""" Implementation of Harwell-Boeing read/write. At the moment not the full Harwell-Boeing format is supported. Supported features are: - assembled, non-symmetric, real matrices - integer for pointer/indices - exponential format for float values, and int format """ # TODO: # - Add more support (symmetric/complex matrices, non-assembled matrices ?) # XXX: reading is reasonably efficient (>= 85 % is in numpy.fromstring), but # takes a lot of memory. Being faster would require compiled code. # write is not efficient. Although not a terribly exciting task, # having reusable facilities to efficiently read/write fortran-formatted files # would be useful outside this module. import warnings import numpy as np from scipy.sparse import csc_matrix from scipy.io.harwell_boeing._fortran_format_parser import \ FortranFormatParser, IntFormat, ExpFormat __all__ = ["MalformedHeader", "hb_read", "hb_write", "HBInfo", "HBFile", "HBMatrixType"] class MalformedHeader(Exception): pass class LineOverflow(Warning): pass def _nbytes_full(fmt, nlines): """Return the number of bytes to read to get every full lines for the given parsed fortran format.""" return (fmt.repeat * fmt.width + 1) * (nlines - 1) class HBInfo(object): @classmethod def from_data(cls, m, title="Default title", key="0", mxtype=None, fmt=None): """Create a HBInfo instance from an existing sparse matrix. Parameters ---------- m : sparse matrix the HBInfo instance will derive its parameters from m title : str Title to put in the HB header key : str Key mxtype : HBMatrixType type of the input matrix fmt : dict not implemented Returns ------- hb_info : HBInfo instance """ m = m.tocsc(copy=False) pointer = m.indptr indices = m.indices values = m.data nrows, ncols = m.shape nnon_zeros = m.nnz if fmt is None: # +1 because HB use one-based indexing (Fortran), and we will write # the indices /pointer as such pointer_fmt = IntFormat.from_number(np.max(pointer+1)) indices_fmt = IntFormat.from_number(np.max(indices+1)) if values.dtype.kind in np.typecodes["AllFloat"]: values_fmt = ExpFormat.from_number(-np.max(np.abs(values))) elif values.dtype.kind in np.typecodes["AllInteger"]: values_fmt = IntFormat.from_number(-np.max(np.abs(values))) else: raise NotImplementedError("type %s not implemented yet" % values.dtype.kind) else: raise NotImplementedError("fmt argument not supported yet.") if mxtype is None: if not np.isrealobj(values): raise ValueError("Complex values not supported yet") if values.dtype.kind in np.typecodes["AllInteger"]: tp = "integer" elif values.dtype.kind in np.typecodes["AllFloat"]: tp = "real" else: raise NotImplementedError("type %s for values not implemented" % values.dtype) mxtype = HBMatrixType(tp, "unsymmetric", "assembled") else: raise ValueError("mxtype argument not handled yet.") def _nlines(fmt, size): nlines = size // fmt.repeat if nlines * fmt.repeat != size: nlines += 1 return nlines pointer_nlines = _nlines(pointer_fmt, pointer.size) indices_nlines = _nlines(indices_fmt, indices.size) values_nlines = _nlines(values_fmt, values.size) total_nlines = pointer_nlines + indices_nlines + values_nlines return cls(title, key, total_nlines, pointer_nlines, indices_nlines, values_nlines, mxtype, nrows, ncols, nnon_zeros, pointer_fmt.fortran_format, indices_fmt.fortran_format, values_fmt.fortran_format) @classmethod def from_file(cls, fid): """Create a HBInfo instance from a file object containing a matrix in the HB format. Parameters ---------- fid : file-like matrix File or file-like object containing a matrix in the HB format. Returns ------- hb_info : HBInfo instance """ # First line line = fid.readline().strip("\n") if not len(line) > 72: raise ValueError("Expected at least 72 characters for first line, " "got: \n%s" % line) title = line[:72] key = line[72:] # Second line line = fid.readline().strip("\n") if not len(line.rstrip()) >= 56: raise ValueError("Expected at least 56 characters for second line, " "got: \n%s" % line) total_nlines = _expect_int(line[:14]) pointer_nlines = _expect_int(line[14:28]) indices_nlines = _expect_int(line[28:42]) values_nlines = _expect_int(line[42:56]) rhs_nlines = line[56:72].strip() if rhs_nlines == '': rhs_nlines = 0 else: rhs_nlines = _expect_int(rhs_nlines) if not rhs_nlines == 0: raise ValueError("Only files without right hand side supported for " "now.") # Third line line = fid.readline().strip("\n") if not len(line) >= 70: raise ValueError("Expected at least 72 character for third line, got:\n" "%s" % line) mxtype_s = line[:3].upper() if not len(mxtype_s) == 3: raise ValueError("mxtype expected to be 3 characters long") mxtype = HBMatrixType.from_fortran(mxtype_s) if mxtype.value_type not in ["real", "integer"]: raise ValueError("Only real or integer matrices supported for " "now (detected %s)" % mxtype) if not mxtype.structure == "unsymmetric": raise ValueError("Only unsymmetric matrices supported for " "now (detected %s)" % mxtype) if not mxtype.storage == "assembled": raise ValueError("Only assembled matrices supported for now") if not line[3:14] == " " * 11: raise ValueError("Malformed data for third line: %s" % line) nrows = _expect_int(line[14:28]) ncols = _expect_int(line[28:42]) nnon_zeros = _expect_int(line[42:56]) nelementals = _expect_int(line[56:70]) if not nelementals == 0: raise ValueError("Unexpected value %d for nltvl (last entry of line 3)" % nelementals) # Fourth line line = fid.readline().strip("\n") ct = line.split() if not len(ct) == 3: raise ValueError("Expected 3 formats, got %s" % ct) return cls(title, key, total_nlines, pointer_nlines, indices_nlines, values_nlines, mxtype, nrows, ncols, nnon_zeros, ct[0], ct[1], ct[2], rhs_nlines, nelementals) def __init__(self, title, key, total_nlines, pointer_nlines, indices_nlines, values_nlines, mxtype, nrows, ncols, nnon_zeros, pointer_format_str, indices_format_str, values_format_str, right_hand_sides_nlines=0, nelementals=0): """Do not use this directly, but the class ctrs (from_* functions).""" self.title = title self.key = key if title is None: title = "No Title" if len(title) > 72: raise ValueError("title cannot be > 72 characters") if key is None: key = "|No Key" if len(key) > 8: warnings.warn("key is > 8 characters (key is %s)" % key, LineOverflow) self.total_nlines = total_nlines self.pointer_nlines = pointer_nlines self.indices_nlines = indices_nlines self.values_nlines = values_nlines parser = FortranFormatParser() pointer_format = parser.parse(pointer_format_str) if not isinstance(pointer_format, IntFormat): raise ValueError("Expected int format for pointer format, got %s" % pointer_format) indices_format = parser.parse(indices_format_str) if not isinstance(indices_format, IntFormat): raise ValueError("Expected int format for indices format, got %s" % indices_format) values_format = parser.parse(values_format_str) if isinstance(values_format, ExpFormat): if mxtype.value_type not in ["real", "complex"]: raise ValueError("Inconsistency between matrix type %s and " "value type %s" % (mxtype, values_format)) values_dtype = np.float64 elif isinstance(values_format, IntFormat): if mxtype.value_type not in ["integer"]: raise ValueError("Inconsistency between matrix type %s and " "value type %s" % (mxtype, values_format)) # XXX: fortran int -> dtype association ? values_dtype = int else: raise ValueError("Unsupported format for values %r" % (values_format,)) self.pointer_format = pointer_format self.indices_format = indices_format self.values_format = values_format self.pointer_dtype = np.int32 self.indices_dtype = np.int32 self.values_dtype = values_dtype