Fix some type issues.

16 files changed, 44 insertions, 44 deletions

diff --git a/pyecsca/sca/scope/picoscope_sdk.py b/pyecsca/sca/scope/picoscope_sdk.py
index b21df09..a198367 100644
--- a/pyecsca/sca/scope/picoscope_sdk.py
+++ b/pyecsca/sca/scope/picoscope_sdk.py
@@ -159,6 +159,8 @@ class PicoScopeSdk(Scope):  # pragma: no cover
         return True
 
     def retrieve(self, channel: str) -> Optional[np.ndarray]:
+        if self.samples is None:
+            raise ValueError
         actual_samples = ctypes.c_int32(self.samples)
         overflow = ctypes.c_int16()
         assert_pico_ok(
@@ -179,6 +181,7 @@ class PicoScopeSdk(Scope):  # pragma: no cover
             raise ValueError
         return method(*args, **kwargs)
 
+
 @public
 class PS5000Scope(PicoScopeSdk):  # pragma: no cover
     MODULE = ps5000
diff --git a/pyecsca/sca/target/binary.py b/pyecsca/sca/target/binary.py
index 9a469b6..cb4c918 100644
--- a/pyecsca/sca/target/binary.py
+++ b/pyecsca/sca/target/binary.py
@@ -14,7 +14,7 @@ class BinaryTarget(SerialTarget):
     debug_output: bool
 
     def __init__(self, binary: Union[str, List[str]], debug_output: bool = False, **kwargs):
-        super().__init__(**kwargs)
+        super().__init__()
         if not isinstance(binary, (str, list)):
             raise TypeError
         if isinstance(binary, str):
@@ -34,7 +34,7 @@ class BinaryTarget(SerialTarget):
         self.process.stdin.write(data.decode())
         self.process.stdin.flush()
 
-    def read(self, num: Optional[int] = 0, timeout: Optional[int] = 0) -> bytes:
+    def read(self, num: int = 0, timeout: int = 0) -> bytes:
         if self.process is None:
             raise ValueError
         if num != 0:
diff --git a/pyecsca/sca/target/chipwhisperer.py b/pyecsca/sca/target/chipwhisperer.py
index 3710195..3dd5686 100644
--- a/pyecsca/sca/target/chipwhisperer.py
+++ b/pyecsca/sca/target/chipwhisperer.py
@@ -36,7 +36,7 @@ class ChipWhispererTarget(Flashable, SimpleSerialTarget):  # pragma: no cover
         self.target.flush()
         self.target.write(data.decode())
 
-    def read(self, num: Optional[int] = 0, timeout: Optional[int] = 0) -> bytes:
+    def read(self, num: int = 0, timeout: int = 0) -> bytes:
         return self.target.read(num, timeout).encode()
 
     def reset(self):
diff --git a/pyecsca/sca/target/flash.py b/pyecsca/sca/target/flash.py
index be3cfb0..bfdb79f 100644
--- a/pyecsca/sca/target/flash.py
+++ b/pyecsca/sca/target/flash.py
@@ -8,4 +8,4 @@ class Flashable(ABC):
 
     @abstractmethod
     def flash(self, fw_path: str) -> bool:
-        ...
\ No newline at end of file
+        ...
diff --git a/pyecsca/sca/target/serial.py b/pyecsca/sca/target/serial.py
index 3c0b5c4..ccde326 100644
--- a/pyecsca/sca/target/serial.py
+++ b/pyecsca/sca/target/serial.py
@@ -14,5 +14,5 @@ class SerialTarget(Target):
         ...
 
     @abstractmethod
-    def read(self, num: Optional[int] = 0, timeout: Optional[int] = 0) -> bytes:
+    def read(self, num: int = 0, timeout: int = 0) -> bytes:
         ...
diff --git a/pyecsca/sca/target/simpleserial.py b/pyecsca/sca/target/simpleserial.py
index 9e26b79..1ad0b68 100644
--- a/pyecsca/sca/target/simpleserial.py
+++ b/pyecsca/sca/target/simpleserial.py
@@ -63,7 +63,7 @@ class SimpleSerialTarget(SerialTarget):
         """
         data = bytes(cmd)
         for i in range(0, len(data), 64):
-            chunk = data[i:i+64]
+            chunk = data[i:i + 64]
             sleep(0.010)
             self.write(chunk)
         self.write(b"\n")
diff --git a/pyecsca/sca/trace/align.py b/pyecsca/sca/trace/align.py
index 643efcf..1c9c216 100644
--- a/pyecsca/sca/trace/align.py
+++ b/pyecsca/sca/trace/align.py
@@ -27,7 +27,7 @@ def align_reference(reference: Trace, *traces: Trace,
                 result_samples[:length - offset] = trace.samples[offset:]
             else:
                 result_samples[-offset:] = trace.samples[:length + offset]
-        result.append(Trace(copy(trace.title), copy(trace.data), result_samples))
+        result.append(Trace(result_samples, copy(trace.title), copy(trace.data)))
     return result
 
