[e9500f]: / docs / old_docs / ybuild / latex / PathFlowAI.log

Download this file

2282 lines (1732 with data), 75.9 kB

This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018) (preloaded format=pdflatex 2018.4.16)  31 JUL 2019 12:33
entering extended mode
 restricted \write18 enabled.
 %&-line parsing enabled.
**PathFlowAI.tex
(./PathFlowAI.tex
LaTeX2e <2018-04-01> patch level 2
Babel <3.18> and hyphenation patterns for 84 language(s) loaded.
(./sphinxmanual.cls
Document Class: sphinxmanual 2018/12/23 v2.0 Document class (Sphinx manual)
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/report.cls
Document Class: report 2014/09/29 v1.4h Standard LaTeX document class
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/size10.clo
File: size10.clo 2014/09/29 v1.4h Standard LaTeX file (size option)
)
\c@part=\count80
\c@chapter=\count81
\c@section=\count82
\c@subsection=\count83
\c@subsubsection=\count84
\c@paragraph=\count85
\c@subparagraph=\count86
\c@figure=\count87
\c@table=\count88
\abovecaptionskip=\skip41
\belowcaptionskip=\skip42
\bibindent=\dimen102
))
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/inputenc.sty
Package: inputenc 2018/04/06 v1.3b Input encoding file
\inpenc@prehook=\toks14
\inpenc@posthook=\toks15
)
   defining Unicode char U+00A0 (decimal 160)
   defining Unicode char U+2500 (decimal 9472)
   defining Unicode char U+2502 (decimal 9474)
   defining Unicode char U+2514 (decimal 9492)
   defining Unicode char U+251C (decimal 9500)
   defining Unicode char U+2572 (decimal 9586)

(/usr/local/texlive/2018/texmf-dist/tex/latex/cmap/cmap.sty
Package: cmap 2008/03/06 v1.0h CMap support: searchable PDF
)
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/fontenc.sty
Package: fontenc 2017/04/05 v2.0i Standard LaTeX package

(/usr/local/texlive/2018/texmf-dist/tex/latex/base/t1enc.def
File: t1enc.def 2017/04/05 v2.0i Standard LaTeX file
LaTeX Font Info:    Redeclaring font encoding T1 on input line 48.
)<<t1.cmap>>)
(/usr/local/texlive/2018/texmf-dist/tex/latex/amsmath/amsmath.sty
Package: amsmath 2017/09/02 v2.17a AMS math features
\@mathmargin=\skip43

For additional information on amsmath, use the `?' option.
(/usr/local/texlive/2018/texmf-dist/tex/latex/amsmath/amstext.sty
Package: amstext 2000/06/29 v2.01 AMS text

(/usr/local/texlive/2018/texmf-dist/tex/latex/amsmath/amsgen.sty
File: amsgen.sty 1999/11/30 v2.0 generic functions
\@emptytoks=\toks16
\ex@=\dimen103
))
(/usr/local/texlive/2018/texmf-dist/tex/latex/amsmath/amsbsy.sty
Package: amsbsy 1999/11/29 v1.2d Bold Symbols
\pmbraise@=\dimen104
)
(/usr/local/texlive/2018/texmf-dist/tex/latex/amsmath/amsopn.sty
Package: amsopn 2016/03/08 v2.02 operator names
)
\inf@bad=\count89
LaTeX Info: Redefining \frac on input line 213.
\uproot@=\count90
\leftroot@=\count91
LaTeX Info: Redefining \overline on input line 375.
\classnum@=\count92
\DOTSCASE@=\count93
LaTeX Info: Redefining \ldots on input line 472.
LaTeX Info: Redefining \dots on input line 475.
LaTeX Info: Redefining \cdots on input line 596.
\Mathstrutbox@=\box26
\strutbox@=\box27
\big@size=\dimen105
LaTeX Font Info:    Redeclaring font encoding OML on input line 712.
LaTeX Font Info:    Redeclaring font encoding OMS on input line 713.
\macc@depth=\count94
\c@MaxMatrixCols=\count95
\dotsspace@=\muskip10
\c@parentequation=\count96
\dspbrk@lvl=\count97
\tag@help=\toks17
\row@=\count98
\column@=\count99
\maxfields@=\count100
\andhelp@=\toks18
\eqnshift@=\dimen106
\alignsep@=\dimen107
\tagshift@=\dimen108
\tagwidth@=\dimen109
\totwidth@=\dimen110
\lineht@=\dimen111
\@envbody=\toks19
\multlinegap=\skip44
\multlinetaggap=\skip45
\mathdisplay@stack=\toks20
LaTeX Info: Redefining \[ on input line 2817.
LaTeX Info: Redefining \] on input line 2818.
)
(/usr/local/texlive/2018/texmf-dist/tex/latex/amsfonts/amssymb.sty
Package: amssymb 2013/01/14 v3.01 AMS font symbols

(/usr/local/texlive/2018/texmf-dist/tex/latex/amsfonts/amsfonts.sty
Package: amsfonts 2013/01/14 v3.01 Basic AMSFonts support
\symAMSa=\mathgroup4
\symAMSb=\mathgroup5
LaTeX Font Info:    Overwriting math alphabet `\mathfrak' in version `bold'
(Font)                  U/euf/m/n --> U/euf/b/n on input line 106.
))
(/usr/local/texlive/2018/texmf-dist/tex/generic/babel/babel.sty
Package: babel 2018/02/14 3.18 The Babel package

(/usr/local/texlive/2018/texmf-dist/tex/generic/babel/switch.def
File: switch.def 2018/02/14 3.18 Babel switching mechanism
)
(/usr/local/texlive/2018/texmf-dist/tex/generic/babel-english/english.ldf
Language: english 2017/06/06 v3.3r English support from the babel system

(/usr/local/texlive/2018/texmf-dist/tex/generic/babel/babel.def
File: babel.def 2018/02/14 3.18 Babel common definitions
\babel@savecnt=\count101
\U@D=\dimen112

(/usr/local/texlive/2018/texmf-dist/tex/generic/babel/txtbabel.def)
\bbl@dirlevel=\count102
)
\l@canadian = a dialect from \language\l@american 
\l@australian = a dialect from \language\l@british 
\l@newzealand = a dialect from \language\l@british 
))
(/usr/local/texlive/2018/texmf-dist/tex/latex/psnfss/times.sty
Package: times 2005/04/12 PSNFSS-v9.2a (SPQR) 
)
(/usr/local/texlive/2018/texmf-dist/tex/latex/fncychap/fncychap.sty
Package: fncychap 2007/07/30 v1.34 LaTeX package (Revised chapters)
\RW=\skip46
\mylen=\skip47
\myhi=\skip48
\px=\skip49
\py=\skip50
\pyy=\skip51
\pxx=\skip52
\c@AlphaCnt=\count103
\c@AlphaDecCnt=\count104
)
(./sphinx.sty
Package: sphinx 2019/06/04 v2.1.1 LaTeX package (Sphinx markup)

(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/ltxcmds.sty
Package: ltxcmds 2016/05/16 v1.23 LaTeX kernel commands for general use (HO)
)
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/graphicx.sty
Package: graphicx 2017/06/01 v1.1a Enhanced LaTeX Graphics (DPC,SPQR)

(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/keyval.sty
Package: keyval 2014/10/28 v1.15 key=value parser (DPC)
\KV@toks@=\toks21
)
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/graphics.sty
Package: graphics 2017/06/25 v1.2c Standard LaTeX Graphics (DPC,SPQR)

(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics/trig.sty
Package: trig 2016/01/03 v1.10 sin cos tan (DPC)
)
(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics-cfg/graphics.cfg
File: graphics.cfg 2016/06/04 v1.11 sample graphics configuration
)
Package graphics Info: Driver file: pdftex.def on input line 99.

(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics-def/pdftex.def
File: pdftex.def 2018/01/08 v1.0l Graphics/color driver for pdftex
))
\Gin@req@height=\dimen113
\Gin@req@width=\dimen114
)
(/usr/local/texlive/2018/texmf-dist/tex/latex/fancyhdr/fancyhdr.sty
Package: fancyhdr 2017/06/30 v3.9a Extensive control of page headers and footer
s
\f@nch@headwidth=\skip53
\f@nch@O@elh=\skip54
\f@nch@O@erh=\skip55
\f@nch@O@olh=\skip56
\f@nch@O@orh=\skip57
\f@nch@O@elf=\skip58
\f@nch@O@erf=\skip59
\f@nch@O@olf=\skip60
\f@nch@O@orf=\skip61
)
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/textcomp.sty
Package: textcomp 2017/04/05 v2.0i Standard LaTeX package
Package textcomp Info: Sub-encoding information:
(textcomp)               5 = only ISO-Adobe without \textcurrency
(textcomp)               4 = 5 + \texteuro
(textcomp)               3 = 4 + \textohm
(textcomp)               2 = 3 + \textestimated + \textcurrency
(textcomp)               1 = TS1 - \textcircled - \t
(textcomp)               0 = TS1 (full)
(textcomp)             Font families with sub-encoding setting implement
(textcomp)             only a restricted character set as indicated.
(textcomp)             Family '?' is the default used for unknown fonts.
(textcomp)             See the documentation for details.
Package textcomp Info: Setting ? sub-encoding to TS1/1 on input line 79.

(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1enc.def
File: ts1enc.def 2001/06/05 v3.0e (jk/car/fm) Standard LaTeX file
Now handling font encoding TS1 ...
... processing UTF-8 mapping file for font encoding TS1

