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Supervisor working

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This commit is contained in:
Florent Guiotte 2018-07-26 16:22:48 +02:00
parent 81d96823e8
commit 4877dab2c4
4 changed files with 106 additions and 632 deletions
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84
Notebooks/YAML Serialization.ipynb
View File

@ -160,6 +160,7 @@
" def __init__(self):\n",
" self._pt = time.process_time()\n",
" self._times = OrderedDict()\n",
" self._stime = time.time()\n",
" \n",
" def time(self, name):\n",
" self._times[name + '_process_time'] = time.process_time() - self._pt\n",
@ -168,8 +169,13 @@
" def get_times(self):\n",
" return self._times\n",
" \n",
"kronos = Kronos()\n",
"start_time = time.time()"
" def get_start_date(self):\n",
" return self._stime\n",
" \n",
" def get_end_date(self):\n",
" return time.time()\n",
" \n",
"kronos = Kronos()"
]
},
{
@ -308,7 +314,7 @@
"\n",
" expe_report['supervisor'] = os.uname()[1]\n",
"\n",
" for timev, datek in zip((start_time, end_time), ('start_date', 'end_date')):\n",
" for timev, datek in zip((kronos.get_start_date(), kronos.get_end_date()), ('start_date', 'end_date')):\n",
" expe_report[datek] = datetime.datetime.fromtimestamp(timev).strftime('Le %d/%m/%Y à %H:%M:%S')\n",
"\n",
" ressources = kronos.get_times()\n",
@ -321,15 +327,6 @@
"expe_report"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"**TODO**\n",
"\n",
"améliorer kronos pour le start et le end time (build and get_times)\n"
]
},
{
"cell_type": "markdown",
"metadata": {},
@ -535,6 +532,69 @@
"desc.run(**expe['descriptors_param'])"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"A = []"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"A.pop()"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"A.count()"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"continue"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"E = Path('./Enrichment')"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"(E / 'Test' / 'aefaef.tif').stem"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"E / ('qwer' + '.tif')"
]
},
{
"cell_type": "code",
"execution_count": null,

572
Notebooks/notebook.tex
View File

@ -1,572 +0,0 @@
% Default to the notebook output style
% Inherit from the specified cell style.
\documentclass[11pt]{article}
\usepackage[T1]{fontenc}
% Nicer default font (+ math font) than Computer Modern for most use cases
\usepackage{mathpazo}
% Basic figure setup, for now with no caption control since it's done
% automatically by Pandoc (which extracts ![](path) syntax from Markdown).
\usepackage{graphicx}
% We will generate all images so they have a width \maxwidth. This means
% that they will get their normal width if they fit onto the page, but
% are scaled down if they would overflow the margins.
\makeatletter
\def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth
\else\Gin@nat@width\fi}
\makeatother
\let\Oldincludegraphics\includegraphics
% Set max figure width to be 80% of text width, for now hardcoded.
\renewcommand{\includegraphics}[1]{\Oldincludegraphics[width=.8\maxwidth]{#1}}
% Ensure that by default, figures have no caption (until we provide a
% proper Figure object with a Caption API and a way to capture that
% in the conversion process - todo).
\usepackage{caption}
\DeclareCaptionLabelFormat{nolabel}{}
\captionsetup{labelformat=nolabel}
\usepackage{adjustbox} % Used to constrain images to a maximum size
\usepackage{xcolor} % Allow colors to be defined
\usepackage{enumerate} % Needed for markdown enumerations to work
\usepackage{geometry} % Used to adjust the document margins
\usepackage{amsmath} % Equations
\usepackage{amssymb} % Equations
\usepackage{textcomp} % defines textquotesingle
% Hack from http://tex.stackexchange.com/a/47451/13684:
\AtBeginDocument{%
\def\PYZsq{\textquotesingle}% Upright quotes in Pygmentized code
}
\usepackage{upquote} % Upright quotes for verbatim code
\usepackage{eurosym} % defines \euro
\usepackage[mathletters]{ucs} % Extended unicode (utf-8) support
\usepackage[utf8x]{inputenc} % Allow utf-8 characters in the tex document
\usepackage{fancyvrb} % verbatim replacement that allows latex
\usepackage{grffile} % extends the file name processing of package graphics
% to support a larger range
% The hyperref package gives us a pdf with properly built
% internal navigation ('pdf bookmarks' for the table of contents,
% internal cross-reference links, web links for URLs, etc.)
