Add Roman jump detection to ramp fitting (#215)

.gitignore

@@ -139,6 +139,9 @@ dmypy.json
 
 # Cython debug symbols
 cython_debug/
+src/stcal/ramp_fitting/ols_cas22/*.c
+src/stcal/ramp_fitting/ols_cas22/*.cpp
+src/stcal/ramp_fitting/ols_cas22/*.html
 
 # setuptools-scm generated module
 src/stcal/_version.py

CHANGES.rst

@@ -3,6 +3,12 @@
 
 - Added ``alignment`` sub-package. [#179]
 
+ramp_fitting
+------------
+
+- Refactor Casertano, et.al, 2022 uneven ramp fitting and incorporate the matching
+  jump detection algorithm into it. [#215]
+
 Changes to API
 --------------
 

setup.py

@@ -6,9 +6,31 @@
 Options.docstrings = True
 Options.annotate = False
 
-extensions = [Extension('stcal.ramp_fitting.ols_cas22',
-                        ['src/stcal/ramp_fitting/ols_cas22.pyx'],
-                        include_dirs=[np.get_include()],
-                        extra_compile_args=['-std=c99'])]
+extensions = [
+    Extension(
+        'stcal.ramp_fitting.ols_cas22._core',
+        ['src/stcal/ramp_fitting/ols_cas22/_core.pyx'],
+        include_dirs=[np.get_include()],
+        language='c++'
+    ),
+    Extension(
+        'stcal.ramp_fitting.ols_cas22._fixed',
+        ['src/stcal/ramp_fitting/ols_cas22/_fixed.pyx'],
+        include_dirs=[np.get_include()],
+        language='c++'
+    ),
+    Extension(
+        'stcal.ramp_fitting.ols_cas22._pixel',
+        ['src/stcal/ramp_fitting/ols_cas22/_pixel.pyx'],
+        include_dirs=[np.get_include()],
+        language='c++'
+    ),
+    Extension(
+        'stcal.ramp_fitting.ols_cas22._fit_ramps',
+        ['src/stcal/ramp_fitting/ols_cas22/_fit_ramps.pyx'],
+        include_dirs=[np.get_include()],
+        language='c++'
+    ),
+]
 
 setup(ext_modules=cythonize(extensions))

src/stcal/ramp_fitting/ols_cas22/__init__.py

@@ -0,0 +1,4 @@
+from ._fit_ramps import fit_ramps, RampFitOutputs
+from ._core import Parameter, Variance, Diff, RampJumpDQ
+
+__all__ = ['fit_ramps', 'RampFitOutputs', 'Parameter', 'Variance', 'Diff', 'RampJumpDQ']

src/stcal/ramp_fitting/ols_cas22/_core.pxd

@@ -0,0 +1,58 @@
+from libcpp.vector cimport vector
+from libcpp.stack cimport stack
+from libcpp.deque cimport deque
+
+
+cdef struct RampIndex:
+    int start
+    int end
+
+
+cdef struct RampFit:
+    float slope
+    float read_var
+    float poisson_var
+
+
+cdef struct RampFits:
+    vector[RampFit] fits
+    vector[RampIndex] index
+    vector[int] jumps
+    RampFit average
+
+
+cdef struct ReadPatternMetadata:
+    vector[float] t_bar
+    vector[float] tau
+    vector[int] n_reads
+
+
+cdef struct Thresh:
+    float intercept
+    float constant
+
+
+cpdef enum Diff:
+    single = 0
+    double = 1
+
+
+cpdef enum Parameter:
+    intercept = 0
+    slope = 1
+
+
+cpdef enum Variance:
+    read_var = 0
+    poisson_var = 1
+    total_var = 2
+
+
+cpdef enum RampJumpDQ:
+    JUMP_DET = 4
+
+
+cpdef float threshold(Thresh thresh, float slope)
+cdef float get_power(float s)
+cdef deque[stack[RampIndex]] init_ramps(int[:, :] dq)
+cpdef ReadPatternMetadata metadata_from_read_pattern(list[list[int]] read_pattern, float read_time)