From 9a9e6f5a76018b5892b2a95135ea2c306068012b Mon Sep 17 00:00:00 2001
From: "Karl D. Gordon" <kgordon@stsci.edu>
Date: Thu, 22 Feb 2024 10:05:28 -0500
Subject: [PATCH] MIRI merging units fixed

---
 measure_extinction/merge_obsspec.py           |  7 ++++---
 measure_extinction/modeldata.py               |  6 +++---
 measure_extinction/stardata.py                |  3 ---
 .../utils/merge_miri_ifu_spec.py              | 20 +++++++++++++------
 4 files changed, 21 insertions(+), 15 deletions(-)

diff --git a/measure_extinction/merge_obsspec.py b/measure_extinction/merge_obsspec.py
index 6aeef57..46fcad7 100644
--- a/measure_extinction/merge_obsspec.py
+++ b/measure_extinction/merge_obsspec.py
@@ -285,7 +285,7 @@ def merge_gen_obsspec(obstables, wave_range, output_resolution=100):
     Parameters
     ----------
     obstables : list of astropy Table objects
-        list of tables containing the observed IRS spectra
+        list of tables containing the observed spectra
         usually the result of reading tables
 
     wave_range : 2 element float
@@ -367,7 +367,7 @@ def merge_irs_obsspec(obstables, output_resolution=150):
     """
     wave_range = [5.0, 40.0] * u.micron
     otable = merge_gen_obsspec(
-        obstables, wave_range, output_resolution=output_resolution
+        obstables, wave_range, output_resolution=output_resolution,
     )
     return otable
 
@@ -421,6 +421,7 @@ def merge_miri_ifu_obsspec(obstables, output_resolution=3000):
     """
     wave_range = [4.8, 29.0] * u.micron
     otable = merge_gen_obsspec(
-        obstables, wave_range, output_resolution=output_resolution
+        obstables, wave_range, output_resolution=output_resolution,
     )
+
     return otable
diff --git a/measure_extinction/modeldata.py b/measure_extinction/modeldata.py
index d81327b..f0fcd2f 100644
--- a/measure_extinction/modeldata.py
+++ b/measure_extinction/modeldata.py
@@ -209,7 +209,7 @@ def stellar_sed(self, params, velocity=None):
 
         return sed
 
-    def dust_extinguished_sed_FM90_G23(self, params, sed, velocity=0.0):
+    def dust_extinguished_sed(self, params, sed, velocity=0.0):
         """
         Dust extinguished sed given the extinction parameters
 
@@ -254,7 +254,7 @@ def dust_extinguished_sed_FM90_G23(self, params, sed, velocity=0.0):
                 params[6],
                 optnir_axav_x.value,
                 optnir_axav_y,
-                [0.2, 11.0],
+                [0.033, 11.0],
                 "FM90_G23_measure_extinction",
             )
             ext_sed[cspec] = sed[cspec] * (10 ** (-0.4 * axav * params[0]))
@@ -270,7 +270,7 @@ def dust_extinguished_sed_FM90_G23(self, params, sed, velocity=0.0):
 
         return ext_sed
 
-    def dust_extinguished_sed(self, params, sed, velocity=0.0):
+    def dust_extinguished_sed_FM04(self, params, sed, velocity=0.0):
         """
         Dust extinguished sed given the extinction parameters
 
diff --git a/measure_extinction/stardata.py b/measure_extinction/stardata.py
index fd2827b..7d0bec1 100644
--- a/measure_extinction/stardata.py
+++ b/measure_extinction/stardata.py
@@ -844,9 +844,6 @@ def read_miri_ifu(self, line, path="./"):
         """
         self.read_spectra(line, path)
 
-        # add units
-        self.fluxes = self.fluxes.value * u.Jy
-        self.uncs = self.uncs.value * u.Jy
         self.fluxes = self.fluxes.to(
             fluxunit, equivalencies=u.spectral_density(self.waves)
         )
diff --git a/measure_extinction/utils/merge_miri_ifu_spec.py b/measure_extinction/utils/merge_miri_ifu_spec.py
index 3575eee..24a6cce 100644
--- a/measure_extinction/utils/merge_miri_ifu_spec.py
+++ b/measure_extinction/utils/merge_miri_ifu_spec.py
@@ -12,7 +12,7 @@
 from measure_extinction.merge_obsspec import merge_miri_ifu_obsspec
 
 
-fluxunit = u.erg / (u.s * u.cm * u.cm * u.angstrom)
+fluxunit = u.erg / (u.cm * u.cm * u.s * u.angstrom)
 
 
 if __name__ == "__main__":
@@ -61,7 +61,6 @@
     mrs_file = f"{outname}_miri_ifu.fits"
     rb_mrs.write(f"{args.outpath}/{mrs_file}", overwrite=True)
 
-
     # plot the original and merged Spectra
     fontsize = 14
     font = {"size": fontsize}
@@ -75,19 +74,28 @@
 
     for ctable in stable:
         gvals = ctable["NPTS"] > 0
+        cfluxes = (
+            ctable["FLUX"]
+            .to(fluxunit, equivalencies=u.spectral_density(ctable["WAVELENGTH"]))
+            .value
+        )
         ax.plot(
             ctable["WAVELENGTH"][gvals],
-            ctable["FLUX"][gvals],
+            cfluxes[gvals],
             "k-",
             alpha=0.5,
             label="orig",
         )
     gvals = rb_mrs["NPTS"] > 0
-    cfluxes = rb_mrs["FLUX"][gvals].data * fluxunit
-    # cfluxes = (rb_mrs["FLUX"][gvals].data * fluxunit).to(u.Jy, equivalencies=u.spectral_density(rb_mrs["WAVELENGTH"].data)).value
+    cfluxes = (
+        rb_mrs["FLUX"]
+        .to(fluxunit, equivalencies=u.spectral_density(ctable["WAVELENGTH"]))
+        .value
+    )
+ 
     ax.plot(
         rb_mrs["WAVELENGTH"][gvals].to(u.micron),
-        cfluxes,
+        rb_mrs["FLUX"][gvals],
         "b-",
         alpha=0.5,
         label="merged",