8000 BUG: Fix deprecation warning on use of `np.fromstring`. by jhlegarreta · Pull Request #706 · nipy/nibabel · GitHub
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BUG: Fix deprecation warning on use of np.fromstring. #706

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BUG: Fix deprecation warning on use of np.fromstring.
Fix deprecation warning on use of `no.fromstring`. Fixes:
```
DeprecationWarning: The binary mode of fromstring is deprecated, as it
behaves surprisingly on unicode inputs. Use frombuffer instead
```

observed in projects using Nibabel, e.g. DIPY:
https://travis-ci.org/nipy/dipy/jobs/471947136
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jhlegarreta committed Dec 25, 2018
commit 347ab8365ccef9609079d84dfabf4d7d0ff03043
4 changes: 2 additions & 2 deletions nibabel/gifti/parse_gifti_fast.py
Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,7 @@ def read_data_block(encoding, endian, ordering, datatype, shape, data):
dec = base64.b64decode(data.encode('ascii'))
dt = data_type_codes.type[datatype]
sh = tuple(shape)
newarr = np.fromstring(dec, dtype=dt)
newarr = np.frombuffer(dec, dtype=dt)
if len(newarr.shape) != len(sh):
newarr = newarr.reshape(sh, order=ord)

Expand All @@ -59,7 +59,7 @@ def read_data_block(encoding, endian, ordering, datatype, shape, data):
zdec = zlib.decompress(dec)
dt = data_type_codes.type[datatype]
sh = tuple(shape)
newarr = np.fromstring(zdec, dtype=dt)
newarr = np.frombuffer(zdec, dtype=dt)
if len(newarr.shape) != len(sh):
newarr = newarr.reshape(sh, order=ord)

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2 changes: 1 addition & 1 deletion nibabel/nifti1.py
Original file line number Diff line number Diff line change
Expand Up @@ -579,7 +579,7 @@ def from_fileobj(klass, fileobj, size, byteswap):
# otherwise there should be a full extension header
if not len(ext_def) == 8:
raise HeaderDataError('failed to read extension header')
ext_def = np.fromstring(ext_def, dtype=np.int32)
ext_def = np.frombuffer(ext_def, dtype=np.int32)
if byteswap:
ext_def = ext_def.byteswap()
# be extra verbose
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2 changes: 1 addition & 1 deletion nibabel/parrec.py
Original file line number Diff line number Diff line change
Expand Up @@ -341,7 +341,7 @@ def _process_gen_dict(gen_dict):
value = props[1](value)
elif len(props) == 3:
# array with dtype and shape
value = np.fromstring(value, props[1], sep=' ')
value = np.frombuffer(value, props[1], sep=' ')
# if shape is None, allow arbitrary length
if props[2] is not None:
value.shape = props[2]
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2 changes: 1 addition & 1 deletion nibabel/streamlines/trk.py
Original file line number Diff line number Diff line change
Expand Up @@ -559,7 +559,7 @@ def _read_header(fileobj):

# Read the header in one block.
header_str = f.read(header_2_dtype.itemsize)
header_rec = np.fromstring(string=header_str, dtype=header_2_dtype)
header_rec = np.frombuffer(string=header_str, dtype=header_2_dtype)

# Check endianness
endianness = native_code
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