diff --git a/EXOSIMS/Completeness/GarrettCompleteness.py b/EXOSIMS/Completeness/GarrettCompleteness.py index d42286860..03b680192 100644 --- a/EXOSIMS/Completeness/GarrettCompleteness.py +++ b/EXOSIMS/Completeness/GarrettCompleteness.py @@ -49,6 +49,9 @@ def __init__(self, order_of_quadrature=15, **specs): self._outspec["order_of_quadrature"] = self.order_of_quadrature + # setting a base filename that isn't mutated by a completeness calculation + self.filename_intcompleteness = self.filename + def completeness_setup(self): """Preform any preliminary calculations needed for this flavor of completeness @@ -206,20 +209,10 @@ def target_completeness(self, TL): int_comp: 1D numpy array of completeness values for each target star """ - - OS = TL.OpticalSystem - if TL.calc_char_int_comp: - mode = list( - filter(lambda mode: "spec" in mode["inst"]["name"], OS.observingModes) - )[0] - else: - mode = list(filter(lambda mode: mode["detectionMode"], OS.observingModes))[ - 0 - ] - # To limit the amount of computation, we want to find the most common # int_dMag value (typically the one the user sets in the input json since # int_dMag is either the user input or the intCutoff_dMag). + vals, counts = np.unique(TL.int_dMag, return_counts=True) self.mode_dMag = vals[np.argwhere(counts == np.max(counts))[0][0]] mode_dMag_mask = TL.int_dMag == self.mode_dMag @@ -234,6 +227,7 @@ def target_completeness(self, TL): ): extstr += "%s: " % att + str(getattr(self.PlanetPopulation, att)) + " " # include mode_dMag and intCutoff_dMag + extstr += ( "%s: " % "mode_dMag" + str(self.mode_dMag) @@ -241,53 +235,111 @@ def target_completeness(self, TL): + " " ) ext = hashlib.md5(extstr.encode("utf-8")).hexdigest() - self.filename += ext - Cpath = os.path.join(self.cachedir, self.filename + ".acomp") - - # calculate separations based on IWA - IWA = mode["IWA"] - OWA = mode["OWA"] - smin = (np.tan(IWA) * TL.dist).to("AU").value - if np.isinf(OWA): - smax = np.array([self.rmax] * len(smin)) - else: - smax = (np.tan(OWA) * TL.dist).to("AU").value - smax[smax > self.rmax] = self.rmax - - int_comp = np.zeros(smin.shape) - # calculate dMags based on maximum dMag - if self.PlanetPopulation.scaleOrbits: - L = np.where(TL.L > 0, TL.L, 1e-10) # take care of zero/negative values - smin = smin / np.sqrt(L) - smax = smax / np.sqrt(L) - dMag_vals = TL.int_dMag - 2.5 * np.log10(L) - separation_mask = smin < self.rmax - int_comp[separation_mask] = self.comp_s( - smin[separation_mask], smax[separation_mask], dMag_vals[separation_mask] - ) + Cpath = os.path.join( + self.cachedir, + self.filename_intcompleteness + + hashlib.md5("int_comp".encode("utf-8")).hexdigest() + + ext + + ".acomp", + ) + + if os.path.exists(Cpath): + self.vprint('Loading cached int completeness file from "%s".' % Cpath) + try: + with open(Cpath, "rb") as ff: + int_comp = pickle.load(ff) + except UnicodeDecodeError: + with open(Cpath, "rb") as ff: + int_comp = pickle.load(ff, encoding="latin1") + self.vprint("int Completeness loaded from cache.") else: - # In this case we find where the mode dMag value is also in the - # separation range and use the vectorized integral since they have - # the same dMag value. Where the dMag values are not the mode we - # must use comp_s which is slower - dMag_vals = TL.int_dMag - separation_mask = smin < self.rmax - dist_s = self.genComp(Cpath, TL) - dist_sv = np.vectorize(dist_s.integral, otypes=[np.float64]) - separation_mode_mask = separation_mask & mode_dMag_mask - separation_not_mode_mask = separation_mask & ~mode_dMag_mask - int_comp[separation_mode_mask] = dist_sv( - smin[separation_mode_mask], smax[separation_mode_mask] - ) - int_comp[separation_not_mode_mask] = self.comp_s( - smin[separation_not_mode_mask], - smax[separation_not_mode_mask], - dMag_vals[separation_not_mode_mask], + + self.vprint('Cached int completeness file not found at "%s".' % Cpath) + self.vprint("Beginning int_comp completeness calculations.") + + OS = TL.OpticalSystem + if TL.calc_char_int_comp: + mode = list( + filter( + lambda mode: "spec" in mode["inst"]["name"], OS.observingModes + ) + )[0] + else: + mode = list( + filter(lambda mode: mode["detectionMode"], OS.observingModes) + )[0] + + # important PlanetPopulation attributes + atts = list(self.PlanetPopulation.