Read the Docs build information Build id: 25917 Project: scs-toolbox Version: latest Commit: e9a355ce4be5f40cd5ed6cfdf83669813c0dc533 Date: 2023-04-05T19:23:35.020206Z State: finished Success: True [rtd-command-info] start-time: 2023-04-05T19:23:36.164881Z, end-time: 2023-04-05T19:23:37.274161Z, duration: 1, exit-code: 0 git clone --no-single-branch --depth 50 https://git.xfel.eu/SCS/ToolBox.git . Cloning into '.'... [rtd-command-info] start-time: 2023-04-05T19:23:37.719204Z, end-time: 2023-04-05T19:23:37.847021Z, duration: 0, exit-code: 0 git checkout --force origin/master Note: checking out 'origin/master'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by performing another checkout. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -b with the checkout command again. Example: git checkout -b HEAD is now at e9a355c Enable GPU acceleration of the BOZ correction determination [rtd-command-info] start-time: 2023-04-05T19:23:37.930202Z, end-time: 2023-04-05T19:23:37.991153Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2023-04-05T19:23:39.297981Z, end-time: 2023-04-05T19:23:44.225920Z, duration: 4, exit-code: 0 python3.7 -mvirtualenv /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/envs/latest Using base prefix '/home/docs/.pyenv/versions/3.7.3' New python executable in /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/envs/latest/bin/python3.7 Also creating executable in /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2023-04-05T19:23:44.317367Z, end-time: 2023-04-05T19:23:45.254716Z, duration: 0, exit-code: 0 /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/envs/latest/bin/python -m pip install --upgrade --no-cache-dir pip Requirement already satisfied: pip in /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/envs/latest/lib/python3.7/site-packages (23.0.1) [rtd-command-info] start-time: 2023-04-05T19:23:45.341448Z, end-time: 2023-04-05T19:23:55.066731Z, duration: 9, exit-code: 0 /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/envs/latest/bin/python -m pip install --upgrade --no-cache-dir jinja2==2.11.3 markupsafe==2.0.1 Pygments==2.3.1 setuptools==41.0.1 docutils==0.14 mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<1.1 Collecting jinja2==2.11.3 Downloading Jinja2-2.11.3-py2.py3-none-any.whl (125 kB) 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Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.0/2.0 MB 132.7 MB/s eta 0:00:00 Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.13-py3-none-any.whl (13 kB) Collecting commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 47.4/47.4 kB 133.2 MB/s eta 0:00:00 Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx<2 Downloading Sphinx-1.8.6-py2.py3-none-any.whl (3.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 50.5 MB/s eta 0:00:00 Collecting sphinx-rtd-theme<0.5 Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.4/6.4 MB 137.2 MB/s eta 0:00:00 Collecting readthedocs-sphinx-ext<1.1 Downloading readthedocs_sphinx_ext-1.0.4-py2.py3-none-any.whl (28 kB) Collecting future Downloading future-0.18.3.tar.gz (840 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 840.9/840.9 kB 207.7 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting requests>=2.0.0 Downloading requests-2.28.2-py3-none-any.whl (62 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.8/62.8 kB 140.2 MB/s eta 0:00:00 Collecting six>=1.5 Downloading six-1.16.0-py2.py3-none-any.whl (11 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.2.0-py2.py3-none-any.whl (93 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 93.0/93.0 kB 106.2 MB/s eta 0:00:00 Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Collecting imagesize Downloading imagesize-1.4.1-py2.py3-none-any.whl (8.8 kB) Collecting packaging Downloading packaging-23.0-py3-none-any.whl (42 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 42.7/42.7 kB 122.9 MB/s eta 0:00:00 Collecting babel!=2.0,>=1.3 Downloading Babel-2.12.1-py3-none-any.whl (10.1 MB) 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sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl (94 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 94.0/94.0 kB 162.3 MB/s eta 0:00:00 Building wheels for collected packages: mock, future Building wheel for mock (setup.py): started Building wheel for mock (setup.py): finished with status 'done' Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23753 sha256=27ef6a92e326bff0873328957dbef46609151ce952bbf32d5a83b17454b5a737 Stored in directory: /tmp/pip-ephem-wheel-cache-8xt9fnz8/wheels/7a/94/b1/0fdc5339a5bd487a5cc15421ec200d9ba3e2aa7190e4a727f1 Building wheel for future (setup.py): started Building wheel for future (setup.py): finished with status 'done' Created wheel for future: filename=future-0.18.3-py3-none-any.whl size=492022 sha256=668f0eefda2adf33238fe1b51a2723420998a40f2f4f6f7c4582609cf0424143 Stored in directory: /tmp/pip-ephem-wheel-cache-8xt9fnz8/wheels/fa/cd/1f/c6b7b50b564983bf3011e8fc75d06047ddc50c07f6e3660b00 Successfully built mock future Installing collected packages: snowballstemmer, pytz, Pygments, mock, docutils, urllib3, sphinxcontrib-serializinghtml, six, setuptools, pillow, packaging, markupsafe, imagesize, idna, future, charset-normalizer, certifi, babel, alabaster, sphinxcontrib-websupport, requests, jinja2, commonmark, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark Attempting uninstall: setuptools Found existing installation: setuptools 67.6.1 Uninstalling setuptools-67.6.1: Successfully uninstalled setuptools-67.6.1 Successfully installed Pygments-2.3.1 alabaster-0.7.13 babel-2.12.1 certifi-2022.12.7 charset-normalizer-3.1.0 commonmark-0.8.1 docutils-0.14 future-0.18.3 idna-3.4 imagesize-1.4.1 jinja2-2.11.3 markupsafe-2.0.1 mock-1.0.1 packaging-23.0 pillow-5.4.1 pytz-2023.3 readthedocs-sphinx-ext-1.0.4 recommonmark-0.5.0 requests-2.28.2 setuptools-41.0.1 six-1.16.0 snowballstemmer-2.2.0 sphinx-1.8.6 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-1.26.15 [rtd-command-info] start-time: 2023-04-05T19:23:55.153858Z, end-time: 2023-04-05T19:24:06.088398Z, duration: 10, exit-code: 0 /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/envs/latest/bin/python -m pip install --exists-action=w --no-cache-dir -r doc/requirements.txt Requirement already satisfied: sphinx in /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/envs/latest/lib/python3.7/site-packages (from -r doc/requirements.txt (line 1)) (1.8.6) Requirement already satisfied: sphinx_rtd_theme in /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/envs/latest/lib/python3.7/site-packages (from -r doc/requirements.txt (line 2)) (0.4.3) Collecting autoapi Downloading autoapi-2.0.1.tar.gz (11 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting sphinx-autoapi Downloading sphinx_autoapi-2.1.0-py2.py3-none-any.whl (53 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 53.9/53.9 kB 2.7 MB/s eta 0:00:00 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packages: webencodings, mistune, fastjsonschema, zipp, wrapt, unidecode, typing-extensions, typed-ast, traitlets, tornado, tinycss2, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, soupsieve, pyzmq, PyYAML, python-dateutil, pyrsistent, Pygments, pkgutil-resolve-name, pandocfilters, nest-asyncio, lazy-object-proxy, jupyterlab-pygments, Jinja2, entrypoints, defusedxml, bleach, attrs, jupyter-core, importlib-resources, importlib-metadata, beautifulsoup4, astroid, sphinx, jupyter-client, jsonschema, sphinx-autoapi, nbformat, autoapi, nbclient, nbconvert, nbsphinx Attempting uninstall: Pygments Found existing installation: Pygments 2.3.1 Uninstalling Pygments-2.3.1: Successfully uninstalled Pygments-2.3.1 Attempting uninstall: Jinja2 Found existing installation: Jinja2 2.11.3 Uninstalling Jinja2-2.11.3: Successfully uninstalled Jinja2-2.11.3 Attempting uninstall: sphinx Found existing installation: Sphinx 1.8.6 Uninstalling Sphinx-1.8.6: Successfully uninstalled Sphinx-1.8.6 Successfully installed Jinja2-3.1.2 PyYAML-6.0 Pygments-2.14.0 astroid-2.15.2 attrs-22.2.0 autoapi-2.0.1 beautifulsoup4-4.12.1 bleach-6.0.0 defusedxml-0.7.1 entrypoints-0.4 fastjsonschema-2.16.3 importlib-metadata-6.1.0 importlib-resources-5.12.0 jsonschema-4.17.3 jupyter-client-7.4.9 jupyter-core-4.12.0 jupyterlab-pygments-0.2.2 lazy-object-proxy-1.9.0 mistune-2.0.5 nbclient-0.7.3 nbconvert-7.3.0 nbformat-5.8.0 nbsphinx-0.9.1 nest-asyncio-1.5.6 pandocfilters-1.5.0 pkgutil-resolve-name-1.3.10 pyrsistent-0.19.3 python-dateutil-2.8.2 pyzmq-25.0.2 soupsieve-2.4 sphinx-5.3.0 sphinx-autoapi-2.1.0 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 tinycss2-1.2.1 tornado-6.2 traitlets-5.9.0 typed-ast-1.5.4 typing-extensions-4.5.0 unidecode-1.3.6 webencodings-0.5.1 wrapt-1.15.0 zipp-3.15.0 [rtd-command-info] start-time: 2023-04-05T19:24:06.819570Z, end-time: 2023-04-05T19:24:06.884574Z, duration: 0, exit-code: 0 cat doc/conf.py # -*- coding: utf-8 -*- # # Configuration file for the Sphinx documentation builder. # # This file does only contain a selection of the most common options. For a # full list see the documentation: # http://www.sphinx-doc.org/en/master/config # -- Path setup -------------------------------------------------------------- # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. # import os import sys sys.path.insert(0, os.path.abspath('..')) import sphinx_rtd_theme # -- Project information ----------------------------------------------------- project = 'SCS Toolbox' copyright = '2021, SCS' author = 'SCS' # The short X.Y version version = '' # The full version, including alpha/beta/rc tags release = '' # -- 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.mathjax', 'sphinx.ext.viewcode', 'sphinx.ext.coverage', 'sphinx.ext.napoleon', 'sphinx.ext.extlinks', # Comment out autoapi to be able to run nbsphinx 'autoapi.extension', 'sphinx_rtd_theme', 'nbsphinx' ] autoapi_dirs = ['../src/toolbox_scs'] autoapi_ignore = ['*/deprecated/*'] extlinks = {'issue': ('https://git.xfel.eu/SCS/ToolBox/-/issues/%s', 'issue:'), 'mr': ('https://git.xfel.eu/SCS/ToolBox/-/merge_requests/%s', 'MR:'), 'commit': ('https://git.xfel.eu/SCS/ToolBox/-/commit/%s', 'commit:') } # Don't add .txt suffix to source files: html_sourcelink_suffix = '' # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] # The suffix(es) of source filenames. # You can specify multiple suffix as a list of string: # # source_suffix = ['.rst', '.md'] source_suffix = '.rst' # The master toctree document. master_doc = 'index' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. # # This is also used if you do content translation