Rename signature to spectrum

Author: kormang

autoclustering.py

@@ -9,15 +9,15 @@
 def find_related_clusters2(image, min_correlation, **kwargs):
     """
         Primitive algorithm that scans image left to right, top to buttom,
-        and assigns pixels/signatures to clusters. When, during scaning it finds
+        and assigns pixels/spectra to clusters. When, during scaning it finds
         pixel that is less than min_correlation correlated with all already found centers,
         algorithm assigns that pixel to new cluster, and that pixel is also new center.
         if kwarg start_centers is not present, then starting center is first pixel.
         Which means, centers are not really centers, but starting pixels of each
         cluster. However, these centers are good potetial starting centers
         to apply K-Means.
         Returns pair of (map of cluster indices, centers).
-        Centers have shape (num_centers, signature_length).
+        Centers have shape (num_centers, spectrum_length).
     """
     from spectral.algorithms.spymath import has_nan, NaNValueError
 
@@ -78,7 +78,7 @@ def find_mincorr_centers(values, centers):
         that is, value that has smallest sum of cosines between itself
         and each of the centers.
         Values and centers should be normalized.
-        Values are of shape (N, signature_length), and centers (sig_len, N).
+        Values are of shape (N, spectrum_length), and centers (spec_len, N).
         Returns pair of value and its index.
     """
     minci = np.argmin(np.sum(np.matmul(values, centers), axis=1))
@@ -149,16 +149,16 @@ def find_mincorr_from_center(values, centers):
 
 def find_maxdist_clusters(image, min_correlation):
     """
-        First finds signature that is least correlated with the average.
+        First finds spectrum that is least correlated with the average.
         It becomes first cluster center.
         Then finds next cluster center, the one that is least correlated
         with average (center) of existing cluster centers.
-        Then the steps are repeated, until there is no more unclassified signatures.
-        After each iteration all signatures that have correlation with new center
+        Then the steps are repeated, until there is no more unclassified spectra.
+        After each iteration all spectra that have correlation with new center
         equal or greater than min_correlation are clussified to belong to this new cluster,
         and excluded from further classification.
         Returns pair of map of indices of clusters,
-        and cluster centers of shape (N, signature_length).
+        and cluster centers of shape (N, spectrum_length).
     """
     from spectral.algorithms.spymath import has_nan, NaNValueError
 

continuummodule.c

@@ -80,54 +80,54 @@ continuum_generic_impl(PyObject *self, PyObject *args,
     if (PyArray_NDIM(ain) == 1) {
       double* datain = (double*)PyArray_DATA(ain);
       double* dataout = (double*)PyArray_DATA(aout);
-      Py_ssize_t signature_length = PyArray_SHAPE(ain)[0];
-      if (signature_length != PyArray_SHAPE(awl)[0]) {
+      Py_ssize_t spectrum_length = PyArray_SHAPE(ain)[0];
+      if (spectrum_length != PyArray_SHAPE(awl)[0]) {
           PyErr_SetString(PyExc_ValueError,
               "In continuum_generic_impl: wavelengths array has incorrect length.");
           return Py_None;
       }
-      continuum_processing_f(datain, dataout, dataawl, signature_length);
+      continuum_processing_f(datain, dataout, dataawl, spectrum_length);
     } else {
-      Py_ssize_t num_signatures = PyArray_SHAPE(ain)[0];
-      Py_ssize_t signature_length = PyArray_SHAPE(ain)[1];
-      if (signature_length != PyArray_SHAPE(awl)[0]) {
+      Py_ssize_t num_spectra = PyArray_SHAPE(ain)[0];
+      Py_ssize_t spectrum_length = PyArray_SHAPE(ain)[1];
+      if (spectrum_length != PyArray_SHAPE(awl)[0]) {
           PyErr_SetString(PyExc_ValueError,
               "In continuum_generic_impl: wavelengths array has incorrect length.");
           return Py_None;
       }
 
       #pragma omp parallel for
-      for (Py_ssize_t i = 0; i < num_signatures; ++i) {
+      for (Py_ssize_t i = 0; i < num_spectra; ++i) {
         double* datain = (double*)(PyArray_DATA(ain)
           + i * PyArray_STRIDES(ain)[0]);
         double* dataout = (double*)(PyArray_DATA(aout)
           + i * PyArray_STRIDES(aout)[0]);
-        continuum_processing_f(datain, dataout, dataawl, signature_length);
+        continuum_processing_f(datain, dataout, dataawl, spectrum_length);
       }
     }
 
     return Py_None;
 }
 
-/* Function accepting 1d array and returning continuum signature. */
+/* Function accepting 1d array and returning continuum spectrum. */
 
