Read the Docs build information Build id: 1104 Project: pydetlib Version: latest Commit: 2caefbcdea5498b51c4311f5538a41d684b7910b Date: 2017-05-17T05:54:31.222198Z State: finished Success: True [rtd-command-info] start-time: 2017-05-17T10:54:42.553000Z, end-time: 2017-05-17T10:54:50.204000Z, duration: 7, exit-code: 0 python3 -mvirtualenv --no-site-packages --no-download /user_builds/pydetlib/envs/latest Using base prefix '/usr' New python executable in /user_builds/pydetlib/envs/latest/bin/python3 Not overwriting existing python script /user_builds/pydetlib/envs/latest/bin/python (you must use /user_builds/pydetlib/envs/latest/bin/python3) Installing setuptools, pip, wheel...done. [rtd-command-info] start-time: 2017-05-17T10:54:50.266000Z, end-time: 2017-05-17T10:55:37.605000Z, duration: 47, exit-code: 0 python /user_builds/pydetlib/envs/latest/bin/pip install --use-wheel -U --cache-dir /user_builds/pydetlib/.cache/pip sphinx==1.3.5 Pygments==2.1.3 setuptools==20.1.1 docutils==0.12 mkdocs==0.15.0 mock==1.0.1 pillow==2.6.1 git+https://github.com/rtfd/readthedocs-sphinx-ext.git@0.6-alpha#egg=readthedocs-sphinx-ext sphinx-rtd-theme==0.1.9 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.5.4 recommonmark==0.1.1 Requirement already up-to-date: sphinx==1.3.5 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages Requirement already up-to-date: Pygments==2.1.3 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages Collecting setuptools==20.1.1 Using cached setuptools-20.1.1-py2.py3-none-any.whl Requirement already up-to-date: docutils==0.12 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages Requirement already up-to-date: mkdocs==0.15.0 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages Requirement already up-to-date: mock==1.0.1 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages Requirement already up-to-date: pillow==2.6.1 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages Collecting readthedocs-sphinx-ext from git+https://github.com/rtfd/readthedocs-sphinx-ext.git@0.6-alpha#egg=readthedocs-sphinx-ext Cloning https://github.com/rtfd/readthedocs-sphinx-ext.git (to 0.6-alpha) to /tmp/pip-build-a6igv16e/readthedocs-sphinx-ext Requirement already up-to-date: sphinx-rtd-theme==0.1.9 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.10-py2.py3-none-any.whl Requirement already up-to-date: commonmark==0.5.4 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages Requirement already up-to-date: recommonmark==0.1.1 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages Collecting Jinja2>=2.3 (from sphinx==1.3.5) Downloading Jinja2-2.9.6-py2.py3-none-any.whl (340kB) Requirement already up-to-date: six>=1.4 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from sphinx==1.3.5) Requirement already up-to-date: snowballstemmer>=1.1 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from sphinx==1.3.5) Collecting babel!=2.0,>=1.3 (from sphinx==1.3.5) Downloading Babel-2.4.0-py2.py3-none-any.whl (6.8MB) Requirement already up-to-date: livereload>=2.3.2 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from mkdocs==0.15.0) Collecting tornado>=4.1 (from mkdocs==0.15.0) Downloading tornado-4.5.1.tar.gz (483kB) Requirement already up-to-date: Markdown>=2.3.1 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from mkdocs==0.15.0) Requirement already up-to-date: PyYAML>=3.10 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from mkdocs==0.15.0) Requirement already up-to-date: mkdocs-bootswatch>=0.1.0 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from mkdocs==0.15.0) Requirement already up-to-date: click>=4.0 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from mkdocs==0.15.0) Requirement already up-to-date: mkdocs-bootstrap>=0.1.1 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from mkdocs==0.15.0) Collecting requests (from readthedocs-sphinx-ext) Downloading requests-2.14.2-py2.py3-none-any.whl (560kB) Requirement already up-to-date: nilsimsa>=0.3.7 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from readthedocs-sphinx-ext) Collecting MarkupSafe>=0.23 (from Jinja2>=2.3->sphinx==1.3.5) Downloading MarkupSafe-1.0.tar.gz Collecting pytz>=0a (from babel!=2.0,>=1.3->sphinx==1.3.5) Downloading pytz-2017.2-py2.py3-none-any.whl (484kB) Requirement already up-to-date: backports_abc>=0.4 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from tornado>=4.1->mkdocs==0.15.0) Building wheels for collected packages: tornado, MarkupSafe Running setup.py bdist_wheel for tornado: started Running setup.py bdist_wheel for tornado: finished with status 'done' Stored in directory: /user_builds/pydetlib/.cache/pip/wheels/84/83/cd/6a04602633457269d161344755e6766d24307189b7a67ff4b7 Running setup.py bdist_wheel for MarkupSafe: started Running setup.py bdist_wheel for MarkupSafe: finished with status 'done' Stored in directory: /user_builds/pydetlib/.cache/pip/wheels/88/a7/30/e39a54a87bcbe25308fa3ca64e8ddc75d9b3e5afa21ee32d57 Successfully built tornado MarkupSafe Installing collected packages: setuptools, requests, readthedocs-sphinx-ext, alabaster, MarkupSafe, Jinja2, pytz, babel, tornado Found existing installation: setuptools 28.8.0 Uninstalling setuptools-28.8.0: Successfully uninstalled setuptools-28.8.0 Found existing installation: requests 2.13.0 Uninstalling requests-2.13.0: Successfully uninstalled requests-2.13.0 Found existing installation: readthedocs-sphinx-ext 0.5.4 Uninstalling readthedocs-sphinx-ext-0.5.4: Successfully uninstalled readthedocs-sphinx-ext-0.5.4 Running setup.py install for readthedocs-sphinx-ext: started Running setup.py install for readthedocs-sphinx-ext: finished with status 'done' Found existing installation: alabaster 0.7.9 Uninstalling alabaster-0.7.9: Successfully uninstalled alabaster-0.7.9 Found existing installation: MarkupSafe 0.23 Uninstalling MarkupSafe-0.23: Successfully uninstalled MarkupSafe-0.23 Found existing installation: Jinja2 2.9.5 Uninstalling Jinja2-2.9.5: Successfully uninstalled Jinja2-2.9.5 Found existing installation: pytz 2016.10 Uninstalling pytz-2016.10: Successfully uninstalled pytz-2016.10 Found existing installation: Babel 2.3.4 Uninstalling Babel-2.3.4: Successfully uninstalled Babel-2.3.4 Found existing installation: tornado 4.4.2 Uninstalling tornado-4.4.2: Successfully uninstalled tornado-4.4.2 Successfully installed Jinja2-2.9.6 MarkupSafe-1.0 alabaster-0.7.10 babel-2.4.0 pytz-2017.2 readthedocs-sphinx-ext-0.5.4 requests-2.14.2 setuptools-20.1.1 tornado-4.5.1 [rtd-command-info] start-time: 2017-05-17T10:55:37.673000Z, end-time: 2017-05-17T10:55:40.159000Z, duration: 2, exit-code: 0 python /user_builds/pydetlib/envs/latest/bin/pip install --exists-action=w --cache-dir /user_builds/pydetlib/.cache/pip -rlib/docs/requirements.txt Requirement already satisfied: ipython in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from -r lib/docs/requirements.txt (line 1)) Requirement already satisfied: ipyparallel in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from -r lib/docs/requirements.txt (line 2)) Requirement already satisfied: jupyter in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from -r lib/docs/requirements.txt (line 3)) Requirement already satisfied: matplotlib>=2.0.0 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from -r lib/docs/requirements.txt (line 4)) Requirement 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html5lib!=0.9999,!=0.99999,<0.99999999,>=0.999 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from bleach->nbconvert->jupyter->-r lib/docs/requirements.txt (line 3)) [rtd-command-info] start-time: 2017-05-17T10:55:41.457000Z, end-time: 2017-05-17T10:55:41.490000Z, duration: 0, exit-code: 0 cat conf.py # -*- coding: utf-8 -*- # # src documentation build configuration file, created by # sphinx-quickstart on Tue Sep 30 09:45:40 2014. # # 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. import sys import os sys.path.append(os.path.abspath("../src/")) from unittest.mock import MagicMock class Mock(MagicMock): @classmethod def __getattr__(cls, name): return Mock() MOCK_MODULES = ['pycuda', 'pycuda.driver', 'pycuda.compiler', 'pycuda.autoinit', 'h5py', 'brewer2mpl', 'matplotlib', 'matplotlib.pyplot', 'matplotlib.colors', 'matplotlib.axes', 'scipy', 'scipy.stats', 'matplotlib.patches', 'scipy.ndimage', 'scipy.ndimage.filters', 'iminuit', 'mpl_toolkits', 'mpl_toolkits.mplot3d', 'mpl_toolkits.axes_grid1', 'mpl_toolkits.axes_grid1.inset_locator', 'pandoc', 'pypandoc'] sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES) # 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('.')) # -- 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.autodoc', 'sphinx.ext.viewcode', 'sphinxcontrib.napoleon', 'sphinx.ext.mathjax', 'sphinx.ext.intersphinx', ] # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] # The suffix of source filenames. source_suffix = '.rst' # The encoding of source files. #source_encoding = 'utf-8-sig' # The master toctree document. master_doc = 'index' # General information about the project. project = u'XFEL Detector Tools' copyright = u'2014, European X-ray Free Electron Laser Facility GmbH' # 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 = '' # The full version, including alpha/beta/rc tags. release = '' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. #language = None # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: #today = '' # Else, today_fmt is used as the format for a strftime call. #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'] # The reST default role (used for this markup: `text`) to use for all # documents. #default_role = None # If true, '()' will be appended to :func: etc. cross-reference text. #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 # If true, sectionauthor and moduleauthor directives will be shown in the # output. They are ignored by default. #show_authors = False # The name of the Pygments (syntax highlighting) style to use. pygments_style = 'sphinx' # A list of ignored prefixes for module index sorting. #modindex_common_prefix = [] # If true, keep warnings as "system message" paragraphs in the built documents. #keep_warnings = False # -- 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 = 'sphinxdoc' # 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 themes here, relative to this directory. #html_theme_path = [] # The name for this set of Sphinx documents. If None, it defaults to # " v documentation". #html_title = None # A shorter title for the navigation bar. Default is the same as html_title. #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 # 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 # 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'] # 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 = [] # 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' # If true, SmartyPants will be used to convert quotes and dashes to # typographically correct entities. #html_use_smartypants = True # Custom sidebar templates, maps document names to template names. #html_sidebars = {} # Additional templates that should be rendered to pages, maps page names to # template names. #html_additional_pages = {} # If false, no module index is generated. #html_domain_indices = True # If false, no index is generated. #html_use_index = True # If true, the index is split into individual pages for each letter. #html_split_index = False # If true, links to the reST sources are added to the pages. #html_show_sourcelink = True # If true, "Created using Sphinx" is shown in the HTML footer. Default is True. #html_show_sphinx = True # If true, "(C) Copyright ..." is shown in the HTML footer. Default is 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 = '' # This is the file name suffix for HTML files (e.g. ".xhtml"). #html_file_suffix = None # Output file base name for HTML help builder. htmlhelp_basename = 'srcdoc' # -- 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': '', } # 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 = [ ('index', 'src.tex', u'XFEL Detector Tools', u'Steffen Hauf', 'manual'), ] # The name of an image file (relative to this directory) to place at the top of # the title page. #latex_logo = None # For "manual" documents, if this is true, then toplevel headings are parts, # not chapters. #latex_use_parts = False # If true, show page references after internal links. #latex_show_pagerefs = False # If true, show URL addresses after external links. #latex_show_urls = False # Documents to append as an appendix to all manuals. #latex_appendices = [] # If false, no module index is generated. #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 = [ ('index', 'src', u'XFEL Detector Tools', [u'Author'], 1) ] # If true, show URL addresses after external links. #man_show_urls = False # -- 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 = [ ('index', 'src', u'XFEL Detector Tools', u'Author', 'src', 'One line description of project.', 'Miscellaneous'), ] # Documents to append as an appendix to all manuals. #texinfo_appendices = [] # If false, no module index is generated. #texinfo_domain_indices = True # How to display URL addresses: 'footnote', 'no', or 'inline'. #texinfo_show_urls = 'footnote' # If true, do not generate a @detailmenu in the "Top" node's menu. #texinfo_no_detailmenu = False # -- Options for Epub output ---------------------------------------------- # Bibliographic Dublin Core info. epub_title = u'XFEL Detector Tools' epub_author = u'Steffen Hauf' epub_publisher = u'European X-ray Free Electron Laser GmbH' epub_copyright = u'2014, Steffen Hauf' # The basename for the epub file. It defaults to the project name. #epub_basename = u'src' # The HTML theme for the epub output. Since the default themes are not optimized # for small screen space, using the same theme for HTML and epub output is # usually not wise. This defaults to 'epub', a theme designed to save visual # space. #epub_theme = 'epub' # The language of the text. It defaults to the language option # or en if the language is not set. #epub_language = '' # The scheme of the identifier. Typical schemes are ISBN or URL. #epub_scheme = '' # 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 tuple containing the cover image and cover page html template filenames. #epub_cover = () # A sequence of (type, uri, title) tuples for the guide element of content.opf. #epub_guide = () # HTML files that should be inserted before the pages created by sphinx. # The format is a list of tuples containing the path and title. #epub_pre_files = [] # HTML files shat should be inserted after the pages created by sphinx. # The format is a list of tuples containing the path and title. #epub_post_files = [] # A list of files that should not be packed into the epub file. epub_exclude_files = ['search.html'] # The depth of the table of contents in toc.ncx. #epub_tocdepth = 3 # Allow duplicate toc entries. #epub_tocdup = True # Choose between 'default' and 'includehidden'. #epub_tocscope = 'default' # Fix unsupported image types using the PIL. #epub_fix_images = False # Scale large images. #epub_max_image_width = 0 # How to display URL addresses: 'footnote', 'no', or 'inline'. #epub_show_urls = 'inline' # If false, no index is generated. #epub_use_index = True autoclass_content = 'both' napoleon_google_docstring = True napoleon_numpy_docstring = True napoleon_include_private_with_doc = True napoleon_include_special_with_doc = False napoleon_use_admonition_for_examples = False napoleon_use_admonition_for_notes = False napoleon_use_admonition_for_references = False napoleon_use_ivar = False napoleon_use_param = True napoleon_use_rtype = True intersphinx_mapping = {'python': ('http://docs.python.org/2.7', None), 'numpy': ('http://docs.scipy.org/doc/numpy/', None), 'scipy': ('http://docs.scipy.org/doc/scipy/reference/', None), 'matplotlib': ('http://matplotlib.sourceforge.net/', None)} ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # import sys import os.path from six import string_types from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix else: SUFFIX = source_suffix[0] else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') html_static_path.append('/rtd_root/readthedocs/templates/sphinx/_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = False if 'html_theme' in globals(): if html_theme in ['default']: # Allow people to bail with a hack of having an html_style if not 'html_style' in globals(): import sphinx_rtd_theme html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(sphinx_rtd_theme.get_html_theme_path()) else: html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] using_rtd_theme = True else: import sphinx_rtd_theme html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(sphinx_rtd_theme.get_html_theme_path()) else: html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] using_rtd_theme = True if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.org/websupport' if 'http' not in settings.MEDIA_URL: websupport2_static_url = '/static/' else: websupport2_static_url = '/media//static' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'MEDIA_URL': "/media/", 'PRODUCTION_DOMAIN': "exflrtd.desy.de", 'versions': [ ("latest", "/en/latest/"), ("stable", "/en/stable/"), ], 'downloads': [ ("pdf", "//exflrtd.desy.de/projects/pydetlib/downloads/pdf/latest/"), ("htmlzip", "//exflrtd.desy.de/projects/pydetlib/downloads/htmlzip/latest/"), ("epub", "//exflrtd.desy.de/projects/pydetlib/downloads/epub/latest/"), ], 'subprojects': [ ], 'slug': 'pydetlib', 'name': u'PyDetLib', 'rtd_language': u'en', 'canonical_url': 'http://exflrtd.desy.de/docs/pydetlib/en/latest/', 'analytics_code': '', 'single_version': False, 'conf_py_path': '/doc/', 'api_host': 'https://readthedocs.org', 'github_user': 'None', 'github_repo': 'None', 'github_version': 'master', 'display_github': False, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-1', 'commit': '2caefbcd', } if 'html_context' in globals(): html_context.update(context) else: html_context = context # Add custom RTD extension if 'extensions' in globals(): extensions.append("readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] [rtd-command-info] start-time: 2017-05-17T10:55:41.978000Z, end-time: 2017-05-17T10:56:12.626000Z, duration: 30, exit-code: 0 python /user_builds/pydetlib/envs/latest/bin/sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.3.5 making output directory... loading translations [en]... done loading intersphinx inventory from http://docs.scipy.org/doc/numpy/objects.inv... loading intersphinx inventory from http://docs.scipy.org/doc/scipy/reference/objects.inv... loading intersphinx inventory from http://docs.python.org/2.7/objects.inv... loading intersphinx inventory from http://matplotlib.sourceforge.net/objects.inv... building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 24 source files that are out of date updating environment: 24 added, 0 changed, 0 removed reading sources... [ 4%] _notebooks/DataGeneratorExample reading sources... [ 8%] _notebooks/PlotExamples reading sources... [ 12%] _notebooks/calculatorCreation reading sources... [ 16%] _notebooks/gainMapStability reading sources... [ 20%] _notebooks/index reading sources... [ 25%] api/XFELDetAna Plotting not available No module named 'matplotlib.collections' reading sources... [ 29%] api/XFELDetAna.algorithms reading sources... [ 33%] api/XFELDetAna.algorithms.gpu reading sources... [ 37%] api/XFELDetAna.algorithms.gpu.kernels reading sources... [ 41%] api/XFELDetAna.core reading sources... [ 45%] api/XFELDetAna.detectors reading sources... [ 50%] api/XFELDetAna.detectors.agipd reading sources... [ 54%] api/XFELDetAna.detectors.fastccd reading sources... [ 58%] api/XFELDetAna.detectors.generator reading sources... [ 62%] api/XFELDetAna.detectors.lpd reading sources... [ 66%] api/XFELDetAna.detectors.pnccd reading sources... [ 70%] api/XFELDetAna.plotting reading sources... 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[100%] installation /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages/IPython/utils/pickleutil.py:3: UserWarning: IPython.utils.pickleutil has moved to ipykernel.pickleutil warn("IPython.utils.pickleutil has moved to ipykernel.pickleutil") /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/DataGeneratorExample.rst:169: WARNING: Inline emphasis start-string without end-string. /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/calculatorCreation.rst:151: WARNING: Inline strong start-string without end-string. /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/calculatorCreation.rst:151: WARNING: Inline strong start-string without end-string. /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.rst:7: WARNING: toctree contains reference to nonexisting document 'api/XFELDetAna.algorithms.cython' /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/algorithms/histogram.py:docstring of XFELDetAna.algorithms.histogram.HistogramCalculator:38: ERROR: Unknown interpreted text role "method". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/algorithms/histogram.py:docstring of XFELDetAna.algorithms.histogram.HistogramCalculator.get:26: WARNING: Definition list ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/algorithms/gpu/correct_common_mode.py:docstring of XFELDetAna.algorithms.gpu.correct_common_mode._gpuCommonMode:11: ERROR: Unexpected indentation. