diff --git a/document/data/plot_notes.txt b/document/data/plot_notes.txt
index bc6adb0056c48b5a1b4e2f3db8169b9c0a39ad99..8f0b7b843666f78f484fd588485b0164bc0d0608 100644
--- a/document/data/plot_notes.txt
+++ b/document/data/plot_notes.txt
@@ -33,6 +33,23 @@ Level_6;ZOrder;AverageCompressionRation
LLC Emerald 1.71823
16 Bit Z Stack 1.88627
-----------------------------------------------
+Level_6;DifferenceNormal_VS_ZOrder
+ GZIP
+ Artemia 105.95400
+ Artemia Flash 109.29308
+ LLC Emerald 101.46799
+ 16 Bit Z Stack 101.15722
+ LZMA
+ Artemia 103.48855
+ Artemia Flash 104.98964
+ LLC Emerald 102.23146
+ 16 Bit Z Stack 101.92729
+ BZIP2
+ Artemia 99.84425
+ Artemia Flash 100.77455
+ LLC Emerald 99.89707
+ 16 Bit Z Stack 98.90801
+-----------------------------------------------
Level_6;NormalOrder;BitsPerPixel
GZIP
Artemia 5.99774
diff --git a/document/data/query.sql b/document/data/query.sql
index f92a6aad75fb45efb1564230d3617cedb55644df..25f99d8c0ad5f7795a89e325f33ab4532e22a63b 100644
--- a/document/data/query.sql
+++ b/document/data/query.sql
@@ -1,27 +1,26 @@
-SELECT subblock, compressionRatio, compressionRatioZ
-FROM LlcEmeralCherry
-WHERE compression = 'BZIP2' AND level = 6
+-- SELECT subblock, compressionRatio, compressionRatioZ
+-- FROM LlcEmeralCherry
+-- WHERE compression = 'GZIP' AND level = 6
+
-/*
SELECT * FROM
(
-SELECT ROUND(AVG(originalSize/1000000.0) / (compressionTimeZ/1000.0),5)
+SELECT ROUND((AVG(compressionRatioZ) / AVG(compressionRatio))*100.0,5)
FROM ArtemiaZSect
WHERE compression = 'GZIP' AND level = 6
) a,
(
-SELECT ROUND(AVG(originalSize/1000000.0) / (compressionTimeZ/1000.0),5)
+SELECT ROUND((AVG(compressionRatioZ) / AVG(compressionRatio))*100.0,5)
FROM ArtemiaFlash
WHERE compression = 'GZIP' AND level = 6
) af,
(
-SELECT ROUND(AVG(originalSize/1000000.0) / (compressionTimeZ/1000.0),5)
+SELECT ROUND((AVG(compressionRatioZ) / AVG(compressionRatio))*100.0,5)
FROM LlcEmeralCherry
WHERE compression = 'GZIP' AND level = 6
) llc,
(
-SELECT ROUND(AVG(originalSize/1000000.0) / (compressionTimeZ/1000.0),5)
+SELECT ROUND((AVG(compressionRatioZ) / AVG(compressionRatio))*100.0,5)
FROM Bit16ZStack
WHERE compression = 'GZIP' AND level = 6
-) b16;
-*/
\ No newline at end of file
+) b16;
\ No newline at end of file
diff --git a/document/document.pdf b/document/document.pdf
index f5376cffc3047d0fccd65f26cdf0e5158ab5b242..95e2f082fe0381e67a482d610b76b45786d76273 100644
Binary files a/document/document.pdf and b/document/document.pdf differ
diff --git a/document/document.tex b/document/document.tex
index 8c6ec99d6b25b5cac16e6f4976d078ddf4fca292..1428f48466d558863cba05144c12f8eef0db7985 100644
--- a/document/document.tex
+++ b/document/document.tex
@@ -32,6 +32,18 @@
(0cm,0cm) rectangle (3pt,0.8em);},
}
}
+\pgfplotsset{%
+ axis line origin/.style args={#1,#2}{
+ x filter/.append code={ % Check for empty or filtered out numbers
+ \ifx\pgfmathresult\empty\else\pgfmathparse{\pgfmathresult-#1}\fi
+ },
+ y filter/.append code={
+ \ifx\pgfmathresult\empty\else\pgfmathparse{\pgfmathresult-#2}\fi
+ },
+ xticklabel=\pgfmathparse{\tick+#1}\pgfmathprintnumber{\pgfmathresult},
+ yticklabel=\pgfmathparse{\tick+#2}\pgfmathprintnumber{\pgfmathresult}
+ }
+}
\author{Moravec Vojtěch}
\title{Metody komprese bioinformatických dat pro přenos na HPC infrastrukturu}
@@ -127,6 +139,12 @@ Nejprve uvedeme 3 metody, kterĂ© se pouĹľĂvajĂ pro bezztrátovou kompresi dat
NáslednÄ› popĂšeme kompresi \bThreed, která se pĹ™Ămo zaměřuje na kompresi obrazĹŻ, zĂskanĂ˝ch z mikroskopĹŻ.