via gettext catalogs. # Usually you set "language" from the command line for these cases. language = None # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This pattern also affects html_static_path and html_extra_path. exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] # The name of the Pygments (syntax highlighting) style to use. pygments_style = None # -- 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 = 'alabaster' html_theme = 'sphinx_rtd_theme' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # documentation. # # html_theme_options = {} # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['_static'] # Custom sidebar templates, must be a dictionary that maps document names # to template names. # # The default sidebars (for documents that don't match any pattern) are # defined by theme itself. Builtin themes are using these templates by # default: ``['localtoc.html', 'relations.html', 'sourcelink.html', # 'searchbox.html']``. # # html_sidebars = {} # -- Options for HTMLHelp output --------------------------------------------- # Output file base name for HTML help builder. htmlhelp_basename = 'SCSToolboxdoc' # -- Options for LaTeX output ------------------------------------------------ latex_elements = { # The paper size ('letterpaper' or 'a4paper'). # # 'papersize': 'letterpaper', # The font size ('10pt', '11pt' or '12pt'). # # 'pointsize': '10pt', # Additional stuff for the LaTeX preamble. # # 'preamble': '', # Latex figure (float) alignment # # 'figure_align': 'htbp', } # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, # author, documentclass [howto, manual, or own class]). latex_documents = [ (master_doc, 'SCSToolbox.tex', 'SCS Toolbox Documentation', 'SCS', 'manual'), ] # -- Options for manual page output ------------------------------------------ # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [ (master_doc, 'scstoolbox', 'SCS Toolbox Documentation', [author], 1) ] # -- Options for Texinfo output ---------------------------------------------- # Grouping the document tree into Texinfo files. List of tuples # (source start file, target name, title, author, # dir menu entry, description, category) texinfo_documents = [ (master_doc, 'SCSToolbox', 'SCS Toolbox Documentation', author, 'SCSToolbox', 'One line description of project.', 'Miscellaneous'), ] # -- Options for Epub output ------------------------------------------------- # Bibliographic Dublin Core info. epub_title = project # The unique identifier of the text. This can be a ISBN number # or the project homepage. # # epub_identifier = '' # A unique identification for the text. # # epub_uid = '' # A list of files that should not be packed into the epub file. epub_exclude_files = ['search.html'] # -- Extension configuration ------------------------------------------------- ########################################################################### # 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 importlib 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 elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' 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') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] if globals().get('websupport2_base_url', False): websupport2_base_url = 'http://rtd.xfel.eu/websupport' websupport2_static_url = '/static/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "media/", 'STATIC_URL': "/static/", 'PRODUCTION_DOMAIN': "rtd.xfel.eu", 'versions': [ ("latest", "/en/latest/"), ], 'downloads': [ ("pdf", "//rtd.xfel.eu/downloads/scs-toolbox/latest/pdf/"), ], 'subprojects': [ ], 'slug': 'scs-toolbox', 'name': u'SCS ToolBox', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'http://rtd.xfel.eu/docs/scs-toolbox/en/latest/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/doc/', 'api_host': 'http://rtd.xfel.eu', 'github_user': 'None', 'proxied_api_host': '/_', 'github_repo': 'None', 'github_version': 'master', 'display_github': False, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'docsearch_disabled': False, 'user_analytics_code': '', 'global_analytics_code': 'None', 'commit': 'e9a355ce', } if 'html_context' in globals(): html_context.update(context) else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' # Make sure our build directory is always excluded exclude_patterns = globals().get('exclude_patterns', []) exclude_patterns.extend(['_build']) [rtd-command-info] start-time: 2023-04-05T19:24:06.972055Z, end-time: 2023-04-05T19:24:35.510062Z, duration: 28, exit-code: 0 python /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/envs/latest/bin/sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v5.3.0 WARNING: Invalid configuration value found: 'language = None'. 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[100%] toolbox_scs.routines.boz [autosummary] generating autosummary for: Analysis_of_Viking_spectrometer_data.ipynb, Azimuthal integration of DSSC with pyFAI.ipynb, BOZ analysis part I.a Correction determination.ipynb, BOZ analysis part I.b Correction validation.ipynb, BOZ analysis part II.1 Small data.ipynb, BOZ analysis part II.2 Binning.ipynb, DSSC create geometry.ipynb, DSSC fine delay with SCS toolbox.ipynb, DSSC scattering time-delay.ipynb, Dask DSSC module binning.ipynb, ..., Loading_data_in_memory.ipynb, PES_spectra_extraction.ipynb, Transient reflectivity measurement.ipynb, bunch_pattern_decoding.rst, changelog.rst, dssc/DSSCBinner.rst, howtos.rst, index.rst, load.rst, maintainers.rst building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 22 source files that are out of date updating environment: [new config] 64 added, 0 changed, 0 removed reading sources... [ 1%] Analysis_of_Viking_spectrometer_data reading sources... 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[ 1%] Analysis_of_Viking_spectrometer_data writing output... [ 3%] Azimuthal integration of DSSC with pyFAI writing output... [ 4%] BOZ analysis part I.a Correction determination writing output... [ 6%] BOZ analysis part I.b Correction validation writing output... [ 7%] BOZ analysis part II.1 Small data writing output... [ 9%] BOZ analysis part II.2 Binning writing output... [ 10%] DSSC create geometry writing output... [ 12%] DSSC fine delay with SCS toolbox writing output... [ 14%] DSSC scattering time-delay writing output... [ 15%] Dask DSSC module binning writing output... [ 17%] HRIXS writing output... [ 18%] How to extract peaks from digitizer traces writing output... [ 20%] Loading_data_in_memory writing output... [ 21%] PES_spectra_extraction writing output... [ 23%] Transient reflectivity measurement writing output... [ 25%] autoapi/index writing output... [ 26%] autoapi/toolbox_scs/base/index writing output... 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[ 50%] autoapi/toolbox_scs/detectors/index writing output... [ 51%] autoapi/toolbox_scs/detectors/pes/index writing output... [ 53%] autoapi/toolbox_scs/detectors/viking/index writing output... [ 54%] autoapi/toolbox_scs/detectors/xgm/index writing output... [ 56%] autoapi/toolbox_scs/index writing output... [ 57%] autoapi/toolbox_scs/load/index writing output... [ 59%] autoapi/toolbox_scs/misc/bunch_pattern/index writing output... [ 60%] autoapi/toolbox_scs/misc/bunch_pattern_external/index writing output... [ 62%] autoapi/toolbox_scs/misc/index writing output... [ 64%] autoapi/toolbox_scs/misc/laser_utils/index writing output... [ 65%] autoapi/toolbox_scs/misc/undulator/index writing output... [ 67%] autoapi/toolbox_scs/mnemonics_machinery/index writing output... [ 68%] autoapi/toolbox_scs/routines/Reflectivity/index writing output... [ 70%] autoapi/toolbox_scs/routines/XAS/index writing output... [ 71%] autoapi/toolbox_scs/routines/boz/index writing output... [ 73%] autoapi/toolbox_scs/routines/index writing output... [ 75%] autoapi/toolbox_scs/routines/knife_edge/index writing output... [ 76%] autoapi/toolbox_scs/test/index writing output... [ 78%] autoapi/toolbox_scs/test/test_dssc_cls/index writing output... [ 79%] autoapi/toolbox_scs/test/test_hrixs/index writing output... [ 81%] autoapi/toolbox_scs/test/test_misc/index writing output... [ 82%] autoapi/toolbox_scs/test/test_top_level/index writing output... [ 84%] autoapi/toolbox_scs/test/test_utils/index writing output... [ 85%] autoapi/toolbox_scs/util/exceptions/index writing output... [ 87%] autoapi/toolbox_scs/util/index writing output... [ 89%] autoapi/toolbox_scs/util/pkg/index writing output... [ 90%] bunch_pattern_decoding writing output... [ 92%] changelog writing output... [ 93%] dssc/DSSCBinner writing output... [ 95%] howtos writing output... [ 96%] index writing output... [ 98%] load writing output... 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/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/misc/index.rst:12: WARNING: Block quote ends without a blank line; unexpected unindent. /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/misc/index.rst:203: ERROR: Unexpected indentation. /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/misc/index.rst:214: ERROR: Unexpected indentation. /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/misc/index.rst:227: ERROR: Unexpected indentation. /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/misc/laser_utils/index.rst:28: ERROR: Unexpected indentation. /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/misc/laser_utils/index.rst:41: ERROR: Unexpected indentation. /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/misc/laser_utils/index.rst:55: ERROR: Unexpected indentation. /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/XAS/index.rst:40: ERROR: Unexpected indentation. /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/XAS/index.rst:7: WARNING: Block quote ends without a blank line; unexpected unindent. /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/XAS/index.rst:47: ERROR: Unexpected indentation. /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/XAS/index.rst:63: ERROR: Unexpected indentation. /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:195: ERROR: Unexpected 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/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:10: WARNING: Block quote ends without a blank line; unexpected unindent. /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:7: WARNING: Definition list ends without a blank line; unexpected unindent. /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:421: ERROR: Unexpected indentation. /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:9: WARNING: Block quote ends without a blank line; unexpected unindent. /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:468: ERROR: Unexpected indentation. 