iu:dZddlmZmZmZmZddlZddlZddlZ ddl m Z ddl m Z ddlmZmZddlmZdd lmZdd lmZdd lmZdd ZddZdZddZddZddZddZdS)zz load_functions -------------- Module for top-level functions that open MRC files and form the main API of the package. )absolute_importdivisionprint_functionunicode_literalsN)utils) Bzip2MrcFile)MAP_IDMAP_ID_OFFSET_BYTES) FutureMrcFile) GzipMrcFile)MrcFile MrcMemmapFc|dkrt}n9|dkrt}n+|"td|t}||d|}||||S)aCreate a new MRC file. Args: name: The file name to use, as a string or :class:`~pathlib.Path`. data: Data to put in the file, as a :class:`numpy array `. The default is :data:`None`, to create an empty file. compression: The compression format to use. Acceptable values are: :data:`None` (the default; for no compression), ``'gzip'`` or ``'bzip2'``. It's good practice to name compressed files with an appropriate extension (for example, ``.mrc.gz`` for gzip) but this is not enforced. overwrite: Flag to force overwriting of an existing file. If :data:`False` and a file of the same name already exists, the file is not overwritten and an exception is raised. Returns: An :class:`~mrcfile.mrcfile.MrcFile` object (or a subclass of it if ``compression`` is specified). Raises: :exc:`ValueError`: If the file already exists and overwrite is :data:`False`. :exc:`ValueError`: If the compression format is not recognised. Warns: RuntimeWarning: If the data array contains Inf or NaN values. gzipbzip2Nz Unknown compression format '{0}'w+mode overwrite)r r ValueErrorformatrset_data)namedata compressionrNewMrcmrcs `/srv/www/vhosts/g4struct/public_html/venv/lib/python3.11/site-packages/mrcfile/load_functions.pynewr!s<f     ; &--// / &DI 6 6 6C  T Jrc0t}t|}tj|rd|vr"t d|tj|d5}| tttz}dddn #1swxYwY|tt dtkr+|dddkrt}n|dddkrt}|||||S) aOpen an MRC file. This function opens both normal and compressed MRC files. Supported compression formats are: gzip, bzip2. It is possible to use this function to create new MRC files (using mode ``w+``) but the :func:`new` function is more flexible. This function offers a permissive read mode for attempting to open corrupt or invalid files. In permissive mode, :mod:`warnings` are issued instead of exceptions if problems with the file are encountered. See :class:`~mrcfile.mrcinterpreter.MrcInterpreter` or the :doc:`usage guide <../usage_guide>` for more information. Args: name: The file name to open, as a string or :class:`~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``. permissive: Read the file 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`. Returns: An :class:`~mrcfile.mrcfile.MrcFile` object (or a :class:`~mrcfile.gzipmrcfile.GzipMrcFile` object if the file is gzipped). 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+`` and the file already exists. (Call :func:`new` with ``overwrite=True`` to deliberately overwrite an existing file.) :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. wzFile '{0}' already exists; use a different name, or delete it first or call 'mrcfile.new()' with 'overwrite=True' to overwrite itrbNssBZ)r permissive header_only)rstrospathexistsrrioopenreadr lenr r r )rrr(r)rfstarts r r/r/LsObF t99D w~~d& $;;AAGOO OWT4  >AFF.V<==E > > > > > > > > > > > > > > > #f++ 6 ) )RaRyK''$rre##% 6$Tj) + + ++s10B--B14B1ct|dd5}|j}dddn #1swxYwY|S)a Read an MRC file's data into a numpy array. This is a convenience function to read the data from an MRC file when there is no need for the file's header information. To read the headers as well, or if you need access to an :class:`~mrcfile.mrcfile.MrcFile` object representing the file, use :func:`mrcfile.open` instead. Args: name: The file name to read, as a string or :class:`~pathlib.Path`. Returns: A :class:`numpy array` containing the data from the file. r#Trr(N)r/rcopy)rrrs r r0r0s d . . .#x}} Ks 9==ct|}d}|drd}n|drd}t||||5}|||_ddddS#1swxYwYdS)aWrite a new MRC file. This is a convenience function to allow data to be quickly written to a file (with optional compression) using just a single function call. However, there is no control over the file's metadata except for optionally setting the voxel size. For more control, or if you need access to an :class:`~mrcfile.mrcfile.MrcFile` object representing the new file, use :func:`mrcfile.new` instead. Args: name: The file name to use, as a string or :class:`~pathlib.Path`. If the name ends with ``.gz`` or ``.bz2``, the file will be compressed using gzip or bzip2 respectively. data: Data to put in the file, as a :class:`numpy array `. The default is :data:`None`, to create an empty file. overwrite: Flag to force overwriting of an existing file. If :data:`False` and a file of the same name already exists, the file is not overwritten and an exception is raised. voxel_size: float | 3-tuple The voxel size to be written in the file header. Raises: :exc:`ValueError`: If the file already exists and overwrite is :data:`False`. Warns: RuntimeWarning: If the data array contains Inf or NaN values. Nz.gzrz.bz2r)r*endswithr! voxel_size)rrrr9rrs r writer:s: t99DK }}U v   T4i 0 0(C  !'CN((((((((((((((((((s A**A.1A.cNtt|ft||S)aOpen an MRC file asynchronously in a separate thread. This allows a file to be opened in the background while the main thread continues with other work. This can be a good way to improve performance if the main thread is busy with intensive computation, but will be less effective if the main thread is itself busy with disk I/O. Multiple files can be opened in the background simultaneously. However, this implementation is relatively crude; each call to this function will start a new thread and immediately use it to start opening a file. If you try to open many large files at the same time, performance will decrease as all of the threads attempt to access the disk at once. You'll also risk running out of memory to store the data from all the files. This function returns a :class:`~mrcfile.future_mrcfile.FutureMrcFile` object, which deliberately mimics the API of the :class:`~concurrent.futures.Future` object from Python 3's :mod:`concurrent.futures` module. (Future versions of this library might return genuine :class:`~concurrent.futures.Future` objects instead.) To get the real :class:`~mrcfile.mrcfile.MrcFile` object from a :class:`~mrcfile.future_mrcfile.FutureMrcFile`, call :meth:`~mrcfile.future_mrcfile.FutureMrcFile.result`. This will block until the file has been read and the :class:`~mrcfile.mrcfile.MrcFile` object is ready. To check if the :class:`~mrcfile.mrcfile.MrcFile` is ready without blocking, call :meth:`~mrcfile.future_mrcfile.FutureMrcFile.running` or :meth:`~mrcfile.future_mrcfile.FutureMrcFile.done`. Args: name: The file name to open, as a string or :class:`~pathlib.Path`. mode: The file mode (one of ``r``, ``r+`` or ``w+``). permissive: Read the file in permissive mode. The default is :data:`False`. Returns: A :class:`~mrcfile.future_mrcfile.FutureMrcFile` object. r5)r r/dictrrr(s r open_asyncr>s&N w$:(N(N(N O OOr"c&t|||S)aOpen a memory-mapped MRC file. This allows much faster opening of large files, because the data is only accessed on disk when a slice is read or written from the data array. See the :class:`~mrcfile.mrcmemmap.MrcMemmap` class documentation for more information. Because the memory-mapped data array accesses the disk directly, compressed files cannot be opened with this function. In all other ways, :func:`mmap` behaves in exactly the same way as :func:`open`. The :class:`~mrcfile.mrcmemmap.MrcMemmap` object returned by this function can be used in exactly the same way as a normal :class:`~mrcfile.mrcfile.MrcFile` object. Args: name: The file name to open, as a string or :class:`~pathlib.Path`. mode: The file mode (one of ``r``, ``r+`` or ``w+``). permissive: Read the file in permissive mode. The default is :data:`False`. Returns: An :class:`~mrcfile.mrcmemmap.MrcMemmap` object. r5rr=s r mmapr@s0 T < < < int8 * mode 1 -> int16 * mode 2 -> float32 * mode 4 -> complex64 * mode 6 -> uint16 The default is 0. fill: An optional value to use to fill the new data array. If :data:`None`, the data array will not be filled and its contents are unspecified. Numpy's usual rules for rounding or rejecting values apply, according to the dtype of the array. overwrite: Flag to force overwriting of an existing file. If :data:`False` and a file of the same name already exists, the file is not overwritten and an exception is raised. extended_header: The extended header object exttyp: The extended header type Returns: A new :class:`~mrcfile.mrcmemmap.MrcMemmap` object. Raises: :exc:`ValueError`: If the MRC mode is invalid. :exc:`ValueError`: If the file already exists and overwrite is :data:`False`. :exc:`ValueError`: If the extended header or any of the dimensions of the shape have a size greater than 2,147,483,647 (and therefore the size cannot be stored in the header). zPNew shape is too large! Found a dimension of size {}. The maximum allowed is {}.rrN.)npiinfoint32maxrrrset_extended_headerheaderexttyprdtype_from_mode _open_memmapupdate_header_from_datarflush) rshapemrc_modefillrextended_headerrHdimrdtypes r new_mmaprSs fCC "(##' ' 'D$fS"(28*<*<*@AACC C ( Dty 9 9 9C" 000 "   !( + +EUE"""!!!  IIKKK Jr")NNF)r#FF)NFN)r#F)rNFNN) __doc__ __future__rrrrr.r+numpyrBr bzip2mrcfiler constantsr r future_mrcfiler gzipmrcfiler mrcfiler mrcmemmaprr!r/r0r:r>r@rSr"r r_s************ &&&&&&22222222))))))$$$$$$ ****ZF+F+F+F+R&%(%(%(%(P'P'P'P'PT====6HHHHHHr"