From c2e4cbcfb33f9a4801bdf5bb5532267d09344d4f Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Tue, 1 May 2018 17:26:21 -0400
Subject: [PATCH 01/72] First pass at XraySpectrum1D

---
 specutils/spectra/xrayspectrum1d.py | 47 +++++++++++++++++++++++++++++
 1 file changed, 47 insertions(+)
 create mode 100644 specutils/spectra/xrayspectrum1d.py

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
new file mode 100644
index 000000000..b7556ad77
--- /dev/null
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -0,0 +1,47 @@
+import logging
+
+import numpy as np
+from astropy import units as u
+from .spectrum1d import Spectrum1D
+
+__all__ = ['XraySpectrum1D']
+
+# For dealing with varied unit string choices
+EV   = ['eV', 'ev']
+KEV  = ['kev', 'keV']
+ANGS = ['angs', 'Angs', 'Angstrom', 'angstrom', 'Angstroms', 'angstroms', 'A', 'a']
+
+def _unit_parser(unit_string):
+    if unit_string in EV:
+        return u.eV
+    if unit_string in KEV:
+        return u.keV
+    if unit_string in ANGS:
+        return u.angstrom
+
+class XraySpectrum1D(Spectrum1D):
+    """
+    Spectrum container for holding X-ray spectrum
+    WIP by eblur
+
+    Parameters
+    ----------
+    bin_lo
+    bin_hi
+    bin_unit
+    counts
+    arf
+    rmf
+    """
+    def __init__(self, bin_lo, bin_hi, bin_unit, counts, arf=None, rmf=None):
+        try:
+            axis_unit = u.Unit(bin_unit)
+        else:
+            axis_unit = _unit_parser(bin_unit)
+
+        bin_mid = 0.5 * (bin_lo + bin_hi) * unit
+        Spectrum1D.__init__(self, spectral_axis=bin_mid, flux=counts)
+
+        self.arf = arf
+        self.rmf = rmf
+        return

From 20c8b289b212ab8a00aad758db7149dc9bb34965 Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Tue, 1 May 2018 17:40:28 -0400
Subject: [PATCH 02/72] Can load an X-ray spectrum

---
 specutils/spectra/__init__.py       | 1 +
 specutils/spectra/xrayspectrum1d.py | 4 ++--
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/specutils/spectra/__init__.py b/specutils/spectra/__init__.py
index 711a16154..95c052b1f 100644
--- a/specutils/spectra/__init__.py
+++ b/specutils/spectra/__init__.py
@@ -5,3 +5,4 @@
 from __future__ import absolute_import
 
 from .spectrum1d import *  # noqa
+from .xrayspectrum1d import *
diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index b7556ad77..d57146f97 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -36,10 +36,10 @@ class XraySpectrum1D(Spectrum1D):
     def __init__(self, bin_lo, bin_hi, bin_unit, counts, arf=None, rmf=None):
         try:
             axis_unit = u.Unit(bin_unit)
-        else:
+        except:
             axis_unit = _unit_parser(bin_unit)
 
-        bin_mid = 0.5 * (bin_lo + bin_hi) * unit
+        bin_mid = 0.5 * (bin_lo + bin_hi) * axis_unit
         Spectrum1D.__init__(self, spectral_axis=bin_mid, flux=counts)
 
         self.arf = arf

From 6ac1c0841b81ec3efe4531423e9ab25cf1415b32 Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Tue, 1 May 2018 17:44:41 -0400
Subject: [PATCH 03/72] Added  attribute

---
 specutils/spectra/xrayspectrum1d.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index d57146f97..b939b40d1 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -45,3 +45,8 @@ def __init__(self, bin_lo, bin_hi, bin_unit, counts, arf=None, rmf=None):
         self.arf = arf
         self.rmf = rmf
         return
+
+    # Convenience function for Xray people
+    @property
+    def counts(self):
+        return self.flux

From 4571350ce927f1dd0934a02b155a9295bb4f138a Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Wed, 2 May 2018 13:53:39 -0400
Subject: [PATCH 04/72] Added ARF and RMF objects

---
 specutils/spectra/xrayspectrum1d.py | 326 +++++++++++++++++++++++++++-
 1 file changed, 325 insertions(+), 1 deletion(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index b939b40d1..e36a500a6 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -4,7 +4,7 @@
 from astropy import units as u
 from .spectrum1d import Spectrum1D
 
-__all__ = ['XraySpectrum1D']
+__all__ = ['XraySpectrum1D', 'ARF', 'RMF']
 
 # For dealing with varied unit string choices
 EV   = ['eV', 'ev']
@@ -50,3 +50,327 @@ def __init__(self, bin_lo, bin_hi, bin_unit, counts, arf=None, rmf=None):
     @property
     def counts(self):
         return self.flux
+
+## ----  Supporting response file objects
+
+class RMF(object):
+    def __init__(self, filename):
+        self._load_rmf(filename)
+        pass
+
+    def _load_rmf(self, filename):
+        """
+        Load an RMF from a FITS file.
+
+        Parameters
+        ----------
+        filename : str
+            The file name with the RMF file
+
+        Attributes
+        ----------
+        n_grp : numpy.ndarray
+            the Array with the number of channels in each
+            channel set
+
+        f_chan : numpy.ndarray
+            The starting channel for each channel group;
+            If an element i in n_grp > 1, then the resulting
+            row entry in f_chan will be a list of length n_grp[i];
+            otherwise it will be a single number
+
+        n_chan : numpy.ndarray
+            The number of channels in each channel group. The same
+            logic as for f_chan applies
+
+        matrix : numpy.ndarray
+            The redistribution matrix as a flattened 1D vector
+
+        energ_lo : numpy.ndarray
+            The lower edges of the energy bins
+
+        energ_hi : numpy.ndarray
+            The upper edges of the energy bins
+
+        detchans : int
+            The number of channels in the detector
+
+        """
+        # open the FITS file and extract the MATRIX extension
+        # which contains the redistribution matrix and
+        # anxillary information
+        hdulist = fits.open(filename)
+
+        # get all the extension names
+        extnames = np.array([h.name for h in hdulist])
+
+        # figure out the right extension to use
+        if "MATRIX" in extnames:
+            h = hdulist["MATRIX"]
+
+        elif "SPECRESP MATRIX" in extnames:
+            h = hdulist["SPECRESP MATRIX"]
+
+        data = h.data
+        hdr = h.header
+        hdulist.close()
+
+        # extract + store the attributes described in the docstring
+        n_grp = np.array(data.field("N_GRP"))
+        f_chan = np.array(data.field('F_CHAN'))
+        n_chan = np.array(data.field("N_CHAN"))
+        matrix = np.array(data.field("MATRIX"))
+
+        self.energ_lo = np.array(data.field("ENERG_LO"))
+        self.energ_hi = np.array(data.field("ENERG_HI"))
+        self.energ_unit = data.columns["ENERG_LO"].unit
+        self.detchans = hdr["DETCHANS"]
+        self.offset = self.__get_tlmin(h)
+
+        # flatten the variable-length arrays
+        self.n_grp, self.f_chan, self.n_chan, self.matrix = \
+                self._flatten_arrays(n_grp, f_chan, n_chan, matrix)
+
+        return
+
+    def __get_tlmin(self, h):
+        """
+        Get the tlmin keyword for `F_CHAN`.
+
+        Parameters
+        ----------
+        h : an astropy.io.fits.hdu.table.BinTableHDU object
+            The extension containing the `F_CHAN` column
+
+        Returns
+        -------
+        tlmin : int
+            The tlmin keyword
+        """
+        # get the header
+        hdr = h.header
+        # get the keys of all
+        keys = np.array(list(hdr.keys()))
+
+        # find the place where the tlmin keyword is defined
+        t = np.array(["TLMIN" in k for k in keys])
+
+        # get the index of the TLMIN keyword
+        tlmin_idx = np.hstack(np.where(t))[0]
+
+        # get the corresponding value
+        tlmin = np.int(list(hdr.items())[tlmin_idx][1])
+
+        return tlmin
+
+    def _flatten_arrays(self, n_grp, f_chan, n_chan, matrix):
+
+        if not len(n_grp) == len(f_chan) == len(n_chan) == len(matrix):
+            raise ValueError("Arrays must be of same length!")
+
+        # find all non-zero groups
+        nz_idx = (n_grp > 0)
+
+        # stack all non-zero rows in the matrix
+        matrix_flat = np.hstack(matrix[nz_idx])
+
+        # stack all nonzero rows in n_chan and f_chan
+        #n_chan_flat = np.hstack(n_chan[nz_idx])
+        #f_chan_flat = np.hstack(f_chan[nz_idx])
+
+        # some matrices actually have more elements
+        # than groups in `n_grp`, so we'll only pick out
+        # those values that have a correspondence in
+        # n_grp
+        f_chan_new = []
+        n_chan_new = []
+        for i,t in enumerate(nz_idx):
+            if t:
+                n = n_grp[i]
+                f = f_chan[i]
+                nc = n_chan[i]
+                if np.size(f) == 1:
+                    f_chan_new.append(f)
+                    n_chan_new.append(nc)
+                else:
+                    f_chan_new.append(f[:n])
+                    n_chan_new.append(nc[:n])
+
+        n_chan_flat = np.hstack(n_chan_new)
+        f_chan_flat = np.hstack(f_chan_new)
+
+        # if n_chan is zero, we'll remove those as well.
+        nz_idx2 = (n_chan_flat > 0)
+        n_chan_flat = n_chan_flat[nz_idx2]
+        f_chan_flat = f_chan_flat[nz_idx2]
+
+        return n_grp, f_chan_flat, n_chan_flat, matrix_flat
+
+    def apply_rmf(self, spec):
+        """
+        Fold the spectrum through the redistribution matrix.
+
+        The redistribution matrix is saved as a flattened 1-dimensional
+        vector to save space. In reality, for each entry in the flux
+        vector, there exists one or more sets of channels that this
+        flux is redistributed into. The additional arrays `n_grp`,
+        `f_chan` and `n_chan` store this information:
+            * `n_group` stores the number of channel groups for each
+              energy bin
+            * `f_chan` stores the *first channel* that each channel
+              for each channel set
+            * `n_chan` stores the number of channels in each channel
+              set
+
+        As a result, for a given energy bin i, we need to look up the
+        number of channel sets in `n_grp` for that energy bin. We
+        then need to loop over the number of channel sets. For each
+        channel set, we look up the first channel into which flux
+        will be distributed as well as the number of channels in the
+        group. We then need to also loop over the these channels and
+        actually use the corresponding elements in the redistribution
+        matrix to redistribute the photon flux into channels.
+
+        All of this is basically a big bookkeeping exercise in making
+        sure to get the indices right.
+
+        Parameters
+        ----------
+        spec : numpy.ndarray
+            The (model) spectrum to be folded
+
+        Returns
+        -------
+        counts : numpy.ndarray
+            The (model) spectrum after folding, in
+            counts/s/channel
+
+        """
+        # get the number of channels in the data
+        nchannels = spec.shape[0]
+
+        # an empty array for the output counts
+        counts = np.zeros(nchannels)
+
+        # index for n_chan and f_chan incrementation
+        k = 0
+
+        # index for the response matrix incrementation
+        resp_idx = 0
+
+        # loop over all channels
+        for i in range(nchannels):
+
+            # this is the current bin in the flux spectrum to
+            # be folded
+            source_bin_i = spec[i]
+
+            # get the current number of groups
+            current_num_groups = self.n_grp[i]
+
+            # loop over the current number of groups
+            for j in range(current_num_groups):
+
+                current_num_chans = int(self.n_chan[k])
+
+                if current_num_chans == 0:
+                    k += 1
+                    resp_idx += current_num_chans
+                    continue
+
+
+                else:
+                    # get the right index for the start of the counts array
+                    # to put the data into
+                    counts_idx = int(self.f_chan[k] - self.offset)
+                    # this is the current number of channels to use
+
+                    k += 1
+                    # add the flux to the subarray of the counts array that starts with
+                    # counts_idx and runs over current_num_chans channels
+                    counts[counts_idx:counts_idx +
+                                      current_num_chans] += self.matrix[resp_idx:resp_idx +
+                                                                                 current_num_chans] * \
+                                                                np.float(source_bin_i)
+                    # iterate the response index for next round
+                    resp_idx += current_num_chans
+
+
+        return counts[:self.detchans]
+
+
+class ARF(object):
+
+    def __init__(self, filename):
+
+        self._load_arf(filename)
+        pass
+
+    def _load_arf(self, filename):
+        """
+        Load an ARF from a FITS file.
+        Parameters
+        ----------
+        filename : str
+            The file name with the RMF file
+        Attributes
+        ----------
+        """
+        # open the FITS file and extract the MATRIX extension
+        # which contains the redistribution matrix and
+        # anxillary information
+        hdulist = fits.open(filename)
+        h = hdulist["SPECRESP"]
+        data = h.data
+        hdr = h.header
+        hdulist.close()
+
+        # extract + store the attributes described in the docstring
+
+        self.e_low  = np.array(data.field("ENERG_LO"))
+        self.e_high = np.array(data.field("ENERG_HI"))
+        self.e_unit = data.columns["ENERG_LO"].unit
+        self.specresp = np.array(data.field("SPECRESP"))
+
+        if "EXPOSURE" in list(hdr.keys()):
+            self.exposure = hdr["EXPOSURE"]
+        else:
+            self.exposure = 1.0
+
+        if "FRACEXPO" in data.columns.names:
+            self.fracexpo = data["FRACEXPO"]
+        else:
+            self.fracexpo = 1.0
+
+        return
+
+    def apply_arf(self, spec, exposure=None):
+        """
+        Fold the spectrum through the ARF.
+        The ARF is a single vector encoding the effective area information
+        about the detector. A such, applying the ARF is a simple
+        multiplication with the input spectrum.
+        Parameters
+        ----------
+        spec : numpy.ndarray
+            The (model) spectrum to be folded
+        exposure : float, default None
+            Value for the exposure time. By default, `apply_arf` will use the
+            exposure keyword from the ARF file. If this exposure time is not
+            correct (for example when simulated spectra use a different exposure
+            time and the ARF from a real observation), one can override the
+            default exposure by setting the `exposure` keyword to the correct
+            value.
+        Returns
+        -------
+        s_arf : numpy.ndarray
+            The (model) spectrum after folding, in
+            counts/s/channel
+        """
+        assert spec.shape[0] == self.specresp.shape[0], "The input spectrum must " \
+                                                      "be of same size as the " \
+                                                      "ARF array."
+        if exposure is None:
+            return np.array(spec) * self.specresp * self.exposure
+        else:
+            return np.array(spec) * self.specresp * exposure

From a92bd09751e7595466ed49bd407d0a94216b585a Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Wed, 2 May 2018 14:07:50 -0400
Subject: [PATCH 05/72] Added assign_rmf and assign_arf methods

---
 specutils/spectra/xrayspectrum1d.py | 29 +++++++++++++++++++++++++++--
 1 file changed, 27 insertions(+), 2 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index e36a500a6..a371b94a5 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -42,8 +42,8 @@ def __init__(self, bin_lo, bin_hi, bin_unit, counts, arf=None, rmf=None):
         bin_mid = 0.5 * (bin_lo + bin_hi) * axis_unit
         Spectrum1D.__init__(self, spectral_axis=bin_mid, flux=counts)
 
-        self.arf = arf
-        self.rmf = rmf
+        self.assign_rmf(rmf)
+        self.assign_arf(rmf)
         return
 
     # Convenience function for Xray people
@@ -51,6 +51,21 @@ def __init__(self, bin_lo, bin_hi, bin_unit, counts, arf=None, rmf=None):
     def counts(self):
         return self.flux
 