TakĂ© zde prozkoumáme techniku pĹ™euspořádánĂ dat, která by mohla vĂ©st k lepšĂm vĂ˝sledkĹŻm komprese.
+Komprese budou hodnoceny pomocĂ kompresnĂho pomÄ›ru, kterĂ˝ je vypoÄŤten následovnÄ›:
+\begin{equation*}
+ \text{kompresnà poměr} = \frac{\text{velikost dat}}{\text{velikost komprimovaných dat}}
+\end{equation*}
+\noindent žádoucà jsou tedy hodnoty většà než $1.0$.
+
\subsection{StandartnĂ metody}
StandartnĂ metody, kterĂ© zde uvedeme, jsou hojnÄ› vyuĹľĂvány v nejrozšĂĹ™eněšjšĂch programech zabĂ˝vajĂcĂ se bezztrátovou kompresĂ. Tyto metody jsou navrĹľeny tak,
@@ -239,14 +257,57 @@ druhé části jsou chyby predikce zakódovány pomocà RLE a Huffmana.
Bezztrátová komprese dosáhla kompresnĂho pomÄ›ru 2,7 kdeĹľto ztrátová WNL komprese dosahuje kompresnĂho pomÄ›ru 5. Chyba lokalizace jedinĂ© molekuly v obrazu vstoupla pouze o 4\%. (Bylo testováno na datasetu zĂskanĂ©m pomocĂ Single-Molecule Localization Microscopy, rozlišenĂ 2-25 nm).
+\newpage
\subsection{Mortonovo kĂłdovánĂ}
-Mortonovo kĂłdovánĂ, je zpĹŻsob mapovánĂ multidimenzionálnĂch dat na jednodimenzionálnĂ data. Jedná se o pĹ™euspořádánĂ dat podle \emph{Z kĹ™ivky}, která jimi
-procházĂ. \emph{Z kĹ™ivka} spadá do skupiny tzv. prostor vyplĹujĂcĂch kĹ™Ăvek. Tyto kĹ™Ăvky obecnÄ› procházĂ kaĹľdĂ˝m bodem prostoru v $n$-dimenzionálnĂ hyperkrychli.
+Mortonovo kĂłdovánĂ, je zpĹŻsob mapovánĂ multidimenzionálnĂch dat na jednodimenzionálnĂ. Jedná se o pĹ™euspořádánĂ dat podle \emph{Z kĹ™ivky}, která jimi
+procházĂ. \emph{Z kĹ™ivka} spadá do skupiny tzv. prostor vyplĹujĂcĂch kĹ™Ăvek, kterĂ© obecnÄ› procházĂ kaĹľdĂ˝m bodem prostoru v $n$-dimenzionálnĂ hyperkrychli.
Na ObrázkĹŻ \ref{fig:zCurve} mĹŻĹľeme vidÄ›t jak probĂhá mapovánĂ 2D prostoru na 1D prostor, pro kaĹľdĂ˝ bod roviny je vypoÄŤtena $Z$ souĹ™adnice,
-pomocĂ kterĂ© následnÄ› seĹ™adĂme jednotlivĂ© body. V našem pĹ™ĂpadÄ› pomocĂ $Z$ souĹ™adnice pĹ™euspořádáme data obrazĹŻ.
+pomocĂ kterĂ© následnÄ› seĹ™adĂme jednotlivĂ© body. $Z$ souĹ™adnice je vypoÄŤtena prolnutĂm bitĹŻ $X$-ovĂ© a $Y$-ovĂ© souĹ™adnice.
+V našem pĹ™ĂpadÄ› pomocĂ $Z$ souĹ™adnice pĹ™euspořádáme data obrazĹŻ.
