Merge pull request #899 from effigies/rf/tobytes

MNT: Drop deprecated ndarray.tostring for tobytes

Author: effigies

nibabel/analyze.py

@@ -509,7 +509,7 @@ def data_to_fileobj(self, data, fileobj, rescale=True):
         >>> str_io = BytesIO()
         >>> data = np.arange(6).reshape(1,2,3)
         >>> hdr.data_to_fileobj(data, str_io)
-        >>> data.astype(np.float64).tostring('F') == str_io.getvalue()
+        >>> data.astype(np.float64).tobytes('F') == str_io.getvalue()
         True
         '''
         data = np.asanyarray(data)

nibabel/benchmarks/bench_fileslice.py

@@ -48,7 +48,7 @@ def run_slices(file_like, repeat=3, offset=0, order='F'):
     times_arr = np.zeros((n_dim, n_slicers))
     with ImageOpener(file_like, 'wb') as fobj:
         fobj.write(b'\0' * offset)
-        fobj.write(arr.tostring(order=order))
+        fobj.write(arr.tobytes(order=order))
     with ImageOpener(file_like, 'rb') as fobj:
         for i, L in enumerate(SHAPE):
             for j, slicer in enumerate(_slices_for_len(L)):

nibabel/dft.py

@@ -144,8 +144,7 @@ def as_png(self, index=None, scale_to_slice=True):
             max = data.max()
             data = data * 255 / (max - min)
         data = data.astype(numpy.uint8)
-        im = frombytes('L', (self.rows, self.columns),
-                       data.tostring())
+        im = frombytes('L', (self.rows, self.columns), data.tobytes())
 
         s = BytesIO()
         im.save(s, 'PNG')
@@ -213,7 +212,7 @@ def as_nifti(self):
         s = BytesIO()
         hdr.write_to(s)
 
-        return s.getvalue() + data.tostring()
+        return s.getvalue() + data.tobytes()
 
     def nifti_size(self):
         return 352 + 2 * len(self.storage_instances) * self.columns * self.rows

nibabel/ecat.py

@@ -981,7 +981,7 @@ def to_file_map(self, file_map=None):
 
             # Write subheader
             subhdr = subheaders.subheaders[index]
-            imgf.write(subhdr.tostring())
+            imgf.write(subhdr.tobytes())
 
             # Seek to the next image block
             pos = imgf.tell()

nibabel/externals/netcdf.py

@@ -421,7 +421,7 @@ def flush(self):
     def _write(self):
         self.fp.seek(0)
         self.fp.write(b'CDF')
-        self.fp.write(array(self.version_byte, '>b').tostring())
+        self.fp.write(array(self.version_byte, '>b').tobytes())
 
         # Write headers and data.
         self._write_numrecs()
@@ -531,7 +531,7 @@ def _write_var_data(self, name):
 
         # Write data.
         if not var.isrec:
-            self.fp.write(var.data.tostring())
+            self.fp.write(var.data.tobytes())
             count = var.data.size * var.data.itemsize
             self._write_var_padding(var, var._vsize - count)
         else:  # record variable
@@ -553,7 +553,7 @@ def _write_var_data(self, name):
                 if not rec.shape and (rec.dtype.byteorder == '<' or
                         (rec.dtype.byteorder == '=' and LITTLE_ENDIAN)):
                     rec = rec.byteswap()
-                self.fp.write(rec.tostring())
+                self.fp.write(rec.tobytes())
                 # Padding
                 count = rec.size * rec.itemsize
                 self._write_var_padding(var, var._vsize - count)
@@ -606,7 +606,7 @@ def _write_att_values(self, values):
         if not values.shape and (values.dtype.byteorder == '<' or
                 (values.dtype.byteorder == '=' and LITTLE_ENDIAN)):
             values = values.byteswap()
-        self.fp.write(values.tostring())
+        self.fp.write(values.tobytes())
         count = values.size * values.itemsize
         self.fp.write(b'\x00' * (-count % 4))  # pad
 
