Read the Docs build information Build id: 10479 Project: pydetlib Version: latest Commit: de20716e388698565c87022accf8f54e001da35b Date: 2019-05-23T00:54:04.578018Z State: finished Success: True [rtd-command-info] start-time: 2019-05-23T05:54:19.115000Z, end-time: 2019-05-23T05:54:38.070000Z, duration: 18, 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: 2019-05-23T05:54:38.134000Z, end-time: 2019-05-23T05:56:24.065000Z, duration: 105, 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 https://files.pythonhosted.org/packages/e8/82/3b5455f74bf9ac0757d09c625b7741e6fc284d7519cffc3babb6c5173cf5/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-62o0qox0/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 Using cached https://files.pythonhosted.org/packages/10/ad/00b090d23a222943eb0eda509720a404f531a439e803f6538f35136cae9e/alabaster-0.7.12-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 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 six>=1.4 (from sphinx==1.3.5) Using cached https://files.pythonhosted.org/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl Collecting babel!=2.0,>=1.3 (from sphinx==1.3.5) Using cached https://files.pythonhosted.org/packages/b8/ad/c6f60602d3ee3d92fbed87675b6fb6a6f9a38c223343ababdb44ba201f10/Babel-2.6.0-py2.py3-none-any.whl Collecting Jinja2>=2.3 (from sphinx==1.3.5) Using cached https://files.pythonhosted.org/packages/1d/e7/fd8b501e7a6dfe492a433deb7b9d833d39ca74916fa8bc63dd1a4947a671/Jinja2-2.10.1-py2.py3-none-any.whl Collecting PyYAML>=3.10 (from mkdocs==0.15.0) Collecting mkdocs-bootstrap>=0.1.1 (from mkdocs==0.15.0) Using cached https://files.pythonhosted.org/packages/e4/26/8823a7e45fad6ede3da31147514fb029dffb134e363bb0f64f7a2bd9448d/mkdocs_bootstrap-1.0.1-py2.py3-none-any.whl Collecting tornado>=4.1 (from mkdocs==0.15.0) Collecting Markdown>=2.3.1 (from mkdocs==0.15.0) Using cached https://files.pythonhosted.org/packages/7a/6b/5600647404ba15545ec37d2f7f58844d690baf2f81f3a60b862e48f29287/Markdown-3.0.1-py2.py3-none-any.whl Collecting mkdocs-bootswatch>=0.1.0 (from mkdocs==0.15.0) Using cached https://files.pythonhosted.org/packages/42/06/1cdc2c3889c3c5803ae830bae3bf7c3fa5a0841109665d93bac81f287088/mkdocs_bootswatch-1.0-py2.py3-none-any.whl Collecting click>=4.0 (from mkdocs==0.15.0) Using cached https://files.pythonhosted.org/packages/fa/37/45185cb5abbc30d7257104c434fe0b07e5a195a6847506c074527aa599ec/Click-7.0-py2.py3-none-any.whl Collecting livereload>=2.3.2 (from mkdocs==0.15.0) Using cached https://files.pythonhosted.org/packages/12/4d/30cfe74402d2e962d66d35da29bf8850b0557b559ce84d09967c8ade859e/livereload-2.6.1-py2.py3-none-any.whl Collecting requests (from readthedocs-sphinx-ext) Using cached https://files.pythonhosted.org/packages/7d/e3/20f3d364d6c8e5d2353c72a67778eb189176f08e873c9900e10c0287b84b/requests-2.21.0-py2.py3-none-any.whl 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 pytz>=0a (from babel!=2.0,>=1.3->sphinx==1.3.5) Using cached https://files.pythonhosted.org/packages/3d/73/fe30c2daaaa0713420d0382b16fbb761409f532c56bdcc514bf7b6262bb6/pytz-2019.1-py2.py3-none-any.whl Collecting MarkupSafe>=0.23 (from Jinja2>=2.3->sphinx==1.3.5) Using cached https://files.pythonhosted.org/packages/99/c9/5d5dcf2aa90f1d4500e92467a04f63b3708ee6e5764b40b2445e767ab8dc/MarkupSafe-1.1.1-cp34-cp34m-manylinux1_x86_64.whl 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) Collecting urllib3<1.25,>=1.21.1 (from requests->readthedocs-sphinx-ext) Using cached https://files.pythonhosted.org/packages/01/11/525b02e4acc0c747de8b6ccdab376331597c569c42ea66ab0a1dbd36eca2/urllib3-1.24.3-py2.py3-none-any.whl Requirement already up-to-date: chardet<3.1.0,>=3.0.2 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from requests->readthedocs-sphinx-ext) Collecting idna<2.9,>=2.5 (from requests->readthedocs-sphinx-ext) Using cached https://files.pythonhosted.org/packages/14/2c/cd551d81dbe15200be1cf41cd03869a46fe7226e7450af7a6545bfc474c9/idna-2.8-py2.py3-none-any.whl Collecting certifi>=2017.4.17 (from requests->readthedocs-sphinx-ext) Using cached https://files.pythonhosted.org/packages/60/75/f692a584e85b7eaba0e03827b3d51f45f571c2e793dd731e598828d380aa/certifi-2019.3.9-py2.py3-none-any.whl Installing collected packages: setuptools, urllib3, idna, certifi, requests, readthedocs-sphinx-ext, alabaster, six, pytz, babel, MarkupSafe, Jinja2, PyYAML, mkdocs-bootstrap, tornado, Markdown, mkdocs-bootswatch, click, livereload Found existing installation: setuptools 28.8.0 Uninstalling setuptools-28.8.0: Successfully uninstalled setuptools-28.8.0 Found existing installation: urllib3 1.21.1 Uninstalling urllib3-1.21.1: Successfully uninstalled urllib3-1.21.1 Found existing installation: idna 2.5 Uninstalling idna-2.5: Successfully uninstalled idna-2.5 Found existing installation: certifi 2017.4.17 Uninstalling certifi-2017.4.17: Successfully uninstalled certifi-2017.4.17 Found existing installation: requests 2.17.3 Uninstalling requests-2.17.3: Successfully uninstalled requests-2.17.3 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 0.7.10 Uninstalling alabaster-0.7.10: Successfully uninstalled alabaster-0.7.10 Found existing installation: six 1.10.0 Uninstalling six-1.10.0: Successfully uninstalled six-1.10.0 Found existing installation: pytz 2017.2 Uninstalling pytz-2017.2: Successfully uninstalled pytz-2017.2 Found existing installation: Babel 2.4.0 Uninstalling Babel-2.4.0: Successfully uninstalled Babel-2.4.0 Found existing installation: MarkupSafe 1.0 Uninstalling MarkupSafe-1.0: Successfully uninstalled MarkupSafe-1.0 Found existing installation: Jinja2 2.9.6 Uninstalling Jinja2-2.9.6: Successfully uninstalled Jinja2-2.9.6 Found existing installation: PyYAML 3.12 Uninstalling PyYAML-3.12: Successfully uninstalled PyYAML-3.12 Found existing installation: mkdocs-bootstrap 0.1.1 Uninstalling mkdocs-bootstrap-0.1.1: Successfully uninstalled mkdocs-bootstrap-0.1.1 Found existing installation: tornado 4.5.1 Uninstalling tornado-4.5.1: Successfully uninstalled tornado-4.5.1 Found existing installation: Markdown 2.6.8 Uninstalling Markdown-2.6.8: Successfully uninstalled Markdown-2.6.8 Found existing installation: mkdocs-bootswatch 0.4.0 Uninstalling mkdocs-bootswatch-0.4.0: Successfully uninstalled mkdocs-bootswatch-0.4.0 Found existing installation: click 6.7 Uninstalling click-6.7: Successfully uninstalled click-6.7 Found existing installation: livereload 2.5.1 Uninstalling livereload-2.5.1: Successfully uninstalled livereload-2.5.1 Successfully installed Jinja2-2.10.1 Markdown-3.0.1 MarkupSafe-1.1.1 PyYAML-5.1 alabaster-0.7.12 babel-2.6.0 certifi-2019.3.9 click-7.0 idna-2.8 livereload-2.6.1 mkdocs-bootstrap-1.0.1 mkdocs-bootswatch-1.0 pytz-2019.1 readthedocs-sphinx-ext-0.5.4 requests-2.21.0 setuptools-20.1.1 six-1.12.0 tornado-5.1.1 urllib3-1.24.3 You are using pip version 9.0.1, however version 19.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. [rtd-command-info] start-time: 2019-05-23T05:56:24.131000Z, end-time: 2019-05-23T05:56:29.799000Z, duration: 5, 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 already satisfied: numpy>=1.12 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from -r lib/docs/requirements.txt (line 5)) Requirement already satisfied: tornado>=4.3 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from -r lib/docs/requirements.txt (line 6)) Requirement already satisfied: pandas==0.18 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from -r lib/docs/requirements.txt (line 7)) Requirement already satisfied: seaborn>=0.7.1 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from -r lib/docs/requirements.txt (line 8)) Requirement already satisfied: brewer2mpl>=1.4 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from -r lib/docs/requirements.txt (line 9)) Requirement already satisfied: dill>=0.2.5 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from -r lib/docs/requirements.txt (line 10)) Requirement already satisfied: sphinxcontrib-napoleon>=0.5.2 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from -r lib/docs/requirements.txt (line 11)) Collecting pypandoc (from -r lib/docs/requirements.txt (line 12)) Requirement already satisfied: traitlets>=4.2 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from ipython->-r lib/docs/requirements.txt (line 1)) Requirement already satisfied: prompt-toolkit<2.0.0,>=1.0.4 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from ipython->-r lib/docs/requirements.txt (line 1)) Requirement already satisfied: pexpect; sys_platform != "win32" in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from ipython->-r lib/docs/requirements.txt (line 1)) Requirement already satisfied: decorator in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from ipython->-r lib/docs/requirements.txt (line 1)) Requirement already satisfied: setuptools>=18.5 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from ipython->-r lib/docs/requirements.txt (line 1)) Requirement already satisfied: pickleshare in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from