 
@@ -198,7 +198,7 @@ def align_dtw_scale(reference: Trace, *traces: Trace, radius: int = 1,
             scale[x] += 1
         result_samples //= scale
         del scale
-        result.append(Trace(copy(trace.title), copy(trace.data), result_samples))
+        result.append(Trace(result_samples, copy(trace.title), copy(trace.data)))
     return result
 
 
@@ -233,5 +233,5 @@ def align_dtw(reference: Trace, *traces: Trace, radius: int = 1, fast: bool = Tr
         # or manually:
         # for x, y in path:
         #    result_samples[x] = trace.samples[y]
-        result.append(Trace(copy(trace.title), copy(trace.data), result_samples))
+        result.append(Trace(result_samples, copy(trace.title), copy(trace.data)))
     return result
diff --git a/pyecsca/sca/trace/combine.py b/pyecsca/sca/trace/combine.py
index c484748..2ab552a 100644
--- a/pyecsca/sca/trace/combine.py
+++ b/pyecsca/sca/trace/combine.py
@@ -16,10 +16,10 @@ def average(*traces: Trace) -> Optional[CombinedTrace]:
     if not traces:
         return None
     if len(traces) == 1:
-        return CombinedTrace(None, None, traces[0].samples.copy(), parents=traces)
+        return CombinedTrace(traces[0].samples.copy(), None, None)
     dtype = traces[0].samples.dtype
     result_samples = np.mean(np.array([trace.samples for trace in traces]), axis=0).astype(dtype)
-    return CombinedTrace(None, None, result_samples, parents=traces)
+    return CombinedTrace(result_samples, None, None)
 
 
 @public
@@ -46,4 +46,4 @@ def standard_deviation(*traces: Trace) -> Optional[CombinedTrace]:
         return None
     dtype = traces[0].samples.dtype
     result_samples = np.std(np.array([trace.samples for trace in traces]), axis=0).astype(dtype)
-    return CombinedTrace(None, None, result_samples, parents=traces)
+    return CombinedTrace(result_samples, None, None)
diff --git a/pyecsca/sca/trace/edit.py b/pyecsca/sca/trace/edit.py
index f01a0dc..f58ad57 100644
--- a/pyecsca/sca/trace/edit.py
+++ b/pyecsca/sca/trace/edit.py
@@ -22,7 +22,7 @@ def trim(trace: Trace, start: int = None, end: int = None) -> Trace:
         end = len(trace.samples)
     if start > end:
         raise ValueError("Invalid trim arguments.")
-    return Trace(copy(trace.title), copy(trace.data), trace.samples[start:end].copy())
+    return Trace(trace.samples[start:end].copy(), copy(trace.title), copy(trace.data))
 
 
 @public
@@ -33,7 +33,7 @@ def reverse(trace: Trace) -> Trace:
     :param trace:
     :return:
     """
-    return Trace(copy(trace.title), copy(trace.data), np.flipud(trace.samples))
+    return Trace(np.flipud(trace.samples), copy(trace.title), copy(trace.data))
 
 
 @public
@@ -51,5 +51,5 @@ def pad(trace: Trace, lengths: Union[Tuple[int, int], int],
         lengths = (lengths, lengths)
     if not isinstance(values, tuple):
         values = (values, values)
-    return Trace(copy(trace.title), copy(trace.data),
-                 np.pad(trace.samples, lengths, "constant", constant_values=values))
+    return Trace(np.pad(trace.samples, lengths, "constant", constant_values=values),
+                 copy(trace.title), copy(trace.data))
diff --git a/pyecsca/sca/trace/filter.py b/pyecsca/sca/trace/filter.py
index 11cc89c..6bb17b9 100644
--- a/pyecsca/sca/trace/filter.py
+++ b/pyecsca/sca/trace/filter.py
@@ -14,7 +14,7 @@ def filter_any(trace: Trace, sampling_frequency: int,
     else:
         b, a = butter(6, cutoff / nyq, btype=band_type, analog=False, output='ba')
     result_samples = lfilter(b, a, trace.samples)
-    return Trace(copy(trace.title), copy(trace.data), result_samples)
+    return Trace(result_samples, copy(trace.title), copy(trace.data))
 