(/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1enc.dfu
File: ts1enc.dfu 2018/04/05 v1.2c UTF-8 support for inputenc
   defining Unicode char U+00A2 (decimal 162)
   defining Unicode char U+00A3 (decimal 163)
   defining Unicode char U+00A4 (decimal 164)
   defining Unicode char U+00A5 (decimal 165)
   defining Unicode char U+00A6 (decimal 166)
   defining Unicode char U+00A7 (decimal 167)
   defining Unicode char U+00A8 (decimal 168)
   defining Unicode char U+00A9 (decimal 169)
   defining Unicode char U+00AA (decimal 170)
   defining Unicode char U+00AC (decimal 172)
   defining Unicode char U+00AE (decimal 174)
   defining Unicode char U+00AF (decimal 175)
   defining Unicode char U+00B0 (decimal 176)
   defining Unicode char U+00B1 (decimal 177)
   defining Unicode char U+00B2 (decimal 178)
   defining Unicode char U+00B3 (decimal 179)
   defining Unicode char U+00B4 (decimal 180)
   defining Unicode char U+00B5 (decimal 181)
   defining Unicode char U+00B6 (decimal 182)
   defining Unicode char U+00B7 (decimal 183)
   defining Unicode char U+00B9 (decimal 185)
   defining Unicode char U+00BA (decimal 186)
   defining Unicode char U+00BC (decimal 188)
   defining Unicode char U+00BD (decimal 189)
   defining Unicode char U+00BE (decimal 190)
   defining Unicode char U+00D7 (decimal 215)
   defining Unicode char U+00F7 (decimal 247)
   defining Unicode char U+0192 (decimal 402)
   defining Unicode char U+02C7 (decimal 711)
   defining Unicode char U+02D8 (decimal 728)
   defining Unicode char U+02DD (decimal 733)
   defining Unicode char U+0E3F (decimal 3647)
   defining Unicode char U+2016 (decimal 8214)
   defining Unicode char U+2020 (decimal 8224)
   defining Unicode char U+2021 (decimal 8225)
   defining Unicode char U+2022 (decimal 8226)
   defining Unicode char U+2030 (decimal 8240)
   defining Unicode char U+2031 (decimal 8241)
   defining Unicode char U+203B (decimal 8251)
   defining Unicode char U+203D (decimal 8253)
   defining Unicode char U+2044 (decimal 8260)
   defining Unicode char U+204E (decimal 8270)
   defining Unicode char U+2052 (decimal 8274)
   defining Unicode char U+20A1 (decimal 8353)
   defining Unicode char U+20A4 (decimal 8356)
   defining Unicode char U+20A6 (decimal 8358)
   defining Unicode char U+20A9 (decimal 8361)
   defining Unicode char U+20AB (decimal 8363)
   defining Unicode char U+20AC (decimal 8364)
   defining Unicode char U+20B1 (decimal 8369)
   defining Unicode char U+2103 (decimal 8451)
   defining Unicode char U+2116 (decimal 8470)
   defining Unicode char U+2117 (decimal 8471)
   defining Unicode char U+211E (decimal 8478)
   defining Unicode char U+2120 (decimal 8480)
   defining Unicode char U+2122 (decimal 8482)
   defining Unicode char U+2126 (decimal 8486)
   defining Unicode char U+2127 (decimal 8487)
   defining Unicode char U+212E (decimal 8494)
   defining Unicode char U+2190 (decimal 8592)
   defining Unicode char U+2191 (decimal 8593)
   defining Unicode char U+2192 (decimal 8594)
   defining Unicode char U+2193 (decimal 8595)
   defining Unicode char U+2329 (decimal 9001)
   defining Unicode char U+232A (decimal 9002)
   defining Unicode char U+2422 (decimal 9250)
   defining Unicode char U+25E6 (decimal 9702)
   defining Unicode char U+25EF (decimal 9711)
   defining Unicode char U+266A (decimal 9834)
   defining Unicode char U+FEFF (decimal 65279)
))
LaTeX Info: Redefining \oldstylenums on input line 334.
Package textcomp Info: Setting cmr sub-encoding to TS1/0 on input line 349.
Package textcomp Info: Setting cmss sub-encoding to TS1/0 on input line 350.
Package textcomp Info: Setting cmtt sub-encoding to TS1/0 on input line 351.
Package textcomp Info: Setting cmvtt sub-encoding to TS1/0 on input line 352.
Package textcomp Info: Setting cmbr sub-encoding to TS1/0 on input line 353.
Package textcomp Info: Setting cmtl sub-encoding to TS1/0 on input line 354.
Package textcomp Info: Setting ccr sub-encoding to TS1/0 on input line 355.
Package textcomp Info: Setting ptm sub-encoding to TS1/4 on input line 356.
Package textcomp Info: Setting pcr sub-encoding to TS1/4 on input line 357.
Package textcomp Info: Setting phv sub-encoding to TS1/4 on input line 358.
Package textcomp Info: Setting ppl sub-encoding to TS1/3 on input line 359.
Package textcomp Info: Setting pag sub-encoding to TS1/4 on input line 360.
Package textcomp Info: Setting pbk sub-encoding to TS1/4 on input line 361.
Package textcomp Info: Setting pnc sub-encoding to TS1/4 on input line 362.
Package textcomp Info: Setting pzc sub-encoding to TS1/4 on input line 363.
Package textcomp Info: Setting bch sub-encoding to TS1/4 on input line 364.
Package textcomp Info: Setting put sub-encoding to TS1/5 on input line 365.
Package textcomp Info: Setting uag sub-encoding to TS1/5 on input line 366.
Package textcomp Info: Setting ugq sub-encoding to TS1/5 on input line 367.
Package textcomp Info: Setting ul8 sub-encoding to TS1/4 on input line 368.
Package textcomp Info: Setting ul9 sub-encoding to TS1/4 on input line 369.
Package textcomp Info: Setting augie sub-encoding to TS1/5 on input line 370.
Package textcomp Info: Setting dayrom sub-encoding to TS1/3 on input line 371.
Package textcomp Info: Setting dayroms sub-encoding to TS1/3 on input line 372.

Package textcomp Info: Setting pxr sub-encoding to TS1/0 on input line 373.
Package textcomp Info: Setting pxss sub-encoding to TS1/0 on input line 374.
Package textcomp Info: Setting pxtt sub-encoding to TS1/0 on input line 375.
Package textcomp Info: Setting txr sub-encoding to TS1/0 on input line 376.
Package textcomp Info: Setting txss sub-encoding to TS1/0 on input line 377.
Package textcomp Info: Setting txtt sub-encoding to TS1/0 on input line 378.
Package textcomp Info: Setting lmr sub-encoding to TS1/0 on input line 379.
Package textcomp Info: Setting lmdh sub-encoding to TS1/0 on input line 380.
Package textcomp Info: Setting lmss sub-encoding to TS1/0 on input line 381.
Package textcomp Info: Setting lmssq sub-encoding to TS1/0 on input line 382.
Package textcomp Info: Setting lmvtt sub-encoding to TS1/0 on input line 383.
Package textcomp Info: Setting lmtt sub-encoding to TS1/0 on input line 384.
Package textcomp Info: Setting qhv sub-encoding to TS1/0 on input line 385.
Package textcomp Info: Setting qag sub-encoding to TS1/0 on input line 386.
Package textcomp Info: Setting qbk sub-encoding to TS1/0 on input line 387.
Package textcomp Info: Setting qcr sub-encoding to TS1/0 on input line 388.
Package textcomp Info: Setting qcs sub-encoding to TS1/0 on input line 389.
Package textcomp Info: Setting qpl sub-encoding to TS1/0 on input line 390.
Package textcomp Info: Setting qtm sub-encoding to TS1/0 on input line 391.
Package textcomp Info: Setting qzc sub-encoding to TS1/0 on input line 392.
Package textcomp Info: Setting qhvc sub-encoding to TS1/0 on input line 393.
Package textcomp Info: Setting futs sub-encoding to TS1/4 on input line 394.
Package textcomp Info: Setting futx sub-encoding to TS1/4 on input line 395.
Package textcomp Info: Setting futj sub-encoding to TS1/4 on input line 396.
Package textcomp Info: Setting hlh sub-encoding to TS1/3 on input line 397.
Package textcomp Info: Setting hls sub-encoding to TS1/3 on input line 398.
Package textcomp Info: Setting hlst sub-encoding to TS1/3 on input line 399.
Package textcomp Info: Setting hlct sub-encoding to TS1/5 on input line 400.
Package textcomp Info: Setting hlx sub-encoding to TS1/5 on input line 401.
Package textcomp Info: Setting hlce sub-encoding to TS1/5 on input line 402.
Package textcomp Info: Setting hlcn sub-encoding to TS1/5 on input line 403.
Package textcomp Info: Setting hlcw sub-encoding to TS1/5 on input line 404.
Package textcomp Info: Setting hlcf sub-encoding to TS1/5 on input line 405.
Package textcomp Info: Setting pplx sub-encoding to TS1/3 on input line 406.
Package textcomp Info: Setting pplj sub-encoding to TS1/3 on input line 407.
Package textcomp Info: Setting ptmx sub-encoding to TS1/4 on input line 408.
Package textcomp Info: Setting ptmj sub-encoding to TS1/4 on input line 409.
)
(/usr/local/texlive/2018/texmf-dist/tex/latex/titlesec/titlesec.sty
Package: titlesec 2016/03/21 v2.10.2 Sectioning titles
\ttl@box=\box28
\beforetitleunit=\skip62
\aftertitleunit=\skip63
\ttl@plus=\dimen115
\ttl@minus=\dimen116
\ttl@toksa=\toks22
\titlewidth=\dimen117
\titlewidthlast=\dimen118
\titlewidthfirst=\dimen119
)
(/usr/local/texlive/2018/texmf-dist/tex/latex/tabulary/tabulary.sty
Package: tabulary 2014/06/11 v0.10 tabulary package (DPC)

(/usr/local/texlive/2018/texmf-dist/tex/latex/tools/array.sty
Package: array 2018/04/07 v2.4g Tabular extension package (FMi)
\col@sep=\dimen120
\ar@mcellbox=\box29
\extrarowheight=\dimen121
\NC@list=\toks23
\extratabsurround=\skip64
\backup@length=\skip65
\ar@cellbox=\box30
)
\TY@count=\count105
\TY@linewidth=\dimen122
\tymin=\dimen123
\tymax=\dimen124
\TY@tablewidth=\dimen125
)
(/usr/local/texlive/2018/texmf-dist/tex/latex/tools/longtable.sty
Package: longtable 2014/10/28 v4.11 Multi-page Table package (DPC)
\LTleft=\skip66
\LTright=\skip67
\LTpre=\skip68
\LTpost=\skip69
\LTchunksize=\count106
\LTcapwidth=\dimen126
\LT@head=\box31
\LT@firsthead=\box32
\LT@foot=\box33
\LT@lastfoot=\box34
\LT@cols=\count107
\LT@rows=\count108
\c@LT@tables=\count109
\c@LT@chunks=\count110
\LT@p@ftn=\toks24
)
(/usr/local/texlive/2018/texmf-dist/tex/latex/varwidth/varwidth.sty
Package: varwidth 2009/03/30 ver 0.92;  Variable-width minipages
\@vwid@box=\box35
\sift@deathcycles=\count111
\@vwid@loff=\dimen127
\@vwid@roff=\dimen128
)
(./sphinxmulticell.sty
Package: sphinxmulticell 2017/02/23 v1.6 better span rows and columns of a tabl
e (Sphinx team)
\sphinx@TY@tablewidth=\dimen129
)
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/makeidx.sty
Package: makeidx 2014/09/29 v1.0m Standard LaTeX package
)
(/usr/local/texlive/2018/texmf-dist/tex/latex/framed/framed.sty
Package: framed 2011/10/22 v 0.96: framed or shaded text with page breaks
\OuterFrameSep=\skip70
\fb@frw=\dimen130
\fb@frh=\dimen131
\FrameRule=\dimen132
\FrameSep=\dimen133
)
(/usr/local/texlive/2018/texmf-dist/tex/latex/xcolor/xcolor.sty
Package: xcolor 2016/05/11 v2.12 LaTeX color extensions (UK)

(/usr/local/texlive/2018/texmf-dist/tex/latex/graphics-cfg/color.cfg
File: color.cfg 2016/01/02 v1.6 sample color configuration
)
Package xcolor Info: Driver file: pdftex.def on input line 225.
Package xcolor Info: Model `cmy' substituted by `cmy0' on input line 1348.
Package xcolor Info: Model `hsb' substituted by `rgb' on input line 1352.
Package xcolor Info: Model `RGB' extended on input line 1364.
Package xcolor Info: Model `HTML' substituted by `rgb' on input line 1366.
Package xcolor Info: Model `Hsb' substituted by `hsb' on input line 1367.
Package xcolor Info: Model `tHsb' substituted by `hsb' on input line 1368.
Package xcolor Info: Model `HSB' substituted by `hsb' on input line 1369.
Package xcolor Info: Model `Gray' substituted by `gray' on input line 1370.
Package xcolor Info: Model `wave' substituted by `hsb' on input line 1371.
)
(/usr/local/texlive/2018/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty
Package: fancyvrb 2008/02/07

Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix 
<2008/02/07> (tvz)
\FV@CodeLineNo=\count112
\FV@InFile=\read1
\FV@TabBox=\box36
\c@FancyVerbLine=\count113
\FV@StepNumber=\count114
\FV@OutFile=\write3
) (./footnotehyper-sphinx.sty
Package: footnotehyper-sphinx 2017/10/27 v1.7 hyperref aware footnote.sty for s
phinx (JFB)
\FNH@notes=\box37
\FNH@width=\dimen134
)
(/usr/local/texlive/2018/texmf-dist/tex/latex/float/float.sty
Package: float 2001/11/08 v1.3d Float enhancements (AL)
\c@float@type=\count115
\float@exts=\toks25
\float@box=\box38
\@float@everytoks=\toks26
\@floatcapt=\box39
)
(/usr/local/texlive/2018/texmf-dist/tex/latex/wrapfig/wrapfig.sty
\wrapoverhang=\dimen135
\WF@size=\dimen136
\c@WF@wrappedlines=\count116
\WF@box=\box40
\WF@everypar=\toks27
Package: wrapfig 2003/01/31  v 3.6
)
(/usr/local/texlive/2018/texmf-dist/tex/latex/parskip/parskip.sty
Package: parskip 2001/04/09 non-zero parskip adjustments
)
(/usr/local/texlive/2018/texmf-dist/tex/latex/base/alltt.sty
Package: alltt 1997/06/16 v2.0g defines alltt environment
)
(/usr/local/texlive/2018/texmf-dist/tex/latex/upquote/upquote.sty
Package: upquote 2012/04/19 v1.3 upright-quote and grave-accent glyphs in verba
tim
)
(/usr/local/texlive/2018/texmf-dist/tex/latex/capt-of/capt-of.sty
Package: capt-of 2009/12/29 v0.2 standard captions outside of floats
)
(/usr/local/texlive/2018/texmf-dist/tex/latex/needspace/needspace.sty
Package: needspace 2010/09/12 v1.3d reserve vertical space
)
(./sphinxhighlight.sty
Package: sphinxhighlight 2016/05/29 stylesheet for highlighting with pygments
)
(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/kvoptions.sty
Package: kvoptions 2016/05/16 v3.12 Key value format for package options (HO)

(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/kvsetkeys.sty
Package: kvsetkeys 2016/05/16 v1.17 Key value parser (HO)

(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/infwarerr.sty
Package: infwarerr 2016/05/16 v1.4 Providing info/warning/error messages (HO)
)
(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/etexcmds.sty
Package: etexcmds 2016/05/16 v1.6 Avoid name clashes with e-TeX commands (HO)

(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/ifluatex.sty
Package: ifluatex 2016/05/16 v1.4 Provides the ifluatex switch (HO)
Package ifluatex Info: LuaTeX not detected.
)
Package etexcmds Info: Could not find \expanded.
(etexcmds)             That can mean that you are not using pdfTeX 1.50 or
(etexcmds)             that some package has redefined \expanded.
(etexcmds)             In the latter case, load this package earlier.
)))
\sphinxverbatimsep=\dimen137
\sphinxverbatimborder=\dimen138
\sphinxshadowsep=\dimen139
\sphinxshadowsize=\dimen140
\sphinxshadowrule=\dimen141
\spx@notice@border=\dimen142
\spx@image@maxheight=\dimen143
\spx@image@box=\dimen144
\c@literalblock=\count117
\sphinxcontinuationbox=\box41
\sphinxvisiblespacebox=\box42
\sphinxVerbatim@TitleBox=\box43
\py@argswidth=\skip71
\lineblockindentation=\skip72
\DUlineblockindent=\skip73
)
(/usr/local/texlive/2018/texmf-dist/tex/latex/geometry/geometry.sty
Package: geometry 2018/03/24 v5.7 Page Geometry

(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/ifpdf.sty
Package: ifpdf 2017/03/15 v3.2 Provides the ifpdf switch
)
(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/ifvtex.sty
Package: ifvtex 2016/05/16 v1.6 Detect VTeX and its facilities (HO)
Package ifvtex Info: VTeX not detected.
)
(/usr/local/texlive/2018/texmf-dist/tex/generic/ifxetex/ifxetex.sty
Package: ifxetex 2010/09/12 v0.6 Provides ifxetex conditional
)
\Gm@cnth=\count118
\Gm@cntv=\count119
\c@Gm@tempcnt=\count120
\Gm@bindingoffset=\dimen145
\Gm@wd@mp=\dimen146
\Gm@odd@mp=\dimen147
\Gm@even@mp=\dimen148
\Gm@layoutwidth=\dimen149
\Gm@layoutheight=\dimen150
\Gm@layouthoffset=\dimen151
\Gm@layoutvoffset=\dimen152
\Gm@dimlist=\toks28
)
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/hyperref.sty
Package: hyperref 2018/02/06 v6.86b Hypertext links for LaTeX

(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/hobsub-hyperref.sty
Package: hobsub-hyperref 2016/05/16 v1.14 Bundle oberdiek, subset hyperref (HO)


(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/hobsub-generic.sty
Package: hobsub-generic 2016/05/16 v1.14 Bundle oberdiek, subset generic (HO)
Package: hobsub 2016/05/16 v1.14 Construct package bundles (HO)
Package hobsub Info: Skipping package `infwarerr' (already loaded).
Package hobsub Info: Skipping package `ltxcmds' (already loaded).
Package hobsub Info: Skipping package `ifluatex' (already loaded).
Package hobsub Info: Skipping package `ifvtex' (already loaded).
Package: intcalc 2016/05/16 v1.2 Expandable calculations with integers (HO)
Package hobsub Info: Skipping package `ifpdf' (already loaded).
Package hobsub Info: Skipping package `etexcmds' (already loaded).
Package hobsub Info: Skipping package `kvsetkeys' (already loaded).
Package: kvdefinekeys 2016/05/16 v1.4 Define keys (HO)
Package: pdftexcmds 2018/01/30 v0.27 Utility functions of pdfTeX for LuaTeX (HO
)
Package pdftexcmds Info: LuaTeX not detected.
Package pdftexcmds Info: \pdf@primitive is available.
Package pdftexcmds Info: \pdf@ifprimitive is available.
Package pdftexcmds Info: \pdfdraftmode found.
Package: pdfescape 2016/05/16 v1.14 Implements pdfTeX's escape features (HO)
Package: bigintcalc 2016/05/16 v1.4 Expandable calculations on big integers (HO
)
Package: bitset 2016/05/16 v1.2 Handle bit-vector datatype (HO)
Package: uniquecounter 2016/05/16 v1.3 Provide unlimited unique counter (HO)
)
Package hobsub Info: Skipping package `hobsub' (already loaded).
Package: letltxmacro 2016/05/16 v1.5 Let assignment for LaTeX macros (HO)
Package: hopatch 2016/05/16 v1.3 Wrapper for package hooks (HO)
Package: xcolor-patch 2016/05/16 xcolor patch
Package: atveryend 2016/05/16 v1.9 Hooks at the very end of document (HO)
Package atveryend Info: \enddocument detected (standard20110627).
Package: atbegshi 2016/06/09 v1.18 At begin shipout hook (HO)
Package: refcount 2016/05/16 v3.5 Data extraction from label references (HO)
Package: hycolor 2016/05/16 v1.8 Color options for hyperref/bookmark (HO)
)
(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/auxhook.sty
Package: auxhook 2016/05/16 v1.4 Hooks for auxiliary files (HO)
)
\@linkdim=\dimen153
\Hy@linkcounter=\count121
\Hy@pagecounter=\count122

(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/pd1enc.def
File: pd1enc.def 2018/02/06 v6.86b Hyperref: PDFDocEncoding definition (HO)
Now handling font encoding PD1 ...
... no UTF-8 mapping file for font encoding PD1
)
\Hy@SavedSpaceFactor=\count123

(/usr/local/texlive/2018/texmf-dist/tex/latex/latexconfig/hyperref.cfg
File: hyperref.cfg 2002/06/06 v1.2 hyperref configuration of TeXLive
)
Package hyperref Info: Option `unicode' set `true' on input line 4383.

(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/puenc.def
File: puenc.def 2018/02/06 v6.86b Hyperref: PDF Unicode definition (HO)
Now handling font encoding PU ...
... no UTF-8 mapping file for font encoding PU
)
Package hyperref Info: Option `colorlinks' set `true' on input line 4383.
Package hyperref Info: Option `breaklinks' set `true' on input line 4383.
Package hyperref Info: Hyper figures OFF on input line 4509.
Package hyperref Info: Link nesting OFF on input line 4514.
Package hyperref Info: Hyper index ON on input line 4517.
Package hyperref Info: Plain pages OFF on input line 4524.
Package hyperref Info: Backreferencing OFF on input line 4529.
Package hyperref Info: Implicit mode ON; LaTeX internals redefined.
Package hyperref Info: Bookmarks ON on input line 4762.
\c@Hy@tempcnt=\count124

(/usr/local/texlive/2018/texmf-dist/tex/latex/url/url.sty
\Urlmuskip=\muskip11
Package: url 2013/09/16  ver 3.4  Verb mode for urls, etc.
)
LaTeX Info: Redefining \url on input line 5115.
\XeTeXLinkMargin=\dimen154
\Fld@menulength=\count125
\Field@Width=\dimen155
\Fld@charsize=\dimen156
Package hyperref Info: Hyper figures OFF on input line 6369.
Package hyperref Info: Link nesting OFF on input line 6374.
Package hyperref Info: Hyper index ON on input line 6377.
Package hyperref Info: backreferencing OFF on input line 6384.
Package hyperref Info: Link coloring ON on input line 6387.
Package hyperref Info: Link coloring with OCG OFF on input line 6394.
Package hyperref Info: PDF/A mode OFF on input line 6399.
LaTeX Info: Redefining \ref on input line 6439.
LaTeX Info: Redefining \pageref on input line 6443.
\Hy@abspage=\count126
\c@Item=\count127
\c@Hfootnote=\count128
)
Package hyperref Info: Driver (autodetected): hpdftex.

(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/hpdftex.def
File: hpdftex.def 2018/02/06 v6.86b Hyperref driver for pdfTeX
\Fld@listcount=\count129
\c@bookmark@seq@number=\count130

(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty
Package: rerunfilecheck 2016/05/16 v1.8 Rerun checks for auxiliary files (HO)
Package uniquecounter Info: New unique counter `rerunfilecheck' on input line 2
82.
)
\Hy@SectionHShift=\skip74
)
(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/hypcap.sty
Package: hypcap 2016/05/16 v1.12 Adjusting the anchors of captions (HO)
)
(./sphinxmessages.sty
Package: sphinxmessages 2019/01/04 v2.0 Localized LaTeX macros (Sphinx team)
)
\@indexfile=\write4
\openout4 = `PathFlowAI.idx'.


Writing index file PathFlowAI.idx
(./PathFlowAI.aux)
\openout1 = `PathFlowAI.aux'.

