def collection(self, value):
if isinstance(value, Spectrum):
# create new collection
self._collection = Collection(name=Spectrum.name, spectra=[value])
if isinstance(value, Collection):
self._collection = value
else:
self._collection = None
def update_artists(self, new_lim=False):
if self.collection is None:
return
#update values being plotted -> redo statistics
self.mean_line = None
self.median_line = None
self.max_line = None
self.min_line = None
self.std_line = None
# save limits
if new_lim == False:
xlim = self.ax.get_xlim()
ylim = self.ax.get_ylim()
# plot
self.ax.clear()
# show statistics
if self.spectrum_mode:
idx = self.listbox.curselection()
if len(idx) == 0:
idx = [self.head]
spectra = [self.collection.spectra[i] for i in idx]
flags = [s.name in self.collection.flags for s in spectra]
print("flags = ", flags)
flag_style = ' '
if self.show_flagged:
flag_style = 'r'
artists = Collection(name='selection', spectra=spectra).plot(
ax=self.ax,
style=list(np.where(flags, flag_style, self.color)),
picker=1)
self.ax.set_title('selection')
# c = str(np.where(spectrum.name in self.collection.flags, 'r', 'k'))
# spectrum.plot(ax=self.ax, label=spectrum.name, c=c)
else:
# red curves for flagged spectra
flag_style = ' '
if self.show_flagged:
flag_style = 'r'
flags = [
s.name in self.collection.flags
for s in self.collection.spectra
]
print("flags = ", flags)
self.collection.plot(ax=self.ax,
style=list(np.where(flags, flag_style, 'k')),
picker=1)
#self.ax.set_title(self.collection.name)
keys = [s.name for s in self.collection.spectra]
artists = self.ax.lines
self.artist_dict = {key: artist for key, artist in zip(keys, artists)}
self.colors = {key: 'black' for key in keys}
self.ax.legend().remove()
self.navbar.setHome(self.ax.get_xlim(), self.ax.get_ylim())
self.canvas.draw()
self.sblabel.config(text="Showing: {}".format(len(artists)))
def _open_dataset(self, directory=None):
directory = directory or \
QtWidgets.QFileDialog.getExistingDirectory(self,
caption="Open Spectra Dataset")
try:
c = Collection(name="collection", directory=directory)
self._directory = directory
self._set_collection(c)
except:
pass
def filter_white(collection,wavelength0=0,wavelength1=10000,group='mean'):
"""Filter out white reference spectra from collection"""
data = collection.data.loc[wavelength0:wavelength1]
mean = data.mean(axis=0)
std = data.std(axis=0)
#a flat-ish spectrum at nearly 1 is probably white
white = (mean > 0.9) & (mean < 1.1) & (std < .03)
good = ~white
if not good.all():
return split_good_bad(collection,good)
return collection,Collection(collection.name+'_filtered')
def read_dir(self):
try:
directory = os.path.split(
filedialog.askopenfilename(filetypes=(
("Supported types", "*.asd *.sed *.sig *.pico"),
("All files", "*"),
)))[0]
except:
return
if not directory:
return
c = Collection(name="collection", directory=directory)
self.set_collection(c)
self.dirLbl.config(text="Viewing: " + directory)
def filter_white(collection, wavelength0=0, wavelength1=10000, group='mean'):
"""Filter white reference spectra from collection
Returns
-------
good: specdal.containers.Collection
A new collection made of the spectra that passed the filter
bad: specdal.containers.Collection
A new collection made of the spectra that failed the filter
"""
data = collection.data.loc[wavelength0:wavelength1]
mean = data.mean(axis=0)
std = data.std(axis=0)
#a flat-ish spectrum at nearly 1 is probably white
white = (mean > 0.9) & (mean < 1.1) & (std < .03)
good = ~white
if not good.all():
return split_good_bad(collection, good)
return collection, Collection(collection.name + '_filtered')
def read_test_data():
path = '~/data/specdal/aidan_data2/ASD'
c = Collection("Test Collection", directory=path)
for i in range(30):
c.flag(c.spectra[i].name)
def update(self):
""" Update the plot """
if self.collection is None:
return
# show statistics
if self.spectrum_mode:
self.ax.clear()
idx = self.listbox.curselection()
if len(idx) == 0:
idx = [self.head]
spectra = [self.collection.spectra[i] for i in idx]
flags = [s.name in self.collection.flags for s in spectra]
print("flags = ", flags)
flag_style = ' '
if self.show_flagged:
flag_style = 'r'
Collection(name='selection', spectra=spectra).plot(
ax=self.ax,
style=list(np.where(flags, flag_style, 'k')),
picker=1)
self.ax.set_title('selection')
# c = str(np.where(spectrum.name in self.collection.flags, 'r', 'k'))
# spectrum.plot(ax=self.ax, label=spectrum.name, c=c)
else:
# red curves for flagged spectra
keys = [s.name for s in self.collection.spectra]
for key in keys:
if key in self.collection.flags:
if self.show_flagged:
self.artist_dict[key].set_visible(True)
self.artist_dict[key].set_color('red')
else:
self.artist_dict[key].set_visible(False)
else:
self.artist_dict[key].set_color(self.colors[key])
self.artist_dict[key].set_visible(True)
if self.show_flagged:
self.sblabel.config(
text="Showing: {}".format(len(self.artist_dict)))
else:
self.sblabel.config(text="Showing: {}".format(
len(self.artist_dict) - len(self.collection.flags)))
'''
self.collection.plot(ax=self.ax,
style=list(np.where(flags, flag_style, 'k')),
picker=1)
self.ax.set_title(self.collection.name)
'''
if self.spectrum_mode:
#self.ax.legend()
pass
else:
#self.ax.legend().remove()
pass
self.ax.set_ylabel(self.collection.measure_type)
#toggle appearance of statistics
if self.mean_line != None: self.mean_line.set_visible(self.mean)
if self.median_line != None: self.median_line.set_visible(self.median)
if self.max_line != None: self.max_line.set_visible(self.max)
if self.min_line != None: self.min_line.set_visible(self.min)
if self.std_line != None: self.std_line.set_visible(self.std)
self.canvas.draw()