\usepackage{hyperref}
\usepackage{longtable} % longtable support required by pandoc >1.10
\usepackage{booktabs} % table support for pandoc > 1.12.2
\usepackage[inline]{enumitem} % IRkernel/repr support (it uses the enumerate* environment)
\usepackage[normalem]{ulem} % ulem is needed to support strikethroughs (\sout)
% normalem makes italics be italics, not underlines
% Colors for the hyperref package
\definecolor{urlcolor}{rgb}{0,.145,.698}
\definecolor{linkcolor}{rgb}{.71,0.21,0.01}
\definecolor{citecolor}{rgb}{.12,.54,.11}
% ANSI colors
\definecolor{ansi-black}{HTML}{3E424D}
\definecolor{ansi-black-intense}{HTML}{282C36}
\definecolor{ansi-red}{HTML}{E75C58}
\definecolor{ansi-red-intense}{HTML}{B22B31}
\definecolor{ansi-green}{HTML}{00A250}
\definecolor{ansi-green-intense}{HTML}{007427}
\definecolor{ansi-yellow}{HTML}{DDB62B}
\definecolor{ansi-yellow-intense}{HTML}{B27D12}
\definecolor{ansi-blue}{HTML}{208FFB}
\definecolor{ansi-blue-intense}{HTML}{0065CA}
\definecolor{ansi-magenta}{HTML}{D160C4}
\definecolor{ansi-magenta-intense}{HTML}{A03196}
\definecolor{ansi-cyan}{HTML}{60C6C8}
\definecolor{ansi-cyan-intense}{HTML}{258F8F}
\definecolor{ansi-white}{HTML}{C5C1B4}
\definecolor{ansi-white-intense}{HTML}{A1A6B2}
% commands and environments needed by pandoc snippets
% extracted from the output of `pandoc -s`
\providecommand{\tightlist}{%
\setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
\DefineVerbatimEnvironment{Highlighting}{Verbatim}{commandchars=\\\{\}}
% Add ',fontsize=\small' for more characters per line
\newenvironment{Shaded}{}{}
\newcommand{\KeywordTok}[1]{\textcolor[rgb]{0.00,0.44,0.13}{\textbf{{#1}}}}
\newcommand{\DataTypeTok}[1]{\textcolor[rgb]{0.56,0.13,0.00}{{#1}}}
\newcommand{\DecValTok}[1]{\textcolor[rgb]{0.25,0.63,0.44}{{#1}}}
\newcommand{\BaseNTok}[1]{\textcolor[rgb]{0.25,0.63,0.44}{{#1}}}
\newcommand{\FloatTok}[1]{\textcolor[rgb]{0.25,0.63,0.44}{{#1}}}
\newcommand{\CharTok}[1]{\textcolor[rgb]{0.25,0.44,0.63}{{#1}}}
\newcommand{\StringTok}[1]{\textcolor[rgb]{0.25,0.44,0.63}{{#1}}}
\newcommand{\CommentTok}[1]{\textcolor[rgb]{0.38,0.63,0.69}{\textit{{#1}}}}
\newcommand{\OtherTok}[1]{\textcolor[rgb]{0.00,0.44,0.13}{{#1}}}
\newcommand{\AlertTok}[1]{\textcolor[rgb]{1.00,0.00,0.00}{\textbf{{#1}}}}
\newcommand{\FunctionTok}[1]{\textcolor[rgb]{0.02,0.16,0.49}{{#1}}}
\newcommand{\RegionMarkerTok}[1]{{#1}}
\newcommand{\ErrorTok}[1]{\textcolor[rgb]{1.00,0.00,0.00}{\textbf{{#1}}}}
\newcommand{\NormalTok}[1]{{#1}}
% Additional commands for more recent versions of Pandoc
\newcommand{\ConstantTok}[1]{\textcolor[rgb]{0.53,0.00,0.00}{{#1}}}
\newcommand{\SpecialCharTok}[1]{\textcolor[rgb]{0.25,0.44,0.63}{{#1}}}
\newcommand{\VerbatimStringTok}[1]{\textcolor[rgb]{0.25,0.44,0.63}{{#1}}}
\newcommand{\SpecialStringTok}[1]{\textcolor[rgb]{0.73,0.40,0.53}{{#1}}}
\newcommand{\ImportTok}[1]{{#1}}
\newcommand{\DocumentationTok}[1]{\textcolor[rgb]{0.73,0.13,0.13}{\textit{{#1}}}}