 
 @public
diff --git a/pyecsca/sca/trace/process.py b/pyecsca/sca/trace/process.py
index 8e983b2..4cdbeff 100644
--- a/pyecsca/sca/trace/process.py
+++ b/pyecsca/sca/trace/process.py
@@ -13,7 +13,7 @@ def absolute(trace: Trace) -> Trace:
     :param trace:
     :return:
     """
-    return Trace(copy(trace.title), copy(trace.data), np.absolute(trace.samples))
+    return Trace(np.absolute(trace.samples), copy(trace.title), copy(trace.data))
 
 
 @public
@@ -24,7 +24,7 @@ def invert(trace: Trace) -> Trace:
     :param trace:
     :return:
     """
-    return Trace(copy(trace.title), copy(trace.data), np.negative(trace.samples))
+    return Trace(np.negative(trace.samples), copy(trace.title), copy(trace.data))
 
 
 @public
@@ -39,7 +39,7 @@ def threshold(trace: Trace, value) -> Trace:
     result_samples = trace.samples.copy()
     result_samples[result_samples <= value] = 0
     result_samples[np.nonzero(result_samples)] = 1
-    return Trace(copy(trace.title), copy(trace.data), result_samples)
+    return Trace(result_samples, copy(trace.title), copy(trace.data))
 
 
 def rolling_window(samples: np.ndarray, window: int) -> np.ndarray:
@@ -57,9 +57,8 @@ def rolling_mean(trace: Trace, window: int) -> Trace:
     :param window:
     :return:
     """
-    return Trace(copy(trace.title), copy(trace.data),
-                 np.mean(rolling_window(trace.samples, window), -1).astype(
-                         dtype=trace.samples.dtype))
+    return Trace(np.mean(rolling_window(trace.samples, window), -1).astype(
+            dtype=trace.samples.dtype), copy(trace.title), copy(trace.data))
 
 
 @public
@@ -71,7 +70,7 @@ def offset(trace: Trace, offset) -> Trace:
     :param offset:
     :return:
     """
-    return Trace(copy(trace.title), copy(trace.data), trace.samples + offset)
+    return Trace(trace.samples + offset, copy(trace.title), copy(trace.data))
 
 
 def root_mean_square(trace: Trace):
@@ -92,12 +91,11 @@ def recenter(trace: Trace) -> Trace:
 
 @public
 def normalize(trace: Trace) -> Trace:
-    return Trace(copy(trace.title), copy(trace.data),
-                 (trace.samples - np.mean(trace.samples)) / np.std(trace.samples))
+    return Trace((trace.samples - np.mean(trace.samples)) / np.std(trace.samples),
+                 copy(trace.title), copy(trace.data))
 
 
 @public
 def normalize_wl(trace: Trace) -> Trace:
-    return Trace(copy(trace.title), copy(trace.data),
-                 (trace.samples - np.mean(trace.samples)) / (
-                         np.std(trace.samples) * len(trace.samples)))
+    return Trace((trace.samples - np.mean(trace.samples)) / (
+            np.std(trace.samples) * len(trace.samples)), copy(trace.title), copy(trace.data))
diff --git a/pyecsca/sca/trace/sampling.py b/pyecsca/sca/trace/sampling.py
index 29dc251..fdd5e5b 100644
--- a/pyecsca/sca/trace/sampling.py
+++ b/pyecsca/sca/trace/sampling.py
@@ -18,7 +18,7 @@ def downsample_average(trace: Trace, factor: int = 2) -> Trace:
     """
     resized = np.resize(trace.samples, len(trace.samples) - (len(trace.samples) % factor))
     result_samples = resized.reshape(-1, factor).mean(axis=1).astype(trace.samples.dtype)
-    return Trace(copy(trace.title), copy(trace.data), result_samples)
+    return Trace(result_samples, copy(trace.title), copy(trace.data))
 
 
 @public
@@ -32,7 +32,7 @@ def downsample_pick(trace: Trace, factor: int = 2, offset: int = 0) -> Trace:
     :return:
     """
     result_samples = trace.samples[offset::factor].copy()
-    return Trace(copy(trace.title), copy(trace.data), result_samples)
+    return Trace(result_samples, copy(trace.title), copy(trace.data))
 
