def convert(source, destination, sourceFormat, destinationFormat):
# converts the matrix at source in sourceFormat to destinationFormat
# then writes out at destination
if not os.path.exists(source):
print("ERROR: load from nonexistent path")
return
if not os.path.isfile(source):
print("ERROR: {0} is not a file".format(source))
return
HERCMATRIX = libHercmIO.readMatrix(source, sourceFormat)
HERCMATRIX.verification = libBXF.generateVerificationSum(HERCMATRIX)
libHercmIO.writeMatrix(destination, destinationFormat, HERCMATRIX)
def readMatrix(filename, form, showProgress=False):
HERCMATRIX = libHercMatrix.hercMatrix()
logging.info("reading matrix {0} in format {1}".format(filename, form))
if (form == 'hercm') or (form == 'bxf'):
# TODO: exception handling
HERCMATRIX = libBXF.read(filename)
elif form == 'mtx':
from scipy import io
from scipy.sparse import csr_matrix
from numpy import array
# reads in an MTX file and converts it to hercm
try:
if showProgress:
print("reading data from file...")
rawMatrix = scipy.sparse.coo_matrix(scipy.io.mmread(filename))
if 'symmetric' in io.mminfo(filename):
HERCMATRIX.symmetry = "SYM"
else:
HERCMATRIX.symmetry = "ASYM"
hercm = {} # needed to generate verification
if showProgress:
print("generating header data..")
hercm['val'] = rawMatrix.data
hercm['col'] = rawMatrix.col.tolist()
hercm['row'] = rawMatrix.row.tolist()
(matrixWidth, matrixHeight) = rawMatrix.shape
HERCMATRIX.height = int(matrixHeight)
HERCMATRIX.width = int(matrixWidth)
vs = libBXF.generateVerificationSum(hercm)
HERCMATRIX.verification = vs
HERCMATRIX.remarks = []
# I'm not sure why has to be hard...
# http://stackoverflow.com/questions/26018781/numpy-is-it-possible-to-preserve-the-dtype-of-columns-when-using-column-stack
if showProgress:
print("preparing matrix data...")
val = numpy.asarray(hercm['val'], dtype='float64')
col = numpy.asarray(hercm['col'], dtype='int32')
row = numpy.asarray(hercm['row'], dtype='int32')
val = numpy.rec.array(val, dtype=[(('val'), numpy.float64)])
col = numpy.rec.array(col, dtype=[(('col'), numpy.int32)])
row = numpy.rec.array(row, dtype=[(('row'), numpy.int32)])
HERCMATRIX.elements = append_fields(row,
'col',
col,
usemask=False,
dtypes=[numpy.int32])
HERCMATRIX.elements = append_fields(HERCMATRIX.elements,
'val',
val,
usemask=False,
dtypes=[numpy.float64])
HERCMATRIX.nzentries = len(HERCMATRIX.elements['val'])
HERCMATRIX.verification = libBXF.generateVerificationSum(
HERCMATRIX)
if showProgress:
print("finished reading matrix")
except IOError as e: # make sure the file exists and is readable
logging.warning("(lsc-480) could not open matrix file")
raise IOError("could not open matrix file for writing...",
str(e))
elif form == 'mat': # matlab matrices
from scipy import io
from scipy import sparse
from numpy import array
try:
rawMatrix = scipy.sparse.coo_matrix(
scipy.io.loadmat(filename)['matrix'])
hercm = {} # needed to generate verification
hercm['val'] = rawMatrix.data
hercm['col'] = rawMatrix.col.tolist()
hercm['row'] = rawMatrix.row.tolist()
(matrixWidth, matrixHeight) = rawMatrix.shape
HERCMATRIX.height = int(matrixHeight)
HERCMATRIX.width = int(matrixWidth)
vs = libBXF.generateVerificationSum(hercm)
HERCMATRIX.verification = vs
HERCMATRIX.remarks = []
# I'm not sure why has to be hard...
# http://stackoverflow.com/questions/26018781/numpy-is-it-possible-to-preserve-the-dtype-of-columns-when-using-column-stack
val = numpy.asarray(hercm['val'], dtype='float64')
col = numpy.asarray(hercm['col'], dtype='int32')
row = numpy.asarray(hercm['row'], dtype='int32')
val = numpy.rec.array(val, dtype=[(('val'), numpy.float64)])
col = numpy.rec.array(col, dtype=[(('col'), numpy.int32)])
row = numpy.rec.array(row, dtype=[(('row'), numpy.int32)])
HERCMATRIX.elements = append_fields(row,
'col',
col,
usemask=False,
dtypes=[numpy.int32])
HERCMATRIX.elements = append_fields(HERCMATRIX.elements,
'val', val, usemask=False, dtypes=[numpy.float64])
HERCMATRIX.nzentries = len(HERCMATRIX.elements['val'])
if HERCMATRIX.checkSymmetry():
HERCMATRIX.symmetry = 'SYM'
HERCMATRIX.verification = libBXF.generateVerificationSum(
HERCMATRIX)
except IOError as e: # make sure the file exists and is readable
logging.warning("(lsc-536)could not open matrix file")
raise IOError("could not open matrix file for writing...",
str(e))
elif form == 'valcol':
HERCMATRIX = libValcolIO.read(filename)
else:
logging.warning("(lsc-545) format {0} is not valid".format(form))
if showProgress:
print("converting matrix to row-major...")
logging.info("converting matrix to row-major")
HERCMATRIX.makeRowMajor()
if showProgress:
print("matrix is now row major")
if HERCMATRIX.symmetry == 'SYM':
logging.info("matrix is symmetric, truncating upper triangle")
if showProgress:
print("matrix is symmetric, truncating upper triangle...")
HERCMATRIX.makeSymmetrical('truncate')
if showProgress:
print("upper triangle truncated")
return HERCMATRIX
def execute(this, arguments, WORKINGMATRIX):
try:
newSum = libBXF.generateVerificationSum(WORKINGMATRIX)
except TypeError:
print("ERROR: could not generate verification sum of empty matrix")
WORKINGMATRIX.verification = newSum
