Handle deprecation of array.{to,from}string (#86).

Author: tboggs

spectral/database/aster.py

@@ -31,7 +31,7 @@
 
 from __future__ import division, print_function, unicode_literals
 
-from spectral.utilities.python23 import IS_PYTHON3
+from spectral.utilities.python23 import IS_PYTHON3, tobytes, frombytes
 
 if IS_PYTHON3:
     readline = lambda fin: fin.readline()
@@ -183,8 +183,8 @@ def _add_signature(
         sql = '''INSERT INTO Spectra (SampleID, SensorCalibrationID, Instrument,
                  Environment, Measurement, XUnit, YUnit, MinWavelength, MaxWavelength,
                  NumValues, XData, YData) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)'''
-        xBlob = sqlite3.Binary(array.array(arraytypecode, xData).tostring())
-        yBlob = sqlite3.Binary(array.array(arraytypecode, yData).tostring())
+        xBlob = sqlite3.Binary(tobytes(array.array(arraytypecode, xData)))
+        yBlob = sqlite3.Binary(tobytes(array.array(arraytypecode, yData)))
         numValues = len(xData)
         self.cursor.execute(
             sql, (
@@ -375,9 +375,9 @@ def get_spectrum(self, spectrumID):
         if len(rows) < 1:
             raise 'Measurement record not found'
         x = array.array(arraytypecode)
-        x.fromstring(rows[0][0])
+        frombytes(x, rows[0][0])
         y = array.array(arraytypecode)
-        y.fromstring(rows[0][1])
+        frombytes(y, rows[0][1])
         return (list(x), list(y))
 
     def get_signature(self, spectrumID):

spectral/io/bilfile.py

@@ -36,7 +36,7 @@
 
 import numpy as np
 from .spyfile import SpyFile, MemmapFile
-from spectral.utilities.python23 import typecode
+from spectral.utilities.python23 import typecode, tobytes, frombytes
 
 byte_typecode = typecode('b')
 
@@ -112,7 +112,7 @@ def read_band(self, band, use_memmap=True):
                    self.ncols, 0)
             vals.fromfile(f, self.ncols * self.sample_size)
 
-        arr = numpy.fromstring(vals.tostring(), dtype=self.dtype)
+        arr = numpy.fromstring(tobytes(vals), dtype=self.dtype)
         arr = arr.reshape((self.nrows, self.ncols))
 
         if self.scale_factor != 1:
@@ -166,7 +166,7 @@ def read_bands(self, bands, use_memmap=True):
                 f.seek(row_offset + bands[j] * self.sample_size * self.ncols, 0)
                 vals.fromfile(f, self.ncols * self.sample_size)
 
-            frame = numpy.fromstring(vals.tostring(), dtype=self.dtype)
+            frame = numpy.fromstring(tobytes(vals), dtype=self.dtype)
             arr[i, :, :] = frame.reshape((len(bands), self.ncols)).transpose()
 
         if self.scale_factor != 1:
@@ -218,7 +218,7 @@ def read_pixel(self, row, col, use_memmap=True):
             f.seek(offset + i * sample_size * ncols, 0)
             vals.fromfile(f, sample_size)
 
-        pixel = numpy.fromstring(vals.tostring(), dtype=self.dtype)
+        pixel = numpy.fromstring(tobytes(vals), dtype=self.dtype)
 
         if self.scale_factor != 1:
             return pixel / float(self.scale_factor)
@@ -301,7 +301,7 @@ def read_subregion(self, row_bounds, col_bounds, bands=None,
             for j in bands:
                 f.seek(rowPos + j * ncols * sampleSize, 0)
                 vals.fromfile(f, nSubCols * sampleSize)
-            subArray = numpy.fromstring(vals.tostring(), dtype=self.dtype)
+            subArray = numpy.fromstring(tobytes(vals), dtype=self.dtype)
             subArray = subArray.reshape((nSubBands, nSubCols))
             arr[i - row_bounds[0], :, :] = numpy.transpose(subArray)
 