\newcommand{\AnnotationTok}[1]{\textcolor[rgb]{0.38,0.63,0.69}{\textbf{\textit{{#1}}}}}
\newcommand{\CommentVarTok}[1]{\textcolor[rgb]{0.38,0.63,0.69}{\textbf{\textit{{#1}}}}}
\newcommand{\VariableTok}[1]{\textcolor[rgb]{0.10,0.09,0.49}{{#1}}}
\newcommand{\ControlFlowTok}[1]{\textcolor[rgb]{0.00,0.44,0.13}{\textbf{{#1}}}}
\newcommand{\OperatorTok}[1]{\textcolor[rgb]{0.40,0.40,0.40}{{#1}}}
\newcommand{\BuiltInTok}[1]{{#1}}
\newcommand{\ExtensionTok}[1]{{#1}}
\newcommand{\PreprocessorTok}[1]{\textcolor[rgb]{0.74,0.48,0.00}{{#1}}}
\newcommand{\AttributeTok}[1]{\textcolor[rgb]{0.49,0.56,0.16}{{#1}}}
\newcommand{\InformationTok}[1]{\textcolor[rgb]{0.38,0.63,0.69}{\textbf{\textit{{#1}}}}}
\newcommand{\WarningTok}[1]{\textcolor[rgb]{0.38,0.63,0.69}{\textbf{\textit{{#1}}}}}
% Define a nice break command that doesn't care if a line doesn't already
% exist.
\def\br{\hspace*{\fill} \\* }
% Math Jax compatability definitions
\def\gt{>}
\def\lt{<}
% Document parameters
\title{Triskele Python Demo}
% Pygments definitions
\makeatletter
\def\PY@reset{\let\PY@it=\relax \let\PY@bf=\relax%
\let\PY@ul=\relax \let\PY@tc=\relax%
\let\PY@bc=\relax \let\PY@ff=\relax}
\def\PY@tok#1{\csname PY@tok@#1\endcsname}
\def\PY@toks#1+{\ifx\relax#1\empty\else%
\PY@tok{#1}\expandafter\PY@toks\fi}
\def\PY@do#1{\PY@bc{\PY@tc{\PY@ul{%
\PY@it{\PY@bf{\PY@ff{#1}}}}}}}
\def\PY#1#2{\PY@reset\PY@toks#1+\relax+\PY@do{#2}}
\expandafter\def\csname PY@tok@w\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.73,0.73,0.73}{##1}}}
\expandafter\def\csname PY@tok@c\endcsname{\let\PY@it=\textit\def\PY@tc##1{\textcolor[rgb]{0.25,0.50,0.50}{##1}}}
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\expandafter\def\csname PY@tok@kp\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.00,0.50,0.00}{##1}}}
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\expandafter\def\csname PY@tok@nn\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.00,0.00,1.00}{##1}}}
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\expandafter\def\csname PY@tok@ge\endcsname{\let\PY@it=\textit}
\expandafter\def\csname PY@tok@gs\endcsname{\let\PY@bf=\textbf}
\expandafter\def\csname PY@tok@gp\endcsname{\let\PY@bf=\textbf\def\PY@tc##1{\textcolor[rgb]{0.00,0.00,0.50}{##1}}}
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\expandafter\def\csname PY@tok@sc\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}}
\expandafter\def\csname PY@tok@dl\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}}
\expandafter\def\csname PY@tok@s2\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.73,0.13,0.13}{##1}}}
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\expandafter\def\csname PY@tok@mh\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}}
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\expandafter\def\csname PY@tok@mo\endcsname{\def\PY@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}}