+    def assign_arf(self, arf_inp):
+        if isinstance(arf_inp, str):
+            self.arf = ARF(arf_inp)
+        else:
+            self.arf = arf_inp
+        return
+
+    def assign_rmf(self, rmf_inp):
+        if isinstance(rmf_inp, str):
+            self.rmf = RMF(rmf_inp)
+        else:
+            self.rmf = rmf_inp
+        return
+
+
 ## ----  Supporting response file objects
 
 class RMF(object):
@@ -69,6 +84,9 @@ def _load_rmf(self, filename):
 
         Attributes
         ----------
+        filename : str
+            The file name that the RMF was drawn from
+
         n_grp : numpy.ndarray
             the Array with the number of channels in each
             channel set
@@ -100,6 +118,7 @@ def _load_rmf(self, filename):
         # which contains the redistribution matrix and
         # anxillary information
         hdulist = fits.open(filename)
+        self.filename = filename
 
         # get all the extension names
         extnames = np.array([h.name for h in hdulist])
@@ -309,17 +328,23 @@ def __init__(self, filename):
     def _load_arf(self, filename):
         """
         Load an ARF from a FITS file.
+
         Parameters
         ----------
         filename : str
             The file name with the RMF file
+
         Attributes
         ----------
+        filename : str
+            The file name that the ARF was drawn from
         """
         # open the FITS file and extract the MATRIX extension
         # which contains the redistribution matrix and
         # anxillary information
         hdulist = fits.open(filename)
+        self.filename = filename
+        
         h = hdulist["SPECRESP"]
         data = h.data
         hdr = h.header

From 7077dc7187ed413b6e39040b821d57aaa645243d Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Wed, 2 May 2018 14:16:13 -0400
Subject: [PATCH 06/72] Added exposure input

---
 specutils/spectra/xrayspectrum1d.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index a371b94a5..51de9e726 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -33,7 +33,7 @@ class XraySpectrum1D(Spectrum1D):
     arf
     rmf
     """
-    def __init__(self, bin_lo, bin_hi, bin_unit, counts, arf=None, rmf=None):
+    def __init__(self, bin_lo, bin_hi, bin_unit, counts, exposure, arf=None, rmf=None):
         try:
             axis_unit = u.Unit(bin_unit)
         except:
@@ -42,6 +42,7 @@ def __init__(self, bin_lo, bin_hi, bin_unit, counts, arf=None, rmf=None):
         bin_mid = 0.5 * (bin_lo + bin_hi) * axis_unit
         Spectrum1D.__init__(self, spectral_axis=bin_mid, flux=counts)
 
+        self.exposure = exposure
         self.assign_rmf(rmf)
         self.assign_arf(rmf)
         return
@@ -344,7 +345,7 @@ def _load_arf(self, filename):
         # anxillary information
         hdulist = fits.open(filename)
         self.filename = filename
-        
+
         h = hdulist["SPECRESP"]
         data = h.data
         hdr = h.header

From 9c8159df3f7b5ce2583459056fca6b7eb77a6a66 Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Wed, 2 May 2018 14:18:22 -0400
Subject: [PATCH 07/72] Fixed bugs

---
 specutils/spectra/xrayspectrum1d.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index 51de9e726..fade12358 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -2,6 +2,7 @@
 
 import numpy as np
 from astropy import units as u
+from astropy.io import fits
 from .spectrum1d import Spectrum1D
 
 __all__ = ['XraySpectrum1D', 'ARF', 'RMF']
@@ -44,7 +45,7 @@ def __init__(self, bin_lo, bin_hi, bin_unit, counts, exposure, arf=None, rmf=Non
 
         self.exposure = exposure
         self.assign_rmf(rmf)
-        self.assign_arf(rmf)
+        self.assign_arf(arf)
         return
 
     # Convenience function for Xray people

From fb5f1b6ed5c088bb3aa7ce0e1787dd25f156ad42 Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Wed, 2 May 2018 14:30:44 -0400
Subject: [PATCH 08/72] Updated docstrings

---
 specutils/spectra/xrayspectrum1d.py | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index fade12358..72c5bd11e 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -112,6 +112,9 @@ def _load_rmf(self, filename):
         energ_hi : numpy.ndarray
             The upper edges of the energy bins
 
+        energ_unit : str
+            Description of the energy units used
+
         detchans : int
             The number of channels in the detector
 
@@ -340,6 +343,28 @@ def _load_arf(self, filename):
         ----------
         filename : str
             The file name that the ARF was drawn from
+
+        e_low : numpy.ndarray
+            The lower edges of the energy bins
+
+        e_high : numpy.ndarray
+            The upper edges of the energy bins
+
+        e_unit : str
+            Description of the energy units used
+
+        specresp : numpy.ndarray
+            Description of the energy dependent telescope response area
+
+        fracexpo : float or numpy.ndarray
+            Fractional exposure time for the spectrum
+            (sometimes constant, sometimes dependent on spectral channel).
+            These values are stored for reference; generally, they are already
+            accounted for in the specresp array.
+
+        exposure :
+            Average exposure time for the dataset
+            (takes telescope dithering into account)
         """
         # open the FITS file and extract the MATRIX extension
         # which contains the redistribution matrix and

From a08d8ae03050f359b7e2dd9b647939133adc2146 Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Wed, 2 May 2018 14:36:08 -0400
Subject: [PATCH 09/72] Store bin and energy units as astropy.units.Unit

---
 specutils/spectra/xrayspectrum1d.py | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index 72c5bd11e..2b98164aa 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -31,6 +31,7 @@ class XraySpectrum1D(Spectrum1D):
     bin_hi
     bin_unit
     counts
+    exposure
     arf
     rmf
     """
@@ -43,6 +44,7 @@ def __init__(self, bin_lo, bin_hi, bin_unit, counts, exposure, arf=None, rmf=Non
         bin_mid = 0.5 * (bin_lo + bin_hi) * axis_unit
         Spectrum1D.__init__(self, spectral_axis=bin_mid, flux=counts)
 
+        self.bin_unit = axis_unit # keep for reference
         self.exposure = exposure
         self.assign_rmf(rmf)
         self.assign_arf(arf)
@@ -112,7 +114,7 @@ def _load_rmf(self, filename):
         energ_hi : numpy.ndarray
             The upper edges of the energy bins
 
-        energ_unit : str
+        energ_unit : astropy.units.Unit
             Description of the energy units used
 
         detchans : int
@@ -147,7 +149,7 @@ def _load_rmf(self, filename):
 
         self.energ_lo = np.array(data.field("ENERG_LO"))
         self.energ_hi = np.array(data.field("ENERG_HI"))
-        self.energ_unit = data.columns["ENERG_LO"].unit
+        self.energ_unit = _unit_parser(data.columns["ENERG_LO"].unit)
         self.detchans = hdr["DETCHANS"]
         self.offset = self.__get_tlmin(h)
 
@@ -350,7 +352,7 @@ def _load_arf(self, filename):
         e_high : numpy.ndarray
             The upper edges of the energy bins
 
-        e_unit : str
+        e_unit : astropy.units.Unit
             Description of the energy units used
 
         specresp : numpy.ndarray
@@ -381,7 +383,7 @@ def _load_arf(self, filename):
 
         self.e_low  = np.array(data.field("ENERG_LO"))
         self.e_high = np.array(data.field("ENERG_HI"))
-        self.e_unit = data.columns["ENERG_LO"].unit
+        self.e_unit = _unit_parser(data.columns["ENERG_LO"].unit)
         self.specresp = np.array(data.field("SPECRESP"))
 
         if "EXPOSURE" in list(hdr.keys()):

From 20ee61df2a27bd8ed6b0a1448393906d3d27130a Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Wed, 2 May 2018 16:31:14 -0400
Subject: [PATCH 10/72] Added bin_lo and hi because wcs.bin_edges did not exist

---
 specutils/spectra/xrayspectrum1d.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index 2b98164aa..d209c988b 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -35,15 +35,18 @@ class XraySpectrum1D(Spectrum1D):
     arf
     rmf
     """
-    def __init__(self, bin_lo, bin_hi, bin_unit, counts, exposure, arf=None, rmf=None):
+    def __init__(self, bin_lo, bin_hi, bin_unit, counts, exposure,
+                 arf=None, rmf=None, **kwargs):
         try:
             axis_unit = u.Unit(bin_unit)
         except:
             axis_unit = _unit_parser(bin_unit)
 
         bin_mid = 0.5 * (bin_lo + bin_hi) * axis_unit
-        Spectrum1D.__init__(self, spectral_axis=bin_mid, flux=counts)
+        Spectrum1D.__init__(self, spectral_axis=bin_mid, flux=counts, **kwargs)
 
+        self.bin_lo = bin_lo
+        self.bin_hi = bin_hi
         self.bin_unit = axis_unit # keep for reference
         self.exposure = exposure
         self.assign_rmf(rmf)

From 6cd49f0ccb7290f97e6812f5a67cd1b1217050e2 Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Wed, 2 May 2018 16:34:35 -0400
Subject: [PATCH 11/72] Added apply_resp method

---
 specutils/spectra/xrayspectrum1d.py | 44 +++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index d209c988b..765e77241 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -72,6 +72,50 @@ def assign_rmf(self, rmf_inp):
             self.rmf = rmf_inp
         return
 
+    def apply_resp(self, mflux, exposure=None):
+        """
+        Given a model flux spectrum, apply the response. In cases where the
+        spectrum has both an ARF and an RMF, apply both. Otherwise, apply
+        whatever response is in RMF.
+
+        The model flux spectrum *must* be created using the same units and
+        bins as in the ARF (where the ARF exists)!
+
+        Parameters
+        ----------
+        mflux : iterable
+            A list or array with the model flux values in ergs/keV/s/cm^-2
+
+        exposure : float, default None
+            By default, the exposure stored in the ARF will be used to compute
+            the total counts per bin over the effective observation time.
+            In cases where this might be incorrect (e.g. for simulated spectra
+            where the pha file might have a different exposure value than the
+            ARF), this keyword provides the functionality to override the
+            default behaviour and manually set the exposure time to use.
+
+        Returns
+        -------
+        count_model : numpy.ndarray
+            The model spectrum in units of counts/bin
+
+        If no ARF file exists, it will return the model flux after applying the RMF
+        If no RMF file exists, it will return the model flux after applying the ARF (with a warning)
+        If no ARF and no RMF, it will return the model flux spectrum (with a warning)
+        """
+
+        if self.arf is not None:
+            mrate  = self.arf.apply_arf(mflux, exposure=exposure)
+        else:
+            mrate = mflux
+
+        if self.rmf is not None:
+            count_model = self.rmf.apply_rmf(mrate)
+            return count_model
+        else:
+            print("Caution: no response file specified")
+            return mrate
+
 
 ## ----  Supporting response file objects
 

From 9c08caaf324c4258e61b046b36d2b0f7ddea0eb4 Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Wed, 2 May 2018 16:52:47 -0400
Subject: [PATCH 12/72] Adjust apply_resp output if spectrum is stored by
 wavelength

---
 specutils/spectra/xrayspectrum1d.py | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index 765e77241..b9f2df62d 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -110,11 +110,18 @@ def apply_resp(self, mflux, exposure=None):
             mrate = mflux
 
         if self.rmf is not None:
-            count_model = self.rmf.apply_rmf(mrate)
-            return count_model
+            result = self.rmf.apply_rmf(mrate)
         else:
             print("Caution: no response file specified")
-            return mrate
+            result = mrate
+
+        # The response is always stored according to energy
+        # If the spectrum is stored in wavelength, reverse the result so it
+        # matches in wavelength space
+        if self.bin_unit.physical_type == 'length':
+            return result[::-1]
+        else:
+            return result
 
 
 ## ----  Supporting response file objects

From 35d09321cf066a833adbec17e940dcf94c3b43f3 Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Wed, 2 May 2018 18:03:29 -0400
Subject: [PATCH 13/72] Don't need bin_unit

---
 specutils/spectra/xrayspectrum1d.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index b9f2df62d..bac3f6e3e 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -47,7 +47,6 @@ def __init__(self, bin_lo, bin_hi, bin_unit, counts, exposure,
 
         self.bin_lo = bin_lo
         self.bin_hi = bin_hi
-        self.bin_unit = axis_unit # keep for reference
         self.exposure = exposure
         self.assign_rmf(rmf)
         self.assign_arf(arf)
@@ -118,7 +117,8 @@ def apply_resp(self, mflux, exposure=None):
         # The response is always stored according to energy
         # If the spectrum is stored in wavelength, reverse the result so it
         # matches in wavelength space
-        if self.bin_unit.physical_type == 'length':
+        if self.spectral_axis.unit.physical_type == 'length':
+            print("reversing output")
             return result[::-1]
         else:
             return result

From da39e47faa109c2d18cf215955aacfa500a62c55 Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Wed, 2 May 2018 18:12:10 -0400
Subject: [PATCH 14/72] Because pha-file wavelength is in reverse order, the
 output from apply_resp is in correct order. No longer need to check

---
 specutils/spectra/xrayspectrum1d.py | 17 ++++++++---------
 1 file changed, 8 insertions(+), 9 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index bac3f6e3e..c054255df 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -34,6 +34,11 @@ class XraySpectrum1D(Spectrum1D):
     exposure
     arf
     rmf
+
+    Attributes
+    ----------
+    model : numpy.ndarray
+        Stores model values
     """
     def __init__(self, bin_lo, bin_hi, bin_unit, counts, exposure,
                  arf=None, rmf=None, **kwargs):
@@ -50,6 +55,7 @@ def __init__(self, bin_lo, bin_hi, bin_unit, counts, exposure,
         self.exposure = exposure
         self.assign_rmf(rmf)
         self.assign_arf(arf)
+        self.model_counts = np.zeros_like(bin_mid)
         return
 
     # Convenience function for Xray people
@@ -114,15 +120,8 @@ def apply_resp(self, mflux, exposure=None):
             print("Caution: no response file specified")
             result = mrate
 
-        # The response is always stored according to energy
-        # If the spectrum is stored in wavelength, reverse the result so it
-        # matches in wavelength space
-        if self.spectral_axis.unit.physical_type == 'length':
-            print("reversing output")
-            return result[::-1]
-        else:
-            return result
-
+        self.model_counts = result
+        return result
 
 ## ----  Supporting response file objects
 

From c5db843592a0d3d525f1bd2cdd587bf157317246 Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Wed, 2 May 2018 18:15:20 -0400
Subject: [PATCH 15/72] added save_model_counts option

---
 specutils/spectra/xrayspectrum1d.py | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index c054255df..cd78d2e49 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -77,7 +77,7 @@ def assign_rmf(self, rmf_inp):
             self.rmf = rmf_inp
         return
 
-    def apply_resp(self, mflux, exposure=None):
+    def apply_resp(self, mflux, exposure=None, store_model_counts=True):
         """
         Given a model flux spectrum, apply the response. In cases where the
         spectrum has both an ARF and an RMF, apply both. Otherwise, apply
@@ -99,9 +99,12 @@ def apply_resp(self, mflux, exposure=None):
             ARF), this keyword provides the functionality to override the
             default behaviour and manually set the exposure time to use.
 