 
 @public
@@ -45,4 +45,4 @@ def downsample_decimate(trace: Trace, factor: int = 2) -> Trace:
     :return:
     """
     result_samples = decimate(trace.samples, factor)
-    return Trace(copy(trace.title), copy(trace.data), result_samples)
+    return Trace(result_samples, copy(trace.title), copy(trace.data))
diff --git a/pyecsca/sca/trace/test.py b/pyecsca/sca/trace/test.py
index f2cfb33..4fc0236 100644
--- a/pyecsca/sca/trace/test.py
+++ b/pyecsca/sca/trace/test.py
@@ -14,7 +14,7 @@ def ttest_func(first_set: Sequence[Trace], second_set: Sequence[Trace],
     first_stack = np.stack([first.samples for first in first_set])
     second_stack = np.stack([second.samples for second in second_set])
     result = ttest_ind(first_stack, second_stack, axis=0, equal_var=equal_var)
-    return CombinedTrace(None, None, result[0], parents=[*first_set, *second_set])
+    return CombinedTrace(result[0], None, None)
 
 
 @public
@@ -61,4 +61,4 @@ def ks_test(first_set: Sequence[Trace], second_set: Sequence[Trace]) -> Optional
     results = np.empty(len(first_set[0].samples), dtype=first_set[0].samples.dtype)
     for i in range(len(first_set[0].samples)):
         results[i] = ks_2samp(first_stack[..., i], second_stack[..., i])[0]
-    return CombinedTrace(None, None, results, parents=[*first_set, *second_set])
+    return CombinedTrace(results, None, None)
diff --git a/pyecsca/sca/trace/trace.py b/pyecsca/sca/trace/trace.py
index 5324a37..18df978 100644
--- a/pyecsca/sca/trace/trace.py
+++ b/pyecsca/sca/trace/trace.py
@@ -11,8 +11,8 @@ class Trace(object):
     data: Optional[bytes]
     samples: ndarray
 
-    def __init__(self, title: Optional[str], data: Optional[bytes],
-                 samples: ndarray, trace_set: Any = None):
+    def __init__(self, samples: ndarray, title: Optional[str], data: Optional[bytes],
+                 trace_set: Any = None):
         self.title = title
         self.data = data
         self.samples = samples
@@ -39,9 +39,9 @@ class Trace(object):
 class CombinedTrace(Trace):
     """A power trace that was combined from other traces, `parents`."""
 
-    def __init__(self, title: Optional[str], data: Optional[bytes],
-                 samples: ndarray, trace_set=None, parents: Sequence[Trace] = None):
-        super().__init__(title, data, samples, trace_set=trace_set)
+    def __init__(self, samples: ndarray, title: Optional[str], data: Optional[bytes],
+                 trace_set=None, parents: Sequence[Trace] = None):
+        super().__init__(samples, title, data, trace_set=trace_set)
         self.parents = None
         if parents is not None:
             self.parents = weakref.WeakSet(parents)
diff --git a/pyecsca/sca/trace_set/chipwhisperer.py b/pyecsca/sca/trace_set/chipwhisperer.py
index d9dcf3f..2b37c6f 100644
--- a/pyecsca/sca/trace_set/chipwhisperer.py
+++ b/pyecsca/sca/trace_set/chipwhisperer.py
@@ -17,7 +17,7 @@ class ChipWhispererTraceSet(TraceSet):
         else:
             data = self.__read_data(path, name)
             trace_data = data["traces"]
-            traces = [Trace(None, None, trace_samples, trace_set=self) for trace_samples in trace_data]
+            traces = [Trace(trace_samples, None, None, trace_set=self) for trace_samples in trace_data]
             del data["traces"]
             config = self.__read_config(path, name)
             super().__init__(*traces, **data, **config)
diff --git a/pyecsca/sca/trace_set/inspector.py b/pyecsca/sca/trace_set/inspector.py
index f9475c0..b07313d 100644
--- a/pyecsca/sca/trace_set/inspector.py
+++ b/pyecsca/sca/trace_set/inspector.py
@@ -197,7 +197,7 @@ class InspectorTraceSet(TraceSet):
                 samples = np.frombuffer(
                         file.read(dtype.itemsize * self.num_samples), dtype,
                         self.num_samples)
-            result.append(Trace(title, data, samples, trace_set=self))
+            result.append(Trace(samples, title, data, trace_set=self))
         return result
 
     def __write(self, file):
@@ -229,9 +229,8 @@ class InspectorTraceSet(TraceSet):
                 file.write(trace.samples.tobytes())
 
     def __scale(self, traces):
-        return list(map(lambda trace: Trace(trace.title, trace.data,
-                                            trace.samples.astype("f4") * self.y_scale,
-                                            trace_set=self),
+        return list(map(lambda trace: Trace(trace.samples.astype("f4") * self.y_scale, trace.title,
+                                            trace.data, trace_set=self),
                         traces))
 
     def save(self, output: Union[Path, str, BinaryIO]):