@@ -386,7 +386,7 @@ def read_subimage(self, rows, cols, bands=None, use_memmap=False):
                            j * d_col +
                            k * d_band, 0)
                     vals.fromfile(f, sample_size)
-        subArray = numpy.fromstring(vals.tostring(), dtype=self.dtype)
+        subArray = numpy.fromstring(tobytes(vals), dtype=self.dtype)
         subArray = subArray.reshape((nSubRows, nSubCols, nSubBands))
 
         if self.scale_factor != 1:
@@ -426,5 +426,5 @@ def read_datum(self, i, j, k, use_memmap=True):
         self.fid.seek(self.offset + i * d_row + j * d_col + k * d_band, 0)
         vals = array.array(byte_typecode)
         vals.fromfile(self.fid, self.sample_size)
-        arr = np.fromstring(vals.tostring(), dtype=self.dtype)
+        arr = np.fromstring(tobytes(vals), dtype=self.dtype)
         return arr.tolist()[0] / float(self.scale_factor)

spectral/io/bipfile.py

@@ -36,7 +36,7 @@
 
 import numpy as np
 from .spyfile import SpyFile, MemmapFile
-from spectral.utilities.python23 import typecode
+from spectral.utilities.python23 import typecode, tobytes, frombytes
 
 byte_typecode = typecode('b')
 
@@ -112,7 +112,7 @@ def read_band(self, band, use_memmap=True):
             f.seek(delta, 1)
         vals.fromfile(f, sample_size)
 
-        arr = np.fromstring(vals.tostring(), dtype=self.dtype)
+        arr = np.fromstring(tobytes(vals), dtype=self.dtype)
         arr = arr.reshape(self.nrows, self.ncols)
 
         if self.scale_factor != 1:
@@ -169,7 +169,7 @@ def read_bands(self, bands, use_memmap=True):
             for j in range(len(bands)):
                 f.seek(pixelOffset + delta_b[j], 0)        # Next band
                 vals.fromfile(f, sample_size)
-        arr = np.fromstring(vals.tostring(), dtype=self.dtype)
+        arr = np.fromstring(tobytes(vals), dtype=self.dtype)
         arr = arr.reshape(self.nrows, self.ncols, len(bands))
 
         if self.scale_factor != 1:
@@ -213,7 +213,7 @@ def read_pixel(self, row, col, use_memmap=True):
         # Pixel format is BIP so read entire pixel.
         vals.fromfile(f, self.nbands * self.sample_size)
 
-        pixel = np.fromstring(vals.tostring(), dtype=self.dtype)
+        pixel = np.fromstring(tobytes(vals), dtype=self.dtype)
 
         if self.scale_factor != 1:
             return pixel / float(self.scale_factor)
@@ -304,7 +304,7 @@ def read_subregion(self, row_bounds, col_bounds, bands=None,
                     for k in range(len(bands)):
                         f.seek(pixelPos + delta_b[k], 0)    # Next band
                         vals.fromfile(f, sample_size)
-        arr = np.fromstring(vals.tostring(), dtype=self.dtype)
+        arr = np.fromstring(tobytes(vals), dtype=self.dtype)
         arr = arr.reshape(nSubRows, nSubCols, nSubBands)
 
         if self.scale_factor != 1:
@@ -391,7 +391,7 @@ def read_subimage(self, rows, cols, bands=None, use_memmap=False):
                                k * d_band, 0)
                         vals.fromfile(f, sample_size)
 
-        arr = np.fromstring(vals.tostring(), dtype=self.dtype)
+        arr = np.fromstring(tobytes(vals), dtype=self.dtype)
         arr = arr.reshape(nSubRows, nSubCols, nSubBands)
 
         if self.scale_factor != 1:
@@ -430,5 +430,5 @@ def read_datum(self, i, j, k, use_memmap=True):
                * (self.nbands * (i * self.ncols + j) + k), 0)
         # Pixel format is BIP so read entire pixel.
         vals.fromfile(f, self.sample_size)
-        arr = np.fromstring(vals.tostring(), dtype=self.dtype)
+        arr = np.fromstring(tobytes(vals), dtype=self.dtype)
         return arr.tolist()[0] / float(self.scale_factor)

spectral/io/bsqfile.py

@@ -36,7 +36,7 @@
 
 import numpy as np
 from .spyfile import SpyFile, MemmapFile
-from spectral.utilities.python23 import typecode
+from spectral.utilities.python23 import typecode, tobytes, frombytes
 
 byte_typecode = typecode('b')
 