\expandafter\def\csname PY@tok@ch\endcsname{\let\PY@it=\textit\def\PY@tc##1{\textcolor[rgb]{0.25,0.50,0.50}{##1}}}
\expandafter\def\csname PY@tok@cm\endcsname{\let\PY@it=\textit\def\PY@tc##1{\textcolor[rgb]{0.25,0.50,0.50}{##1}}}
\expandafter\def\csname PY@tok@cpf\endcsname{\let\PY@it=\textit\def\PY@tc##1{\textcolor[rgb]{0.25,0.50,0.50}{##1}}}
\expandafter\def\csname PY@tok@c1\endcsname{\let\PY@it=\textit\def\PY@tc##1{\textcolor[rgb]{0.25,0.50,0.50}{##1}}}
\expandafter\def\csname PY@tok@cs\endcsname{\let\PY@it=\textit\def\PY@tc##1{\textcolor[rgb]{0.25,0.50,0.50}{##1}}}
\def\PYZbs{\char`\\}
\def\PYZus{\char`\_}
\def\PYZob{\char`\{}
\def\PYZcb{\char`\}}
\def\PYZca{\char`\^}
\def\PYZam{\char`\&}
\def\PYZlt{\char`\<}
\def\PYZgt{\char`\>}
\def\PYZsh{\char`\#}
\def\PYZpc{\char`\%}
\def\PYZdl{\char`\$}
\def\PYZhy{\char`\-}
\def\PYZsq{\char`\'}
\def\PYZdq{\char`\"}
\def\PYZti{\char`\~}
% for compatibility with earlier versions
\def\PYZat{@}
\def\PYZlb{[}
\def\PYZrb{]}
\makeatother
% Exact colors from NB
\definecolor{incolor}{rgb}{0.0, 0.0, 0.5}
\definecolor{outcolor}{rgb}{0.545, 0.0, 0.0}
% Prevent overflowing lines due to hard-to-break entities
\sloppy
% Setup hyperref package
\hypersetup{
breaklinks=true, % so long urls are correctly broken across lines
colorlinks=true,
urlcolor=urlcolor,
linkcolor=linkcolor,
citecolor=citecolor,
}
% Slightly bigger margins than the latex defaults
\geometry{verbose,tmargin=1in,bmargin=1in,lmargin=1in,rmargin=1in}
\begin{document}
\maketitle
\hypertarget{init}{%
\section{Init}\label{init}}
\begin{Verbatim}[commandchars=\\\{\}]
{\color{incolor}In [{\color{incolor}1}]:} \PY{k+kn}{import} \PY{n+nn}{numpy} \PY{k}{as} \PY{n+nn}{np}
\PY{k+kn}{import} \PY{n+nn}{matplotlib}\PY{n+nn}{.}\PY{n+nn}{pyplot} \PY{k}{as} \PY{n+nn}{plt}
\end{Verbatim}
\hypertarget{import-triskele}{%
\subsection{Import Triskele}\label{import-triskele}}
I did not install triskele-python on my system folders, so this is a
trick to load the module outside the triskele project.
\begin{Verbatim}[commandchars=\\\{\}]
{\color{incolor}In [{\color{incolor}2}]:} \PY{k+kn}{import} \PY{n+nn}{sys}
\PY{n}{sys}\PY{o}{.}\PY{n}{path}\PY{o}{.}\PY{n}{append}\PY{p}{(}\PY{l+s+s1}{\PYZsq{}}\PY{l+s+s1}{../triskele/python/}\PY{l+s+s1}{\PYZsq{}}\PY{p}{)} \PY{c+c1}{\PYZsh{} Change with your triskele install path}
\PY{k+kn}{import} \PY{n+nn}{triskele}
\end{Verbatim}
\hypertarget{simple-test}{%
\section{Simple test}\label{simple-test}}
Just to test the python import and the triskele compilation. Create an
array with random values.
\begin{Verbatim}[commandchars=\\\{\}]
{\color{incolor}In [{\color{incolor}3}]:} \PY{n}{raster} \PY{o}{=} \PY{n}{np}\PY{o}{.}\PY{n}{random}\PY{o}{.}\PY{n}{randint}\PY{p}{(}\PY{l+m+mi}{0}\PY{p}{,} \PY{l+m+mi}{255}\PY{p}{,} \PY{p}{(}\PY{l+m+mi}{1000}\PY{p}{,} \PY{l+m+mi}{1000}\PY{p}{)}\PY{p}{)}
\end{Verbatim}
Create the instance of triskele object with the array to filter.