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/core/reader.py:docstring of XFELDetAna.core.reader.ChunkReader.readChunks:8: WARNING: Definition list ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.rst:7: WARNING: toctree contains reference to nonexisting document 'api/XFELDetAna.detectors.dssc' /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.plotting.rst:7: WARNING: autodoc: failed to import module 'XFELDetAna.plotting.heatmap'; the following exception was raised: Traceback (most recent call last): File "/user_builds/pydetlib/envs/latest/lib/python3.4/site-packages/sphinx/ext/autodoc.py", line 385, in import_object __import__(self.modname) File "/user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/plotting/heatmap.py", line 246, in import matplotlib.collections as mcoll ImportError: No module named 'matplotlib.collections' /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.util.rst:7: WARNING: __all__ should be a list of strings, not .wrapped at 0x7f08d575b510> (in module XFELDetAna.util.knumpy) -- ignoring __all__ /user_builds/pydetlib/checkouts/latest/lib/docs/examples/DataGeneratorExample.rst:161: WARNING: Inline emphasis start-string without end-string. /user_builds/pydetlib/checkouts/latest/lib/docs/index.rst:7: WARNING: Title underline too short. Welcome to XFEL Detector Tools' documentation! =============================== looking for now-outdated files... none found pickling environment... done checking consistency... /user_builds/pydetlib/checkouts/latest/lib/docs/examples/DataGeneratorExample.rst:: WARNING: document isn't included in any toctree /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst:: WARNING: document isn't included in any toctree /user_builds/pydetlib/checkouts/latest/lib/docs/examples/gainMapStability.rst:: WARNING: document isn't included in any toctree done preparing documents... done writing output... [ 4%] _notebooks/DataGeneratorExample writing output... [ 8%] _notebooks/PlotExamples writing output... [ 12%] _notebooks/calculatorCreation writing output... [ 16%] _notebooks/gainMapStability writing output... [ 20%] _notebooks/index writing output... [ 25%] api/XFELDetAna writing output... [ 29%] api/XFELDetAna.algorithms writing output... 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[rtd-command-info] start-time: 2017-05-17T10:56:41.950000Z, end-time: 2017-05-17T10:57:01.033000Z, duration: 19, exit-code: 0 python /user_builds/pydetlib/envs/latest/bin/sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia Running Sphinx v1.3.5 making output directory... loading translations [en]... done loading pickled environment... done loading intersphinx inventory from http://matplotlib.sourceforge.net/objects.inv... loading intersphinx inventory from http://docs.scipy.org/doc/scipy/reference/objects.inv... loading intersphinx inventory from http://docs.python.org/2.7/objects.inv... loading intersphinx inventory from http://docs.scipy.org/doc/numpy/objects.inv... building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: 0 added, 8 changed, 0 removed reading sources... 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[rtd-command-info] start-time: 2017-05-17T10:57:02.072000Z, end-time: 2017-05-17T10:57:20.022000Z, duration: 17, exit-code: 0 python /user_builds/pydetlib/envs/latest/bin/sphinx-build -b latex -D language=en -d _build/doctrees . _build/latex Running Sphinx v1.3.5 making output directory... loading translations [en]... done loading pickled environment... not yet created loading intersphinx inventory from http://matplotlib.sourceforge.net/objects.inv... loading intersphinx inventory from http://docs.scipy.org/doc/scipy/reference/objects.inv... loading intersphinx inventory from http://docs.scipy.org/doc/numpy/objects.inv... loading intersphinx inventory from http://docs.python.org/2.7/objects.inv... building [mo]: targets for 0 po files that are out of date building [latex]: all documents updating environment: 24 added, 0 changed, 0 removed reading sources... [ 4%] _notebooks/DataGeneratorExample reading sources... [ 8%] _notebooks/PlotExamples reading sources... 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[100%] installation /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages/IPython/utils/pickleutil.py:3: UserWarning: IPython.utils.pickleutil has moved to ipykernel.pickleutil warn("IPython.utils.pickleutil has moved to ipykernel.pickleutil") /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/DataGeneratorExample.rst:169: WARNING: Inline emphasis start-string without end-string. /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/calculatorCreation.rst:151: WARNING: Inline strong start-string without end-string. /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/calculatorCreation.rst:151: WARNING: Inline strong start-string without end-string. /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.rst:7: WARNING: toctree contains reference to nonexisting document 'api/XFELDetAna.algorithms.cython' /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/algorithms/histogram.py:docstring of XFELDetAna.algorithms.histogram.HistogramCalculator:38: ERROR: Unknown interpreted text role "method". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/algorithms/histogram.py:docstring of XFELDetAna.algorithms.histogram.HistogramCalculator.get:26: WARNING: Definition list ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/algorithms/gpu/correct_common_mode.py:docstring of XFELDetAna.algorithms.gpu.correct_common_mode._gpuCommonMode:11: ERROR: Unexpected indentation. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/core/reader.py:docstring of XFELDetAna.core.reader.ChunkReader.readChunks:8: WARNING: Definition list ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.rst:7: WARNING: toctree contains reference to nonexisting document 'api/XFELDetAna.detectors.dssc' /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.plotting.rst:7: WARNING: autodoc: failed to import module 'XFELDetAna.plotting.heatmap'; the following exception was raised: Traceback (most recent call last): File "/user_builds/pydetlib/envs/latest/lib/python3.4/site-packages/sphinx/ext/autodoc.py", line 385, in import_object __import__(self.modname) File "/user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/plotting/heatmap.py", line 246, in import matplotlib.collections as mcoll ImportError: No module named 'matplotlib.collections' /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.util.rst:7: WARNING: __all__ should be a list of strings, not .wrapped at 0x7f031c8afea0> (in module XFELDetAna.util.knumpy) -- ignoring __all__ /user_builds/pydetlib/checkouts/latest/lib/docs/examples/DataGeneratorExample.rst:161: WARNING: Inline emphasis start-string without end-string. /user_builds/pydetlib/checkouts/latest/lib/docs/index.rst:7: WARNING: Title underline too short. Welcome to XFEL Detector Tools' documentation! =============================== looking for now-outdated files... none found pickling environment... done checking consistency... /user_builds/pydetlib/checkouts/latest/lib/docs/examples/DataGeneratorExample.rst:: WARNING: document isn't included in any toctree /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst:: WARNING: document isn't included in any toctree /user_builds/pydetlib/checkouts/latest/lib/docs/examples/gainMapStability.rst:: WARNING: document isn't included in any toctree done processing src.tex... index installation _notebooks/index _notebooks/gainMapStability _notebooks/DataGeneratorExample _notebooks/calculatorCreation _notebooks/PlotExamples api/modules api/XFELDetAna api/XFELDetAna.algorithms api/XFELDetAna.algorithms.gpu api/XFELDetAna.algorithms.gpu.kernels api/XFELDetAna.core api/XFELDetAna.detectors api/XFELDetAna.detectors.agipd api/XFELDetAna.detectors.fastccd api/XFELDetAna.detectors.generator api/XFELDetAna.detectors.lpd api/XFELDetAna.detectors.pnccd api/XFELDetAna.plotting api/XFELDetAna.util resolving references... /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.rst:18: WARNING: undefined label: _gainmapstability (if the link has no caption the label must precede a section header) writing... done copying images... _notebooks/gainMapStability_files/gainMapStability_4_0.png _notebooks/PlotExamples_files/PlotExamples_36_0.png _notebooks/DataGeneratorExample_files/DataGeneratorExample_23_1.png _notebooks/gainMapStability_files/gainMapStability_12_1.png _notebooks/gainMapStability_files/gainMapStability_12_2.png _notebooks/PlotExamples_files/PlotExamples_22_1.png _notebooks/PlotExamples_files/PlotExamples_18_0.png _notebooks/PlotExamples_files/PlotExamples_4_0.png _notebooks/gainMapStability_files/gainMapStability_10_0.png _notebooks/DataGeneratorExample_files/DataGeneratorExample_23_2.png _notebooks/PlotExamples_files/PlotExamples_8_1.png _notebooks/gainMapStability_files/gainMapStability_11_0.png _notebooks/DataGeneratorExample_files/DataGeneratorExample_21_1.png _notebooks/PlotExamples_files/PlotExamples_6_1.png _notebooks/DataGeneratorExample_files/DataGeneratorExample_25_0.png _notebooks/PlotExamples_files/PlotExamples_30_0.png _notebooks/DataGeneratorExample_files/DataGeneratorExample_39_1.png _notebooks/DataGeneratorExample_files/DataGeneratorExample_46_1.png _notebooks/PlotExamples_files/PlotExamples_16_0.png _notebooks/PlotExamples_files/PlotExamples_12_0.png _notebooks/DataGeneratorExample_files/DataGeneratorExample_25_1.png _notebooks/PlotExamples_files/PlotExamples_26_0.png _notebooks/DataGeneratorExample_files/DataGeneratorExample_41_0.png _notebooks/PlotExamples_files/PlotExamples_34_0.png _notebooks/gainMapStability_files/gainMapStability_12_3.png _notebooks/PlotExamples_files/PlotExamples_14_0.png _notebooks/PlotExamples_files/PlotExamples_20_0.png _notebooks/PlotExamples_files/PlotExamples_28_0.png _notebooks/PlotExamples_files/PlotExamples_14_1.png _notebooks/PlotExamples_files/PlotExamples_8_0.png _notebooks/gainMapStability_files/gainMapStability_12_7.png _notebooks/gainMapStability_files/gainMapStability_12_4.png _notebooks/gainMapStability_files/gainMapStability_13_0.png _notebooks/PlotExamples_files/PlotExamples_22_2.png _notebooks/gainMapStability_files/gainMapStability_12_10.png _notebooks/PlotExamples_files/PlotExamples_8_2.png _notebooks/PlotExamples_files/PlotExamples_24_0.png _notebooks/DataGeneratorExample_files/DataGeneratorExample_31_0.png _notebooks/PlotExamples_files/PlotExamples_32_0.png _notebooks/DataGeneratorExample_files/DataGeneratorExample_21_0.png _notebooks/PlotExamples_files/PlotExamples_2_0.png _notebooks/gainMapStability_files/gainMapStability_12_9.png _notebooks/gainMapStability_files/gainMapStability_16_0.png _notebooks/DataGeneratorExample_files/DataGeneratorExample_41_1.png _notebooks/gainMapStability_files/gainMapStability_9_0.png _notebooks/PlotExamples_files/PlotExamples_38_0.png _notebooks/PlotExamples_files/PlotExamples_6_0.png _notebooks/PlotExamples_files/PlotExamples_4_1.png _notebooks/gainMapStability_files/gainMapStability_12_8.png _notebooks/PlotExamples_files/PlotExamples_42_0.png _notebooks/DataGeneratorExample_files/DataGeneratorExample_37_0.png _notebooks/DataGeneratorExample_files/DataGeneratorExample_27_1.png _notebooks/gainMapStability_files/gainMapStability_12_6.png _notebooks/DataGeneratorExample_files/DataGeneratorExample_14_1.png _notebooks/PlotExamples_files/PlotExamples_40_0.png _notebooks/gainMapStability_files/gainMapStability_12_5.png _notebooks/PlotExamples_files/PlotExamples_10_1.png _notebooks/PlotExamples_files/PlotExamples_10_0.png copying TeX support files... done build succeeded, 17 warnings. 