Feature/make slit illum interactive

geminidr/gmos/parameters_gmos_longslit.py

@@ -31,21 +31,37 @@ def setDefaults(self):
 
 
 class makeSlitIllumConfig(config.Config):
-    bins = config.Field("Total number of bins across the dispersion axis.",
-                        int, None, optional=True)
-    border = config.Field("Size of the border added to the reconstructed slit illumination image",
-                          int, 0, optional=True)
-    debug_plot = config.Field("Create diagnosis plots?",
-                              bool, False, optional=True)
-    smooth_order = config.Field("Spline order to smooth binned data",
-                                int, 3, optional=True)
+    bins = config.Field("Either total number of bins across the dispersion axis, "
+                        "or a comma-separated list \n                                          "
+                        "of pixel coordinate pairs defining then dispersion bins, e.g. 1:300,301:500",
+                        (int, str), None, optional=True)
+    regions = config.Field("Sample regions along the slit", str, None, optional=True)
     suffix = config.Field("Filename suffix",
                           str, "_slitIllum", optional=True)
-    x_order = config.Field("Order of the x-component of the Chebyshev2D model used to reconstruct data",
-                           int, 4, optional=True)
-    y_order = config.Field("Order of the y-component of the Chebyshev2D model used to reconstruct data",
-                           int, 4, optional=True)
-
+    function = config.ChoiceField("Fitting function to use for bin fitting (spatial direction)", str,
+                           allowed={"spline3": "Cubic spline",
+                                    "chebyshev": "Chebyshev polynomial",
+                                    "legendre": "Legendre polynomial",
+                                    "spline1": "Linear spline"},
+                           default="spline3", optional=False)
+    order = config.Field("Order of the bin fitting function",
+                                int, 20, optional=True)
+    hsigma = config.RangeField("High rejection threshold (sigma) of the bin fit",
+                               float, 3., min=0)
+    lsigma = config.RangeField("Low rejection threshold (sigma) of the bin fit",
+                               float, 3., min=0)
+    niter = config.RangeField("Maximum number of iterations",
+                              int, 3, min = 0, optional=True)
+    grow = config.RangeField("Growth radius for rejected pixels of the bin fit",
+                             float, 0, min=0, optional=True)
+    interp_order = config.RangeField("Order of the spline interpolator",
+                            int, 3, min=1, max=5, optional=True)
+    debug_boundary_ext = config.Field("Extrapolate outside interpolation interval? If 'False'" 
+                            "boundary values are used", bool, False, optional=True)
+    interactive = config.Field("Set to activate an interactive preview to fine tune the input parameters",
+                               bool, False, optional=True)
+    border = config.Field("Size of the border added to the reconstructed slit illumination image",
+                          int, 2, optional=True)
 
 class normalizeFlatConfig(config.core_1Dfitting_config):
     suffix = config.Field("Filename suffix", str, "_normalized", optional=True)

geminidr/gmos/tests/longslit/test_make_slit_illum.py

@@ -1,8 +1,6 @@
 #!/usr/bin/env python
 """
-Tests for the `makeSlitIllum` primitive. The primitive itself is
-defined in :mod:`~geminidr.core.primitives_spect` but these tests use GMOS Spect
-data.
+Tests for the `makeSlitIllum` primitive.
 """
 import os
 import pytest
@@ -49,7 +47,7 @@ def test_create_slit_illumination_with_mosaicked_data(ad, change_working_dir, re
     constant.
 
     There are several ways of doing this but, given the noise levels, we bin
-    the data, fit a polynomium, and check that the fitted polynomium has its 1st
+    the data, fit a polynomial, and check that the fitted polynomial has its 1st
     and 2nd coefficients almost zero.
     """
     plot = request.config.getoption("--do-plots")
@@ -63,7 +61,7 @@ def test_create_slit_illumination_with_mosaicked_data(ad, change_working_dir, re
         assert hasattr(ad[0], "wcs")
 
         p = primitives_gmos_longslit.GMOSLongslit([ad])
-        p.makeSlitIllum(bins=25, border=10, debug_plot=plot)
+        p.makeSlitIllum(bins=25, border=10)
         slit_illum_ad = p.writeOutputs(
             suffix="_mosaickedSlitIllum",  strip=True)[0]
 
@@ -122,7 +120,7 @@ def test_create_slit_illumination_with_multi_extension_data(ad, change_working_d
         cwd = os.getcwd()
         print("Running tests inside folder:\n  {}".format(cwd))
         p = primitives_gmos_longslit.GMOSLongslit([ad])
-        p.makeSlitIllum(bins=25, border=10, debug_plot=plot)
+        p.makeSlitIllum(bins=25, border=10)
         slit_illum_ad = p.writeOutputs()[0]
 
         for ext, slit_ext in zip(ad, slit_illum_ad):