def load_blank(self, blank_fn):
results = jwslib.read_file(blank_fn)
error = True
if results[0] == jwslib.JWS_ERROR_SUCCESS:
blank_header = results[1]
blank_channels = results[2]
if len(blank_channels) < 1:
self.error(_("Error: Blank has no channel data.\n"))
else:
error = False
elif results[0] == jwslib.JWS_ERROR_COULD_NOT_READ_FILE:
self.error( _("Error reading blank file %(#)s:\n%(##)s\n") % \
{'#':blank_fn, '##':results[1] } )
elif results[0] == jwslib.JWS_ERROR_INVALID_FILE:
self.error(
_("Invalid blank file %(#)s:\n%(##)s\n") % {
'#': blank_fn,
'##': results[1]
})
else:
self.error(_("Unknown error loading blank\n"))
if error:
return None
else:
return (blank_header, blank_channels)
def test2():
import jwslib
import sys
results = jwslib.read_file("spc.jws")
if results[0] == jwslib.JWS_ERROR_SUCCESS:
header = results[1]
channels = results[2]
else:
sys.exit(-1)
channels[0] = mean_movement(channels[0], 25)
jwslib.dump_channel_data('feo3.txt', header, channels)
def test2():
import jwslib
import sys
results = jwslib.read_file("spc.jws")
if results[0] == jwslib.JWS_ERROR_SUCCESS:
header = results[1]
channels = results[2]
else:
sys.exit(-1)
channels[0] = mean_movement(channels[0], 25)
jwslib.dump_channel_data('feo3.txt', header, channels)
def test3():
import jwslib
import sys
results = jwslib.read_file("spc.jws")
if results[0] == jwslib.JWS_ERROR_SUCCESS:
header = results[1]
channels = results[2]
else:
sys.exit(-1)
original = channels[0]
for i in range(5, 25, 2):
channels[0] = sgolayfilt(original, 1, i)
jwslib.dump_channel_data('spc_sg_1_%d.txt' % i, header, channels)
def test3():
import jwslib
import sys
results = jwslib.read_file("spc.jws")
if results[0] == jwslib.JWS_ERROR_SUCCESS:
header = results[1]
channels = results[2]
else:
sys.exit(-1)
original = channels[0]
for i in range(5,25,2):
channels[0] = sgolayfilt(original, 1, i)
jwslib.dump_channel_data('spc_sg_1_%d.txt'%i, header, channels)
def show_spectrum_file(self, input_fn, options=None):
results = jwslib.read_file(input_fn)
error = True
if results[0] == jwslib.JWS_ERROR_SUCCESS:
header = results[1]
channels = results[2]
if len(channels) > 0:
error = False
if error:
return False
else:
if options is not None:
self.options = options
self.show_spectrum(header, channels)
return True
def __init__(self, input_fn, options=ProcessOptions(), parent=None):
results = jwslib.read_file(input_fn)
error = True
if results[0] == jwslib.JWS_ERROR_SUCCESS:
header = results[1]
channels = results[2]
if len(channels) > 0:
error = False
if error:
raise Exception, "File %s could not be loaded" % input_fn
(head, tail) = os.path.split(input_fn) # head=path; tail=nombre arch.
title = _("Showing %s") % tail
SmoothingSelectionDialog.__init__(self, header, channels, options,
parent, title,
(gtk.STOCK_CLOSE, gtk.RESPONSE_OK))
def __init__(self, path):
self.path = path
from jwslib import read_file
t = read_file(self.path)
self.header = t[1]
if t[0] != 0:
print t[1]
raise Exception("Invalid file")
if len(t[2]) == 1:
self.y_data = np.array(t[2][0])
self.y_data_norm = (self.y_data - self.y_data.min()) / (self.y_data.max() - self.y_data.min())
else:
raise Exception("Multiple channels")
self.x_data = np.linspace(self.header.x_for_first_point, self.header.x_for_last_point, num=self.header.point_number)
def _update_preview_cb(self, widget):
input_fn = self.get_preview_filename()
error = True
if input_fn is not None:
results = jwslib.read_file(input_fn)
if results[0] == jwslib.JWS_ERROR_SUCCESS:
header = results[1]
channels = results[2]
if len(channels) > 0:
error = False
if not error:
xdata = arange(
header.x_for_first_point, #start
header.x_for_last_point + header.x_increment, #end+incr.
header.x_increment) #increment
ellipticity = array(channels[0], float32)
self.figure.clear()
p = self.figure.add_subplot(111)
p.plot(xdata, ellipticity)
self.canvas.draw()
self.set_preview_widget_active(not error)
def load_blank(self, blank_fn):
results = jwslib.read_file(blank_fn)
error = True
if results[0] == jwslib.JWS_ERROR_SUCCESS:
blank_header = results[1]
blank_channels = results[2]
if len(blank_channels) < 1:
self.error(_("Error: Blank has no channel data.\n"))
else:
error = False
elif results[0] == jwslib.JWS_ERROR_COULD_NOT_READ_FILE:
self.error( _("Error reading blank file %(#)s:\n%(##)s\n") % \
{'#':blank_fn, '##':results[1] } )
elif results[0] == jwslib.JWS_ERROR_INVALID_FILE:
self.error(_("Invalid blank file %(#)s:\n%(##)s\n") % {'#':blank_fn, '##':results[1]})
else:
self.error(_("Unknown error loading blank\n"))
if error:
return None
else:
return (blank_header, blank_channels)
def _update_preview_cb(self, widget):
input_fn = self.get_preview_filename()
error = True
if input_fn is not None:
results = jwslib.read_file(input_fn)
if results[0] == jwslib.JWS_ERROR_SUCCESS:
header = results[1]
channels = results[2]
if len(channels) > 0:
error = False
if not error:
xdata = arange(
header.x_for_first_point, # start
header.x_for_last_point + header.x_increment, # end+incr.
