B -§,c'ã@sLdZddlmZmZmZmZddlZddlZddlm Z Gdd„de ƒZ dS)zŒ mrcfile ------- Module which exports the :class:`MrcFile` class. Classes: :class:`MrcFile`: An object which represents an MRC file. é)Úabsolute_importÚdivisionÚprint_functionÚunicode_literalsNé)ÚMrcInterpretercsveZdZdZd‡fdd„ Zdd„Zdd „Zd‡fd d „ Z‡fd d „Zdd„Z ‡fdd„Z dd„Z d‡fdd„ Z ‡Z S)ÚMrcFilea 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). ÚrFc s¾tt|ƒjfd|i|—Ž|dkr0td |¡ƒ‚t|ƒ}d|kr^tj |¡r^|s^td |¡ƒ‚||_ |j dk|_ |  |¡y d|krŽ|  ¡n |  |¡Wntk r¸| ¡‚YnXdS)aÆInitialise 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. Ú permissive)r zr+zw+zMode '{0}' not supportedÚwz=File '{0}' already exists; set overwrite=True to overwrite itr N)ÚsuperrÚ__init__Ú ValueErrorÚformatÚstrÚosÚpathÚexistsÚ_modeZ _read_onlyÚ _open_fileZ_create_default_attributesÚ_readÚ ExceptionÚ _close_file)ÚselfÚnameÚmodeZ overwriter Ú header_onlyÚkwargs)Ú __class__©ú.lib/python3.7/site-packages/mrcfile/mrcfile.pyr 4s",   zMrcFile.__init__cCsd |jj|j¡S)NzMrcFile('{0}', mode='{1}'))rÚ _iostreamrr)rrrr Ú__repr__xs zMrcFile.__repr__cCst||jdƒ|_dS)z,Open a file object to use as the I/O stream.ÚbN)Úopenrr!)rrrrr r|szMrcFile._open_filecs |j d¡tt|ƒ |¡dS)z5Override _read() to move back to start of file first.rN)r!Úseekr rr)rr)rrr r€s z MrcFile._readcsj| ¡}|jj|jj}||}tt|ƒj|d|jdk rf|jj}||krfd ||¡}t   |t ¡dS)zAOverride _read_data() to check file size matches data block size.)Z max_bytesNz*MRC file is {0} bytes larger than expected) Ú_get_file_sizeÚheaderÚnbytesZnsymbtr rÚ _read_dataÚdatarÚwarningsÚwarnÚRuntimeWarning)rÚ file_sizeZ header_sizeZremaining_file_sizeZ data_sizeÚmsg)rrr r)…s  zMrcFile._read_datacCs8|j ¡}|j dtj¡|j ¡}|j |tj¡|S)z8Return the size of the underlying file object, in bytes.r)r!Útellr%rÚSEEK_ENDÚSEEK_SET)rÚposÚsizerrr r&•s   zMrcFile._get_file_sizecstt|ƒ ¡| ¡dS)zÊFlush 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)r rÚcloser)r)rrr r5sz MrcFile.closecCs|j ¡dS)zClose the file object.N)r!r5)rrrr r¦szMrcFile._close_fileNcsrtt|ƒj|d}|jdk r^| ¡}|jj|jj|jj}||krntd  ||¡|dd}ntd|dd}|S)aˆ 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. )Ú print_fileNzgFile is larger than expected. Actual size: {0} bytes; expected size: {1} bytes (calculated from header))ÚfileFz4Data block could not be read - file size not checked) r rÚvalidater*r&r'r(Zextended_headerÚprintr)rr6Zvalidr.Zmrc_size)rrr r8ªs. zMrcFile.validate)r FFF)F)N)Ú__name__Ú __module__Ú __qualname__Ú__doc__r r"rrr)r&r5rr8Ú __classcell__rr)rr rsC  r) r=Z __future__rrrrrr+Zmrcinterpreterrrrrrr Ú s