ipython->-r lib/docs/requirements.txt (line 1)) Requirement already satisfied: pygments in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from ipython->-r lib/docs/requirements.txt (line 1)) Requirement already satisfied: simplegeneric>0.8 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from ipython->-r lib/docs/requirements.txt (line 1)) Requirement already satisfied: python-dateutil>=2.1 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from ipyparallel->-r lib/docs/requirements.txt (line 2)) Requirement already satisfied: jupyter-client in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from ipyparallel->-r lib/docs/requirements.txt (line 2)) Requirement already satisfied: pyzmq>=13 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from ipyparallel->-r lib/docs/requirements.txt (line 2)) Requirement already satisfied: ipython-genutils in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from ipyparallel->-r lib/docs/requirements.txt (line 2)) Requirement already satisfied: ipykernel in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from ipyparallel->-r lib/docs/requirements.txt (line 2)) Requirement already satisfied: qtconsole in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from jupyter->-r lib/docs/requirements.txt (line 3)) Requirement already satisfied: jupyter-console in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from jupyter->-r lib/docs/requirements.txt (line 3)) Requirement already satisfied: ipywidgets in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from jupyter->-r lib/docs/requirements.txt (line 3)) Requirement already satisfied: nbconvert in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from jupyter->-r lib/docs/requirements.txt (line 3)) Requirement already satisfied: notebook in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from jupyter->-r lib/docs/requirements.txt (line 3)) Requirement already satisfied: six>=1.10 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from matplotlib>=2.0.0->-r lib/docs/requirements.txt (line 4)) Requirement already satisfied: pytz in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from matplotlib>=2.0.0->-r lib/docs/requirements.txt (line 4)) Requirement already satisfied: cycler>=0.10 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from matplotlib>=2.0.0->-r lib/docs/requirements.txt (line 4)) Requirement already satisfied: pyparsing!=2.0.0,!=2.0.4,!=2.1.2,!=2.1.6,>=1.5.6 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from matplotlib>=2.0.0->-r lib/docs/requirements.txt (line 4)) Requirement already satisfied: backports-abc>=0.4 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from tornado>=4.3->-r lib/docs/requirements.txt (line 6)) Requirement already satisfied: scipy in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from seaborn>=0.7.1->-r lib/docs/requirements.txt (line 8)) Requirement already satisfied: pockets>=0.3 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from sphinxcontrib-napoleon>=0.5.2->-r lib/docs/requirements.txt (line 11)) Requirement already satisfied: pip>=8.1.0 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from pypandoc->-r lib/docs/requirements.txt (line 12)) Requirement already satisfied: wheel>=0.25.0 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from pypandoc->-r lib/docs/requirements.txt (line 12)) Requirement already satisfied: wcwidth in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from prompt-toolkit<2.0.0,>=1.0.4->ipython->-r lib/docs/requirements.txt (line 1)) Requirement already satisfied: ptyprocess>=0.5 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from pexpect; sys_platform != "win32"->ipython->-r lib/docs/requirements.txt (line 1)) Requirement already satisfied: jupyter-core in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from jupyter-client->ipyparallel->-r lib/docs/requirements.txt (line 2)) Requirement already satisfied: widgetsnbextension>=1.2.6 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from ipywidgets->jupyter->-r lib/docs/requirements.txt (line 3)) Requirement already satisfied: pandocfilters>=1.4.1 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from nbconvert->jupyter->-r lib/docs/requirements.txt (line 3)) Requirement already satisfied: jinja2 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from nbconvert->jupyter->-r lib/docs/requirements.txt (line 3)) Requirement already satisfied: testpath in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from nbconvert->jupyter->-r lib/docs/requirements.txt (line 3)) Requirement already satisfied: mistune!