Merge pull request #81 from natashabatalha/dev

Stage PandExo 3 Update

Author: natashabatalha

docs/conf.py

@@ -49,7 +49,7 @@
 
 # General information about the project.
 project = u'PandExo'
-copyright = u'2016, Natasha Batalha;Kevin Stevenson'
+copyright = u'Updated 2022'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

docs/installation.rst

@@ -11,16 +11,31 @@ PandExo requires downloading **three folders**: 1) JWST instrument info, 2) stel
 
 JWST Reference Data
 ````````````````````
-JWST Reference data has been updated to 2.0!
+JWST Reference data has been updated to 3.0!
 
 .. warning::
-    Reference data for PandExo/Pandeia 1.X is not compatible with PandExo/Pandeia 2.0. Please always ensure that your reference data is up to date with the software (e.g. reference data 2.0 should match software release 2.0)
+    Reference data must match the software version. For example Pandeia reference data 3.0 should match Pandeia verions software release 3.0, and that should match PandExo 3.0)
 
-The new reference data is located `here for v2p0 <https://stsci.app.box.com/v/pandeia-refdata-v2p0-jwst>`_. More information on `pandeia installation can be found here <https://outerspace.stsci.edu/display/PEN/Pandeia+Engine+Installation>`_
+The new reference data is located `here for v3p0 <https://stsci.app.box.com/v/pandeia-refdata-v3p0-jwst>`_. More information on `pandeia installation can be found here <https://outerspace.stsci.edu/display/PEN/Pandeia+Engine+Installation>`_
 
 
 After you have downloaded the reference data, create environment variable (`more resources on how to create environment variables are located here <https://natashabatalha.github.io/picaso/installation.html#create-environment-variable>`_). 
 
+You can verify your installation by opening up a terminal with access to the conda installation, and type
+
+.. code-block:: bash 
+
+    python -c "import pandeia.engine; pandeia.engine.pandeia_version()"
+
+If properly installed and configured, it should show the refdata version and synphot data directory, like this:
+
+.. code-block:: bash 
+
+    Pandeia Engine version:  3.0
+    Pandeia RefData version:  3.0
+    Pysynphot Data:  /your/data/directory/synphot
+
+
 .. code-block:: bash 
 
     echo 'export pandeia_refdata="$USRDIR/pandeia_data"' >>~/.bash_profile
@@ -41,7 +56,7 @@ Create your environment variable:
 
 Normalization Files  
 ````````````````````
-New to PandExo 2.0, **users now have to download the master table of all pysynphot throughput tables.** 
+New to PandExo >2.0, **users now have to download the master table of all pysynphot throughput tables.** 
 
 `Download the file here <https://archive.stsci.edu/hlsps/reference-atlases/hlsp_reference-atlases_hst_multi_everything_multi_v11_sed.tar>`_
 

pandexo/engine/justplotit.py

@@ -548,14 +548,20 @@ def jwst_2d_det(result_dict, plot=True, output_file='det2d.html'):
     out = result_dict['PandeiaOutTrans']
     data = out['2d']['detector']
 
+    if 'miri' in result_dict['input']['Instrument']: 
+        width=300
+        height=800
+    else: 
+        width=800
+        height=300
 
     xr, yr = data.shape
 
     plot_detector_2d = Figure(tools="pan,wheel_zoom,box_zoom,reset,hover,save",
                          x_range=[0, yr], y_range=[0, xr],
                          x_axis_label='Pixel', y_axis_label='Spatial',
                          title="2D Detector Image",
-                        width=800, height=300)
+                        width=width, height=height)
 
     plot_detector_2d.image(image=[data], x=[0], y=[0], dh=[xr], dw=[yr],
                       palette="Spectral11")
@@ -593,11 +599,19 @@ def jwst_2d_sat(result_dict, plot=True, output_file='sat2d.html'):
     out = result_dict['PandeiaOutTrans']
     data = out['2d']['saturation']
     xr, yr = data.shape
+
+    if 'miri' in result_dict['input']['Instrument']: 
+        width=300
+        height=800
+    else: 
+        width=800
+        height=300
+        
     plot_sat_2d = Figure(tools=TOOLS,
                          x_range=[0, yr], y_range=[0, xr],
                          x_axis_label='Pixel', y_axis_label='Spatial',
                          title="Saturation",
-                        width=800, height=300)
+                        width=width, height=height)
 
     plot_sat_2d.image(image=[data], x=[0], y=[0], dh=[xr], dw=[yr],
                       palette="Spectral11")

pandexo/engine/reference/miri_input.json

@@ -6,10 +6,19 @@
             "target": true,
             "position": {
                 "ang_unit": "arcsec",
-                "xoff": 0.0,
-                "yoff": 0.0
+                "x_offset": 0.0,
+                "y_offset": 0.0
+            },
+            "shape":{
+                "geometry": "point"
             },
             "spectrum": {
+                "extinction": {
+                    "bandpass": "j",
+                    "law": "mw_rv_31",
+                    "unit": "mag",
+                    "value": 0.0                    
+                },
                 "normalization": {
                      "type": "none"},
                 "sed": {

