def do_proc_F1(dinp, doutp, parameter):
"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 !
F1widgets = [
'Processing F1: ',
widgets.Percentage(), ' ',
widgets.Bar(marker='-', left='[', right=']'),
widgets.ETA()
]
pbar = pg.ProgressBar(widgets=F1widgets,
maxval=scan).start() #, fd=sys.stdout)
for i in xrange(scan):
c = dinp.col(i)
apod(c, size)
c.rfft()
# get statistics
buff = c.get_buffer()
b = buff.copy()
for i in range(10):
b = b[b - b.mean() < 3 * b.std()]
# computed ridge and remove
if parameter.do_F1 and parameter.do_rem_ridge:
c -= b.mean()
# clean for compression
if parameter.compress_outfile:
threshold = parameter.compress_level * b.std()
c.zeroing(threshold)
c = hmclear(c)
doutp.set_col(i, c)
pbar.update(i)
pbar.finish()
def do_proc_F2mp(dinp, doutp, parameter):
"do the F2 processing in MP"
size = doutp.axis2.size
scan = min(dinp.size1,
doutp.size1) # min() because no need to do extra work !
F2widgets = [
'Processing F2: ',
widgets.Percentage(), ' ',
widgets.Bar(marker='-', left='[', right=']'),
widgets.ETA()
]
pbar = pg.ProgressBar(widgets=F2widgets,
maxval=scan).start() #, fd=sys.stdout)
xarg = iterargF2(dinp, size, scan) # construct iterator for main loop
if parameter.mp: # means multiprocessing //
res = Pool.imap(_do_proc_F2, xarg)
for i, r in enumerate(res):
doutp.set_row(i, r)
pbar.update(i + 1)
elif mpiutil.MPI_size > 1: # code for MPI processing //
res = mpiutil.enum_imap(_do_proc_F2, xarg) # apply it
for i, r in res: # and get results
doutp.set_row(i, r)
pbar.update(i + 1)
else: # plain non //
res = imap(_do_proc_F2, xarg)
for i, r in enumerate(res):
doutp.set_row(i, r)
pbar.update(i + 1)
pbar.finish()
def do_proc_F1_modu(dinp, doutp, parameter):
"as do_proc_F1, but applies hypercomplex modulus() at the end"
size = 2 * doutp.axis1.size
scan = min(dinp.size2, doutp.size2)
F1widgets = [
'Processing F1 modu: ',
widgets.Percentage(), ' ',
widgets.Bar(marker='-', left='[', right=']'),
widgets.ETA()
]
pbar = pg.ProgressBar(widgets=F1widgets,
maxval=scan).start() #, fd=sys.stdout)
d = FTICRData(buffer=np.zeros(
(2 * doutp.size1, 2))) # 2 columns - used for hypercomplex modulus
for i in xrange(scan):
d.chsize(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()
# recover buffer
c = d.col(0)
# get statistics
buff = c.get_buffer()
b = buff.copy()
for i in range(10):
b = b[b - b.mean() < 3 * b.std()]
# computed ridge and remove
if parameter.do_F1 and parameter.do_rem_ridge:
c -= b.mean()
# clean for compression
if parameter.compress_outfile:
threshold = parameter.compress_level * b.std()
c.zeroing(threshold)
c = hmclear(c)
doutp.set_col(i, c)
pbar.update(i + 1)
pbar.finish()
def do_proc_F2(dinp, doutp, parameter):
"do the F2 processing - serial code"
size = doutp.axis2.size
scan = min(dinp.size1,
doutp.size1) # min() because no need to do extra work !
#scan = dinp.size1 # when was it done?