+        store_model_counts : bool
+            If True, the output will also be stored in self.model_counts
+
         Returns
         -------
-        count_model : numpy.ndarray
+        model_counts : numpy.ndarray
             The model spectrum in units of counts/bin
 
         If no ARF file exists, it will return the model flux after applying the RMF
@@ -120,7 +123,8 @@ def apply_resp(self, mflux, exposure=None):
             print("Caution: no response file specified")
             result = mrate
 
-        self.model_counts = result
+        if store_model_counts:
+            self.model_counts = result
         return result
 
 ## ----  Supporting response file objects

From 291be38f142345a331d996655c8816ee4feea696 Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Thu, 3 May 2018 10:06:41 -0400
Subject: [PATCH 16/72] Changed my mind on model_counts thing for now

---
 specutils/spectra/xrayspectrum1d.py | 10 +---------
 1 file changed, 1 insertion(+), 9 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index cd78d2e49..7b342cb96 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -34,11 +34,6 @@ class XraySpectrum1D(Spectrum1D):
     exposure
     arf
     rmf
-
-    Attributes
-    ----------
-    model : numpy.ndarray
-        Stores model values
     """
     def __init__(self, bin_lo, bin_hi, bin_unit, counts, exposure,
                  arf=None, rmf=None, **kwargs):
@@ -55,7 +50,6 @@ def __init__(self, bin_lo, bin_hi, bin_unit, counts, exposure,
         self.exposure = exposure
         self.assign_rmf(rmf)
         self.assign_arf(arf)
-        self.model_counts = np.zeros_like(bin_mid)
         return
 
     # Convenience function for Xray people
@@ -77,7 +71,7 @@ def assign_rmf(self, rmf_inp):
             self.rmf = rmf_inp
         return
 
-    def apply_resp(self, mflux, exposure=None, store_model_counts=True):
+    def apply_resp(self, mflux, exposure=None):
         """
         Given a model flux spectrum, apply the response. In cases where the
         spectrum has both an ARF and an RMF, apply both. Otherwise, apply
@@ -123,8 +117,6 @@ def apply_resp(self, mflux, exposure=None, store_model_counts=True):
             print("Caution: no response file specified")
             result = mrate
 
-        if store_model_counts:
-            self.model_counts = result
         return result
 
 ## ----  Supporting response file objects

From fcd9e25667931d27b1597ca1826429975481d354 Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Wed, 23 May 2018 18:27:59 -0500
Subject: [PATCH 17/72] Hard coded in a rest_value

---
 specutils/spectra/xrayspectrum1d.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index 7b342cb96..2c5f4d86e 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -36,14 +36,15 @@ class XraySpectrum1D(Spectrum1D):
     rmf
     """
     def __init__(self, bin_lo, bin_hi, bin_unit, counts, exposure,
-                 arf=None, rmf=None, **kwargs):
+                 arf=None, rmf=None, rest_value=0.0, **kwargs):
         try:
             axis_unit = u.Unit(bin_unit)
         except:
             axis_unit = _unit_parser(bin_unit)
 
         bin_mid = 0.5 * (bin_lo + bin_hi) * axis_unit
-        Spectrum1D.__init__(self, spectral_axis=bin_mid, flux=counts, **kwargs)
+        Spectrum1D.__init__(self, spectral_axis=bin_mid, flux=counts,
+                            rest_value=rest_value, **kwargs)
 
         self.bin_lo = bin_lo
         self.bin_hi = bin_hi

From fe8c1b5beec19de16bb86995a7a72af8842a6ef0 Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Wed, 23 May 2018 18:29:31 -0500
Subject: [PATCH 18/72] Added unit to rest_value

---
 specutils/spectra/xrayspectrum1d.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index 2c5f4d86e..d700837b7 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -36,7 +36,7 @@ class XraySpectrum1D(Spectrum1D):
     rmf
     """
     def __init__(self, bin_lo, bin_hi, bin_unit, counts, exposure,
-                 arf=None, rmf=None, rest_value=0.0, **kwargs):
+                 arf=None, rmf=None, rest_value=0.0 * u.angstrom, **kwargs):
         try:
             axis_unit = u.Unit(bin_unit)
         except:

From 1c7f27d1eb41ccdafe874565cfc724c17d8885a8 Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Wed, 23 May 2018 18:47:34 -0500
Subject: [PATCH 19/72] Commented out distracting print statements

---
 specutils/spectra/xrayspectrum1d.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index d700837b7..ceb3f9fdf 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -110,12 +110,13 @@ def apply_resp(self, mflux, exposure=None):
         if self.arf is not None:
             mrate  = self.arf.apply_arf(mflux, exposure=exposure)
         else:
+            #print("Caution: no ARF file specified")
             mrate = mflux
 
         if self.rmf is not None:
             result = self.rmf.apply_rmf(mrate)
         else:
-            print("Caution: no response file specified")
+            #print("Caution: no RMF file specified")
             result = mrate
 
         return result

From c6f5aaa55f4cb784def23effb8f50a4f54ec6f69 Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Wed, 23 May 2018 19:00:00 -0500
Subject: [PATCH 20/72] Wrote tests

---
 specutils/tests/test_xrayspectrum1d.py | 35 ++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)
 create mode 100644 specutils/tests/test_xrayspectrum1d.py

diff --git a/specutils/tests/test_xrayspectrum1d.py b/specutils/tests/test_xrayspectrum1d.py
new file mode 100644
index 000000000..f8792a7ff
--- /dev/null
+++ b/specutils/tests/test_xrayspectrum1d.py
@@ -0,0 +1,35 @@
+import numpy as np
+from scipy import optimize
+import astropy.units as u
+from astropy.modeling.powerlaws import PowerLaw1D
+from specutils import XraySpectrum1D
+
+def test_create_from_arrays():
+    # Test that XraySpectrum1D can be initialized
+    amp0, alpha0 = 3.e-3, 2.0
+    powlaw0 = PowerLaw1D(amplitude=amp0, alpha=alpha0, x_0=1.e3)
+    energy = np.linspace(0.2, 10.0, 8000)
+    elo = energy[:-1]
+    ehi = energy[1:]
+    emid = 0.5 * (elo + ehi)
+    counts = np.random.poisson(lam=powlaw0(emid), size=len(emid))
+    test_spec = XraySpectrum1D(elo, ehi, u.keV, counts, exposure=1.0)
+    return test_spec
+
+def test_call_spectrum():
+    # Test that the XraySpectrum1D has attributes that make it unique
+    # to X-ray spectrum
+    test_spec = test_create_from_arrays()
+    assert len(test_spec.counts) == len(test_spec.spectral_axis)
+    assert len(test_spec.bin_lo) == len(test_spec.spectral_axis)
+    assert len(test_spec.bin_hi) == len(test_spec.spectral_axis)
+    return
+
+def test_apply_model():
+    # Test that one can evaluate XraySpectrum1D with a model
+    test_spec = test_create_from_arrays()
+    new_model = PowerLaw1D(amplitude=5.e-3, alpha=1.8, x_0=1.e3)
+    model_flux = new_model(test_spec.spectral_axis.value)
+    ymodel = test_spec.apply_resp(model_flux)
+    assert len(ymodel) == len(test_spec.spectral_axis)
+    return

From c1929350e17a1a62917e69834acc5cd042fcbacc Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Wed, 23 May 2018 19:17:48 -0500
Subject: [PATCH 21/72] Added docstrings

---
 specutils/spectra/xrayspectrum1d.py | 67 +++++++++++++++++++++++++++--
 1 file changed, 64 insertions(+), 3 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index ceb3f9fdf..0b72ccedf 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -13,6 +13,9 @@
 ANGS = ['angs', 'Angs', 'Angstrom', 'angstrom', 'Angstroms', 'angstroms', 'A', 'a']
 
 def _unit_parser(unit_string):
+    """
+    A function for matching unit strings to the correct Astropy unit
+    """
     if unit_string in EV:
         return u.eV
     if unit_string in KEV:
@@ -22,17 +25,51 @@ def _unit_parser(unit_string):
 
 class XraySpectrum1D(Spectrum1D):
     """
-    Spectrum container for holding X-ray spectrum
-    WIP by eblur
+    Spectrum properties specific to X-ray data
 
     Parameters
     ----------
+    bin_lo : numpy.ndarray
+        The left edges for bin values
+
+    bin_hi : numpy.ndarray
+        The right edges for bin values
+
+    bin_unit : string OR astropy.units.Unit
+        Unit for the bin values
+
+    counts : numpy.ndarray
+        Counts histogram for the X-ray spectrum
+
+    exposure : float
+        Exposure time for the dataset
+
+    arf : specutils.ARF or string, default None
+        Strings will be passed to ARF.__init__
+        All other input types are stored as arf attribute
+
+    rmf : specutils.RMF or string, default None
+        Strings will be passed to RMF.__init__
+        All other input types are stored as rmf attribute
+
+    rest_value : astropy.units.Quantity, default 0 Angstrom
+        See Spectrum1D rest_value input
+
+    Attributes
+    ----------
+    Inherits from Spectrum1D object.
+    The following inputs are stored as additional attributes.
+
     bin_lo
+
     bin_hi
-    bin_unit
+
     counts
+
     exposure
+
     arf
+
     rmf
     """
     def __init__(self, bin_lo, bin_hi, bin_unit, counts, exposure,
@@ -59,6 +96,18 @@ def counts(self):
         return self.flux
 
     def assign_arf(self, arf_inp):
+        """
+        Assign an ARF object to the XraySpectrum1D object
+
+        Input
+        -----
+        arf_inp : string
+            File name for the ARF (FITS file)
+
+        Returns
+        -------
+        Modifies the XraySpectrum1D.arf attribute
+        """
         if isinstance(arf_inp, str):
             self.arf = ARF(arf_inp)
         else:
@@ -66,6 +115,18 @@ def assign_arf(self, arf_inp):
         return
 
     def assign_rmf(self, rmf_inp):
+        """
+        Assign an RMF object to the XraySpectrum1D object
+
+        Input
+        -----
+        rmf_inp : string
+            File name for the RMF (FITS file)
+
+        Returns
+        -------
+        Modifies the XraySpectrum1D.rmf attribute
+        """
         if isinstance(rmf_inp, str):
             self.rmf = RMF(rmf_inp)
         else:

From 3314f7dfd7c30ea7389495e129f763091c319990 Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Wed, 23 May 2018 19:19:32 -0500
Subject: [PATCH 22/72] Removed scipy dependence

---
 specutils/tests/test_xrayspectrum1d.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/specutils/tests/test_xrayspectrum1d.py b/specutils/tests/test_xrayspectrum1d.py
index f8792a7ff..53fbae5c0 100644
--- a/specutils/tests/test_xrayspectrum1d.py
+++ b/specutils/tests/test_xrayspectrum1d.py
@@ -1,5 +1,4 @@
 import numpy as np
-from scipy import optimize
 import astropy.units as u
 from astropy.modeling.powerlaws import PowerLaw1D
 from specutils import XraySpectrum1D

From 801e3b661213eb7ba273bf69d415204b2dbf5a8a Mon Sep 17 00:00:00 2001
From: eblur <lia@astro.wisc.edu>
Date: Fri, 1 Jun 2018 10:56:46 -0500
Subject: [PATCH 23/72] Spelled out acronyms, link to edu materials

---
 specutils/spectra/xrayspectrum1d.py | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index 0b72ccedf..05e9cc892 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -12,6 +12,9 @@
 KEV  = ['kev', 'keV']
 ANGS = ['angs', 'Angs', 'Angstrom', 'angstrom', 'Angstroms', 'angstroms', 'A', 'a']
 
+## An introduction to X-ray analysis can be found here:
+## http://cxc.cfa.harvard.edu/xrayschool/talks/intro_xray_analysis.pdf
+
 def _unit_parser(unit_string):
     """
     A function for matching unit strings to the correct Astropy unit
@@ -97,12 +100,12 @@ def counts(self):
 
     def assign_arf(self, arf_inp):
         """
-        Assign an ARF object to the XraySpectrum1D object
+        Assign an area response file (ARF) object to the XraySpectrum1D object
 
         Input
         -----
         arf_inp : string
-            File name for the ARF (FITS file)
+            File name for the area response file (FITS file)
 
         Returns
         -------
@@ -116,12 +119,12 @@ def assign_arf(self, arf_inp):
 
     def assign_rmf(self, rmf_inp):
         """
-        Assign an RMF object to the XraySpectrum1D object
+        Assign a response matrix file (RMF) object to the XraySpectrum1D object
 
         Input
         -----
         rmf_inp : string
-            File name for the RMF (FITS file)
+            File name for the response matrix file (FITS file)
 
         Returns
         -------
@@ -191,7 +194,7 @@ def __init__(self, filename):
 
     def _load_rmf(self, filename):
         """
-        Load an RMF from a FITS file.
+        Load a response matrix file (RMF) from a FITS file.
 
         Parameters
         ----------
@@ -446,7 +449,7 @@ def __init__(self, filename):
 
     def _load_arf(self, filename):
         """
-        Load an ARF from a FITS file.
+        Load an area response file (ARF) from a FITS file.
 
         Parameters
         ----------
@@ -512,7 +515,7 @@ def _load_arf(self, filename):
 
     def apply_arf(self, spec, exposure=None):
         """
-        Fold the spectrum through the ARF.
+        Fold the spectrum through the area response file (ARF).
         The ARF is a single vector encoding the effective area information
         about the detector. A such, applying the ARF is a simple
         multiplication with the input spectrum.

From 4dff31686315a0342673ae173534a6d8f59a0ff7 Mon Sep 17 00:00:00 2001
From: eblur <lia@astro.wisc.edu>
Date: Fri, 1 Jun 2018 11:05:22 -0500
Subject: [PATCH 24/72] Added option to specify RMF FITS extension for response
 matrix

---
 specutils/spectra/xrayspectrum1d.py | 18 +++++++++++++++---
 1 file changed, 15 insertions(+), 3 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index 05e9cc892..68460d8b6 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -136,7 +136,7 @@ def assign_rmf(self, rmf_inp):
             self.rmf = rmf_inp
         return
 
-    def apply_resp(self, mflux, exposure=None):
+    def apply_response(self, mflux, exposure=None):
         """
         Given a model flux spectrum, apply the response. In cases where the
         spectrum has both an ARF and an RMF, apply both. Otherwise, apply
@@ -192,7 +192,7 @@ def __init__(self, filename):
         self._load_rmf(filename)
         pass
 
-    def _load_rmf(self, filename):
+    def _load_rmf(self, filename, extension=None):
         """
         Load a response matrix file (RMF) from a FITS file.
 