\begin{Verbatim}[commandchars=\\\{\}]
{\color{incolor}In [{\color{incolor}4}]:} \PY{n}{ap\PYZus{}random} \PY{o}{=} \PY{n}{triskele}\PY{o}{.}\PY{n}{Triskele}\PY{p}{(}\PY{n}{raster}\PY{p}{)}
\end{Verbatim}
Filter the raster with this method :
\begin{Verbatim}[commandchars=\\\{\}]
{\color{incolor}In [{\color{incolor}5}]:} \PY{n}{filtered\PYZus{}raster} \PY{o}{=} \PY{n}{ap\PYZus{}random}\PY{o}{.}\PY{n}{filter}\PY{p}{(}\PY{p}{)}
\PY{n+nb}{print}\PY{p}{(}\PY{n}{filtered\PYZus{}raster}\PY{p}{)}
\end{Verbatim}
\begin{Verbatim}[commandchars=\\\{\}]
STDOUT:
Input:/tmp/infile.tif [1000,1000] (1 chanels of Byte)
Crop topLeft:(0,0) size:[1000,1000] band:[0]
Output:/tmp/outfile.tif
core count:24
STDERR:
*** apGenerator done!
Leaf Count Mean Min Max
max 1 1000000 1000000 1000000
Comp Count Mean Min Max
max 1 347157 347157 347157
Time Sum Count Mean Min Max
build tree 00:00:00.086426 1 00:00:00.086426 00:00:00.086426 00:00:00.086426
setup 00:00:00.038795 1 00:00:00.038795 00:00:00.038795 00:00:00.038795
parents 00:00:00.026013 1 00:00:00.026013 00:00:00.026013 00:00:00.026013
merge 00:00:00.005112 1 00:00:00.005112 00:00:00.005112 00:00:00.005112
index 00:00:00.006034 1 00:00:00.006034 00:00:00.006034 00:00:00.006034
compress 00:00:00.008091 1 00:00:00.008091 00:00:00.008091 00:00:00.008091
children 00:00:00.108123 1 00:00:00.108123 00:00:00.108123 00:00:00.108123
area 00:00:00.004463 1 00:00:00.004463 00:00:00.004463 00:00:00.004463
[[194 125 164 {\ldots} 213 182 168]
[ 25 48 242 {\ldots} 229 16 143]
[ 7 207 212 {\ldots} 112 94 100]
{\ldots}
[227 180 185 {\ldots} 34 10 229]
[129 149 27 {\ldots} 217 66 195]
[145 203 251 {\ldots} 186 116 165]]
\end{Verbatim}
If there is no error so far everything is okay.
Theoretically the filtered output should be a copy of the input. (it's
not, there is something going on along the edges, we should tell
François !)
\hypertarget{attribute-filter}{%
\subsection{Attribute filter}\label{attribute-filter}}
With \texttt{filter} method you can ask for specific attributes
filtering. The results are stacked.
\begin{Verbatim}[commandchars=\\\{\}]
{\color{incolor}In [{\color{incolor}6}]:} \PY{n}{filtered\PYZus{}rasters} \PY{o}{=} \PY{n}{ap\PYZus{}random}\PY{o}{.}\PY{n}{filter}\PY{p}{(}\PY{n}{area}\PY{o}{=}\PY{p}{[}\PY{l+m+mi}{10}\PY{p}{,} \PY{l+m+mi}{100}\PY{p}{,} \PY{l+m+mf}{1e3}\PY{p}{]}\PY{p}{)}
\PY{n+nb}{print}\PY{p}{(}\PY{n}{filtered\PYZus{}rasters}\PY{o}{.}\PY{n}{shape}\PY{p}{)}
\end{Verbatim}
\begin{Verbatim}[commandchars=\\\{\}]
STDOUT:
Input:/tmp/infile.tif [1000,1000] (1 chanels of Byte)
Crop topLeft:(0,0) size:[1000,1000] band:[0]
Output:/tmp/outfile.tif
core count:24
STDERR:
*** apGenerator done!
Leaf Count Mean Min Max
max 1 1000000 1000000 1000000
Comp Count Mean Min Max
max 1 347157 347157 347157
Time Sum Count Mean Min Max
build tree 00:00:00.094336 1 00:00:00.094336 00:00:00.094336 00:00:00.094336
setup 00:00:00.040030 1 00:00:00.040030 00:00:00.040030 00:00:00.040030
parents 00:00:00.034337 1 00:00:00.034337 00:00:00.034337 00:00:00.034337
merge 00:00:00.004679 1 00:00:00.004679 00:00:00.004679 00:00:00.004679
index 00:00:00.005624 1 00:00:00.005624 00:00:00.005624 00:00:00.005624
compress 00:00:00.007514 1 00:00:00.007514 00:00:00.007514 00:00:00.007514
children 00:00:00.113179 1 00:00:00.113179 00:00:00.113179 00:00:00.113179
area 00:00:00.004390 1 00:00:00.004390 00:00:00.004390 00:00:00.004390
filtering 00:00:00.007614 1 00:00:00.007614 00:00:00.007614 00:00:00.007614
(1000, 1000, 4)
\end{Verbatim}
I don't know if you can see the signature with yout IDE :
\texttt{filter(tree=\textquotesingle{}max-tree\textquotesingle{},\ area=None,\ standard\_deviation=None,\ moment\_of\_inertia=None)}
The parameters are the same than apGenerator from François, I should
write the doc\ldots{}
\hypertarget{advanced-test}{%
\section{Advanced test}\label{advanced-test}}
With a real example.
Load a TIFF file with 4 bands :
\begin{Verbatim}[commandchars=\\\{\}]
{\color{incolor}In [{\color{incolor}7}]:} \PY{n}{raster} \PY{o}{=} \PY{n}{triskele}\PY{o}{.}\PY{n}{read}\PY{p}{(}\PY{l+s+s1}{\PYZsq{}}\PY{l+s+s1}{../triskele/data/10m.tif}\PY{l+s+s1}{\PYZsq{}}\PY{p}{)}
\PY{n+nb}{print}\PY{p}{(}\PY{n}{raster}\PY{o}{.}\PY{n}{shape}\PY{p}{)}
\PY{n}{plt}\PY{o}{.}\PY{n}{imshow}\PY{p}{(}\PY{n}{raster}\PY{p}{)}
\PY{n}{plt}\PY{o}{.}\PY{n}{show}\PY{p}{(}\PY{p}{)}
\end{Verbatim}
\begin{Verbatim}[commandchars=\\\{\}]
(291, 685, 4)
\end{Verbatim}
\begin{center}
\adjustimage{max size={0.9\linewidth}{0.9\paperheight}}{output_14_1.png}
\end{center}
{ \hspace*{\fill} \\}
Create the instance with some tweaks.
\begin{Verbatim}[commandchars=\\\{\}]
{\color{incolor}In [{\color{incolor}8}]:} \PY{n}{ap\PYZus{}10m} \PY{o}{=} \PY{n}{triskele}\PY{o}{.}\PY{n}{Triskele}\PY{p}{(}\PY{n}{raster}\PY{p}{,} \PY{n}{verbose}\PY{o}{=}\PY{k+kc}{False}\PY{p}{)} \PY{c+c1}{\PYZsh{} Verbose False to hide apGenerator gibbering :p}
\end{Verbatim}
Filter as you wish :
\begin{Verbatim}[commandchars=\\\{\}]
{\color{incolor}In [{\color{incolor}9}]:} \PY{n}{tree} \PY{o}{=} \PY{l+s+s1}{\PYZsq{}}\PY{l+s+s1}{tos\PYZhy{}tree}\PY{l+s+s1}{\PYZsq{}} \PY{c+c1}{\PYZsh{} \PYZob{}\PYZsq{}max\PYZhy{}tree\PYZsq{}, \PYZsq{}min\PYZhy{}tree\PYZsq{}, ...\PYZcb{}}
\PY{n}{area} \PY{o}{=} \PY{p}{[}\PY{l+m+mi}{100}\PY{p}{,} \PY{l+m+mf}{1e3}\PY{p}{,} \PY{l+m+mf}{1e4}\PY{p}{]}
\PY{n}{standard\PYZus{}deviation} \PY{o}{=} \PY{k+kc}{None}
\PY{n}{moment\PYZus{}of\PYZus{}inertia} \PY{o}{=} \PY{k+kc}{None}
\PY{n}{filtered\PYZus{}rasters} \PY{o}{=} \PY{n}{ap\PYZus{}10m}\PY{o}{.}\PY{n}{filter}\PY{p}{(}\PY{n}{tree}\PY{o}{=}\PY{n}{tree}\PY{p}{,} \PY{n}{area}\PY{o}{=}\PY{n}{area}\PY{p}{,} \PY{n}{standard\PYZus{}deviation}\PY{o}{=}\PY{n}{standard\PYZus{}deviation}\PY{p}{,} \PY{n}{moment\PYZus{}of\PYZus{}inertia}\PY{o}{=}\PY{n}{moment\PYZus{}of\PYZus{}inertia}\PY{p}{)}