=0.6 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from nbconvert->jupyter->-r lib/docs/requirements.txt (line 3)) Requirement already satisfied: entrypoints>=0.2.2 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from nbconvert->jupyter->-r lib/docs/requirements.txt (line 3)) Requirement already satisfied: bleach in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from nbconvert->jupyter->-r lib/docs/requirements.txt (line 3)) Requirement already satisfied: nbformat in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from nbconvert->jupyter->-r lib/docs/requirements.txt (line 3)) Requirement already satisfied: terminado>=0.3.3; sys_platform != "win32" in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from notebook->jupyter->-r lib/docs/requirements.txt (line 3)) Requirement already satisfied: MarkupSafe>=0.23 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from jinja2->nbconvert->jupyter->-r lib/docs/requirements.txt (line 3)) Requirement already satisfied: 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)) Requirement already satisfied: jsonschema!=2.5.0,>=2.4 in /user_builds/pydetlib/envs/latest/lib/python3.4/site-packages (from nbformat->nbconvert->jupyter->-r lib/docs/requirements.txt (line 3)) Installing collected packages: pypandoc Successfully installed pypandoc-1.4 You are using pip version 9.0.1, however version 19.1.1 is available. You should consider upgrading via the 'pip install --upgrade pip' command. [rtd-command-info] start-time: 2019-05-23T05:56:31.934000Z, end-time: 2019-05-23T05:56:31.995000Z, 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': 'de20716e', } 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: 2019-05-23T05:56:33.291000Z, end-time: 2019-05-23T05:56:57.379000Z, duration: 24, 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://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 [readthedocs]: targets for 5 source files that are out of date updating environment: 5 added, 0 changed, 0 removed reading sources... 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WARNING: html_static_path entry '/user_builds/pydetlib/checkouts/latest/lib/docs/_static' does not exist WARNING: html_static_path entry '/rtd_root/readthedocs/templates/sphinx/_static' does not exist done copying extra files... done dumping search index in English (code: en) ... done dumping object inventory... done build succeeded, 7 warnings. [rtd-command-info] start-time: 2019-05-23T05:57:26.776000Z, end-time: 2019-05-23T05:57:41.031000Z, duration: 14, 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://docs.scipy.org/doc/numpy/objects.inv... 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... building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: 0 added, 1 changed, 19 removed reading sources... [100%] examples/PlotExamples 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 assembling single document... 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 /user_builds/pydetlib/checkouts/latest/lib/docs/_notebooks/DataGeneratorExample.rst:508: WARNING: undefined label: gainmapstability (if the link has no caption the label must precede a section header) /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... /user_builds/pydetlib/checkouts/latest/lib/docs/index.rst:13: WARNING: toctree contains reference to nonexisting document '_notebooks/index' /user_builds/pydetlib/checkouts/latest/lib/docs/index.rst:13: WARNING: toctree contains reference to nonexisting document 'api/modules' /user_builds/pydetlib/checkouts/latest/lib/docs/index.rst:13: WARNING: toctree contains reference to nonexisting document '_notebooks/index' /user_builds/pydetlib/checkouts/latest/lib/docs/index.rst:13: WARNING: toctree contains reference to nonexisting document 'api/modules' done writing additional files... copying static files... 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[rtd-command-info] start-time: 2019-05-23T05:57:42.189000Z, end-time: 2019-05-23T05:57:54.663000Z, duration: 12, 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... done loading intersphinx inventory from http://docs.scipy.org/doc/numpy/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/scipy/reference/objects.inv... building [mo]: targets for 0 po files that are out of date building [latex]: all documents updating environment: 0 added, 1 changed, 19 removed reading sources... [100%] examples/PlotExamples 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/_notebooks/DataGeneratorExample.rst:508: WARNING: undefined label: gainmapstability (if the link has no caption the label must precede a section header) /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 TeX support files... done build succeeded, 5 warnings. 