From c23dfc1fcfee6285287029796ddbec6201199f19 Mon Sep 17 00:00:00 2001
From: Philipp Schmidt <philipp.schmidt@xfel.eu>
Date: Wed, 11 May 2022 15:55:52 +0200
Subject: [PATCH] Add native implementation for LPD correction loop
---
setup.py | 7 ++++
src/cal_tools/lpdalgs.pyx | 72 +++++++++++++++++++++++++++++++++++++++
2 files changed, 79 insertions(+)
create mode 100644 src/cal_tools/lpdalgs.pyx
diff --git a/setup.py b/setup.py
index 42847f5dc..bc5896c9b 100644
--- a/setup.py
+++ b/setup.py
@@ -18,6 +18,13 @@ ext_modules = [
extra_compile_args=["-fopenmp", "-march=native"],
extra_link_args=["-fopenmp"],
),
+ Extension(
+ 'cal_tools.lpdalgs',
+ ['src/cal_tools/lpdalgs.pyx'],
+ include_dirs=[numpy.get_include()],
+ extra_compile_args=['-O3', '-fopenmp', '-march=native'],
+ extra_link_args=['-fopenmp'],
+ )
]
diff --git a/src/cal_tools/lpdalgs.pyx b/src/cal_tools/lpdalgs.pyx
new file mode 100644
index 000000000..635dc07de
--- /dev/null
+++ b/src/cal_tools/lpdalgs.pyx
@@ -0,0 +1,72 @@
+from cython cimport boundscheck, wraparound, cdivision
+from cython.view cimport contiguous
+from cython.parallel cimport prange
+
+from cal_tools.enums import BadPixels
+
+ctypedef unsigned short cell_t
+ctypedef unsigned short data_t
+ctypedef float pixel_t
+ctypedef unsigned char gain_t
+ctypedef unsigned int mask_t
+
+cdef mask_t WRONG_GAIN_VALUE = BadPixels.WRONG_GAIN_VALUE, \
+ VALUE_OUT_OF_RANGE = BadPixels.VALUE_OUT_OF_RANGE, \
+ VALUE_IS_NAN = BadPixels.VALUE_IS_NAN
+
+
+@boundscheck(False)
+@wraparound(False)
+@cdivision(True)
+def correct_lpd_frames(
+ # (pulse, x, y)
+ data_t[:, :, ::contiguous] in_data,
+ cell_t[::contiguous] in_cell,
+
+ # (pulse, x, y)
+ pixel_t[:, :, ::contiguous] out_pixels,
+ gain_t[:, :, ::contiguous] out_gain,
+ mask_t[:, :, ::contiguous] out_mask,
+
+ # (x, y, cell, gain)
+ float[:, :, :, ::contiguous] ccv_offset,
+ float[:, :, :, ::contiguous] ccv_gain,
+ mask_t[:, :, :, ::contiguous] ccv_mask,
+
+ int num_threads=1,
+):
+ cdef int frame, ss, fs
+ cdef cell_t cell
+ cdef pixel_t pixel
+ cdef gain_t gain
+ cdef mask_t mask
+
+ for frame in prange(in_data.shape[0], nogil=True, num_threads=num_threads):
+ for ss in range(in_data.shape[1]):
+ for fs in range(in_data.shape[2]):
+ cell = in_cell[frame]
+ pixel = <pixel_t>(in_data[frame, ss, fs] & 0b0000111111111111)
+ gain = in_data[frame, ss, fs] & 0b0000000000000011
+
+ if gain <= 2:
+ mask = ccv_mask[ss, fs, cell, gain]
+ else:
+ pixel = 0.0
+ gain = 0
+ mask = WRONG_GAIN_VALUE
+
+ pixel = pixel - ccv_offset[ss, fs, cell, gain]
+
+ if ccv_gain[ss, fs, cell, gain] != 0.0:
+ pixel = pixel * ccv_gain[ss, fs, cell, gain]
+ else:
+ pixel = 0.0
+ mask = mask | VALUE_IS_NAN
+
+ if pixel > 1e7 or pixel < -1e7:
+ pixel = 0.0
+ mask = mask | VALUE_OUT_OF_RANGE
+
+ out_pixels[frame, ss, fs] = pixel
+ out_gain[frame, ss, fs] = gain
+ out_mask[frame, ss, fs] = mask
--
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