@@ -201,6 +201,10 @@ def _load_rmf(self, filename):
         filename : str
             The file name with the RMF file
 
+        extension : str (default None)
+            FITS file extinction keyword, if the response matrix is stored
+            under an extension other tham "MATRIX" or "SPECRESP MATRIX"
+
         Attributes
         ----------
         filename : str
@@ -246,12 +250,20 @@ def _load_rmf(self, filename):
         extnames = np.array([h.name for h in hdulist])
 
         # figure out the right extension to use
-        if "MATRIX" in extnames:
+        if extension is not None:
+            h = hdulist[extension]
+
+        elif "MATRIX" in extnames:
             h = hdulist["MATRIX"]
 
         elif "SPECRESP MATRIX" in extnames:
             h = hdulist["SPECRESP MATRIX"]
 
+        else:
+            print("Cannot find common FITS file extension for response matrix values")
+            print("Please set the `extension` keyword")
+            return
+
         data = h.data
         hdr = h.header
         hdulist.close()

From cdf337340b76068a7b90ba81add91c6efbbbdb60 Mon Sep 17 00:00:00 2001
From: eblur <lia@astro.wisc.edu>
Date: Fri, 1 Jun 2018 11:15:09 -0500
Subject: [PATCH 25/72] corrected typos

---
 specutils/spectra/xrayspectrum1d.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index 68460d8b6..e2eb6ce9c 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -202,8 +202,8 @@ def _load_rmf(self, filename, extension=None):
             The file name with the RMF file
 
         extension : str (default None)
-            FITS file extinction keyword, if the response matrix is stored
-            under an extension other tham "MATRIX" or "SPECRESP MATRIX"
+            FITS file extension keyword, if the response matrix is stored
+            under an extension other than "MATRIX" or "SPECRESP MATRIX"
 
         Attributes
         ----------
@@ -466,7 +466,7 @@ def _load_arf(self, filename):
         Parameters
         ----------
         filename : str
-            The file name with the RMF file
+            The file name with the ARF file
 
         Attributes
         ----------

From 2e4724cc88652ee19ef19b450b7aa74152d4dbb3 Mon Sep 17 00:00:00 2001
From: eblur <lia@astro.wisc.edu>
Date: Fri, 1 Jun 2018 11:19:14 -0500
Subject: [PATCH 26/72] Removing superfluous returns and pass

---
 specutils/spectra/xrayspectrum1d.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index e2eb6ce9c..610dea245 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -91,7 +91,6 @@ def __init__(self, bin_lo, bin_hi, bin_unit, counts, exposure,
         self.exposure = exposure
         self.assign_rmf(rmf)
         self.assign_arf(arf)
-        return
 
     # Convenience function for Xray people
     @property
@@ -115,7 +114,6 @@ def assign_arf(self, arf_inp):
             self.arf = ARF(arf_inp)
         else:
             self.arf = arf_inp
-        return
 
     def assign_rmf(self, rmf_inp):
         """
@@ -190,7 +188,6 @@ def apply_response(self, mflux, exposure=None):
 class RMF(object):
     def __init__(self, filename):
         self._load_rmf(filename)
-        pass
 
     def _load_rmf(self, filename, extension=None):
         """

From a8a82450189dc3a4fb2863740e40797e58e0ddac Mon Sep 17 00:00:00 2001
From: eblur <lia@astro.wisc.edu>
Date: Fri, 1 Jun 2018 11:22:03 -0500
Subject: [PATCH 27/72] Catch ValueError

---
 specutils/spectra/xrayspectrum1d.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index 610dea245..34b34e7d8 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -79,7 +79,7 @@ def __init__(self, bin_lo, bin_hi, bin_unit, counts, exposure,
                  arf=None, rmf=None, rest_value=0.0 * u.angstrom, **kwargs):
         try:
             axis_unit = u.Unit(bin_unit)
-        except:
+        except ValueError:
             axis_unit = _unit_parser(bin_unit)
 
         bin_mid = 0.5 * (bin_lo + bin_hi) * axis_unit

From 5d4d52c7453759d762544389f1239f582d0627d5 Mon Sep 17 00:00:00 2001
From: eblur <lia@astro.wisc.edu>
Date: Fri, 1 Jun 2018 11:27:25 -0500
Subject: [PATCH 28/72] Spelled out ARF and RMF class names

---
 specutils/spectra/xrayspectrum1d.py | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index 34b34e7d8..3c452c7d3 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -5,7 +5,7 @@
 from astropy.io import fits
 from .spectrum1d import Spectrum1D
 
-__all__ = ['XraySpectrum1D', 'ARF', 'RMF']
+__all__ = ['XraySpectrum1D', 'AreaResponse', 'ResponseMatrix']
 
 # For dealing with varied unit string choices
 EV   = ['eV', 'ev']
@@ -47,12 +47,12 @@ class XraySpectrum1D(Spectrum1D):
     exposure : float
         Exposure time for the dataset
 
-    arf : specutils.ARF or string, default None
-        Strings will be passed to ARF.__init__
+    arf : specutils.AreaResponse or string, default None
+        Strings will be passed to AreaResponse.__init__
         All other input types are stored as arf attribute
 
-    rmf : specutils.RMF or string, default None
-        Strings will be passed to RMF.__init__
+    rmf : specutils.ResponseMatrix or string, default None
+        Strings will be passed to ResponseMatrix.__init__
         All other input types are stored as rmf attribute
 
     rest_value : astropy.units.Quantity, default 0 Angstrom
@@ -111,7 +111,7 @@ def assign_arf(self, arf_inp):
         Modifies the XraySpectrum1D.arf attribute
         """
         if isinstance(arf_inp, str):
-            self.arf = ARF(arf_inp)
+            self.arf = AreaResponse(arf_inp)
         else:
             self.arf = arf_inp
 
@@ -129,7 +129,7 @@ def assign_rmf(self, rmf_inp):
         Modifies the XraySpectrum1D.rmf attribute
         """
         if isinstance(rmf_inp, str):
-            self.rmf = RMF(rmf_inp)
+            self.rmf = ResponseMatrix(rmf_inp)
         else:
             self.rmf = rmf_inp
         return
@@ -185,7 +185,7 @@ def apply_response(self, mflux, exposure=None):
 
 ## ----  Supporting response file objects
 
-class RMF(object):
+class ResponseMatrix(object):
     def __init__(self, filename):
         self._load_rmf(filename)
 
@@ -449,7 +449,7 @@ def apply_rmf(self, spec):
         return counts[:self.detchans]
 
 
-class ARF(object):
+class AreaResponse(object):
 
     def __init__(self, filename):
 

From a297c452cdee7f22b15ebc52585a7712f95b29f9 Mon Sep 17 00:00:00 2001
From: eblur <lia@astro.wisc.edu>
Date: Fri, 1 Jun 2018 11:30:06 -0500
Subject: [PATCH 29/72] updated docstring

---
 specutils/spectra/xrayspectrum1d.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index 3c452c7d3..cb99d21f8 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -137,8 +137,8 @@ def assign_rmf(self, rmf_inp):
     def apply_response(self, mflux, exposure=None):
         """
         Given a model flux spectrum, apply the response. In cases where the
-        spectrum has both an ARF and an RMF, apply both. Otherwise, apply
-        whatever response is in RMF.
+        spectrum has both an area response file (ARF) and a response matrix
+        file (RMF), apply both. Otherwise, apply whatever response is in RMF.
 
         The model flux spectrum *must* be created using the same units and
         bins as in the ARF (where the ARF exists)!

From 86f4a3b73772a05674f5fd7a2ed156aa018bab9b Mon Sep 17 00:00:00 2001
From: eblur <lia@astro.wisc.edu>
Date: Fri, 1 Jun 2018 11:34:47 -0500
Subject: [PATCH 30/72] Updated tests

---
 specutils/tests/test_xrayspectrum1d.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/specutils/tests/test_xrayspectrum1d.py b/specutils/tests/test_xrayspectrum1d.py
index 53fbae5c0..1e1f45bbe 100644
--- a/specutils/tests/test_xrayspectrum1d.py
+++ b/specutils/tests/test_xrayspectrum1d.py
@@ -29,6 +29,6 @@ def test_apply_model():
     test_spec = test_create_from_arrays()
     new_model = PowerLaw1D(amplitude=5.e-3, alpha=1.8, x_0=1.e3)
     model_flux = new_model(test_spec.spectral_axis.value)
-    ymodel = test_spec.apply_resp(model_flux)
+    ymodel = test_spec.apply_response(model_flux)
     assert len(ymodel) == len(test_spec.spectral_axis)
     return

From 769c923b6ba83719db4cf79f3443801e5b0384d9 Mon Sep 17 00:00:00 2001
From: Lia Corrales <lia@astro.wisc.edu>
Date: Tue, 12 Jun 2018 20:38:39 +0200
Subject: [PATCH 31/72] initialize attributes to None before loading from file

---
 specutils/spectra/xrayspectrum1d.py | 31 +++++++++++++++++++++--------
 1 file changed, 23 insertions(+), 8 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index cb99d21f8..5d98c79bc 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -187,9 +187,6 @@ def apply_response(self, mflux, exposure=None):
 
 class ResponseMatrix(object):
     def __init__(self, filename):
-        self._load_rmf(filename)
-
-    def _load_rmf(self, filename, extension=None):
         """
         Load a response matrix file (RMF) from a FITS file.
 
@@ -237,6 +234,19 @@ def _load_rmf(self, filename, extension=None):
             The number of channels in the detector
 
         """
+        self.filename = ""
+        self.offset = None
+        self.n_grp = None
+        self.f_chan = None
+        self.n_chan = None
+        self.matrix = None
+        self.energ_lo = None
+        self.energ_hi = None
+        self.energ_unit = None
+        self.detchans = None
+        self._load_rmf(filename)
+
+    def _load_rmf(self, filename, extension=None):
         # open the FITS file and extract the MATRIX extension
         # which contains the redistribution matrix and
         # anxillary information
@@ -452,11 +462,6 @@ def apply_rmf(self, spec):
 class AreaResponse(object):
 
     def __init__(self, filename):
-
-        self._load_arf(filename)
-        pass
-
-    def _load_arf(self, filename):
         """
         Load an area response file (ARF) from a FITS file.
 
@@ -492,6 +497,16 @@ def _load_arf(self, filename):
             Average exposure time for the dataset
             (takes telescope dithering into account)
         """
+        self.filename = ""
+        self.e_low = None
+        self.e_high = None
+        self.e_unit = None
+        self.specresp = None
+        self.fracexpo = None
+        self.exposure = None
+        self._load_arf(filename)
+
+    def _load_arf(self, filename):
         # open the FITS file and extract the MATRIX extension
         # which contains the redistribution matrix and
         # anxillary information

From a89af6bc769d05fabd86350a0a12ac3518adedc3 Mon Sep 17 00:00:00 2001
From: Lia Corrales <lia@astro.wisc.edu>
Date: Tue, 12 Jun 2018 20:39:55 +0200
Subject: [PATCH 32/72] save filename attribute for attempting load function

---
 specutils/spectra/xrayspectrum1d.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index 5d98c79bc..58dcc3b73 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -234,7 +234,7 @@ def __init__(self, filename):
             The number of channels in the detector
 
         """
-        self.filename = ""
+        self.filename = filename
         self.offset = None
         self.n_grp = None
         self.f_chan = None
@@ -251,7 +251,6 @@ def _load_rmf(self, filename, extension=None):
         # which contains the redistribution matrix and
         # anxillary information
         hdulist = fits.open(filename)
-        self.filename = filename
 
         # get all the extension names
         extnames = np.array([h.name for h in hdulist])
@@ -497,7 +496,7 @@ def __init__(self, filename):
             Average exposure time for the dataset
             (takes telescope dithering into account)
         """
-        self.filename = ""
+        self.filename = filename
         self.e_low = None
         self.e_high = None
         self.e_unit = None
@@ -511,7 +510,6 @@ def _load_arf(self, filename):
         # which contains the redistribution matrix and
         # anxillary information
         hdulist = fits.open(filename)
-        self.filename = filename
 
         h = hdulist["SPECRESP"]
         data = h.data

From dfb9475112ea70dde9444eac8516fc5efaee1dea Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Tue, 1 May 2018 17:26:21 -0400
Subject: [PATCH 33/72] First pass at XraySpectrum1D

---
 specutils/spectra/xrayspectrum1d.py | 47 +++++++++++++++++++++++++++++
 1 file changed, 47 insertions(+)
 create mode 100644 specutils/spectra/xrayspectrum1d.py

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
new file mode 100644
index 000000000..b7556ad77
--- /dev/null
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -0,0 +1,47 @@
+import logging
+
+import numpy as np
+from astropy import units as u
+from .spectrum1d import Spectrum1D
+
+__all__ = ['XraySpectrum1D']
+
+# For dealing with varied unit string choices
+EV   = ['eV', 'ev']
+KEV  = ['kev', 'keV']
+ANGS = ['angs', 'Angs', 'Angstrom', 'angstrom', 'Angstroms', 'angstroms', 'A', 'a']
+
+def _unit_parser(unit_string):
+    if unit_string in EV:
+        return u.eV
+    if unit_string in KEV:
+        return u.keV
+    if unit_string in ANGS:
+        return u.angstrom
+
+class XraySpectrum1D(Spectrum1D):
+    """
+    Spectrum container for holding X-ray spectrum
+    WIP by eblur
+
+    Parameters
+    ----------
+    bin_lo
+    bin_hi
+    bin_unit
+    counts
+    arf
+    rmf
+    """
+    def __init__(self, bin_lo, bin_hi, bin_unit, counts, arf=None, rmf=None):
+        try:
+            axis_unit = u.Unit(bin_unit)
+        else:
+            axis_unit = _unit_parser(bin_unit)
+
+        bin_mid = 0.5 * (bin_lo + bin_hi) * unit
+        Spectrum1D.__init__(self, spectral_axis=bin_mid, flux=counts)
+
+        self.arf = arf
+        self.rmf = rmf
+        return

From 2fa21425147157573e5c416de8d3a9678036be08 Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Tue, 1 May 2018 17:40:28 -0400
Subject: [PATCH 34/72] Can load an X-ray spectrum

---
 specutils/spectra/__init__.py       | 4 ++++
 specutils/spectra/xrayspectrum1d.py | 4 ++--
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/specutils/spectra/__init__.py b/specutils/spectra/__init__.py
index 8ce324ecb..05d5d14c4 100644
--- a/specutils/spectra/__init__.py
+++ b/specutils/spectra/__init__.py
@@ -3,6 +3,10 @@
 `~astropy.nddata.NDData`-inherited classes used for storing the spectrum data.
 """
 from .spectrum1d import *  # noqa
+<<<<<<< HEAD
 from .spectral_region import *  # noqa
 from .spectrum_collection import *  #noqa
 from .spectrum_list import * #noqa
+=======
+from .xrayspectrum1d import *
+>>>>>>> Can load an X-ray spectrum
diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index b7556ad77..d57146f97 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -36,10 +36,10 @@ class XraySpectrum1D(Spectrum1D):
     def __init__(self, bin_lo, bin_hi, bin_unit, counts, arf=None, rmf=None):
         try:
             axis_unit = u.Unit(bin_unit)
-        else:
+        except:
             axis_unit = _unit_parser(bin_unit)
 
-        bin_mid = 0.5 * (bin_lo + bin_hi) * unit
+        bin_mid = 0.5 * (bin_lo + bin_hi) * axis_unit
         Spectrum1D.__init__(self, spectral_axis=bin_mid, flux=counts)
 
         self.arf = arf

From 0f37ccd0668398c6f31ae73f32fbd13b110a673a Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Tue, 1 May 2018 17:44:41 -0400
Subject: [PATCH 35/72] Added  attribute

---
 specutils/spectra/xrayspectrum1d.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index d57146f97..b939b40d1 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -45,3 +45,8 @@ def __init__(self, bin_lo, bin_hi, bin_unit, counts, arf=None, rmf=None):
         self.arf = arf
         self.rmf = rmf
         return
+
+    # Convenience function for Xray people
+    @property
+    def counts(self):
+        return self.flux

From 56612ca4badb7127f5a1186aaa771c849d132797 Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Wed, 2 May 2018 13:53:39 -0400
Subject: [PATCH 36/72] Added ARF and RMF objects

---
 specutils/spectra/xrayspectrum1d.py | 326 +++++++++++++++++++++++++++-
 1 file changed, 325 insertions(+), 1 deletion(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index b939b40d1..e36a500a6 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -4,7 +4,7 @@
 from astropy import units as u
 from .spectrum1d import Spectrum1D
 
-__all__ = ['XraySpectrum1D']
+__all__ = ['XraySpectrum1D', 'ARF', 'RMF']
 