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/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:531: ERROR: Unexpected indentation. /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/boz/index.rst:550: ERROR: Unexpected indentation. /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:86: ERROR: Unexpected indentation. /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:7: WARNING: Block quote ends without a blank line; unexpected unindent. /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:93: ERROR: Unexpected indentation. /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:109: ERROR: Unexpected indentation. /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:250: ERROR: Unexpected indentation. /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:9: WARNING: Block quote ends without a blank line; unexpected unindent. /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:320: ERROR: Unexpected indentation. /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:8: WARNING: Block quote ends without a blank line; unexpected unindent. /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:7: WARNING: Definition list ends without a blank line; unexpected unindent. /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:351: ERROR: Unexpected indentation. /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:10: WARNING: Block quote ends without a blank line; unexpected unindent. /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:7: WARNING: Definition list ends without a blank line; unexpected unindent. /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:476: ERROR: Unexpected indentation. /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/routines/index.rst:9: WARNING: Block quote ends without a blank line; unexpected unindent. 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/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/test/test_top_level/index.rst:27: WARNING: Block quote ends without a blank line; unexpected unindent. /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/test/test_utils/index.rst:72: ERROR: Unexpected indentation. /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/autoapi/toolbox_scs/test/test_utils/index.rst:27: WARNING: Block quote ends without a blank line; unexpected unindent. /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/changelog.rst:38: ERROR: Unknown interpreted text role "rm". /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/index.rst:128: CRITICAL: Title level inconsistent: Contribute ~~~~~~~~~~ WARNING: nbsphinx_widgets_path not given and ipywidgets module unavailable looking for now-outdated files... none found pickling environment... done checking consistency... /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Analysis_of_Viking_spectrometer_data.ipynb: WARNING: document isn't included in any toctree /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/Azimuthal integration of DSSC with pyFAI.ipynb: WARNING: document isn't included in any toctree /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/BOZ analysis part I.a Correction determination.ipynb: WARNING: document isn't included in any toctree /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/BOZ analysis part I.b Correction validation.ipynb: WARNING: document isn't included in any toctree /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/BOZ analysis part II.1 Small data.ipynb: WARNING: document isn't included in any toctree 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/usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/dssc/DSSCBinner.rst: WARNING: document isn't included in any toctree /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/load.rst: WARNING: document isn't included in any toctree done processing SCSToolbox.tex... index howtos maintainers changelog autoapi/index autoapi/toolbox_scs/index autoapi/toolbox_scs/base/index autoapi/toolbox_scs/base/tests/index autoapi/toolbox_scs/base/tests/test_knife_edge/index autoapi/toolbox_scs/base/knife_edge/index autoapi/toolbox_scs/detectors/index autoapi/toolbox_scs/detectors/azimuthal_integrator/index autoapi/toolbox_scs/detectors/bam_detectors/index autoapi/toolbox_scs/detectors/digitizers/index autoapi/toolbox_scs/detectors/dssc/index autoapi/toolbox_scs/detectors/dssc_data/index autoapi/toolbox_scs/detectors/dssc_misc/index autoapi/toolbox_scs/detectors/dssc_plot/index autoapi/toolbox_scs/detectors/dssc_processing/index autoapi/toolbox_scs/detectors/fccd/index autoapi/toolbox_scs/detectors/hrixs/index autoapi/toolbox_scs/detectors/pes/index autoapi/toolbox_scs/detectors/viking/index autoapi/toolbox_scs/detectors/xgm/index autoapi/toolbox_scs/misc/index autoapi/toolbox_scs/misc/bunch_pattern/index autoapi/toolbox_scs/misc/bunch_pattern_external/index autoapi/toolbox_scs/misc/laser_utils/index autoapi/toolbox_scs/misc/undulator/index autoapi/toolbox_scs/routines/index autoapi/toolbox_scs/routines/Reflectivity/index autoapi/toolbox_scs/routines/XAS/index autoapi/toolbox_scs/routines/boz/index autoapi/toolbox_scs/routines/knife_edge/index autoapi/toolbox_scs/test/index autoapi/toolbox_scs/test/test_dssc_cls/index autoapi/toolbox_scs/test/test_hrixs/index autoapi/toolbox_scs/test/test_misc/index autoapi/toolbox_scs/test/test_top_level/index autoapi/toolbox_scs/test/test_utils/index autoapi/toolbox_scs/util/index autoapi/toolbox_scs/util/exceptions/index autoapi/toolbox_scs/util/pkg/index autoapi/toolbox_scs/constants/index autoapi/toolbox_scs/load/index autoapi/toolbox_scs/mnemonics_machinery/index resolving references... done writing... done copying images... [ 50%] metadata.png copying images... [100%] sview.png copying TeX support files... copying TeX support files... done build succeeded, 153 warnings. The LaTeX files are in _build/latex. Run 'make' in that directory to run these through (pdf)latex (use `make latexpdf' here to do that automatically). [rtd-command-info] start-time: 2023-04-05T19:25:00.442665Z, end-time: 2023-04-05T19:25:00.513023Z, duration: 0, exit-code: 0 cat latexmkrc $latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S'; $makeindex = 'makeindex -s python.ist %O -o %D %S'; add_cus_dep( "glo", "gls", 0, "makeglo" ); sub makeglo { return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" ); } [rtd-command-info] start-time: 2023-04-05T19:25:00.596881Z, end-time: 2023-04-05T19:25:05.937952Z, duration: 5, exit-code: 0 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=scs-toolbox -interaction=nonstopmode Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 4, chunk 1. Subroutine makeglo redefined at (eval 11) line 7, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 4, chunk 1. Latexmk: This is Latexmk, John Collins, 1 January 2015, version: 4.41. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/bin/latexmk line 7482. Rule 'pdflatex': Rules & subrules not known to be previously run: pdflatex Rule 'pdflatex': The following rules & subrules became out-of-date: 'pdflatex' ------------ Run number 1 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="scs-toolbox" "SCSToolbox.tex"' ------------ Latexmk: applying rule 'pdflatex'... 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LaTeX Warning: Reference `autoapi/toolbox_scs/util/pkg/index:module-toolbox_scs .util.pkg' on page 159 undefined on input line 20983. [159] No file scs-toolbox.ind. Package longtable Warning: Table widths have changed. Rerun LaTeX. (./scs-toolbox.aux) Package rerunfilecheck Warning: File `scs-toolbox.out' has changed. (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/texmf/fonts/enc /dvips/tex-gyre/q-ec.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc}{ /usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc} Output written on scs-toolbox.pdf (163 pages, 675718 bytes). Transcript written on scs-toolbox.log. Latexmk: Index file 'scs-toolbox.idx' was written Latexmk: Missing input file: 'scs-toolbox.ind' from line 'No file scs-toolbox.ind.' 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AzimuthalIntegrator Underfull \hbox (badness 10000) in paragraph at lines 49--51 []\T1/txtt/m/n/10 _calc_indices() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool- Underfull \hbox (badness 10000) in paragraph at lines 49--51 \T1/qtm/m/it/10 box_scs.detectors.AzimuthalIntegrator Underfull \hbox (badness 10000) in paragraph at lines 51--53 []\T1/txtt/m/n/10 _calc_indices() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool- Overfull \hbox (49.47249pt too wide) in paragraph at lines 51--53 \T1/qtm/m/it/10 box_scs.detectors.azimuthal_integrator.AzimuthalIntegrator Underfull \hbox (badness 10000) in paragraph at lines 55--57 []\T1/txtt/m/n/10 _calc_polar_mask() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool- Underfull \hbox (badness 10000) in paragraph at lines 55--57 \T1/qtm/m/it/10 box_scs.detectors.AzimuthalIntegrator Underfull \hbox (badness 10000) in paragraph at lines 57--59 []\T1/txtt/m/n/10 _calc_polar_mask() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool- Overfull \hbox (49.47249pt too wide) in paragraph at lines 57--59 \T1/qtm/m/it/10 box_scs.detectors.azimuthal_integrator.AzimuthalIntegrator Underfull \hbox (badness 10000) in paragraph at lines 61--63 []\T1/txtt/m/n/10 _with_values() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule too l- Underfull \hbox (badness 10000) in paragraph at lines 66--68 []\T1/txtt/m/n/10 add_attributes() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool- Underfull \hbox (badness 10000) in paragraph at lines 66--68 \T1/qtm/m/it/10 box_scs.detectors.dssc.DSSCFormatter Underfull \hbox (badness 10000) in paragraph at lines 68--70 []\T1/txtt/m/n/10 add_attributes() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool- Underfull \hbox (badness 10000) in paragraph at lines 68--70 \T1/qtm/m/it/10 box_scs.detectors.DSSCFormatter method\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 70--71 []\T1/txtt/m/n/10 add_attributes() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs .DSSCFormatter Underfull \hbox (badness 10000) in paragraph at lines 73--74 []\T1/txtt/m/n/10 add_binner() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.det ectors.DSSCBinner Underfull \hbox (badness 10000) in paragraph at lines 75--77 []\T1/txtt/m/n/10 add_dataArray() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool- Underfull \hbox (badness 10000) in paragraph at lines 75--77 \T1/qtm/m/it/10 box_scs.detectors.dssc.DSSCFormatter [161] Underfull \hbox (badness 10000) in paragraph at lines 