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Commit 21d3a549 authored by Vojtěch Moravec's avatar Vojtěch Moravec
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Updated document.

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.gitignore
+ 3
− 1
View file @ 21d3a549
......@@ -14,4 +14,6 @@ czi_example_data/
*.out
*.bbl
*.blg
*.fdb_latexmk
\ No newline at end of file
*.fdb_latexmk
.vs/
[Oo]bj
README.md
+ 1
− 0
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......@@ -11,6 +11,7 @@
- Jaký je vztah mezi obrázky v CZI souboru?
- Dala by se použít nějaká komprese vzhledem k `referenčním` obrázkům? (vztah mezi obrazy, jak jsou posunuty atd.)
- Možná se podívat co je to ten HDF5, ale spíš se zaměřit na CZI formát.
- Jaké obrázky jsou komprimované pomocí B3D a s jakýmy výsledky?
<!-- Popsat formát CZI, HDF5
......
czi-format/inspector/czi-inspector.sln 0 → 100644
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View file @ 21d3a549

Microsoft Visual Studio Solution File, Format Version 12.00
# Visual Studio 15
VisualStudioVersion = 15.0.28307.168
MinimumVisualStudioVersion = 10.0.40219.1
Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "czi-inspector", "czi-inspector\czi-inspector.csproj", "{CC796EBE-77A0-442F-A44F-0863E03B2F54}"
EndProject
Global
GlobalSection(SolutionConfigurationPlatforms) = preSolution
Debug|Any CPU = Debug|Any CPU
Release|Any CPU = Release|Any CPU
EndGlobalSection
GlobalSection(ProjectConfigurationPlatforms) = postSolution
{CC796EBE-77A0-442F-A44F-0863E03B2F54}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
{CC796EBE-77A0-442F-A44F-0863E03B2F54}.Debug|Any CPU.Build.0 = Debug|Any CPU
{CC796EBE-77A0-442F-A44F-0863E03B2F54}.Release|Any CPU.ActiveCfg = Release|Any CPU
{CC796EBE-77A0-442F-A44F-0863E03B2F54}.Release|Any CPU.Build.0 = Release|Any CPU
EndGlobalSection
GlobalSection(SolutionProperties) = preSolution
HideSolutionNode = FALSE
EndGlobalSection
GlobalSection(ExtensibilityGlobals) = postSolution
SolutionGuid = {E88F4F44-F469-4F79-B35D-08A631D14253}
EndGlobalSection
EndGlobal
czi-format/inspector/czi-inspector/Program.cs 0 → 100644
+ 54
− 0
View file @ 21d3a549
using System;
using System.Diagnostics;
using System.IO;
using System.Text;
using System.Text.RegularExpressions;
namespace czi_inspector
{
class Program
{
static void Main(string[] args)
{
string file = args[0];
string substring = args[1];
string encoding = args[2];
Regex regex = new Regex(substring, RegexOptions.IgnoreCase);
Encoding selectedEncoding = GetEncoding(encoding);
const int bufferSize = 1024;
byte[] buffer = new byte[bufferSize];
int count = 0;
Stopwatch stopwatch = new Stopwatch();
stopwatch.Start();
//var wholeFileBuffer = File.ReadAllBytes(file);
//string wholeFileString = selectedEncoding.GetString(wholeFileBuffer);
//count = regex.Matches(substring).Count;
using (FileStream reader = new FileStream(file, FileMode.Open, FileAccess.Read))
{
while (reader.Read(buffer, 0, bufferSize) > 0)
{
string bufferString = selectedEncoding.GetString(buffer);
var matches = regex.Matches(bufferString).Count;
count += matches;
if (matches > 0)
Console.WriteLine(bufferString);
}
}
stopwatch.Stop();
Console.WriteLine("Found: {0} occurencies of {1} in file {2} in {3} ms.", count, substring, file, stopwatch.Elapsed.TotalMilliseconds);
}