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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 ) [58] 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 , [59] 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 , [60] 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 , [62] 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 , [63] 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 [64] 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 , [65] [66] 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 , [67] 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 , [68] 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=\\\{\}] [71] [72] 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. [73] 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} [75] Underfull \hbox (badness 5711) in paragraph at lines 5049--5052 []\T1/ptm/m/n/10 the iden-ti-fied pat- [76] 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 , [78] 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 , [79] 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 , [80] 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 , [81] [82] 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 , [83] [84] [85] [86] 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 , [87] Underfull \hbox (badness 10000) in paragraph at lines 6513--6515 []\T1/ptm/m/n/10 Usually the [88] [89] 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. [90] [91] [92] [93] [94] [95] [96] [97] [98] [99] [100] [101] [102] [103] [104] [105] 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- [106] 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- [107] [108] Chapter 5. No file src.ind. [109] (./src.aux) Package rerunfilecheck Warning: File `src.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. 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 (113 pages, 437297 bytes). Transcript written on src.log. [rtd-command-info] start-time: 2019-05-23T05:57:56.661000Z, end-time: 2019-05-23T05:57:56.733000Z, 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. [rtd-command-info] start-time: 2019-05-23T05:57:56.793000Z, end-time: 2019-05-23T05:57:58.924000Z, duration: 2, exit-code: 0 pdflatex -interaction=nonstopmode /user_builds/pydetlib/checkouts/latest/doc/_build/latex/src.tex This is pdfTeX, Version 3.14159265-2.6-1.40.15 (TeX Live 2015/dev/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (/user_builds/pydetlib/checkouts/latest/doc/_build/latex/src.tex LaTeX2e <2014/05/01> Babel <3.9l> and hyphenation patterns for 2 languages loaded. 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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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See the pdftex.def package documentation for explanation. Type H for immediate help. ... l.3076 ...otExamples_files/PlotExamples_40_0}.png} LaTeX Warning: File `{_notebooks/PlotExamples_files/PlotExamples_42_0}.png' not found on input line 3091. ! Package pdftex.def Error: File `_notebooks/PlotExamples_files/PlotExamples_42 _0.png' not found. See the pdftex.def package documentation for explanation. Type H for immediate help. ... l.3091 ...otExamples_files/PlotExamples_42_0}.png} LaTeX Warning: File `{_notebooks/PlotExamples_files/PlotExamples_42_0}.png' not found on input line 3091. ! Package pdftex.def Error: File `_notebooks/PlotExamples_files/PlotExamples_42 _0.png' not found. See the pdftex.def package documentation for explanation. Type H for immediate help. ... l.3091 ...otExamples_files/PlotExamples_42_0}.png} [55] [56] 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 ) [57] 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 , 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(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 ) [58] 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 , [59] 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 , [60] 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 , [62] 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 , [63] 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 [64] 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 , [65] [66] 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 , [67] 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 , [68] 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=\\\{\}] [71] [72] 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. [73] 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} [75] Underfull \hbox (badness 5711) in paragraph at lines 5049--5052 []\T1/ptm/m/n/10 the iden-ti-fied pat- [76] 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 , [78] 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 , [79] 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 , [80] 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 , [81] [82] 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 , [83] [84] [85] [86] 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 , [87] Underfull \hbox (badness 10000) in paragraph at lines 6513--6515 []\T1/ptm/m/n/10 Usually the [88] [89] 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. [90] [91] [92] [93] [94] [95] [96] [97] [98] [99] [100] [101] [102] [103] [104] [105] 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- [106] 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- [107] [108] Chapter 5. (./src.ind [109] [110] 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 38--39 []\T1/ptm/m/n/10 apply_along_axis() (in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 39--40 []\T1/ptm/m/n/10 apply_over_axes() (in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 63--64 []\T1/ptm/m/n/10 asarray_chkfinite() (in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 64--65 []\T1/ptm/m/n/10 ascontiguousarray() (in mod-ule XFELDe- [111] Underfull \hbox (badness 10000) in paragraph at lines 76--77 []\T1/ptm/m/n/10 axis_scales (XFELDe-tAna.util.knumpy.krbarray at- Underfull \hbox (badness 10000) in paragraph at lines 82--83 []\T1/ptm/m/n/10 badPixelMaskFromNoiseAndOffset() (in mod-ule Underfull \hbox (badness 10000) in paragraph at lines 86--87 []\T1/ptm/m/n/10 baseArrayType (XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 86--87 \T1/ptm/m/n/10 tAna.util.knumpy.krbMaskedArray at-tribute), Overfull \hbox (2.81924pt too wide) in paragraph at lines 94--95 []\T1/ptm/m/n/10 BLOCK (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- 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- [112] 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 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- [113] 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 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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), [114] 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 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tAna.algorithms.correction.CorrectionBase Underfull \hbox (badness 10000) in paragraph at lines 467--468 []\T1/ptm/m/n/10 makeReport() (XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 467--468 \T1/ptm/m/n/10 tAna.core.mapcalculator.MapCalculator Underfull \hbox (badness 10000) in paragraph at lines 468--469 []\T1/ptm/m/n/10 MapCalculator (class in XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 477--478 []\T1/ptm/m/n/10 MaxCalculator (class in XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 480--481 []\T1/ptm/m/n/10 maximum_sctype() (in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 481--482 []\T1/ptm/m/n/10 MAY_SHARE_BOUNDS() (in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 482--483 []\T1/ptm/m/n/10 MAY_SHARE_EXACT() (in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 483--484 []\T1/ptm/m/n/10 may_share_memory() (in mod-ule XFELDe- Underfull \hbox (badness 10000) in 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SHIFT_OVERFLOW() (in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 702--703 []\T1/ptm/m/n/10 SHIFT_UNDERFLOW() (in mod-ule XFELDe- Underfull \hbox (badness 10000) in paragraph at lines 706--707 []\T1/ptm/m/n/10 simplePlot() (in mod-ule XFELDe- [119] Underfull \hbox (badness 10000) in paragraph at lines 722--723 []\T1/ptm/m/n/10 stackable (XFELDe-tAna.util.knumpy.axisMeaning Underfull \hbox (badness 10000) in paragraph at lines 723--724 []\T1/ptm/m/n/10 stackable (XFELDe-tAna.util.knumpy.imageZAxis Underfull \hbox (badness 10000) in paragraph at lines 724--725 []\T1/ptm/m/n/10 stackable (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 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 [120] 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 [121]) (./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 (125 pages, 488975 bytes). Transcript written on src.log. 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