77--79 []\T1/txtt/m/n/10 add_dataArray() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool- Underfull \hbox (badness 10000) in paragraph at lines 77--79 \T1/qtm/m/it/10 box_scs.detectors.DSSCFormatter method\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 79--80 []\T1/txtt/m/n/10 add_dataArray() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs. DSSCFormatter Underfull \hbox (badness 10000) in paragraph at lines 81--82 []\T1/txtt/m/n/10 aggregate() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.dete ctors.hrixs.hRIXS Underfull \hbox (badness 5475) in paragraph at lines 83--84 []\T1/txtt/m/n/10 aggregator() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.det ectors.hRIXS method\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 84--85 []\T1/txtt/m/n/10 aggregator() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.det ectors.hrixs.hRIXS Underfull \hbox (badness 10000) in paragraph at lines 87--89 []\T1/txtt/m/n/10 aggregators \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.dete ctors.hrixs.hRIXS at- Underfull \hbox (badness 10000) in paragraph at lines 92--94 []\T1/txtt/m/n/10 align_ol_to_fel_pId() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod- ule tool- Underfull \hbox (badness 10000) in paragraph at lines 96--97 []\T1/txtt/m/n/10 average_module() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule t ool- Underfull \hbox (badness 10000) in paragraph at lines 101--103 []\T1/txtt/m/n/10 AzimuthalIntegrator \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in tool- Underfull \hbox (badness 10000) in paragraph at lines 101--103 \T1/qtm/m/it/10 box_scs.detectors.azimuthal_integrator\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 104--106 []\T1/txtt/m/n/10 AzimuthalIntegratorDSSC \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in tool- Underfull \hbox (badness 10000) in paragraph at lines 106--108 []\T1/txtt/m/n/10 AzimuthalIntegratorDSSC \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in tool- Underfull \hbox (badness 10000) in paragraph at lines 106--108 \T1/qtm/m/it/10 box_scs.detectors.azimuthal_integrator\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 114--115 []\T1/txtt/m/n/10 binning() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.detect ors.fccd.FastCCD Underfull \hbox (badness 5985) in paragraph at lines 118--119 []\T1/txtt/m/n/10 BL_POLY_DEG \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.dete ctors.Viking at-tribute\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 119--121 []\T1/txtt/m/n/10 BL_POLY_DEG \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.dete ctors.viking.Viking Underfull \hbox (badness 10000) in paragraph at lines 122--124 []\T1/txtt/m/n/10 BL_SIGNAL_RANGE \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs. detectors.Viking at- Underfull \hbox (badness 10000) in paragraph at lines 130--131 []\T1/txtt/m/n/10 calc_q() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.Azimuth alIntegrator method\T1/qtm/m/n/10 ), Overfull \hbox (71.93236pt too wide) in paragraph at lines 131--133 []\T1/txtt/m/n/10 calc_q() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.detecto rs.azimuthal_integrator.AzimuthalIntegrator Underfull \hbox (badness 10000) in paragraph at lines 133--135 []\T1/txtt/m/n/10 calc_q() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.detecto rs.AzimuthalIntegrator Underfull \hbox (badness 10000) in paragraph at lines 136--138 []\T1/txtt/m/n/10 calibrate() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.dete ctors.viking.Viking Underfull \hbox (badness 10000) in paragraph at lines 141--142 []\T1/txtt/m/n/10 calibrate_xgm() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule to ol- Underfull \hbox (badness 10000) in paragraph at lines 143--144 []\T1/txtt/m/n/10 centroid() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.detec tors.hrixs.hRIXS Underfull \hbox (badness 10000) in paragraph at lines 146--148 []\T1/txtt/m/n/10 centroid_one() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.d etectors.hrixs.hRIXS Underfull \hbox (badness 10000) in paragraph at lines 150--152 []\T1/txtt/m/n/10 centroid_two() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.d etectors.hrixs.hRIXS Underfull \hbox (badness 10000) in paragraph at lines 154--155 []\T1/txtt/m/n/10 check_peak_params() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ul e tool- Underfull \hbox (badness 10000) in paragraph at lines 155--157 []\T1/txtt/m/n/10 check_peak_params() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ul e tool- Underfull \hbox (badness 10000) in paragraph at lines 157--159 []\T1/txtt/m/n/10 cleanup_tmp_dir() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule tool- Underfull \hbox (badness 10000) in paragraph at lines 159--161 []\T1/txtt/m/n/10 collect_fastccd_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool- Underfull \hbox (badness 10000) in paragraph at lines 159--161 \T1/qtm/m/it/10 box_scs.detectors.fccd.FastCCD method\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 161--163 []\T1/txtt/m/n/10 combine_files() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool- Underfull \hbox (badness 10000) in paragraph at lines 161--163 \T1/qtm/m/it/10 box_scs.detectors.dssc.DSSCFormatter Underfull \hbox (badness 10000) in paragraph at lines 163--165 []\T1/txtt/m/n/10 combine_files() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool- Underfull \hbox (badness 10000) in paragraph at lines 163--165 \T1/qtm/m/it/10 box_scs.detectors.DSSCFormatter method\T1/qtm/m/n/10 ), [162] Underfull \hbox (badness 10000) in 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cs.DSSCBinner Underfull \hbox (badness 10000) in paragraph at lines 188--190 []\T1/txtt/m/n/10 dask_load_persistently() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool - Underfull \hbox (badness 10000) in paragraph at lines 188--190 \T1/qtm/m/it/10 box_scs.routines.boz.parameters method\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 190--192 []\T1/txtt/m/n/10 dask_load_persistently() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool - Underfull \hbox (badness 10000) in paragraph at lines 196--198 []\T1/txtt/m/n/10 define_scan() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.de tectors.fccd.FastCCD Underfull \hbox (badness 10000) in paragraph at lines 200--202 []\T1/txtt/m/n/10 degToRelPower() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule to ol- Underfull \hbox (badness 10000) in paragraph at lines 204--206 []\T1/txtt/m/n/10 delayToPosition() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule tool- Underfull \hbox (badness 10000) in paragraph at lines 222--224 []\T1/txtt/m/n/10 e_per_counts() 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cs.parameters Underfull \hbox (badness 10000) in paragraph at lines 264--266 []\T1/txtt/m/n/10 flat_field_guess() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool- Underfull \hbox (badness 10000) in paragraph at lines 264--266 \T1/qtm/m/it/10 box_scs.routines.boz.parameters method\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 270--272 []\T1/txtt/m/n/10 fluenceCalibration() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u le tool- Underfull \hbox (badness 10000) in paragraph at lines 273--274 []\T1/txtt/m/n/10 from_run() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.detec tors.hrixs.hRIXS Underfull \hbox (badness 10000) in paragraph at lines 275--277 []\T1/txtt/m/n/10 from_run() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.detec tors.viking.Viking Underfull \hbox (badness 10000) in paragraph at lines 286--288 []\T1/txtt/m/n/10 get_bam() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule tool- Underfull \hbox (badness 10000) in paragraph at lines 290--292 []\T1/txtt/m/n/10 get_bam_params() 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[]\T1/txtt/m/n/10 get_camera_params() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_ scs.Viking method\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 303--305 []\T1/txtt/m/n/10 get_data_formatted() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u le tool- Underfull \hbox (badness 10000) in paragraph at lines 305--307 []\T1/txtt/m/n/10 get_data_formatted() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u le tool- Underfull \hbox (badness 10000) in paragraph at lines 308--310 []\T1/txtt/m/n/10 get_dig_avg_trace() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ul e tool- Underfull \hbox (badness 10000) in paragraph at lines 310--312 []\T1/txtt/m/n/10 get_dig_avg_trace() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ul e tool- Underfull \hbox (badness 10000) in paragraph at lines 313--315 []\T1/txtt/m/n/10 get_digitizer_peaks() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod- ule tool- Underfull \hbox (badness 10000) in paragraph at lines 315--317 []\T1/txtt/m/n/10 get_digitizer_peaks() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod- ule tool- Underfull \hbox (badness 10000) in paragraph at lines 318--320 []\T1/txtt/m/n/10 get_flat_field() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool- Underfull \hbox (badness 10000) in paragraph at lines 318--320 \T1/qtm/m/it/10 box_scs.routines.boz.parameters method\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 320--322 []\T1/txtt/m/n/10 get_flat_field() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs .routines.parameters Underfull \hbox (badness 10000) in paragraph at lines 323--324 []\T1/txtt/m/n/10 get_Fnl() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.routin es.boz.parameters Underfull \hbox (badness 5519) in paragraph at lines 324--325 []\T1/txtt/m/n/10 get_Fnl() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.routin es.parameters method\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 325--327 []\T1/txtt/m/n/10 get_info() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.detec tors.dssc.DSSCBinner Underfull \hbox (badness 10000) in paragraph at lines 327--328 []\T1/txtt/m/n/10 get_info() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.detec tors.DSSCBinner Underfull \hbox (badness 10000) in paragraph at lines 331--333 []\T1/txtt/m/n/10 get_laser_peaks() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule tool- Underfull \hbox (badness 10000) in paragraph at lines 334--336 []\T1/txtt/m/n/10 get_mask() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.routi nes.boz.parameters Underfull \hbox (badness 6220) in paragraph at lines 338--340 []\T1/txtt/m/n/10 get_mask_idx() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.r outines.boz.parameters Underfull \hbox (badness 