chianti emission model (#123)

* New folder for chianti files

* Adding CHIANTI_hybrid.geny file

* Adding CHIANTI_photospheric.geny file

* Created a dictionary with _abundance_model_file_path

* Importing packages

* Setting a _abundance_model_data dictionary

* Updating folder name

* Correction to methods of importing files.

* Updating name to be more define as filter name.

* Re-defining method of getting data from geny files

* Creating a function to call data from geny file

* Defing file type name

* Define users input for abundance to retrun the correct data set.

* Updated functions to take data from requested abundance file

* Code return users requested abundance file

* Updating text strings and doc strings in the functions

* Add two articles that reference the new abundance file

* Updating site to having information about the new abundance files

* Adding a link reference for XRT temperature response with other choice of abundances

* Adding information about Additional Abundances

* Fixing text details

* Updating information in the glossary related to the TR.

* Adding more information to Additional Abundances section

* Update xrtpy/response/temperature_response.py

Co-authored-by: Nick Murphy <namurphy@cfa.harvard.edu>

* Update xrtpy/response/temperature_response.py

Co-authored-by: Nick Murphy <namurphy@cfa.harvard.edu>

* Update docs/bibliography.bib

Co-authored-by: Nick Murphy <namurphy@cfa.harvard.edu>

* Update xrtpy/response/temperature_response.py

Co-authored-by: Nick Murphy <namurphy@cfa.harvard.edu>

* Update xrtpy/response/temperature_response.py

Co-authored-by: Nick Murphy <namurphy@cfa.harvard.edu>

* Update xrtpy/response/temperature_response.py

Co-authored-by: Nick Murphy <namurphy@cfa.harvard.edu>

* Creating a private function

* clarified meaning of the version function

* Correction the method of calling a function in the effective area code

* Updating temperature function name

* Adding a TIP on how to call a different abundance model

* Fixing head info to reference easier in a different rst file

* Adding text to give user information about using abundance_model in command line

* Removed package

* IDL testing text file - Temp Resp.

* IDL testing text file - Temp Resp.

* IDL testing text file - Temp Resp.

* IDL testing text file - Temp Resp.

* IDL photospheric testing text file - Temperature Response

* IDL photospheric testing text file - Temperature Response

* IDL photospheric testing text file - Temperature Response

* IDL hybrid testing text file: 2022 - Temperature Response

* IDL hybrid testing text file: 2021 - Temperature Response

* IDL hybrid testing text file: 2019 - Temperature Response

* IDL hybrid testing text file: 2017 - Temperature Response

* IDL hybrid testing text file: 2015 - Temperature Response

* IDL hybrid testing text file: 2013 - Temperature Response

* IDL hybrid testing text file: 2011 - Temperature Response

* IDL hybrid testing text file: 2009 - Temperature Response

* IDL hybrid testing text file: 2007 - Temperature Response

* Updating folder name

* Name correction to data I am calling

* Updated the path to the testing data.

* Correction to folder name;

* Updated name - coronal o.g. test file

* TR Hybrid test for the moment, will merge all TR test.

* TR Photospheric test for the moment, will merge all TR test.

* Updated directory to getting test files.

* Updated directory to getting test files.

* Updated directory to getting test files.

* Updated directory to getting test files.

* New dictionary to call IDL testing file paths

* Update code to look for all new abundance files

* Removed used code

* Updating xrt_teem to take other abundance

* Cleaned up code

* Updated doc information about these abundance

* Correction to title

* Updated word choice

* Updated path method to reference the dic.

* Working on testing all abundance in a single test

* Returning into stadard test

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Updated docstring in xrt_teem to reflect the fact that abundance_model is now a parameter

* Fixed format of string literal in docstring in xrt_teem

---------

Co-authored-by: Nick Murphy <namurphy@cfa.harvard.edu>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Jonathan Slavin <jslavin@cfa.harvard.edu>