 PyDoc_STRVAR(continuum_continuum_doc,
-"continuum(signature)\n\
+"continuum(spectrum)\n\
 \n\
-Return continuum of the signature.");
+Return continuum of the spectrum.");
 
 static PyObject *
 continuum_continuum(PyObject *self, PyObject *args)
 {
     return continuum_generic_impl(self, args, &continuum);
 }
 
-/* Function accepting 1d array and returning continuum removed signature. */
+/* Function accepting 1d array and returning continuum removed spectrum. */
 
 PyDoc_STRVAR(continuum_continuum_removed_doc,
-"continuum_removed(signature)\n\
+"continuum_removed(spectrum)\n\
 \n\
-Return continuum removed signature.");
+Return continuum removed spectrum.");
 
 static PyObject *
 continuum_continuum_removed(PyObject *self, PyObject *args)

custo_math_funcs.py

@@ -70,7 +70,7 @@ def bspline2_from_points(points, xs):
         x_stitching_points.append(bspline2x_t(1.0, p0, p1, p2))
 
     # Fill results with pairs (i, y(i)),
-    # where i is x coordinate and also index in signature array,
+    # where i is x coordinate and also index in spectrum array,
     # and y(i) is respective  y coordinate of bspline2.
     results = np.empty(len(xs))
     filled_i = 0
@@ -227,7 +227,7 @@ def bspline3_from_points(points, xs):
         x_stitching_points.append(bspline3x_t(1.0, p0, p1, p2, p3))
 
     # Fill results with pairs (i, y(i)),
-    # where i is x coordinate and also index in signature array,
+    # where i is x coordinate and also index in spectrum array,
     # and y(i) is respective  y coordinate of bspline3.
     results = np.empty(len(xs))
     filled_i = 0

explore.py

@@ -47,11 +47,11 @@ def show_centers(centers, title, labels):
 #for i in range(data.shape[2]):
 #    save_rgb('./aerodrom_channels/' + str(i+1) + '.png', data[:, :, i])
 
-signatures = np.empty((5, data.shape[2]))
+spectra = np.empty((5, data.shape[2]))
 labels = [u"вода", u"загрязнённая вода", u"бетон", u"болото", u"почва"]
 positions = [(863, 369), (999, 519), (1199, 422), (1056, 352), (357, 585)]
 for i in range(len(positions)):
-    signatures[i] = data[positions[i][0], positions[i][1]]
+    spectra[i] = data[positions[i][0], positions[i][1]]
 
-show_centers(signatures, u'Сигнатуры некоторых точек изображения', labels)
+show_centers(spectra, u'Сигнатуры некоторых точек изображения', labels)
 

gsus_splib_utils/__init__.py

@@ -6,10 +6,10 @@
 from spectral import *
 
 class SpectralData:
-    def __init__(self, signature = None, libname = None,
+    def __init__(self, spectrum = None, libname = None,
                  record = None, description = None, spectrometer = None,
                  purity = None, measurement_type = None, spectrometer_data = None):
-        self.signature = signature
+        self.spectrum = spectrum
         self.libname = libname
         self.record = record
         self.description = description
@@ -25,11 +25,11 @@ def header(self):
                                                self.purity, self.measurement_type)
 
     def __repr__(self):
-        sig_lines = ['{:.5E}'.format(s) for s in self.signature]
-        return self.header() + '\n' + ('\n'.join(sig_lines))
+        spectra_lines = ['{:.5E}'.format(s) for s in self.spectrum]
+        return self.header() + '\n' + ('\n'.join(spectra_lines))
 
     def __str__(self):
-        return self.header() + ' \t {} channels'.format(len(self.signature))
+        return self.header() + ' \t {} channels'.format(len(self.spectrum))
 
     @staticmethod
     def parse_header(header_line):
@@ -61,41 +61,41 @@ def read_from_file(filename):
             libname, record, description, spectrometer, purity, measurment_type = \
                 SpectralData.parse_header(header_line.strip())
 
-            signature = []
+            spectrum = []
             for line in f:
                 try:
-                    signature.append(float(line.strip()))
+                    spectrum.append(float(line.strip()))
                 except:
                     pass
 
             spectrometer_data = SpectrometerData.get_by_name(spectrometer)
 