F2widgets = [
'Processing F2: ',
widgets.Percentage(), ' ',
widgets.Bar(marker='-', left='[', right=']'),
widgets.ETA()
]
pbar = pg.ProgressBar(widgets=F2widgets,
maxval=scan).start() #, fd=sys.stdout)
print("############ in do_proc_F2 #########")
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(doutp.report())
#print dir(doutp)
for i in xrange(scan):
r = dinp.row(i)
apod(r, size)
r.rfft()
if parameter.compress_outfile:
r = hmclear(r)
doutp.set_row(i, r)
pbar.update(i + 1)
if interfproc:
output = open('InterfProc/progbar.pkl', 'wb')
pb = ['F2', int((i + 1) / float(scan) * 100)]
pickle.dump(pb, output)
output.close()
pbar.finish()
def do_palma(npkd,
miniSNR=32,
mppool=None,
nbiter=1000,
lamda=0.1,
uncertainty=1.2,
precision=1E-8):
"""
realize PALMA computation on each column of the 2D datasets
dataset should have been prepared with prepare_palma()
the noise in the initial spectrum is analysed on the first DOSY increment
then each column is processed with palma() if its intensity is sufficient
miniSNR: determines the minimum Signal to Noise Ratio of the signal for allowing the processing
mppool: if passed as a multiprocessing.Pool, it will be used for parallel processing
the other parameters are transparently passed to palma()
"""
import multiprocessing as mp
import itertools
from spike.util import progressbar as pg
from spike.util import widgets
# local functions
def palmaiter(npkd):
"iterator for // processing around palma() using mp.pool.imap()"
#for c in npkd.xcol(): #
for icol in np.random.permutation(
npkd.size2): # create a randomized range
c = npkd.col(icol)
yield (icol, c, N, valmini, nbiter, lamda, precision, uncertainty)
# prepare
if mppool is not None:
if isinstance(mppool, mp.pool.Pool):
paral = True
else:
raise Exception(
"parameter mpool should be either None or of multiprocessing.Pool type"
)
else:
paral = False
npkd.check2D()
K = npkd.axis1.K
M, N = K.shape
output = npkd.copy()
output.chsize(sz1=N)
chi2 = np.zeros(
npkd.size2) # this vector contains the final chi2 for each column
noise = spike.util.signal_tools.findnoiselevel(npkd.row(0).get_buffer())
valmini = noise * miniSNR
# loop
xarg = palmaiter(npkd)
wdg = [
'PALMA: ',
widgets.Percentage(), ' ',
widgets.Bar(marker='-', left='[', right=']'),
widgets.ETA()
]
pbar = pg.ProgressBar(widgets=wdg,
maxval=npkd.size2).start() #, fd=sys.stdout)
if paral:
result = mppool.imap(process, xarg)
else:
result = itertools.imap(process, xarg)
# collect
for ii, res in enumerate(result):
# if icol%50 == 0 :
# print ("DOSY # %d / %d"%(icol,npkd.size2))
pbar.update(ii + 1)
sys.stdout.flush()
icol, c, lchi2 = res
chi2[icol] = lchi2
output.set_col(icol, c)
# for icol in range(npkd.size2):
# #if icol%10 ==0: print (icol, "iteration")
# c = npkd.col(icol)
# if (c[0] > miniSNR*noise):
# y = c.get_buffer()
# c = c.palma(N, nbiter=nbiter, lamda!!, precision=precision, uncertainty=uncertainty)
# chi2[icol] = np.linalg.norm(y-np.dot(K,c.get_buffer()))
# else:
# c = c.set_buffer(np.zeros(N))
# result.set_col(icol, c)
pbar.finish()
output.axis1.chi2 = chi2
return output
def Import_and_Process_LC(folder,
outfile="LC-MS.msh5",
compress=False,
comp_level=3.0,
downsample=True,
dparameters=None):
"""
Entry point to import sets of LC-MS spectra
processing is done on the fly
It creates and returns a HDF5 file containing the data-set
compression is active if (compress=True).
comp_level is the ratio (in x sigma) under which values are set to 0.0
downsample is applied if (downsample=True).