pandexo/engine/reference/nircam_input.json

@@ -5,10 +5,19 @@
             "target": true,
             "position": {
                 "ang_unit": "arcsec",
-                "xoff": 0.0,
-                "yoff": 0.0
+                "x_offset": 0.0,
+                "y_offset": 0.0
+            },
+            "shape": {
+                "geometry": "point"
             },
             "spectrum": {
+                "extinction": {
+                    "bandpass": "j",
+                    "law": "mw_rv_31",
+                    "unit": "mag",
+                    "value": 0.0
+                },
                 "normalization": {
                      "type": "none"},
                 "sed": {

pandexo/engine/reference/niriss_input.json

@@ -5,10 +5,19 @@
             "target": true,
             "position": {
                 "ang_unit": "arcsec",
-                "xoff": 0.0,
-                "yoff": 0.0
+                "x_offset": 0.0,
+                "y_offset": 0.0
+            },
+            "shape": {
+                "geometry": "point"
             },
             "spectrum": {
+                "extinction": {
+                    "bandpass": "j",
+                    "law": "mw_rv_31",
+                    "unit": "mag",
+                    "value": 0.0
+                },
                 "normalization": {
                      "type": "none"},
                 "sed": {
@@ -18,7 +27,6 @@
                 "lines": []
                     }
                 }],
-
     "background_level": "medium",
     "background":"ecliptic",
     "calculation":{
@@ -54,6 +62,7 @@
     },
     "strategy": {
             "method": "soss",
-            "order":1
+            "order":1,
+            "background_subtraction": false
             }
 }

pandexo/engine/reference/nirspec_input.json

@@ -5,10 +5,19 @@
             "target": true,
             "position": {
                 "ang_unit": "arcsec",
-                "xoff": 0.0,
-                "yoff": 0.0
+                "x_offset": 0.0,
+                "y_offset": 0.0
             },
+            "shape": {
+                    "geometry": "point"
+                },
             "spectrum": {
+                "extinction": {
+                    "bandpass": "j",
+                    "law": "mw_rv_31",
+                    "unit": "mag",
+                    "value": 0.0
+                },
                 "normalization": {
                      "type": "none"},
                 "sed": {

pandexo/engine/utils/plotters.py

@@ -385,11 +385,18 @@ def create_component_jwst(result_dict):
 
     xr, yr = data.shape
 
+    if 'miri' in result_dict['input']['Instrument']: 
+        width=300
+        height=800
+    else: 
+        width=800
+        height=300
+        
     plot_detector_2d = Figure(tools="pan,wheel_zoom,box_zoom,reset,hover,save",
                          x_range=[0, yr], y_range=[0, xr],
                          x_axis_label='Pixel', y_axis_label='Spatial',
                          title="2D Detector Image",
-                        width=800, height=300)
+                        width=width, height=height)
 
     plot_detector_2d.image(image=[data], x=[0], y=[0], dh=[xr], dw=[yr],
                       palette="Spectral11")
@@ -405,7 +412,7 @@ def create_component_jwst(result_dict):
                          x_range=[0, yr], y_range=[0, xr],
                          x_axis_label='Pixel', y_axis_label='Spatial',
                          title="Signal-to-Noise Ratio",
-                        width=800, height=300)
+                        width=width, height=height)
 
     plot_snr_2d.image(image=[data], x=[0], y=[0], dh=[xr], dw=[yr],
                       palette="Spectral11")
@@ -420,7 +427,7 @@ def create_component_jwst(result_dict):
                          x_range=[0, yr], y_range=[0, xr],
                          x_axis_label='Pixel', y_axis_label='Spatial',
                          title="Saturation",
-                        width=800, height=300)
+                        width=width, height=height)
 
     plot_sat_2d.image(image=[data], x=[0], y=[0], dh=[xr], dw=[yr],
                       palette="Spectral11")

setup.py

@@ -41,14 +41,11 @@
 # also be placed in the setup.cfg, as will be demonstrated in a future update
 # to this sample package.
 
-if sys.version_info < (3,0): 
-    pandas_version = '==0.24.0'
-else:
-    pandas_version = '>=0.25.0'
+
 setup(
 
     name='pandexo.engine',
-    version='2.0.0',
+    version='3.0.0',
     summary='pandexo transiting exoplanet simulator',
     description_file='README.rst',
     author='Natasha Batalha at NASA Ames',
@@ -92,11 +89,11 @@
     # },
 
     install_requires=[
-          'pandeia.engine==2.0',
+          'pandeia.engine==3.0',
           'numpy',
           'bokeh==3.0.2',
           'tornado',
-          'pandas'+pandas_version,
+          'pandas',
           'joblib',
           'photutils',
           'astropy',