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[46] [47 <./DataGeneratorExample_21_0.png>] [48 <./DataGeneratorExample_21_1.png>] [49 <./DataGeneratorExample_23_1.png>] [50 <./DataGeneratorExample_23_2.png>] [51 <./DataGeneratorExample_25_0.png>] [52 <./DataGeneratorExample_25_1.png>] [53 <./DataGeneratorExample_27_1.png>] [54 <./DataGeneratorExample_31_0.png>] LaTeX Warning: Hyper reference `api/XFELDetAna.algorithms:XFELDetAna.algorithms .characterize_relgain.GainMapCalculator' on page 55 undefined on input line 179 2. LaTeX Warning: Hyper reference `_notebooks/gainMapStability:gainmapstability' o n page 55 undefined on input line 1792. [55] [56] Underfull \vbox (badness 3138) detected at line 1904 [57 <./DataGeneratorExample_37_0.png>] LaTeX Warning: Hyper reference `api/XFELDetAna.algorithms:XFELDetAna.algorithms .correct_relgain.RelativeGainCorrection' on page 58 undefined on input line 191 6. [58 <./DataGeneratorExample_39_1.png>] [59 <./DataGeneratorExample_41_0.png>] [60 <./DataGeneratorExample_41_1.png>] [61 <./DataGeneratorExample_46_1.png>] [62] [63] [64] Overfull \vbox (0.71227pt too high) detected at line 2345 [65] Underfull \vbox (badness 10000) detected at line 2345 Underfull \vbox (badness 10000) detected at line 2345 [66] [67] [68 <./PlotExamples_2_0.png>] [69 <./PlotExamples_4_0.png> <./PlotExamples_4_1.png >] [70 <./PlotExamples_6_0.p ng> <./PlotExamples_6_1.png>] [71 <./PlotExamples_8_0.p ng> <./PlotExamples_8_1.png>] [72 <./PlotExamples_8_2.png>] [73 <./PlotExamples_10_ 0.png> <./PlotExamples_10_1.png>] [74 <./PlotExamples_12_0.png>] [75 <./PlotExamples_14_0.png> <./PlotExamples_14_1. png>] [76 <./PlotExamples_16_ 0.png>] [77 <./PlotExamples_18_ 0.png> <./PlotExamples_20_0.png>] [78] [79 <./PlotExamples_22_ 1.png> <./PlotExamples_22_2.png>] [80 <./PlotExamples_24_ 0.png>] [81] [82 <./PlotExample s_26_0.png>] [83 <./PlotExamples_28_ 0.png>] [84 <./PlotExamples_30_ 0.png>] [85 <./PlotExamples_32_ 0.png>] [86 <./PlotExamples_34_ 0.png>] [87 <./PlotExamples_36_ 0.png>] [88 <./PlotExamples_38_ 0.png>] [89 <./PlotExamples_40_ 0.png>] [90 <./PlotExamples_42_0.png>] Chapter 4. Overfull \hbox (92.52464pt too wide) in paragraph at lines 3170--3170 []\T1/ptm/m/it/10 datalength\T1/ptm/m/n/10 , Overfull \hbox (58.5348pt too wide) in paragraph at lines 3170--3170 \T1/ptm/m/it/10 re- Overfull \hbox (67.24477pt too wide) in paragraph at lines 3170--3170 \T1/ptm/m/it/10 turn- Overfull \hbox (100.91441pt too wide) in paragraph at lines 3170--3170 \T1/ptm/m/it/10 Stats=False\T1/pcr/m/n/10 ) [91] Overfull \hbox (68.52464pt too wide) in paragraph at lines 3176--3176 []\T1/ptm/m/it/10 datalength\T1/ptm/m/n/10 , Overfull \hbox (34.5348pt too wide) in paragraph at lines 3176--3176 \T1/ptm/m/it/10 re- Overfull \hbox (43.24477pt too wide) in paragraph at lines 3176--3176 \T1/ptm/m/it/10 turn- Overfull \hbox (48.6947pt too wide) in paragraph at lines 3176--3176 \T1/ptm/m/it/10 Stats\T1/pcr/m/n/10 ) Overfull \hbox (72.02464pt too wide) in paragraph at lines 3182--3182 []\T1/ptm/m/it/10 datalength\T1/pcr/m/n/10 ) Overfull \hbox (21.52492pt too wide) in paragraph at lines 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noiseMap=None\T1/pcr/m/n/10 ) [92] Underfull \hbox (badness 10000) in paragraph at lines 3277--3277 \T1/ptm/m/it/10 crange=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3277--3277 \T1/ptm/m/it/10 noisemap=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3277--3277 \T1/ptm/m/it/10 shape=None\T1/ptm/m/n/10 , [93] Underfull \hbox (badness 10000) in paragraph at lines 3316--3316 []\T1/ptm/m/it/10 a\T1/ptm/m/n/10 , \T1/ptm/m/it/10 di-rec-tion\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3316--3316 \T1/ptm/m/it/10 block-Size\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3316--3316 \T1/ptm/m/it/10 m\T1/ptm/m/n/10 , \T1/ptm/m/it/10 crange\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3316--3316 \T1/ptm/m/it/10 shape=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3316--3316 \T1/ptm/m/it/10 keep- Underfull \hbox (badness 10000) in paragraph 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[96] Underfull \hbox (badness 10000) in paragraph at lines 3660--3660 []\T1/ptm/m/it/10 shape\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3660--3660 \T1/ptm/m/it/10 peakEs- Underfull \hbox (badness 10000) in paragraph at lines 3660--3660 \T1/ptm/m/it/10 ti-mates\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3660--3660 \T1/ptm/m/it/10 al-lowed-Devs\T1/ptm/m/n/10 , Overfull \hbox (13.54419pt too wide) in paragraph at lines 3660--3660 \T1/ptm/m/it/10 noiseMap=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3660--3660 \T1/ptm/m/it/10 nCells=1\T1/ptm/m/n/10 , Overfull \hbox (14.64417pt too wide) in paragraph at lines 3660--3660 \T1/ptm/m/it/10 method='means'\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3660--3660 \T1/ptm/m/it/10 de-vi-a-tion- Overfull \hbox (8.28375pt too wide) in paragraph at lines 3660--3660 \T1/ptm/m/it/10 Type='relative'\T1/ptm/m/n/10 , Overfull \hbox (0.94408pt too wide) in paragraph at lines 3660--3660 \T1/ptm/m/it/10 dType=\T1/ptm/m/n/10 , LaTeX Warning: Hyper reference `api/XFELDetAna.core:XFELDetAna.core.mapcalculat or.MapCalculator' on page 97 undefined on input line 3661. [97] Underfull \hbox (badness 10000) in paragraph at lines 3779--3782 []\T1/pcr/b/n/10 restrictPeaks \T1/ptm/m/n/10 (\T1/pcr/m/sl/10 List of peak ind exes to restrict evaluation [98] Underfull \hbox (badness 10000) in paragraph at lines 3907--3907 []\T1/ptm/m/it/10 shape\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3907--3907 \T1/ptm/m/it/10 block-Size\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3907--3907 \T1/ptm/m/it/10 ori-en- Underfull \hbox (badness 10000) in paragraph at lines 3907--3907 \T1/ptm/m/it/10 ta-tion\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3907--3907 \T1/ptm/m/it/10 cores=4\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3907--3907 \T1/ptm/m/it/10 nCells=1\T1/ptm/m/n/10 , Overfull \hbox (12.94408pt too wide) in paragraph at lines 3907--3907 \T1/ptm/m/it/10 dType=\T1/ptm/m/n/10 , LaTeX Warning: Hyper reference `api/XFELDetAna.core:XFELDetAna.core.mapcalculat or.MapCalculator' on page 99 undefined on input line 3908. 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[101] Underfull \hbox (badness 10000) in paragraph at lines 4171--4171 []\T1/ptm/m/it/10 shape\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4171--4171 \T1/ptm/m/it/10 gain-Map\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4171--4171 \T1/ptm/m/it/10 nCells=1\T1/ptm/m/n/10 , Overfull \hbox (0.94408pt too wide) in paragraph at lines 4171--4171 \T1/ptm/m/it/10 dType=\T1/ptm/m/n/10 , LaTeX Warning: Hyper reference `api/XFELDetAna.algorithms:XFELDetAna.algorithms .correction.CorrectionBase' on page 102 undefined on input line 4172. Underfull \hbox (badness 10000) in paragraph at lines 4245--4245 \T1/ptm/m/it/10 dType=\T1/ptm/m/n/10 , LaTeX Warning: Hyper reference `api/XFELDetAna.core:XFELDetAna.core.mapcalculat or.MapCalculator' on page 102 undefined on input line 4246. [102] Underfull \hbox (badness 10000) in paragraph at lines 4378--4378 []\T1/ptm/m/it/10 shape\T1/ptm/m/n/10 , \T1/ptm/m/it/10 bins\T1/ptm/m/n/10 , \T 1/ptm/m/it/10 range\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4378--4378 \T1/ptm/m/it/10 nCells=1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 dType= for immediate help. ... l.4554 \begin{Verbatim}[commandchars=\\\{\}] [105] LaTeX Warning: Hyper reference `api/XFELDetAna.core:XFELDetAna.core.mapcalculat or.MapCalculator' on page 106 undefined on input line 4650. [106] Underfull \hbox (badness 10000) in paragraph at lines 4787--4788 []\T1/pcr/b/n/10 function. For any 1-d vector in this list it will be Underfull \hbox (badness 10000) in paragraph at lines 4790--4791 []\T1/pcr/b/n/10 to mask/remove data as is done with the data block. Underfull \hbox (badness 10000) in paragraph at lines 4796--4797 []\T1/pcr/b/n/10 where True denotes remove of an image at this position. 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(rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on src.pdf (150 pages, 3157601 bytes). Transcript written on src.log. [rtd-command-info] start-time: 2017-05-17T10:57:26.653000Z, end-time: 2017-05-17T10:57:26.723000Z, duration: 0, exit-code: 0 makeindex -s python.ist src.idx This is makeindex, version 2.15 [TeX Live 2015/dev] (kpathsea + Thai support). Scanning style file ./python.ist......done (6 attributes redefined, 0 ignored). Scanning input file src.idx....done (770 entries accepted, 0 rejected). Sorting entries.........done (8605 comparisons). Generating output file src.ind....done (875 lines written, 0 warnings). Output written in src.ind. Transcript written in src.ilg. 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[1] [2] [1] [2] Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [3] [4] Chapter 2. [5] [6] Chapter 3. ! LaTeX Error: Bad math environment delimiter. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.197 \end{gather} ! Missing \endgroup inserted. \endgroup l.197 \end{gather} ! Missing } inserted. } l.197 \end{gather} ! LaTeX Error: \begin{split} on input line 197 ended by \end{equation*}. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.197 \end{gather} ! Missing $ inserted. $ l.197 \end{gather} ! Missing } inserted. } l.197 \end{gather} ! Missing \cr inserted. \cr l.197 \end{gather} ! Missing { inserted. { l.197 \end{gather} ! Missing $ inserted. $ l.197 \end{gather} ! Missing } inserted. } l.197 \end{gather} ! Missing { inserted. { l.197 \end{gather} ! Missing } inserted. } l.197 \end{gather} ! LaTeX Error: \begin{gather} on input line 195 ended by \end{split}. 