Fixes in numpy array alignment

alignedarray.py

@@ -19,16 +19,17 @@ def aligned_empty(shape, byteAlignment=32, dtype=np.float64, byteOffset=0, order
         tmp = np.empty(N * d.itemsize + byteAlignment, dtype=np.uint8)
         address = tmp.__array_interface__['data'][0]
         offset = (byteAlignment - (address + byteOffset) % byteAlignment) % byteAlignment
+        t1 = tmp[offset:offset + N * d.itemsize]
         return tmp[offset:offset + N * d.itemsize].view(dtype=d).reshape(shape, order=order)
     else:
         if order == 'C':
             ndim0 = shape[-1]
             dim0 = -1
-            ndim1 = shape[-2]
+            ndim1 = np.prod(shape[:-1])
         else:
             ndim0 = shape[0]
             dim0 = 0
-            ndim1 = shape[1]
+            ndim1 = np.prod(shape[1:])
         d = np.dtype(dtype)
 
         assert byteAlignment >= d.itemsize and byteAlignment % d.itemsize == 0

datahandling/serial_datahandling.py

@@ -103,6 +103,9 @@ class SerialDataHandling(DataHandling):
         cpuArr = createNumpyArrayWithLayout(layout=layoutTuple, alignment=alignment, byteOffset=byteOffset, **kwargs)
         cpuArr.fill(np.inf)
 
+        if alignment and gpu:
+            raise NotImplementedError("Alignment for GPU fields not supported")
+
         if cpu:
             if name in self.cpuArrays:
                 raise ValueError("CPU Field with this name already exists")
@@ -113,8 +116,7 @@ class SerialDataHandling(DataHandling):
             self.gpuArrays[name] = gpuarray.to_gpu(cpuArr)
 
         assert all(f.name != name for f in self.fields.values()), "Symbolic field with this name already exists"
-        self.fields[name] = Field.createFixedSize(name, shape=kwargs['shape'], indexDimensions=indexDimensions,
-                                                  dtype=kwargs['dtype'], layout=layoutTuple)
+        self.fields[name] = Field.createFromNumpyArray(name, cpuArr, indexDimensions=indexDimensions)
         self.fields[name].latexName = latexName
         return self.fields[name]
 

field.py

@@ -502,7 +502,7 @@ def createNumpyArrayWithLayout(shape, layout, alignment=False, byteOffset=0, **k
     else:
         if alignment is True:
             alignment = 8 * 4
-        res = aligned_empty(shape, alignment, byteOffset=byteOffset)
+        res = aligned_empty(shape, alignment, byteOffset=byteOffset, **kwargs)
 
     for a, b in reversed(swaps):
         res = res.swapaxes(a, b)