Merge pull request #113 from spacetelescope/v1.36.0

V1.36.0

History.rst

@@ -1,14 +1,18 @@
 Change Log for SPEC_PLOTS
 =========================
 
-v1.35.1 - 2023 Aug. 4  
+v1.36.0 - 2024 Feb. 9
+-----------------
+* Added basic support HST Hubble Advanced Spectral Products (HASP)
+
+v1.35.1 - 2023 Aug. 4
 -----------------
 * Added support for flux uncertainties being in FLUX_ERROR column
   instead of ERROR column for JWST x1d FITS files.
 * Fixed readability of y-axis tick labels by adjusting font size,
   angle, and padding.
 
-v1.35.0 - 2023 Jul. 31 
+v1.35.0 - 2023 Jul. 31
 -----------------
 * Added required config file for ReadTheDocs.
 * Updated package dependencies to newer versions.

setup.py

@@ -20,6 +20,7 @@
       license="MIT",
       packages=["spec_plots", "spec_plots.utils", "spec_plots.utils.specutils",
                 "spec_plots.utils.specutils_cos",
+                "spec_plots.utils.specutils_hasp",
                 "spec_plots.utils.specutils_jwst",
                 "spec_plots.utils.specutils_stis"],
       install_requires=["astropy>=5.2.2", "matplotlib>=3.7.1", "numpy>=1.24.3",

spec_plots.egg-info/PKG-INFO

@@ -1,9 +1,13 @@
 Metadata-Version: 2.1
-Name: spec-plots
-Version: 1.35.1
+Name: spec_plots
+Version: 1.36.0
 Summary: Create preview plots of HST or JWST spectra.
 Home-page: https://github.com/spacetelescope/spec_plots
 Author: Scott W. Fleming
 Author-email: [email protected]
 License: MIT
 Classifier: Programming Language :: Python :: 3
+Requires-Dist: astropy>=5.2.2
+Requires-Dist: matplotlib>=3.7.1
+Requires-Dist: numpy>=1.24.3
+Requires-Dist: future>=0.18.3

spec_plots.egg-info/SOURCES.txt

@@ -36,6 +36,10 @@ spec_plots/utils/specutils_cos/get_segment_names.py
 spec_plots/utils/specutils_cos/make_fits.py
 spec_plots/utils/specutils_cos/plotspec.py
 spec_plots/utils/specutils_cos/readspec.py
+spec_plots/utils/specutils_hasp/__init__.py
+spec_plots/utils/specutils_hasp/haspspectrum.py
+spec_plots/utils/specutils_hasp/plotspec.py
+spec_plots/utils/specutils_hasp/readspec.py
 spec_plots/utils/specutils_jwst/__init__.py
 spec_plots/utils/specutils_jwst/jwstspectrum.py
 spec_plots/utils/specutils_jwst/plotspec.py

spec_plots/__init__.py

@@ -8,4 +8,4 @@
 
 from __future__ import absolute_import
 
-__version__ = '1.35.1'
+__version__ = '1.36.0'

spec_plots/docs/API/conf.py

@@ -12,7 +12,9 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import mock,os,sys
+import unittest.mock as mock
+import os
+import sys
 
 MOCK_MODULES = ['astropy', 'astropy.io', 'matplotlib', 'matplotlib.pyplot', 'matplotlib.ticker', 'matplotlib.collections', 'numpy', 'future', 'future.builtins']
 for mod_name in MOCK_MODULES:
@@ -26,6 +28,7 @@
 sys.path.insert(0, os.path.abspath('../../utils/'))
 sys.path.insert(0, os.path.abspath('../../utils/specutils/'))
 sys.path.insert(0, os.path.abspath('../../utils/specutils_cos/'))
+sys.path.insert(0, os.path.abspath('../../utils/specutils_hasp/'))
 sys.path.insert(0, os.path.abspath('../../utils/specutils_jwst/'))
 sys.path.insert(0, os.path.abspath('../../utils/specutils_stis/'))
 