LaTeX Font Info:    Checking defaults for OML/cmm/m/it on input line 81.
LaTeX Font Info:    ... okay on input line 81.
LaTeX Font Info:    Checking defaults for T1/cmr/m/n on input line 81.
LaTeX Font Info:    ... okay on input line 81.
LaTeX Font Info:    Checking defaults for OT1/cmr/m/n on input line 81.
LaTeX Font Info:    ... okay on input line 81.
LaTeX Font Info:    Checking defaults for OMS/cmsy/m/n on input line 81.
LaTeX Font Info:    ... okay on input line 81.
LaTeX Font Info:    Checking defaults for OMX/cmex/m/n on input line 81.
LaTeX Font Info:    ... okay on input line 81.
LaTeX Font Info:    Checking defaults for U/cmr/m/n on input line 81.
LaTeX Font Info:    ... okay on input line 81.
LaTeX Font Info:    Checking defaults for TS1/cmr/m/n on input line 81.
LaTeX Font Info:    Try loading font information for TS1+cmr on input line 81.
 (/usr/local/texlive/2018/texmf-dist/tex/latex/base/ts1cmr.fd
File: ts1cmr.fd 2014/09/29 v2.5h Standard LaTeX font definitions
)
LaTeX Font Info:    ... okay on input line 81.
LaTeX Font Info:    Checking defaults for PD1/pdf/m/n on input line 81.
LaTeX Font Info:    ... okay on input line 81.
LaTeX Font Info:    Checking defaults for PU/pdf/m/n on input line 81.
LaTeX Font Info:    ... okay on input line 81.
LaTeX Font Info:    Try loading font information for T1+ptm on input line 81.
 (/usr/local/texlive/2018/texmf-dist/tex/latex/psnfss/t1ptm.fd
File: t1ptm.fd 2001/06/04 font definitions for T1/ptm.
)
(/usr/local/texlive/2018/texmf-dist/tex/context/base/mkii/supp-pdf.mkii
[Loading MPS to PDF converter (version 2006.09.02).]
\scratchcounter=\count131
\scratchdimen=\dimen157
\scratchbox=\box44
\nofMPsegments=\count132
\nofMParguments=\count133
\everyMPshowfont=\toks29
\MPscratchCnt=\count134
\MPscratchDim=\dimen158
\MPnumerator=\count135
\makeMPintoPDFobject=\count136
\everyMPtoPDFconversion=\toks30
) (/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty
Package: epstopdf-base 2016/05/15 v2.6 Base part for package epstopdf

(/usr/local/texlive/2018/texmf-dist/tex/latex/oberdiek/grfext.sty
Package: grfext 2016/05/16 v1.2 Manage graphics extensions (HO)
)
Package epstopdf-base Info: Redefining graphics rule for `.eps' on input line 4
38.
Package grfext Info: Graphics extension search list:
(grfext)             [.pdf,.png,.jpg,.mps,.jpeg,.jbig2,.jb2,.PDF,.PNG,.JPG,.JPE
G,.JBIG2,.JB2,.eps]
(grfext)             \AppendGraphicsExtensions on input line 456.

(/usr/local/texlive/2018/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg
File: epstopdf-sys.cfg 2010/07/13 v1.3 Configuration of (r)epstopdf for TeX Liv
e
))
*geometry* driver: auto-detecting
*geometry* detected driver: pdftex
*geometry* verbose mode - [ preamble ] result:
* driver: pdftex
* paper: letterpaper
* layout: <same size as paper>
* layoutoffset:(h,v)=(0.0pt,0.0pt)
* modes: twoside 
* h-part:(L,W,R)=(72.26999pt, 469.75502pt, 72.26999pt)
* v-part:(T,H,B)=(72.26999pt, 650.43001pt, 72.26999pt)
* \paperwidth=614.295pt
* \paperheight=794.96999pt
* \textwidth=469.75502pt
* \textheight=650.43001pt
* \oddsidemargin=0.0pt
* \evensidemargin=0.0pt
* \topmargin=-37.0pt
* \headheight=12.0pt
* \headsep=25.0pt
* \topskip=10.0pt
* \footskip=30.0pt
* \marginparwidth=36.135pt
* \marginparsep=11.0pt
* \columnsep=10.0pt
* \skip\footins=9.0pt plus 4.0pt minus 2.0pt
* \hoffset=0.0pt
* \voffset=0.0pt
* \mag=1000
* \@twocolumnfalse
* \@twosidetrue
* \@mparswitchtrue
* \@reversemarginfalse
* (1in=72.27pt=25.4mm, 1cm=28.453pt)

\AtBeginShipoutBox=\box45
Package hyperref Info: Link coloring ON on input line 81.
(/usr/local/texlive/2018/texmf-dist/tex/latex/hyperref/nameref.sty
Package: nameref 2016/05/21 v2.44 Cross-referencing by name of section

(/usr/local/texlive/2018/texmf-dist/tex/generic/oberdiek/gettitlestring.sty
Package: gettitlestring 2016/05/16 v1.5 Cleanup title references (HO)
)
\c@section@level=\count137
)
LaTeX Info: Redefining \ref on input line 81.
LaTeX Info: Redefining \pageref on input line 81.
LaTeX Info: Redefining \nameref on input line 81.

(./PathFlowAI.out) (./PathFlowAI.out)
\@outlinefile=\write5
\openout5 = `PathFlowAI.out'.

Package hyperref Info: Option `pageanchor' set `false' on input line 84.
LaTeX Font Info:    Try loading font information for T1+phv on input line 84.

(/usr/local/texlive/2018/texmf-dist/tex/latex/psnfss/t1phv.fd
File: t1phv.fd 2001/06/04 scalable font definitions for T1/phv.
)
LaTeX Font Info:    Font shape `T1/phv/bx/n' in size <10> not available
(Font)              Font shape `T1/phv/b/n' tried instead on input line 84.
LaTeX Font Info:    Font shape `T1/phv/bx/n' in size <24.88> not available
(Font)              Font shape `T1/phv/b/n' tried instead on input line 84.
LaTeX Font Info:    Font shape `T1/phv/bx/it' in size <10> not available
(Font)              Font shape `T1/phv/b/it' tried instead on input line 84.
LaTeX Font Info:    Font shape `T1/phv/b/it' in size <10> not available
(Font)              Font shape `T1/phv/b/sl' tried instead on input line 84.
LaTeX Font Info:    Font shape `T1/phv/bx/it' in size <17.28> not available
(Font)              Font shape `T1/phv/b/it' tried instead on input line 84.
LaTeX Font Info:    Font shape `T1/phv/b/it' in size <17.28> not available
(Font)              Font shape `T1/phv/b/sl' tried instead on input line 84.
LaTeX Font Info:    Font shape `T1/phv/bx/n' in size <17.28> not available
(Font)              Font shape `T1/phv/b/n' tried instead on input line 84.
<<ot1.cmap>><<oml.cmap>><<oms.cmap>><<omx.cmap>>
LaTeX Font Info:    Try loading font information for U+msa on input line 84.

(/usr/local/texlive/2018/texmf-dist/tex/latex/amsfonts/umsa.fd
File: umsa.fd 2013/01/14 v3.01 AMS symbols A
)
LaTeX Font Info:    Try loading font information for U+msb on input line 84.

(/usr/local/texlive/2018/texmf-dist/tex/latex/amsfonts/umsb.fd
File: umsb.fd 2013/01/14 v3.01 AMS symbols B
)
LaTeX Font Info:    Font shape `T1/phv/bx/n' in size <12> not available
(Font)              Font shape `T1/phv/b/n' tried instead on input line 84.
 [1

{/usr/local/texlive/2018/texmf-var/fonts/map/pdftex/updmap/pdftex.map}] [2


]
LaTeX Font Info:    Font shape `T1/phv/bx/n' in size <14.4> not available
(Font)              Font shape `T1/phv/b/n' tried instead on input line 86.

(./PathFlowAI.toc
LaTeX Font Info:    Font shape `T1/ptm/bx/n' in size <10> not available
(Font)              Font shape `T1/ptm/b/n' tried instead on input line 2.
)
\tf@toc=\write6
\openout6 = `PathFlowAI.toc'.

 [1

] [2

]
<1.jpeg, id=149, 1027.84pt x 770.88pt>
LaTeX Font Info:    Try loading font information for T1+pcr on input line 91.

(/usr/local/texlive/2018/texmf-dist/tex/latex/psnfss/t1pcr.fd
File: t1pcr.fd 2001/06/04 font definitions for T1/pcr.
)
File: 1.jpeg Graphic file (type jpg)
<use 1.jpeg>
Package pdftex.def Info: 1.jpeg  used on input line 91.
(pdftex.def)             Requested size: 361.3491pt x 271.01184pt.
<2.jpeg, id=150, 1027.84pt x 770.88pt>
File: 2.jpeg Graphic file (type jpg)
<use 2.jpeg>
Package pdftex.def Info: 2.jpeg  used on input line 93.
(pdftex.def)             Requested size: 361.3491pt x 271.01184pt.
<3.jpeg, id=151, 1027.84pt x 770.88pt>
File: 3.jpeg Graphic file (type jpg)
<use 3.jpeg>
Package pdftex.def Info: 3.jpeg  used on input line 95.
(pdftex.def)             Requested size: 361.3491pt x 271.01184pt.
 [1 <./1.jpeg> <./2.jpeg>]
<4.jpeg, id=157, 1027.84pt x 770.88pt>
File: 4.jpeg Graphic file (type jpg)
<use 4.jpeg>
Package pdftex.def Info: 4.jpeg  used on input line 97.
(pdftex.def)             Requested size: 361.3491pt x 271.01184pt.
 [2 <./3.jpeg> <./4.jpeg>]
Chapter 1.
LaTeX Font Info:    Font shape `T1/pcr/bx/n' in size <10> not available
(Font)              Font shape `T1/pcr/b/n' tried instead on input line 109.
[3

] [4] [5] [6

]
Chapter 2.
[7] [8] [9] [10] [11] [12

]
Chapter 3.
[13] [14

]
Chapter 4.

Underfull \hbox (badness 10000) in paragraph at lines 1017--1017
[]\T1/ptm/m/it/10 dataset_df\T1/ptm/m/n/10 , \T1/ptm/m/it/10 set\T1/ptm/m/n/10 
, \T1/ptm/m/it/10 patch_info_file\T1/ptm/m/n/10 ,
 []


Underfull \hbox (badness 10000) in paragraph at lines 1017--1017
\T1/ptm/m/it/10 trans-form-ers\T1/ptm/m/n/10 , \T1/ptm/m/it/10 in-put_dir\T1/pt
m/m/n/10 , \T1/ptm/m/it/10 tar-
 []


Underfull \hbox (badness 10000) in paragraph at lines 1017--1017
\T1/ptm/m/it/10 get_names\T1/ptm/m/n/10 , \T1/ptm/m/it/10 pos_annotation_class\
T1/ptm/m/n/10 ,
 []


Underfull \hbox (badness 10000) in paragraph at lines 1017--1017
\T1/ptm/m/it/10 other_annotations=[]\T1/ptm/m/n/10 ,
 []


Underfull \hbox (badness 10000) in paragraph at lines 1017--1017
\T1/ptm/m/it/10 seg-men-ta-tion=False\T1/ptm/m/n/10 ,
 []


Underfull \hbox (badness 10000) in paragraph at lines 1017--1017
\T1/ptm/m/it/10 patch_size=224\T1/ptm/m/n/10 , \T1/ptm/m/it/10 fix_names=True\T
1/ptm/m/n/10 ,
 []


Underfull \hbox (badness 10000) in paragraph at lines 1017--1017
\T1/ptm/m/it/10 target_segmentation_class=-
 []


Underfull \hbox (badness 10000) in paragraph at lines 1017--1017
\T1/ptm/m/it/10 1\T1/ptm/m/n/10 , \T1/ptm/m/it/10 tar-get_threshold=0.0\T1/ptm/
m/n/10 ,
 []


Underfull \hbox (badness 10000) in paragraph at lines 1017--1017
\T1/ptm/m/it/10 over-sam-pling_factor=1.0\T1/ptm/m/n/10 ,
 []


Underfull \hbox (badness 10000) in paragraph at lines 1017--1017
\T1/ptm/m/it/10 n_segmentation_classes=4\T1/ptm/m/n/10 ,
 []


Underfull \hbox (badness 10000) in paragraph at lines 1017--1017
\T1/ptm/m/it/10 gdl=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 mt_bce=False\T1/ptm/m
/n/10 , \T1/ptm/m/it/10 clas-
 []

[15]
LaTeX Font Info:    Font shape `T1/pcr/m/it' in size <10> not available
(Font)              Font shape `T1/pcr/m/sl' tried instead on input line 1098.
 [16] [17] [18]
Chapter 5.
LaTeX Font Info:    Try loading font information for TS1+ptm on input line 1397
.
(/usr/local/texlive/2018/texmf-dist/tex/latex/psnfss/ts1ptm.fd
File: ts1ptm.fd 2001/06/04 font definitions for TS1/ptm.
) [19

]
Overfull \hbox (6.0pt too wide) in paragraph at lines 1600--1600
[]| 
 []


Underfull \hbox (badness 10000) in paragraph at lines 1--1663
[][]$\T1/ptm/m/n/10 https : / / raw . githubusercontent . com / inferno-[]pytor
ch / inferno / 0561e8a95cde6bfc5e10a3609841b7b0ca5b03ca /
 []

[20] [21]
Overfull \hbox (6.0pt too wide) in paragraph at lines 1847--1847
[]| 
 []


Underfull \hbox (badness 10000) in paragraph at lines 1--1919
[][]$\T1/ptm/m/n/10 https : / / raw . githubusercontent . com / inferno-[]pytor
ch / inferno / 0561e8a95cde6bfc5e10a3609841b7b0ca5b03ca /
 []


Underfull \hbox (badness 10000) in paragraph at lines 1--1945
[][]$\T1/ptm/m/n/10 https : / / raw . githubusercontent . com / inferno-[]pytor
ch / inferno / 0561e8a95cde6bfc5e10a3609841b7b0ca5b03ca /
 []

[22] [23] [24

]
Chapter 6.

