ig:~dZddlmZmZmZmZddlZddlZddl m Z ddl m Z ddl mZddlmZGd d eZdS) z mrcinterpreter -------------- Module which exports the :class:`MrcInterpreter` class. Classes: :class:`MrcInterpreter`: An object which can interpret an I/O stream as MRC data. )absolute_importdivisionprint_functionunicode_literalsN)utils) HEADER_DTYPE) MrcObject)MAP_IDcdeZdZdZdfd ZdZdZdZddZd Z d Z dd Z d Z dZ dZxZS)MrcInterpretera An object which interprets an I/O stream as MRC / CCP4 map data. The header and data are handled as numpy arrays - see :class:`~mrcfile.mrcobject.MrcObject` for details. :class:`MrcInterpreter` can be used directly, but it is mostly intended as a superclass to provide common stream-handling functionality. This can be used by subclasses which will handle opening and closing the stream. This class implements the :meth:`~object.__enter__` and :meth:`~object.__exit__` special methods which allow it to be used by the Python context manager in a :keyword:`with` block. This ensures that :meth:`close` is called after the object is finished with. When reading the I/O stream, a :exc:`ValueError` is raised if the data is invalid in one of the following ways: #. The header's ``map`` field is not set correctly to confirm the file type. #. The machine stamp is invalid and so the data's byte order cannot be determined. #. The mode number is not recognised. Currently accepted modes are 0, 1, 2, 4 and 6. #. The file is not large enough for the specified extended header size. #. The data block is not large enough for the specified data type and dimensions. :class:`MrcInterpreter` offers a permissive read mode for handling problematic files. If ``permissive`` is set to :data:`True` and any of the validity checks fails, a :mod:`warning ` is issued instead of an exception, and file interpretation continues. If the mode number is invalid or the data block is too small, the :attr:`~mrcfile.mrcobject.MrcObject.data` attribute will be set to :data:`None`. In this case, it might be possible to inspect and correct the header, and then call :meth:`_read` again to read the data correctly. See the :doc:`usage guide <../usage_guide>` for more details. Methods: * :meth:`flush` * :meth:`close` Methods relevant to subclasses: * :meth:`_read` * :meth:`_read_data` * :meth:`_read_bytearray_from_stream` NFc tt|jdi|||_||_|j||dSdS)aIInitialise a new MrcInterpreter object. This initialiser reads the stream if it is given. In general, subclasses should call :meth:`__init__` without giving an ``iostream`` argument, then set the ``_iostream`` attribute themselves and call :meth:`_read` when ready. To use the MrcInterpreter class directly, pass a stream when creating the object (or for a write-only stream, create an MrcInterpreter with no stream, call :meth:`._create_default_attributes` and set the ``_iostream`` attribute directly). Args: iostream: The I/O stream to use to read and write MRC data. The default is :data:`None`. permissive: Read the stream in permissive mode. 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 ``iostream`` is given, the data it contains cannot be interpreted as a valid MRC file and ``permissive`` is :data:`False`. Warns: RuntimeWarning: If ``iostream`` is given, the data it contains cannot be interpreted as a valid MRC file and ``permissive`` is :data:`True`. N)superr __init__ _iostream _permissive_read)selfiostream permissive header_onlykwargs __class__s `/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/mrcfile/mrcinterpreter.pyrzMrcInterpreter.__init__Qsb@ -nd##,66v666!% > % JJ{ # # # # # & %c|S)zCalled by the context manager at the start of a :keyword:`with` block. Returns: This object (``self``). rrs r __enter__zMrcInterpreter.__enter__zs  rc.|dS)zCalled by the context manager at the end of a :keyword:`with` block. This ensures that the :meth:`close` method is called. N)close)rexc_typeexc_valexc_tbs r__exit__zMrcInterpreter.__exit__s rcR |dS#t$rYdSwxYw)zAttempt to flush the stream when this object is garbage collected. It's better not to rely on this - instead, use a :keyword:`with` block or explicitly call the :meth:`close` method. N)r! Exceptionrs r__del__zMrcInterpreter.