def do_proc_F2(dinp, doutp):
"scan all rows of dinp, apply proc() and store into doutp"
size = doutp.axis2.size
#scan = min(dinp.size1, doutp.size1) # min() because no need to do extra work !
scan = dinp.size1
widgets = ['Processing F2: ', pg.Percentage(), ' ', pg.Bar(marker='-',left='[',right=']'), pg.ETA()]
pbar= pg.ProgressBar(widgets=widgets, maxval=scan) #, fd=sys.stdout)
print("dinp.axis1.itype ",dinp.axis1.itype)
print("dinp.axis2.itype ",dinp.axis2.itype)
print("doutp.axis1.itype ",doutp.axis1.itype)
print("doutp.axis2.itype ",doutp.axis2.itype)
print("dinp.axis1.size ",dinp.axis1.size)
print("dinp.axis2.size ",dinp.axis2.size)
print("doutp.axis1.size ",doutp.axis1.size)
print("doutp.axis2.size ",doutp.axis2.size)
print(doutp.report())
print(dir(doutp))
for i in xrange( scan):
# if i%(scan/16) == 0: # print avancement
# print "proc row %d / %d"%(i,scan)
r = dinp.row(i)
apod(r, size)
r.rfft()
doutp.set_row(i,r)
pbar.update(i+1)
pbar.finish()
def do_proc_F1_modu(dinp, doutp):
"as do_proc_F1, but applies hypercomplex modulus() at the end"
size = 2 * doutp.axis1.size
scan = doutp.size2
# scan = doutp.size2
widgets = [
'Processing F1 modu: ',
pg.Percentage(), ' ',
pg.Bar(marker='-', left='[', right=']'),
pg.ETA()
]
pbar = pg.ProgressBar(widgets=widgets, maxval=scan) #, fd=sys.stdout)
for i in xrange(scan):
# if i%(scan/16) == 0: # print avancement
# print "proc col %d / %d"%(i,scan)
d = FTICRData(buffer=np.zeros(
(2 * doutp.size1, 2))) # 2 columns - used for hypercomplex modulus
for off in (0, 1):
p = dinp.col(2 * i + off)
apod(p, size)
p.rfft()
d.set_col(off, p)
d.axis1.itype = 1
d.axis2.itype = 1
d.modulus()
doutp.set_col(i, d.col(0))
pbar.update(i + 1)
pbar.finish()
def do_proc_F1_flip_modu(dinp, doutp, parameter, nproc=None):
"as do_proc_F1, but applies flip and then complex modulus() at the end"
size = 2*doutp.axis1.size
scan = min(dinp.size2, doutp.size2)
# scan = doutp.size2
widgets = ['Processing F1 flip-modu: ', pg.Percentage(), ' ', pg.Bar(marker='-',left='[',right=']'), pg.ETA()]
pbar= pg.ProgressBar(widgets=widgets, maxval=scan) #, fd=sys.stdout)
shift = doutp.axis1.mztoi( doutp.axis1.highmass ) # frequency shift in points, computed from location of highmass
hshift = doutp.axis1.itoh(shift) # the same in Hz
rot = dinp.axis1.mztoi( dinp.axis1.highmass ) # but correction is applied in the starting space
print("LEFT_POINT", shift)
doutp.axis1.left_point = shift
doutp.axis1.specwidth += hshift # correction of specwidth
if mpiutil.MPI_size>1: # MAD : KLUDGE
nproc = 0
if nproc==None:
print("doutp.axis1.itype ",doutp.axis1.itype)
d = FTICRData( buffer=np.zeros((dinp.size1,2)) ) # 2 columns - used for hypercomplex modulus
for i in xrange( scan ):
for off in (0,1):
p = dinp.col(2*i+off)
d.set_col(off, p )
d.axis1.itype = 0
d.axis2.itype = 1
d.f1demodu(rot)
p = d.col(0)
apod(p, size) # avant ou apres ???