private static Encoding GetEncoding(string encoding)
{
encoding = encoding.ToUpper();
if (encoding == "ASCII") return Encoding.ASCII;
if (encoding == "UTF8") return Encoding.UTF8;
if (encoding == "UNICODE") return Encoding.Unicode;
if (encoding == "UTF32") return Encoding.UTF32;
throw new Exception("Try different encoding, currently supported: ASCII, UTF8, UTF32, UNICODE.");
}
}
}
czi-format/inspector/czi-inspector/czi-inspector.csproj 0 → 100644
+ 9
− 0
View file @ 21d3a549
<Project Sdk="Microsoft.NET.Sdk">
<PropertyGroup>
<OutputType>Exe</OutputType>
<TargetFramework>netcoreapp2.1</TargetFramework>
<RootNamespace>czi_inspector</RootNamespace>
</PropertyGroup>
</Project>
document/citations.bib
+ 15
− 2
View file @ 21d3a549
......@@ -3,5 +3,18 @@
title = ZISRAW (CZI) File Format",
year = 2016,
number = "MC33879",
note = "Version 1.2.2"
}
\ No newline at end of file
note = "Version 1.2.2",
}
@article {Balazs164624,
author = {Balazs, Balint and Deschamps, Joran and Albert, Marvin and Ries, Jonas and Hufnagel, Lars},
title = {A real-time compression library for microscopy images},
elocation-id = {164624},
year = {2017},
doi = {10.1101/164624},
publisher = {Cold Spring Harbor Laboratory},
abstract = {Fluorescence imaging techniques such as single molecule localization microscopy, high-content screening and light-sheet microscopy are producing ever-larger datasets, which poses increasing challenges in data handling and data sharing. Here, we introduce a real-time compression library that allows for very fast (beyond 1 GB/s) compression and de-compression of microscopy datasets during acquisition. In addition to an efficient lossless mode, our algorithm also includes a lossy option, which limits pixel deviations to the intrinsic noise level of the image and yields compression ratio of up to 100-fold. We present a detailed performance analysis of the different compression modes for various biological samples and imaging modalities.},
URL = {https://www.biorxiv.org/content/early/2017/07/21/164624},
eprint = {https://www.biorxiv.org/content/early/2017/07/21/164624.full.pdf},
journal = {bioRxiv}
}
document/diploma.cls 0 → 100644
+ 547
− 0
View file @ 21d3a549
%%
%% This is file `diploma.cls',
%% generated with the docstrip utility.
%%
%% The original source files were:
%%
%% VersionInfo.dtx
%% Introduction.dtx
%% UserManual.dtx
%% ImplementationBeginning.dtx
%% Constants.dtx
%% VariablesDeclaration.dtx
%% BaseClassAndPackages.dtx
%% OptionsDeclaration.dtx
%% PublicMacros.dtx
%% InternalMacros.dtx
%% SourceCodeListings.dtx
%% ImplementationFinale.dtx
%%
%% IMPORTANT NOTICE:
%%
%% For the copyright see the source file.
%%
%% Any modified versions of this file must be renamed
%% with new filenames distinct from diploma.cls.
%%
%% For distribution of the original source see the terms
%% for copying and modification in the file VersionInfo.dtx Introduction.dtx UserManual.dtx ImplementationBeginning.dtx Constants.dtx VariablesDeclaration.dtx BaseClassAndPackages.dtx OptionsDeclaration.dtx PublicMacros.dtx InternalMacros.dtx SourceCodeListings.dtx ImplementationFinale.dtx.
%%
%% This generated file may be distributed as long as the
%% original source files, as listed above, are part of the
%% same distribution. (The sources need not necessarily be
%% in the same archive or directory.)