@@ -109,7 +109,7 @@ def read_band(self, band, use_memmap=True):
         f.seek(offset, 0)
         vals.fromfile(f, self.nrows * self.ncols * self.sample_size)
 
-        arr = np.fromstring(vals.tostring(), dtype=self.dtype)
+        arr = np.fromstring(tobytes(vals), dtype=self.dtype)
         arr = arr.reshape(self.nrows, self.ncols)
 
         if self.scale_factor != 1:
@@ -162,7 +162,7 @@ def read_bands(self, bands, use_memmap=False):
             f.seek(offset, 0)
             vals.fromfile(f, self.nrows * self.ncols * self.sample_size)
 
-            band = np.fromstring(vals.tostring(), dtype=self.dtype)
+            band = np.fromstring(tobytes(vals), dtype=self.dtype)
             arr[:, :, j] = band.reshape(self.nrows, self.ncols)
 
         if self.scale_factor != 1:
@@ -219,7 +219,7 @@ def read_pixel(self, row, col, use_memmap=True):
                    + col * sampleSize, 0)
             vals.fromfile(f, sampleSize)
 
-        pixel = np.fromstring(vals.tostring(), dtype=self.dtype)
+        pixel = np.fromstring(tobytes(vals), dtype=self.dtype)
 
         if self.scale_factor != 1:
             return pixel / float(self.scale_factor)
@@ -305,7 +305,7 @@ def read_subregion(self, row_bounds, col_bounds, bands=None,
                        + j * rowSize
                        + colStartOffset, 0)
                 vals.fromfile(f, nSubCols * sampleSize)
-            subArray = np.fromstring(vals.tostring(),
+            subArray = np.fromstring(tobytes(vals),
                                      dtype=self.dtype).reshape((nSubRows,
                                                                 nSubCols))
             arr[:, :, i] = subArray
@@ -397,7 +397,7 @@ def read_subimage(self, rows, cols, bands=None, use_memmap=False):
                            + rowOffset
                            + k * sampleSize, 0)
                     vals.fromfile(f, sampleSize)
-        arr = np.fromstring(vals.tostring(), dtype=self.dtype)
+        arr = np.fromstring(tobytes(vals), dtype=self.dtype)
         arr = arr.reshape(nSubBands, nSubRows, nSubCols)
         arr = np.transpose(arr, (1, 2, 0))
 
@@ -441,5 +441,5 @@ def read_datum(self, i, j, k, use_memmap=True):
                          + j) * sampleSize, 0)
         vals = array.array(byte_typecode)
         vals.fromfile(self.fid, sampleSize)
-        arr = np.fromstring(vals.tostring(), dtype=self.dtype)
+        arr = np.fromstring(tobytes(vals), dtype=self.dtype)
         return arr.tolist()[0] / float(self.scale_factor)

spectral/io/spyfile.py

@@ -114,6 +114,7 @@
 import numpy as np
 from spectral import SpyException
 from spectral.spectral import Image
+from spectral.utilities.python23 import typecode, tobytes, frombytes
 
 class FileNotFoundError(SpyException):
     pass
@@ -222,7 +223,6 @@ def load(self, **kwargs):
         '''
         import spectral
         from spectral.spectral import ImageArray
-        from spectral.utilities.python23 import typecode
         from array import array
         import warnings
         from spectral.algorithms.spymath import has_nan, NaNValueWarning
@@ -235,7 +235,7 @@ def load(self, **kwargs):
         self.fid.seek(self.offset)
         data.fromfile(self.fid, self.nrows * self.ncols *
                       self.nbands * self.sample_size)
-        npArray = np.fromstring(data.tostring(), dtype=self.dtype)
+        npArray = np.fromstring(tobytes(data), dtype=self.dtype)
         if self.interleave == spectral.BIL:
             npArray.shape = (self.nrows, self.nbands, self.ncols)
             npArray = npArray.transpose([0, 2, 1])

spectral/utilities/python23.py

@@ -61,3 +61,11 @@ def is_string(s):
 else:
     def is_string(s):
         return isinstance(s, basestring)
+
+# array.tostring is deprecated in python3
+if IS_PYTHON3:
+    tobytes = lambda array: array.tobytes()
+    frombytes = lambda array, src: array.frombytes(src)
+else:
+    tobytes = lambda array: array.tostring()
+    frombytes = lambda array, src: array.fromstring(src)