@@ -791,15 +791,15 @@ def _pack_begin(self, begin):
             self._pack_int64(begin)
 
     def _pack_int(self, value):
-        self.fp.write(array(value, '>i').tostring())
+        self.fp.write(array(value, '>i').tobytes())
     _pack_int32 = _pack_int
 
     def _unpack_int(self):
         return int(frombuffer(self.fp.read(4), '>i')[0])
     _unpack_int32 = _unpack_int
 
     def _pack_int64(self, value):
-        self.fp.write(array(value, '>q').tostring())
+        self.fp.write(array(value, '>q').tobytes())
 
     def _unpack_int64(self):
         return frombuffer(self.fp.read(8), '>q')[0]
@@ -1045,7 +1045,7 @@ def _get_encoded_fill_value(self):
         """
         if '_FillValue' in self._attributes:
             fill_value = np.array(self._attributes['_FillValue'],
-                                  dtype=self.data.dtype).tostring()
+                                  dtype=self.data.dtype).tobytes()
             if len(fill_value) == self.itemsize():
                 return fill_value
             else:

nibabel/freesurfer/io.py

@@ -613,7 +613,7 @@ def _serialize_volume_info(volume_info):
             if not (np.array_equal(volume_info[key], [20]) or np.array_equal(
                     volume_info[key], [2, 0, 20])):
                 warnings.warn("Unknown extension code.")
-            strings.append(np.array(volume_info[key], dtype='>i4').tostring())
+            strings.append(np.array(volume_info[key], dtype='>i4').tobytes())
         elif key in ('valid', 'filename'):
             val = volume_info[key]
             strings.append('{0} = {1}\n'.format(key, val).encode('utf-8'))

nibabel/freesurfer/mghformat.py

@@ -407,7 +407,7 @@ def writehdr_to(self, fileobj):
                                   buffer=self.binaryblock)
         # goto the very beginning of the file-like obj
         fileobj.seek(0)
-        fileobj.write(hdr_nofooter.tostring())
+        fileobj.write(hdr_nofooter.tobytes())
 
     def writeftr_to(self, fileobj):
         ''' Write footer to fileobj
@@ -427,7 +427,7 @@ def writeftr_to(self, fileobj):
         ftr_nd = np.ndarray((), dtype=self._ftrdtype,
                             buffer=self.binaryblock, offset=ftr_loc_in_hdr)
         fileobj.seek(self.get_footer_offset())
-        fileobj.write(ftr_nd.tostring())
+        fileobj.write(ftr_nd.tobytes())
 
     def copy(self):
         ''' Return copy of structure '''

nibabel/freesurfer/tests/test_io.py

@@ -309,7 +309,7 @@ def gen_old_annot_file(fpath, nverts, labels, rgba, names):
         # number of vertices
         fbytes += struct.pack(dt, nverts)
         # vertices + annotation values
-        fbytes += bytes(vdata.astype(dt).tostring())
+        fbytes += vdata.astype(dt).tobytes()
         # is there a colour table?
         fbytes += struct.pack(dt, 1)
         # number of entries in colour table
@@ -321,7 +321,7 @@ def gen_old_annot_file(fpath, nverts, labels, rgba, names):
             # length of entry name (+1 for terminating byte)
             fbytes += struct.pack(dt, len(names[i]) + 1)
             fbytes += names[i].encode('ascii') + b'\x00'
-            fbytes += bytes(rgba[i, :].astype(dt).tostring())
+            fbytes += rgba[i, :].astype(dt).tobytes()
         with open(fpath, 'wb') as f:
             f.write(fbytes)
     with InTemporaryDirectory():

nibabel/gifti/gifti.py

@@ -281,7 +281,7 @@ def _data_tag_element(dataarray, encoding, dtype, ordering):
         # XXX Accommodating data_tag API - don't try to fix dtype
         if isinstance(dtype, str):
             dtype = dataarray.dtype
-        out = np.asanyarray(dataarray, dtype).tostring(order)
+        out = np.asanyarray(dataarray, dtype).tobytes(order)
         if enclabel == 'B64GZ':
             out = zlib.compress(out)
         da = base64.b64encode(out).decode()

nibabel/nicom/tests/test_dicomwrappers.py

@@ -618,7 +618,7 @@ def test_data_real(self):
         # data hash depends on the endianness
         if endian_codes[data.dtype.byteorder] == '>':
             data = data.byteswap()
-        dat_str = data.tostring()
+        dat_str = data.tobytes()
         assert_equal(sha1(dat_str).hexdigest(),
                      '149323269b0af92baa7508e19ca315240f77fa8c')