Underfull \hbox (badness 10000) in paragraph at lines 2004--2004
[]\T1/ptm/m/it/10 dataset\T1/ptm/m/n/10 , \T1/ptm/m/it/10 in-dices=None\T1/ptm/
m/n/10 ,
 []

[25] [26

]
Chapter 7.

Underfull \hbox (badness 10000) in paragraph at lines 2024--2024
[]\T1/ptm/m/it/10 optimizer\T1/ptm/m/n/10 , \T1/ptm/m/it/10 T_max\T1/ptm/m/n/10
 ,
 []


Underfull \hbox (badness 10000) in paragraph at lines 2024--2024
\T1/ptm/m/it/10 eta_min=0\T1/ptm/m/n/10 ,
 []


Underfull \hbox (badness 10000) in paragraph at lines 2024--2024
\T1/ptm/m/it/10 last_epoch=-1\T1/ptm/m/n/10 ,
 []


Underfull \hbox (badness 10000) in paragraph at lines 2024--2024
\T1/ptm/m/it/10 T_mult=1.0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 al-
 []


Overfull \hbox (6.0pt too wide) in paragraph at lines 2106--2106
[]| 
 []


Overfull \hbox (6.0pt too wide) in paragraph at lines 2106--2106
[]| 
 []


Overfull \hbox (6.0pt too wide) in paragraph at lines 2106--2106
[]| 
 []


Overfull \hbox (6.0pt too wide) in paragraph at lines 2106--2106
[]| 
 []

[27] [28]
Chapter 8.

Underfull \hbox (badness 10000) in paragraph at lines 2307--2307
[]\T1/ptm/m/it/10 dask_arr_dict\T1/ptm/m/n/10 , \T1/ptm/m/it/10 patch_info_db\T
1/ptm/m/n/10 , \T1/ptm/m/it/10 com-
 []


Underfull \hbox (badness 10000) in paragraph at lines 2307--2307
\T1/ptm/m/it/10 pres-sion_factor=3\T1/ptm/m/n/10 , \T1/ptm/m/it/10 al-pha=0.5\T
1/ptm/m/n/10 ,
 []


Underfull \hbox (badness 10000) in paragraph at lines 2307--2307
\T1/ptm/m/it/10 patch_size=224\T1/ptm/m/n/10 , \T1/ptm/m/it/10 no_db=False\T1/p
tm/m/n/10 ,
 []


Underfull \hbox (badness 10000) in paragraph at lines 2307--2307
\T1/ptm/m/it/10 plot_annotation=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 seg-men-t
a-
 []


Underfull \hbox (badness 10000) in paragraph at lines 2307--2307
\T1/ptm/m/it/10 tion=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 n_segmentation_class
es=4\T1/ptm/m/n/10 ,
 []

[29

]
Underfull \hbox (badness 5374) in paragraph at lines 2370--2371
[]|[][]\T1/pcr/m/sl/10 add_custom_segmentation[][]\T1/ptm/m/n/10 (self, base-na
me,
 []

[30]
Underfull \hbox (badness 10000) in paragraph at lines 2547--2547
[]\T1/ptm/m/it/10 image_file\T1/ptm/m/n/10 , \T1/ptm/m/it/10 com-pres-sion_fact
or=2.0\T1/ptm/m/n/10 ,
 []

[31]
Underfull \hbox (badness 5189) in paragraph at lines 2569--2569
\T1/ptm/m/it/10 name\T1/ptm/m/n/10 , \T1/ptm/m/it/10 n_outputs=1\T1/ptm/m/n/10 
, \T1/ptm/m/it/10 method='deep'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 lo-cal_smoothin
g=0.0\T1/ptm/m/n/10 ,
 []


Underfull \hbox (badness 10000) in paragraph at lines 2612--2612
[]\T1/ptm/m/it/10 dask_arr_dict\T1/ptm/m/n/10 , \T1/ptm/m/it/10 em-bed-dings_fi
le\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ID=None\T1/ptm/m/n/10 ,
 []


Underfull \hbox (badness 10000) in paragraph at lines 2612--2612
\T1/ptm/m/it/10 cval=1.0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 im-age_res=300.0\T1/pt
m/m/n/10 , \T1/ptm/m/it/10 out-putf-
 []


Underfull \hbox (badness 10000) in paragraph at lines 2612--2612
\T1/ptm/m/it/10 name='output_embedding.png'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 mpl
_scatter=True\T1/ptm/m/n/10 ,
 []


Underfull \hbox (badness 10000) in paragraph at lines 2612--2612
\T1/ptm/m/it/10 re-move_background_annotation=''\T1/ptm/m/n/10 ,
 []


Underfull \hbox (badness 10000) in paragraph at lines 2612--2612
\T1/ptm/m/it/10 max_background_area=0.01\T1/ptm/m/n/10 , \T1/ptm/m/it/10 zoom=0
.05\T1/ptm/m/n/10 ,
 []

[32] [33] [34

]
Chapter 9.
[35]
Underfull \hbox (badness 10000) in paragraph at lines 2933--2933
[]\T1/ptm/m/it/10 basename\T1/ptm/m/n/10 , \T1/ptm/m/it/10 in-put_dir='./'\T1/p
tm/m/n/10 , \T1/ptm/m/it/10 an-no-ta-tions=[]\T1/ptm/m/n/10 ,
 []


Underfull \hbox (badness 10000) in paragraph at lines 2933--2933
\T1/ptm/m/it/10 thresh-old=0.5\T1/ptm/m/n/10 , \T1/ptm/m/it/10 patch_size=224\T
1/ptm/m/n/10 , \T1/ptm/m/it/10 gen-er-
 []


Underfull \hbox (badness 10000) in paragraph at lines 2933--2933
\T1/ptm/m/it/10 ate_finetune_segmentation=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10
 tar-
 []


Underfull \hbox (badness 10000) in paragraph at lines 2933--2933
\T1/ptm/m/it/10 get_class=0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 in-ten-sity_thresho
ld=100.0\T1/ptm/m/n/10 ,
 []


Underfull \hbox (badness 10000) in paragraph at lines 2933--2933
\T1/ptm/m/it/10 tar-get_threshold=0.0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 adj_mask=
''\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ba-
 []

[36]
Underfull \hbox (badness 10000) in paragraph at lines 3004--3004
[]\T1/ptm/m/it/10 basename\T1/ptm/m/n/10 , \T1/ptm/m/it/10 in-put_dir='./'\T1/p
tm/m/n/10 , \T1/ptm/m/it/10 an-no-ta-
 []


Underfull \hbox (badness 10000) in paragraph at lines 3004--3004
\T1/ptm/m/it/10 tions=[]\T1/ptm/m/n/10 , \T1/ptm/m/it/10 thresh-old=0.5\T1/ptm/
m/n/10 , \T1/ptm/m/it/10 patch_size=224\T1/ptm/m/n/10 ,
 []


Underfull \hbox (badness 10000) in paragraph at lines 3004--3004
\T1/ptm/m/it/10 out_db='patch_info.db'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 gen-er-
 []


Underfull \hbox (badness 10000) in paragraph at lines 3004--3004
\T1/ptm/m/it/10 ate_finetune_segmentation=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10
 tar-
 []


Underfull \hbox (badness 10000) in paragraph at lines 3004--3004
\T1/ptm/m/it/10 get_class=0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 in-ten-sity_thresho
ld=100.0\T1/ptm/m/n/10 ,
 []


Underfull \hbox (badness 10000) in paragraph at lines 3004--3004
\T1/ptm/m/it/10 tar-get_threshold=0.0\T1/ptm/m/n/10 , \T1/ptm/m/it/10 adj_mask=
''\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ba-
 []

[37] [38]
Underfull \hbox (badness 10000) in paragraph at lines 3216--3216
[]\T1/ptm/m/it/10 svs_file\T1/ptm/m/n/10 , \T1/ptm/m/it/10 xml_file=None\T1/ptm
/m/n/10 , \T1/ptm/m/it/10 npy_mask=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 an-no-t
a-
 []

LaTeX Font Info:    Try loading font information for TS1+pcr on input line 1.
(/usr/local/texlive/2018/texmf-dist/tex/latex/psnfss/ts1pcr.fd
File: ts1pcr.fd 2001/06/04 font definitions for TS1/pcr.
)
LaTeX Font Info:    Font shape `TS1/pcr/bx/n' in size <10> not available
(Font)              Font shape `TS1/pcr/b/n' tried instead on input line 1.
 [39]
Underfull \hbox (badness 10000) in paragraph at lines 3343--3343
[]\T1/ptm/m/it/10 xml_file\T1/ptm/m/n/10 , \T1/ptm/m/it/10 an-no-ta-tion_name='
'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 re-
 []


Underfull \hbox (badness 10000) in paragraph at lines 3420--3420
[]\T1/ptm/m/it/10 svs_file\T1/ptm/m/n/10 , \T1/ptm/m/it/10 xml_file=None\T1/ptm
/m/n/10 ,
 []


Underfull \hbox (badness 10000) in paragraph at lines 3420--3420
\T1/ptm/m/it/10 npy_mask=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 an-no-ta-tions=[]
\T1/ptm/m/n/10 ,
 []


Underfull \hbox (badness 10000) in paragraph at lines 3420--3420
\T1/ptm/m/it/10 out_zarr='output_zarr.zarr'\T1/ptm/m/n/10 ,
 []

[40]
Underfull \hbox (badness 10000) in paragraph at lines 3451--3451
[]\T1/ptm/m/it/10 basenames\T1/ptm/m/n/10 , \T1/ptm/m/it/10 in-put_dir='./'\T1/
ptm/m/n/10 , \T1/ptm/m/it/10 an-no-ta-tions=[]\T1/ptm/m/n/10 ,
 []


Underfull \hbox (badness 10000) in paragraph at lines 3451--3451
\T1/ptm/m/it/10 thresh-old=0.5\T1/ptm/m/n/10 , \T1/ptm/m/it/10 patch_size=224\T
1/ptm/m/n/10 , \T1/ptm/m/it/10 out-
 []