 # For dealing with varied unit string choices
 EV   = ['eV', 'ev']
@@ -50,3 +50,327 @@ def __init__(self, bin_lo, bin_hi, bin_unit, counts, arf=None, rmf=None):
     @property
     def counts(self):
         return self.flux
+
+## ----  Supporting response file objects
+
+class RMF(object):
+    def __init__(self, filename):
+        self._load_rmf(filename)
+        pass
+
+    def _load_rmf(self, filename):
+        """
+        Load an RMF from a FITS file.
+
+        Parameters
+        ----------
+        filename : str
+            The file name with the RMF file
+
+        Attributes
+        ----------
+        n_grp : numpy.ndarray
+            the Array with the number of channels in each
+            channel set
+
+        f_chan : numpy.ndarray
+            The starting channel for each channel group;
+            If an element i in n_grp > 1, then the resulting
+            row entry in f_chan will be a list of length n_grp[i];
+            otherwise it will be a single number
+
+        n_chan : numpy.ndarray
+            The number of channels in each channel group. The same
+            logic as for f_chan applies
+
+        matrix : numpy.ndarray
+            The redistribution matrix as a flattened 1D vector
+
+        energ_lo : numpy.ndarray
+            The lower edges of the energy bins
+
+        energ_hi : numpy.ndarray
+            The upper edges of the energy bins
+
+        detchans : int
+            The number of channels in the detector
+
+        """
+        # open the FITS file and extract the MATRIX extension
+        # which contains the redistribution matrix and
+        # anxillary information
+        hdulist = fits.open(filename)
+
+        # get all the extension names
+        extnames = np.array([h.name for h in hdulist])
+
+        # figure out the right extension to use
+        if "MATRIX" in extnames:
+            h = hdulist["MATRIX"]
+
+        elif "SPECRESP MATRIX" in extnames:
+            h = hdulist["SPECRESP MATRIX"]
+
+        data = h.data
+        hdr = h.header
+        hdulist.close()
+
+        # extract + store the attributes described in the docstring
+        n_grp = np.array(data.field("N_GRP"))
+        f_chan = np.array(data.field('F_CHAN'))
+        n_chan = np.array(data.field("N_CHAN"))
+        matrix = np.array(data.field("MATRIX"))
+
+        self.energ_lo = np.array(data.field("ENERG_LO"))
+        self.energ_hi = np.array(data.field("ENERG_HI"))
+        self.energ_unit = data.columns["ENERG_LO"].unit
+        self.detchans = hdr["DETCHANS"]
+        self.offset = self.__get_tlmin(h)
+
+        # flatten the variable-length arrays
+        self.n_grp, self.f_chan, self.n_chan, self.matrix = \
+                self._flatten_arrays(n_grp, f_chan, n_chan, matrix)
+
+        return
+
+    def __get_tlmin(self, h):
+        """
+        Get the tlmin keyword for `F_CHAN`.
+
+        Parameters
+        ----------
+        h : an astropy.io.fits.hdu.table.BinTableHDU object
+            The extension containing the `F_CHAN` column
+
+        Returns
+        -------
+        tlmin : int
+            The tlmin keyword
+        """
+        # get the header
+        hdr = h.header
+        # get the keys of all
+        keys = np.array(list(hdr.keys()))
+
+        # find the place where the tlmin keyword is defined
+        t = np.array(["TLMIN" in k for k in keys])
+
+        # get the index of the TLMIN keyword
+        tlmin_idx = np.hstack(np.where(t))[0]
+
+        # get the corresponding value
+        tlmin = np.int(list(hdr.items())[tlmin_idx][1])
+
+        return tlmin
+
+    def _flatten_arrays(self, n_grp, f_chan, n_chan, matrix):
+
+        if not len(n_grp) == len(f_chan) == len(n_chan) == len(matrix):
+            raise ValueError("Arrays must be of same length!")
+
+        # find all non-zero groups
+        nz_idx = (n_grp > 0)
+
+        # stack all non-zero rows in the matrix
+        matrix_flat = np.hstack(matrix[nz_idx])
+
+        # stack all nonzero rows in n_chan and f_chan
+        #n_chan_flat = np.hstack(n_chan[nz_idx])
+        #f_chan_flat = np.hstack(f_chan[nz_idx])
+
+        # some matrices actually have more elements
+        # than groups in `n_grp`, so we'll only pick out
+        # those values that have a correspondence in
+        # n_grp
+        f_chan_new = []
+        n_chan_new = []
+        for i,t in enumerate(nz_idx):
+            if t:
+                n = n_grp[i]
+                f = f_chan[i]
+                nc = n_chan[i]
+                if np.size(f) == 1:
+                    f_chan_new.append(f)
+                    n_chan_new.append(nc)
+                else:
+                    f_chan_new.append(f[:n])
+                    n_chan_new.append(nc[:n])
+
+        n_chan_flat = np.hstack(n_chan_new)
+        f_chan_flat = np.hstack(f_chan_new)
+
+        # if n_chan is zero, we'll remove those as well.
+        nz_idx2 = (n_chan_flat > 0)
+        n_chan_flat = n_chan_flat[nz_idx2]
+        f_chan_flat = f_chan_flat[nz_idx2]
+
+        return n_grp, f_chan_flat, n_chan_flat, matrix_flat
+
+    def apply_rmf(self, spec):
+        """
+        Fold the spectrum through the redistribution matrix.
+
+        The redistribution matrix is saved as a flattened 1-dimensional
+        vector to save space. In reality, for each entry in the flux
+        vector, there exists one or more sets of channels that this
+        flux is redistributed into. The additional arrays `n_grp`,
+        `f_chan` and `n_chan` store this information:
+            * `n_group` stores the number of channel groups for each
+              energy bin
+            * `f_chan` stores the *first channel* that each channel
+              for each channel set
+            * `n_chan` stores the number of channels in each channel
+              set
+
+        As a result, for a given energy bin i, we need to look up the
+        number of channel sets in `n_grp` for that energy bin. We
+        then need to loop over the number of channel sets. For each
+        channel set, we look up the first channel into which flux
+        will be distributed as well as the number of channels in the
+        group. We then need to also loop over the these channels and
+        actually use the corresponding elements in the redistribution
+        matrix to redistribute the photon flux into channels.
+
+        All of this is basically a big bookkeeping exercise in making
+        sure to get the indices right.
+
+        Parameters
+        ----------
+        spec : numpy.ndarray
+            The (model) spectrum to be folded
+
+        Returns
+        -------
+        counts : numpy.ndarray
+            The (model) spectrum after folding, in
+            counts/s/channel
+
+        """
+        # get the number of channels in the data
+        nchannels = spec.shape[0]
+
+        # an empty array for the output counts
+        counts = np.zeros(nchannels)
+
+        # index for n_chan and f_chan incrementation
+        k = 0
+
+        # index for the response matrix incrementation
+        resp_idx = 0
+
+        # loop over all channels
+        for i in range(nchannels):
+
+            # this is the current bin in the flux spectrum to
+            # be folded
+            source_bin_i = spec[i]
+
+            # get the current number of groups
+            current_num_groups = self.n_grp[i]
+
+            # loop over the current number of groups
+            for j in range(current_num_groups):
+
+                current_num_chans = int(self.n_chan[k])
+
+                if current_num_chans == 0:
+                    k += 1
+                    resp_idx += current_num_chans
+                    continue
+
+
+                else:
+                    # get the right index for the start of the counts array
+                    # to put the data into
+                    counts_idx = int(self.f_chan[k] - self.offset)
+                    # this is the current number of channels to use
+
+                    k += 1
+                    # add the flux to the subarray of the counts array that starts with
+                    # counts_idx and runs over current_num_chans channels
+                    counts[counts_idx:counts_idx +
+                                      current_num_chans] += self.matrix[resp_idx:resp_idx +
+                                                                                 current_num_chans] * \
+                                                                np.float(source_bin_i)
+                    # iterate the response index for next round
+                    resp_idx += current_num_chans
+
+
+        return counts[:self.detchans]
+
+
+class ARF(object):
+
+    def __init__(self, filename):
+
+        self._load_arf(filename)
+        pass
+
+    def _load_arf(self, filename):
+        """
+        Load an ARF from a FITS file.
+        Parameters
+        ----------
+        filename : str
+            The file name with the RMF file
+        Attributes
+        ----------
+        """
+        # open the FITS file and extract the MATRIX extension
+        # which contains the redistribution matrix and
+        # anxillary information
+        hdulist = fits.open(filename)
+        h = hdulist["SPECRESP"]
+        data = h.data
+        hdr = h.header
+        hdulist.close()
+
+        # extract + store the attributes described in the docstring
+
+        self.e_low  = np.array(data.field("ENERG_LO"))
+        self.e_high = np.array(data.field("ENERG_HI"))
+        self.e_unit = data.columns["ENERG_LO"].unit
+        self.specresp = np.array(data.field("SPECRESP"))
+
+        if "EXPOSURE" in list(hdr.keys()):
+            self.exposure = hdr["EXPOSURE"]
+        else:
+            self.exposure = 1.0
+
+        if "FRACEXPO" in data.columns.names:
+            self.fracexpo = data["FRACEXPO"]
+        else:
+            self.fracexpo = 1.0
+
+        return
+
+    def apply_arf(self, spec, exposure=None):
+        """
+        Fold the spectrum through the ARF.
+        The ARF is a single vector encoding the effective area information
+        about the detector. A such, applying the ARF is a simple
+        multiplication with the input spectrum.
+        Parameters
+        ----------
+        spec : numpy.ndarray
+            The (model) spectrum to be folded
+        exposure : float, default None
+            Value for the exposure time. By default, `apply_arf` will use the
+            exposure keyword from the ARF file. If this exposure time is not
+            correct (for example when simulated spectra use a different exposure
+            time and the ARF from a real observation), one can override the
+            default exposure by setting the `exposure` keyword to the correct
+            value.
+        Returns
+        -------
+        s_arf : numpy.ndarray
+            The (model) spectrum after folding, in
+            counts/s/channel
+        """
+        assert spec.shape[0] == self.specresp.shape[0], "The input spectrum must " \
+                                                      "be of same size as the " \
+                                                      "ARF array."
+        if exposure is None:
+            return np.array(spec) * self.specresp * self.exposure
+        else:
+            return np.array(spec) * self.specresp * exposure

From b7303e75966516657bb8ae88a5e1b5f4dd3cda2b Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Wed, 2 May 2018 14:07:50 -0400
Subject: [PATCH 37/72] Added assign_rmf and assign_arf methods

---
 specutils/spectra/xrayspectrum1d.py | 29 +++++++++++++++++++++++++++--
 1 file changed, 27 insertions(+), 2 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index e36a500a6..a371b94a5 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -42,8 +42,8 @@ def __init__(self, bin_lo, bin_hi, bin_unit, counts, arf=None, rmf=None):
         bin_mid = 0.5 * (bin_lo + bin_hi) * axis_unit
         Spectrum1D.__init__(self, spectral_axis=bin_mid, flux=counts)
 
-        self.arf = arf
-        self.rmf = rmf
+        self.assign_rmf(rmf)
+        self.assign_arf(rmf)
         return
 
     # Convenience function for Xray people
@@ -51,6 +51,21 @@ def __init__(self, bin_lo, bin_hi, bin_unit, counts, arf=None, rmf=None):
     def counts(self):
         return self.flux
 
+    def assign_arf(self, arf_inp):
+        if isinstance(arf_inp, str):
+            self.arf = ARF(arf_inp)
+        else:
+            self.arf = arf_inp
+        return
+
+    def assign_rmf(self, rmf_inp):
+        if isinstance(rmf_inp, str):
+            self.rmf = RMF(rmf_inp)
+        else:
+            self.rmf = rmf_inp
+        return
+
+
 ## ----  Supporting response file objects
 
 class RMF(object):
@@ -69,6 +84,9 @@ def _load_rmf(self, filename):
 
         Attributes
         ----------
+        filename : str
+            The file name that the RMF was drawn from
+
         n_grp : numpy.ndarray
             the Array with the number of channels in each
             channel set
@@ -100,6 +118,7 @@ def _load_rmf(self, filename):
         # which contains the redistribution matrix and
         # anxillary information
         hdulist = fits.open(filename)
+        self.filename = filename
 
         # get all the extension names
         extnames = np.array([h.name for h in hdulist])
@@ -309,17 +328,23 @@ def __init__(self, filename):
     def _load_arf(self, filename):
         """
         Load an ARF from a FITS file.
+
         Parameters
         ----------
         filename : str
             The file name with the RMF file
+
         Attributes
         ----------
+        filename : str
+            The file name that the ARF was drawn from
         """
         # open the FITS file and extract the MATRIX extension
         # which contains the redistribution matrix and
         # anxillary information
         hdulist = fits.open(filename)
+        self.filename = filename
+        
         h = hdulist["SPECRESP"]
         data = h.data
         hdr = h.header

From 003b63696503f64d17f44671bc6995fc3b9b9224 Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Wed, 2 May 2018 14:16:13 -0400
Subject: [PATCH 38/72] Added exposure input

---
 specutils/spectra/xrayspectrum1d.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index a371b94a5..51de9e726 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -33,7 +33,7 @@ class XraySpectrum1D(Spectrum1D):
     arf
     rmf
     """
-    def __init__(self, bin_lo, bin_hi, bin_unit, counts, arf=None, rmf=None):
+    def __init__(self, bin_lo, bin_hi, bin_unit, counts, exposure, arf=None, rmf=None):
         try:
             axis_unit = u.Unit(bin_unit)
         except:
@@ -42,6 +42,7 @@ def __init__(self, bin_lo, bin_hi, bin_unit, counts, arf=None, rmf=None):
         bin_mid = 0.5 * (bin_lo + bin_hi) * axis_unit
         Spectrum1D.__init__(self, spectral_axis=bin_mid, flux=counts)
 
+        self.exposure = exposure
         self.assign_rmf(rmf)
         self.assign_arf(rmf)
         return
@@ -344,7 +345,7 @@ def _load_arf(self, filename):
         # anxillary information
         hdulist = fits.open(filename)
         self.filename = filename
-        
+
         h = hdulist["SPECRESP"]
         data = h.data
         hdr = h.header

From ce4349e4e76c20c69bbedc0fab8a154fbc165796 Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Wed, 2 May 2018 14:18:22 -0400
Subject: [PATCH 39/72] Fixed bugs

---
 specutils/spectra/xrayspectrum1d.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index 51de9e726..fade12358 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -2,6 +2,7 @@
 
 import numpy as np
 from astropy import units as u
+from astropy.io import fits
 from .spectrum1d import Spectrum1D
 
 __all__ = ['XraySpectrum1D', 'ARF', 'RMF']
@@ -44,7 +45,7 @@ def __init__(self, bin_lo, bin_hi, bin_unit, counts, exposure, arf=None, rmf=Non
 
         self.exposure = exposure
         self.assign_rmf(rmf)
-        self.assign_arf(rmf)
+        self.assign_arf(arf)
         return
 
     # Convenience function for Xray people

From 753ab5eb08f712fa53ab2f78a41d941fcbd3da32 Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Wed, 2 May 2018 14:30:44 -0400
Subject: [PATCH 40/72] Updated docstrings

---
 specutils/spectra/xrayspectrum1d.py | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index fade12358..72c5bd11e 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -112,6 +112,9 @@ def _load_rmf(self, filename):
         energ_hi : numpy.ndarray
             The upper edges of the energy bins
 
+        energ_unit : str
+            Description of the energy units used
+
         detchans : int
             The number of channels in the detector
 
@@ -340,6 +343,28 @@ def _load_arf(self, filename):
         ----------
         filename : str
             The file name that the ARF was drawn from
+
+        e_low : numpy.ndarray
+            The lower edges of the energy bins
+
+        e_high : numpy.ndarray
+            The upper edges of the energy bins
+
+        e_unit : str
+            Description of the energy units used
+
+        specresp : numpy.ndarray
+            Description of the energy dependent telescope response area
+
+        fracexpo : float or numpy.ndarray
+            Fractional exposure time for the spectrum
+            (sometimes constant, sometimes dependent on spectral channel).
+            These values are stored for reference; generally, they are already
+            accounted for in the specresp array.
+
+        exposure :
+            Average exposure time for the dataset
+            (takes telescope dithering into account)
         """
         # open the FITS file and extract the MATRIX extension
         # which contains the redistribution matrix and

From 4f195e1be723c2b9e833156ac47de979fdd693f8 Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Wed, 2 May 2018 14:36:08 -0400
Subject: [PATCH 41/72] Store bin and energy units as astropy.units.Unit

---
 specutils/spectra/xrayspectrum1d.py | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index 72c5bd11e..2b98164aa 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -31,6 +31,7 @@ class XraySpectrum1D(Spectrum1D):
     bin_hi
     bin_unit
     counts
+    exposure
     arf
     rmf
     """
@@ -43,6 +44,7 @@ def __init__(self, bin_lo, bin_hi, bin_unit, counts, exposure, arf=None, rmf=Non
         bin_mid = 0.5 * (bin_lo + bin_hi) * axis_unit
         Spectrum1D.__init__(self, spectral_axis=bin_mid, flux=counts)
 
