new GNIRS keyhole imaging tutorial.

geminidr/doc/tutorials/GNIRSImg-DRTutorial/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = python -msphinx
+SPHINXPROJ    = TutorialSeries-GNIRSImagingDataReductionwithDRAGONS
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

geminidr/doc/tutorials/GNIRSImg-DRTutorial/_static/css/custom_code.css

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+
+/* , a .rst-content tt, a .rst-content code */
+
+.rst-content code.xref {
+    background-color: transparent;
+    border: solid 1px transparent;
+    color: #2980B9;
+    padding: 0px 0px;
+    font-size: 80%;
+    }
+
+.rst-content code.xref:hover {
+    /* border: solid 1px #e1e4e5; */
+    text-decoration: underline;
+    }
+

geminidr/doc/tutorials/GNIRSImg-DRTutorial/_static/fonts.css

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+.red {
+  color: red;
+}
+
+.blue {
+  color: blue;
+}
+
+.green {
+  color: green;
+}
+
+.yellow {
+  color: yellow;
+}
+
+.gray {
+  color: gray;
+}
+
+.lightgray {
+  color: lightgray;
+}
+
+.small {
+  font-size: 80%;
+}
+
+.large {
+  font-size: 120%;
+}
+
+.bolditalic {
+  font-weight: bold;
+  font-style: italic;
+}

geminidr/doc/tutorials/GNIRSImg-DRTutorial/_static/rtd_theme_overrides.css

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+/* override RTD table width restrictions */
+
+@media screen and (min-width: 767px) {
+
+  .wy-table-responsive table td, .wy-table-responsive table th {
+      /* !important prevents the common CSS stylesheets from 
+         overriding this as on RTD the are loaded after this stylesheet */
+      white-space: normal !important;
+  } 
+
+  .wy-table-responsive {
+      /* margin-bottom: 24px; */ 
+      /* max-width: 100%; */
+      overflow: visible !important;
+  }
+
+  .wy-nav-content {
+      max-width: 1200px !important;
+  }
+}

geminidr/doc/tutorials/GNIRSImg-DRTutorial/_static/todo-styles.css

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+div.admonition-todo {
+border-top: 2px solid red;
+border-bottom: 2px solid red;
+border-left: 2px solid red;
+border-right: 2px solid red;
+background-color: #ff6347
+}

geminidr/doc/tutorials/GNIRSImg-DRTutorial/conf.py

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+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+#
+# Tutorial Series - GNIRS Imaging Data Reduction with DRAGONS documentation build configuration file, created by
+# sphinx-quickstart on Tue May 14 11:01:35 2019.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+# 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.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# 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.intersphinx',
+    'sphinx.ext.todo',
+    'sphinx.ext.imgmath']
+
+# Add any paths that contain templates here, relative to this directory.
+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'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = 'Tutorial Series - GNIRS Imaging Data Reduction with DRAGONS'
+copyright = '2019, Kathleen Labrie'
+author = 'Kathleen Labrie'
+
+# 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 = '1.0'
+# The full version, including alpha/beta/rc tags.
+release = '1.0.0'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# 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
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This patterns also effect to html_static_path and html_extra_path
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = True
+
+
+# -- Options for HTML output ----------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+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 = {}
+
+# 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']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# This is required for the alabaster theme
+# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
+# html_sidebars = {
+#     '**': [
+#         'about.html',
+#         'navigation.html',
+#         'relations.html',  # needs 'show_related': True theme option to display
+#         'searchbox.html',
+#         'donate.html',
+#     ]
+# }
+
+
+# -- Options for HTMLHelp output ------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'TutorialSeries-GNIRSImgDRDRAGONS'
+
+
+# -- 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',
+}
+
+# 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, 'TutorialSeries-GNIRSImgDRDRAGONS.tex', 'Tutorial Series - GNIRS Imaging Data Reduction with DRAGONS Documentation',
+     'Kathleen Labrie', 'manual'),
+]
+
+
+# -- 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, 'tutorialseries-gnirsimgdrdragons', 'Tutorial Series - GNIRS Imaging Data Reduction with DRAGONS Documentation',
+     [author], 1)
+]
+
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, 'TutorialSeries-GNIRSImgDRDRAGONS', 'Tutorial Series - GNIRS Imaging Data Reduction with DRAGONS Documentation',
+     author, 'TutorialSeries-GNIRSImagingDataReductionwithDRAGONS', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+
+# -- Options for Epub output ----------------------------------------------
+
+# Bibliographic Dublin Core info.
+epub_title = project
+epub_author = author
+epub_publisher = author
+epub_copyright = copyright
+
+# The unique identifier of the text. This can be a ISBN number
+# or the project homepage.
+#
+# epub_identifier = ''
+
+# A unique identification for the text.
+#
+# epub_uid = ''
+
+# A list of files that should not be packed into the epub file.
+epub_exclude_files = ['search.html']
+
+
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {'https://docs.python.org/': None}
+
+# ------
+
+# Adding style in order to have the todos show up in a red box
+def setup(app):
+    app.add_stylesheet('todo-styles.css')
+    app.add_stylesheet('rtf_theme_overrides.css')
+    app.add_stylesheet('css/rtd_theme_overrides_references.css')
+    app.add_stylesheet('fonts.css')
+
+