10000) in paragraph at lines 340--342 []\T1/txtt/m/n/10 get_mask_idx() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.r outines.parameters Underfull \hbox (badness 5475) in paragraph at lines 342--343 []\T1/txtt/m/n/10 get_params() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.det ectors.hRIXS method\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 343--345 []\T1/txtt/m/n/10 get_params() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.det ectors.hrixs.hRIXS Underfull \hbox (badness 10000) in paragraph at lines 346--348 []\T1/txtt/m/n/10 get_params() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.det ectors.viking.Viking [164] Underfull \hbox (badness 10000) in paragraph at lines 352--354 []\T1/txtt/m/n/10 get_peaks() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule tool- Underfull \hbox (badness 10000) in paragraph at lines 356--358 []\T1/txtt/m/n/10 get_pes_params() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule t ool- Underfull \hbox (badness 10000) in paragraph at lines 362--363 []\T1/txtt/m/n/10 get_roi_pixel_pos() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ul e tool- Underfull \hbox (badness 10000) in paragraph at lines 363--365 []\T1/txtt/m/n/10 get_roi_pixel_pos() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ul e tool- Underfull \hbox (badness 10000) in paragraph at lines 367--369 []\T1/txtt/m/n/10 get_sase_pId() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule too l- Underfull \hbox (badness 10000) in paragraph at lines 369--371 []\T1/txtt/m/n/10 get_tim_binned() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool- Underfull \hbox (badness 10000) in paragraph at lines 369--371 \T1/qtm/m/it/10 box_scs.detectors.dssc.DSSCBinner method\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 376--378 []\T1/txtt/m/n/10 get_tim_peaks() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule to ol- Underfull \hbox (badness 10000) in paragraph at lines 379--380 []\T1/txtt/m/n/10 get_undulator_config() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod -ule tool- Underfull \hbox (badness 10000) in paragraph at lines 380--382 []\T1/txtt/m/n/10 get_undulator_config() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod -ule tool- Underfull \hbox (badness 10000) in paragraph at lines 386--388 []\T1/txtt/m/n/10 get_xgm_binned() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool- Underfull \hbox (badness 10000) in paragraph at lines 386--388 \T1/qtm/m/it/10 box_scs.detectors.dssc.DSSCBinner method\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 392--393 []\T1/txtt/m/n/10 get_xgm_formatted() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ul e tool- Underfull \hbox (badness 10000) in paragraph at lines 393--395 []\T1/txtt/m/n/10 get_xgm_formatted() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ul e tool- Underfull \hbox (badness 10000) in paragraph at lines 400--402 []\T1/txtt/m/n/10 histogram_module() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule tool- Underfull \hbox (badness 10000) in paragraph at lines 409--410 []\T1/txtt/m/n/10 inspect_correction() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u le tool- Underfull \hbox (badness 10000) in paragraph at lines 410--412 []\T1/txtt/m/n/10 inspect_correction() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u le tool- Underfull \hbox (badness 10000) in paragraph at lines 415--416 []\T1/txtt/m/n/10 inspect_flat_field_domain() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 i n mod-ule tool- Underfull \hbox (badness 10000) in paragraph at lines 416--418 []\T1/txtt/m/n/10 inspect_flat_field_domain() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 i n mod-ule tool- Underfull \hbox (badness 10000) in paragraph at lines 418--420 []\T1/txtt/m/n/10 inspect_flat_field_domain() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 i n mod-ule tool- Underfull \hbox (badness 10000) in paragraph at lines 424--425 []\T1/txtt/m/n/10 inspect_histogram() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ul e tool- Underfull \hbox (badness 10000) in paragraph at lines 425--427 []\T1/txtt/m/n/10 inspect_histogram() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ul e tool- Underfull \hbox (badness 10000) in paragraph at lines 429--430 []\T1/txtt/m/n/10 inspect_nl_fit() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule t ool- Underfull \hbox (badness 10000) in paragraph at lines 431--433 []\T1/txtt/m/n/10 inspect_plane_fitting() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mo d-ule tool- Underfull \hbox (badness 10000) in paragraph at lines 433--435 []\T1/txtt/m/n/10 inspect_plane_fitting() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mo d-ule tool- Underfull \hbox (badness 10000) in paragraph at lines 439--440 []\T1/txtt/m/n/10 inspect_saturation() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u le tool- [165] Underfull \hbox (badness 10000) in paragraph at lines 440--442 []\T1/txtt/m/n/10 inspect_saturation() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u le tool- Underfull \hbox (badness 10000) in paragraph at lines 443--444 []\T1/txtt/m/n/10 integrate() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.dete ctors.hrixs.hRIXS Underfull \hbox (badness 10000) in paragraph at lines 445--447 []\T1/txtt/m/n/10 integrate() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.dete ctors.viking.Viking Underfull \hbox (badness 10000) in paragraph at lines 451--453 []\T1/txtt/m/n/10 is_ppl() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule tool- Underfull \hbox (badness 10000) in paragraph at lines 455--457 []\T1/txtt/m/n/10 is_pulse_at() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule tool - 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tool-box_scs.routines. boz.parameters class Underfull \hbox (badness 10000) in paragraph at lines 493--495 []\T1/txtt/m/n/10 load_binned() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.de tectors.fccd.FastCCD Underfull \hbox (badness 10000) in paragraph at lines 496--497 []\T1/txtt/m/n/10 load_dark() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.dete ctors.hrixs.hRIXS Underfull \hbox (badness 10000) in paragraph at lines 498--500 []\T1/txtt/m/n/10 load_dark() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.dete ctors.viking.Viking Underfull \hbox (badness 10000) in paragraph at lines 504--506 []\T1/txtt/m/n/10 load_dssc_info() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule t ool- Underfull \hbox (badness 10000) in paragraph at lines 508--510 []\T1/txtt/m/n/10 load_dssc_module() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule tool- Underfull \hbox (badness 10000) in paragraph at lines 510--512 []\T1/txtt/m/n/10 load_gain() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.dete ctors.fccd.FastCCD Underfull \hbox (badness 10000) in paragraph at lines 514--516 []\T1/txtt/m/n/10 load_mask() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule tool- Underfull \hbox (badness 10000) in paragraph at lines 516--518 []\T1/txtt/m/n/10 load_mask() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.dete ctors.fccd.FastCCD Underfull \hbox (badness 10000) in paragraph at lines 520--522 []\T1/txtt/m/n/10 load_tim() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.detec tors.dssc.DSSCBinner Underfull \hbox (badness 10000) in paragraph at lines 522--523 []\T1/txtt/m/n/10 load_tim() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.detec tors.DSSCBinner Underfull \hbox (badness 10000) in paragraph at lines 526--528 []\T1/txtt/m/n/10 load_xarray() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule tool - Underfull \hbox (badness 10000) in paragraph at lines 528--530 []\T1/txtt/m/n/10 load_xgm() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.detec tors.dssc.DSSCBinner Underfull \hbox (badness 10000) in paragraph at lines 530--531 []\T1/txtt/m/n/10 load_xgm() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.detec tors.DSSCBinner [166] Underfull \hbox (badness 10000) in paragraph at lines 544--546 []\T1/txtt/m/n/10 mnemonics_for_run() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ul e tool- Underfull \hbox (badness 10000) in paragraph at lines 551--552 []| \T1/txtt/m/n/10 toolbox_scs.base.tests.test_knife_edge\T1/qtm/m/n/10 , Overfull \hbox (13.12186pt too wide) in paragraph at lines 554--555 []| \T1/txtt/m/n/10 toolbox_scs.detectors.azimuthal_integrator\T1/qtm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 570--571 []| \T1/txtt/m/n/10 toolbox_scs.misc.bunch_pattern_external\T1/qtm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 604--605 []\T1/txtt/m/n/10 normalize() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.dete ctors.hrixs.hRIXS Underfull \hbox (badness 10000) in paragraph at lines 608--610 []\T1/txtt/m/n/10 npulses_has_changed() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod- ule tool- Underfull 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\T1/qtm/m/n/10 (\T1/qtm/m/it/10 too l- Underfull \hbox (badness 10000) in paragraph at lines 639--641 \T1/qtm/m/it/10 box_scs.detectors.fccd.FastCCD method\T1/qtm/m/n/10 ), [167] Underfull \hbox (badness 10000) in paragraph at lines 641--643 []\T1/txtt/m/n/10 plot_binner() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule tool - Underfull \hbox (badness 10000) in paragraph at lines 643--645 []\T1/txtt/m/n/10 plot_binner_hist() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule tool- Underfull \hbox (badness 10000) in paragraph at lines 645--647 []\T1/txtt/m/n/10 plot_FastCCD() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.d etectors.fccd.FastCCD Underfull \hbox (badness 10000) in paragraph at lines 647--649 []\T1/txtt/m/n/10 plot_hist_processed() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod- ule tool- Underfull \hbox (badness 10000) in paragraph at lines 649--651 []\T1/txtt/m/n/10 plot_scan() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.dete ctors.fccd.FastCCD Underfull \hbox (badness 10000) in paragraph at lines 653--655 []\T1/txtt/m/n/10 plot_xgm_threshold() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u le tool- Underfull \hbox (badness 10000) in paragraph at lines 657--659 []\T1/txtt/m/n/10 positionToDelay() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule tool- Underfull \hbox (badness 10000) in paragraph at lines 662--664 []\T1/txtt/m/n/10 process_data() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool- Underfull \hbox (badness 10000) in paragraph at lines 662--664 \T1/qtm/m/it/10 box_scs.detectors.dssc.DSSCBinner method\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 