These two parameters are efficient but it takes time.
dparameters if present, is a dictionnary copied into the final file as json
"""
from spike.File import Solarix, Apex
# from spike.File.Solarix import locate_acquisition, read_param
from spike.NPKData import TimeAxis, copyaxes
from spike.File import HDF5File as hf
from spike.util import progressbar as pg
from spike.util import widgets
from spike.FTICR import FTICRData
for _importer in (Solarix, Apex):
try:
parfilename = _importer.locate_acquisition(folder)
params = _importer.read_param(parfilename)
sizeF2 = int(params["TD"])
importer = _importer
break
except:
print("***************************************")
print(params)
else:
raise Exception("could not import data-set - unrecognized format")
# get chromatogram
minu, tic, maxpk = import_scan(os.path.join(folder, "scan.xml"))
# Import parameters : size in F1 and F2
sizeF1 = len(minu)
sizeF2 = int(params["TD"])
if os.path.isfile(os.path.join(folder, "ser")):
fname = os.path.join(folder, "ser")
else:
raise Exception(
"You are dealing with 1D data, you should use Import_1D")
#size, specwidth, offset, left_point, highmass, calibA, calibB, calibC, lowfreq, highfreq
data = FTICRData(dim=2) # create dummy LCMS
data.axis1 = TimeAxis(size=sizeF1,
tabval=np.array(minu),
importunit="min",
currentunit='min')
data.axis2.size = 1 * sizeF2 # The processing below might change the size, so we anticipate here !
data.axis2.specwidth = float(params["SW_h"])
found = False # search for excitation bandwidth
try:
data.axis2.lowfreq, data.axis2.highfreq = read_ExciteSweep(
locate_ExciteSweep(folder))
found = True
except:
pass
if not found:
try:
data.axis2.highfreq = float(params["EXC_Freq_High"])
except:
data.axis2.highfreq = data.axis2.calibA / float(
params["EXC_low"]) # on Apex version
try:
data.axis2.lowfreq = float(params["EXC_Freq_Low"])
except:
data.axis2.lowfreq = data.axis2.calibA / float(
params["EXC_hi"]) # on Apex version
data.axis2.highmass = float(params["MW_high"])
data.axis2.left_point = 0
data.axis2.offset = 0.0
data.axis2.calibA = float(params["ML1"])
data.axis2.calibB = float(params["ML2"])
data.axis2.calibC = float(params["ML3"])
if not math.isclose(data.axis2.calibC, 0.0):
print('Using 3 parameters calibration, Warning calibB is -ML2')
data.axis2.calibB *= -1
data.params = params # add the parameters to the data-set
HF = hf.HDF5File(outfile, "w")
if compress:
HF.set_compression(True)
HF.create_from_template(data, group='resol1')
HF.store_internal_object(params,
h5name='params') # store params in the file
# then store files xx.methods and scan.xml
HF.store_internal_file(parfilename)
HF.store_internal_file(os.path.join(folder, "scan.xml"))
try:
HF.store_internal_file(locate_ExciteSweep(folder))
except:
print('ExciteSweep file not stored')
data.hdf5file = HF # I need a link back to the file in order to close it
# Start processing - first computes sizes and sub-datasets
print(data)
datalist = [] # remembers all downsampled dataset
maxvalues = [
0.0
] # remembers max values in all datasets - main and downsampled
if downsample:
allsizes = comp_sizes(data.size1, data.size2)
for i, (si1, si2) in enumerate(allsizes):
datai = FTICRData(dim=2)
copyaxes(data, datai)
datai.axis1.size = si1
datai.axis2.size = si2
HF.create_from_template(datai, group='resol%d' % (i + 2))
datalist.append(datai)
maxvalues.append(0.0)
# Then go through input file
if sys.maxsize == 2**31 - 1: # the flag used by array depends on architecture - here on 32bit
flag = 'l' # Apex files are in int32
else: # here in 64bit
flag = 'i' # strange, but works here.