docs/bibliography.bib

@@ -68,3 +68,29 @@ @ARTICLE{feldman:1992
   pages = {202-220},
   doi = {10.1088/0031-8949/46/3/002}
 }
+@ARTICLE{Fludra:1999,
+       author = {{Fludra}, A. and {Schmelz}, J.~T.},
+        title = "{The absolute coronal abundances of sulfur, calcium, and iron from Yohkoh-BCS flare spectra}",
+      journal = "{Astronomy \& Astrophysics}",
+     keywords = {SUN: ABUNDANCES, SUN: CORONA, SUN: FLARES, SUN: X-RAYS, GAMMA RAYS},
+         year = 1999,
+        month = aug,
+       volume = {348},
+        pages = {286-294},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/1999A&A...348..286F},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+@ARTICLE{Grevesse:2007,
+       author = {{Grevesse}, N. and {Asplund}, M. and {Sauval}, A.~J.},
+        title = "{The Solar Chemical Composition}",
+      journal = {\ssr},
+     keywords = {Sun: abundances, photosphere, corona},
+         year = 2007,
+        month = jun,
+       volume = {130},
+       number = {1-4},
+        pages = {105-114},
+          doi = {10.1007/s11214-007-9173-7},
+       adsurl = {https://ui.adsabs.harvard.edu/abs/2007SSRv..130..105G},
+      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}

docs/getting_started.rst

@@ -28,15 +28,32 @@ Refer to the `SolarSoft XRT Analysis Guide`_ for more information about the inst
 Temperature Response
 --------------------
 XRTpy produces the temperature response for each XRT filter channel, assuming a spectral emission model, refer to :cite:t:`narukage:2011` and :cite:t:`narukage:2014`.
-XRTpy default emission model is from CHIANTI. This structure contains data and information about a plasma emission model, as a function of wavelength and temperature.
-The default model assumes coronal abundances :cite:t:`feldman:1992`.
+The XRT default emission model is `CHIANTI`_ atomic database version 10.0 with coronal abundances :cite:t:`feldman:1992`. This structure contains data and information about a plasma emission model, as a function of wavelength and temperature.
+
+
+Abundance Model
+---------------------
+The standard XRT temperature response routines are calculated assuming `CHIANTI`_ coronal abundances, :cite:t:`feldman:1992`.
+In addition, XRTpy offers the ability to choose two other sets of `CHIANTI`_ abundances i.e. Hybrid and Photospheric.
+The Hybrid abundances are base on :cite:t:`Fludra:1999` and Photospheric abundances are base on :cite:t:`Grevesse:2007`.
+The `CHIANTI`_ files contain data and information about a plasma emission model, as a function of wavelength and temperature.
+Visit `XRT temperature response with other choice of abundances`_ for future detailed information.
 
 .. note::
-   XRTpy has future plans to accept other plasma emission spectra models.
+    XRTpy has future plans to accept other plasma emission spectra models.
+
+XRTpy defaults to using CHIANTI `"coronal"` abundance. You are able to specify the other abundances by defining the abundance type name
+i.e. `"hybrid"` or `"photospheric"` in `abundance_model`. For example:
+
+.. code-block:: bash
+
+   xrtpy.response.TemperatureResponseFundamental('Al-poly', '2022/07/04T23:43:12', abundance_model = 'Hybrid')
+
+The `abundance_model` method is used in the same format in `xrt_teem`.
 
 Deriving Temperature and Emission Measure for a Pair of Images
 --------------------------------------------------------------
-XRTpy provides a routine, xrt_teem, that employs the objects listed above to derive the temperature and emission measure in for a given pair of images using the filter ratio method. This uses the same methods as in the SolarSoft IDL routine of the same name.
+XRTpy provides a routine, `xrt_teem`, that employs the objects listed above to derive the temperature and emission measure in for a given pair of images using the filter ratio method. This uses the same methods as in the SolarSoft IDL routine of the same name.
 
 
 X-Ray Filter Channel
@@ -71,5 +88,8 @@ in the `SolarSoft XRT Analysis Guide`_ for more information about the XRT filter
     that selects the titanium-on-polyimide filter, then the string would be ``'Ti-poly'``. The process is the same for all XRT
     filter channels.
 
+
+.. _CHIANTI: https://www.chiantidatabase.org/chianti_database_history.html
 .. _SolarSoft XRT Analysis Guide: https://xrt.cfa.harvard.edu/resources/documents/XAG/XAG.pdf
 .. _xrt-cfa-harvard: https://xrt.cfa.harvard.edu/index.php
+.. _XRT temperature response with other choice of abundances: http://solar.physics.montana.edu/takeda/xrt_response/xrt_resp.html

docs/glossary.rst

@@ -9,12 +9,19 @@ Glossary
 .. glossary::
    :sorted:
 
-   Temperature
-      Temperature :math:`T`, is a `~astropy.units.Quantity` with units of temperature (e.g., kelvin).
+   DN
+      Data number (DN) per unit.
+
+   Contamination (related to the XRT)
+      Contaminating material has accumulated on the XRT CCD and focal plane filters (FPFs), causing a decrease in sensitivity.
+      Refer to Section 2.5.3 `Contamination` in the `SolarSoft XRT Analysis Guide`_ in the `SolarSoft XRT Analysis Guide`_ for
+      more information about the XRT contamination.
 