__dict__) + extstr = "" + for att in sorted(atts, key=str.lower): + if ( + not callable(getattr(self.PlanetPopulation, att)) + and att != "PlanetPhysicalModel" + ): + extstr += ( + "%s: " % att + str(getattr(self.PlanetPopulation, att)) + " " + ) + # include mode_dMag and intCutoff_dMag + extstr += ( + "%s: " % "mode_dMag" + + str(self.mode_dMag) + + f"intCutoff_dMag: {TL.intCutoff_dMag}" + + " " ) - # ensure that completeness values are between 0 and 1 - int_comp = np.clip(int_comp, 0.0, 1.0) + ext = hashlib.md5(extstr.encode("utf-8")).hexdigest() + Cpath_aux = os.path.join(self.cachedir, self.filename + ext + ".acomp") + self.filename += ext + + # calculate separations based on IWA + IWA = mode["IWA"] + OWA = mode["OWA"] + smin = (np.tan(IWA) * TL.dist).to("AU").value + if np.isinf(OWA): + smax = np.array([self.rmax] * len(smin)) + else: + smax = (np.tan(OWA) * TL.dist).to("AU").value + smax[smax > self.rmax] = self.rmax + + int_comp = np.zeros(smin.shape) + # calculate dMags based on maximum dMag + if self.PlanetPopulation.scaleOrbits: + L = np.where(TL.L > 0, TL.L, 1e-10) # take care of zero/negative values + smin = smin / np.sqrt(L) + smax = smax / np.sqrt(L) + dMag_vals = TL.int_dMag - 2.5 * np.log10(L) + separation_mask = smin < self.rmax + int_comp[separation_mask] = self.comp_s( + smin[separation_mask], + smax[separation_mask], + dMag_vals[separation_mask], + ) + else: + # In this case we find where the mode dMag value is also in the + # separation range and use the vectorized integral since they have + # the same dMag value. Where the dMag values are not the mode we + # must use comp_s which is slower + dMag_vals = TL.int_dMag + separation_mask = smin < self.rmax + dist_s = self.genComp(Cpath_aux, TL) + dist_sv = np.vectorize(dist_s.integral, otypes=[np.float64]) + separation_mode_mask = separation_mask & mode_dMag_mask + separation_not_mode_mask = separation_mask & ~mode_dMag_mask + int_comp[separation_mode_mask] = dist_sv( + smin[separation_mode_mask], smax[separation_mode_mask] + ) + int_comp[separation_not_mode_mask] = self.comp_s( + smin[separation_not_mode_mask], + smax[separation_not_mode_mask], + dMag_vals[separation_not_mode_mask], + ) + # ensure that completeness values are between 0 and 1 + int_comp = np.clip(int_comp, 0.0, 1.0) + with open(Cpath, "wb") as ff: + pickle.dump(int_comp, ff) + self.vprint("Int Completeness data stored in %s" % Cpath) return int_comp def genComp(self, Cpath, TL): @@ -308,7 +360,7 @@ def genComp(self, Cpath, TL): if os.path.exists(Cpath): # dist_s interpolant already exists for parameters - self.vprint("Loading cached completeness file from %s" % Cpath) + self.vprint("Loading cached completeness pdf file from %s" % Cpath) try: with open(Cpath, "rb") as ff: H = pickle.load(ff) @@ -334,7 +386,7 @@ def genComp(self, Cpath, TL): H = {"dist_s": dist_s} with open(Cpath, "wb") as ff: pickle.dump(H, ff) - self.vprint("Completeness data stored in %s" % Cpath) + self.vprint("Completeness pdf data stored in %s" % Cpath) return dist_s diff --git a/documentation/conf.py b/documentation/conf.py index 10a6e0336..af4f4bff8 100644 --- a/documentation/conf.py +++ b/documentation/conf.py @@ -19,56 +19,56 @@ # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. -#sys.path.insert(0, os.path.abspath('.')) -sys.path.insert(0, os.path.abspath('..')) +# sys.path.insert(0, os.path.abspath('.')) +sys.path.insert(0, os.path.abspath("..")) # -- General configuration ------------------------------------------------ # If your documentation needs a minimal Sphinx version, state it here. -#needs_sphinx = '1.0' +# needs_sphinx = '1.0' # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ - 'sphinx.ext.autodoc', - 'sphinx.ext.napoleon', - 'sphinx.ext.todo', - 'sphinx.ext.coverage', - 'sphinx.ext.mathjax', - 'sphinx.ext.ifconfig', - 'sphinx.ext.viewcode', - 'sphinx.ext.intersphinx', - 'sphinxcontrib.mermaid' + "sphinx.ext.autodoc", + "sphinx.ext.napoleon", + "sphinx.ext.todo", + "sphinx.ext.coverage", + "sphinx.ext.mathjax", + "sphinx.ext.ifconfig", + "sphinx.ext.viewcode", + "sphinx.ext.intersphinx", + "sphinxcontrib.mermaid", ] # Add any paths