geminidr/doc/tutorials/GNIRSImg-DRTutorial/datasets.rst

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+.. datasets.rst
+
+.. _datasets:
+
+********************************
+Setting up and tutorial datasets
+********************************
+
+.. _datasetup:
+
+Downloading the tutorial datasets
+=================================
+
+All the data needed to run this tutorial are found in the tutorial's data
+package (KL??? name of the package, with URL).  Download it and unpack it
+somewhere convenient.
+
+.. highlight:: bash
+
+::
+
+    cd <somewhere convenient>
+    tar xvzf KL???
+
+The datasets are found in the subdirectory ``gnirsimg_tutorial/playdata``, and we
+will work in the subdirectory named ``gnirsimg_tutorial/playground``.
+
+.. note:: All the raw data can also be downloaded from the Gemini Observatory
+   Archive.  Using the tutorial data package is probably more convenient.
+
+
+Datasets descriptions
+=====================
+
+.. _datakeyhole:
+
+Dataset for example 1: Point source through the acquisition keyhole
+-------------------------------------------------------------------
+
+This is a GNIRS acquisition keyhole imaging observation of a point source.
+The observation sequence uses dither on target.  Dithered observations
+nearby in time will be use for sky subtraction of each frame.
+
+The calibrations we use for this example include:
+
+* Darks for the science frames
+* Flats, as a sequence of lamps-on and lamps-off exposures
+
+Here is the files breakdown.  They are included in a tutorial data package.
+They can also be downloaded from the Gemini Observatory Archive (GOA).
+
++---------------+--------------------------------------------+
+| Science       || N20120117S0014-33 (J-band, on-target)     |
++---------------+--------------------------------------------+
+| Science darks || N20120102S0538-547 (60 sec, like Science) |
++---------------+--------------------------------------------+
+| Flats         || N20120117S0034-41 (lamps-on)              |
+|               || N20120117S0042-49 (lamps-off)             |
++---------------+--------------------------------------------+
+
+A note about finding the darks in the GOA.  Since GNIRS is not an imager and
+imaging through the keyhole is done only in extreme circumstances, the archive
+does not have calibration association rules for the darks in this case.  One
+needs to manually search for the darks.  Here is the search that was done to
+find the darks for this observation sequence:
+
+* Set a date range around the dates of the science observations.  In this case
+  we used "20120101-20120131".
+* Set **Instrument** to GNIRS.
+* Set **Obs.Type** to DARK.
+* Set the exposure time to 60 seconds.
+* On the result table, select the darks with a "Pass" setting in the "QA" column.