664--666 []\T1/txtt/m/n/10 process_data() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.d etectors.DSSCBinner Underfull \hbox (badness 10000) in paragraph at lines 666--667 []\T1/txtt/m/n/10 process_data() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.D SSCBinner method\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 668--669 []\T1/txtt/m/n/10 process_dssc_data() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ul e tool- Underfull \hbox (badness 10000) in paragraph at lines 669--671 []\T1/txtt/m/n/10 process_dssc_data() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ul e tool- Underfull \hbox (badness 10000) in paragraph at lines 673--674 []\T1/txtt/m/n/10 process_module() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule t ool- Underfull \hbox (badness 10000) in paragraph at lines 674--676 []\T1/txtt/m/n/10 process_one_module() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u le tool- Underfull \hbox (badness 10000) in paragraph at lines 686--688 []\T1/txtt/m/n/10 pulsePatternInfo() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule tool- Underfull \hbox (badness 10000) in paragraph at lines 692--694 []\T1/txtt/m/n/10 quickmask_DSSC_ASIC() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod- ule tool- Underfull \hbox (badness 10000) in paragraph at lines 694--696 []\T1/txtt/m/n/10 quickmask_DSSC_ASIC() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod- ule tool- Underfull \hbox (badness 10000) in paragraph at lines 701--703 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(rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information){/usr/share/texmf/fonts/enc /dvips/tex-gyre/q-ec.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc}{ /usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc} Output written on scs-toolbox.pdf (175 pages, 753151 bytes). Transcript written on scs-toolbox.log. Latexmk: Index file 'scs-toolbox.idx' was written Latexmk: References changed. Latexmk: Log file says output to 'scs-toolbox.pdf' Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'scs-toolbox.aux' 'scs-toolbox.out' 'scs-toolbox.toc' ------------ Run number 3 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="scs-toolbox" "SCSToolbox.tex"' ------------ Latexmk: applying rule 'pdflatex'... 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[]|[][]\T1/txtt/m/sl/10 get_xgm_formatted[][]\T1/qtm/m/n/10 (run_obj, xgm_name, [29] [30] Underfull \hbox (badness 5817) in paragraph at lines 3361--3361 []|[][]\T1/txtt/m/sl/10 plot_xgm_threshold[][]\T1/qtm/m/n/10 (xgm[, xgm_min, xg m_max, Underfull \hbox (badness 5817) in paragraph at lines 3361--3361 []|[][]\T1/txtt/m/sl/10 plot_xgm_threshold[][]\T1/qtm/m/n/10 (xgm[, xgm_min, xg m_max, [31] Underfull \hbox (badness 10000) in paragraph at lines 3433--3433 []|[][]\T1/txtt/m/sl/10 process_dssc_data[][]\T1/qtm/m/n/10 (proposal, run_nr, mod-ule, Underfull \hbox (badness 10000) in paragraph at lines 3433--3433 []|[][]\T1/txtt/m/sl/10 process_dssc_data[][]\T1/qtm/m/n/10 (proposal, run_nr, mod-ule, [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] Underfull \hbox (badness 10000) in paragraph at lines 5461--5461 []|[][]\T1/txtt/m/sl/10 check_peak_params[][]\T1/qtm/m/n/10 (run, mnemonic[, ra w_trace, Underfull \hbox (badness 10000) in paragraph at lines 5461--5461 []|[][]\T1/txtt/m/sl/10 get_digitizer_peaks[][]\T1/qtm/m/n/10 (run[, mnemon-ics , Underfull \hbox (badness 10000) in paragraph at lines 5461--5461 []|[][]\T1/txtt/m/sl/10 get_xgm_formatted[][]\T1/qtm/m/n/10 (run_obj, xgm_name, Underfull \hbox (badness 10000) in paragraph at lines 5461--5461 []|[][]\T1/txtt/m/sl/10 process_dssc_data[][]\T1/qtm/m/n/10 (proposal, run_nr, mod-ule, Underfull \hbox (badness 10000) in paragraph at lines 5461--5461 []|[][]\T1/txtt/m/sl/10 check_peak_params[][]\T1/qtm/m/n/10 (run, mnemonic[, ra w_trace, Underfull \hbox (badness 10000) in paragraph at lines 5461--5461 []|[][]\T1/txtt/m/sl/10 get_digitizer_peaks[][]\T1/qtm/m/n/10 (run[, mnemon-ics , Underfull \hbox (badness 10000) in paragraph at lines 5461--5461 []|[][]\T1/txtt/m/sl/10 get_xgm_formatted[][]\T1/qtm/m/n/10 (run_obj, xgm_name, Underfull \hbox (badness 10000) in paragraph at lines 5461--5461 []|[][]\T1/txtt/m/sl/10 process_dssc_data[][]\T1/qtm/m/n/10 (proposal, run_nr, mod-ule, [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] [57] [58] [59] [60] [61] [62] [63] [64] [65] Underfull \hbox (badness 10000) in paragraph at lines 8136--8136 []|[][]\T1/txtt/m/sl/10 get_sase_pId[][]\T1/qtm/m/n/10 (run[, loc, run_mnemonic s, bpt, Underfull \hbox (badness 10000) in paragraph at lines 8136--8136 []|[][]\T1/txtt/m/sl/10 get_sase_pId[][]\T1/qtm/m/n/10 (run[, loc, run_mnemonic s, bpt, [66] [67] [68] Underfull \hbox (badness 10000) in paragraph at lines 8559--8559 []|[][]\T1/txtt/m/sl/10 fluenceCalibration[][]\T1/qtm/m/n/10 (hwp, power_mW, np ulses, Underfull \hbox (badness 10000) in paragraph at lines 8559--8559 []|[][]\T1/txtt/m/sl/10 fluenceCalibration[][]\T1/qtm/m/n/10 (hwp, power_mW, np ulses, [69] [70] Underfull \hbox (badness 10000) in paragraph at lines 8970--8970 []|[][]\T1/txtt/m/sl/10 get_sase_pId[][]\T1/qtm/m/n/10 (run[, loc, run_mnemonic s, bpt, Underfull \hbox (badness 10000) in paragraph at lines 8970--8970 []|[][]\T1/txtt/m/sl/10 fluenceCalibration[][]\T1/qtm/m/n/10 (hwp, power_mW, np ulses, Underfull \hbox (badness 10000) in paragraph at lines 8970--8970 []|[][]\T1/txtt/m/sl/10 get_sase_pId[][]\T1/qtm/m/n/10 (run[, loc, run_mnemonic s, bpt, Underfull \hbox (badness 10000) in paragraph at lines 8970--8970 []|[][]\T1/txtt/m/sl/10 fluenceCalibration[][]\T1/qtm/m/n/10 (hwp, power_mW, np ulses, [71] [72] [73] [74] [75] [76] [77] [78] Underfull \hbox (badness 10000) in paragraph at lines 10081--10081 []|[][]\T1/txtt/m/sl/10 inspect_histogram[][]\T1/qtm/m/n/10 (arr[, arr_dark, ma sk, ex- Underfull \hbox (badness 10000) in paragraph at lines 10081--10081 []|[][]\T1/txtt/m/sl/10 compute_flat_field_correction[][]\T1/qtm/m/n/10 (rois, params[, Underfull \hbox (badness 7362) in paragraph at lines 10081--10081 []|[][]\T1/txtt/m/sl/10 process[][]\T1/qtm/m/n/10 (Fmodel, arr_dark, arr, tid, rois, mask, Underfull \hbox (badness 10000) in paragraph at lines 10081--10081 []|[][]\T1/txtt/m/sl/10 inspect_histogram[][]\T1/qtm/m/n/10 (arr[, arr_dark, ma sk, ex- Underfull \hbox (badness 10000) in paragraph at lines 10081--10081 []|[][]\T1/txtt/m/sl/10 compute_flat_field_correction[][]\T1/qtm/m/n/10 (rois, params[, Underfull \hbox (badness 7362) in paragraph at lines 10081--10081 []|[][]\T1/txtt/m/sl/10 process[][]\T1/qtm/m/n/10 (Fmodel, arr_dark, arr, tid, rois, mask, [79] [80] [81] [82] [83] [84] [85] [86] [87] [88] [89] [90] Underfull \hbox (badness 10000) in paragraph at lines 11444--11446 []|[][]\T1/txtt/m/sl/10 inspect_histogram[][]\T1/qtm/m/n/10 (arr[, arr_dark, ma sk, ex- Underfull \hbox (badness 10000) in paragraph at lines 11472--11474 []|[][]\T1/txtt/m/sl/10 compute_flat_field_correction[][]\T1/qtm/m/n/10 (rois, params[, Underfull \hbox (badness 7362) in paragraph at lines 11598--11600 []|[][]\T1/txtt/m/sl/10 process[][]\T1/qtm/m/n/10 (Fmodel, arr_dark, arr, tid, rois, mask, [91] [92] [93] [94] [95] [96] [97] [98] [99] [100] [101] [102] [103] [104] [105] [106] [107] [108] [109] [110] [111] [112] Underfull \hbox (badness 5970) in paragraph at lines 14773--14776 []\T1/txtt/bx/n/10 extract_bam \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 bool\T1/qtm/m/n /10 ) ^^U If True, ex-tracts the val-ues from BAM vari-ables (e.g. [113] [114] [115] [116] Underfull \hbox (badness 10000) in paragraph at lines 15297--15299 []|[][]\T1/txtt/m/sl/10 check_peak_params[][]\T1/qtm/m/n/10 (run, mnemonic[, ra w_trace, Underfull \hbox (badness 10000) in paragraph at lines 15304--15306 []|[][]\T1/txtt/m/sl/10 get_digitizer_peaks[][]\T1/qtm/m/n/10 (run[, mnemon-ics , Underfull \hbox (badness 10000) in paragraph at lines 15381--15383 []|[][]\T1/txtt/m/sl/10 get_xgm_formatted[][]\T1/qtm/m/n/10 (run_obj, xgm_name, Underfull \hbox (badness 10000) in paragraph at lines 15409--15411 []|[][]\T1/txtt/m/sl/10 process_dssc_data[][]\T1/qtm/m/n/10 (proposal, run_nr, mod-ule, Underfull \hbox (badness 10000) in paragraph at lines 15500--15502 []|[][]\T1/txtt/m/sl/10 get_sase_pId[][]\T1/qtm/m/n/10 (run[, loc, run_mnemonic s, bpt, [117] Underfull \hbox (badness 10000) in paragraph at lines 15577--15579 []|[][]\T1/txtt/m/sl/10 fluenceCalibration[][]\T1/qtm/m/n/10 (hwp, power_mW, np ulses, Underfull \hbox (badness 10000) in paragraph at lines 15647--15649 []|[][]\T1/txtt/m/sl/10 inspect_histogram[][]\T1/qtm/m/n/10 (arr[, arr_dark, ma sk, ex- Underfull \hbox (badness 10000) in paragraph at lines 15675--15677 []|[][]\T1/txtt/m/sl/10 compute_flat_field_correction[][]\T1/qtm/m/n/10 (rois, params[, [118] Underfull \hbox (badness 7362) in paragraph at lines 15801--15803 []|[][]\T1/txtt/m/sl/10 process[][]\T1/qtm/m/n/10 (Fmodel, arr_dark, arr, tid, rois, mask, [119] [120] [121] [122] [123] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133] [134] [135] [136] [137] [138] [139] [140] Underfull \hbox (badness 5970) in paragraph at lines 18705--18708 []\T1/txtt/bx/n/10 extract_bam \T1/qtm/m/n/10 (\T1/txtt/m/sl/10 bool\T1/qtm/m/n /10 ) ^^U If True, ex-tracts the val-ues from BAM vari-ables (e.g. [141] [142] [143] [144] [145] [146] [147] [148] [149] [150] [151] [152] [153] [154] [155] [156] [157] [158] Underfull \hbox (badness 10000) in paragraph at lines 20950--20951 []\T1/txtt/m/n/10 toolbox_scs.detectors.azimuthal_integrator\T1/qtm/m/n/10 , [159] (./scs-toolbox.ind [160] Overfull \hbox (82.43233pt too wide) in paragraph at lines 18--20 []\T1/txtt/m/n/10 __call__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.detec tors.azimuthal_integrator.AzimuthalIntegrator Underfull \hbox (badness 10000) in paragraph at lines 22--24 []\T1/txtt/m/n/10 __del__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.detect ors.dssc.DSSCBinner Underfull \hbox (badness 10000) in paragraph at lines 24--26 []\T1/txtt/m/n/10 __del__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.detect ors.fccd.FastCCD Underfull \hbox (badness 10000) in paragraph at lines 27--29 []\T1/txtt/m/n/10 __str__() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.routin es.boz.parameters Underfull \hbox (badness 5519) in paragraph at lines 29--30 []\T1/txtt/m/n/10 __str__() 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tool-box_scs. 