-            return SpectralData(np.array(signature),
+            return SpectralData(np.array(spectrum),
                                 libname, record, description,
                                 spectrometer, purity, measurment_type,
                                 spectrometer_data)
 
     def replace_invalid(self, value):
-        self.signature[self.signature < 0.0] = value
+        self.spectrum[self.spectrum < 0.0] = value
         return self
 
     def interpolate_invalid(self, kind='slinear'):
-        full_xs = list(range(len(self.signature)))
-        xs = [x for x, y in zip(full_xs, self.signature) if y > 0.0]
-        ys = [y for y in self.signature if y > 0.0]
+        full_xs = list(range(len(self.spectrum)))
+        xs = [x for x, y in zip(full_xs, self.spectrum) if y > 0.0]
+        ys = [y for y in self.spectrum if y > 0.0]
         if xs[0] > full_xs[0]:
             xs.insert(0, full_xs[0])
             ys.insert(0, ys[0])
         if xs[-1] < full_xs[-1]:
             xs.append(full_xs[-1])
             ys.append(ys[-1])
         f = scipy.interpolate.interp1d(xs, ys, kind=kind, assume_sorted=True)
-        self.signature = f(full_xs)
+        self.spectrum = f(full_xs)
         return self
 
     def resample_as(self, spectrometer_name, with_fixed_dest = False):
         """
-            Returns signature resampled to different spectrometer.
+            Returns spectrum resampled to different spectrometer.
         """
         dest = SpectrometerData.get_by_name(spectrometer_name)
         dest_wl = dest.wavelengths
@@ -108,16 +108,16 @@ def resample_as(self, spectrometer_name, with_fixed_dest = False):
 
     def resample_at(self, dest_wl, dest_bw = None):
         """
-            Returns signature resampled to different spectrometer.
+            Returns spectrum resampled to different spectrometer.
         """
         resampler = BandResampler(self.spectrometer_data.wavelengths, dest_wl,
                                   self.spectrometer_data.bandwidths, dest_bw)
-        return resampler(self.signature)
+        return resampler(self.spectrum)
 
 
     def interpolate_as(self, spectrometer_name, with_fixed_dest = True, kind='quadratic'):
         """
-            Returns signature interpoleted at wavelengths of different spectrometer,
+            Returns spectrum interpoleted at wavelengths of different spectrometer,
             based on wavelengths and reflectances of original.
         """
         dest = SpectrometerData.get_by_name(spectrometer_name)
@@ -129,37 +129,37 @@ def interpolate_as(self, spectrometer_name, with_fixed_dest = True, kind='quadra
 
     def interpolate_at(self, dest_wl, kind='quadratic'):
         """
-            Returns signature interpoleted at specified wavelengths,
+            Returns spectrum interpoleted at specified wavelengths,
             based on wavelengths and reflectances of original.
         """
         xs = self.wavelengths()
-        ys = self.signature
+        ys = self.spectrum
         f = scipy.interpolate.interp1d(xs, ys, kind=kind, assume_sorted=True, fill_value='extrapolate')
         return f(dest_wl)
 
     def in_range(self, min_wl, max_wl):
         """
-            Return wavelengths and signature part between min wavelength and max wavelength.
+            Return wavelengths and spectrum part between min wavelength and max wavelength.
         """
         src_wavelengths = self.spectrometer_data.wavelengths
         min_wl = max(src_wavelengths[0], min_wl)
         max_wl = min(src_wavelengths[-1], max_wl)
         min_index = np.argmax(src_wavelengths >= min_wl)
         max_index = np.argmax(src_wavelengths > max_wl)
         range_wl = src_wavelengths[min_index:max_index]
-        range_sig = self.signature[min_index:max_index]
-        return range_wl, range_sig
+        range_spec = self.spectrum[min_index:max_index]
+        return range_wl, range_spec
 
     def in_range_of(self, spectrometer_name):
         """
-            Return wavelengths and signature part that overlaps with other spectrometer.
+            Return wavelengths and spectrum part that overlaps with other spectrometer.
         """
         dest_wavelengths = SpectrometerData.get_by_name(spectrometer_name).wavelengths
         return self.in_range(dest_wavelengths[0], dest_wavelengths[-1])
 
     def fix(self):
         self.interpolate_invalid()
-        self.signature = self.resample_as(self.spectrometer, True)
+        self.spectrum = self.resample_as(self.spectrometer, True)
         self.fixed = True
         self._wavelengths = np.sort(self.spectrometer_data.wavelengths)
         return self
@@ -182,7 +182,7 @@ def header(self):
                                                 self.spectrometer_name, self.description)
 
     def __repr__(self):
-        sig_lines = ['{:.5E}'.format(s) for s in self.signature]
+        spectra_lines = ['{:.5E}'.format(s) for s in self.spectrum]
         return self.header() + '\n' + ('\n'.join(wavelengths))
 
     def __str__(self):