self.pointer_nlines = pointer_nlines self.pointer_nbytes_full = _nbytes_full(pointer_format, pointer_nlines) self.indices_nlines = indices_nlines self.indices_nbytes_full = _nbytes_full(indices_format, indices_nlines) self.values_nlines = values_nlines self.values_nbytes_full = _nbytes_full(values_format, values_nlines) self.nrows = nrows self.ncols = ncols self.nnon_zeros = nnon_zeros self.nelementals = nelementals self.mxtype = mxtype def dump(self): """Gives the header corresponding to this instance as a string.""" header = [self.title.ljust(72) + self.key.ljust(8)] header.append("%14d%14d%14d%14d" % (self.total_nlines, self.pointer_nlines, self.indices_nlines, self.values_nlines)) header.append("%14s%14d%14d%14d%14d" % (self.mxtype.fortran_format.ljust(14), self.nrows, self.ncols, self.nnon_zeros, 0)) pffmt = self.pointer_format.fortran_format iffmt = self.indices_format.fortran_format vffmt = self.values_format.fortran_format header.append("%16s%16s%20s" % (pffmt.ljust(16), iffmt.ljust(16), vffmt.ljust(20))) return "\n".join(header) def _expect_int(value, msg=None): try: return int(value) except ValueError: if msg is None: msg = "Expected an int, got %s" raise ValueError(msg % value) def _read_hb_data(content, header): # XXX: look at a way to reduce memory here (big string creation) ptr_string = "".join([content.read(header.pointer_nbytes_full), content.readline()]) ptr = np.fromstring(ptr_string, dtype=int, sep=' ') ind_string = "".join([content.read(header.indices_nbytes_full), content.readline()]) ind = np.fromstring(ind_string, dtype=int, sep=' ') val_string = "".join([content.read(header.values_nbytes_full), content.readline()]) val = np.fromstring(val_string, dtype=header.values_dtype, sep=' ') try: return csc_matrix((val, ind-1, ptr-1), shape=(header.nrows, header.ncols)) except ValueError as e: raise e def _write_data(m, fid, header): m = m.tocsc(copy=False) def write_array(f, ar, nlines, fmt): # ar_nlines is the number of full lines, n is the number of items per # line, ffmt the fortran format pyfmt = fmt.python_format pyfmt_full = pyfmt * fmt.repeat # for each array to write, we first write the full lines, and special # case for partial line full = ar[:(nlines - 1) * fmt.repeat] for row in full.reshape((nlines-1, fmt.repeat)): f.write(pyfmt_full % tuple(row) + "\n") nremain = ar.size - full.size if nremain > 0: f.write((pyfmt * nremain) % tuple(ar[ar.size - nremain:]) + "\n") fid.write(header.dump()) fid.write("\n") # +1 is for Fortran one-based indexing write_array(fid, m.indptr+1, header.pointer_nlines, header.pointer_format) write_array(fid, m.indices+1, header.indices_nlines, header.indices_format) write_array(fid, m.data, header.values_nlines, header.values_format) class HBMatrixType(object): """Class to hold the matrix type.""" # q2f* translates qualified names to Fortran character _q2f_type = { "real": "R", "complex": "C", "pattern": "P", "integer": "I", } _q2f_structure = { "symmetric": "S", "unsymmetric": "U", "hermitian": "H", "skewsymmetric": "Z", "rectangular": "R" } _q2f_storage = { "assembled": "A", "elemental": "E", } _f2q_type = dict([(j, i) for i, j in _q2f_type.items()]) _f2q_structure = dict([(j, i) for i, j in _q2f_structure.items()]) _f2q_storage = dict([(j, i) for i, j in _q2f_storage.items()]) @classmethod def from_fortran(cls, fmt): if not len(fmt) == 3: raise ValueError("Fortran format for matrix type should be 3 " "characters long") try: value_type = cls._f2q_type[fmt[0]] structure = cls._f2q_structure[fmt[1]] storage = cls._f2q_storage[fmt[2]] return cls(value_type, structure, storage) except KeyError: raise ValueError("Unrecognized format %s" % fmt) def __init__(self, value_type, structure, storage="assembled"): self.value_type = value_type self.structure = structure