Merge pull request #1459 from SpiNNakerManchester/fix_numpy

Try to fix numpy v2 things
SpiNNakerManchester · Jun 21, 2024 · 1319cea · 1319cea
2 parents eabcd07 + 3473a19
commit 1319cea
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Showing 4 changed files with 16 additions and 9 deletions.
diff --git a/spynnaker/pyNN/models/common/param_generator_data.py b/spynnaker/pyNN/models/common/param_generator_data.py
@@ -14,7 +14,7 @@
 from typing import Any, Union, cast
 
 import numpy
-from numpy import uint32
+from numpy import uint32, int32
 from numpy.typing import NDArray
 from typing_extensions import TypeAlias
 
@@ -117,7 +117,8 @@ def param_generator_params(values: _ParamType) -> NDArray[uint32]:
     """
     if numpy.isscalar(values):
         return numpy.array(
-            [DataType.S1615.encode_as_int(cast(float, values))], dtype=uint32)
+            [DataType.S1615.encode_as_int(cast(float, values))],
+            dtype=int32).view(uint32)
 
     if isinstance(values, RandomDistribution):
         parameters = (
@@ -129,7 +130,7 @@ def param_generator_params(values: _ParamType) -> NDArray[uint32]:
             for param in parameters if param is not None)
         params = [
             DataType.S1615.encode_as_int(param) for param in parameters]
-        return numpy.array(params, dtype=uint32)
+        return numpy.array(params, dtype=int32).view(uint32)
 
     raise ValueError(f"Unexpected value {values}")
 

diff --git a/spynnaker/pyNN/models/neuron/synapse_dynamics/synapse_dynamics_structural_common.py b/spynnaker/pyNN/models/neuron/synapse_dynamics/synapse_dynamics_structural_common.py
@@ -382,7 +382,7 @@ def __write_post_to_pre_table(
                        for row in rows]
 
         # Finally make the table and write it out
-        post_to_pre = numpy.core.records.fromarrays(
+        post_to_pre = numpy.rec.fromarrays(
             numpy.concatenate(padded_rows).T, formats="u1, u1, u2").view("u4")
         if len(post_to_pre) != vertex_slice.n_atoms * self.s_max:
             raise ValueError(

diff --git a/spynnaker/pyNN/models/projection.py b/spynnaker/pyNN/models/projection.py
@@ -23,7 +23,7 @@
 from numpy.typing import NDArray
 from typing_extensions import Literal, TypeAlias
 
-from pyNN.recording.files import StandardTextFile, BaseFile
+from pyNN.recording.files import BaseFile
 from pyNN.space import Space as PyNNSpace
 
 from spinn_utilities.config_holder import get_config_bool
@@ -376,11 +376,17 @@ def __save_callback(save_file: Union[str, BaseFile],
             data = data.astype(dtype)
         npdata = numpy.nan_to_num(cast(NDArray, data))
         if isinstance(save_file, str):
-            data_file = StandardTextFile(save_file, mode='wb')
+            data_file = open(save_file, mode='wb')
         else:
             data_file = save_file
         try:
-            data_file.write(npdata, metadata)
+            header_lines = [
+                f"# {key} = {value}" for key, value in metadata.items()]
+            header = "\n".join(header_lines) + '\n'
+            data_file.write(header.encode('utf-8'))
+            # write data
+            numpy.savetxt(data_file, npdata, delimiter='\t')
+            data_file.close()
         finally:
             data_file.close()
 

diff --git a/spynnaker/pyNN/utilities/neo_buffer_database.py b/spynnaker/pyNN/utilities/neo_buffer_database.py
@@ -24,7 +24,7 @@
     TYPE_CHECKING)
 
 import numpy
-from numpy import floating, integer, uint8
+from numpy import floating, integer, uint8, uint32
 from numpy.typing import NDArray
 import quantities
 import neo  # type: ignore[import]
@@ -644,7 +644,7 @@ def __get_eieio_spike_by_region(
             key_bytes = eieio_header.eieio_type.key_bytes
             keys = numpy.frombuffer(
                 spike_data, dtype=f"<u{key_bytes}",
-                count=eieio_header.count, offset=data_offset)
+                count=eieio_header.count, offset=data_offset).astype(uint32)
             keys = numpy.bitwise_and(keys, inv_colour_mask)
             local_ids = numpy.array([indices[key] for key in keys])
             neuron_ids = slice_ids[local_ids]