From 4eb78216789fb125f983ca57ddaa11a044b44da4 Mon Sep 17 00:00:00 2001
From: David Hammer <dhammer@mailbox.org>
Date: Tue, 27 Jun 2023 15:59:21 +0200
Subject: [PATCH] Use faster common mode (row / col) for ePix100, too
---
src/calng/corrections/Epix100Correction.py | 19 ++++++++-----------
src/calng/corrections/PnccdCorrection.py | 5 +++--
src/calng/kernels/common_cpu.pyx | 12 ++++++------
src/tests/test_pnccd_kernels.py | 1 -
4 files changed, 17 insertions(+), 20 deletions(-)
diff --git a/src/calng/corrections/Epix100Correction.py b/src/calng/corrections/Epix100Correction.py
index 98411ecd..9c7df5c2 100644
--- a/src/calng/corrections/Epix100Correction.py
+++ b/src/calng/corrections/Epix100Correction.py
@@ -21,6 +21,7 @@ from .. import (
utils,
)
from .._version import version as deviceVersion
+from ..kernels import common_cython
class Constants(enum.Enum):
@@ -251,11 +252,11 @@ class Epix100CpuRunner(base_kernel_runner.BaseKernelRunner):
if flags & CorrectionFlags.COMMONMODE:
# per rectangular block that looks like something is going on
- masked = np.ma.masked_array(
- data=output,
- mask=(self._q_bad_pixel_map[q] != 0)
- | (output > self._q_noise_map[q] * cm_noise_sigma),
- )
+ cm_mask=(
+ (self._q_bad_pixel_map[q] != 0)
+ | (output > self._q_noise_map[q] * cm_noise_sigma)
+ ).astype(np.uint8, copy=False)
+ masked = np.ma.masked_array(data=output, mask=cm_mask)
if cm_block:
for block in np.hsplit(masked, 4):
if block.count() < block.size * cm_min_frac:
@@ -263,14 +264,10 @@ class Epix100CpuRunner(base_kernel_runner.BaseKernelRunner):
block.data[:] -= np.ma.median(block)
if cm_row:
- subset_rows = masked.count(axis=1) >= masked.shape[1] * cm_min_frac
- output[subset_rows] -= np.ma.median(
- masked[subset_rows], axis=1, keepdims=True
- )
+ common_cython.cm_fs(output, cm_mask, cm_noise_sigma, cm_min_frac)
if cm_col:
- subset_cols = masked.count(axis=0) >= masked.shape[0] * cm_min_frac
- output[:, subset_cols] -= np.ma.median(masked[:, subset_cols], axis=0)
+ common_cython.cm_ss(output, cm_mask, cm_noise_sigma, cm_min_frac)
if flags & CorrectionFlags.RELGAIN:
output *= self._q_rel_gain_map[q]
diff --git a/src/calng/corrections/PnccdCorrection.py b/src/calng/corrections/PnccdCorrection.py
index 36b8ee15..4a8c1491 100644
--- a/src/calng/corrections/PnccdCorrection.py
+++ b/src/calng/corrections/PnccdCorrection.py
@@ -259,8 +259,9 @@ class PnccdCpuRunner(base_kernel_runner.BaseKernelRunner):
output -= self._q_offset_map[q]
if flags & CorrectionFlags.COMMONMODE:
- cm_mask = (self._q_bad_pixel_map[q] != 0) | (
- output > self._q_noise_map[q] * cm_noise_sigma
+ cm_mask = (
+ (self._q_bad_pixel_map[q] != 0)
+ | (output > self._q_noise_map[q] * cm_noise_sigma)
).astype(np.uint8, copy=False)
if cm_row:
common_cython.cm_fs(
diff --git a/src/calng/kernels/common_cpu.pyx b/src/calng/kernels/common_cpu.pyx
index fc61d6d0..893015f2 100644
--- a/src/calng/kernels/common_cpu.pyx
+++ b/src/calng/kernels/common_cpu.pyx
@@ -48,7 +48,7 @@ def cm_ss(
float ratio,
):
# transposing to give std::nth_element contiguous input
- cdef float[:, ::1] a = np.empty_like(np.transpose(data), order="C")
+ cdef float[:, ::1] aux = np.empty_like(np.transpose(data), order="C")
cdef int num_dark, min_dark, i, j, k
cdef float median
min_dark = <int>(<float>data.shape[1] * ratio)
@@ -56,15 +56,15 @@ def cm_ss(
num_dark = 0
for i in range(data.shape[0]):
if mask[i, j] == 0:
- a[j, num_dark] = data[i, j]
+ aux[j, num_dark] = data[i, j]
num_dark = num_dark + 1
if num_dark < min_dark:
continue
k = num_dark // 2
- nth_element(&a[j, 0], (&a[j, 0]) + k, (&a[j, 0]) + <int>num_dark)
- median = a[j, k]
+ nth_element(&aux[j, 0], (&aux[j, 0]) + k, (&aux[j, 0]) + <int>num_dark)
+ median = aux[j, k]
if num_dark % 2 == 0:
- nth_element(&a[j, 0], (&a[j, 0]) + k - 1, (&a[j, 0]) + <int>num_dark)
- median = median / 2 + a[j, k - 1] / 2
+ nth_element(&aux[j, 0], (&aux[j, 0]) + k - 1, (&aux[j, 0]) + <int>num_dark)
+ median = median / 2 + aux[j, k - 1] / 2
for i in range(data.shape[0]):
data[i, j] = data[i, j] - median
diff --git a/src/tests/test_pnccd_kernels.py b/src/tests/test_pnccd_kernels.py
index 470eb025..18f438fa 100644
--- a/src/tests/test_pnccd_kernels.py
+++ b/src/tests/test_pnccd_kernels.py
@@ -20,7 +20,6 @@ def test_common_mode():
subset_ss = masked.count(axis=0) >= masked.shape[0] * cm_min_frac
data[:, subset_ss] -= np.ma.median(masked[:, subset_ss], axis=0)
-
data_shape = (1024, 1024)
data = (np.random.random(data_shape) * 1000).astype(np.uint16)
runner = PnccdCpuRunner(1024, 1024, 1, 1)
--
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