From 9887e2d3749b0e2df53570490a04709c6af2dfbb Mon Sep 17 00:00:00 2001
From: Eduardo Gonzalez Solares <eglez@ast.cam.ac.uk>
Date: Thu, 9 May 2019 16:03:21 +0100
Subject: [PATCH] Cythonize get_coords function
---
.gitignore | 1 +
setup.py | 3 ++
stpt_pipeline/settings.py | 2 +-
stpt_pipeline/stpt_displacement.py | 46 ------------------------------
stpt_pipeline/utils.pyx | 37 ++++++++++++++++++++++++
5 files changed, 42 insertions(+), 47 deletions(-)
create mode 100644 stpt_pipeline/utils.pyx
diff --git a/.gitignore b/.gitignore
index 4542d77..d4f6506 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,6 +5,7 @@ __pycache__/
# C extensions
*.so
+utils.c
# Distribution / packaging
.Python
diff --git a/setup.py b/setup.py
index 8d9e046..4f2224a 100644
--- a/setup.py
+++ b/setup.py
@@ -1,3 +1,5 @@
+from Cython.Build import cythonize
+from setuptools.extension import Extension
from setuptools import find_packages, setup
with open('README.rst') as readme_file:
@@ -32,6 +34,7 @@ setup(
keywords='stpt_pipeline',
name='stpt_pipeline',
packages=find_packages(include=['stpt_pipeline']),
+ ext_modules=cythonize(Extension('stpt_pipeline.utils', ['stpt_pipeline/utils.pyx'])),
setup_requires=setup_requirements,
test_suite='tests',
tests_require=test_requirements,
diff --git a/stpt_pipeline/settings.py b/stpt_pipeline/settings.py
index 0df7039..fe613b0 100644
--- a/stpt_pipeline/settings.py
+++ b/stpt_pipeline/settings.py
@@ -25,4 +25,4 @@ class Settings:
do_flat = True
do_defringe = False
channel_to_use = 4
- cof_dist = np.array([3.93716645e-05, -7.37696218e-02, 2.52457306e01]) / 2.0
+ cof_dist = (3.93716645e-05 / 2, -7.37696218e-02 / 2, 2.52457306e01 / 2)
diff --git a/stpt_pipeline/stpt_displacement.py b/stpt_pipeline/stpt_displacement.py
index 1f7b53b..91d0b1d 100644
--- a/stpt_pipeline/stpt_displacement.py
+++ b/stpt_pipeline/stpt_displacement.py
@@ -60,52 +60,6 @@ def defringe(img):
return fr_img
-#
-# Â get_coords is the function that feeds geometric_transform
-# in order to correct for the optical distortion of the detector.
-#
-def get_coords(coords, cof, center_x, max_x, direct=True):
- """[summary]
-
- Parameters
- ----------
- coords : [type]
- [description]
- cof : [type]
- [description]
- center_x : [type]
- [description]
- max_x : [type]
- [description]
- direct : bool, optional
- [description], by default True
-
- Returns
- -------
- [type]
- [description]
- """
- max_desp = cof[0] * coords[1] ** 2 + cof[1] * coords[1] + cof[2]
- dy_cof = max_desp / (max_x - center_x) ** 2
- if direct:
- if coords[0] > center_x:
- sign = 1
- else:
- sign = -1
- xi = np.abs(coords[0] - center_x)
- return (center_x + sign * (xi + dy_cof * xi ** 2), coords[1])
- else:
- if coords[0] > center_x + cof[2]:
- sign = 1
- else:
- sign = -1
- xi = np.abs(coords[0] - center_x - cof[2])
- return (
- center_x + sign * (np.sqrt(1 + 4 * dy_cof * xi) - 1) / (2 * dy_cof),
- coords[1],
- )
-
-
def magic_function(x, flat=1): # TODO: Call this some other name
"""[summary]
diff --git a/stpt_pipeline/utils.pyx b/stpt_pipeline/utils.pyx
new file mode 100644
index 0000000..d54b9cc
--- /dev/null
+++ b/stpt_pipeline/utils.pyx
@@ -0,0 +1,37 @@
+from libc.math cimport abs
+
+def get_coords(tuple coords, tuple cof, float center_x, float max_x):
+ """[summary]
+
+ Parameters
+ ----------
+ coords : [type]
+ [description]
+ cof : [type]
+ [description]
+ center_x : [type]
+ [description]
+ max_x : [type]
+ [description]
+
+ Returns
+ -------
+ [type]
+ [description]
+ """
+ cdef float max_desp, dy_cof, xi, r0, r1
+ cdef int c0, c1, sign
+ cdef tuple res
+ c0 = coords[0]
+ c1 = coords[1]
+ max_desp = cof[0] * c1 ** 2 + cof[1] * c1 + cof[2]
+ dy_cof = max_desp / (max_x - center_x) ** 2
+ if c0 > center_x:
+ sign = 1
+ else:
+ sign = -1
+ xi = abs(c0 - center_x)
+ r0 = center_x + sign * (xi + dy_cof * xi ** 2)
+ res = (r0, c1)
+ return res
+
\ No newline at end of file
--
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