self.storage = storage if value_type not in self._q2f_type: raise ValueError("Unrecognized type %s" % value_type) if structure not in self._q2f_structure: raise ValueError("Unrecognized structure %s" % structure) if storage not in self._q2f_storage: raise ValueError("Unrecognized storage %s" % storage) @property def fortran_format(self): return self._q2f_type[self.value_type] + \ self._q2f_structure[self.structure] + \ self._q2f_storage[self.storage] def __repr__(self): return "HBMatrixType(%s, %s, %s)" % \ (self.value_type, self.structure, self.storage) class HBFile(object): def __init__(self, file, hb_info=None): """Create a HBFile instance. Parameters ---------- file : file-object StringIO work as well hb_info : HBInfo, optional Should be given as an argument for writing, in which case the file should be writable. """ self._fid = file if hb_info is None: self._hb_info = HBInfo.from_file(file) else: #raise IOError("file %s is not writable, and hb_info " # "was given." % file) self._hb_info = hb_info @property def title(self): return self._hb_info.title @property def key(self): return self._hb_info.key @property def type(self): return self._hb_info.mxtype.value_type @property def structure(self): return self._hb_info.mxtype.structure @property def storage(self): return self._hb_info.mxtype.storage def read_matrix(self): return _read_hb_data(self._fid, self._hb_info) def write_matrix(self, m): return _write_data(m, self._fid, self._hb_info) def hb_read(path_or_open_file): """Read HB-format file. Parameters ---------- path_or_open_file : path-like or file-like If a file-like object, it is used as-is. Otherwise, it is opened before reading. Returns ------- data : scipy.sparse.csc_matrix instance The data read from the HB file as a sparse matrix. Notes ----- At the moment not the full Harwell-Boeing format is supported. Supported features are: - assembled, non-symmetric, real matrices - integer for pointer/indices - exponential format for float values, and int format Examples -------- We can read and write a harwell-boeing format file: >>> from scipy.io.harwell_boeing import hb_read, hb_write >>> from scipy.sparse import csr_matrix, eye >>> data = csr_matrix(eye(3)) # create a sparse matrix >>> hb_write("data.hb", data) # write a hb file >>> print(hb_read("data.hb")) # read a hb file (0, 0) 1.0 (1, 1) 1.0 (2, 2) 1.0 """ def _get_matrix(fid): hb = HBFile(fid) return hb.read_matrix() if hasattr(path_or_open_file, 'read'): return _get_matrix(path_or_open_file) else: with open(path_or_open_file) as f: return _get_matrix(f) def hb_write(path_or_open_file, m, hb_info=None): """Write HB-format file. Parameters ---------- path_or_open_file : path-like or file-like If a file-like object, it is used as-is. Otherwise, it is opened before writing. m : sparse-matrix the sparse matrix to write hb_info : HBInfo contains the meta-data for write Returns ------- None Notes ----- At the moment not the full Harwell-Boeing format is supported. Supported features are: - assembled, non-symmetric, real matrices - integer for pointer/indices - exponential format for float values, and int format Examples -------- We can read and write a harwell-boeing format file: >>> from scipy.io.harwell_boeing import hb_read, hb_write >>> from scipy.sparse import csr_matrix, eye >>> data = csr_matrix(eye(3)) # create a sparse matrix >>> hb_write("data.hb", data) # write a hb file >>> print(hb_read("data.hb")) # read a hb file (0, 0) 1.0 (1, 1) 1.0 (2, 2) 1.0 """ m = m.tocsc(copy=False) if hb_info is None: hb_info = HBInfo.from_data(m) def _set_matrix(fid): hb = HBFile(fid, hb_info) return hb.write_matrix(m) if hasattr(path_or_open_file, 'write'): return _set_matrix(path_or_open_file) else: with open(path_or_open_file, 'w') as f: return _set_matrix(f)