@@ -55,7 +58,7 @@
 
 # General information about the project.
 project = u'spec_plots'
-copyright = u'2014,2015,2016 Scott W. Fleming'
+copyright = u'2014,2015,2016,2017,2018,2019,2020,2021,2022,2023,2024 Scott W. Fleming'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

spec_plots/docs/API/index.rst

@@ -3,7 +3,7 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Documentation for MAST's openSAIL project: spec_plots
+Documentation for MAST's spectral preview generator: spec_plots
 =====================================================
 
 Contents:

spec_plots/docs/API/modules.rst

@@ -6,5 +6,6 @@ Utility Modules, Including Instrument-Specific READ and PLOT Modules
 
    utils.specutils
    utils.specutils_cos
+   utils.specutils_hasp
    utils.specutils_jwst
    utils.specutils_stis

spec_plots/docs/API/utils.specutils_hasp.rst

@@ -0,0 +1,20 @@
+utils.specutils_hasp package
+============================
+
+haspspectrum
+---------------------------------------
+
+.. automodule:: utils.specutils_hasp.haspspectrum
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+plotspec
+-----------------------------------
+
+.. autofunction:: utils.specutils_hasp.plotspec
+
+readspec
+-----------------------------------
+
+.. autofunction:: utils.specutils_hasp.readspec

spec_plots/docs/README_DEVELOPERS.txt

@@ -16,7 +16,7 @@ Best Practices for Development Of A New Branch
 
 8.)  After doing a final commit of the branch, make sure all Github Issues are closed for that branch, or re-assigned if punting to a later build for that Issue.
 
-9.)  After regression testing is finished and all Issues assigned to this branch are closed or moved to a future build, initiate a pull request and merge into master.
+9.)  After regression testing is finished and all Issues assigned to this branch are closed or moved to a future build, initiate a pull request and merge into main.
 
 10.)  To upload to PyPI with twine: twine upload dist/*, with the -u and -p options.
 

spec_plots/make_hst_spec_previews.py

@@ -17,8 +17,9 @@
 from __future__ import absolute_import
 from __future__ import print_function
 import argparse
-from os import path
 from builtins import str
+from os import path
+import sys
 #--------------------
 # External Imports
 #--------------------
@@ -27,7 +28,7 @@
 #--------------------
 # Package Imports
 #--------------------
-from spec_plots.utils import specutils, specutils_cos, specutils_stis
+from spec_plots.utils import specutils, specutils_cos, specutils_stis, specutils_hasp
 from spec_plots import __version__
 
 FLUX_SCALE_FACTOR_DEFAULT = 10.
@@ -43,7 +44,7 @@
 
 #--------------------
 
-class HSTSpecPrevError(Exception, object):
+class HSTSpecPrevError(Exception):
     """
     This class defines a generic Exception to use for errors raised in
     MAKE_HST_SPEC_PREVIEWS.  It simply prints the given string when raising the
@@ -99,7 +100,8 @@ def check_input_options(args):
 
 def get_instrument_name(input_file):
     """
-    Retrieves the instrument name from a FITS file primary header.
+    Determines whether the input file is for HASP (Hubbble Advanced
+    Spectral Product).
 
     :param input_file: Name of input FITS file.
 
@@ -124,11 +126,28 @@ def get_instrument_name(input_file):
         except KeyError:
             print("*** MAKE_HST_SPEC_PREVIEWS ERROR: INSTRUME keyword not"
                   " found in this file's primary header: " + input_file)
-            exit(1)
+            sys.exit()
     return this_instrument.strip().upper()
 
