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 _load_files(self):
files = None
filters = 'All files (*.*)|*.*|Dat files (*.dat)|*.dat|Txt files (*.txt)|*.txt'
dialog = wx.FileDialog(self,
'Select a file',
self.current_directory,
style=wx.FD_OPEN | wx.FD_MULTIPLE,
wildcard=filters)
# Show the dialog and get user input
if dialog.ShowModal() == wx.ID_OK:
files = dialog.GetPaths()
# Destroy the dialog
dialog.Destroy()
if files is not None:
if not isinstance(files, list):
files = [
files,
]
data = SASFileIO.load_files(files)
self.current_directory = os.path.dirname(files[0])
self.add_items(data)
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 loadIFTMs(self, filename_list):
"""Load GNOM .ift/.out files."""
print('Please wait while loading files...', file=self._stdout)
iftm_list = []
try:
for each_filename in filename_list:
file_ext = os.path.splitext(each_filename)[1]
if file_ext == '.ift' or file_ext == '.out':
iftm, _ = SASFileIO.loadFile(each_filename,
self._raw_settings)
if isinstance(iftm, list):
iftm_list.extend(iftm)
else:
iftm_list.append(iftm)
except (SASExceptions.UnrecognizedDataFormat,
SASExceptions.WrongImageFormat) as error:
self.error_printer.showDataFormatError(
os.path.split(each_filename)[1])
raise error
except SASExceptions.HeaderLoadError as error:
print(
str(error), 'Error Loading Headerfile:'
'Please check that the header file is in the directory with the data.',
file=self._stdout)
raise error
except SASExceptions.MaskSizeError as error:
print(str(error),
'Saved mask does not fit loaded image',
file=self._stdout)
raise error
except SASExceptions.HeaderMaskLoadError as error:
print(str(error),
'Mask information was not found in header',
file=self._stdout)
raise error
return iftm_list
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
def loadSASMs(self, filename_list):
"""Load image or dat files."""
print('Please wait while loading files...', file=self._stdout)
sasm_list = []
do_auto_save = self._raw_settings.get('AutoSaveOnImageFiles')
try:
for each_filename in filename_list:
# file_ext = os.path.splitext(each_filename)[1]
sasm, img = SASFileIO.loadFile(each_filename,
self._raw_settings)
if img is not None:
# qrange = sasm.getQrange()
start_point = self._raw_settings.get('StartPoint')
end_point = self._raw_settings.get('EndPoint')
if isinstance(sasm, list):
qrange = (start_point,
len(sasm[0].getBinnedQ()) - end_point)
for each_sasm in sasm:
each_sasm.setQrange(qrange)
else:
qrange = (start_point,
len(sasm.getBinnedQ()) - end_point)
sasm.setQrange(qrange)
if do_auto_save:
save_path = self._raw_settings.get('ProcessedFilePath')
try:
if isinstance(sasm, list):
for each in sasm:
self.saveSASM(each, '.dat', save_path)
else:
self.saveSASM(sasm, '.dat', save_path)
except IOError as error:
self._raw_settings.set('AutoSaveOnImageFiles',
False)
do_auto_save = False
if isinstance(sasm, list):
sasm_list.extend(sasm)
else:
sasm_list.append(sasm)
except (SASExceptions.UnrecognizedDataFormat,
SASExceptions.WrongImageFormat) as error:
self.error_printer.showDataFormatError(
os.path.split(each_filename)[1])
raise error
except SASExceptions.HeaderLoadError as error:
print(
str(error), 'Error Loading Headerfile:'
'Please check that the header file is in the directory with the data.',
file=self._stdout)
raise error
except SASExceptions.MaskSizeError as error:
print(str(error),
'Saved mask does not fit loaded image',
file=self._stdout)
raise error
except SASExceptions.HeaderMaskLoadError as error:
print(str(error),
'Mask information was not found in header',
file=self._stdout)
raise error
return sasm_list