spectre = FTICRData(shape=(sizeF2, )) # to handle FT
projection = FTICRData(buffer=np.zeros(sizeF2)) # to accumulate projection
projection.axis1 = data.axis2.copy()
Impwidgets = [
'Importing: ',
widgets.Percentage(), ' ',
widgets.Bar(marker='-', left='[', right=']'),
widgets.ETA()
]
pbar = pg.ProgressBar(widgets=Impwidgets, maxval=sizeF1,
fd=sys.stdout).start()
with open(fname, "rb") as f:
ipacket = 0
szpacket = 10
packet = np.zeros(
(szpacket,
sizeF2)) # store by packet to increase compression speed
for i1 in range(sizeF1):
absmax = 0.0
#print(i1, ipacket, end=' ')
tbuf = f.read(4 * sizeF2)
if len(tbuf) != 4 * sizeF2:
break
abuf = np.array(array.array(flag, tbuf), dtype=float)
# processing
spectre.set_buffer(abuf)
spectre.adapt_size()
spectre.hamming().zf(2).rfft().modulus() # double the size
mu, sigma = spectre.robust_stats(iterations=5)
spectre.buffer -= mu
if compress:
spectre.zeroing(sigma * comp_level).eroding()
packet[ipacket, :] = spectre.buffer[:] # store into packet
np.maximum(projection.buffer,
spectre.buffer,
out=projection.buffer) # projection
if (ipacket + 1) % szpacket == 0: # and dump every szpacket
maxvalues[0] = max(maxvalues[0],
abs(packet.max())) # compute max
data.buffer[i1 - (szpacket - 1):i1 +
1, :] = packet[:, :] # and copy
packet[:, :] = 0.0
ipacket = 0
else:
ipacket += 1
# now downsample
for idt, datai in enumerate(datalist):
if i1 % (sizeF1 // datai.size1) == 0: # modulo the size ratio
ii1 = (i1 * datai.size1) // sizeF1
spectre.set_buffer(abuf)
spectre.adapt_size()
spectre.chsize(
datai.size2).hamming().zf(2).rfft().modulus()
mu, sigma = spectre.robust_stats(iterations=5)
spectre.buffer -= mu
if compress:
spectre.zeroing(sigma * comp_level).eroding()
maxvalues[idt + 1] = max(
maxvalues[idt + 1],
spectre.absmax) # compute max (0 is full spectrum)
datai.buffer[ii1, :] = spectre.buffer[:]
pbar.update(i1)
# flush the remaining packet
maxvalues[0] = max(maxvalues[0], abs(packet[:ipacket, :].max()))
data.buffer[i1 - ipacket:i1, :] = packet[:ipacket, :]
# store maxvalues in the file
HF.store_internal_object(maxvalues, h5name='maxvalues')
if dparameters is not None:
HF.store_internal_object(dparameters, h5name='import_parameters')
# then write projection as 'projectionF2'
proj = FTICRData(dim=1)
proj.axis1 = data.axis2.copy()
HF.create_from_template(proj, group='projectionF2')
proj.buffer[:] = projection.buffer[:]
pbar.finish()
HF.flush()
return data
def do_proc_F1_demodu_modu(dinp, doutp, parameter):
"as do_proc_F1, but applies demodu and then complex modulus() at the end"
size = 2 * doutp.axis1.size
scan = min(dinp.size2, doutp.size2)
F1widgets = [
'Processing F1 demodu-modulus: ',
widgets.Percentage(), ' ',
widgets.Bar(marker='-', left='[', right=']'),
widgets.ETA()
]
pbar = pg.ProgressBar(widgets=F1widgets,
maxval=scan).start() #, fd=sys.stdout)
if parameter.freq_f1demodu == 0: # means not given in .mscf file -> compute from highmass
hshift = dinp.axis2.lowfreq # frequency shift in points, computed from lowfreq of excitation pulse - assumiing the pulse was from high to low !