 #--------------------
 
+def is_hasp_product(input_file):
+    """
+    Retrieves the instrument name from a FITS file primary header.
+
+    :param input_file: Name of input FITS file.
+
+    :type input_file: str
+
+    :returns: bool -- Returns True if the filename ends in _cspec.fits.
+    """
+
+    if input_file.endswith("_cspec.fits"):
+        return True
+    return False
+
+#--------------------
+
 def make_hst_spec_previews(input_file, flux_scale_factor=
                            FLUX_SCALE_FACTOR_DEFAULT, fluxerr_scale_factor=
                            FLUXERR_SCALE_FACTOR_DEFAULT, n_consecutive=
@@ -227,13 +246,50 @@ def make_hst_spec_previews(input_file, flux_scale_factor=
             if ofile is not None:
                 if ofile[-4:] == '.png':
                     print("  Output file: " + ofile)
-                    print("  Output file: " + ofile.strip('\.png') +
+                    print("  Output file: " + ofile.split('.png')[0] +
                           '_thumb.png')
                 else:
                     print("  Output file: " + ofile)
             else:
                 print("  Plotting to screen.")
 
+    # Handle previews for HASP products.
+    if is_hasp_product(input_file):
+        if verbose:
+            print("HASP product")
+        # Get wavelengths, fluxes, flux uncertainties.
+        hasp_spectrum = specutils_hasp.readspec(input_file)
+
+        # Make "large-size" plot.
+        for out_type, out_file in zip(output_type, output_files):
+            if out_type != 'fits':
+                # Make "large-size" plot
+                hasp_plot_metrics = specutils.calc_plot_metrics("hasp",
+                    hasp_spectrum.wavelengths,
+                    hasp_spectrum.fluxes,
+                    hasp_spectrum.fluxerrs,
+                    hasp_spectrum.dqs,
+                    1, flux_scale_factor, fluxerr_scale_factor)
+                specutils_hasp.plotspec(hasp_spectrum,
+                                        out_type, out_file,
+                                        flux_scale_factor, fluxerr_scale_factor,
+                                        hasp_plot_metrics,
+                                        dpi_val=dpi_val, output_size=1024,
+                                        debug=debug, full_ylabels=full_ylabels,
+                                        optimize=optimize)
+
+                # Make "thumbnail-size" plot, if requested.  Notice that in this
+                # case we always plot just the first association, by passing only
+                # `stitched_spectra[0]`.
+                if not debug:
+                    specutils_hasp.plotspec(hasp_spectrum,
+                                            out_type, out_file,
+                                            flux_scale_factor, fluxerr_scale_factor,
+                                            hasp_plot_metrics,
+                                            dpi_val=dpi_val,
+                                            output_size=128, optimize=optimize)
+        return
+
     # Read in the FITS file to determine which instrument it comes from.
     # Print the name of the instrument found in the header if verbose is turned
     # on.

spec_plots/make_jwst_spec_previews.py

@@ -17,8 +17,9 @@
 from __future__ import absolute_import
 from __future__ import print_function
 import argparse
-from os import path
 from builtins import str
+from os import path
+import sys
 #--------------------
 # External Imports
 #--------------------
@@ -43,7 +44,7 @@
 
 #--------------------
 
-class JWSTSpecPrevError(Exception, object):
+class JWSTSpecPrevError(Exception):
     """
     This class defines a generic Exception to use for errors raised in
     MAKE_JWST_SPEC_PREVIEWS.  It simply prints the given string when raising the
@@ -124,7 +125,7 @@ def get_instrument_name(input_file):
         except KeyError:
             print("*** MAKE_JWST_SPEC_PREVIEWS ERROR: INSTRUME keyword not"
                   " found in this file's primary header: " + input_file)
-            exit(1)
+            sys.exit()
     return this_instrument.strip().upper()
 
 #--------------------
@@ -228,7 +229,7 @@ def make_jwst_spec_previews(input_file, flux_scale_factor=
             if ofile is not None:
                 if ofile[-4:] == '.png':
                     print("  Output file: " + ofile)
-                    print("  Output file: " + ofile.strip('\.png') +
+                    print("  Output file: " + ofile.split('.png')[0] +
                           '_thumb.png')
                 else:
                     print("  Output file: " + ofile)

