def _calcGNOM(self, dmax):
start = int(self.spinctrlIDs['qstart'])
end = int(self.spinctrlIDs['qend'])
self.gnom_settings['npts'] = 0
path = self.raw_settings.get('GnomFilePath') # TODO: temp path
cwd = os.getcwd()
savename = 't_dat.dat'
while os.path.isfile(os.path.join(path, savename)):
savename = 't' + savename
outname = 't_out.out'
while os.path.isfile(os.path.join(path, outname)):
outname = 't' + outname
save_sasm = SASM.SASM(
copy.deepcopy(self.curr_sasm.i), copy.deepcopy(self.curr_sasm.q),
copy.deepcopy(self.curr_sasm.err),
copy.deepcopy(self.curr_sasm.getAllParameters()))
save_sasm.setParameter('filename', savename)
save_sasm.setQrange((start, end))
try:
SASFileIO.saveMeasurement(
save_sasm, path, self.raw_settings, filetype='.dat')
except SASExceptions.HeaderSaveError as error:
printer = ErrorPrinter(self.raw_settings, self._stdout)
printer.showSaveError('header')
os.chdir(path)
try:
iftm = SASCalc.runGnom(
savename,
outname,
dmax,
self.gnom_settings,
new_gnom=self.new_gnom,
raw_settings=self.raw_settings)
except SASExceptions.NoATSASError as error:
print('Error running GNOM/DATGNOM:', str(error), file=self._stdout)
self.cleanupGNOM(path, savename, outname)
os.chdir(cwd)
return None
os.chdir(cwd)
# self.cleanupGNOM(path, savename, outname)
return iftm
def saveSASM(self, sasm, filetype='dat', save_path=''):
"""Save SASM object to file."""
newext = filetype
filename = sasm.getParameter('filename')
check_filename, _ = os.path.splitext(filename)
check_filename = check_filename + newext
filepath = os.path.join(save_path, check_filename)
# file_exists = os.path.isfile(filepath)
filepath = save_path
try:
SASFileIO.saveMeasurement(sasm,
filepath,
self._raw_settings,
filetype=newext)
except SASExceptions.HeaderSaveError:
self.error_printer.showSaveError('header')
def saveIFTM(self, iftm, save_path):
"""Save IFTM object to file."""
if iftm.getParameter('algorithm') == 'GNOM':
newext = '.out'
else:
newext = '.ift'
filename = iftm.getParameter('filename')
check_filename, ext = os.path.splitext(filename)
check_filename = check_filename + newext
filepath = os.path.join(save_path, check_filename)
# file_exists = os.path.isfile(filepath)
filepath = save_path
try:
SASFileIO.saveMeasurement(
iftm, filepath, self.raw_settings, filetype=newext)
except SASExceptions.HeaderSaveError:
printer = ErrorPrinter(self.raw_settings, self._stdout)
printer.showSaveError('header')
def _initGNOM(self, sasm):
analysis_dict = sasm.getParameter('analysis')
if 'GNOM' in analysis_dict:
iftm = self._initGnomValues(sasm)
assert False
else:
path = self.raw_settings.get('GnomFilePath') # TODO: temp files?
cwd = os.getcwd()
savename = 't_dat.dat'
while os.path.isfile(os.path.join(path, savename)):
savename = 't' + savename
save_sasm = SASM.SASM(
copy.deepcopy(sasm.i), copy.deepcopy(sasm.q),
copy.deepcopy(sasm.err),
copy.deepcopy(sasm.getAllParameters()))
save_sasm.setParameter('filename', savename)
save_sasm.setQrange(sasm.getQrange())
try:
SASFileIO.saveMeasurement(
save_sasm, path, self.raw_settings, filetype='.dat')
except SASExceptions.HeaderSaveError as error:
printer = ErrorPrinter(self.raw_settings, self._stdout)
printer.showSaveError('header')
os.chdir(path)
try:
init_iftm = SASCalc.runDatgnom(savename, sasm,
self.raw_settings)
except SASExceptions.NoATSASError as error:
print(
'Error running GNOM/DATGNOM:',
str(error),
file=self._stdout)
self.cleanupGNOM(path, savename=savename)
os.chdir(cwd)
return None
os.chdir(cwd)
if init_iftm is None:
outname = 't_datgnom.out'
while os.path.isfile(outname):
outname = 't' + outname
if 'guinier' in analysis_dict:
rg = float(analysis_dict['guinier']['Rg'][0]) # TODO: [0]?
dmax = int(rg * 3.) #Mostly arbitrary guess at Dmax
print("????:", rg)
else:
print(
'No DMAX found warning:',
'No Guinier analysis found, arbirary value 80 will be set to DMAX.',
file=self._stdout)
dmax = 80 #Completely arbitrary default setting for Dmax
os.chdir(path)
try:
init_iftm = SASCalc.runGnom(
savename,
outname,
dmax,
self.gnom_settings,
new_gnom=self.new_gnom,
raw_settings=self.raw_settings)
except SASExceptions.NoATSASError as error:
print(
'Error running GNOM/DATGNOM',
str(error),
file=self._stdout)
self.cleanupGNOM(path, savename=savename, outname=outname)
os.chdir(cwd)
return None
os.chdir(cwd)
self.cleanupGNOM(path, outname=outname)
self.cleanupGNOM(path, savename=savename)
iftm = self._initDatgnomValues(sasm, init_iftm)
# plotPanel.plotPr(iftm)
return iftm