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')
 

nibabel/nifti1.py

@@ -376,7 +376,7 @@ def write_to(self, fileobj, byteswap):
         extinfo = np.array((rawsize, self._code), dtype=np.int32)
         if byteswap:
             extinfo = extinfo.byteswap()
-        fileobj.write(extinfo.tostring())
+        fileobj.write(extinfo.tobytes())
         # followed by the actual extension content
         # XXX if mangling upon load is implemented, it should be reverted here
         fileobj.write(self._mangle(self._content))

nibabel/spatialimages.py

@@ -266,7 +266,7 @@ def data_to_fileobj(self, data, fileobj, rescale=True):
         '''
         data = np.asarray(data)
         dtype = self.get_data_dtype()
-        fileobj.write(data.astype(dtype).tostring(order=self.data_layout))
+        fileobj.write(data.astype(dtype).tobytes(order=self.data_layout))
 
     def data_from_fileobj(self, fileobj):
         ''' Read binary image data from `fileobj` '''

nibabel/streamlines/tck.py

@@ -205,7 +205,7 @@ def save(self, fileobj):
                 self._finalize_header(f, header, offset=beginning)
 
                 # Add the EOF_DELIMITER.
-                f.write(asbytes(self.EOF_DELIMITER.tostring()))
+                f.write(self.EOF_DELIMITER.tobytes())
                 return
 
             data_for_streamline = first_item.data_for_streamline
@@ -224,13 +224,13 @@ def save(self, fileobj):
 
             for t in tractogram:
                 data = np.r_[t.streamline, self.FIBER_DELIMITER]
-                f.write(data.astype(dtype).tostring())
+                f.write(data.astype(dtype).tobytes())
                 nb_streamlines += 1
 
             header[Field.NB_STREAMLINES] = nb_streamlines
 
             # Add the EOF_DELIMITER.
-            f.write(asbytes(self.EOF_DELIMITER.tostring()))
+            f.write(asbytes(self.EOF_DELIMITER.tobytes()))
             self._finalize_header(f, header, offset=beginning)
 
     @staticmethod

nibabel/streamlines/tests/test_tck.py

@@ -129,8 +129,8 @@ def test_load_file_with_wrong_information(self):
         assert_raises(HeaderError, TckFile.load, BytesIO(new_tck_file))
 
         # Simulate a TCK file which is missing a streamline delimiter.
-        eos = TckFile.FIBER_DELIMITER.tostring()
-        eof = TckFile.EOF_DELIMITER.tostring()
+        eos = TckFile.FIBER_DELIMITER.tobytes()
+        eof = TckFile.EOF_DELIMITER.tobytes()
         new_tck_file = tck_file[:-(len(eos) + len(eof))] + tck_file[-len(eof):]
 
         # Force TCK loading to use buffering.

nibabel/streamlines/trk.py

@@ -438,7 +438,7 @@ def save(self, fileobj):
             beginning = f.tell()
 
             # Write temporary header that we will update at the end
-            f.write(header.tostring())
+            f.write(header.tobytes())
 
             i4_dtype = np.dtype("<i4")  # Always save in little-endian.
             f4_dtype = np.dtype("<f4")  # Always save in little-endian.
@@ -467,7 +467,7 @@ def save(self, fileobj):
                 header[Field.NB_PROPERTIES_PER_STREAMLINE] = 0
                 # Overwrite header with updated one.
                 f.seek(beginning, os.SEEK_SET)
-                f.write(header.tostring())
+                f.write(header.tobytes())
                 return
 
             # Update field 'property_name' using 'data_per_streamline'.
@@ -523,8 +523,8 @@ def save(self, fileobj):
                 data = struct.pack(i4_dtype.str[:-1], len(points))
                 pts_scalars = np.concatenate(
                     [points, scalars], axis=1).astype(f4_dtype)
-                data += pts_scalars.tostring()
-                data += properties.tostring()
+                data += pts_scalars.tobytes()
+                data += properties.tobytes()
                 f.write(data)
 
                 nb_streamlines += 1
@@ -552,7 +552,7 @@ def save(self, fileobj):
 
             # Overwrite header with updated one.
             f.seek(beginning, os.SEEK_SET)
-            f.write(header.tostring())
+            f.write(header.tobytes())
 