that contain templates here, relative to this directory. -templates_path = ['_templates'] +templates_path = ["_templates"] # The suffix(es) of source filenames. # You can specify multiple suffix as a list of string: # source_suffix = ['.rst', '.md'] -source_suffix = '.rst' +source_suffix = ".rst" # The encoding of source files. -#source_encoding = 'utf-8-sig' +# source_encoding = 'utf-8-sig' # The master toctree document. -master_doc = 'index' +master_doc = "index" # General information about the project. -project = u'EXOSIMS' -copyright = u'2015 - 2023, SIOSlab' -author = u'SIOSlab' +project = "EXOSIMS" +copyright = "2015 - 2023, SIOSlab" +author = "SIOSlab" # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # # The short X.Y version. -#version = '2.1' +# version = '2.1' # The full version, including alpha/beta/rc tags. -#release = '2.1.0' +# release = '2.1.0' with open(os.path.join("..", "EXOSIMS", "__init__.py"), "r") as f: version_file = f.read() @@ -86,41 +86,41 @@ # # This is also used if you do content translation via gettext catalogs. # Usually you set "language" from the command line for these cases. -#language = None +# language = None # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: -#today = '' +# today = '' # Else, today_fmt is used as the format for a strftime call. -#today_fmt = '%B %d, %Y' +# today_fmt = '%B %d, %Y' # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. -exclude_patterns = ['_build', '.DS_Store'] +exclude_patterns = ["_build", ".DS_Store"] # The reST default role (used for this markup: `text`) to use for all # documents. -#default_role = None +# default_role = None # If true, '()' will be appended to :func: etc. cross-reference text. -#add_function_parentheses = True +# add_function_parentheses = True # If true, the current module name will be prepended to all description # unit titles (such as .. function::). -#add_module_names = True +# add_module_names = True # If true, sectionauthor and moduleauthor directives will be shown in the # output. They are ignored by default. -#show_authors = False +# show_authors = False # The name of the Pygments (syntax highlighting) style to use. -pygments_style = 'sphinx' +pygments_style = "sphinx" # A list of ignored prefixes for module index sorting. -#modindex_common_prefix = [] +# modindex_common_prefix = [] # If true, keep warnings as "system message" paragraphs in the built documents. -#keep_warnings = False +# keep_warnings = False # If true, `todo` and `todoList` produce output, else they produce nothing. todo_include_todos = True @@ -130,164 +130,157 @@ # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. -#html_theme = 'alabaster' +# html_theme = 'alabaster' html_theme = "sphinx_rtd_theme" # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # documentation. -#html_theme_options = {} -#html_theme_options = {'fixed_sidebar':'true', +# html_theme_options = {} +# html_theme_options = {'fixed_sidebar':'true', # 'logo': 'logo.png', # 'sidebar_collapse':'true' # } -html_theme_options = {'collapse_navigation': False} +html_theme_options = {"collapse_navigation": False} # Add any paths that contain custom themes here, relative to this directory. -#html_theme_path = [] +# html_theme_path = [] # The name for this set of Sphinx documents. If None, it defaults to # " v documentation". -#html_title = None +# html_title = None # A shorter title for the navigation bar. Default is the same as html_title. -#html_short_title = None +# html_short_title = None # The name of an image file (relative to this directory) to place at the top # of the sidebar. -#html_logo = None -#html_logo = os.path.join("..","EXOSIMS_cropped.png") +# html_logo = None +# html_logo = os.path.join("..","EXOSIMS_cropped.png") # The name of an image file (within the static path) to use as favicon of the # docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 # pixels large. -#html_favicon = None +# html_favicon = None # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ['_static'] -html_css_files = ['css/custom.css'] +html_static_path = ["_static"] +html_css_files = ["css/custom.css"] # Add any extra paths that contain custom files (such as robots.txt or # .htaccess) here, relative