spec_plots/utils/specutils/calc_plot_metrics.py

@@ -103,4 +103,3 @@ def calc_plot_metrics(instrument, wls, fls, flerrs, dqs, n_consecutive,
                 optimal_xaxis_range, "avoid_regions":avoid_regions,
             "y_axis_range":y_axis_range, "line_collection":linecoll}
 #--------------------
-

spec_plots/utils/specutils/edge_trim.py

@@ -118,6 +118,7 @@ def _set_plot_xrange_test(instrument, flux_values, flux_err_values, median_flux,
     # Return array of boolean values for the edge_trim test.
     if numpy.isfinite(median_flux):
         bool_results = [((instrument == "cos" and x != 0. and check_fluxes) or
+                         (instrument == "hasp" and x != 0. and check_fluxes) or
                          (instrument == "stis" and x != 0. and check_fluxes) or
                          (instrument == "miri" and x != 0. and check_fluxes) or
                          (not check_fluxes))
@@ -132,6 +133,8 @@ def _set_plot_xrange_test(instrument, flux_values, flux_err_values, median_flux,
                               is_bad_dq(instrument, z) and check_dqs) or
                              (instrument == "cos" and not
                               is_bad_dq(instrument, z) and check_dqs) or
+                             (instrument == "hasp" and not
+                              is_bad_dq(instrument, z) and check_dqs) or
                              (instrument == "miri" and not
                               is_bad_dq(instrument, z) and check_dqs) or
                              (not check_dqs))
@@ -217,7 +220,7 @@ def edge_trim(instrument, fluxes, fluxerrs, dqs, n_consecutive, median_flux,
 
     # First run the xrange test on the first and last 100 elements (for
     # speed).  If no good indices are found within those ranges, then and only
-    # then will we run it on the entire array. """
+    # then will we run it on the entire array.
     where_good_fluxes_nodq = numpy.where(numpy.asarray(_set_plot_xrange_test(
         instrument, numpy.concatenate((fluxes[0:edge_size],
                                        fluxes[-1*edge_size:])),

spec_plots/utils/specutils/is_bad_dq.py

@@ -43,21 +43,22 @@ def is_bad_dq(instrument, dqs):
     if instrument == "cos":
         if isinstance(dqs, numpy.ndarray):
             return numpy.asarray([x < 1 for x in dqs])
-        else:
-            return dqs < 1
+        return dqs < 1
 
-    elif instrument == "stis":
+    if instrument == "hasp":
         if isinstance(dqs, numpy.ndarray):
-            return numpy.asarray([x != 0 and x != 16 for x in dqs])
-        else:
-            return dqs != 0 and dqs != 16
+            return numpy.asarray([x < 1 for x in dqs])
+        return dqs < 1
+
+    if instrument == "stis":
+        if isinstance(dqs, numpy.ndarray):
+            return numpy.asarray([x not in (0, 16) for x in dqs])
+        return dqs not in (0, 16)
 
-    elif instrument in ["miri", "nirspec", "niriss"]:
+    if instrument in ["miri", "nirspec", "niriss"]:
         if isinstance(dqs, numpy.ndarray):
             return numpy.asarray([x < 1 for x in dqs])
-        else:
-            return dqs < 1
+        return dqs < 1
 
-    else:
-        return numpy.asarray([])
+    return numpy.asarray([])
 #--------------------

spec_plots/utils/specutils/set_plot_yrange.py

@@ -108,10 +108,8 @@ def set_plot_yrange(wavelengths, fluxes, avoid_regions=None, wl_range=None):
     if min_flux != max_flux:
         if min_flux - ybuffer > 0.:
             return [min_flux-ybuffer, max_flux+ybuffer]
-        else:
-            # We don't want the y-axis range to be TOO far negative, so limit
-            # it to be close to the lowest data point. """
-            return [1.1*min_flux, max_flux+ybuffer]
-    else:
-        return [min_flux-1., max_flux+1.]
+        # We don't want the y-axis range to be TOO far negative, so limit
+        # it to be close to the lowest data point.
+        return [1.1*min_flux, max_flux+ybuffer]
+    return [min_flux-1., max_flux+1.]
 #--------------------