else:
hshift = parameter.freq_f1demodu
shift = doutp.axis1.htoi(hshift)
rot = dinp.axis1.htoi(
hshift) # rot correction is applied in the starting space
# sampling
if parameter.samplingfile is not None: # NUS
dinp.axis1.load_sampling(
parameter.samplingfile
) # load sampling file, and compute rot in non-NUS space
cdinp = dinp.col(0)
cdinp.zf()
rot = cdinp.axis1.htoi(hshift)
# print( "11111111", shift, rot)
del (cdinp)
if debug > 0: print("LEFT_POINT", shift)
doutp.axis1.offsetfreq = hshift
xarg = iterarg(dinp, rot, size,
parameter) # construct iterator for main loop
if parameter.mp: # means multiprocessing //
res = Pool.imap(_do_proc_F1_demodu_modu, xarg)
for i, buf in enumerate(res):
doutp.buffer[:, i] = buf
# doutp.set_col(i,p)
pbar.update(i + 1)
elif mpiutil.MPI_size > 1: # code for MPI processing //
res = mpiutil.enum_imap(_do_proc_F1_demodu_modu, xarg) # apply it
for i, buf in res: # and get results
doutp.buffer[:, i] = buf
# doutp.set_col(i, p)
pbar.update(i + 1)
if interfproc:
output = open('InterfProc/progbar.pkl', 'wb')
pb = ['F1', int((i + 1) / float(scan) * 100)]
pickle.dump(pb, output) # for Qt progressbar
output.close()
if interfproc:
output = open('InterfProc/progbar.pkl', 'wb')
pb = ['end']
pickle.dump(pb, output) # for Qt progressbar
output.close()
else: # plain non //
res = imap(_do_proc_F1_demodu_modu, xarg)
for i, buf in enumerate(res):
doutp.buffer[:, i] = buf
# doutp.set_col(i,p)
pbar.update(i + 1)
pbar.finish()
def Import_and_Process_LC(folder,
nProc=1,
outfile="LC-MS.msh5",
compress=False,
comp_level=3.0,
downsample=True,
dparameters=None):
"""
Entry point to import sets of LC-MS spectra
processing is done on the fly
It creates and returns a HDF5 file containing the data-set
compression is active if (compress=True).
comp_level is the ratio (in x sigma) under which values are set to 0.0
downsample is applied if (downsample=True).
These two parameters are efficient but it takes time.
dparameters if present, is a dictionnary copied into the final file as json
"""
import multiprocessing as mp
from spike.File import Solarix, Apex
# from spike.File.Solarix import locate_acquisition, read_param
from spike.NPKData import TimeAxis, copyaxes
from spike.File import HDF5File as hf
from spike.util import progressbar as pg
from spike.util import widgets
from spike.FTICR import FTICRData
if nProc > 1:
print("** running on %d processors" % nProc)
Pool = mp.Pool(nProc)
for _importer in (Solarix, Apex):
try:
parfilename = _importer.locate_acquisition(folder)
params = _importer.read_param(parfilename)
sizeF2 = int(params["TD"])
importer = _importer
break
except:
#print("***************************************")
#print(params)
pass
else:
raise Exception("could not import data-set - unrecognized format")
# get chromatogram
minu, tic, maxpk = import_scan(os.path.join(folder, "scan.xml"))
# Import parameters : size in F1 and F2
sizeF1 = len(minu)
sizeF2 = int(params["TD"])
if os.path.isfile(os.path.join(folder, "ser")):
fname = os.path.join(folder, "ser")
else:
raise Exception(
"You are dealing with 1D data, you should use Import_1D")
#size, specwidth, offset, left_point, highmass, calibA, calibB, calibC, lowfreq, highfreq
data = FTICRData(dim=2) # create dummy LCMS
data.axis1 = TimeAxis(size=sizeF1,
tabval=np.array(minu),
importunit="min",
currentunit='min')
data.axis2.size = 1 * sizeF2 # The processing below might change the size, so we anticipate here !
