def subtract(self, readpath, sample, blank, fraction=0, writepath= '../manual', analysispath='../analysis', analyse=True):
if fraction > 0:
fraction = round(fraction, 1)
try:
sampleDat = DatFile(os.path.join(readpath, sample))
blankDat = DatFile(os.path.join(readpath, blank))
except IOError:
print "File Doesn't Exist"
return -1
sampleNum = int(sampleDat.fileindex)
blankNum = int(blankDat.fileindex)
sampleNumLen = len(sampleDat.fileindex)
blankNumLen = len(blankDat.fileindex)
sampleRoot = os.path.splitext(sampleDat.rootname)[0]
blankRoot = os.path.splitext(blankDat.rootname)[0]
if not os.path.exists(writepath):
writepath = os.path.abspath(os.path.join(readpath,writepath))
if not os.path.exists(writepath):
try:
os.mkdir(writepath)
except OSError:
if not os.path.isdir(writepath):
print 'dat write path ' + writepath + ' invalid, file not written'
raise
if analyse:
if not os.path.exists(analysispath):
analysispath = os.path.abspath(os.path.join(readpath,analysispath))
if not os.path.exists(analysispath):
try:
os.mkdir(analysispath)
except OSError:
if not os.path.isdir(analysispath):
print 'analysis write path invalid, file not written'
raise
num = 0
while True:
try:
sampleTemp = DatFile(datfile=os.path.join(readpath, ''.join([sampleRoot, '_', str(sampleNum).zfill(sampleNumLen), '.dat'])))
blankTemp = DatFile(datfile=os.path.join(readpath, ''.join([blankRoot, '_', str(blankNum).zfill(blankNumLen), '.dat'])))
fraction_string = ''
if fraction > 0:
blank2 = '{}_{:04d}.dat'.format(blankTemp.rootname_rmext, int(blankTemp.fileindex)+1)
blankTemp2 = DatFile(os.path.join(readpath, blank2))
blankTemp = dat.average([blankTemp, blankTemp2], [fraction, 1-fraction])
fraction_string = '_{:.0f}'.format(100*fraction)
subtractedDat = dat.subtract(sampleTemp, blankTemp)
filename = os.path.join(writepath, ''.join([os.path.splitext(subtractedDat.rootname)[0], '_', str(sampleNum).zfill(sampleNumLen), '_', str(blankNum).zfill(blankNumLen), fraction_string, '.dat']))
subtractedDat.save(filename)
if analyse:
pipeline = PipelineLite.PipelineLite(filename, analysispath)
pipeline.runPipeline()
sampleNum += 1
blankNum += 1
num += 1
except IOError as e:
print 'IO'
break
except OSError as e:
print 'OS'
break
except Exception:
raise
return num
def subtract(self, target=None):
while True:
buffer_, item = (yield)
if target:
target.send(dat.subtract(item, buffer_))
def subtract(self,
readpath,
sample,
blank,
fraction=0,
writepath='../manual',
analysispath='../analysis',
analyse=True):
if fraction > 0:
fraction = round(fraction, 1)
try:
sampleDat = DatFile(os.path.join(readpath, sample))
blankDat = DatFile(os.path.join(readpath, blank))
except IOError:
print "File Doesn't Exist"
return -1
sampleNum = int(sampleDat.fileindex)
blankNum = int(blankDat.fileindex)
sampleNumLen = len(sampleDat.fileindex)
blankNumLen = len(blankDat.fileindex)
sampleRoot = os.path.splitext(sampleDat.rootname)[0]
blankRoot = os.path.splitext(blankDat.rootname)[0]
if not os.path.exists(writepath):
writepath = os.path.abspath(os.path.join(readpath, writepath))
if not os.path.exists(writepath):
try:
os.mkdir(writepath)
except OSError:
if not os.path.isdir(writepath):
print 'dat write path ' + writepath + ' invalid, file not written'
raise
if analyse:
if not os.path.exists(analysispath):
analysispath = os.path.abspath(
os.path.join(readpath, analysispath))
if not os.path.exists(analysispath):
try:
os.mkdir(analysispath)
except OSError:
if not os.path.isdir(analysispath):
print 'analysis write path invalid, file not written'
raise
num = 0
while True:
try:
sampleTemp = DatFile(datfile=os.path.join(
readpath, ''.join([
sampleRoot, '_',
str(sampleNum).zfill(sampleNumLen), '.dat'
])))
blankTemp = DatFile(datfile=os.path.join(
readpath, ''.join([
blankRoot, '_',
str(blankNum).zfill(blankNumLen), '.dat'
])))
fraction_string = ''
if fraction > 0:
blank2 = '{}_{:04d}.dat'.format(
blankTemp.rootname_rmext,
int(blankTemp.fileindex) + 1)
blankTemp2 = DatFile(os.path.join(readpath, blank2))
blankTemp = dat.average([blankTemp, blankTemp2],
[fraction, 1 - fraction])
fraction_string = '_{:.0f}'.format(100 * fraction)
subtractedDat = dat.subtract(sampleTemp, blankTemp)
filename = os.path.join(
writepath, ''.join([
os.path.splitext(subtractedDat.rootname)[0], '_',
str(sampleNum).zfill(sampleNumLen), '_',
str(blankNum).zfill(blankNumLen), fraction_string,
'.dat'
]))
subtractedDat.save(filename)
if analyse:
pipeline = PipelineLite.PipelineLite(
filename, analysispath)
pipeline.runPipeline()
sampleNum += 1
blankNum += 1
num += 1
except IOError as e:
print 'IO'
break
except OSError as e:
print 'OS'
break
except Exception:
raise
return num