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Extra \endgroup. \endgroup l.237 \end{itemize} (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [8] Underfull \vbox (badness 10000) detected at line 477 Underfull \vbox (badness 10000) detected at line 477 [9] Underfull \vbox (badness 10000) detected at line 477 Underfull \vbox (badness 10000) detected at line 477 [10] Underfull \vbox (badness 10000) detected at line 477 Underfull \vbox (badness 10000) detected at line 477 [11] [12] [13 <./gainM apStability_4_0.png>] Underfull \vbox (badness 10000) detected at line 695 [14] Underfull \vbox (badness 10000) detected at line 695 Underfull \vbox (badness 10000) detected at line 695 [15] [16] Underfull \vbox (badness 10000) detected at line 812 Underfull \vbox (badness 10000) detected at line 812 [17] [18] Underfull \vbox (badness 1122) detected at line 904 [19 <./gainMapStability_9_0.png>] Underfull \vbox (badness 10000) detected at line 904 Underfull \vbox (badness 10000) detected at line 904 [20] [21] Underfull \vbox (badness 10000) detected at line 975 [22 <./gainMapStability_10_0.png>] Underfull \vbox (badness 10000) detected at line 975 Underfull \vbox (badness 10000) detected at line 975 [23] Underfull \vbox (badness 10000) detected at line 1018 [24 <./gainMapStability_11_0.png>] [25] [26 <./gainMapS tability_12_1.png>] [27 <./gainMapS tability_12_2.png>] [28 <./gainMapS tability_12_3.png>] [29 <./gainMapS tability_12_4.png>] [30 <./gainMapS tability_12_5.png>] [31 <./gainMapS tability_12_6.png>] [32 <./gainMapS tability_12_7.png>] [33 <./gainMa pStability_12_8.png>] [34 <./gainMapStability_12_9.png>] Underfull \vbox (badness 5970) detected at line 1068 [35 <./gainMapStability_12_10.png>] Overfull \vbox (0.57379pt too high) detected at line 1167 [36 <./gainMapStability_13_0.png>] Underfull \vbox (badness 10000) detected at line 1167 Underfull \vbox (badness 10000) detected at line 1167 [37] Underfull \vbox (badness 2302) detected at line 1262 [38] [39] [40 <./gai nMapStability_16_0.png>] [41] [42] [43] [44] [45 <./DataGeneratorExample_14_1.png>] [46] [47 <./DataGeneratorExample_21_0.png>] [48 <./DataGeneratorExample_21_1.png>] [49 <./DataGeneratorExample_23_1.png>] [50 <./DataGeneratorExample_23_2.png>] [51 <./DataGeneratorExample_25_0.png>] [52 <./DataGeneratorExample_25_1.png>] [53 <./DataGeneratorExample_27_1.png>] [54 <./DataGeneratorExample_31_0.png>] [55] [56] Underfull \vbox (badness 3138) detected at line 1904 [57 <./DataGeneratorExample_37_0.png>] [58 <./DataGeneratorExample_39_1.png>] [59 <./DataGeneratorExample_41_0.png>] [60 <./DataGeneratorExample_41_1.png>] [61 <./DataGeneratorExample_46_1.png>] [62] [63] [64] Overfull \vbox (0.71227pt too high) detected at line 2345 [65] Underfull \vbox (badness 10000) detected at line 2345 Underfull \vbox (badness 10000) detected at line 2345 [66] [67] [68 <./PlotExamples_2_0.png>] [69 <./PlotExamples_4_0.png> <./PlotExamples_4_1.png >] [70 <./PlotExamples_6_0.p ng> <./PlotExamples_6_1.png>] [71 <./PlotExamples_8_0.p ng> <./PlotExamples_8_1.png>] [72 <./PlotExamples_8_2.png>] [73 <./PlotExamples_10_ 0.png> <./PlotExamples_10_1.png>] [74 <./PlotExamples_12_0.png>] [75 <./PlotExamples_14_0.png> <./PlotExamples_14_1. png>] [76 <./PlotExamples_16_ 0.png>] [77 <./PlotExamples_18_ 0.png> <./PlotExamples_20_0.png>] [78] [79 <./PlotExamples_22_ 1.png> <./PlotExamples_22_2.png>] [80 <./PlotExamples_24_ 0.png>] [81] [82 <./PlotExample s_26_0.png>] [83 <./PlotExamples_28_ 0.png>] [84 <./PlotExamples_30_ 0.png>] [85 <./PlotExamples_32_ 0.png>] [86 <./PlotExamples_34_ 0.png>] [87 <./PlotExamples_36_ 0.png>] [88 <./PlotExamples_38_ 0.png>] [89 <./PlotExamples_40_ 0.png>] [90 <./PlotExamples_42_0.png>] Chapter 4. Overfull \hbox (92.52464pt too wide) in paragraph at lines 3170--3170 []\T1/ptm/m/it/10 datalength\T1/ptm/m/n/10 , Overfull \hbox (58.5348pt too wide) in paragraph at lines 3170--3170 \T1/ptm/m/it/10 re- Overfull \hbox (67.24477pt too wide) in paragraph at lines 3170--3170 \T1/ptm/m/it/10 turn- Overfull \hbox (100.91441pt too wide) in paragraph at lines 3170--3170 \T1/ptm/m/it/10 Stats=False\T1/pcr/m/n/10 ) [91] Overfull \hbox (68.52464pt too wide) in paragraph at lines 3176--3176 []\T1/ptm/m/it/10 datalength\T1/ptm/m/n/10 , Overfull \hbox (34.5348pt too wide) in paragraph at lines 3176--3176 \T1/ptm/m/it/10 re- Overfull \hbox (43.24477pt too wide) in paragraph at lines 3176--3176 \T1/ptm/m/it/10 turn- Overfull \hbox (48.6947pt too wide) in paragraph at lines 3176--3176 \T1/ptm/m/it/10 Stats\T1/pcr/m/n/10 ) Overfull \hbox (72.02464pt too wide) in paragraph at lines 3182--3182 []\T1/ptm/m/it/10 datalength\T1/pcr/m/n/10 ) Overfull \hbox (21.52492pt too wide) in paragraph at lines 3188--3188 []\T1/ptm/m/it/10 lo\T1/ptm/m/n/10 , Overfull \hbox (21.52492pt too wide) in paragraph at lines 3188--3188 \T1/ptm/m/it/10 hi\T1/ptm/m/n/10 , Overfull \hbox (21.36488pt too wide) in paragraph at lines 3188--3188 \T1/ptm/m/it/10 r\T1/pcr/m/n/10 ) Overfull \hbox (72.24475pt too wide) in paragraph at lines 3194--3194 []\T1/ptm/m/it/10 length\T1/pcr/m/n/10 ) Overfull \hbox (87.52492pt too wide) in paragraph at lines 3203--3203 []\T1/ptm/m/it/10 lo\T1/ptm/m/n/10 , Overfull \hbox (91.02492pt too wide) in paragraph at lines 3203--3203 \T1/ptm/m/it/10 hi\T1/pcr/m/n/10 ) Overfull \hbox (34.49384pt too wide) in paragraph at lines 3238--3238 []\T1/ptm/m/it/10 statsPerPixel=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3238--3238 \T1/ptm/m/it/10 statsPer- Underfull \hbox (badness 10000) in paragraph at lines 3238--3238 \T1/ptm/m/it/10 Me-m-o- Overfull \hbox (6.96422pt too wide) in paragraph at lines 3238--3238 \T1/ptm/m/it/10 ryCell=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3238--3238 \T1/ptm/m/it/10 statsPer- Overfull \hbox (4.18445pt too wide) in paragraph at lines 3238--3238 \T1/ptm/m/it/10 Pulse=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3238--3238 \T1/ptm/m/it/10 statsPer- Overfull \hbox (1.9646pt too wide) in paragraph at lines 3238--3238 \T1/ptm/m/it/10 Gain=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3238--3238 \T1/ptm/m/it/10 std=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3238--3238 \T1/ptm/m/it/10 min- Underfull \hbox (badness 10000) in paragraph at lines 3238--3238 \T1/ptm/m/it/10 Max=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3238--3238 \T1/ptm/m/it/10 gain- Underfull \hbox (badness 10000) in paragraph at lines 3238--3238 \T1/ptm/m/it/10 Map=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3238--3238 \T1/ptm/m/it/10 me- Underfull \hbox (badness 10000) in paragraph at lines 3238--3238 \T1/ptm/m/it/10 dian=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3238--3238 \T1/ptm/m/it/10 thresh-old- Overfull \hbox (1.60475pt too wide) in paragraph at lines 3238--3238 \T1/ptm/m/it/10 High=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3238--3238 \T1/ptm/m/it/10 thresh-old- Underfull \hbox (badness 10000) in paragraph at lines 3238--3238 \T1/ptm/m/it/10 Low=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3238--3238 \T1/ptm/m/it/10 thresh- Underfull \hbox (badness 10000) in paragraph at lines 3238--3238 \T1/ptm/m/it/10 oldA-gain-st- Overfull \hbox (4.74438pt too wide) in paragraph at lines 3238--3238 \T1/ptm/m/it/10 Noise=False\T1/ptm/m/n/10 , Overfull \hbox (17.90439pt too wide) in paragraph at lines 3238--3238 \T1/ptm/m/it/10 cellTable=None\T1/ptm/m/n/10 , Overfull \hbox (24.54457pt too wide) in paragraph at lines 3238--3238 \T1/ptm/m/it/10 noiseMap=None\T1/pcr/m/n/10 ) [92] Underfull \hbox (badness 10000) in paragraph at lines 3277--3277 \T1/ptm/m/it/10 crange=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3277--3277 \T1/ptm/m/it/10 noisemap=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3277--3277 \T1/ptm/m/it/10 shape=None\T1/ptm/m/n/10 , [93] Underfull \hbox (badness 10000) in paragraph at lines 3316--3316 []\T1/ptm/m/it/10 a\T1/ptm/m/n/10 , \T1/ptm/m/it/10 di-rec-tion\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3316--3316 \T1/ptm/m/it/10 block-Size\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3316--3316 \T1/ptm/m/it/10 m\T1/ptm/m/n/10 , \T1/ptm/m/it/10 crange\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3316--3316 \T1/ptm/m/it/10 shape=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3316--3316 \T1/ptm/m/it/10 keep- Underfull \hbox (badness 10000) in paragraph at lines 3352--3352 []\T1/ptm/m/it/10 a\T1/ptm/m/n/10 , \T1/ptm/m/it/10 di-rec-tion\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3352--3352 \T1/ptm/m/it/10 block-Size\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3352--3352 \T1/ptm/m/it/10 noisemap\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3352--3352 \T1/ptm/m/it/10 crange\T1/ptm/m/n/10 , \T1/ptm/m/it/10 mem- Underfull \hbox (badness 10000) in paragraph at lines 3352--3352 \T1/ptm/m/it/10 Cells\T1/ptm/m/n/10 , \T1/ptm/m/it/10 stack\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3352--3352 \T1/ptm/m/it/10 sig\T1/ptm/m/n/10 , \T1/ptm/m/it/10 bs=4\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3352--3352 \T1/ptm/m/it/10 cellTable=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3352--3352 \T1/ptm/m/it/10 gain- Underfull \hbox (badness 10000) in paragraph at lines 3352--3352 \T1/ptm/m/it/10 Code=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3352--3352 \T1/ptm/m/it/10 shape=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3352--3352 \T1/ptm/m/it/10 keep- Underfull \hbox (badness 10000) in paragraph at lines 3352--3352 \T1/ptm/m/it/10 OnGpu=False\T1/ptm/m/n/10 , [94] Underfull \hbox (badness 5175) in paragraph at lines 3424--3424 []\T1/ptm/m/it/10 shape\T1/ptm/m/n/10 , \T1/ptm/m/it/10 noisemap\T1/ptm/m/n/10 , \T1/ptm/m/it/10 axis\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3458--3458 []\T1/ptm/m/it/10 shape\T1/ptm/m/n/10 , \T1/ptm/m/it/10 nCells=1\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3458--3458 \T1/ptm/m/it/10 dType=\T1/ptm/m/n/10 , [96] Underfull \hbox (badness 10000) in paragraph at lines 3660--3660 []\T1/ptm/m/it/10 shape\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3660--3660 \T1/ptm/m/it/10 peakEs- Underfull \hbox (badness 10000) in paragraph at lines 3660--3660 \T1/ptm/m/it/10 ti-mates\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3660--3660 \T1/ptm/m/it/10 al-lowed-Devs\T1/ptm/m/n/10 , Overfull \hbox (13.54419pt too wide) in paragraph at lines 3660--3660 \T1/ptm/m/it/10 noiseMap=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3660--3660 \T1/ptm/m/it/10 nCells=1\T1/ptm/m/n/10 , Overfull \hbox (14.64417pt too wide) in paragraph at lines 3660--3660 \T1/ptm/m/it/10 method='means'\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3660--3660 \T1/ptm/m/it/10 de-vi-a-tion- Overfull \hbox (8.28375pt too wide) in paragraph at lines 3660--3660 \T1/ptm/m/it/10 Type='relative'\T1/ptm/m/n/10 , Overfull \hbox (0.94408pt too wide) in paragraph at lines 3660--3660 \T1/ptm/m/it/10 dType=\T1/ptm/m/n/10 , [97] Underfull \hbox (badness 10000) in paragraph at lines 3779--3782 []\T1/pcr/b/n/10 restrictPeaks \T1/ptm/m/n/10 (\T1/pcr/m/sl/10 List of peak ind exes to restrict evaluation [98] Underfull \hbox (badness 10000) in paragraph at lines 3907--3907 []\T1/ptm/m/it/10 shape\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3907--3907 \T1/ptm/m/it/10 block-Size\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3907--3907 \T1/ptm/m/it/10 ori-en- Underfull \hbox (badness 10000) in paragraph at lines 3907--3907 \T1/ptm/m/it/10 ta-tion\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3907--3907 \T1/ptm/m/it/10 cores=4\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3907--3907 \T1/ptm/m/it/10 nCells=1\T1/ptm/m/n/10 , Overfull \hbox (12.94408pt too wide) in paragraph at lines 3907--3907 \T1/ptm/m/it/10 dType=\T1/ptm/m/n/10 , [99] [100] Underfull \hbox (badness 10000) in paragraph at lines 4049--4049 \T1/ptm/m/it/10 dType=\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4111--4111 []\T1/ptm/m/it/10 shape\T1/ptm/m/n/10 , \T1/ptm/m/it/10 off- Underfull \hbox (badness 10000) in paragraph at lines 4111--4111 \T1/ptm/m/it/10 setMap\T1/ptm/m/n/10 , \T1/ptm/m/it/10 nCells=1\T1/ptm/m/n/10 , [101] Underfull \hbox (badness 10000) in paragraph at lines 4171--4171 []\T1/ptm/m/it/10 shape\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4171--4171 \T1/ptm/m/it/10 gain-Map\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4171--4171 \T1/ptm/m/it/10 nCells=1\T1/ptm/m/n/10 , Overfull \hbox (0.94408pt too wide) in paragraph at lines 4171--4171 \T1/ptm/m/it/10 dType=\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4245--4245 \T1/ptm/m/it/10 dType=\T1/ptm/m/n/10 , [102] Underfull \hbox (badness 10000) in paragraph at lines 4378--4378 []\T1/ptm/m/it/10 shape\T1/ptm/m/n/10 , \T1/ptm/m/it/10 bins\T1/ptm/m/n/10 , \T 1/ptm/m/it/10 range\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4378--4378 \T1/ptm/m/it/10 nCells=1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 dType= for immediate help. ... l.4554 \begin{Verbatim}[commandchars=\\\{\}] [105] [106] Underfull \hbox (badness 10000) in paragraph at lines 4787--4788 []\T1/pcr/b/n/10 function. For any 1-d vector in this list it will be Underfull \hbox (badness 10000) in paragraph at lines 4790--4791 []\T1/pcr/b/n/10 to mask/remove data as is done with the data block. Underfull \hbox (badness 10000) in paragraph at lines 4796--4797 []\T1/pcr/b/n/10 where True denotes remove of an image at this position. Underfull \hbox (badness 10000) in paragraph at lines 4799--4800 []\T1/pcr/b/n/10 indices is given, the evaluation function is NOT evaluated. [107] Underfull \hbox (badness 10000) in paragraph at lines 4820--4820 \T1/ptm/m/it/10 dType=\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4888--4888 \T1/ptm/m/it/10 ry-Thresh-old\T1/ptm/m/n/10 , \T1/ptm/m/it/10 sec-ondary- Underfull \hbox (badness 10000) in paragraph at lines 4888--4888 \T1/ptm/m/it/10 Thresh-old\T1/ptm/m/n/10 , \T1/ptm/m/it/10 up-perThresh- Underfull \hbox (badness 10000) in paragraph at lines 4888--4888 \T1/ptm/m/it/10 old\T1/ptm/m/n/10 , \T1/ptm/m/it/10 tag-FirstS-in-gles=0\T1/ptm /m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4888--4888 \T1/ptm/m/it/10 nCells=1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 dType= for immediate help. ... l.5011 \item {} \begin{description} [109] Underfull \hbox (badness 5711) in paragraph at lines 5049--5052 []\T1/ptm/m/n/10 the iden-ti-fied pat- [110] Underfull \hbox (badness 10000) in paragraph at lines 5194--5194 []\T1/ptm/m/it/10 shape, selectionList=[-1], Underfull \hbox (badness 10000) in paragraph at lines 5194--5194 \T1/ptm/m/it/10 nCells=1, dType=\T1/ptm/m/n/10 , \T1/ptm/m/it/10 statsPer-Pixel=False\T 1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5320--5320 \T1/ptm/m/it/10 statsPer-Me-m-o-ryCell=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5320--5320 \T1/ptm/m/it/10 statsPer-Pulse=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 statsPer- Underfull \hbox (badness 10000) in paragraph at lines 5320--5320 \T1/ptm/m/it/10 Gain=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 thresh-old- Underfull \hbox (badness 10000) in paragraph at lines 5320--5320 \T1/ptm/m/it/10 High=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 thresh-old- Underfull \hbox (badness 10000) in paragraph at lines 5320--5320 \T1/ptm/m/it/10 Low=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 thresh-oldA-gain- Underfull \hbox (badness 10000) in paragraph at lines 5320--5320 \T1/ptm/m/it/10 st-Noise=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 std=True\T1/ptm/ m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5320--5320 \T1/ptm/m/it/10 min-Max=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 mean=True\T1/ptm/m /n/10 , Underfull \hbox (badness 10000) in paragraph at lines 5320--5320 \T1/ptm/m/it/10 gains=1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 pulses=None\T1/ptm/m/n/ 10 , [112] Underfull \hbox (badness 10000) in paragraph at lines 5502--5502 []\T1/ptm/m/it/10 offsetmap\T1/ptm/m/n/10 , \T1/ptm/m/it/10 noisemap\T1/ptm/m/n /10 , [113] Underfull \hbox (badness 10000) in paragraph at lines 5600--5600 []\T1/ptm/m/it/10 offsetmap\T1/ptm/m/n/10 , \T1/ptm/m/it/10 noisemap\T1/ptm/m/n /10 , [114] Underfull \hbox (badness 10000) in paragraph at lines 5674--5674 []\T1/ptm/m/it/10 shape\T1/ptm/m/n/10 , \T1/ptm/m/it/10 nCells=1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 dType=\T1/ptm/m/n/10 , \T1/ptm/m/it/10 par-al-lel=Tru e\T1/ptm/m/n/10 , [115] [116] Underfull \hbox (badness 10000) in paragraph at lines 5970--5970 []\T1/ptm/m/it/10 functionsToProfile\T1/ptm/m/n/10 , \T1/ptm/m/it/10 val-uesTo- VaryCpu\T1/ptm/m/n/10 , \T1/ptm/m/it/10 val-uesTo- Underfull \hbox (badness 10000) in paragraph at lines 5970--5970 \T1/ptm/m/it/10 VaryGpu=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 nRe-peats=None\T1/ ptm/m/n/10 , \T1/ptm/m/it/10 val-uesTo-P-re- Underfull \hbox (badness 10000) in paragraph at lines 5982--5982 []\T1/ptm/m/it/10 filename\T1/ptm/m/n/10 , \T1/ptm/m/it/10 read-Fun\T1/ptm/m/n/ 10 , \T1/ptm/m/it/10 size\T1/ptm/m/n/10 , \T1/ptm/m/it/10 chunk-Size\T1/ptm/m/n /10 , \T1/ptm/m/it/10 *args\T1/ptm/m/n/10 , [117] [118] [119] [120] Underfull \hbox (badness 10000) in paragraph at lines 6347--6347 []\T1/ptm/m/it/10 filename\T1/ptm/m/n/10 , \T1/ptm/m/it/10 path='/stream'\T1/pt m/m/n/10 , [121] Underfull \hbox (badness 10000) in paragraph at lines 6513--6515 []\T1/ptm/m/n/10 Usually the [122] [123] Underfull \hbox (badness 6792) in paragraph at lines 6748--6748 []\T1/ptm/m/it/10 data\T1/ptm/m/n/10 , \T1/ptm/m/it/10 axes\T1/ptm/m/n/10 , \T1 /ptm/m/it/10 ax-is-Names\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ti-tle=None\T1/ptm/m/n /10 , Underfull \hbox (badness 10000) in paragraph at lines 6774--6775 []\T1/pcr/b/n/10 will be passed to the matplotlib fill_between() function. [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] Underfull \hbox (badness 10000) in paragraph at lines 10117--10117 []\T1/ptm/m/it/10 host=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 port=None\T1/ptm/m/ n/10 , \T1/ptm/m/it/10 read-Han- [140] Underfull \hbox (badness 10000) in paragraph at lines 10137--10137 []\T1/ptm/m/it/10 host=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 port=None\T1/ptm/m/ n/10 , \T1/ptm/m/it/10 read-Han- [141] [142] Chapter 5. [143] [144] Overfull \hbox (0.6225pt too wide) in paragraph at lines 10414--10415 []\T1/pcr/m/n/10 XFELDetAna.algorithms.characterize_cti\T1/ptm/m/n/10 , Overfull \hbox (12.6225pt too wide) in paragraph at lines 10415--10416 []\T1/pcr/m/n/10 XFELDetAna.algorithms.characterize_noise\T1/ptm/m/n/10 , Overfull \hbox (18.6225pt too wide) in paragraph at lines 10416--10417 []\T1/pcr/m/n/10 XFELDetAna.algorithms.characterize_offset\T1/ptm/m/n/10 , Overfull \hbox (24.6225pt too wide) in paragraph at lines 10417--10418 []\T1/pcr/m/n/10 XFELDetAna.algorithms.characterize_relgain\T1/ptm/m/n/10 , Overfull \hbox (18.6225pt too wide) in paragraph at lines 10418--10419 []\T1/pcr/m/n/10 XFELDetAna.algorithms.correct_common_mode\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 10420--10421 []\T1/pcr/m/n/10 XFELDetAna.algorithms.correct_offset\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 10421--10422 []\T1/pcr/m/n/10 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too wide) in paragraph at lines 10431--10432 []\T1/pcr/m/n/10 XFELDetAna.algorithms.gpu.kernels.correct_relgain\T1/ptm/m/n/1 0 , Overfull \hbox (48.6225pt too wide) in paragraph at lines 10432--10433 []\T1/pcr/m/n/10 XFELDetAna.algorithms.gpu.kernels.split_events\T1/ptm/m/n/10 , Overfull \hbox (36.6225pt too wide) in paragraph at lines 10433--10434 []\T1/pcr/m/n/10 XFELDetAna.algorithms.gpu.kernels.statistics\T1/ptm/m/n/10 , Overfull \hbox (0.6225pt too wide) in paragraph at lines 10434--10435 []\T1/pcr/m/n/10 XFELDetAna.algorithms.gpu.kernels.util\T1/ptm/m/n/10 , Overfull \hbox (60.6225pt too wide) in paragraph at lines 10435--10436 []\T1/pcr/m/n/10 XFELDetAna.algorithms.gpu.kernels.xfelgpukernels\T1/ptm/m/n/10 , Overfull \hbox (0.6225pt too wide) in paragraph at lines 10436--10437 []\T1/pcr/m/n/10 XFELDetAna.algorithms.gpu.split_events\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 10437--10438 []\T1/pcr/m/n/10 XFELDetAna.algorithms.gpu.statistics\T1/ptm/m/n/10 , Overfull \hbox (18.6225pt too wide) in paragraph at lines 10439--10440 []\T1/pcr/m/n/10 XFELDetAna.algorithms.gpu.xfelcalgputools\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 10458--10459 []\T1/pcr/m/n/10 XFELDetAna.detectors.generator.reader\T1/ptm/m/n/10 , [145] [146] (./src.ind Underfull \hbox (badness 10000) in paragraph at lines 5--6 []\T1/ptm/m/n/10 _axisFuncWrapper() (in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 6--7 []\T1/ptm/m/n/10 _decorateModule() (in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 7--8 []\T1/ptm/m/n/10 _fill_between_steps() (in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 8--10 []\T1/ptm/m/n/10 _gpuCommonMode() (in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 