Fix integration with rest of stcal

src/stcal/ramp_fitting/ols_cas22/_fit_ramps.pyx

@@ -34,8 +34,8 @@ def fit_ramps(np.ndarray[float, ndim=2] resultants,
         the resultants in electrons
     dq : np.ndarry[n_resultants, n_pixel]
         the dq array.  dq != 0 implies bad pixel / CR.
-    read noise : float
-        the read noise in electrons
+    read_noise : np.ndarray[n_pixel]
+        the read noise in electrons for each pixel
     read_time : float
         Time to perform a readout. For Roman data, this is FRAME_TIME.
     read_pattern : list[list[int]]

src/stcal/ramp_fitting/ols_cas22_fit.py

@@ -33,7 +33,7 @@
 import numpy as np
 
 from . import ols_cas22
-from .ols_cas22_util import ma_table_to_tau, ma_table_to_tbar, readpattern_to_matable
+from .ols_cas22_util import ma_table_to_tau, ma_table_to_tbar, read_pattern_to_ma_table, ma_table_to_read_pattern
 
 
 def fit_ramps_casertano(resultants, dq, read_noise, read_time, ma_table=None, read_pattern=None, use_jump=False):
@@ -76,7 +76,7 @@ def fit_ramps_casertano(resultants, dq, read_noise, read_time, ma_table=None, re
     # Get the Multi-accum table, either as given or from the read pattern
     if read_pattern is None:
         if ma_table is not None:
-            read_pattern = ma_table_to_readpattern(ma_table)
+            read_pattern = ma_table_to_read_pattern(ma_table)
     if read_pattern is None:
         raise RuntimeError('One of `ma_table` or `read_pattern` must be given.')
 
@@ -86,8 +86,7 @@ def fit_ramps_casertano(resultants, dq, read_noise, read_time, ma_table=None, re
 
     resultants = np.array(resultants).astype(np.float32)
 
-    dq = np.array(dq).astype(np.float32)
-
+    dq = np.array(dq).astype(np.int32)
     if np.ndim(read_noise) <= 1:
         read_noise = read_noise * np.ones(resultants.shape[1:])
     read_noise = np.array(read_noise).astype(np.float32)
@@ -112,12 +111,12 @@ def fit_ramps_casertano(resultants, dq, read_noise, read_time, ma_table=None, re
 
     # Extract the data request from the ramp fits
     for index, ramp_fit in enumerate(ramp_fits):
-        parameters[1, :] = ramp_fit['average']['slope']
+        parameters[index, 1] = ramp_fit['average']['slope']
 
-        variances[0, :] = ramp_fit['average']['read_var']
-        variances[1, :] = ramp_fit['average']['poisson_var']
+        variances[index, 0] = ramp_fit['average']['read_var']
+        variances[index, 1] = ramp_fit['average']['poisson_var']
 
-    variances[2, :] = variances[0, :] + variances[1, :]
+    variances[:, 2] = (variances[:, 0] + variances[:, 1]).astype(np.float32)
 
     if resultants.shape != orig_shape:
         parameters = parameters[0]

src/stcal/ramp_fitting/ols_cas22_util.py

@@ -2,10 +2,14 @@
 """
 import numpy as np
 
-__all__ = ['ma_table_to_tau', 'ma_table_to_tbar']
+__all__ = [
+    'ma_table_to_read_pattern',
+    'ma_table_to_tau',
+    'ma_table_to_tbar',
+    'read_pattern_to_ma_table']
 
 
-def matable_to_readpattern(ma_table):
+def ma_table_to_read_pattern(ma_table):
     """Convert read patterns to multi-accum lists
 
     Using Roman terminology, a "read pattern" is a list of resultants. Each element of this list
@@ -26,7 +30,7 @@ def matable_to_readpattern(ma_table):
     [[1, 1], [2, 2], [4, 1], [5, 4], [9,2], [11,1]]
 
     The example above, using this function, should perform as follows:
-    >>> matable_to_readpattern([[1, 1], [2, 2], [4, 1], [5, 4], [9,2], [11,1]])
+    >>> ma_table_to_read_pattern([[1, 1], [2, 2], [4, 1], [5, 4], [9,2], [11,1]])
     [[1], [2, 3], [4], [5, 6, 7, 8], [9, 10], [11]]
 
     Parameters
@@ -123,7 +127,7 @@ def ma_table_to_tbar(ma_table, read_time):
     return meantimes
 
 
-def readpattern_to_matable(read_pattern):
+def read_pattern_to_ma_table(read_pattern):
     """Convert read patterns to multi-accum lists
 
     Using Roman terminology, a "read pattern" is a list of resultants. Each element of this list
@@ -144,7 +148,7 @@ def readpattern_to_matable(read_pattern):
     [[1, 1], [2, 2], [4, 1], [5, 4], [9,2], [11,1]]
 
     The example above, using this function, should perform as follows:
-    >>> readpattern_to_matable([[1], [2, 3], [4], [5, 6, 7, 8], [9, 10], [11]])
+    >>> read_pattern_to_ma_table([[1], [2, 3], [4], [5, 6, 7, 8], [9, 10], [11]])
     [[1, 1], [2, 2], [4, 1], [5, 4], [9, 2], [11, 1]]
 
     Parameters

tests/test_ramp_fitting_cas22.py

@@ -14,22 +14,22 @@
 ROMAN_READ_TIME = 3.04
 
 
-def test_matable_to_readpattern():
+def test_ma_table_to_read_pattern():
     """Test conversion from read pattern to multi-accum table"""
     ma_table = [[1, 1], [2, 2], [4, 1], [5, 4], [9,2], [11,1]]
     expected = [[1], [2, 3], [4], [5, 6, 7, 8], [9, 10], [11]]
 
-    result = ols_cas22_util.matable_to_readpattern(ma_table)
+    result = ols_cas22_util.ma_table_to_read_pattern(ma_table)
 
     assert result == expected
 
 
-def test_readpattern_to_matable():
+def test_read_pattern_to_ma_table():
     """Test conversion from read pattern to multi-accum table"""
     pattern = [[1], [2, 3], [4], [5, 6, 7, 8], [9, 10], [11]]
     expected = [[1, 1], [2, 2], [4, 1], [5, 4], [9,2], [11,1]]
 
-    result = ols_cas22_util.readpattern_to_matable(pattern)
+    result = ols_cas22_util.read_pattern_to_ma_table(pattern)
 
     assert result == expected
 
@@ -38,14 +38,18 @@ def test_simulated_ramps():
     ntrial = 100000
     ma_table, flux, read_noise, resultants = simulate_many_ramps(ntrial=ntrial)
 
+    dq = np.zeros(resultants.shape, dtype=np.int32)
+    read_noise = np.ones(resultants.shape[1], dtype=np.float32) * read_noise
+
     par, var = ramp.fit_ramps_casertano(
-        resultants, resultants * 0, read_noise, ROMAN_READ_TIME, ma_table=ma_table)
+        resultants, dq, read_noise, ROMAN_READ_TIME, ma_table=ma_table)
+
     chi2dof_slope = np.sum((par[:, 1] - flux)**2 / var[:, 2]) / ntrial
     assert np.abs(chi2dof_slope - 1) < 0.03
 
     # now let's mark a bunch of the ramps as compromised.
     bad = np.random.uniform(size=resultants.shape) > 0.7
-    dq = resultants * 0 + bad
+    dq += bad
     par, var = ramp.fit_ramps_casertano(
         resultants, dq, read_noise, ROMAN_READ_TIME, ma_table=ma_table)
     # only use okay ramps