+        self.bin_unit = axis_unit # keep for reference
         self.exposure = exposure
         self.assign_rmf(rmf)
         self.assign_arf(arf)
@@ -112,7 +114,7 @@ def _load_rmf(self, filename):
         energ_hi : numpy.ndarray
             The upper edges of the energy bins
 
-        energ_unit : str
+        energ_unit : astropy.units.Unit
             Description of the energy units used
 
         detchans : int
@@ -147,7 +149,7 @@ def _load_rmf(self, filename):
 
         self.energ_lo = np.array(data.field("ENERG_LO"))
         self.energ_hi = np.array(data.field("ENERG_HI"))
-        self.energ_unit = data.columns["ENERG_LO"].unit
+        self.energ_unit = _unit_parser(data.columns["ENERG_LO"].unit)
         self.detchans = hdr["DETCHANS"]
         self.offset = self.__get_tlmin(h)
 
@@ -350,7 +352,7 @@ def _load_arf(self, filename):
         e_high : numpy.ndarray
             The upper edges of the energy bins
 
-        e_unit : str
+        e_unit : astropy.units.Unit
             Description of the energy units used
 
         specresp : numpy.ndarray
@@ -381,7 +383,7 @@ def _load_arf(self, filename):
 
         self.e_low  = np.array(data.field("ENERG_LO"))
         self.e_high = np.array(data.field("ENERG_HI"))
-        self.e_unit = data.columns["ENERG_LO"].unit
+        self.e_unit = _unit_parser(data.columns["ENERG_LO"].unit)
         self.specresp = np.array(data.field("SPECRESP"))
 
         if "EXPOSURE" in list(hdr.keys()):

From 67493c523e1f30624db50cca1e204319fc1fa942 Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Wed, 2 May 2018 16:31:14 -0400
Subject: [PATCH 42/72] Added bin_lo and hi because wcs.bin_edges did not exist

---
 specutils/spectra/xrayspectrum1d.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index 2b98164aa..d209c988b 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -35,15 +35,18 @@ class XraySpectrum1D(Spectrum1D):
     arf
     rmf
     """
-    def __init__(self, bin_lo, bin_hi, bin_unit, counts, exposure, arf=None, rmf=None):
+    def __init__(self, bin_lo, bin_hi, bin_unit, counts, exposure,
+                 arf=None, rmf=None, **kwargs):
         try:
             axis_unit = u.Unit(bin_unit)
         except:
             axis_unit = _unit_parser(bin_unit)
 
         bin_mid = 0.5 * (bin_lo + bin_hi) * axis_unit
-        Spectrum1D.__init__(self, spectral_axis=bin_mid, flux=counts)
+        Spectrum1D.__init__(self, spectral_axis=bin_mid, flux=counts, **kwargs)
 
+        self.bin_lo = bin_lo
+        self.bin_hi = bin_hi
         self.bin_unit = axis_unit # keep for reference
         self.exposure = exposure
         self.assign_rmf(rmf)

From 7974939f7a92a44b437aad94a8c31b202e59e14f Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Wed, 2 May 2018 16:34:35 -0400
Subject: [PATCH 43/72] Added apply_resp method

---
 specutils/spectra/xrayspectrum1d.py | 44 +++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index d209c988b..765e77241 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -72,6 +72,50 @@ def assign_rmf(self, rmf_inp):
             self.rmf = rmf_inp
         return
 
+    def apply_resp(self, mflux, exposure=None):
+        """
+        Given a model flux spectrum, apply the response. In cases where the
+        spectrum has both an ARF and an RMF, apply both. Otherwise, apply
+        whatever response is in RMF.
+
+        The model flux spectrum *must* be created using the same units and
+        bins as in the ARF (where the ARF exists)!
+
+        Parameters
+        ----------
+        mflux : iterable
+            A list or array with the model flux values in ergs/keV/s/cm^-2
+
+        exposure : float, default None
+            By default, the exposure stored in the ARF will be used to compute
+            the total counts per bin over the effective observation time.
+            In cases where this might be incorrect (e.g. for simulated spectra
+            where the pha file might have a different exposure value than the
+            ARF), this keyword provides the functionality to override the
+            default behaviour and manually set the exposure time to use.
+
+        Returns
+        -------
+        count_model : numpy.ndarray
+            The model spectrum in units of counts/bin
+
+        If no ARF file exists, it will return the model flux after applying the RMF
+        If no RMF file exists, it will return the model flux after applying the ARF (with a warning)
+        If no ARF and no RMF, it will return the model flux spectrum (with a warning)
+        """
+
+        if self.arf is not None:
+            mrate  = self.arf.apply_arf(mflux, exposure=exposure)
+        else:
+            mrate = mflux
+
+        if self.rmf is not None:
+            count_model = self.rmf.apply_rmf(mrate)
+            return count_model
+        else:
+            print("Caution: no response file specified")
+            return mrate
+
 
 ## ----  Supporting response file objects
 

From 7f54eaeaca2e3d132d76da83789986fce76abf7e Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Wed, 2 May 2018 16:52:47 -0400
Subject: [PATCH 44/72] Adjust apply_resp output if spectrum is stored by
 wavelength

---
 specutils/spectra/xrayspectrum1d.py | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index 765e77241..b9f2df62d 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -110,11 +110,18 @@ def apply_resp(self, mflux, exposure=None):
             mrate = mflux
 
         if self.rmf is not None:
-            count_model = self.rmf.apply_rmf(mrate)
-            return count_model
+            result = self.rmf.apply_rmf(mrate)
         else:
             print("Caution: no response file specified")
-            return mrate
+            result = mrate
+
+        # The response is always stored according to energy
+        # If the spectrum is stored in wavelength, reverse the result so it
+        # matches in wavelength space
+        if self.bin_unit.physical_type == 'length':
+            return result[::-1]
+        else:
+            return result
 
 
 ## ----  Supporting response file objects

From 5eded3d6b2716a25795144687a9cf35b1ce04939 Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Wed, 2 May 2018 18:03:29 -0400
Subject: [PATCH 45/72] Don't need bin_unit

---
 specutils/spectra/xrayspectrum1d.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index b9f2df62d..bac3f6e3e 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -47,7 +47,6 @@ def __init__(self, bin_lo, bin_hi, bin_unit, counts, exposure,
 
         self.bin_lo = bin_lo
         self.bin_hi = bin_hi
-        self.bin_unit = axis_unit # keep for reference
         self.exposure = exposure
         self.assign_rmf(rmf)
         self.assign_arf(arf)
@@ -118,7 +117,8 @@ def apply_resp(self, mflux, exposure=None):
         # The response is always stored according to energy
         # If the spectrum is stored in wavelength, reverse the result so it
         # matches in wavelength space
-        if self.bin_unit.physical_type == 'length':
+        if self.spectral_axis.unit.physical_type == 'length':
+            print("reversing output")
             return result[::-1]
         else:
             return result

From 6705068c79c934eec26af075c8a3aab9c45490df Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Wed, 2 May 2018 18:12:10 -0400
Subject: [PATCH 46/72] Because pha-file wavelength is in reverse order, the
 output from apply_resp is in correct order. No longer need to check

---
 specutils/spectra/xrayspectrum1d.py | 17 ++++++++---------
 1 file changed, 8 insertions(+), 9 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index bac3f6e3e..c054255df 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -34,6 +34,11 @@ class XraySpectrum1D(Spectrum1D):
     exposure
     arf
     rmf
+
+    Attributes
+    ----------
+    model : numpy.ndarray
+        Stores model values
     """
     def __init__(self, bin_lo, bin_hi, bin_unit, counts, exposure,
                  arf=None, rmf=None, **kwargs):
@@ -50,6 +55,7 @@ def __init__(self, bin_lo, bin_hi, bin_unit, counts, exposure,
         self.exposure = exposure
         self.assign_rmf(rmf)
         self.assign_arf(arf)
+        self.model_counts = np.zeros_like(bin_mid)
         return
 
     # Convenience function for Xray people
@@ -114,15 +120,8 @@ def apply_resp(self, mflux, exposure=None):
             print("Caution: no response file specified")
             result = mrate
 
-        # The response is always stored according to energy
-        # If the spectrum is stored in wavelength, reverse the result so it
-        # matches in wavelength space
-        if self.spectral_axis.unit.physical_type == 'length':
-            print("reversing output")
-            return result[::-1]
-        else:
-            return result
-
+        self.model_counts = result
+        return result
 
 ## ----  Supporting response file objects
 

From 80d559d6c62b192fada371b9be12fa6905aed65e Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Wed, 2 May 2018 18:15:20 -0400
Subject: [PATCH 47/72] added save_model_counts option

---
 specutils/spectra/xrayspectrum1d.py | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index c054255df..cd78d2e49 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -77,7 +77,7 @@ def assign_rmf(self, rmf_inp):
             self.rmf = rmf_inp
         return
 
-    def apply_resp(self, mflux, exposure=None):
+    def apply_resp(self, mflux, exposure=None, store_model_counts=True):
         """
         Given a model flux spectrum, apply the response. In cases where the
         spectrum has both an ARF and an RMF, apply both. Otherwise, apply
@@ -99,9 +99,12 @@ def apply_resp(self, mflux, exposure=None):
             ARF), this keyword provides the functionality to override the
             default behaviour and manually set the exposure time to use.
 
+        store_model_counts : bool
+            If True, the output will also be stored in self.model_counts
+
         Returns
         -------
-        count_model : numpy.ndarray
+        model_counts : numpy.ndarray
             The model spectrum in units of counts/bin
 
         If no ARF file exists, it will return the model flux after applying the RMF
@@ -120,7 +123,8 @@ def apply_resp(self, mflux, exposure=None):
             print("Caution: no response file specified")
             result = mrate
 
-        self.model_counts = result
+        if store_model_counts:
+            self.model_counts = result
         return result
 
 ## ----  Supporting response file objects

From 73535d9344d037824362a7e9fb7cbe679661c089 Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Thu, 3 May 2018 10:06:41 -0400
Subject: [PATCH 48/72] Changed my mind on model_counts thing for now

---
 specutils/spectra/xrayspectrum1d.py | 10 +---------
 1 file changed, 1 insertion(+), 9 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index cd78d2e49..7b342cb96 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -34,11 +34,6 @@ class XraySpectrum1D(Spectrum1D):
     exposure
     arf
     rmf
-
-    Attributes
-    ----------
-    model : numpy.ndarray
-        Stores model values
     """
     def __init__(self, bin_lo, bin_hi, bin_unit, counts, exposure,
                  arf=None, rmf=None, **kwargs):
@@ -55,7 +50,6 @@ def __init__(self, bin_lo, bin_hi, bin_unit, counts, exposure,
         self.exposure = exposure
         self.assign_rmf(rmf)
         self.assign_arf(arf)
-        self.model_counts = np.zeros_like(bin_mid)
         return
 
     # Convenience function for Xray people
@@ -77,7 +71,7 @@ def assign_rmf(self, rmf_inp):
             self.rmf = rmf_inp
         return
 
-    def apply_resp(self, mflux, exposure=None, store_model_counts=True):
+    def apply_resp(self, mflux, exposure=None):
         """
         Given a model flux spectrum, apply the response. In cases where the
         spectrum has both an ARF and an RMF, apply both. Otherwise, apply
@@ -123,8 +117,6 @@ def apply_resp(self, mflux, exposure=None, store_model_counts=True):
             print("Caution: no response file specified")
             result = mrate
 
-        if store_model_counts:
-            self.model_counts = result
         return result
 
 ## ----  Supporting response file objects

From e9be1099fea9034f52ba8ba8e6e30e1b2610b682 Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Wed, 23 May 2018 18:27:59 -0500
Subject: [PATCH 49/72] Hard coded in a rest_value

---
 specutils/spectra/xrayspectrum1d.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index 7b342cb96..2c5f4d86e 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -36,14 +36,15 @@ class XraySpectrum1D(Spectrum1D):
     rmf
     """
     def __init__(self, bin_lo, bin_hi, bin_unit, counts, exposure,
-                 arf=None, rmf=None, **kwargs):
+                 arf=None, rmf=None, rest_value=0.0, **kwargs):
         try:
             axis_unit = u.Unit(bin_unit)
         except:
             axis_unit = _unit_parser(bin_unit)
 
         bin_mid = 0.5 * (bin_lo + bin_hi) * axis_unit
-        Spectrum1D.__init__(self, spectral_axis=bin_mid, flux=counts, **kwargs)
+        Spectrum1D.__init__(self, spectral_axis=bin_mid, flux=counts,
+                            rest_value=rest_value, **kwargs)
 
         self.bin_lo = bin_lo
         self.bin_hi = bin_hi

From baa613c99e45bd8b78412e4c0b999f5143962a07 Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Wed, 23 May 2018 18:29:31 -0500
Subject: [PATCH 50/72] Added unit to rest_value

---
 specutils/spectra/xrayspectrum1d.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index 2c5f4d86e..d700837b7 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -36,7 +36,7 @@ class XraySpectrum1D(Spectrum1D):
     rmf
     """
     def __init__(self, bin_lo, bin_hi, bin_unit, counts, exposure,
-                 arf=None, rmf=None, rest_value=0.0, **kwargs):
+                 arf=None, rmf=None, rest_value=0.0 * u.angstrom, **kwargs):
         try:
             axis_unit = u.Unit(bin_unit)
         except:

From 56b4c1afdd8f667365ac005d804a30ca27ae10d1 Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Wed, 23 May 2018 18:47:34 -0500
Subject: [PATCH 51/72] Commented out distracting print statements

---
 specutils/spectra/xrayspectrum1d.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index d700837b7..ceb3f9fdf 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -110,12 +110,13 @@ def apply_resp(self, mflux, exposure=None):
         if self.arf is not None:
             mrate  = self.arf.apply_arf(mflux, exposure=exposure)
         else:
+            #print("Caution: no ARF file specified")
             mrate = mflux
 
         if self.rmf is not None:
             result = self.rmf.apply_rmf(mrate)
         else:
-            print("Caution: no response file specified")
+            #print("Caution: no RMF file specified")
             result = mrate
 
         return result

From afb6333c6337a5104eaf4684cd2be1e7aa53105f Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Wed, 23 May 2018 19:00:00 -0500
Subject: [PATCH 52/72] Wrote tests

---
 specutils/tests/test_xrayspectrum1d.py | 35 ++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)
 create mode 100644 specutils/tests/test_xrayspectrum1d.py

diff --git a/specutils/tests/test_xrayspectrum1d.py b/specutils/tests/test_xrayspectrum1d.py
new file mode 100644
index 000000000..f8792a7ff
--- /dev/null
+++ b/specutils/tests/test_xrayspectrum1d.py
@@ -0,0 +1,35 @@
+import numpy as np
+from scipy import optimize
+import astropy.units as u
+from astropy.modeling.powerlaws import PowerLaw1D
+from specutils import XraySpectrum1D
+
+def test_create_from_arrays():
+    # Test that XraySpectrum1D can be initialized
+    amp0, alpha0 = 3.e-3, 2.0
+    powlaw0 = PowerLaw1D(amplitude=amp0, alpha=alpha0, x_0=1.e3)
+    energy = np.linspace(0.2, 10.0, 8000)
+    elo = energy[:-1]
+    ehi = energy[1:]
+    emid = 0.5 * (elo + ehi)
+    counts = np.random.poisson(lam=powlaw0(emid), size=len(emid))
+    test_spec = XraySpectrum1D(elo, ehi, u.keV, counts, exposure=1.0)
+    return test_spec
+
+def test_call_spectrum():
+    # Test that the XraySpectrum1D has attributes that make it unique
+    # to X-ray spectrum
+    test_spec = test_create_from_arrays()
+    assert len(test_spec.counts) == len(test_spec.spectral_axis)
+    assert len(test_spec.bin_lo) == len(test_spec.spectral_axis)
+    assert len(test_spec.bin_hi) == len(test_spec.spectral_axis)
+    return
+
+def test_apply_model():
+    # Test that one can evaluate XraySpectrum1D with a model
+    test_spec = test_create_from_arrays()
+    new_model = PowerLaw1D(amplitude=5.e-3, alpha=1.8, x_0=1.e3)
+    model_flux = new_model(test_spec.spectral_axis.value)
+    ymodel = test_spec.apply_resp(model_flux)
+    assert len(ymodel) == len(test_spec.spectral_axis)
+    return