if parameter.do_rqrd:
p.buffer = urQRd(p.buffer,parameter.rqrd_rank) #integrated rQRd
p.rfft()
p.modulus()
#print "p.axis1.itype ", p.axis1.itype
doutp.set_col(i,p)
pbar.update(i+1)
elif nproc >1:
import multiprocessing as mp
xarg = iterarg(dinp, rot, size, parameter.do_rqrd, parameter.rqrd_rank)
pool = mp.Pool(nproc)
res = pool.map(_do_proc_F1_flip_modu, xarg)
for i,p in enumerate(res):
doutp.set_col(i,p)
pbar.update(i+1)
elif nproc == 0: # 0 means MPI
mpiutil.mprint('MPI NEW STYLE')
xarg = iterarg(dinp, rot, size, parameter.do_rqrd, parameter.rqrd_rank)
res = mpiutil.enum_imap(_do_proc_F1_flip_modu, xarg) # apply it
for i,p in res: # and get results
doutp.set_col(i,p)
pbar.update(i+1)
else:
raise Exception("We have an internal problem n.1 here !")
pbar.finish()
def do_proc_F1(dinp, doutp):
"scan all cols of dinp, apply proc() and store into doutp"
size = doutp.axis1.size
scan = min(dinp.size2, doutp.size2) # min() because no need to do extra work !
widgets = ['Processing F1: ', pg.Percentage(), ' ', pg.Bar(marker='-',left='[',right=']'), pg.ETA()]
pbar= pg.ProgressBar(widgets=widgets, maxval=scan) #, fd=sys.stdout)
for i in xrange( scan):
# if i%(scan/16) == 0: # print avancement
# print "proc col %d / %d"%(i,scan)
c = dinp.col(i)
apod(c, size)
c.rfft()
doutp.set_col(i,c)
pbar.update(i)
pbar.finish()
def main():
"""does the whole job,
if we are running in MPI, this is only called by job #0
all other jobs are running mpi.slave()
"""
argv = sys.argv
if len(argv) != 2:
print("""
syntax is :
(mpirun -np N) python program configfile.mscf
""")
sys.exit(1)
# get parameters
configfile = argv[1]
cp = NPKConfigParser()
cp.readfp(open(configfile))
infile = cp.getword("Cadzow", "namein")
print("infile", infile)
outfile = cp.getword("Cadzow", "nameout")
print("outfile", outfile)
algo = cp.getword("Cadzow", "algorithm")
print("algorithm", algo)
n_of_line = cp.getint("Cadzow", "n_of_lines", 70)
print("n_of_line", n_of_line)
n_of_iter = cp.getint("Cadzow", "n_of_iters", 1)
print("n_of_iter", n_of_iter)
orda = cp.getint("Cadzow", "order", 500)
print("order", orda)
n_of_column = cp.getint("Cadzow", "n_of_column", 100)
print("n_of_column", n_of_column)
progress = cp.getboolean("Cadzow", "progress", True)
d0 = load_input(infile)
d0.check2D() # raise error if not a 2D
Set_Table_Param()
hfar = HDF5File(outfile, "w", debug=0) # OUTFILE
d1 = FTICRData(dim=2) # create dummy 2D
copyaxes(d0, d1) # copy axes from d0 to d1
group = 'resol1'
hfar.create_from_template(d1, group)
# prepare index and method
if n_of_column == 0:
indexes = range(d0.size2) # process all
else:
indexes = selectcol(d0, n_of_column) # selections
if algo == "Cadzow":
meth = cadz
elif algo == "rQRd": #
meth = rqr
else:
raise ("wrong algo")
# then loop
t0 = time.time()
if progress:
widgets = [
'Processing %s: ' % (algo),
pg.Percentage(), ' ',
pg.Bar(marker='-', left='[', right=']'),
pg.ETA()
]
pbar = pg.ProgressBar(widgets=widgets,
maxval=len(indexes)) #, fd=sys.stdout)
d1D = d0.col(0) # template
xarg = iterarg(indexes, d0, n_of_line, n_of_iter, orda)
if mpiutil.MPI_size > 1: # means we are running under MPI !
mpiutil.mprint('MPI Master job - starting slave jobs - ')
res = mpiutil.enum_imap(meth, xarg) # apply it
for i, p in res: # and get results
d1D.buffer = p
d1.set_col(indexes[i], d1D)
if progress: pbar.update(i + 1)
else:
import itertools
res = itertools.imap(meth, xarg) # apply it
for i, p in enumerate(res): # and get results
d1D.buffer = p
d1.set_col(indexes[i], d1D)
if progress: pbar.update(i + 1)
print("Processing time : ", time.time() - t0)