__del__s:   JJLLLLL    DD s  &&c|||s|dSdS)a1Read the header, extended header and data from the I/O stream. Before calling this method, the stream should be open and positioned at the start of the header. This method will advance the stream to the end of the data block (or the end of the extended header if ``header_only`` is :data:`True`. Args: header_only: Only read the header and extended header from the stream. The default is :data:`False`. Raises: :exc:`ValueError`: If the data in the stream cannot be interpreted as a valid MRC file and ``permissive`` is :data:`False`. Warns: RuntimeWarning: If the data in the stream cannot be interpreted as a valid MRC file and ``permissive`` is :data:`True`. N) _read_header_read_extended_header _read_data)rrs rrzMrcInterpreter._readsP(  ""$$$  OO       rc|tj\}}|tjkrtdt j|tdtj}t|j ddtddkr3d}|j rtj|tnt| t!j|j}nI#t$r<}|j r*d}tjt'|tnYd}~nd}~wwxYw|j||_|j r t!j|jn#t$r |j|jj}t!j||j|_t!j|j}d}tj|||jjjtn#t$rYnwxYwYnwxYw|j |j_||_dS) aRead the MRC header from the I/O stream. The header will be read from the current stream position, and the stream will be advanced by 1024 bytes. Raises: :exc:`ValueError`: If the data in the stream cannot be interpreted as a valid MRC file and ``permissive`` is :data:`False`. Warns: RuntimeWarning: If the data in the stream cannot be interpreted as a valid MRC file and ``permissive`` is :data:`True`. z)Couldn't read enough bytes for MRC headerdtyperNz=Map ID string not found - not an MRC file, or file is corrupt>>FFrJJOOPRP[\\   RaR F2A2J . .9C & c>2222 oo% #>FL$)$>v}$M$MM\CM#**]FK_extended_headerr4r5r6rHrIrJ)rext_header_arrrMrOs rr+z$MrcInterpreter._read_extended_headers$&*%E%Ec$+J\F]F]%^%^"  * * *RF4;-z::  & c>222(,% oo% " nD I I I48O0C#---rrcR tj|j}nT#t$rG}|jr:t jd|td|_ Yd}~dSd}~wwxYwtj |j}|j }|D]}||z}|dkrU||krOd||}|jr#t j|td|_ dSt|| |\}} | |krOd|| }|jr#t j|td|_ dSt|tj||||_ |j |j j_dS)aRead the data array from the stream. This method uses information from the header to set the data array's shape and dtype. Args: max_bytes: Read at most this many bytes from the stream. If zero or negative, the full size of the data block as defined in the header will be read, even if this is very large. Raises: :exc:`ValueError`: If the stream is not long enough to contain the data indicated by the header and ``permissive`` is :data:`False`. Warns: RuntimeWarning: If the stream is not long enough to contain the data indicated by the header and ``permissive`` is :data:`True`. z{0} - data block cannot be readNrz1Expected {0} bytes in data block but limit is {1}z8Expected {0} bytes in data block but could only read {1}r.)rdata_dtype_from_headerrNr4rr<r=rFr>_datadata_shape_from_headerr3r2r5r6r7rHrIrJ) r max_bytesr/rQshapenbytes axis_lengthrOdata_arrrMs rr,zMrcInterpreter._read_datas* 0==EE     ?FFsKK,...!  ,T[99  " "K k !FF q==Vi//FF69--  & c>222!  oo%#??GG*   MF6:..  & c>222!  oo%]85999AA%HH )-%8 """s A-;A('A((A-c\t|}|j|}||fS)aRead a :class:`bytearray` from the stream. This default implementation relies on the stream implementing the :meth:`~io.BufferedIOBase.readinto` method to avoid copying the new array while creating the mutable :class:`bytearray`. Subclasses should override this if their stream does not support :meth:`~io.BufferedIOBase.readinto`. Returns: A 2-tuple of the :class:`bytearray` and the number of bytes that were read from the stream. ) bytearrayrreadinto)rnumber_of_bytes result_arrayrMs rr2z*MrcInterpreter._read_bytearray_from_streamYs1!11 ^,,\:: Z''rc|j |jjs|d|_d|_|dS)z=Flush to the stream and clear the header and data attributes.N)rKrclosedflushrX _close_datars rr!zMrcInterpreter.closejsH < #DN,A # JJLLL $ rc|js|jd|j|j|j|j|jt j|j|j |j dSdS)aoFlush the header and data arrays to the I/O stream. This implementation seeks to the start of the stream, writes the header, extended header and data arrays, and then truncates the stream. Subclasses should override this implementation for streams which do not support :meth:`~io.IOBase.seek` or :meth:`~io.IOBase.truncate`. rN) rHrseekwriterNextended_headerr5ascontiguousarraydatatruncaterjrs rrjzMrcInterpreter.flushrs # N   " " " N  - - - N !5 6 6 6 N !5di!@!@ A A A N # # % % % N " " " " "  # #r)NFF)F)r)__name__ __module__ __qualname____doc__rrr%r(rr*r+r,r2r!rj __classcell__)rs@rr r s00d'$'$'$'$'$'$R   2GGGR D D DD=9=9=9=9~((("#######rr )rv __future__rrrrr<numpyr5rdtypesr mrcobjectr constantsr r rrrr~s  ************ d#d#d#d#d#Yd#d#d#d#d#r