From a15b101ec3b083b34924569bc6cd704542572ddf Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Wed, 23 May 2018 19:17:48 -0500
Subject: [PATCH 53/72] Added docstrings

---
 specutils/spectra/xrayspectrum1d.py | 67 +++++++++++++++++++++++++++--
 1 file changed, 64 insertions(+), 3 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index ceb3f9fdf..0b72ccedf 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -13,6 +13,9 @@
 ANGS = ['angs', 'Angs', 'Angstrom', 'angstrom', 'Angstroms', 'angstroms', 'A', 'a']
 
 def _unit_parser(unit_string):
+    """
+    A function for matching unit strings to the correct Astropy unit
+    """
     if unit_string in EV:
         return u.eV
     if unit_string in KEV:
@@ -22,17 +25,51 @@ def _unit_parser(unit_string):
 
 class XraySpectrum1D(Spectrum1D):
     """
-    Spectrum container for holding X-ray spectrum
-    WIP by eblur
+    Spectrum properties specific to X-ray data
 
     Parameters
     ----------
+    bin_lo : numpy.ndarray
+        The left edges for bin values
+
+    bin_hi : numpy.ndarray
+        The right edges for bin values
+
+    bin_unit : string OR astropy.units.Unit
+        Unit for the bin values
+
+    counts : numpy.ndarray
+        Counts histogram for the X-ray spectrum
+
+    exposure : float
+        Exposure time for the dataset
+
+    arf : specutils.ARF or string, default None
+        Strings will be passed to ARF.__init__
+        All other input types are stored as arf attribute
+
+    rmf : specutils.RMF or string, default None
+        Strings will be passed to RMF.__init__
+        All other input types are stored as rmf attribute
+
+    rest_value : astropy.units.Quantity, default 0 Angstrom
+        See Spectrum1D rest_value input
+
+    Attributes
+    ----------
+    Inherits from Spectrum1D object.
+    The following inputs are stored as additional attributes.
+
     bin_lo
+
     bin_hi
-    bin_unit
+
     counts
+
     exposure
+
     arf
+
     rmf
     """
     def __init__(self, bin_lo, bin_hi, bin_unit, counts, exposure,
@@ -59,6 +96,18 @@ def counts(self):
         return self.flux
 
     def assign_arf(self, arf_inp):
+        """
+        Assign an ARF object to the XraySpectrum1D object
+
+        Input
+        -----
+        arf_inp : string
+            File name for the ARF (FITS file)
+
+        Returns
+        -------
+        Modifies the XraySpectrum1D.arf attribute
+        """
         if isinstance(arf_inp, str):
             self.arf = ARF(arf_inp)
         else:
@@ -66,6 +115,18 @@ def assign_arf(self, arf_inp):
         return
 
     def assign_rmf(self, rmf_inp):
+        """
+        Assign an RMF object to the XraySpectrum1D object
+
+        Input
+        -----
+        rmf_inp : string
+            File name for the RMF (FITS file)
+
+        Returns
+        -------
+        Modifies the XraySpectrum1D.rmf attribute
+        """
         if isinstance(rmf_inp, str):
             self.rmf = RMF(rmf_inp)
         else:

From 4ba7b5829c400d13d2bc976d241b6fb80981881d Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Wed, 23 May 2018 19:19:32 -0500
Subject: [PATCH 54/72] Removed scipy dependence

---
 specutils/tests/test_xrayspectrum1d.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/specutils/tests/test_xrayspectrum1d.py b/specutils/tests/test_xrayspectrum1d.py
index f8792a7ff..53fbae5c0 100644
--- a/specutils/tests/test_xrayspectrum1d.py
+++ b/specutils/tests/test_xrayspectrum1d.py
@@ -1,5 +1,4 @@
 import numpy as np
-from scipy import optimize
 import astropy.units as u
 from astropy.modeling.powerlaws import PowerLaw1D
 from specutils import XraySpectrum1D

From f5a996a0175e8c36d1a12c91c6109ebb27fe1495 Mon Sep 17 00:00:00 2001
From: eblur <lia@astro.wisc.edu>
Date: Fri, 1 Jun 2018 10:56:46 -0500
Subject: [PATCH 55/72] Spelled out acronyms, link to edu materials

---
 specutils/spectra/xrayspectrum1d.py | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index 0b72ccedf..05e9cc892 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -12,6 +12,9 @@
 KEV  = ['kev', 'keV']
 ANGS = ['angs', 'Angs', 'Angstrom', 'angstrom', 'Angstroms', 'angstroms', 'A', 'a']
 
+## An introduction to X-ray analysis can be found here:
+## http://cxc.cfa.harvard.edu/xrayschool/talks/intro_xray_analysis.pdf
+
 def _unit_parser(unit_string):
     """
     A function for matching unit strings to the correct Astropy unit
@@ -97,12 +100,12 @@ def counts(self):
 
     def assign_arf(self, arf_inp):
         """
-        Assign an ARF object to the XraySpectrum1D object
+        Assign an area response file (ARF) object to the XraySpectrum1D object
 
         Input
         -----
         arf_inp : string
-            File name for the ARF (FITS file)
+            File name for the area response file (FITS file)
 
         Returns
         -------
@@ -116,12 +119,12 @@ def assign_arf(self, arf_inp):
 
     def assign_rmf(self, rmf_inp):
         """
-        Assign an RMF object to the XraySpectrum1D object
+        Assign a response matrix file (RMF) object to the XraySpectrum1D object
 
         Input
         -----
         rmf_inp : string
-            File name for the RMF (FITS file)
+            File name for the response matrix file (FITS file)
 
         Returns
         -------
@@ -191,7 +194,7 @@ def __init__(self, filename):
 
     def _load_rmf(self, filename):
         """
-        Load an RMF from a FITS file.
+        Load a response matrix file (RMF) from a FITS file.
 
         Parameters
         ----------
@@ -446,7 +449,7 @@ def __init__(self, filename):
 
     def _load_arf(self, filename):
         """
-        Load an ARF from a FITS file.
+        Load an area response file (ARF) from a FITS file.
 
         Parameters
         ----------
@@ -512,7 +515,7 @@ def _load_arf(self, filename):
 
     def apply_arf(self, spec, exposure=None):
         """
-        Fold the spectrum through the ARF.
+        Fold the spectrum through the area response file (ARF).
         The ARF is a single vector encoding the effective area information
         about the detector. A such, applying the ARF is a simple
         multiplication with the input spectrum.

From eed588cdb5c6c785d059ba77d6d120ed8c6208f6 Mon Sep 17 00:00:00 2001
From: eblur <lia@astro.wisc.edu>
Date: Fri, 1 Jun 2018 11:05:22 -0500
Subject: [PATCH 56/72] Added option to specify RMF FITS extension for response
 matrix

---
 specutils/spectra/xrayspectrum1d.py | 18 +++++++++++++++---
 1 file changed, 15 insertions(+), 3 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index 05e9cc892..68460d8b6 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -136,7 +136,7 @@ def assign_rmf(self, rmf_inp):
             self.rmf = rmf_inp
         return
 
-    def apply_resp(self, mflux, exposure=None):
+    def apply_response(self, mflux, exposure=None):
         """
         Given a model flux spectrum, apply the response. In cases where the
         spectrum has both an ARF and an RMF, apply both. Otherwise, apply
@@ -192,7 +192,7 @@ def __init__(self, filename):
         self._load_rmf(filename)
         pass
 
-    def _load_rmf(self, filename):
+    def _load_rmf(self, filename, extension=None):
         """
         Load a response matrix file (RMF) from a FITS file.
 
@@ -201,6 +201,10 @@ def _load_rmf(self, filename):
         filename : str
             The file name with the RMF file
 
+        extension : str (default None)
+            FITS file extinction keyword, if the response matrix is stored
+            under an extension other tham "MATRIX" or "SPECRESP MATRIX"
+
         Attributes
         ----------
         filename : str
@@ -246,12 +250,20 @@ def _load_rmf(self, filename):
         extnames = np.array([h.name for h in hdulist])
 
         # figure out the right extension to use
-        if "MATRIX" in extnames:
+        if extension is not None:
+            h = hdulist[extension]
+
+        elif "MATRIX" in extnames:
             h = hdulist["MATRIX"]
 
         elif "SPECRESP MATRIX" in extnames:
             h = hdulist["SPECRESP MATRIX"]
 
+        else:
+            print("Cannot find common FITS file extension for response matrix values")
+            print("Please set the `extension` keyword")
+            return
+
         data = h.data
         hdr = h.header
         hdulist.close()

From 0fa3718a048314f120c9d2bb63a88af574db2496 Mon Sep 17 00:00:00 2001
From: eblur <lia@astro.wisc.edu>
Date: Fri, 1 Jun 2018 11:15:09 -0500
Subject: [PATCH 57/72] corrected typos

---
 specutils/spectra/xrayspectrum1d.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index 68460d8b6..e2eb6ce9c 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -202,8 +202,8 @@ def _load_rmf(self, filename, extension=None):
             The file name with the RMF file
 
         extension : str (default None)
-            FITS file extinction keyword, if the response matrix is stored
-            under an extension other tham "MATRIX" or "SPECRESP MATRIX"
+            FITS file extension keyword, if the response matrix is stored
+            under an extension other than "MATRIX" or "SPECRESP MATRIX"
 
         Attributes
         ----------
@@ -466,7 +466,7 @@ def _load_arf(self, filename):
         Parameters
         ----------
         filename : str
-            The file name with the RMF file
+            The file name with the ARF file
 
         Attributes
         ----------

From aa458114d39d123c8fb0e93a00f84a7e492bbf94 Mon Sep 17 00:00:00 2001
From: eblur <lia@astro.wisc.edu>
Date: Fri, 1 Jun 2018 11:19:14 -0500
Subject: [PATCH 58/72] Removing superfluous returns and pass

---
 specutils/spectra/xrayspectrum1d.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index e2eb6ce9c..610dea245 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -91,7 +91,6 @@ def __init__(self, bin_lo, bin_hi, bin_unit, counts, exposure,
         self.exposure = exposure
         self.assign_rmf(rmf)
         self.assign_arf(arf)
-        return
 
     # Convenience function for Xray people
     @property
@@ -115,7 +114,6 @@ def assign_arf(self, arf_inp):
             self.arf = ARF(arf_inp)
         else:
             self.arf = arf_inp
-        return
 
     def assign_rmf(self, rmf_inp):
         """
@@ -190,7 +188,6 @@ def apply_response(self, mflux, exposure=None):
 class RMF(object):
     def __init__(self, filename):
         self._load_rmf(filename)
-        pass
 
     def _load_rmf(self, filename, extension=None):
         """

From 674ae640e7627528b241b780513ac15d9f55a882 Mon Sep 17 00:00:00 2001
From: eblur <lia@astro.wisc.edu>
Date: Fri, 1 Jun 2018 11:22:03 -0500
Subject: [PATCH 59/72] Catch ValueError

---
 specutils/spectra/xrayspectrum1d.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index 610dea245..34b34e7d8 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -79,7 +79,7 @@ def __init__(self, bin_lo, bin_hi, bin_unit, counts, exposure,
                  arf=None, rmf=None, rest_value=0.0 * u.angstrom, **kwargs):
         try:
             axis_unit = u.Unit(bin_unit)
-        except:
+        except ValueError:
             axis_unit = _unit_parser(bin_unit)
 
         bin_mid = 0.5 * (bin_lo + bin_hi) * axis_unit

From 029f8abee7243cdec11506162860e90fec4e5e99 Mon Sep 17 00:00:00 2001
From: eblur <lia@astro.wisc.edu>
Date: Fri, 1 Jun 2018 11:27:25 -0500
Subject: [PATCH 60/72] Spelled out ARF and RMF class names

---
 specutils/spectra/xrayspectrum1d.py | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index 34b34e7d8..3c452c7d3 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -5,7 +5,7 @@
 from astropy.io import fits
 from .spectrum1d import Spectrum1D
 
-__all__ = ['XraySpectrum1D', 'ARF', 'RMF']
+__all__ = ['XraySpectrum1D', 'AreaResponse', 'ResponseMatrix']
 
 # For dealing with varied unit string choices
 EV   = ['eV', 'ev']
@@ -47,12 +47,12 @@ class XraySpectrum1D(Spectrum1D):
     exposure : float
         Exposure time for the dataset
 
-    arf : specutils.ARF or string, default None
-        Strings will be passed to ARF.__init__
+    arf : specutils.AreaResponse or string, default None
+        Strings will be passed to AreaResponse.__init__
         All other input types are stored as arf attribute
 
-    rmf : specutils.RMF or string, default None
-        Strings will be passed to RMF.__init__
+    rmf : specutils.ResponseMatrix or string, default None
+        Strings will be passed to ResponseMatrix.__init__
         All other input types are stored as rmf attribute
 
     rest_value : astropy.units.Quantity, default 0 Angstrom
@@ -111,7 +111,7 @@ def assign_arf(self, arf_inp):
         Modifies the XraySpectrum1D.arf attribute
         """
         if isinstance(arf_inp, str):
-            self.arf = ARF(arf_inp)
+            self.arf = AreaResponse(arf_inp)
         else:
             self.arf = arf_inp
 
@@ -129,7 +129,7 @@ def assign_rmf(self, rmf_inp):
         Modifies the XraySpectrum1D.rmf attribute
         """
         if isinstance(rmf_inp, str):
-            self.rmf = RMF(rmf_inp)
+            self.rmf = ResponseMatrix(rmf_inp)
         else:
             self.rmf = rmf_inp
         return
@@ -185,7 +185,7 @@ def apply_response(self, mflux, exposure=None):
 
 ## ----  Supporting response file objects
 
-class RMF(object):
+class ResponseMatrix(object):
     def __init__(self, filename):
         self._load_rmf(filename)
 
@@ -449,7 +449,7 @@ def apply_rmf(self, spec):
         return counts[:self.detchans]
 
 
-class ARF(object):
+class AreaResponse(object):
 
     def __init__(self, filename):
 

From 2590b7a05e957ca5cf77213916a35a7e9982fdfc Mon Sep 17 00:00:00 2001
From: eblur <lia@astro.wisc.edu>
Date: Fri, 1 Jun 2018 11:30:06 -0500
Subject: [PATCH 61/72] updated docstring

---
 specutils/spectra/xrayspectrum1d.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index 3c452c7d3..cb99d21f8 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -137,8 +137,8 @@ def assign_rmf(self, rmf_inp):
     def apply_response(self, mflux, exposure=None):
         """
         Given a model flux spectrum, apply the response. In cases where the
-        spectrum has both an ARF and an RMF, apply both. Otherwise, apply
-        whatever response is in RMF.
+        spectrum has both an area response file (ARF) and a response matrix
+        file (RMF), apply both. Otherwise, apply whatever response is in RMF.
 
         The model flux spectrum *must* be created using the same units and
         bins as in the ARF (where the ARF exists)!