\def\fileversion{4.03}
\def\filedate{2017/03/31}
\def\docdate{31. března 2018}
\NeedsTeXFormat{LaTeX2e}
\ProvidesClass{diploma}[\filedate\space \fileversion\space diploma LaTeX document class]
\RequirePackage{ifthen}
\newcommand{\Dipl@BachelorThesis}{0}
\newcommand{\Dipl@BachelorPractice}{1}
\newcommand{\Dipl@MasterThesis}{2}
\newcommand{\Dipl@PhDThesis}{3}
\newcommand{\Dipl@CzechLanguage}{0}
\newcommand{\Dipl@EnglishLanguage}{1}
\newcommand{\Dipl@SlovakLanguage}{2}
\newtoks\Dipl@UniversityName
\Dipl@UniversityName={No university name is given}
\newtoks\Dipl@FacultyName
\Dipl@FacultyName={No faculty name is given}
\newtoks\Dipl@DepartmentName
\Dipl@DepartmentName={No department name is given}
\newtoks\Dipl@ThesisAuthor
\Dipl@ThesisAuthor={No author name is given}
\newtoks\Dipl@CzechThesisTitle
\Dipl@CzechThesisTitle={No Czech or Slovak thesis title is given}
\newtoks\Dipl@EnglishThesisTitle
\Dipl@EnglishThesisTitle={No English thesis title is given}
\newtoks\Dipl@SubmissionDate
\Dipl@SubmissionDate={No submission date is given}
\newtoks\Dipl@ThesisAssignmentImagePath
\Dipl@ThesisAssignmentImagePath={}
\newtoks\Dipl@AuthorDeclaration
\Dipl@AuthorDeclaration={}
\newtoks\Dipl@AuthorDeclarationImageFile
\Dipl@AuthorDeclarationImageFile={}
\newtoks\Dipl@CooperatingPersonsDeclaration
\Dipl@CooperatingPersonsDeclaration={}
\newtoks\Dipl@ThesisAccessRestriction
\Dipl@ThesisAccessRestriction={}
\newtoks\Dipl@CooperatingPersonsDeclarationImageFile
\Dipl@CooperatingPersonsDeclarationImageFile={}
\newtoks\Dipl@Thanks
\Dipl@Thanks={}
\newtoks\Dipl@CzechAbstract
\Dipl@CzechAbstract={No Czech or Slovak abstract is given}
\newtoks\Dipl@CzechKeywords
\Dipl@CzechKeywords={No Czech or Slovak keywords are given}
\newtoks\Dipl@EnglishAbstract
\Dipl@EnglishAbstract={No English abstract is given}
\newtoks\Dipl@EnglishKeywords
\Dipl@EnglishKeywords={No English keywords are given}
\newtoks\Dipl@Acronyms
\Dipl@Acronyms={}
\newtoks\Dipl@DefaultSourceCodeLanguage
\Dipl@DefaultSourceCodeLanguage={java}
\newboolean{Dipl@IsPublicPart}
\setboolean{Dipl@IsPublicPart}{true}
\newboolean{Dipl@AuthorIsMale}
\setboolean{Dipl@AuthorIsMale}{true}
\newboolean{Dipl@PrintCooperatingPersonsDeclaration}
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\newboolean{Dipl@IsAppendix}
\setboolean{Dipl@IsAppendix}{false}
\newcounter{Dipl@CurrentThesisType}
\setcounter{Dipl@CurrentThesisType}{\Dipl@MasterThesis}
\newcounter{Dipl@CurrentThesisLanguage}
\setcounter{Dipl@CurrentThesisLanguage}{\Dipl@CzechLanguage}
\newcounter{Dipl@ThesisAssignmentImageCounter}
\LoadClass[11pt]{article}
\RequirePackage[czech,english,slovak]{babel}
\RequirePackage[T1]{fontenc}
\RequirePackage{lmodern}
\RequirePackage[a4paper,includefoot,nohead,marginparwidth=0mm,marginparsep=0mm,left=30mm,right=20mm,top=30mm,bottom=30mm]{geometry}
\RequirePackage{booktabs}
\RequirePackage{graphicx}
\RequirePackage[final]{listings}
\RequirePackage{longtable}
\RequirePackage{rotating}
\RequirePackage{setspace}
\RequirePackage{theorem}
\RequirePackage{titlesec}
\RequirePackage[nottoc,notindex,section]{tocbibind}
\RequirePackage{totcount}