    Temperature response
       Instrument temperature response function, for a filter-channel. Units are
       DN cm\ :sup:`5` s\ :sup:`−1` pix\ :sup:`-1`\ .
 
    Solar-emission-spectra
       A set of plasma emission spectra for a set of temperature.
+
+.. _SolarSoft XRT Analysis Guide: https://xrt.cfa.harvard.edu/resources/documents/XAG/XAG.pdf

xrtpy/response/temperature_response.py

@@ -4,7 +4,6 @@
 
 import numpy as np
 import scipy.io
-import sunpy.time
 
 from astropy import units as u
 from astropy.constants import c, h
@@ -18,107 +17,155 @@
 _h_eV_s = h.to(u.eV * u.s).value
 
 
-_CHIANTI_filename = (
-    Path(__file__).parent.absolute() / "data" / "XRT_emiss_model.default_CHIANTI.geny"
-)
-_CHIANTI_file = scipy.io.readsav(_CHIANTI_filename)
-_XRT_emiss_model_file = _CHIANTI_file["p0"]
-
-
-CHIANTI_file = {
-    "abundance_model": _XRT_emiss_model_file["ABUND_MODEL"][0],
-    "dens_model": _XRT_emiss_model_file["DENS_MODEL"][0],
-    "ioneq_model": _XRT_emiss_model_file["IONEQ_MODEL"][0],
-    "name": _XRT_emiss_model_file["NAME"][0],
-    "spectra": _XRT_emiss_model_file["SPEC"],
-    "spectra_units": _XRT_emiss_model_file["SPEC_UNITS"][0],
-    "temperature": _XRT_emiss_model_file["TEMP"][0],
-    "temp_units": _XRT_emiss_model_file["TEMP_UNITS"][0],
-    "tlength": _XRT_emiss_model_file["TLENGTH"][0],
-    "wlength": _XRT_emiss_model_file["WLENGTH"][0],
-    "wavelength": _XRT_emiss_model_file["WAVE"][0],
-    "wavelength_units": _XRT_emiss_model_file["WAVE_UNITS"][0],
+_abundance_model_file_path = {
+    "coronal_abundance_path": Path(__file__).parent.absolute()
+    / "data/chianti_emission_models"
+    / "XRT_emiss_model.default_CHIANTI.geny",
+    "hybrid_abundance_path": Path(__file__).parent.absolute()
+    / "data/chianti_emission_models"
+    / "XRT_emiss_model.default_CHIANTI_photospheric.geny",
+    "photospheric_abundance_path": Path(__file__).parent.absolute()
+    / "data/chianti_emission_models"
+    / "XRT_emiss_model.default_CHIANTI_hybrid.geny",
 }
 
+_abundance_model_data = {
+    "coronal": scipy.io.readsav(_abundance_model_file_path["coronal_abundance_path"])[
+        "p0"
+    ],
+    "hybrid": scipy.io.readsav(_abundance_model_file_path["hybrid_abundance_path"])[
+        "p0"
+    ],
+    "photospheric": scipy.io.readsav(
+        _abundance_model_file_path["photospheric_abundance_path"]
+    )["p0"],
+}
+
+list_of_abundance_name = ["coronal", "hybrid", "photospheric"]
+
+
+def _resolve_abundance_model_type(abundance_model):
+    """Formats and checks users abundance model input name."""
+    if not isinstance(abundance_model, str):
+        raise TypeError("Abundance model name must be a string")
+    abundance_name = abundance_model.lower()
+    if abundance_name not in list_of_abundance_name:
+        raise ValueError(
+            f"\n{abundance_name} is not a current abundance model for XRTpy.\n"
+            "Available abundance models:\n"
+            "'coronal', 'hybrid', and 'photospheric'.\n"
+        )
+    return abundance_name
+
 
 class TemperatureResponseFundamental:
     """Produce the temperature response for each XRT x-ray channel, assuming a spectral emission model."""
 