8--10 \T1/ptm/m/n/10 tAna.algorithms.gpu.correct_common_mode), Underfull \hbox (badness 10000) in paragraph at lines 10--12 []\T1/ptm/m/n/10 _gpuCommonMode2D() (in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 10--12 \T1/ptm/m/n/10 tAna.algorithms.gpu.correct_common_mode), Underfull \hbox (badness 10000) in paragraph at lines 12--14 []\T1/ptm/m/n/10 _gpuCommonMode3D() (in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 12--14 \T1/ptm/m/n/10 tAna.algorithms.gpu.correct_common_mode), Underfull \hbox (badness 10000) in paragraph at lines 21--22 []\T1/ptm/m/n/10 add_can_expand (XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 21--22 \T1/ptm/m/n/10 tAna.util.knumpy.krbMaskedArray at-tribute), Underfull \hbox (badness 10000) in paragraph at lines 24--25 []\T1/ptm/m/n/10 add_newdoc_ufunc() (in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 29--30 []\T1/ptm/m/n/10 ALLOW_THREADS() (in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 34--35 []\T1/ptm/m/n/10 AND (XFELDe-tAna.algorithms.selection.DataSelector Underfull \hbox (badness 10000) in paragraph at lines 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(XFELDe-tAna.algorithms.selection.DataSelector Underfull \hbox (badness 10000) in paragraph at lines 96--97 []\T1/ptm/m/n/10 broadcast_arrays() (in mod-ule XFELDe- Overfull \hbox (28.38911pt too wide) in paragraph at lines 112--113 []\T1/ptm/m/n/10 classify() (XFELDe-tAna.algorithms.split_event.PatternClassifi er Underfull \hbox (badness 10000) in paragraph at lines 115--116 []\T1/ptm/m/n/10 close() (XFELDe-tAna.util.p2pInterface.P2pInterface Underfull \hbox (badness 10000) in paragraph at lines 116--118 []\T1/ptm/m/n/10 collect_incoming_data() (XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 120--122 []\T1/ptm/m/n/10 commonmode3d (in mod-ule XFELDe- Overfull \hbox (26.93044pt too wide) in paragraph at lines 120--122 \T1/ptm/m/n/10 tAna.algorithms.gpu.kernels.correct_common_mode), Underfull \hbox (badness 10000) in paragraph at lines 122--124 []\T1/ptm/m/n/10 commonmode3dBitonic (in mod-ule XFELDe- Overfull \hbox (26.93044pt too wide) in paragraph at lines 122--124 \T1/ptm/m/n/10 tAna.algorithms.gpu.kernels.correct_common_mode), Underfull \hbox (badness 10000) in paragraph at lines 124--126 []\T1/ptm/m/n/10 commonmode3dBitonicZ1 (in mod-ule XFELDe- Overfull \hbox (26.93044pt too wide) in paragraph at lines 124--126 \T1/ptm/m/n/10 tAna.algorithms.gpu.kernels.correct_common_mode), Underfull \hbox (badness 10000) in paragraph at lines 126--128 []\T1/ptm/m/n/10 commonmode3dNetwork() (in mod-ule XFELDe- Overfull \hbox (61.3601pt too wide) in paragraph at lines 126--128 \T1/ptm/m/n/10 tAna.algorithms.gpu.kernels.correct_common_mode_batcher), Underfull \hbox (badness 10000) in paragraph at lines 128--129 []\T1/ptm/m/n/10 CommonModeCorrection (class in XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 128--129 \T1/ptm/m/n/10 tAna.algorithms.correct_common_mode), Underfull \hbox (badness 10000) in paragraph at lines 129--130 []\T1/ptm/m/n/10 compare_chararrays() (in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 131--132 []\T1/ptm/m/n/10 ComplexWarning() (in mod-ule XFELDe- [148] Overfull \hbox (114.4592pt too wide) in paragraph at lines 142--144 []\T1/ptm/m/n/10 correct() (XFELDe-tAna.algorithms.correct_common_mode.CommonMo deCorrection Overfull \hbox (18.89969pt too wide) in paragraph at lines 144--145 []\T1/ptm/m/n/10 correct() (XFELDe-tAna.algorithms.correction.CorrectionBase Overfull \hbox (16.03978pt too wide) in paragraph at lines 145--146 []\T1/ptm/m/n/10 correct() (XFELDe-tAna.algorithms.unitary.UnitaryCalculator Underfull \hbox (badness 10000) in paragraph at lines 146--147 []\T1/ptm/m/n/10 CorrectionBase (class in XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 153--154 []\T1/ptm/m/n/10 CTICalculator (class in XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 154--155 []\T1/ptm/m/n/10 CTICorrection (class in XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 167--168 []\T1/ptm/m/n/10 dataReceiver() (in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 168--169 []\T1/ptm/m/n/10 DataSelector (class in XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 170--171 []\T1/ptm/m/n/10 datetime_as_string() (in mod-ule XFELDe- Overfull \hbox (3.15033pt too wide) in paragraph at lines 172--173 []\T1/ptm/m/n/10 debug() (XFELDe-tAna.core.mapcalculator.MapCalculator Underfull \hbox (badness 10000) in paragraph at lines 173--174 []\T1/ptm/m/n/10 defaultBlockSize (in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 179--180 []\T1/ptm/m/n/10 deprecate_with_doc() (in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 182--183 []\T1/ptm/m/n/10 diag_indices_from() (in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 203--204 []\T1/ptm/m/n/10 enable() (XFELDe-tAna.core.profiler.Profiler method), Underfull \hbox (badness 10000) in paragraph at lines 204--205 []\T1/ptm/m/n/10 enabledClasses() (XFELDe-tAna.core.profiler.Profiler Underfull \hbox (badness 10000) in paragraph at lines 205--206 []\T1/ptm/m/n/10 enablePrettyPlot() (in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 207--208 []\T1/ptm/m/n/10 enforce_setting (XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 207--208 \T1/ptm/m/n/10 tAna.util.knumpy.krbMaskedArray at-tribute), Underfull \hbox (badness 10000) in paragraph at lines 208--209 []\T1/ptm/m/n/10 enforce_stackable (XFELDe-tAna.util.knumpy.krbarray Underfull \hbox (badness 10000) in paragraph at lines 209--210 []\T1/ptm/m/n/10 enforce_stackable (XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 209--210 \T1/ptm/m/n/10 tAna.util.knumpy.krbMaskedArray at-tribute), Underfull \hbox (badness 10000) in paragraph at lines 212--213 []\T1/ptm/m/n/10 ERR_DEFAULT() (in mod-ule XFELDe- [149] Underfull \hbox (badness 10000) in paragraph at lines 232--233 []\T1/ptm/m/n/10 fastCopyAndTranspose() (in mod-ule XFELDe- Overfull \hbox (20.57932pt too wide) in paragraph at lines 235--236 []\T1/ptm/m/n/10 fill() (XFELDe-tAna.algorithms.characterize_cti.CTICalculator Overfull \hbox (38.90915pt too wide) in paragraph at lines 236--237 []\T1/ptm/m/n/10 fill() (XFELDe-tAna.algorithms.characterize_noise.NoiseCalcula tor Overfull \hbox (41.72897pt too wide) in paragraph at lines 237--238 []\T1/ptm/m/n/10 fill() (XFELDe-tAna.algorithms.characterize_offset.OffsetCalcu lator Overfull \hbox (59.95905pt too wide) in paragraph at lines 238--240 []\T1/ptm/m/n/10 fill() (XFELDe-tAna.algorithms.characterize_relgain.GainMapCal culator Overfull \hbox (23.38934pt too wide) in paragraph at lines 240--241 []\T1/ptm/m/n/10 fill() (XFELDe-tAna.algorithms.histogram.HistogramCalculator Underfull \hbox (badness 10000) in paragraph at lines 241--242 []\T1/ptm/m/n/10 fill() (XFELDe-tAna.algorithms.statistics.StatCalculator Overfull \hbox (5.04953pt too wide) in paragraph at lines 243--244 []\T1/ptm/m/n/10 filter() (XFELDe-tAna.algorithms.selection.ThresholdFilter Underfull \hbox (badness 10000) in paragraph at lines 245--246 []\T1/ptm/m/n/10 find_common_type() (in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 260--261 []\T1/ptm/m/n/10 found_terminator() (XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 261--262 []\T1/ptm/m/n/10 FPE_DIVIDEBYZERO() (in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 263--264 []\T1/ptm/m/n/10 FPE_OVERFLOW() (in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 264--265 []\T1/ptm/m/n/10 FPE_UNDERFLOW() (in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 279--280 []\T1/ptm/m/n/10 GainMapCalculator (class in XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 280--281 []\T1/ptm/m/n/10 gainMultiMapsToSingle() (in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 281--283 []\T1/ptm/m/n/10 generateNetwork() (in mod-ule XFELDe- Overfull \hbox (61.3601pt too wide) in paragraph at lines 281--283 \T1/ptm/m/n/10 tAna.algorithms.gpu.kernels.correct_common_mode_batcher), Underfull \hbox (badness 10000) in paragraph at lines 283--284 []\T1/ptm/m/n/10 generates_report() (in mod-ule XFELDe- Overfull \hbox (21.67943pt too wide) in paragraph at lines 286--287 []\T1/ptm/m/n/10 get() (XFELDe-tAna.algorithms.characterize_cti.CTICalculator Overfull \hbox (40.00926pt too wide) in paragraph at lines 287--288 []\T1/ptm/m/n/10 get() (XFELDe-tAna.algorithms.characterize_noise.NoiseCalculat or Overfull \hbox (42.82909pt too wide) in paragraph at lines 288--289 []\T1/ptm/m/n/10 get() (XFELDe-tAna.algorithms.characterize_offset.OffsetCalcul ator Overfull \hbox (61.05916pt too wide) in paragraph at lines 289--291 []\T1/ptm/m/n/10 get() (XFELDe-tAna.algorithms.characterize_relgain.GainMapCalc ulator [150] Overfull \hbox (98.9194pt too wide) in paragraph at lines 291--293 []\T1/ptm/m/n/10 get() (XFELDe-tAna.algorithms.correct_common_mode.CommonModeCo rrection Overfull \hbox (24.48946pt too wide) in paragraph at lines 293--294 []\T1/ptm/m/n/10 get() (XFELDe-tAna.algorithms.histogram.HistogramCalculator Underfull \hbox (badness 6428) in paragraph at lines 296--297 []\T1/ptm/m/n/10 get() (XFELDe-tAna.algorithms.statistics.MinCalculator Underfull \hbox (badness 10000) in paragraph at lines 297--298 []\T1/ptm/m/n/10 get() (XFELDe-tAna.algorithms.statistics.StatCalculator Underfull \hbox (badness 10000) in paragraph at lines 298--299 []\T1/ptm/m/n/10 get() (XFELDe-tAna.algorithms.statistics.StdCalculator Underfull \hbox (badness 10000) in paragraph at lines 302--303 []\T1/ptm/m/n/10 get_printoptions() (in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 304--305 []\T1/ptm/m/n/10 get_respects_scales (XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 304--305 \T1/ptm/m/n/10 tAna.util.knumpy.krbMaskedArray at-tribute), Underfull \hbox (badness 10000) in paragraph at lines 306--307 []\T1/ptm/m/n/10 getCoordinatesForIndices() (XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 307--308 []\T1/ptm/m/n/10 getDataSize() (in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 308--309 []\T1/ptm/m/n/10 getDataSize() (in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 309--310 []\T1/ptm/m/n/10 getDataSize() (in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 310--311 []\T1/ptm/m/n/10 getDataSize() (in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 311--312 []\T1/ptm/m/n/10 getDataSize() (in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 315--316 []\T1/ptm/m/n/10 getFormattedLog() (XFELDe-tAna.core.profiler.Profiler Underfull \hbox (badness 10000) in paragraph at lines 317--318 []\T1/ptm/m/n/10 getGPUInfo() (XFELDe-tAna.core.profiler.Profiler Underfull \hbox (badness 10000) in paragraph at lines 318--319 []\T1/ptm/m/n/10 getHardwareInfo() (XFELDe-tAna.core.profiler.Profiler Overfull \hbox (10.60907pt too wide) in paragraph at lines 319--320 []\T1/ptm/m/n/10 getMax() (XFELDe-tAna.algorithms.statistics.StatCalculator Underfull \hbox (badness 10000) in paragraph at lines 320--321 []\T1/ptm/m/n/10 getMaxEntry() (XFELDe-tAna.core.profiler.Profiler Overfull \hbox (15.04901pt too wide) in paragraph at lines 321--322 []\T1/ptm/m/n/10 getMean() (XFELDe-tAna.algorithms.statistics.StatCalculator Overfull \hbox (87.71883pt too wide) in paragraph at lines 322--324 []\T1/ptm/m/n/10 getMeans() (XFELDe-tAna.algorithms.characterize_relgain.GainMa pCalculator Overfull \hbox (8.94902pt too wide) in paragraph at lines 324--325 []\T1/ptm/m/n/10 getMin() (XFELDe-tAna.algorithms.statistics.StatCalculator Underfull \hbox (badness 10000) in paragraph at lines 325--326 []\T1/ptm/m/n/10 getMinEntry() (XFELDe-tAna.core.profiler.Profiler Overfull \hbox (64.74887pt too wide) in paragraph at lines 326--328 []\T1/ptm/m/n/10 getOffset() (XFELDe-tAna.algorithms.characterize_noise.NoiseCa lculator Underfull \hbox (badness 10000) in paragraph at lines 328--330 []\T1/ptm/m/n/10 getPatternStats() (XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 328--330 \T1/ptm/m/n/10 tAna.algorithms.split_event.PatternClassifier Underfull \hbox (badness 10000) in paragraph at lines 330--332 []\T1/ptm/m/n/10 getRawPeaks() (XFELDe- Overfull \hbox (40.28964pt too wide) in paragraph at lines 330--332 \T1/ptm/m/n/10 tAna.algorithms.characterize_relgain.GainMapCalculator Overfull \hbox (15.56999pt too wide) in paragraph at lines 332--333 []\T1/ptm/m/n/10 getShape() (XFELDe-tAna.core.mapcalculator.MapCalculator Underfull \hbox (badness 10000) in paragraph at lines 333--335 []\T1/ptm/m/n/10 getSigmas() (XFELDe- Overfull \hbox (40.28964pt too wide) in paragraph at lines 333--335 \T1/ptm/m/n/10 tAna.algorithms.characterize_relgain.GainMapCalculator Overfull \hbox (5.61906pt too wide) in paragraph at lines 335--336 []\T1/ptm/m/n/10 getStd() (XFELDe-tAna.algorithms.statistics.StatCalculator Underfull \hbox (badness 10000) in paragraph at lines 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[]\T1/ptm/m/n/10 median3dNetwork() (in mod-ule XFELDe- Overfull \hbox (61.3601pt too wide) in paragraph at lines 491--493 \T1/ptm/m/n/10 tAna.algorithms.gpu.kernels.correct_common_mode_batcher), Underfull \hbox (badness 10000) in paragraph at lines 497--498 []\T1/ptm/m/n/10 min_scalar_type() (in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 498--499 []\T1/ptm/m/n/10 MinCalculator (class in XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 504--505 []\T1/ptm/m/n/10 ModuleDeprecationWarning() (in mod-ule XFELDe- [153] Underfull \hbox (badness 10000) in paragraph at lines 538--539 []\T1/ptm/m/n/10 NoiseCalculator (class in XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 549--551 []\T1/ptm/m/n/10 oddeven_merge() (in mod-ule XFELDe- Overfull \hbox (61.3601pt too wide) in paragraph at lines 549--551 \T1/ptm/m/n/10 tAna.algorithms.gpu.kernels.correct_common_mode_batcher), Underfull \hbox (badness 10000) in paragraph at lines 551--553 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(XFELDe-tAna.util.knumpy.pulseAxis at- Underfull \hbox (badness 10000) in paragraph at lines 725--726 []\T1/ptm/m/n/10 stackable (XFELDe-tAna.util.knumpy.stackAxis at- Underfull \hbox (badness 10000) in paragraph at lines 727--728 []\T1/ptm/m/n/10 StatCalculator (class in XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 728--730 []\T1/ptm/m/n/10 statisticsCalculator() (in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 731--732 []\T1/ptm/m/n/10 StdCalculator (class in XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 734--735 []\T1/ptm/m/n/10 surfacePlot2dGrid() (in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 746--747 []\T1/ptm/m/n/10 ThresholdFilter (class in XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 752--753 []\T1/ptm/m/n/10 transpose3d (in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 757--758 []\T1/ptm/m/n/10 tril_indices_from() (in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 761--762 []\T1/ptm/m/n/10 triu_indices_from() (in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 773--774 []\T1/ptm/m/n/10 UFUNC_PYVALS_NAME() (in mod-ule XFELDe- Overfull \hbox (13.15033pt too wide) in paragraph at lines 774--775 []\T1/ptm/m/n/10 undebug() (XFELDe-tAna.core.mapcalculator.MapCalculator [156] Underfull \hbox (badness 10000) in paragraph at lines 777--778 []\T1/ptm/m/n/10 UnitaryCalculator (class in XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 789--790 []\T1/ptm/m/n/10 VisibleDeprecationWarning() (in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 799--800 []\T1/ptm/m/n/10 write() (XFELDe-tAna.util.p2pInterface.AsyncServer Underfull \hbox (badness 10000) in paragraph at lines 800--801 []\T1/ptm/m/n/10 write() (XFELDe-tAna.util.p2pInterface.P2pInterface Underfull \hbox (badness 10000) in paragraph at lines 807--808 []\T1/ptm/m/n/10 XFELDetAna.algorithms.characterize_noise (mod-ule), Underfull \hbox (badness 10000) in paragraph at lines 808--809 []\T1/ptm/m/n/10 XFELDetAna.algorithms.characterize_offset (mod-ule), Underfull \hbox (badness 10000) in paragraph at lines 816--817 []\T1/ptm/m/n/10 XFELDetAna.algorithms.gpu.correct_common_mode Underfull \hbox (badness 7613) in paragraph at lines 818--819 []\T1/ptm/m/n/10 XFELDetAna.algorithms.gpu.correct_relgain (mod-ule), Overfull \hbox (17.76027pt too wide) in paragraph at lines 820--821 []\T1/ptm/m/n/10 XFELDetAna.algorithms.gpu.kernels.correct_common_mode Overfull \hbox (52.18994pt too wide) in paragraph at lines 821--822 []\T1/ptm/m/n/10 XFELDetAna.algorithms.gpu.kernels.correct_common_mode_batcher Underfull \hbox (badness 10000) in paragraph at lines 822--823 []\T1/ptm/m/n/10 XFELDetAna.algorithms.gpu.kernels.correct_offset Underfull \hbox (badness 10000) in paragraph at lines 823--824 []\T1/ptm/m/n/10 XFELDetAna.algorithms.gpu.kernels.correct_relgain Underfull \hbox (badness 10000) in paragraph at lines 827--828 []\T1/ptm/m/n/10 XFELDetAna.algorithms.gpu.kernels.xfelgpukernels [157] [158]) (./src.aux) Package rerunfilecheck Warning: File `src.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on src.pdf (162 pages, 3221756 bytes). Transcript written on src.log. [rtd-command-info] start-time: 2017-05-17T10:57:33.265000Z, end-time: 2017-05-17T10:57:33.293000Z, duration: 0, exit-code: 0 mv -f /user_builds/pydetlib/checkouts/latest/doc/_build/latex/src.pdf /user_builds/pydetlib/artifacts/latest/sphinx_pdf/pydetlib.pdf [rtd-command-info] start-time: 2017-05-17T10:57:34.325000Z, end-time: 2017-05-17T10:57:54.443000Z, duration: 20, exit-code: 0 python /user_builds/pydetlib/envs/latest/bin/sphinx-build -T -b epub -d _build/doctrees-epub -D language=en . _build/epub Running Sphinx v1.3.5 making output directory... loading translations [en]... done loading pickled environment... done loading intersphinx inventory from http://docs.scipy.org/doc/scipy/reference/objects.inv... loading intersphinx inventory from http://docs.python.org/2.7/objects.inv... loading intersphinx inventory from http://matplotlib.sourceforge.net/objects.inv... loading intersphinx inventory from http://docs.scipy.org/doc/numpy/objects.inv... building [mo]: targets for 0 po files that are out of date building [epub]: targets for 24 source files that are out of date updating environment: 0 added, 8 changed, 0 removed reading sources... [ 12%] api/XFELDetAna Plotting not available No module named 'matplotlib.collections' reading sources... [ 25%] api/XFELDetAna.algorithms reading sources... [ 37%] api/XFELDetAna.algorithms.gpu reading sources... [ 50%] api/XFELDetAna.algorithms.gpu.kernels reading sources... [ 62%] api/XFELDetAna.core reading sources... [ 75%] api/XFELDetAna.detectors reading sources... [ 87%] api/XFELDetAna.plotting reading sources... [100%] api/XFELDetAna.util /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages/IPython/utils/pickleutil.py:3: UserWarning: IPython.utils.pickleutil has moved to ipykernel.pickleutil warn("IPython.utils.pickleutil has moved to ipykernel.pickleutil") /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.algorithms.rst:7: WARNING: toctree contains reference to nonexisting document 'api/XFELDetAna.algorithms.cython' /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/algorithms/histogram.py:docstring of XFELDetAna.algorithms.histogram.HistogramCalculator:38: ERROR: Unknown interpreted text role "method". /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/algorithms/histogram.py:docstring of XFELDetAna.algorithms.histogram.HistogramCalculator.get:26: WARNING: Definition list ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/algorithms/gpu/correct_common_mode.py:docstring of XFELDetAna.algorithms.gpu.correct_common_mode._gpuCommonMode:11: ERROR: Unexpected indentation. /user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/core/reader.py:docstring of XFELDetAna.core.reader.ChunkReader.readChunks:8: WARNING: Definition list ends without a blank line; unexpected unindent. /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.detectors.rst:7: WARNING: toctree contains reference to nonexisting document 'api/XFELDetAna.detectors.dssc' /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.plotting.rst:7: WARNING: autodoc: failed to import module 'XFELDetAna.plotting.heatmap'; the following exception was raised: Traceback (most recent call last): File "/user_builds/pydetlib/envs/latest/lib/python3.4/site-packages/sphinx/ext/autodoc.py", line 385, in import_object __import__(self.modname) File "/user_builds/pydetlib/checkouts/latest/lib/src/XFELDetAna/plotting/heatmap.py", line 246, in import matplotlib.collections as mcoll ImportError: No module named 'matplotlib.collections' /user_builds/pydetlib/checkouts/latest/lib/docs/api/XFELDetAna.util.rst:7: WARNING: __all__ should be a list of strings, not .wrapped at 0x7f178335f7b8> (in module XFELDetAna.util.knumpy) -- ignoring __all__ looking for now-outdated files... none found pickling environment... done checking consistency... /user_builds/pydetlib/checkouts/latest/lib/docs/examples/DataGeneratorExample.rst:: WARNING: document isn't included in any toctree /user_builds/pydetlib/checkouts/latest/lib/docs/examples/PlotExamples.rst:: WARNING: document isn't included in any toctree /user_builds/pydetlib/checkouts/latest/lib/docs/examples/gainMapStability.rst:: WARNING: document isn't included in any toctree done preparing documents... done writing output... 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