\RequirePackage{xcolor}
\RequirePackage[a-1b]{pdfx}
\RequirePackage[utf8]{inputenc}
\DeclareOption{czech}
{
\setcounter{Dipl@CurrentThesisLanguage}{\Dipl@CzechLanguage}
\Dipl@UniversityName={VŠB -- Technická univerzita Ostrava}
\Dipl@FacultyName={Fakulta elektrotechniky a informatiky}
}
\DeclareOption{english}
{
\setcounter{Dipl@CurrentThesisLanguage}{\Dipl@EnglishLanguage}
\Dipl@UniversityName={VŠB -- Technical University of Ostrava}
\Dipl@FacultyName={Faculty of Electrical Engineering and Computer Science}
}
\DeclareOption{slovak}
{
\setcounter{Dipl@CurrentThesisLanguage}{\Dipl@SlovakLanguage}
\Dipl@UniversityName={VŠB -- Technická univerzita Ostrava}
\Dipl@FacultyName={Fakulta elektrotechniky a informatiky}
}
\DeclareOption{bachelor}
{
\setcounter{Dipl@CurrentThesisType}{\Dipl@BachelorThesis}
\Dipl@CooperatingPersonsDeclaration={\Dipl@IfEnglish{I hereby agree to the publishing of the bachelor's thesis as per s. 26, ss. 9 of the Study and Examination Regulations for Bachelor's Degree Programmes at VŠB -- Technical University of Ostrava.}{Souhlasím se zveřejněním této bakalářské práce dle požadavků čl.\ 26, odst.\ 9 Studijního a~zkušebního řádu pro studium v bakalářských programech VŠB-TU Ostrava.}}
}
\DeclareOption{bachelorpractice}
{
\setcounter{Dipl@CurrentThesisType}{\Dipl@BachelorPractice}
\Dipl@CzechThesisTitle={Absolvování individuální odborné praxe}
\Dipl@EnglishThesisTitle={Individual Professional Practice in the Company}
\Dipl@CooperatingPersonsDeclaration={\Dipl@IfEnglish{I hereby agree to the publishing of the bachelor's thesis as per s. 26, ss. 9 of the Study and Examination Regulations for Bachelor's Degree Programmes at VŠB -- Technical University of Ostrava.}{Souhlasím se zveřejněním této bakalářské práce dle požadavků čl.\ 26, odst.\ 9 Studijního a~zkušebního řádu pro studium v bakalářských programech VŠB-TU Ostrava.}}
}
\DeclareOption{master}
{
\setcounter{Dipl@CurrentThesisType}{\Dipl@MasterThesis}
\Dipl@CooperatingPersonsDeclaration={\Dipl@IfEnglish{I hereby agree to the publishing of the master's thesis as per s. 26, ss. 9 of the Study and Examination Regulations for Master's Degree Programmes at VŠB -- Technical University of Ostrava.}{Souhlasím se zveřejněním této diplomové práce dle požadavků čl.\ 26, odst.\ 9 Studijního a~zkušebního řádu pro studium v magisterských programech VŠB-TU Ostrava.}}
}
\DeclareOption{phd}{\setcounter{Dipl@CurrentThesisType}{\Dipl@PhDThesis}}
\DeclareOption{public}{\setboolean{Dipl@IsPublicPart}{true}}
\DeclareOption{nonpublic}{\setboolean{Dipl@IsPublicPart}{false}}
\DeclareOption{cpdeclaration}{\setboolean{Dipl@PrintCooperatingPersonsDeclaration}{true}}
\DeclareOption{dept410}{\Dipl@DepartmentName={\Dipl@IfEnglish{Department of Electrical Power Engineering}{Katedra elektroenergetiky}}}
\DeclareOption{dept420}{\Dipl@DepartmentName={\Dipl@IfEnglish{Department of Electrical Engineering}{Katedra elektrotechniky}}}
\DeclareOption{dept430}{\Dipl@DepartmentName={\Dipl@IfEnglish{Department of Electronics}{Katedra elektroniky}}}
\DeclareOption{dept440}{\Dipl@DepartmentName={\Dipl@IfEnglish{Department of Telecommunications}{Katedra telekomunikační techniky}}}