LaTeX Font Info:    Font shape `T1/pcr/bx/n' in size <9> not available
(Font)              Font shape `T1/pcr/b/n' tried instead on input line 3537.
[41] [42]
Chapter 10.
[43

] [44

] [45


] (./PathFlowAI.ind [46


]
Underfull \hbox (badness 10000) in paragraph at lines 9--10
[]| \T1/pcr/m/n/10 pathflowai-monitor command line
 []


Underfull \hbox (badness 10000) in paragraph at lines 10--11
[]| \T1/pcr/m/n/10 pathflowai-preprocess command line
 []


Underfull \hbox (badness 10000) in paragraph at lines 11--12
[]| \T1/pcr/m/n/10 pathflowai-visualize command line
 []


Overfull \hbox (54.1225pt too wide) in paragraph at lines 13--15
[]| \T1/pcr/m/n/10 pathflowai-visualize-overlay_new_annotations
 []


Overfull \hbox (36.1225pt too wide) in paragraph at lines 16--18
[]| \T1/pcr/m/n/10 pathflowai-preprocess-preprocess_pipeline
 []


Overfull \hbox (6.1225pt too wide) in paragraph at lines 18--19
[]| \T1/pcr/m/n/10 pathflowai-visualize-plot_embeddings
 []


Overfull \hbox (12.1225pt too wide) in paragraph at lines 20--21
[]| \T1/pcr/m/n/10 pathflowai-visualize-plot_predictions
 []


Overfull \hbox (12.1225pt too wide) in paragraph at lines 22--23
[]| \T1/pcr/m/n/10 pathflowai-visualize-plot_predictions
 []


Overfull \hbox (36.1225pt too wide) in paragraph at lines 24--26
[]| \T1/pcr/m/n/10 pathflowai-preprocess-preprocess_pipeline
 []


Overfull \hbox (12.1225pt too wide) in paragraph at lines 27--28
[]| \T1/pcr/m/n/10 pathflowai-visualize-plot_predictions
 []


Overfull \hbox (36.1225pt too wide) in paragraph at lines 29--31
[]| \T1/pcr/m/n/10 pathflowai-preprocess-preprocess_pipeline
 []


Overfull \hbox (60.1225pt too wide) in paragraph at lines 31--33
[]| \T1/pcr/m/n/10 pathflowai-preprocess-remove_basename_from_db
 []


Underfull \hbox (badness 10000) in paragraph at lines 33--34
[]| \T1/pcr/m/n/10 pathflowai-visualize-extract_patch
 []


Overfull \hbox (6.1225pt too wide) in paragraph at lines 34--35
[]| \T1/pcr/m/n/10 pathflowai-visualize-plot_embeddings
 []


Overfull \hbox (72.1225pt too wide) in paragraph at lines 35--37
[]| \T1/pcr/m/n/10 pathflowai-visualize-plot_image_umap_embeddings
 []


Overfull \hbox (12.1225pt too wide) in paragraph at lines 37--38
[]| \T1/pcr/m/n/10 pathflowai-visualize-plot_predictions
 []


Overfull \hbox (36.1225pt too wide) in paragraph at lines 39--41
[]| \T1/pcr/m/n/10 pathflowai-preprocess-preprocess_pipeline
 []


Underfull \hbox (badness 10000) in paragraph at lines 42--43
[]| \T1/pcr/m/n/10 pathflowai-visualize-shapley_plot
 []


Underfull \hbox (badness 10000) in paragraph at lines 43--44
[]\T1/pcr/m/n/10 -c, --custom_segmentation
 []


Underfull \hbox (badness 10000) in paragraph at lines 44--45
[]| \T1/pcr/m/n/10 pathflowai-visualize-extract_patch
 []


Overfull \hbox (12.1225pt too wide) in paragraph at lines 45--46
[]| \T1/pcr/m/n/10 pathflowai-visualize-plot_predictions
 []


Underfull \hbox (badness 10000) in paragraph at lines 46--47
[]\T1/pcr/m/n/10 -cf, --compression_factor
 []


Overfull \hbox (54.1225pt too wide) in paragraph at lines 47--49
[]| \T1/pcr/m/n/10 pathflowai-visualize-overlay_new_annotations
 []


Underfull \hbox (badness 10000) in paragraph at lines 49--50
[]| \T1/pcr/m/n/10 pathflowai-visualize-plot_image
 []


Overfull \hbox (12.1225pt too wide) in paragraph at lines 50--51
[]| \T1/pcr/m/n/10 pathflowai-visualize-plot_predictions
 []


Underfull \hbox (badness 10000) in paragraph at lines 51--52
[]\T1/pcr/m/n/10 -csv, --records_output_csv
 []


Underfull \hbox (badness 10000) in paragraph at lines 52--53
[]| \T1/pcr/m/n/10 pathflowai-monitor-monitor_usage
 []


Underfull \hbox (badness 10000) in paragraph at lines 54--55
[]| \T1/pcr/m/n/10 pathflowai-monitor-monitor_usage
 []


Overfull \hbox (72.1225pt too wide) in paragraph at lines 56--58
[]| \T1/pcr/m/n/10 pathflowai-visualize-plot_image_umap_embeddings
 []


Underfull \hbox (badness 10000) in paragraph at lines 58--59
[]\T1/pcr/m/n/10 -fr, --from_annotations
 []


Underfull \hbox (badness 10000) in paragraph at lines 59--60
[]| \T1/pcr/m/n/10 pathflowai-preprocess-alter_masks
 []


Overfull \hbox (42.1225pt too wide) in paragraph at lines 60--62
[]| \T1/pcr/m/n/10 pathflowai-preprocess-collapse_annotations
 []


Overfull \hbox (36.1225pt too wide) in paragraph at lines 63--65
[]| \T1/pcr/m/n/10 pathflowai-preprocess-preprocess_pipeline
 []


Overfull \hbox (6.1225pt too wide) in paragraph at lines 66--67
[]| \T1/pcr/m/n/10 pathflowai-visualize-plot_embeddings
 []


Underfull \hbox (badness 10000) in paragraph at lines 68--69
[]| \T1/pcr/m/n/10 pathflowai-visualize-plot_image
 []

[47

]
Overfull \hbox (54.1225pt too wide) in paragraph at lines 70--72
[]| \T1/pcr/m/n/10 pathflowai-visualize-overlay_new_annotations
 []


Overfull \hbox (36.1225pt too wide) in paragraph at lines 73--75
[]| \T1/pcr/m/n/10 pathflowai-preprocess-preprocess_pipeline
 []


Underfull \hbox (badness 10000) in paragraph at lines 75--76
[]| \T1/pcr/m/n/10 pathflowai-visualize-extract_patch
 []


Overfull \hbox (72.1225pt too wide) in paragraph at lines 76--78
[]| \T1/pcr/m/n/10 pathflowai-visualize-plot_image_umap_embeddings
 []


Overfull \hbox (12.1225pt too wide) in paragraph at lines 78--79
[]| \T1/pcr/m/n/10 pathflowai-visualize-plot_predictions
 []


Overfull \hbox (42.1225pt too wide) in paragraph at lines 80--82
[]| \T1/pcr/m/n/10 pathflowai-preprocess-collapse_annotations
 []


Overfull \hbox (60.1225pt too wide) in paragraph at lines 82--84
[]| \T1/pcr/m/n/10 pathflowai-preprocess-remove_basename_from_db
 []


Underfull \hbox (badness 10000) in paragraph at lines 85--86
[]| \T1/pcr/m/n/10 pathflowai-preprocess-alter_masks
 []


Underfull \hbox (badness 10000) in paragraph at lines 86--87
[]\T1/pcr/m/n/10 -it, --intensity_threshold
 []


Overfull \hbox (36.1225pt too wide) in paragraph at lines 87--89
[]| \T1/pcr/m/n/10 pathflowai-preprocess-preprocess_pipeline
 []


Underfull \hbox (badness 10000) in paragraph at lines 90--91
[]| \T1/pcr/m/n/10 pathflowai-visualize-shapley_plot
 []


Underfull \hbox (badness 10000) in paragraph at lines 92--93
[]| \T1/pcr/m/n/10 pathflowai-visualize-shapley_plot
 []


Underfull \hbox (badness 10000) in paragraph at lines 93--94
[]\T1/pcr/m/n/10 -ma, --max_background_area
 []


Overfull \hbox (42.1225pt too wide) in paragraph at lines 94--96
[]| \T1/pcr/m/n/10 pathflowai-preprocess-collapse_annotations
 []


Overfull \hbox (6.1225pt too wide) in paragraph at lines 96--97
[]| \T1/pcr/m/n/10 pathflowai-visualize-plot_embeddings
 []


Overfull \hbox (72.1225pt too wide) in paragraph at lines 97--99
[]| \T1/pcr/m/n/10 pathflowai-visualize-plot_image_umap_embeddings
 []


Overfull \hbox (72.1225pt too wide) in paragraph at lines 100--102
[]| \T1/pcr/m/n/10 pathflowai-visualize-plot_image_umap_embeddings
 []


Underfull \hbox (badness 10000) in paragraph at lines 103--104
[]| \T1/pcr/m/n/10 pathflowai-visualize-shapley_plot
 []


Overfull \hbox (36.1225pt too wide) in paragraph at lines 105--107
[]| \T1/pcr/m/n/10 pathflowai-preprocess-preprocess_pipeline
 []


Overfull \hbox (6.1225pt too wide) in paragraph at lines 107--108
[]| \T1/pcr/m/n/10 pathflowai-visualize-plot_embeddings
 []


Overfull \hbox (72.1225pt too wide) in paragraph at lines 108--110
[]| \T1/pcr/m/n/10 pathflowai-visualize-plot_image_umap_embeddings
 []


Overfull \hbox (36.1225pt too wide) in paragraph at lines 111--113
[]| \T1/pcr/m/n/10 pathflowai-preprocess-preprocess_pipeline
 []


Underfull \hbox (badness 10000) in paragraph at lines 114--115
[]| \T1/pcr/m/n/10 pathflowai-visualize-shapley_plot
 []


Underfull \hbox (badness 10000) in paragraph at lines 116--117
[]| \T1/pcr/m/n/10 pathflowai-preprocess-alter_masks
 []


Overfull \hbox (42.1225pt too wide) in paragraph at lines 118--120
[]| \T1/pcr/m/n/10 pathflowai-preprocess-collapse_annotations
 []


Overfull \hbox (60.1225pt too wide) in paragraph at lines 120--122
[]| \T1/pcr/m/n/10 pathflowai-preprocess-remove_basename_from_db
 []


Overfull \hbox (54.1225pt too wide) in paragraph at lines 123--125
[]| \T1/pcr/m/n/10 pathflowai-visualize-overlay_new_annotations
 []


Overfull \hbox (72.1225pt too wide) in paragraph at lines 125--127
[]| \T1/pcr/m/n/10 pathflowai-visualize-plot_image_umap_embeddings
 []


Underfull \hbox (badness 10000) in paragraph at lines 127--128
[]| \T1/pcr/m/n/10 pathflowai-visualize-shapley_plot
 []


Underfull \hbox (badness 10000) in paragraph at lines 129--130
[]| \T1/pcr/m/n/10 pathflowai-visualize-extract_patch
 []


Underfull \hbox (badness 10000) in paragraph at lines 130--131
[]| \T1/pcr/m/n/10 pathflowai-visualize-plot_image
 []