data.axis2.specwidth = float(params["SW_h"])
found = False # search for excitation bandwidth
try:
data.axis2.lowfreq, data.axis2.highfreq = read_ExciteSweep(
locate_ExciteSweep(folder))
found = True
except:
pass
if not found:
try:
data.axis2.highfreq = float(params["EXC_Freq_High"])
except:
data.axis2.highfreq = data.axis2.calibA / float(
params["EXC_low"]) # on Apex version
try:
data.axis2.lowfreq = float(params["EXC_Freq_Low"])
except:
data.axis2.lowfreq = data.axis2.calibA / float(
params["EXC_hi"]) # on Apex version
data.axis2.highmass = float(params["MW_high"])
data.axis2.left_point = 0
data.axis2.offset = 0.0
data.axis2.calibA = float(params["ML1"])
data.axis2.calibB = float(params["ML2"])
data.axis2.calibC = float(params["ML3"])
if not math.isclose(data.axis2.calibC, 0.0):
print('Using 3 parameters calibration, Warning calibB is -ML2')
data.axis2.calibB *= -1
data.params = params # add the parameters to the data-set
HF = hf.HDF5File(outfile, "w")
if compress:
HF.set_compression(True)
HF.create_from_template(data, group='resol1')
HF.store_internal_object(params,
h5name='params') # store params in the file
# then store files xx.methods and scan.xml
HF.store_internal_file(parfilename)
HF.store_internal_file(os.path.join(folder, "scan.xml"))
try:
HF.store_internal_file(locate_ExciteSweep(folder))
except:
print('ExciteSweep file not found')
data.hdf5file = HF # I need a link back to the file in order to close it
# Start processing - first computes sizes and sub-datasets
print(data)
datalist = [] # remembers all downsampled dataset
maxvalues = [
0.0
] # remembers max values in all datasets - main and downsampled
if downsample:
allsizes = comp_sizes(data.size1, data.size2)
for i, (si1, si2) in enumerate(allsizes):
datai = FTICRData(dim=2)
copyaxes(data, datai)
datai.axis1.size = si1
datai.axis2.size = si2
HF.create_from_template(datai, group='resol%d' % (i + 2))
datalist.append(datai)
maxvalues.append(0.0)
# Then go through input file
projection = FTICRData(buffer=np.zeros(sizeF2)) # to accumulate projection
projection.axis1 = data.axis2.copy()
Impwidgets = [
'Importing: ',
widgets.Percentage(), ' ',
widgets.Bar(marker='-', left='[', right=']'),
widgets.ETA()
]
pbar = pg.ProgressBar(widgets=Impwidgets, maxval=sizeF1,
fd=sys.stdout).start()
with open(fname, "rb") as f:
ipacket = 0
szpacket = 11
packet = np.zeros(
(szpacket,
sizeF2)) # store by packet to increase compression speed
absmax = 0.0
xarg = iterargF2(f, sizeF1, sizeF2, compress, comp_level,
allsizes) # construct iterator for main loop
if nProc > 1:
res = Pool.imap(processF2row,
xarg) # multiproc processing using Pool
else:
res = map(processF2row, xarg) # plain single proc processing
for i1, spectres in enumerate(res): # and get results
spectre = spectres.pop(0)
packet[ipacket, :] = spectre.buffer[:] # store into packet
np.maximum(projection.buffer,
spectre.buffer,
out=projection.buffer) # projection
if (ipacket + 1) % szpacket == 0: # and dump every szpacket
maxvalues[0] = max(maxvalues[0],
abs(packet.max())) # compute max
data.buffer[i1 - (szpacket - 1):i1 +
1, :] = packet[:, :] # and copy
packet[:, :] = 0.0
ipacket = 0
else:
ipacket += 1
# now downsample
for idt, spectre in enumerate(spectres):
datai = datalist[idt]
if i1 % (sizeF1 // datai.size1) == 0: # modulo the size ratio
ii1 = (i1 * datai.size1) // sizeF1
maxvalues[idt + 1] = max(
maxvalues[idt + 1],
spectre.absmax) # compute max (0 is full spectrum)
datai.buffer[ii1, :] = spectre.buffer[:]
pbar.update(i1 + 1)
last = i1
# flush the remaining packet
maxvalues[0] = max(maxvalues[0], abs(packet[:ipacket, :].max()))
data.buffer[last - ipacket:last, :] = packet[:ipacket, :]
pbar.finish()
# then write projection as 'projectionF2'
print('writing projections')
proj = FTICRData(dim=1)
proj.axis1 = data.axis2.copy()
HF.create_from_template(proj, group='projectionF2')
proj.buffer[:] = projection.buffer[:]
# store maxvalues in the file
print('writing max abs value')
HF.store_internal_object(maxvalues, h5name='maxvalues')
print('writing parameters')
if dparameters is not None:
HF.store_internal_object(dparameters, h5name='import_parameters')
# and close
HF.flush()
if nProc > 1:
Pool.close() # finally closes multiprocessing slaves
return data
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)