to this directory. These files are copied # directly to the root of the documentation. -#html_extra_path = [] +# html_extra_path = [] # If not '', a 'Last updated on:' timestamp is inserted at every page bottom, # using the given strftime format. -#html_last_updated_fmt = '%b %d, %Y' +# html_last_updated_fmt = '%b %d, %Y' # If true, SmartyPants will be used to convert quotes and dashes to # typographically correct entities. -#html_use_smartypants = True +# html_use_smartypants = True # Custom sidebar templates, maps document names to template names. -#html_sidebars = {} +# html_sidebars = {} # Additional templates that should be rendered to pages, maps page names to # template names. -#html_additional_pages = {} +# html_additional_pages = {} # If false, no module index is generated. -#html_domain_indices = True +# html_domain_indices = True # If false, no index is generated. -#html_use_index = True +# html_use_index = True # If true, the index is split into individual pages for each letter. -#html_split_index = False +# html_split_index = False # If true, links to the reST sources are added to the pages. -#html_show_sourcelink = True +# html_show_sourcelink = True # If true, "Created using Sphinx" is shown in the HTML footer. Default is True. -#html_show_sphinx = True +# html_show_sphinx = True # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. -#html_show_copyright = True +# html_show_copyright = True # If true, an OpenSearch description file will be output, and all pages will # contain a tag referring to it. The value of this option must be the # base URL from which the finished HTML is served. -#html_use_opensearch = '' +# html_use_opensearch = '' # This is the file name suffix for HTML files (e.g. ".xhtml"). -#html_file_suffix = None +# html_file_suffix = None # Language to be used for generating the HTML full-text search index. # Sphinx supports the following languages: # 'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja' # 'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr' -#html_search_language = 'en' +# html_search_language = 'en' # A dictionary with options for the search language support, empty by default. # Now only 'ja' uses this config value -#html_search_options = {'type': 'default'} +# html_search_options = {'type': 'default'} # The name of a javascript file (relative to the configuration directory) that # implements a search results scorer. If empty, the default will be used. -#html_search_scorer = 'scorer.js' +# html_search_scorer = 'scorer.js' # Output file base name for HTML help builder. -htmlhelp_basename = 'EXOSIMSdoc' +htmlhelp_basename = "EXOSIMSdoc" # -- Options for LaTeX output --------------------------------------------- latex_elements = { -# The paper size ('letterpaper' or 'a4paper'). -#'papersize': 'letterpaper', - -# The font size ('10pt', '11pt' or '12pt'). -#'pointsize': '10pt', - -# Additional stuff for the LaTeX preamble. -#'preamble': '', - -# Latex figure (float) alignment -#'figure_align': 'htbp', + # The paper size ('letterpaper' or 'a4paper'). + #'papersize': 'letterpaper', + # The font size ('10pt', '11pt' or '12pt'). + #'pointsize': '10pt', + # Additional stuff for the LaTeX preamble. + #'preamble': '', + # Latex figure (float) alignment + #'figure_align': 'htbp', } # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, # author, documentclass [howto, manual, or own class]). latex_documents = [ - (master_doc, 'EXOSIMS.tex', u'EXOSIMS Documentation', - u'SIOSlab', 'manual'), + (master_doc, "EXOSIMS.tex", "EXOSIMS Documentation", "SIOSlab", "manual"), ] # The name of an image file (relative to this directory) to place at the top of # the title page. -#latex_logo = None +# latex_logo = None # For "manual" documents, if this is true, then toplevel headings are parts, # not chapters. -#latex_use_parts = False +# latex_use_parts = False # If true, show page references after internal links. -#latex_show_pagerefs = False +# latex_show_pagerefs = False # If true, show URL addresses after external links. -#latex_show_urls = False +# latex_show_urls = False # Documents to append as an appendix to all manuals. -#latex_appendices = [] +# latex_appendices = [] # If false, no