Overfull \hbox (12.1225pt too wide) in paragraph at lines 131--132
[]| \T1/pcr/m/n/10 pathflowai-visualize-plot_predictions
 []


Underfull \hbox (badness 10000) in paragraph at lines 132--133
[]\T1/pcr/m/n/10 -o, --plotly_output_file
 []


Overfull \hbox (6.1225pt too wide) in paragraph at lines 133--134
[]| \T1/pcr/m/n/10 pathflowai-visualize-plot_embeddings
 []


Underfull \hbox (badness 10000) in paragraph at lines 134--135
[]\T1/pcr/m/n/10 -ocf, --original_compression_factor
 []


Overfull \hbox (54.1225pt too wide) in paragraph at lines 135--137
[]| \T1/pcr/m/n/10 pathflowai-visualize-overlay_new_annotations
 []


Overfull \hbox (36.1225pt too wide) in paragraph at lines 138--140
[]| \T1/pcr/m/n/10 pathflowai-preprocess-preprocess_pipeline
 []


Underfull \hbox (badness 10000) in paragraph at lines 141--142
[]| \T1/pcr/m/n/10 pathflowai-visualize-extract_patch
 []


Overfull \hbox (12.1225pt too wide) in paragraph at lines 142--143
[]| \T1/pcr/m/n/10 pathflowai-visualize-plot_predictions
 []


Underfull \hbox (badness 10000) in paragraph at lines 144--145
[]| \T1/pcr/m/n/10 pathflowai-visualize-shapley_plot
 []


Overfull \hbox (36.1225pt too wide) in paragraph at lines 146--148
[]| \T1/pcr/m/n/10 pathflowai-preprocess-preprocess_pipeline
 []


Overfull \hbox (36.1225pt too wide) in paragraph at lines 149--151
[]| \T1/pcr/m/n/10 pathflowai-preprocess-preprocess_pipeline
 []


Overfull \hbox (42.1225pt too wide) in paragraph at lines 152--154
[]| \T1/pcr/m/n/10 pathflowai-preprocess-collapse_annotations
 []

[48]
Overfull \hbox (36.1225pt too wide) in paragraph at lines 154--156
[]| \T1/pcr/m/n/10 pathflowai-preprocess-preprocess_pipeline
 []


Overfull \hbox (60.1225pt too wide) in paragraph at lines 156--158
[]| \T1/pcr/m/n/10 pathflowai-preprocess-remove_basename_from_db
 []


Underfull \hbox (badness 10000) in paragraph at lines 158--159
[]| \T1/pcr/m/n/10 pathflowai-visualize-extract_patch
 []


Overfull \hbox (12.1225pt too wide) in paragraph at lines 159--160
[]| \T1/pcr/m/n/10 pathflowai-visualize-plot_predictions
 []


Underfull \hbox (badness 10000) in paragraph at lines 160--161
[]\T1/pcr/m/n/10 -rb, --remove_background_annotation
 []


Overfull \hbox (42.1225pt too wide) in paragraph at lines 161--163
[]| \T1/pcr/m/n/10 pathflowai-preprocess-collapse_annotations
 []


Overfull \hbox (6.1225pt too wide) in paragraph at lines 163--164
[]| \T1/pcr/m/n/10 pathflowai-visualize-plot_embeddings
 []


Overfull \hbox (72.1225pt too wide) in paragraph at lines 164--166
[]| \T1/pcr/m/n/10 pathflowai-visualize-plot_image_umap_embeddings
 []


Underfull \hbox (badness 10000) in paragraph at lines 167--168
[]| \T1/pcr/m/n/10 pathflowai-visualize-extract_patch
 []


Overfull \hbox (12.1225pt too wide) in paragraph at lines 168--169
[]| \T1/pcr/m/n/10 pathflowai-visualize-plot_predictions
 []


Underfull \hbox (badness 10000) in paragraph at lines 169--170
[]\T1/pcr/m/n/10 -sc, --n_segmentation_classes
 []


Underfull \hbox (badness 10000) in paragraph at lines 170--171
[]| \T1/pcr/m/n/10 pathflowai-visualize-extract_patch
 []


Overfull \hbox (12.1225pt too wide) in paragraph at lines 171--172
[]| \T1/pcr/m/n/10 pathflowai-visualize-plot_predictions
 []


Overfull \hbox (72.1225pt too wide) in paragraph at lines 173--175
[]| \T1/pcr/m/n/10 pathflowai-visualize-plot_image_umap_embeddings
 []


Overfull \hbox (12.1225pt too wide) in paragraph at lines 176--177
[]| \T1/pcr/m/n/10 pathflowai-visualize-plot_predictions
 []


Overfull \hbox (72.1225pt too wide) in paragraph at lines 178--180
[]| \T1/pcr/m/n/10 pathflowai-visualize-plot_image_umap_embeddings
 []


Overfull \hbox (36.1225pt too wide) in paragraph at lines 181--183
[]| \T1/pcr/m/n/10 pathflowai-preprocess-preprocess_pipeline
 []


Underfull \hbox (badness 10000) in paragraph at lines 183--184
[]\T1/pcr/m/n/10 -tc, --target_segmentation_class
 []


Overfull \hbox (36.1225pt too wide) in paragraph at lines 184--186
[]| \T1/pcr/m/n/10 pathflowai-preprocess-preprocess_pipeline
 []


Overfull \hbox (12.1225pt too wide) in paragraph at lines 187--188
[]| \T1/pcr/m/n/10 pathflowai-visualize-plot_predictions
 []


Underfull \hbox (badness 10000) in paragraph at lines 189--190
[]| \T1/pcr/m/n/10 pathflowai-preprocess-alter_masks
 []


Overfull \hbox (42.1225pt too wide) in paragraph at lines 190--192
[]| \T1/pcr/m/n/10 pathflowai-preprocess-collapse_annotations
 []


Underfull \hbox (badness 10000) in paragraph at lines 192--193
[]\T1/pcr/m/n/10 -tt, --target_threshold
 []


Overfull \hbox (36.1225pt too wide) in paragraph at lines 193--195
[]| \T1/pcr/m/n/10 pathflowai-preprocess-preprocess_pipeline
 []


Underfull \hbox (badness 10000) in paragraph at lines 196--197
[]| \T1/pcr/m/n/10 pathflowai-monitor-monitor_usage
 []


Underfull \hbox (badness 10000) in paragraph at lines 198--199
[]| \T1/pcr/m/n/10 pathflowai-visualize-extract_patch
 []


Underfull \hbox (badness 10000) in paragraph at lines 200--201
[]| \T1/pcr/m/n/10 pathflowai-visualize-extract_patch
 []


Overfull \hbox (72.1225pt too wide) in paragraph at lines 202--204
[]| \T1/pcr/m/n/10 pathflowai-visualize-plot_image_umap_embeddings
 []


Underfull \hbox (badness 10000) in paragraph at lines 207--209
[]\T1/pcr/m/n/10 add_custom_segmentation() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 path
-
 []


Underfull \hbox (badness 10000) in paragraph at lines 207--209
\T1/ptm/m/it/10 flowai.visualize.PredictionPlotter method\T1/ptm/m/n/10 ),
 []


Underfull \hbox (badness 10000) in paragraph at lines 217--219
[]\T1/pcr/m/n/10 binarize_annotations() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 path-
 []


Underfull \hbox (badness 10000) in paragraph at lines 217--219
\T1/ptm/m/it/10 flowai.datasets.DynamicImageDataset
 []


Underfull \hbox (badness 10000) in paragraph at lines 227--229
[]\T1/pcr/m/n/10 CosineAnnealingWithRestartsLR \T1/ptm/m/n/10 (\T1/ptm/m/it/10 
class in
 []


Underfull \hbox (badness 10000) in paragraph at lines 229--230
[]\T1/pcr/m/n/10 create_purple_mask() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul
e path-
 []


Underfull \hbox (badness 10000) in paragraph at lines 230--232
[]\T1/pcr/m/n/10 create_sparse_annotation_arrays() \T1/ptm/m/n/10 (\T1/ptm/m/it
/10 in
 []


Underfull \hbox (badness 10000) in paragraph at lines 232--233
[]\T1/pcr/m/n/10 create_train_val_test() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod
-ule path-
 []


Underfull \hbox (badness 10000) in paragraph at lines 233--234
[]\T1/pcr/m/n/10 create_transforms() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule
 path-
 []


Underfull \hbox (badness 10000) in paragraph at lines 239--240
[]\T1/pcr/m/n/10 DynamicImageDataset \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in p
ath-
 []

[49]
Underfull \hbox (badness 10000) in paragraph at lines 254--255
[]\T1/pcr/m/n/10 forward() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 path-flowai.losses.G
eneralizedDiceLoss
 []


Underfull \hbox (badness 10000) in paragraph at lines 260--262
[]\T1/pcr/m/n/10 generate_image() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 path-
 []


Underfull \hbox (badness 10000) in paragraph at lines 260--262
\T1/ptm/m/it/10 flowai.visualize.PredictionPlotter method\T1/ptm/m/n/10 ),
 []


Underfull \hbox (badness 10000) in paragraph at lines 263--265
[]\T1/pcr/m/n/10 get_class_weights() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 path-
 []


Underfull \hbox (badness 10000) in paragraph at lines 263--265
\T1/ptm/m/it/10 flowai.datasets.DynamicImageDataset
 []


Underfull \hbox (badness 10000) in paragraph at lines 265--266
[]\T1/pcr/m/n/10 get_data_transforms() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u
le path-
 []


Underfull \hbox (badness 10000) in paragraph at lines 268--269
[]\T1/pcr/m/n/10 grab_interior_points() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-
ule path-
 []


Underfull \hbox (badness 10000) in paragraph at lines 274--275
[]\T1/pcr/m/n/10 ImbalancedDatasetSampler \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class
 in path-
 []


Underfull \hbox (badness 10000) in paragraph at lines 284--285
[]\T1/pcr/m/n/10 load_process_image() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul
e path-
 []


Underfull \hbox (badness 10000) in paragraph at lines 295--297
[]\T1/pcr/m/n/10 output_image() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 path-
 []


Underfull \hbox (badness 10000) in paragraph at lines 295--297
\T1/ptm/m/it/10 flowai.visualize.PredictionPlotter method\T1/ptm/m/n/10 ),
 []


Underfull \hbox (badness 10000) in paragraph at lines 304--305
[]\T1/pcr/m/n/10 pathflowai-monitor-monitor_usage
 []


Underfull \hbox (badness 10000) in paragraph at lines 305--307
[]| \T1/pcr/m/n/10 -csv, --records_output_csv
 []


Underfull \hbox (badness 10000) in paragraph at lines 309--310
[]\T1/pcr/m/n/10 pathflowai-preprocess command line
 []


Underfull \hbox (badness 10000) in paragraph at lines 311--312
[]\T1/pcr/m/n/10 pathflowai-preprocess-alter_masks
 []


Underfull \hbox (badness 10000) in paragraph at lines 312--314
[]| \T1/pcr/m/n/10 -fr, --from_annotations
 []


Underfull \hbox (badness 10000) in paragraph at lines 316--318
[]| \T1/pcr/m/n/10 -to, --to_annotations
 []


Overfull \hbox (22.1225pt too wide) in paragraph at lines 318--319
[]\T1/pcr/m/n/10 pathflowai-preprocess-collapse_annotations
 []


Underfull \hbox (badness 10000) in paragraph at lines 319--321
[]| \T1/pcr/m/n/10 -fr, --from_annotations
 []


Underfull \hbox (badness 10000) in paragraph at lines 321--323
[]| \T1/pcr/m/n/10 -i, --input_patch_db
 []