\PY{n+nb}{print}\PY{p}{(}\PY{n}{filtered\PYZus{}rasters}\PY{o}{.}\PY{n}{shape}\PY{p}{)}
\end{Verbatim}
\begin{Verbatim}[commandchars=\\\{\}]
(291, 685, 16)
\end{Verbatim}
\hypertarget{display-results}{%
\subsection{Display results}\label{display-results}}
\begin{Verbatim}[commandchars=\\\{\}]
{\color{incolor}In [{\color{incolor}10}]:} \PY{k}{for} \PY{n}{i} \PY{o+ow}{in} \PY{n+nb}{range}\PY{p}{(}\PY{n}{filtered\PYZus{}rasters}\PY{o}{.}\PY{n}{shape}\PY{p}{[}\PY{l+m+mi}{2}\PY{p}{]}\PY{p}{)}\PY{p}{:}
\PY{n}{plt}\PY{o}{.}\PY{n}{imshow}\PY{p}{(}\PY{n}{filtered\PYZus{}rasters}\PY{p}{[}\PY{p}{:}\PY{p}{,}\PY{p}{:}\PY{p}{,}\PY{n}{i}\PY{p}{]}\PY{p}{)}
\PY{n}{plt}\PY{o}{.}\PY{n}{show}\PY{p}{(}\PY{p}{)}
\end{Verbatim}
\begin{center}
\adjustimage{max size={0.9\linewidth}{0.9\paperheight}}{output_20_0.png}
\end{center}
{ \hspace*{\fill} \\}
\begin{center}
\adjustimage{max size={0.9\linewidth}{0.9\paperheight}}{output_20_1.png}
\end{center}
{ \hspace*{\fill} \\}
\begin{center}
\adjustimage{max size={0.9\linewidth}{0.9\paperheight}}{output_20_2.png}
\end{center}
{ \hspace*{\fill} \\}
\begin{center}
\adjustimage{max size={0.9\linewidth}{0.9\paperheight}}{output_20_3.png}
\end{center}
{ \hspace*{\fill} \\}
\begin{center}
\adjustimage{max size={0.9\linewidth}{0.9\paperheight}}{output_20_4.png}
\end{center}
{ \hspace*{\fill} \\}
\begin{center}
\adjustimage{max size={0.9\linewidth}{0.9\paperheight}}{output_20_5.png}
\end{center}
{ \hspace*{\fill} \\}
\begin{center}
\adjustimage{max size={0.9\linewidth}{0.9\paperheight}}{output_20_6.png}
\end{center}
{ \hspace*{\fill} \\}
\begin{center}
\adjustimage{max size={0.9\linewidth}{0.9\paperheight}}{output_20_7.png}
\end{center}
{ \hspace*{\fill} \\}
\begin{center}
\adjustimage{max size={0.9\linewidth}{0.9\paperheight}}{output_20_8.png}
\end{center}
{ \hspace*{\fill} \\}
\begin{center}
\adjustimage{max size={0.9\linewidth}{0.9\paperheight}}{output_20_9.png}
\end{center}
{ \hspace*{\fill} \\}
\begin{center}
\adjustimage{max size={0.9\linewidth}{0.9\paperheight}}{output_20_10.png}
\end{center}
{ \hspace*{\fill} \\}
\begin{center}
\adjustimage{max size={0.9\linewidth}{0.9\paperheight}}{output_20_11.png}
\end{center}
{ \hspace*{\fill} \\}
\begin{center}
\adjustimage{max size={0.9\linewidth}{0.9\paperheight}}{output_20_12.png}
\end{center}
{ \hspace*{\fill} \\}
\begin{center}
\adjustimage{max size={0.9\linewidth}{0.9\paperheight}}{output_20_13.png}
\end{center}
{ \hspace*{\fill} \\}
\begin{center}
\adjustimage{max size={0.9\linewidth}{0.9\paperheight}}{output_20_14.png}
\end{center}
{ \hspace*{\fill} \\}
\begin{center}
\adjustimage{max size={0.9\linewidth}{0.9\paperheight}}{output_20_15.png}
\end{center}
{ \hspace*{\fill} \\}
% Add a bibliography block to the postdoc
\end{document}

47
supervisor.py
View File

@ -38,7 +38,10 @@ def setup_yaml():
yaml.add_representer(OrderedDict, represent_dict_order)
setup_yaml()
test_dir = Path('./Tests')
enrichment_dir = Path('./Enrichment/')
test_dir = enrichment_dir / 'Tests'
staging_dir = enrichment_dir / 'Staging'
result_dir = enrichment_dir / 'Results'
def update_queue():
tmp_queue = list()
@ -60,11 +63,22 @@ def run(expe_file):
with open(expe_file) as f:
expe = OrderedDict(yaml.safe_load(f)['expe'])