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DSSCFormatter Underfull \hbox (badness 10000) in paragraph at lines 81--82 []\T1/txtt/m/n/10 aggregate() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.dete ctors.hrixs.hRIXS Underfull \hbox (badness 5475) in paragraph at lines 83--84 []\T1/txtt/m/n/10 aggregator() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.det ectors.hRIXS method\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 84--85 []\T1/txtt/m/n/10 aggregator() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.det ectors.hrixs.hRIXS Underfull \hbox (badness 10000) in paragraph at lines 87--89 []\T1/txtt/m/n/10 aggregators \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.dete ctors.hrixs.hRIXS at- Underfull \hbox (badness 10000) in paragraph at lines 92--94 []\T1/txtt/m/n/10 align_ol_to_fel_pId() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod- ule tool- Underfull \hbox (badness 10000) in paragraph at lines 96--97 []\T1/txtt/m/n/10 average_module() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule t ool- Underfull \hbox (badness 10000) in paragraph at lines 101--103 []\T1/txtt/m/n/10 AzimuthalIntegrator \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in tool- Underfull \hbox (badness 10000) in paragraph at lines 101--103 \T1/qtm/m/it/10 box_scs.detectors.azimuthal_integrator\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 104--106 []\T1/txtt/m/n/10 AzimuthalIntegratorDSSC \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in tool- Underfull \hbox (badness 10000) in paragraph at lines 106--108 []\T1/txtt/m/n/10 AzimuthalIntegratorDSSC \T1/qtm/m/n/10 (\T1/qtm/m/it/10 class in tool- Underfull \hbox (badness 10000) in paragraph at lines 106--108 \T1/qtm/m/it/10 box_scs.detectors.azimuthal_integrator\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 114--115 []\T1/txtt/m/n/10 binning() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.detect ors.fccd.FastCCD Underfull \hbox (badness 5985) in paragraph at lines 118--119 []\T1/txtt/m/n/10 BL_POLY_DEG \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.dete ctors.Viking at-tribute\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 119--121 []\T1/txtt/m/n/10 BL_POLY_DEG \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.dete ctors.viking.Viking Underfull \hbox (badness 10000) in paragraph at lines 122--124 []\T1/txtt/m/n/10 BL_SIGNAL_RANGE \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs. detectors.Viking at- Underfull \hbox (badness 10000) in paragraph at lines 130--131 []\T1/txtt/m/n/10 calc_q() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.Azimuth alIntegrator method\T1/qtm/m/n/10 ), Overfull \hbox (71.93236pt too wide) in paragraph at lines 131--133 []\T1/txtt/m/n/10 calc_q() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.detecto rs.azimuthal_integrator.AzimuthalIntegrator Underfull \hbox (badness 10000) in paragraph at lines 133--135 []\T1/txtt/m/n/10 calc_q() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.detecto rs.AzimuthalIntegrator Underfull \hbox (badness 10000) in paragraph at lines 136--138 []\T1/txtt/m/n/10 calibrate() 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tool- Underfull \hbox (badness 10000) in paragraph at lines 157--159 []\T1/txtt/m/n/10 cleanup_tmp_dir() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule tool- Underfull \hbox (badness 10000) in paragraph at lines 159--161 []\T1/txtt/m/n/10 collect_fastccd_file() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool- Underfull \hbox (badness 10000) in paragraph at lines 159--161 \T1/qtm/m/it/10 box_scs.detectors.fccd.FastCCD method\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 161--163 []\T1/txtt/m/n/10 combine_files() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool- Underfull \hbox (badness 10000) in paragraph at lines 161--163 \T1/qtm/m/it/10 box_scs.detectors.dssc.DSSCFormatter Underfull \hbox (badness 10000) in paragraph at lines 163--165 []\T1/txtt/m/n/10 combine_files() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool- Underfull \hbox (badness 10000) in paragraph at lines 163--165 \T1/qtm/m/it/10 box_scs.detectors.DSSCFormatter method\T1/qtm/m/n/10 ), [162] Underfull \hbox (badness 10000) in 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DSSCFormatter Underfull \hbox (badness 10000) in paragraph at lines 175--176 []\T1/txtt/m/n/10 create_dssc_bins() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule tool- Underfull \hbox (badness 10000) in paragraph at lines 176--178 []\T1/txtt/m/n/10 create_dssc_bins() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule tool- Underfull \hbox (badness 10000) in paragraph at lines 178--180 []\T1/txtt/m/n/10 create_pulsemask() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool- Underfull \hbox (badness 10000) in paragraph at lines 178--180 \T1/qtm/m/it/10 box_scs.detectors.dssc.DSSCBinner method\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 180--182 []\T1/txtt/m/n/10 create_pulsemask() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool- Underfull \hbox (badness 10000) in paragraph at lines 180--182 \T1/qtm/m/it/10 box_scs.detectors.DSSCBinner method\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 182--183 []\T1/txtt/m/n/10 create_pulsemask() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_s cs.DSSCBinner Underfull \hbox (badness 10000) in paragraph at lines 188--190 []\T1/txtt/m/n/10 dask_load_persistently() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool - Underfull \hbox (badness 10000) in paragraph at lines 188--190 \T1/qtm/m/it/10 box_scs.routines.boz.parameters method\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 190--192 []\T1/txtt/m/n/10 dask_load_persistently() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool - Underfull \hbox (badness 10000) in paragraph at lines 196--198 []\T1/txtt/m/n/10 define_scan() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.de tectors.fccd.FastCCD Underfull \hbox (badness 10000) in paragraph at lines 200--202 []\T1/txtt/m/n/10 degToRelPower() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule to ol- Underfull \hbox (badness 10000) in paragraph at lines 204--206 []\T1/txtt/m/n/10 delayToPosition() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule tool- Underfull \hbox (badness 10000) in paragraph at lines 222--224 []\T1/txtt/m/n/10 e_per_counts() 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cs.parameters Underfull \hbox (badness 10000) in paragraph at lines 264--266 []\T1/txtt/m/n/10 flat_field_guess() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool- Underfull \hbox (badness 10000) in paragraph at lines 264--266 \T1/qtm/m/it/10 box_scs.routines.boz.parameters method\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 270--272 []\T1/txtt/m/n/10 fluenceCalibration() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u le tool- Underfull \hbox (badness 10000) in paragraph at lines 273--274 []\T1/txtt/m/n/10 from_run() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.detec tors.hrixs.hRIXS Underfull \hbox (badness 10000) in paragraph at lines 275--277 []\T1/txtt/m/n/10 from_run() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.detec tors.viking.Viking Underfull \hbox (badness 10000) in paragraph at lines 286--288 []\T1/txtt/m/n/10 get_bam() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule tool- Underfull \hbox (badness 10000) in paragraph at lines 290--292 []\T1/txtt/m/n/10 get_bam_params() 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[]\T1/txtt/m/n/10 get_camera_params() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_ scs.Viking method\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 303--305 []\T1/txtt/m/n/10 get_data_formatted() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u le tool- Underfull \hbox (badness 10000) in paragraph at lines 305--307 []\T1/txtt/m/n/10 get_data_formatted() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u le tool- Underfull \hbox (badness 10000) in paragraph at lines 308--310 []\T1/txtt/m/n/10 get_dig_avg_trace() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ul e tool- Underfull \hbox (badness 10000) in paragraph at lines 310--312 []\T1/txtt/m/n/10 get_dig_avg_trace() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ul e tool- Underfull \hbox (badness 10000) in paragraph at lines 313--315 []\T1/txtt/m/n/10 get_digitizer_peaks() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod- ule tool- Underfull \hbox (badness 10000) in paragraph at lines 315--317 []\T1/txtt/m/n/10 get_digitizer_peaks() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod- ule tool- Underfull \hbox (badness 10000) in paragraph at lines 318--320 []\T1/txtt/m/n/10 get_flat_field() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool- Underfull \hbox (badness 10000) in paragraph at lines 318--320 \T1/qtm/m/it/10 box_scs.routines.boz.parameters method\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 320--322 []\T1/txtt/m/n/10 get_flat_field() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs .routines.parameters Underfull \hbox (badness 10000) in paragraph at lines 323--324 []\T1/txtt/m/n/10 get_Fnl() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.routin es.boz.parameters Underfull \hbox (badness 5519) in paragraph at lines 324--325 []\T1/txtt/m/n/10 get_Fnl() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.routin es.parameters method\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 325--327 []\T1/txtt/m/n/10 get_info() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.detec tors.dssc.DSSCBinner Underfull \hbox (badness 10000) in paragraph at lines 327--328 []\T1/txtt/m/n/10 get_info() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.detec tors.DSSCBinner Underfull \hbox (badness 10000) in paragraph at lines 331--333 []\T1/txtt/m/n/10 get_laser_peaks() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule tool- Underfull \hbox (badness 10000) in paragraph at lines 334--336 []\T1/txtt/m/n/10 get_mask() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.routi nes.boz.parameters Underfull \hbox (badness 6220) in paragraph at lines 338--340 []\T1/txtt/m/n/10 get_mask_idx() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.r outines.boz.parameters Underfull \hbox (badness 10000) in paragraph at lines 340--342 []\T1/txtt/m/n/10 get_mask_idx() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.r outines.parameters Underfull \hbox (badness 5475) in paragraph at lines 342--343 []\T1/txtt/m/n/10 get_params() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.det ectors.hRIXS method\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 343--345 []\T1/txtt/m/n/10 get_params() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.det ectors.hrixs.hRIXS Underfull \hbox (badness 10000) in paragraph at lines 346--348 []\T1/txtt/m/n/10 get_params() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.det ectors.viking.Viking [164] Underfull \hbox (badness 10000) in paragraph at lines 352--354 []\T1/txtt/m/n/10 get_peaks() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule tool- Underfull \hbox (badness 10000) in paragraph at lines 356--358 []\T1/txtt/m/n/10 get_pes_params() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule t ool- Underfull \hbox (badness 10000) in paragraph at lines 362--363 []\T1/txtt/m/n/10 get_roi_pixel_pos() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ul e tool- Underfull \hbox (badness 10000) in paragraph at lines 363--365 []\T1/txtt/m/n/10 get_roi_pixel_pos() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ul e tool- Underfull \hbox (badness 10000) in paragraph at lines 367--369 []\T1/txtt/m/n/10 get_sase_pId() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule too l- Underfull \hbox (badness 10000) in paragraph at lines 369--371 []\T1/txtt/m/n/10 get_tim_binned() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool- Underfull \hbox (badness 10000) in paragraph at lines 369--371 \T1/qtm/m/it/10 box_scs.detectors.dssc.DSSCBinner method\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 376--378 []\T1/txtt/m/n/10 get_tim_peaks() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule to ol- Underfull \hbox (badness 10000) in paragraph at lines 379--380 []\T1/txtt/m/n/10 get_undulator_config() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod -ule tool- Underfull \hbox (badness 10000) in paragraph at lines 380--382 []\T1/txtt/m/n/10 get_undulator_config() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod -ule tool- Underfull \hbox (badness 10000) in paragraph at lines 386--388 []\T1/txtt/m/n/10 get_xgm_binned() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool- Underfull \hbox (badness 10000) in paragraph at lines 386--388 \T1/qtm/m/it/10 box_scs.detectors.dssc.DSSCBinner method\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 392--393 []\T1/txtt/m/n/10 get_xgm_formatted() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ul e tool- Underfull \hbox (badness 10000) in paragraph at lines 393--395 []\T1/txtt/m/n/10 get_xgm_formatted() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ul e tool- Underfull \hbox (badness 10000) in paragraph at lines 400--402 []\T1/txtt/m/n/10 histogram_module() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule tool- Underfull \hbox (badness 10000) in paragraph at lines 409--410 []\T1/txtt/m/n/10 inspect_correction() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u le tool- Underfull \hbox (badness 10000) in paragraph at lines 410--412 []\T1/txtt/m/n/10 inspect_correction() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u le tool- Underfull \hbox (badness 10000) in paragraph at lines 415--416 []\T1/txtt/m/n/10 inspect_flat_field_domain() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 i n mod-ule tool- Underfull \hbox (badness 10000) in paragraph at lines 416--418 []\T1/txtt/m/n/10 inspect_flat_field_domain() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 i n mod-ule tool- Underfull \hbox (badness 10000) in paragraph at lines 418--420 []\T1/txtt/m/n/10 inspect_flat_field_domain() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 i n mod-ule tool- Underfull \hbox (badness 10000) in paragraph at lines 424--425 []\T1/txtt/m/n/10 inspect_histogram() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ul e tool- Underfull \hbox (badness 10000) in paragraph at lines 425--427 []\T1/txtt/m/n/10 inspect_histogram() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ul e tool- Underfull \hbox (badness 10000) in paragraph at lines 429--430 []\T1/txtt/m/n/10 inspect_nl_fit() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule t ool- Underfull \hbox (badness 10000) in paragraph at lines 431--433 []\T1/txtt/m/n/10 inspect_plane_fitting() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mo d-ule tool- Underfull \hbox (badness 10000) in paragraph at lines 433--435 []\T1/txtt/m/n/10 inspect_plane_fitting() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mo d-ule tool- Underfull \hbox (badness 10000) in paragraph at lines 439--440 []\T1/txtt/m/n/10 inspect_saturation() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u le tool- [165] Underfull \hbox (badness 10000) in paragraph at lines 440--442 []\T1/txtt/m/n/10 inspect_saturation() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-u le tool- Underfull \hbox (badness 10000) in paragraph at lines 443--444 []\T1/txtt/m/n/10 integrate() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.dete ctors.hrixs.hRIXS Underfull \hbox (badness 10000) in paragraph at lines 445--447 []\T1/txtt/m/n/10 integrate() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.dete ctors.viking.Viking Underfull \hbox (badness 10000) in paragraph at lines 451--453 []\T1/txtt/m/n/10 is_ppl() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule tool- Underfull \hbox (badness 10000) in paragraph at lines 455--457 []\T1/txtt/m/n/10 is_pulse_at() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule tool - 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tool-box_scs.routines. boz.parameters class Underfull \hbox (badness 10000) in paragraph at lines 493--495 []\T1/txtt/m/n/10 load_binned() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.de tectors.fccd.FastCCD Underfull \hbox (badness 10000) in paragraph at lines 496--497 []\T1/txtt/m/n/10 load_dark() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.dete ctors.hrixs.hRIXS Underfull \hbox (badness 10000) in paragraph at lines 498--500 []\T1/txtt/m/n/10 load_dark() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.dete ctors.viking.Viking Underfull \hbox (badness 10000) in paragraph at lines 504--506 []\T1/txtt/m/n/10 load_dssc_info() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule t ool- Underfull \hbox (badness 10000) in paragraph at lines 508--510 []\T1/txtt/m/n/10 load_dssc_module() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule tool- Underfull \hbox (badness 10000) in paragraph at lines 510--512 []\T1/txtt/m/n/10 load_gain() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.dete ctors.fccd.FastCCD Underfull 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10000) in paragraph at lines 829--831 []\T1/txtt/m/n/10 test_normalization_all() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool - Underfull \hbox (badness 10000) in paragraph at lines 829--831 \T1/qtm/m/it/10 box_scs.test.test_dssc_cls.TestDSSC method\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 831--833 []\T1/txtt/m/n/10 test_openrun() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool- Underfull \hbox (badness 10000) in paragraph at lines 831--833 \T1/qtm/m/it/10 box_scs.test.test_top_level.TestToolbox Underfull \hbox (badness 10000) in paragraph at lines 833--835 []\T1/txtt/m/n/10 test_openrunpath() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool- Underfull \hbox (badness 10000) in paragraph at lines 833--835 \T1/qtm/m/it/10 box_scs.test.test_top_level.TestToolbox Underfull \hbox (badness 10000) in paragraph at lines 835--837 []\T1/txtt/m/n/10 test_prepare_arrays_nans() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule tool- Underfull \hbox (badness 10000) in paragraph at lines 837--839 []\T1/txtt/m/n/10 test_prepare_arrays_range() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 i n mod-ule tool- Underfull \hbox (badness 10000) in paragraph at lines 839--841 []\T1/txtt/m/n/10 test_prepare_arrays_size() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule tool- Underfull \hbox (badness 10000) in paragraph at lines 841--843 []\T1/txtt/m/n/10 test_processing_quick() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool- Underfull \hbox (badness 10000) in paragraph at lines 841--843 \T1/qtm/m/it/10 box_scs.test.test_dssc_cls.TestDSSC method\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 843--845 []\T1/txtt/m/n/10 test_pulsePatternInfo() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool- Underfull \hbox (badness 10000) in paragraph at lines 845--847 []\T1/txtt/m/n/10 test_range_mask() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 in mod-ule tool- Underfull \hbox (badness 10000) in paragraph at lines 847--849 []\T1/txtt/m/n/10 test_rundir1() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool- Underfull \hbox (badness 10000) in paragraph at lines 849--851 []\T1/txtt/m/n/10 test_rundir2() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool- Underfull \hbox (badness 10000) in paragraph at lines 851--853 []\T1/txtt/m/n/10 test_rundir3() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool- Underfull \hbox (badness 10000) in paragraph at lines 853--855 []\T1/txtt/m/n/10 test_use_xgm_tim() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool- Underfull \hbox (badness 10000) in paragraph at lines 853--855 \T1/qtm/m/it/10 box_scs.test.test_dssc_cls.TestDSSC method\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 862--863 []\T1/txtt/m/n/10 THRESHOLD \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.detect ors.hrixs.hRIXS at- [170] Underfull \hbox (badness 10000) in paragraph at lines 962--963 []\T1/txtt/m/n/10 use_gpu() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.routin es.boz.parameters Underfull \hbox (badness 5519) in paragraph at lines 963--964 []\T1/txtt/m/n/10 use_gpu() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.routin es.parameters method\T1/qtm/m/n/10 ), Underfull \hbox (badness 10000) in paragraph at lines 989--991 []\T1/txtt/m/n/10 xgm_filter() \T1/qtm/m/n/10 (\T1/qtm/m/it/10 tool-box_scs.det ectors.fccd.FastCCD [171]) (./scs-toolbox.aux) ) (see the transcript file for additional information){/usr/share/texmf/fonts/enc /dvips/tex-gyre/q-ec.enc}{/usr/share/texmf/fonts/enc/dvips/tex-gyre/q-ts1.enc}{ /usr/share/texlive/texmf-dist/fonts/enc/dvips/base/8r.enc} Output written on scs-toolbox.pdf (175 pages, 753662 bytes). Transcript written on scs-toolbox.log. Latexmk: Index file 'scs-toolbox.idx' was written Latexmk: Log file says output to 'scs-toolbox.pdf' Latexmk: All targets (scs-toolbox.pdf) are up-to-date [rtd-command-info] start-time: 2023-04-05T19:25:06.046629Z, end-time: 2023-04-05T19:25:06.105700Z, duration: 0, exit-code: 0 mv -f /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/checkouts/latest/doc/_build/latex/scs-toolbox.pdf /usr/src/app/checkouts/readthedocs.org/user_builds/scs-toolbox/artifacts/latest/sphinx_pdf/scs-toolbox.pdf