     @staticmethod
     def _read_header(fileobj):

nibabel/tests/test_arrayproxy.py

@@ -67,7 +67,7 @@ def test_init():
     dtype = np.int32
     arr = np.arange(24, dtype=dtype).reshape(shape)
     bio.seek(16)
-    bio.write(arr.tostring(order='F'))
+    bio.write(arr.tobytes(order='F'))
     hdr = FunkyHeader(shape)
     ap = ArrayProxy(bio, hdr)
     assert_true(ap.file_like is bio)
@@ -84,7 +84,7 @@ def test_init():
     # C order also possible
     bio = BytesIO()
     bio.seek(16)
-    bio.write(arr.tostring(order='C'))
+    bio.write(arr.tobytes(order='C'))
     ap = CArrayProxy(bio, FunkyHeader((2, 3, 4)))
     assert_array_equal(np.asarray(ap), arr)
     # Illegal init
@@ -97,7 +97,7 @@ def test_tuplespec():
     dtype = np.int32
     arr = np.arange(24, dtype=dtype).reshape(shape)
     bio.seek(16)
-    bio.write(arr.tostring(order='F'))
+    bio.write(arr.tobytes(order='F'))
     # Create equivalent header and tuple specs
     hdr = FunkyHeader(shape)
     tuple_spec = (hdr.get_data_shape(), hdr.get_data_dtype(),
@@ -125,7 +125,7 @@ def write_raw_data(arr, hdr, fileobj):
     hdr.set_data_shape(arr.shape)
     hdr.set_data_dtype(arr.dtype)
     fileobj.write(b'\x00' * hdr.get_data_offset())
-    fileobj.write(arr.tostring(order='F'))
+    fileobj.write(arr.tobytes(order='F'))
 
 
 def test_nifti1_init():
@@ -163,15 +163,15 @@ def test_proxy_slicing():
             for order, klass in ('F', ArrayProxy), ('C', CArrayProxy):
                 fobj = BytesIO()
                 fobj.write(b'\0' * offset)
-                fobj.write(arr.tostring(order=order))
+                fobj.write(arr.tobytes(order=order))
                 prox = klass(fobj, hdr)
                 for sliceobj in slicer_samples(shape):
                     assert_array_equal(arr[sliceobj], prox[sliceobj])
     # Check slicing works with scaling
     hdr.set_slope_inter(2.0, 1.0)
     fobj = BytesIO()
     fobj.write(b'\0' * offset)
-    fobj.write(arr.tostring(order='F'))
+    fobj.write(arr.tobytes(order='F'))
     prox = ArrayProxy(fobj, hdr)
     sliceobj = (None, slice(None), 1, -1)
     assert_array_equal(arr[sliceobj] * 2.0 + 1.0, prox[sliceobj])
@@ -199,7 +199,7 @@ def test_reshape_dataobj():
     bio = BytesIO()
     prox = ArrayProxy(bio, hdr)
     arr = np.arange(np.prod(shape), dtype=prox.dtype).reshape(shape)
-    bio.write(b'\x00' * prox.offset + arr.tostring(order='F'))
+    bio.write(b'\x00' * prox.offset + arr.tobytes(order='F'))
     assert_array_equal(prox, arr)
     assert_array_equal(reshape_dataobj(prox, (2, 3, 4)),
                        np.reshape(arr, (2, 3, 4)))
@@ -245,7 +245,7 @@ def get_slope_inter(self):
     # Check standard read works
     arr = np.arange(24, dtype=np.int32).reshape(shape, order='F')
     bio.write(b'\x00' * hdr.get_data_offset())
-    bio.write(arr.tostring(order='F'))
+    bio.write(arr.tobytes(order='F'))
     prox = ArrayProxy(bio, hdr)
     assert_array_almost_equal(np.array(prox), arr * 2.1 + 3.14)
     # Check unscaled read works
@@ -294,7 +294,7 @@ def check_mmap(hdr, offset, proxy_class,
     with InTemporaryDirectory():
         with open(fname, 'wb') as fobj:
             fobj.write(b' ' * offset)
-            fobj.write(arr.tostring(order='F'))
+            fobj.write(arr.tobytes(order='F'))
         for mmap, expected_mode in (
                 # mmap value, expected memmap mode
                 # mmap=None -> no mmap value
@@ -405,10 +405,10 @@ def test_keep_file_open_true_false_invalid():
             # create the test data file
             if filetype == 'gz':
                 with gzip.open(fname, 'wb') as fobj:
-                    fobj.write(data.tostring(order='F'))
+                    fobj.write(data.tobytes(order='F'))
             else:
                 with open(fname, 'wb') as fobj:
-                    fobj.write(data.tostring(order='F'))
+                    fobj.write(data.tobytes(order='F'))
             # pass in a file name or open file handle. If the latter, we open
             # two file handles, because we're going to create two proxies
             # below.
@@ -459,7 +459,7 @@ def test_keep_file_open_true_false_invalid():
     with InTemporaryDirectory():
         fname = 'testdata'
         with open(fname, 'wb') as fobj:
-            fobj.write(data.tostring(order='F'))
+            fobj.write(data.tobytes(order='F'))
 
         for invalid_kfo in (55, 'auto', 'cauto'):
             with assert_raises(ValueError):