\image{0.5}{ZCurve.pdf}{fig:zCurve}{Mortonovo kĂłdovánĂ}
+\begin{tikzpicture}
+ \begin{axis}[
+ ybar,
+ %xlabel = {},
+ ylabel = {ProcentualnĂ zmÄ›na kompresnĂho pomÄ›ru},
+ axis line origin={0,100},
+ width=0.8\linewidth,
+ symbolic x coords={{Artemia},{Artemia Flash}, {LLC Emerald}, {16 Bit Z Stack}},
+ legend pos = outer north east,
+ x tick label style={
+ rotate=90,
+ anchor=east,
+ },
+ xtick=data,
+ nodes near coords,
+ every node near coord/.append style={rotate=90},
+ ]
+ % gzip
+ \addplot coordinates {
+ ({Artemia},105.95400)
+ ({Artemia Flash},109.29308)
+ ({LLC Emerald},101.46799)
+ ({16 Bit Z Stack},101.15722)
+ };
+ % lzma
+ \addplot coordinates {
+ ({Artemia},103.4885)
+ ({Artemia Flash},104.98964)
+ ({LLC Emerald},102.23146)
+ ({16 Bit Z Stack},101.92729)
+ };
+ % bzip2
+ \addplot coordinates {
+ ({Artemia},99.84425)
+ ({Artemia Flash},100.77455)
+ ({LLC Emerald},99.89707)
+ ({16 Bit Z Stack},98.90801)
+ };
+ \legend{gzip,lzma,bzip2}
+ \end{axis}
+\end{tikzpicture}
\bibliography{citations}
\bibliographystyle{ieeetr}
diff --git a/document/figures/ZCurve.pdf b/document/figures/ZCurve.pdf
index 498d390d4eef751b8e75e215d292eaf5ffd8058f..39777938ade06e687140eba262607e31e3e3782a 100644
Binary files a/document/figures/ZCurve.pdf and b/document/figures/ZCurve.pdf differ
diff --git a/document/figures/ZCurve.svg b/document/figures/ZCurve.svg
index bda1a202b61374cebf4df19e75004c9a16e5461a..f61d19e99cd10319aac474c25a3b56e3a70bb917 100644
--- a/document/figures/ZCurve.svg
+++ b/document/figures/ZCurve.svg
@@ -140,6 +140,17 @@
style="fill-rule:evenodd;stroke:#000000;stroke-width:1pt;stroke-opacity:1;fill:#000000;fill-opacity:1"
transform="scale(0.8) translate(12.5,0)" />
</marker>
+ <clipPath
+ clipPathUnits="userSpaceOnUse"
+ id="clipPath3898">
+ <rect
+ style="fill:none;fill-opacity:1;stroke:#000000;stroke-width:1;stroke-linecap:butt;stroke-linejoin:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1;paint-order:normal"
+ id="rect3900"
+ width="92.597198"
+ height="92.59977"
+ x="0"
+ y="0" />
+ </clipPath>
</defs>
<sodipodi:namedview
id="base"
@@ -148,9 +159,9 @@
borderopacity="1.0"
inkscape:pageopacity="0.0"
inkscape:pageshadow="2"
- inkscape:zoom="1.4142136"
- inkscape:cx="205.39342"
- inkscape:cy="892.49327"
+ inkscape:zoom="2.0000001"
+ inkscape:cx="213.32306"
+ inkscape:cy="929.36493"
inkscape:document-units="mm"
inkscape:current-layer="layer1"
showgrid="true"
@@ -193,18 +204,18 @@
style="display:inline">
<path
d="M 0,0 V 296.99999 M 18.520833,0 V 296.99999 M 37.041666,0 V 296.99999 M 55.562499,0 V 296.99999 M 74.083332,0 V 296.99999 M 92.604165,0 V 296.99999 M 111.125,0 V 296.99999 M 129.64583,0 V 296.99999 M 148.16666,0 V 296.99999 M 166.6875,0 V 296.99999 M 185.20833,0 V 296.99999 M 203.72916,0 V 296.99999 M 0,0 H 210 M 0,18.520833 H 210 M 0,37.041666 H 210 M 0,55.562499 H 210 M 0,74.083332 H 210 M 0,92.604165 H 210 M 0,111.125 H 210 M 0,129.64583 H 210 M 0,148.16666 H 210 M 0,166.6875 H 210 M 0,185.20833 H 210 M 0,203.72916 H 210 M 0,222.24999 H 210 M 0,240.77083 H 210 M 0,259.29166 H 210 M 0,277.81249 H 210 M 0,296.33333 h 210"
- style="display:none;fill:none;stroke:#000000;stroke-width:0.30000001;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
+ style="display:inline;fill:none;stroke:#000000;stroke-width:0.30000001;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
id="path4548"
inkscape:connector-curvature="0"
- inkscape:label="Grid" />
+ inkscape:label="Grid"
+ clip-path="url(#clipPath3898)" />
<path
- style="fill:none;fill-opacity:1;stroke:#000000;stroke-width:1.5;stroke-linecap:butt;stroke-linejoin:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:0.27374303;paint-order:normal"
+ style="display:inline;fill:none;fill-opacity:1;stroke:#000000;stroke-width:1.5;stroke-linecap:butt;stroke-linejoin:round;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:0.27374303;paint-order:normal"
d="M 27.78125,27.124992 H 46.302083 L 27.78125,45.645825 H 46.302083 L 64.822917,27.124992 H 83.34375 L 64.822917,45.645825 H 83.34375 L 27.78125,64.166658 H 46.302083 L 27.78125,82.687492 H 46.302083 L 64.822917,64.166658 H 83.34375 L 64.822917,82.687492 H 83.34375"
id="path5179"
inkscape:connector-curvature="0"
inkscape:label="ZCurve"
- sodipodi:nodetypes="cccccccccccccccc"
- sodipodi:insensitive="true" />
+ sodipodi:nodetypes="cccccccccccccccc" />
<path
style="fill:none;stroke:#000000;stroke-width:1;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
d="m 18.475006,18.448349 74.12916,0.07768"
@@ -273,7 +284,7 @@
y="8.868742"
x="10.816911"
id="tspan4554"
- sodipodi:role="line">Y</tspan></text>
+ sodipodi:role="line">X</tspan></text>
<text
id="text4552"
y="17.335409"
@@ -285,7 +296,7 @@
y="17.335409"
x="0.97151697"
id="tspan4550"
- sodipodi:role="line">X</tspan></text>
+ sodipodi:role="line">Y</tspan></text>
<text
inkscape:label="x3"
id="text4595"