def run(self):
# load spectrometer measurement
spectrometer_reader = SpectrometerReader()
spectrometer_msi = spectrometer_reader.read(self.input()[0].path)
# the wavelengths recorded by the spectrometer
spectrometer_wavelengths = spectrometer_msi.get_wavelengths()
spectrometer_white = spectrometer_reader.read(
os.path.join(sc.get_full_dir("DATA_FOLDER"),
"spectrometer_whitebalance",
"white_IL_1_OO_20ms.txt"))
spectrometer_dark = spectrometer_reader.read(
os.path.join(sc.get_full_dir("DATA_FOLDER"),
"spectrometer_whitebalance", "dark_1_OO_20ms.txt"))
msimani.dark_correction(spectrometer_white, spectrometer_dark)
white_interpolator = interp1d(spectrometer_white.get_wavelengths(),
spectrometer_white.get_image(),
bounds_error=False,
fill_value=0.)
white_interpolated = white_interpolator(spectrometer_wavelengths)
camera_qe = pd.read_csv(self.input()[2].path)
camera_qe_interpolator = interp1d(camera_qe["wavelengths"] * 10**-9,
camera_qe["quantum efficiency"],
bounds_error=False,
fill_value=0.)
camera_qe_interpolated = \
camera_qe_interpolator(spectrometer_wavelengths)
# camera batch creation:
new_reflectances = []
for band in self.input()[1]:
df_filter = pd.read_csv(band.path)
interpolator = interp1d(df_filter["wavelengths"],
df_filter["reflectances"],
assume_sorted=False,
bounds_error=False)
# use this to create new reflectances
interpolated_filter = interpolator(spectrometer_wavelengths)
# if a wavelength cannot be interpolated, set it to 0
interpolated_filter = np.nan_to_num(interpolated_filter)
# account for cameras quantum efficiency
interpolated_filter *= camera_qe_interpolated * white_interpolated
# normalize band response
#normalize(interpolated_filter.reshape(1, -1), norm='l1', copy=False)
folded_reflectance = np.dot(spectrometer_msi.get_image(),
interpolated_filter)
new_reflectances.append(folded_reflectance)
plt.plot(interpolated_filter)
new_reflectances = np.array(new_reflectances).T
spectrometer_msi.set_image(
new_reflectances, wavelengths=sc.other["RECORDED_WAVELENGTHS"])
# write it
nrrd_writer = NrrdWriter(spectrometer_msi)
nrrd_writer.write(self.output().path)
def run(self):
reader = SpectrometerReader()
filter_transmission = reader.read(self.input().path)
# filter high and low _wavelengths
wavelengths = filter_transmission.get_wavelengths()
fi_image = filter_transmission.get_image()
fi_image[wavelengths < 450 * 10**-9] = 0.0
fi_image[wavelengths > 720 * 10**-9] = 0.0
# filter elements farther away than +- 30nm
file_name = os.path.split(self.input_file)[1]
name_to_float = float(os.path.splitext(file_name)[0])
fi_image[wavelengths < (name_to_float - 30) * 10**-9] = 0.0
fi_image[wavelengths > (name_to_float + 30) * 10**-9] = 0.0
# elements < 0 are set to 0.
fi_image[fi_image < 0.0] = 0.0
# write it to a dataframe
df = pd.DataFrame()
df["wavelengths"] = wavelengths
df["reflectances"] = fi_image
df.to_csv(self.output().path, index=False)
def setUp(self):
self.exampleFileName = "./msi/data/Transmission_15-49-35-978_filter700nm.txt"
self.reader = SpectrometerReader()
