be one of the supported mode numbers: 0, 1, 2, 4, 6 or 12. (Note that MRC modes 3 and 101 are also valid according to the MRC 2014 specification but are not supported by mrcfile.) #. Map and cell dimensions: The header fields ``nx``, ``ny``, ``nz``, ``mx``, ``my``, ``mz``, ``cella.x``, ``cella.y`` and ``cella.z`` must all be positive numbers. #. Axis mapping: Header fields ``mapc``, ``mapr`` and ``maps`` must contain the values 1, 2, and 3 (in any order). #. Volume stack dimensions: If the spacegroup is in the range 401--630, representing a volume stack, the ``nz`` field should be exactly divisible by ``mz`` to represent the number of volumes in the stack. #. Header labels: The ``nlabl`` field should be set to indicate the number of labels in use, and the labels in use should appear first in the label array. #. MRC format version: The ``nversion`` field should be 20140 or 20141 for compliance with the MRC2014 standard. #. Extended header type: If an extended header is present, the ``exttyp`` field should be set to indicate the type of extended header. #. Data statistics: The statistics in the header should be correct for the actual data in the file, or marked as undetermined. #. File size: The size of the file on disk should match the expected size calculated from the MRC header. Args: print_file: The output text stream to use for printing messages about the validation. This is passed directly to the ``file`` argument of Python's :func:`print` function. The default is :data:`None`, which means output will be printed to :data:`sys.stdout`. Returns: :data:`True` if the file is valid, or :data:`False` if the file does not meet the MRC format specification in any way. ) print_fileNzgFile is larger than expected. Actual size: {0} bytes; expected size: {1} bytes (calculated from header))fileFz4Data block could not be read - file size not checked) rr validater9r3r4r5extended_headerprintr)rrLvalidr=mrc_sizer%s r&rNzMrcFile.validates\gt$$---DD 9 ++--I *.56)*+HX%%Jvi22%'''' H! # # # #E r+)r FFF)F)N)__name__ __module__ __qualname____doc__rr*rrr8r3rIrrN __classcell__)r%s@r&r r s 2DI"BBBBBBH???666000000 33333&AAAAAAAAAAr+r ) rV __future__rrrrrr:mrcinterpreterrr rr+r&rZs  ************ ******UUUUUnUUUUUr+