From f6b66f52196879cdce5f63854b19f563c6172944 Mon Sep 17 00:00:00 2001
From: eblur <lia@astro.wisc.edu>
Date: Fri, 1 Jun 2018 11:34:47 -0500
Subject: [PATCH 62/72] Updated tests

---
 specutils/tests/test_xrayspectrum1d.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/specutils/tests/test_xrayspectrum1d.py b/specutils/tests/test_xrayspectrum1d.py
index 53fbae5c0..1e1f45bbe 100644
--- a/specutils/tests/test_xrayspectrum1d.py
+++ b/specutils/tests/test_xrayspectrum1d.py
@@ -29,6 +29,6 @@ def test_apply_model():
     test_spec = test_create_from_arrays()
     new_model = PowerLaw1D(amplitude=5.e-3, alpha=1.8, x_0=1.e3)
     model_flux = new_model(test_spec.spectral_axis.value)
-    ymodel = test_spec.apply_resp(model_flux)
+    ymodel = test_spec.apply_response(model_flux)
     assert len(ymodel) == len(test_spec.spectral_axis)
     return

From 4111295c4a990873bb7f75ac0c7d221e212e3fc2 Mon Sep 17 00:00:00 2001
From: Lia Corrales <lia@astro.wisc.edu>
Date: Tue, 12 Jun 2018 20:38:39 +0200
Subject: [PATCH 63/72] initialize attributes to None before loading from file

---
 specutils/spectra/xrayspectrum1d.py | 31 +++++++++++++++++++++--------
 1 file changed, 23 insertions(+), 8 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index cb99d21f8..5d98c79bc 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -187,9 +187,6 @@ def apply_response(self, mflux, exposure=None):
 
 class ResponseMatrix(object):
     def __init__(self, filename):
-        self._load_rmf(filename)
-
-    def _load_rmf(self, filename, extension=None):
         """
         Load a response matrix file (RMF) from a FITS file.
 
@@ -237,6 +234,19 @@ def _load_rmf(self, filename, extension=None):
             The number of channels in the detector
 
         """
+        self.filename = ""
+        self.offset = None
+        self.n_grp = None
+        self.f_chan = None
+        self.n_chan = None
+        self.matrix = None
+        self.energ_lo = None
+        self.energ_hi = None
+        self.energ_unit = None
+        self.detchans = None
+        self._load_rmf(filename)
+
+    def _load_rmf(self, filename, extension=None):
         # open the FITS file and extract the MATRIX extension
         # which contains the redistribution matrix and
         # anxillary information
@@ -452,11 +462,6 @@ def apply_rmf(self, spec):
 class AreaResponse(object):
 
     def __init__(self, filename):
-
-        self._load_arf(filename)
-        pass
-
-    def _load_arf(self, filename):
         """
         Load an area response file (ARF) from a FITS file.
 
@@ -492,6 +497,16 @@ def _load_arf(self, filename):
             Average exposure time for the dataset
             (takes telescope dithering into account)
         """
+        self.filename = ""
+        self.e_low = None
+        self.e_high = None
+        self.e_unit = None
+        self.specresp = None
+        self.fracexpo = None
+        self.exposure = None
+        self._load_arf(filename)
+
+    def _load_arf(self, filename):
         # open the FITS file and extract the MATRIX extension
         # which contains the redistribution matrix and
         # anxillary information

From 8a1aa62787b3058068ca3e1c63fbaf9eaaf3f097 Mon Sep 17 00:00:00 2001
From: Lia Corrales <lia@astro.wisc.edu>
Date: Tue, 12 Jun 2018 20:39:55 +0200
Subject: [PATCH 64/72] save filename attribute for attempting load function

---
 specutils/spectra/xrayspectrum1d.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index 5d98c79bc..58dcc3b73 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -234,7 +234,7 @@ def __init__(self, filename):
             The number of channels in the detector
 
         """
-        self.filename = ""
+        self.filename = filename
         self.offset = None
         self.n_grp = None
         self.f_chan = None
@@ -251,7 +251,6 @@ def _load_rmf(self, filename, extension=None):
         # which contains the redistribution matrix and
         # anxillary information
         hdulist = fits.open(filename)
-        self.filename = filename
 
         # get all the extension names
         extnames = np.array([h.name for h in hdulist])
@@ -497,7 +496,7 @@ def __init__(self, filename):
             Average exposure time for the dataset
             (takes telescope dithering into account)
         """
-        self.filename = ""
+        self.filename = filename
         self.e_low = None
         self.e_high = None
         self.e_unit = None
@@ -511,7 +510,6 @@ def _load_arf(self, filename):
         # which contains the redistribution matrix and
         # anxillary information
         hdulist = fits.open(filename)
-        self.filename = filename
 
         h = hdulist["SPECRESP"]
         data = h.data

From 4afde8f7e1d28f2146f8e50a57ac850a655a79c2 Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Thu, 6 Dec 2018 13:30:05 -0700
Subject: [PATCH 65/72] [skip ci] provide xrayspectrum1d

---
 specutils/spectra/__init__.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/specutils/spectra/__init__.py b/specutils/spectra/__init__.py
index 05d5d14c4..d03dac32a 100644
--- a/specutils/spectra/__init__.py
+++ b/specutils/spectra/__init__.py
@@ -3,10 +3,8 @@
 `~astropy.nddata.NDData`-inherited classes used for storing the spectrum data.
 """
 from .spectrum1d import *  # noqa
-<<<<<<< HEAD
 from .spectral_region import *  # noqa
 from .spectrum_collection import *  #noqa
 from .spectrum_list import * #noqa
-=======
+
 from .xrayspectrum1d import *
->>>>>>> Can load an X-ray spectrum

From 90f8ad6871bde4a1b0353bc9a85f381682369458 Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Thu, 6 Dec 2018 13:57:25 -0700
Subject: [PATCH 66/72] specutils flux input needs units

---
 specutils/tests/test_xrayspectrum1d.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/specutils/tests/test_xrayspectrum1d.py b/specutils/tests/test_xrayspectrum1d.py
index 1e1f45bbe..4317bc836 100644
--- a/specutils/tests/test_xrayspectrum1d.py
+++ b/specutils/tests/test_xrayspectrum1d.py
@@ -11,7 +11,7 @@ def test_create_from_arrays():
     elo = energy[:-1]
     ehi = energy[1:]
     emid = 0.5 * (elo + ehi)
-    counts = np.random.poisson(lam=powlaw0(emid), size=len(emid))
+    counts = np.random.poisson(lam=powlaw0(emid), size=len(emid)) * u.ct
     test_spec = XraySpectrum1D(elo, ehi, u.keV, counts, exposure=1.0)
     return test_spec
 

From fa80d2440a18430d62541d895da0681977d1650a Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Thu, 6 Dec 2018 14:32:03 -0700
Subject: [PATCH 67/72] attempting to fix docstrings

---
 specutils/spectra/xrayspectrum1d.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index 58dcc3b73..c82d0cced 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -541,10 +541,12 @@ def apply_arf(self, spec, exposure=None):
         The ARF is a single vector encoding the effective area information
         about the detector. A such, applying the ARF is a simple
         multiplication with the input spectrum.
+
         Parameters
         ----------
         spec : numpy.ndarray
             The (model) spectrum to be folded
+
         exposure : float, default None
             Value for the exposure time. By default, `apply_arf` will use the
             exposure keyword from the ARF file. If this exposure time is not
@@ -552,6 +554,7 @@ def apply_arf(self, spec, exposure=None):
             time and the ARF from a real observation), one can override the
             default exposure by setting the `exposure` keyword to the correct
             value.
+
         Returns
         -------
         s_arf : numpy.ndarray

From f14e9afd4095372b2b0359d043517f62eb859021 Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Thu, 6 Dec 2018 14:54:07 -0700
Subject: [PATCH 68/72] further docstring fixes for sphinx

---
 specutils/spectra/xrayspectrum1d.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index c82d0cced..ce0771053 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -41,7 +41,7 @@ class XraySpectrum1D(Spectrum1D):
     bin_unit : string OR astropy.units.Unit
         Unit for the bin values
 
-    counts : numpy.ndarray
+    counts : astropy.Quantity array
         Counts histogram for the X-ray spectrum
 
     exposure : float
@@ -374,10 +374,13 @@ def apply_rmf(self, spec):
         vector, there exists one or more sets of channels that this
         flux is redistributed into. The additional arrays `n_grp`,
         `f_chan` and `n_chan` store this information:
+        
             * `n_group` stores the number of channel groups for each
               energy bin
+
             * `f_chan` stores the *first channel* that each channel
               for each channel set
+
             * `n_chan` stores the number of channels in each channel
               set
 

From eecce756203afcafdaac91e80a05ce7769b56e25 Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Thu, 6 Dec 2018 17:18:41 -0700
Subject: [PATCH 69/72] added extension keyword to _load_arf

---
 specutils/spectra/xrayspectrum1d.py | 25 +++++++++++++++++++------
 1 file changed, 19 insertions(+), 6 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index ce0771053..102bc16d4 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -374,7 +374,7 @@ def apply_rmf(self, spec):
         vector, there exists one or more sets of channels that this
         flux is redistributed into. The additional arrays `n_grp`,
         `f_chan` and `n_chan` store this information:
-        
+
             * `n_group` stores the number of channel groups for each
               energy bin
 
@@ -508,13 +508,26 @@ def __init__(self, filename):
         self.exposure = None
         self._load_arf(filename)
 
-    def _load_arf(self, filename):
-        # open the FITS file and extract the MATRIX extension
-        # which contains the redistribution matrix and
-        # anxillary information
+    def _load_arf(self, filename, extension=None):
+        # open the FITS file and extract the SPECRESP extension
+        # which contains the spectral response for the telescope
         hdulist = fits.open(filename)
 
-        h = hdulist["SPECRESP"]
+        # get all the extension names
+        extnames = np.array([h.name for h in hdulist])
+
+        # figure out the right extension to use
+        if extension is not None:
+            h = hdulist[extension]
+
+        elif 'SPECRESP' in extnames:
+            h = hdulist['SPECRESP']
+
+        else:
+            print("Cannot find common FITS file extension for spectral response")
+            print("Please set the `extension` keyword")
+            return
+
         data = h.data
         hdr = h.header
         hdulist.close()

From bdc5a418efbe49e659f015baffe7e85dbeef232d Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Thu, 6 Dec 2018 17:22:01 -0700
Subject: [PATCH 70/72] updated init and load calls with extension keyword

---
 specutils/spectra/xrayspectrum1d.py | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index 102bc16d4..5ed8365e7 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -186,7 +186,7 @@ def apply_response(self, mflux, exposure=None):
 ## ----  Supporting response file objects
 
 class ResponseMatrix(object):
-    def __init__(self, filename):
+    def __init__(self, filename, extension=None):
         """
         Load a response matrix file (RMF) from a FITS file.
 
@@ -244,7 +244,7 @@ def __init__(self, filename):
         self.energ_hi = None
         self.energ_unit = None
         self.detchans = None
-        self._load_rmf(filename)
+        self._load_rmf(filename, extension=extension)
 
     def _load_rmf(self, filename, extension=None):
         # open the FITS file and extract the MATRIX extension
@@ -463,7 +463,7 @@ def apply_rmf(self, spec):
 
 class AreaResponse(object):
 
-    def __init__(self, filename):
+    def __init__(self, filename, extension=None):
         """
         Load an area response file (ARF) from a FITS file.
 
@@ -472,6 +472,10 @@ def __init__(self, filename):
         filename : str
             The file name with the ARF file
 
+        extension : str (default None)
+            FITS file extension keyword, if the spectral response is stored
+            under an extension other than "SPECRESP"
+
         Attributes
         ----------
         filename : str
@@ -506,7 +510,7 @@ def __init__(self, filename):
         self.specresp = None
         self.fracexpo = None
         self.exposure = None
-        self._load_arf(filename)
+        self._load_arf(filename, extension=extension)
 
     def _load_arf(self, filename, extension=None):
         # open the FITS file and extract the SPECRESP extension

From 3fef5b91c9fece08e5005887ab6b3b660510c3b2 Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Fri, 7 Dec 2018 13:53:48 -0700
Subject: [PATCH 71/72] XraySpectrum1d uses astropy.Quantity for all inputs

---
 specutils/spectra/xrayspectrum1d.py | 17 +++++------------
 1 file changed, 5 insertions(+), 12 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index 5ed8365e7..28bfb7742 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -32,19 +32,16 @@ class XraySpectrum1D(Spectrum1D):
 
     Parameters
     ----------
-    bin_lo : numpy.ndarray
+    bin_lo : astropy.Quantity
         The left edges for bin values
 
-    bin_hi : numpy.ndarray
+    bin_hi : astropy.Quantity
         The right edges for bin values
 
-    bin_unit : string OR astropy.units.Unit
-        Unit for the bin values
-
-    counts : astropy.Quantity array
+    counts : astropy.Quantity
         Counts histogram for the X-ray spectrum
 
-    exposure : float
+    exposure : astropy.Quantity
         Exposure time for the dataset
 
     arf : specutils.AreaResponse or string, default None
@@ -77,12 +74,8 @@ class XraySpectrum1D(Spectrum1D):
     """
     def __init__(self, bin_lo, bin_hi, bin_unit, counts, exposure,
                  arf=None, rmf=None, rest_value=0.0 * u.angstrom, **kwargs):
-        try:
-            axis_unit = u.Unit(bin_unit)
-        except ValueError:
-            axis_unit = _unit_parser(bin_unit)
 
-        bin_mid = 0.5 * (bin_lo + bin_hi) * axis_unit
+        bin_mid = 0.5 * (bin_lo + bin_hi)
         Spectrum1D.__init__(self, spectral_axis=bin_mid, flux=counts,
                             rest_value=rest_value, **kwargs)
 

From 8b4b945e83c66c7edae91e3e6b30ca4d1e5c6207 Mon Sep 17 00:00:00 2001
From: Lia Corrales <liac@umich.edu>
Date: Fri, 7 Dec 2018 13:58:56 -0700
Subject: [PATCH 72/72] tested xrayspectrum1d with quantity inputs

---
 specutils/spectra/xrayspectrum1d.py    | 2 +-
 specutils/tests/test_xrayspectrum1d.py | 8 ++++----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/specutils/spectra/xrayspectrum1d.py b/specutils/spectra/xrayspectrum1d.py
index 28bfb7742..68f12da3f 100644
--- a/specutils/spectra/xrayspectrum1d.py
+++ b/specutils/spectra/xrayspectrum1d.py
@@ -72,7 +72,7 @@ class XraySpectrum1D(Spectrum1D):
 
     rmf
     """
-    def __init__(self, bin_lo, bin_hi, bin_unit, counts, exposure,
+    def __init__(self, bin_lo, bin_hi, counts, exposure,
                  arf=None, rmf=None, rest_value=0.0 * u.angstrom, **kwargs):
 
         bin_mid = 0.5 * (bin_lo + bin_hi)
diff --git a/specutils/tests/test_xrayspectrum1d.py b/specutils/tests/test_xrayspectrum1d.py
index 4317bc836..6a561307f 100644
--- a/specutils/tests/test_xrayspectrum1d.py
+++ b/specutils/tests/test_xrayspectrum1d.py
@@ -8,11 +8,11 @@ def test_create_from_arrays():
     amp0, alpha0 = 3.e-3, 2.0
     powlaw0 = PowerLaw1D(amplitude=amp0, alpha=alpha0, x_0=1.e3)
     energy = np.linspace(0.2, 10.0, 8000)
-    elo = energy[:-1]
-    ehi = energy[1:]
+    elo = energy[:-1] * u.keV
+    ehi = energy[1:] * u.keV
     emid = 0.5 * (elo + ehi)
-    counts = np.random.poisson(lam=powlaw0(emid), size=len(emid)) * u.ct
-    test_spec = XraySpectrum1D(elo, ehi, u.keV, counts, exposure=1.0)
+    counts = np.random.poisson(lam=powlaw0(emid.value), size=len(emid)) * u.ct
+    test_spec = XraySpectrum1D(elo, ehi, counts, exposure=1.0*u.second)
     return test_spec
 
 def test_call_spectrum():