-    def __init__(self, filter_name, observation_date):
+    def __init__(self, filter_name, observation_date, abundance_model="coronal"):
         self._name = resolve_filter_name(filter_name)
+        self._channel = Channel(self.filter_name)
+        # self.observation_date = self.observation_date
+        self._abundance_model = _resolve_abundance_model_type(abundance_model)
         self._effective_area_fundamental = EffectiveAreaFundamental(
-            self.name, observation_date
+            self._name, observation_date
         )
-        self._channel = Channel(self.name)
 
     @property
-    def name(self):
+    def filter_name(self):
         """Name of searched filter."""
         return self._name
 
+    @property
+    def abundances(self) -> str:
+        """Defined the name of the requested abundance model as a string."""
+        return self._abundance_model
+
     @property
     def observation_date(self):
         """Date of observation."""
         return self._effective_area_fundamental.observation_date
 
     @property
-    def CHIANTI_version(self):
-        """Name of the emission model."""
-        return CHIANTI_file["name"]
+    def get_abundance_data(self):
+        """Returning the requested abundance data that is used to calculate the temperature response."""
+        abundance_type_name = self.abundances
+        data = _abundance_model_data[abundance_type_name]
+        if abundance_type_name not in list_of_abundance_name:
+            ValueError("Unable to process data. ")
+
+        return {
+            "abundance_model_info": data["ABUND_MODEL"][0],
+            "dens_model": data["DENS_MODEL"][0],
+            "ioneq_model": data["IONEQ_MODEL"][0],
+            "name": data["NAME"][0],
+            "spectra": data["SPEC"],
+            "spectra_units": data["SPEC_UNITS"][0],
+            "temperature": data["TEMP"][0],
+            "temp_units": data["TEMP_UNITS"][0],
+            "tlength": data["TLENGTH"][0],
+            "wlength": data["WLENGTH"][0],
+            "wavelength": data["WAVE"][0],
+            "wavelength_units": data["WAVE_UNITS"][0],
+        }
+
+    @property
+    def chianti_abundance_version(self):
+        """Version of the chianti abundance model."""
+        return self.get_abundance_data["name"]
 
     @property
-    def abundance_model(self):
+    def abundance_model_information(self):
         """A brief description of what abundance model was used in the creation of the emission spectra."""
-        return CHIANTI_file["abundance_model"]
+        return self.get_abundance_data["abundance_model_info"]
 
     @property
     def density_model(self):
         """A brief description of the plasma density, emission measure,or differential emission measure that was used in the creation of the emission spectra."""
-        return CHIANTI_file["dens_model"]
+        return self.get_abundance_data["dens_model"]
 
     @property
     def ionization_model(self):
         """A brief description of that ionization equilibrium model was used in the creation of the emission spectra."""
-        return CHIANTI_file["ioneq_model"]
+        return self.get_abundance_data["ioneq_model"]
 
     @property
     @u.quantity_input
     def CHIANTI_temperature(self):
-        """CHIANTI temperatures in kelvin."""
-        return u.Quantity(CHIANTI_file["temperature"] * u.K)
+        """Emission model temperatures in kelvin."""
+        return u.Quantity(self.get_abundance_data["temperature"] * u.K)
 
     @property
-    def CHIANTI_file_spectra(self):
-        """CHIANTI file spectra."""
-        return CHIANTI_file["spectra"]
+    def file_spectra(self):
+        """Emission model file spectra."""
+        return self.get_abundance_data["spectra"][0]
 
     @property
     @u.quantity_input
-    def CHIANTI_wavelength(self):
-        """CHIANTI file wavelength values in Å."""
-        return u.Quantity(CHIANTI_file["wavelength"] * u.Angstrom)
+    def wavelength(self):
+        """Emission model file wavelength values in Å."""
+        return u.Quantity(self.get_abundance_data["wavelength"] * u.Angstrom)
 
     @property
     @u.quantity_input
     def channel_wavelength(self):
         """Array of wavelengths for every X-ray channel in Å."""
-        return u.Quantity((Channel(self.name).wavelength[:3993]) * u.photon)
+        return u.Quantity((Channel(self.filter_name).wavelength[:3993]) * u.photon)
 
     @property
     def focal_len(self):
         """Focal length of the telescope in units of cm."""
-        return Channel(self.name).geometry.geometry_focal_len
+        return Channel(self.filter_name).geometry.geometry_focal_len
 
     @property
     def ev_per_electron(self):
         """Amount of energy it takes to dislodge 1 electron in the CCD."""
-        return Channel(self.name).ccd.ccd_energy_per_electron
+        return Channel(self.filter_name).ccd.ccd_energy_per_electron
 
     @property
     @u.quantity_input
     def pixel_size(self) -> u.cm:
         """CCD pixel size. Units converted from μm to cm."""
-        ccd_pixel_size = Channel(self.name).ccd.ccd_pixel_size
+        ccd_pixel_size = Channel(self.filter_name).ccd.ccd_pixel_size
         return ccd_pixel_size.to(u.cm)
 