header.x_increment,
) # increment
ellipticity = array(channels[0], float32)
self.figure.clear()
p = self.figure.add_subplot(111)
p.plot(xdata, ellipticity)
self.canvas.draw()
self.set_preview_widget_active(not error)
def process_file(self, input_fn, dilution_factor, blank_header,
blank_channels, options):
# Read input file
error = True
results = jwslib.read_file(input_fn)
if results[0] == jwslib.JWS_ERROR_SUCCESS:
error = False
elif results[0] == jwslib.JWS_ERROR_COULD_NOT_READ_FILE:
self.error(
_("Error reading jws file %(#)s:\n%(##)s\n") % {
'#': input_fn,
'##': results[1]
})
elif results[0] == jwslib.JWS_ERROR_INVALID_FILE:
self.error(
_("Invalid file %(#)s:\n%(##)s\n") % {
'#': input_fn,
'##': results[1]
})
else:
self.error(_("Unknown error loading %s\n") % input_fn)
if error:
return None
header = results[1]
channels = results[2]
n_channels = len(channels)
# Print information about the file
self.print_header_info(header, input_fn)
self.info(_("Read data for %d channels\n") % n_channels)
# Exit if we don't have channel data to process
if n_channels < 1:
self.error(_("Error: This file has no channel data\n"))
return None
ellipticity = array(channels[0], float32)
# Subtract blank
if options.subtract_blank:
error = True
if blank_header.point_number < header.point_number:
self.error(
_("Error: Blank has not enough data to be subtracted to input.\n"
))
elif blank_header.x_for_first_point != header.x_for_first_point:
self.error(
_("Error: Blank has no data in the wavelength range of input.\n"
))
else:
error = False
if error:
return None
blank = array(blank_channels[0][:len(channels[0])], float32)
subtract(ellipticity, blank, ellipticity)
# Make ellipticity at 260nm 0
if options.subtract260 and options.subtract_blank:
if header.x_for_first_point == 260.0:
self.info(_("Making ellipticity at 260nm 0...\n"))
subtract(ellipticity, ellipticity[0], ellipticity)
# Apply smoothing
if options.smoothing:
self.info(_("Applying smoothing...\n"))
m = options.get_clamped_m()
if options.smoothing_type == "mm":
ellipticity = pysmoothing.mean_movement(ellipticity, m)
elif options.smoothing_type == "sg":
p = options.get_clamped_p()
ellipticity = pysmoothing.sgolayfilt(ellipticity, p, m)
ellipticity = array(ellipticity, float32)
# Apply correction factor:
if options.correct:
multiply(ellipticity, options.correction_factor, ellipticity)
if options.correct_dilution:
multiply(ellipticity, dilution_factor, ellipticity)
channels[0] = list(ellipticity)
return (header, channels)
def process_file(self, input_fn, dilution_factor, blank_header, blank_channels, options):
# Read input file
error = True
results = jwslib.read_file(input_fn)
if results[0] == jwslib.JWS_ERROR_SUCCESS:
error = False
elif results[0] == jwslib.JWS_ERROR_COULD_NOT_READ_FILE:
self.error(_("Error reading jws file %(#)s:\n%(##)s\n") % {'#':input_fn, '##':results[1]} )
elif results[0] == jwslib.JWS_ERROR_INVALID_FILE:
self.error(_("Invalid file %(#)s:\n%(##)s\n") % {'#':input_fn, '##':results[1]})
else:
self.error(_("Unknown error loading %s\n") % input_fn)
if error:
return None
header = results[1]
channels = results[2]
n_channels = len(channels)
# Print information about the file
self.print_header_info(header, input_fn)
self.info(_("Read data for %d channels\n") % n_channels)
# Exit if we don't have channel data to process
if n_channels < 1:
self.error(_("Error: This file has no channel data\n"))
return None
ellipticity = array(channels[0], float32)
# Subtract blank
if options.subtract_blank:
error = True
if blank_header.point_number < header.point_number:
self.error(_("Error: Blank has not enough data to be subtracted to input.\n"))
elif blank_header.x_for_first_point != header.x_for_first_point:
self.error(_("Error: Blank has no data in the wavelength range of input.\n"))
else:
error = False
if error:
return None
blank = array(blank_channels[0][:len(channels[0])], float32)
subtract(ellipticity, blank, ellipticity)
# Make ellipticity at 260nm 0
if options.subtract260 and options.subtract_blank:
if header.x_for_first_point == 260.0:
self.info(_("Making ellipticity at 260nm 0...\n"))
subtract(ellipticity, ellipticity[0], ellipticity)
# Apply smoothing
if options.smoothing:
self.info(_("Applying smoothing...\n"))
m = options.get_clamped_m()
if options.smoothing_type == "mm":
ellipticity = pysmoothing.mean_movement(ellipticity, m)
elif options.smoothing_type == "sg":
p = options.get_clamped_p()
ellipticity = pysmoothing.sgolayfilt(ellipticity, p, m)
ellipticity = array(ellipticity, float32)
# Apply correction factor:
if options.correct:
multiply(ellipticity, options.correction_factor, ellipticity)
if options.correct_dilution:
multiply(ellipticity, dilution_factor, ellipticity)
channels[0] = list(ellipticity)
return (header, channels)
