From 96425e225765b4bd60e7d4ff9dc726e071d602d1 Mon Sep 17 00:00:00 2001
From: Tamas Gal <tgal@km3net.de>
Date: Thu, 23 Jan 2020 17:42:31 +0100
Subject: [PATCH] Improve performance of bit parsing
---
km3io/daq.py | 36 ++++++++++++++++++++++++------------
tests/test_daq.py | 8 ++++----
2 files changed, 28 insertions(+), 16 deletions(-)
diff --git a/km3io/daq.py b/km3io/daq.py
index dd314f0..f5bad1b 100644
--- a/km3io/daq.py
+++ b/km3io/daq.py
@@ -13,6 +13,8 @@ MINIMAL_RATE_HZ = 2.0e3
MAXIMAL_RATE_HZ = 2.0e6
RATE_FACTOR = np.log(MAXIMAL_RATE_HZ / MINIMAL_RATE_HZ) / 255
+CHANNEL_BITS_TEMPLATE = np.zeros(31, dtype=bool)
+
@nb.vectorize([
nb.int32(nb.int8),
@@ -28,20 +30,30 @@ def get_rate(value):
return MINIMAL_RATE_HZ * np.exp(value * RATE_FACTOR)
-def unpack_bits(value):
- """Helper to unpack bits to bool flags (little endian)
+@nb.guvectorize(
+ "void(i8, b1[:], b1[:])", "(), (n) -> (n)", target="parallel", nopython=True
+ )
+def unpack_bits(value, bits_template, out):
+ """Return a boolean array for a value's bit representation.
+
+ This function also accepts arrays as input, the output shape will be
+ NxM where N is the number of input values and M the length of the
+ ``bits_template`` array, which is just a dummy array, due to the weird
+ signature system of numba.
Parameters
----------
- value : int32
- The integer value to be parsed.
+ value: int or np.array(int) with shape (N,)
+ The binary value of containing the bit information
+ bits_template: np.array() with shape (M,)
+ The template for the output array, the only important is its shape
+
+ Returns
+ -------
+ np.array(bool) either with shape (M,) or (N, M)
"""
- value = np.array(value).astype(np.int32)
- value = value.reshape(-1, 1)
- value = value.view(np.uint8)
- value = np.flip(value, axis=1)
- length = value.shape[0]
- return np.unpackbits(value).reshape(length, -1).astype(bool)
+ for i in range(bits_template.shape[0]):
+ out[30 - i] = value & (1 << i) > 0
def get_channel_flags(value):
@@ -53,8 +65,8 @@ def get_channel_flags(value):
The integer value to be parsed.
"""
channel_bits = np.bitwise_and(value, 0x3FFFFFFF)
- flags = unpack_bits(channel_bits)
- return np.flip(flags, axis=1)[:, :31]
+ flags = unpack_bits(channel_bits, CHANNEL_BITS_TEMPLATE)
+ return np.flip(flags, axis=-1)
def get_number_udp_packets(value):
diff --git a/tests/test_daq.py b/tests/test_daq.py
index 6858cd6..16ed42a 100644
--- a/tests/test_daq.py
+++ b/tests/test_daq.py
@@ -185,7 +185,7 @@ class TestSummaryslices(unittest.TestCase):
}
for dom_id, fifo_status in dct_fifo_stat.items():
frame = s[s.dom_id == dom_id]
- assert any(get_channel_flags(frame.fifo[0])[0]) == fifo_status
+ assert any(get_channel_flags(frame.fifo[0])) == fifo_status
def test_has_udp_trailer(self):
s = self.ss.slices[0]
@@ -244,7 +244,7 @@ class TestSummaryslices(unittest.TestCase):
}
for dom_id, high_rate_veto in dct_high_rate_veto.items():
frame = s[s.dom_id == dom_id]
- assert any(get_channel_flags(frame.hrv[0])[0]) == high_rate_veto
+ assert any(get_channel_flags(frame.hrv[0])) == high_rate_veto
def test_max_sequence_number(self):
s = self.ss.slices[0]
@@ -344,7 +344,7 @@ class TestSummaryslices(unittest.TestCase):
frame = s[s.dom_id == dom_id]
assert any([
a == b
- for a, b in zip(get_channel_flags(frame.hrv[0])[0], hrv_flags)
+ for a, b in zip(get_channel_flags(frame.hrv[0]), hrv_flags)
])
def test_fifo_flags(self):
@@ -391,7 +391,7 @@ class TestSummaryslices(unittest.TestCase):
frame = s[s.dom_id == dom_id]
assert any([
a == b for a, b in zip(
- get_channel_flags(frame.fifo[0])[0], fifo_flags)
+ get_channel_flags(frame.fifo[0]), fifo_flags)
])
--
GitLab