module index is generated. -#latex_domain_indices = True +# latex_domain_indices = True # -- Options for manual page output --------------------------------------- # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). -man_pages = [ - (master_doc, 'exosims', u'EXOSIMS Documentation', - [author], 1) -] +man_pages = [(master_doc, "exosims", "EXOSIMS Documentation", [author], 1)] # If true, show URL addresses after external links. -#man_show_urls = False +# man_show_urls = False # -- Options for Texinfo output ------------------------------------------- @@ -296,37 +289,45 @@ # (source start file, target name, title, author, # dir menu entry, description, category) texinfo_documents = [ - (master_doc, 'EXOSIMS', u'EXOSIMS Documentation', - author, 'EXOSIMS', 'One line description of project.', - 'Miscellaneous'), + ( + master_doc, + "EXOSIMS", + "EXOSIMS Documentation", + author, + "EXOSIMS", + "One line description of project.", + "Miscellaneous", + ), ] # Documents to append as an appendix to all manuals. -#texinfo_appendices = [] +# texinfo_appendices = [] # If false, no module index is generated. -#texinfo_domain_indices = True +# texinfo_domain_indices = True # How to display URL addresses: 'footnote', 'no', or 'inline'. -#texinfo_show_urls = 'footnote' +# texinfo_show_urls = 'footnote' # If true, do not generate a @detailmenu in the "Top" node's menu. -#texinfo_no_detailmenu = False +# texinfo_no_detailmenu = False numfig = True -intersphinx_mapping = {'python': ('https://docs.python.org/3', None), - 'astropy': ('https://docs.astropy.org/en/stable/', None), - 'numpy': ('https://numpy.org/doc/stable/', None), - 'scipy': ('https://docs.scipy.org/doc/scipy/', None), - 'matplotlib': ('https://matplotlib.org/stable/', None), - 'synphot': ('https://synphot.readthedocs.io/en/latest/', None)} +intersphinx_mapping = { + "python": ("https://docs.python.org/3", None), + "astropy": ("https://docs.astropy.org/en/stable/", None), + "numpy": ("https://numpy.org/doc/stable/", None), + "scipy": ("https://docs.scipy.org/doc/scipy/", None), + "matplotlib": ("https://matplotlib.org/stable/", None), + "synphot": ("https://synphot.readthedocs.io/en/latest/", None), +} # add latex customization mathjax3_config = { - 'tex':{ - 'macros':{ - "intd": ["\\,\\mathrm{d}#1",1], + "tex": { + "macros": { + "intd": ["\\,\\mathrm{d}#1", 1], "mf": "\\mathbf", "mc": "\\mathcal", } @@ -334,7 +335,7 @@ } latex_elements = { - 'preamble': r""" + "preamble": r""" \def\bs{\boldsymbol} \def\mf{\mathbf} \def\mb{\mathbb} @@ -345,5 +346,5 @@ """, } -mermaid_params = ['-p' 'puppeteer-config.json'] -mermaid_version = "9.4.0" # temporary until next sphinxcontrib.mermaid release +mermaid_params = ["-p" "puppeteer-config.json"] +mermaid_version = "9.4.0" # temporary until next sphinxcontrib.mermaid release diff --git a/tools/evenlyDistributePointsOnSphere.py b/tools/evenlyDistributePointsOnSphere.py index 336d4f7a2..005d753e6 100644 --- a/tools/evenlyDistributePointsOnSphere.py +++ b/tools/evenlyDistributePointsOnSphere.py @@ -10,8 +10,8 @@ import os import matplotlib -if ( - ("DISPLAY" not in os.environ) and ("indows" not in os.environ["OS"]) +if ("DISPLAY" not in os.environ) and ( + "indows" not in os.environ["OS"] ): # Check environment for keys import matplotlib.pyplot as plt @@ -73,9 +73,7 @@ def f(vv): xyzpoints = np.asarray([[xx[i], yy[i], zz[i]] for i in np.arange(len(zz))]) # Calculates the sum(min(dij)**3.) distances, inds = pt_pt_distances(xyzpoints) - return sum( - 1.0 / np.asarray(distances) - ) # -sum(np.asarray(distances)**2.) + return sum(1.0 / np.asarray(distances)) # -sum(np.asarray(distances)**2.) # squares and sums each point-to-closest point distances diff --git a/tools/gen_spectral_library_index.py b/tools/gen_spectral_library_index.py index fea842c6f..c5f8963aa 100644 --- a/tools/gen_spectral_library_index.py +++ b/tools/gen_spectral_library_index.py @@ -185,5 +185,5 @@ # filter by luminosity class tmp3 = specclasses[specclasses[:, 2] == tmp[2]] # next get the closest numerical spectral class representation - row = tmp3[np.argmin(np.abs(tmp3[:,3] - tmp2))] + row = tmp3[np.argmin(np.abs(tmp3[:, 3] - tmp2))] print(f"{s} matched to {row[0]}{row[1]}{row[2]}")