### Keep track of time
kronos = Kronos()
### Compute hashes
expe_hashes = compute_hashes(expe)
### Keep track of time
kronos = Kronos()
### Create output names
oname = '{}_{}'.format(expe_file.stem, expe_hashes['global'][:6])
oname_yml = oname + '.yml'
oname_tif = oname + '.tif'
### Create partial report
expe_report = create_report(kronos)
### Stage expe
write_expe_file(staging_dir / oname_yml, expe, expe_hashes, expe_report)
### Compute descriptors
descriptors = compute_descriptors(expe)
@ -78,22 +92,23 @@ def run(expe_file):
metrics = run_metrics(expe, classification)
kronos.time('metrics')
### Create report
### Create complete report
expe_report = create_report(kronos)
### Name and write prediction
oname = '{}_{}'.format(Path(expe_file).stem, expe_hashes['global'][:6])
oname_tif = oname + '.tif'
triskele.write(oname_tif, classification)
triskele.write(result_dir / oname_tif, classification)
### Write report and results
oname_yml = oname + '.yml'
with open(oname_yml, 'w') as of:
write_expe_file(result_dir / oname_yml, expe, expe_hashes, expe_report, oname_tif, metrics)
def write_expe_file(file, expe, hashes=None, report=None, classification=None, results=None):
with open(file, 'w') as of:
yaml.dump(OrderedDict({'expe': expe,
'expe_hashes': expe_hashes,
'expe_report': expe_report,
'expe_classification': oname_tif,
'expe_results': metrics}),
'expe_hashes': hashes,
'expe_report': report,
'expe_classification': classification,
'expe_results': results}),
of, default_flow_style=False, encoding=None, allow_unicode=True)
@ -170,7 +185,7 @@ def create_report(kronos):
expe_report['supervisor'] = os.uname()[1]
for timev, datek in zip((kronos.get_start_date(), kronos.get_end_date()), ('start_date', 'end_date')):
expe_report[datek] = datetime.datetime.fromtimestamp(timev).strftime('Le %d/%m/%Y à %H:%M:%S')
expe_report[datek] = datetime.datetime.fromtimestamp(timev).strftime('Le %d/%m/%Y à %H:%M:%S') if timev is not None else None
ressources = kronos.get_times()
ressources['ram'] = None
@ -184,10 +199,12 @@ class Kronos(object):
self._pt = time.process_time()
self._times = OrderedDict()
self._stime = time.time()
self._etime = None
def time(self, name):
self._times[name + '_process_time'] = time.process_time() - self._pt
self._pt = time.process_time()
self._etime = time.time()
def get_times(self):
return self._times
@ -196,7 +213,7 @@ class Kronos(object):
return self._stime
def get_end_date(self):
return time.time()
return self._etime
def watch_folder():

31
test.yml
View File

@ -1,31 +0,0 @@
expe:
name: Première expérience
date: 9 juillet 2018
priority: 1
ground_truth: '../Data/ground_truth/2018_IEEE_GRSS_DFC_GT_TR.tif'
descriptors_script:
name: Descriptors.dfc_aps
parameters:
treshold: 1e4
rasters:
- '../Data/phase1_rasters/DEM+B_C123/UH17_GEM051_TR.tif'
- '../Data/phase1_rasters/DEM_C123_3msr/UH17_GEG051_TR.tif'
areas: [100, 1000]
moi: [.5, .9]
cross_validation:
name: CrossValidationGenerator.APsCVG
parameters:
n_test: 2
classifier:
name: sklearn.ensemble.RandomForestClassifier
parameters:
n_jobs: -1
random_state: 0
n_estimators: 50
min_samples_leaf: 10
expe_hashes:
ground_truth: XXX
descriptors_script: XXX
cross_validation: XXX
classifier: XXX
global: XXX