Underfull \hbox (badness 10000) in paragraph at lines 323--325
[]| \T1/pcr/m/n/10 -ma, --max_background_area
 []


Underfull \hbox (badness 10000) in paragraph at lines 325--327
[]| \T1/pcr/m/n/10 -o, --output_patch_db
 []


Underfull \hbox (badness 10000) in paragraph at lines 328--330
[]| \T1/pcr/m/n/10 -rb, --remove_background_annotation
 []


Underfull \hbox (badness 10000) in paragraph at lines 330--332
[]| \T1/pcr/m/n/10 -to, --to_annotations
 []


Overfull \hbox (16.1225pt too wide) in paragraph at lines 332--333
[]\T1/pcr/m/n/10 pathflowai-preprocess-preprocess_pipeline
 []

[50]
Overfull \hbox (2.6225pt too wide) in paragraph at lines 337--338
[]| \T1/pcr/m/n/10 -g, --generate_finetune_segmentation\T1/ptm/m/n/10 ,
 []


Underfull \hbox (badness 10000) in paragraph at lines 339--341
[]| \T1/pcr/m/n/10 -it, --intensity_threshold
 []


Underfull \hbox (badness 10000) in paragraph at lines 348--350
[]| \T1/pcr/m/n/10 -tc, --target_segmentation_class
 []


Underfull \hbox (badness 10000) in paragraph at lines 350--352
[]| \T1/pcr/m/n/10 -tt, --target_threshold
 []


Overfull \hbox (40.1225pt too wide) in paragraph at lines 352--353
[]\T1/pcr/m/n/10 pathflowai-preprocess-remove_basename_from_db
 []


Underfull \hbox (badness 10000) in paragraph at lines 354--356
[]| \T1/pcr/m/n/10 -i, --input_patch_db
 []


Underfull \hbox (badness 10000) in paragraph at lines 356--358
[]| \T1/pcr/m/n/10 -o, --output_patch_db
 []


Underfull \hbox (badness 10000) in paragraph at lines 359--360
[]\T1/pcr/m/n/10 pathflowai-visualize command line
 []


Underfull \hbox (badness 10000) in paragraph at lines 361--362
[]\T1/pcr/m/n/10 pathflowai-visualize-extract_patch
 []


Underfull \hbox (badness 10000) in paragraph at lines 363--365
[]| \T1/pcr/m/n/10 -c, --custom_segmentation
 []


Underfull \hbox (badness 10000) in paragraph at lines 367--369
[]| \T1/pcr/m/n/10 -p, --patch_info_file
 []


Underfull \hbox (badness 10000) in paragraph at lines 371--373
[]| \T1/pcr/m/n/10 -sc, --n_segmentation_classes
 []


Overfull \hbox (34.1225pt too wide) in paragraph at lines 375--376
[]\T1/pcr/m/n/10 pathflowai-visualize-overlay_new_annotations
 []


Underfull \hbox (badness 10000) in paragraph at lines 376--378
[]| \T1/pcr/m/n/10 -a, --annotation_txt
 []


Underfull \hbox (badness 10000) in paragraph at lines 378--380
[]| \T1/pcr/m/n/10 -cf, --compression_factor
 []


Underfull \hbox (badness 10000) in paragraph at lines 381--382
[]| \T1/pcr/m/n/10 -o, --outputfilename
 []


Underfull \hbox (badness 10000) in paragraph at lines 382--384
[]| \T1/pcr/m/n/10 -ocf, --original_compression_factor
 []


Underfull \hbox (badness 10000) in paragraph at lines 384--385
[]\T1/pcr/m/n/10 pathflowai-visualize-plot_embeddings
 []


Underfull \hbox (badness 10000) in paragraph at lines 387--389
[]| \T1/pcr/m/n/10 -i, --embeddings_file
 []


Underfull \hbox (badness 10000) in paragraph at lines 389--391
[]| \T1/pcr/m/n/10 -ma, --max_background_area
 []


Underfull \hbox (badness 10000) in paragraph at lines 392--394
[]| \T1/pcr/m/n/10 -o, --plotly_output_file
 []


Underfull \hbox (badness 10000) in paragraph at lines 394--396
[]| \T1/pcr/m/n/10 -rb, --remove_background_annotation
 []


Underfull \hbox (badness 10000) in paragraph at lines 396--397
[]\T1/pcr/m/n/10 pathflowai-visualize-plot_image
 []


Underfull \hbox (badness 10000) in paragraph at lines 397--399
[]| \T1/pcr/m/n/10 -cf, --compression_factor
 []


Overfull \hbox (52.1225pt too wide) in paragraph at lines 401--402
[]\T1/pcr/m/n/10 pathflowai-visualize-plot_image_umap_embeddings
 []


Underfull \hbox (badness 10000) in paragraph at lines 403--405
[]| \T1/pcr/m/n/10 -e, --embeddings_file
 []


Underfull \hbox (badness 10000) in paragraph at lines 406--408
[]| \T1/pcr/m/n/10 -ma, --max_background_area
 []


Underfull \hbox (badness 10000) in paragraph at lines 410--411
[]| \T1/pcr/m/n/10 -o, --outputfilename
 []


Underfull \hbox (badness 10000) in paragraph at lines 411--413
[]| \T1/pcr/m/n/10 -rb, --remove_background_annotation
 []


Underfull \hbox (badness 10000) in paragraph at lines 416--417
[]\T1/pcr/m/n/10 pathflowai-visualize-plot_predictions
 []


Underfull \hbox (badness 10000) in paragraph at lines 417--419
[]| \T1/pcr/m/n/10 -ac, --annotation_col
 []


Underfull \hbox (badness 10000) in paragraph at lines 422--424
[]| \T1/pcr/m/n/10 -c, --custom_segmentation
 []


Underfull \hbox (badness 10000) in paragraph at lines 424--426
[]| \T1/pcr/m/n/10 -cf, --compression_factor
 []


Underfull \hbox (badness 10000) in paragraph at lines 428--430
[]| \T1/pcr/m/n/10 -p, --patch_info_file
 []

[51]
Underfull \hbox (badness 10000) in paragraph at lines 432--434
[]| \T1/pcr/m/n/10 -sc, --n_segmentation_classes
 []


Underfull \hbox (badness 10000) in paragraph at lines 434--436
[]| \T1/pcr/m/n/10 -sf, --scaling_factor
 []


Underfull \hbox (badness 10000) in paragraph at lines 437--438
[]\T1/pcr/m/n/10 pathflowai-visualize-shapley_plot
 []


Underfull \hbox (badness 10000) in paragraph at lines 439--441
[]| \T1/pcr/m/n/10 -l, --local_smoothing
 []


Underfull \hbox (badness 10000) in paragraph at lines 444--446
[]| \T1/pcr/m/n/10 -o, --outputfilename
 []


Underfull \hbox (badness 10000) in paragraph at lines 456--457
[]\T1/pcr/m/n/10 plot_umap_images() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule 
path-
 []


Overfull \hbox (13.36089pt too wide) in paragraph at lines 465--467
[]\T1/pcr/m/n/10 retain_ID() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 path-flowai.datase
ts.DynamicImageDataset
 []


Underfull \hbox (badness 10000) in paragraph at lines 468--469
[]\T1/pcr/m/n/10 return_image_coord() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ul
e path-
 []


Underfull \hbox (badness 10000) in paragraph at lines 469--471
[]\T1/pcr/m/n/10 return_image_in_boxes_dict() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 i
n mod-ule
 []


Underfull \hbox (badness 10000) in paragraph at lines 471--473
[]\T1/pcr/m/n/10 return_patch() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 path-
 []


Underfull \hbox (badness 10000) in paragraph at lines 471--473
\T1/ptm/m/it/10 flowai.visualize.PredictionPlotter method\T1/ptm/m/n/10 ),
 []


Underfull \hbox (badness 10000) in paragraph at lines 473--475
[]\T1/pcr/m/n/10 run_preprocessing_pipeline() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 i
n mod-ule
 []


Underfull \hbox (badness 10000) in paragraph at lines 478--479
[]\T1/pcr/m/n/10 save_all_patch_info() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u
le path-
 []


Underfull \hbox (badness 5119) in paragraph at lines 484--486
[]\T1/pcr/m/n/10 segmentation_transform() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mo
d-ule path-
 []


Underfull \hbox (badness 10000) in paragraph at lines 488--490
[]\T1/pcr/m/n/10 split_by_ID() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 path-
 []


Underfull \hbox (badness 10000) in paragraph at lines 488--490
\T1/ptm/m/it/10 flowai.datasets.DynamicImageDataset
 []


Overfull \hbox (13.36089pt too wide) in paragraph at lines 492--494
[]\T1/pcr/m/n/10 subsample() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 path-flowai.datase
ts.DynamicImageDataset
 []

[52])
Package atveryend Info: Empty hook `BeforeClearDocument' on input line 3590.
Package atveryend Info: Empty hook `AfterLastShipout' on input line 3590.
 (./PathFlowAI.aux)
Package atveryend Info: Executing hook `AtVeryEndDocument' on input line 3590.
Package atveryend Info: Executing hook `AtEndAfterFileList' on input line 3590.

Package rerunfilecheck Info: File `PathFlowAI.out' has not changed.
(rerunfilecheck)             Checksum: E363130B6B10C2E90972D6DBA7908EA7;3074.
Package atveryend Info: Empty hook `AtVeryVeryEnd' on input line 3590.
 ) 
Here is how much of TeX's memory you used:
 13847 strings out of 492649
 200259 string characters out of 6129622
 301709 words of memory out of 5000000
 17150 multiletter control sequences out of 15000+600000
 50630 words of font info for 74 fonts, out of 8000000 for 9000
 1142 hyphenation exceptions out of 8191
 37i,16n,45p,758b,666s stack positions out of 5000i,500n,10000p,200000b,80000s
{/usr/local/texlive/2018/texmf-dist/fonts/enc/dvips/base/8r.enc}</usr/local/t
exlive/2018/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi10.pfb></usr/local/te
xlive/2018/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi5.pfb></usr/local/texl
ive/2018/texmf-dist/fonts/type1/public/amsfonts/cm/cmmi7.pfb></usr/local/texliv
e/2018/texmf-dist/fonts/type1/public/amsfonts/cm/cmr10.pfb></usr/local/texlive/
2018/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/local/texlive/2
018/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy5.pfb></usr/local/texlive/201
8/texmf-dist/fonts/type1/urw/courier/ucrb8a.pfb></usr/local/texlive/2018/texmf-
dist/fonts/type1/urw/courier/ucrr8a.pfb></usr/local/texlive/2018/texmf-dist/fon
ts/type1/urw/courier/ucrro8a.pfb></usr/local/texlive/2018/texmf-dist/fonts/type
1/urw/helvetic/uhvb8a.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/urw/h
elvetic/uhvbo8a.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/urw/helveti
c/uhvr8a.pfb></usr/local/texlive/2018/texmf-dist/fonts/type1/urw/times/utmb8a.p
fb></usr/local/texlive/2018/texmf-dist/fonts/type1/urw/times/utmr8a.pfb></usr/l
ocal/texlive/2018/texmf-dist/fonts/type1/urw/times/utmri8a.pfb>
Output written on PathFlowAI.pdf (56 pages, 1468332 bytes).
PDF statistics:
 1014 PDF objects out of 1200 (max. 8388607)
 922 compressed objects within 10 object streams
 273 named destinations out of 1000 (max. 500000)
 233 words of extra memory for PDF output out of 10000 (max. 10000000)