Added iris.sg.background module for FUV background subtraction. (#9)

Author: roytsmart

docs/index.rst

@@ -74,7 +74,7 @@ and display as a false-color movie.
     velocity_max = +100 * u.km / u.s
 
     # Define the spectral normalization curve
-    spd_max = np.percentile(
+    spd_max = np.nanpercentile(
         a=obs.outputs,
         q=99.5,
         axis=axis_txy,

iris/sg/__init__.py

@@ -2,8 +2,10 @@
 Represent and manipulate data captured using the IRIS spectrograph
 """
 
+from . import background
 from ._spectrograph import SpectrographObservation
 
 __all__ = [
+    "background",
     "SpectrographObservation",
 ]

iris/sg/_spectrograph.py

@@ -60,7 +60,7 @@ class SpectrographObservation(
             wavelength=obs.inputs.wavelength.mean(("detector_x", "detector_y")),
             axis=obs.axis_wavelength,
             spd_min=0 * u.DN,
-            spd_max=np.percentile(
+            spd_max=np.nanpercentile(
                 a=obs.outputs,
                 q=99,
                 axis=(obs.axis_time, obs.axis_detector_x, obs.axis_detector_y),
@@ -316,7 +316,10 @@ def from_fits(
         self.inputs.time.ndarray = astropy.time.Time(
             val=self.inputs.time.ndarray,
             format="jd",
-        ).isot
+        )
+
+        where_invalid = self.outputs < -10 * u.DN
+        self.outputs[where_invalid] = np.nan
 
         return self
 

iris/sg/background/__init__.py

@@ -0,0 +1,25 @@
+"""
+Utilities for estimating the stray light background of FUV spectrograph images.
+"""
+
+from ._background import (
+    model_background,
+    model_spectral_line,
+    model_total,
+    fit,
+    average,
+    subtract_spectral_line,
+    smooth,
+    estimate,
+)
+
+__all__ = [
+    "model_background",
+    "model_spectral_line",
+    "model_total",
+    "fit",
+    "average",
+    "subtract_spectral_line",
+    "smooth",
+    "estimate",
+]