     @property
@@ -133,7 +180,9 @@ def spectra(self) -> u.photon * u.cm**3 / (u.sr * u.s * u.Angstrom):
         spectra_interpolate = []
         for i in range(61):
             interpolater = interpolate.interp1d(
-                self.CHIANTI_wavelength, CHIANTI_file["spectra"][0][i], kind="linear"
+                self.wavelength,
+                self.file_spectra[i],
+                kind="linear",
             )
             spectra_interpolate.append(interpolater(self.channel_wavelength))
         return spectra_interpolate * (
@@ -142,6 +191,7 @@ def spectra(self) -> u.photon * u.cm**3 / (u.sr * u.s * u.Angstrom):
 
     @u.quantity_input
     def effective_area(self) -> u.cm**2:
+        # return effective_area(self.filter_name, self.observation_date)
         return self._effective_area_fundamental.effective_area()
 
     @u.quantity_input
@@ -166,7 +216,7 @@ def integration(self) -> u.electron * u.cm**5 / (u.s * u.pix):
     @u.quantity_input
     def ccd_gain_right(self) -> u.electron / u.DN:
         """Provide the camera gain in electrons per data number."""
-        return Channel(self.name).ccd.ccd_gain_right
+        return Channel(self.filter_name).ccd.ccd_gain_right
 
     @u.quantity_input
     def temperature_response(self) -> u.DN * u.cm**5 / (u.s * u.pix):

xrtpy/response/tests/data/temperature_response_hybrid_IDL_testing_files/Al_med/Al_med_22Sept2007_temperature_response_hybrid.txt

@@ -0,0 +1,66 @@
+Temperature Response: IDL Results
+Abundance_model hybrid
+Filter Al-med
+observation_date 22-Sept-2007  22:45:45
+Temperature Temperature Response
+      100000.   2.19654e-36
+      112202.   2.83905e-36
+      125893.   4.11514e-36
+      141254.   6.46438e-36
+      158489.   1.02296e-35
+      177828.   1.55973e-35
+      199526.   2.25359e-35
+      223872.   3.07464e-35
+      251189.   3.89549e-35
+      281838.   4.40142e-35
+      316228.   4.64052e-35
+      354814.   5.33387e-35
+      398107.   6.73237e-35
+      446684.   8.62099e-35
+      501187.   1.12587e-34
+      562341.   1.96639e-34
+      630958.   7.20764e-34
+      707946.   3.59215e-33
+      794328.   1.61838e-32
+      891251.   6.42349e-32
+  1.00000e+06   2.33399e-31
+  1.12202e+06   7.84793e-31
+  1.25893e+06   2.37168e-30
+  1.41254e+06   6.34721e-30
+  1.58489e+06   1.52579e-29
+  1.77828e+06   3.36681e-29
+  1.99526e+06   6.97998e-29
+  2.23872e+06   1.36832e-28
+  2.51189e+06   2.49099e-28
+  2.81838e+06   4.19238e-28
+  3.16228e+06   6.59565e-28
+  3.54814e+06   9.80474e-28
+  3.98107e+06   1.38720e-27
+  4.46684e+06   1.87501e-27
+  5.01187e+06   2.42907e-27
+  5.62341e+06   3.02825e-27
+  6.30958e+06   3.64568e-27
+  7.07946e+06   4.25010e-27
+  7.94328e+06   4.81729e-27
+  8.91250e+06   5.34668e-27
+  1.00000e+07   5.84188e-27
+  1.12202e+07   6.22687e-27
+  1.25893e+07   6.30359e-27
+  1.41254e+07   5.96482e-27
+  1.58489e+07   5.37829e-27
+  1.77828e+07   4.77259e-27
+  1.99526e+07   4.25235e-27
+  2.23872e+07   3.83292e-27
+  2.51189e+07   3.50310e-27
+  2.81838e+07   3.24246e-27
+  3.16228e+07   3.03185e-27
+  3.54814e+07   2.85659e-27
+  3.98108e+07   2.70554e-27
+  4.46684e+07   2.57191e-27
+  5.01187e+07   2.45039e-27
+  5.62341e+07   2.33929e-27
+  6.30958e+07   2.23732e-27
+  7.07946e+07   2.14467e-27
+  7.94328e+07   2.06166e-27
+  8.91251e+07   1.98826e-27
+  1.00000e+08   1.92372e-27