\DeclareOption{dept450}{\Dipl@DepartmentName={\Dipl@IfEnglish{Department of Cybernetics and Biomedical Engineering}{Katedra kybernetiky a biomedicínského inženýrství}}}
\DeclareOption{dept460}{\Dipl@DepartmentName={\Dipl@IfEnglish{Department of Computer Science}{Katedra informatiky}}}
\DeclareOption{dept470}{\Dipl@DepartmentName={\Dipl@IfEnglish{Department of Applied Mathematics}{Katedra aplikované matematiky}}}
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{
\setboolean{Dipl@AuthorIsMale}{true}
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{
\Dipl@AuthorDeclaration={\Dipl@IfEnglish{I hereby declare that this bachelor's thesis was written by myself. I have quoted all the references I have drawn upon.}{Prohlašuji, že jsem tuto bakalářskou práci vypracoval samostatně. Uvedl jsem všechny literární prameny a publikace, ze kterých jsem čerpal.}}
}
{\relax}
\ifthenelse{\value{Dipl@CurrentThesisType}=\Dipl@MasterThesis}
{
\Dipl@AuthorDeclaration={\Dipl@IfEnglish{I hereby declare that this master's thesis was written by myself. I have quoted all the references I have drawn upon.}{Prohlašuji, že jsem tuto diplomovou práci vypracoval samostatně. Uvedl jsem všechny literární prameny a publikace, ze kterých jsem čerpal.}}
}
{\relax}
}
\DeclareOption{female}
{
\setboolean{Dipl@AuthorIsMale}{false}
\ifthenelse{\(\value{Dipl@CurrentThesisType}=\Dipl@BachelorThesis\) \or \(\value{Dipl@CurrentThesisType}=\Dipl@BachelorPractice\)}
{
\Dipl@AuthorDeclaration={\Dipl@IfEnglish{I hereby declare that this bachelor's thesis was written by myself. I have quoted all the references I have drawn upon.}{Prohlašuji, že jsem tuto bakalářskou práci vypracovala samostatně. Uvedla jsem všechny literární prameny a publikace, ze kterých jsem čerpala.}}
}
{\relax}
\ifthenelse{\value{Dipl@CurrentThesisType}=\Dipl@MasterThesis}
{
\Dipl@AuthorDeclaration={\Dipl@IfEnglish{I hereby declare that this master's thesis was written by myself. I have quoted all the references I have drawn upon.}{Prohlašuji, že jsem tuto diplomovou práci vypracovala samostatně. Uvedla jsem všechny literární prameny a publikace, ze kterých jsem čerpala.}}
}
{\relax}
}
\DeclareOption{ansic}{\Dipl@DefaultSourceCodeLanguage={ansic}}
\DeclareOption{bash}{\Dipl@DefaultSourceCodeLanguage={bash}}
\DeclareOption{cil}{\Dipl@DefaultSourceCodeLanguage={cil}}
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\DeclareOption{tcltk}{\Dipl@DefaultSourceCodeLanguage={tcltk}}
\DeclareOption{vb}{\Dipl@DefaultSourceCodeLanguage={vb}}
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\DeclareOption{xml}{\Dipl@DefaultSourceCodeLanguage={xml}}
\DeclareOption{xslt}{\Dipl@DefaultSourceCodeLanguage={xslt}}
\DeclareOption*{\PassOptionsToClass{\CurrentOption}{article}}
\ProcessOptions
\newcommand{\ThesisAuthor}[1]{\Dipl@ThesisAuthor={#1}}
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\newcommand{\EnglishThesisTitle}[1]{\ifthenelse{\value{Dipl@CurrentThesisType}=\Dipl@BachelorPractice}{\relax}{\Dipl@EnglishThesisTitle={#1}}}
\newcommand{\SubmissionDate}[1]{\Dipl@SubmissionDate={#1}}
\newcommand{\ThesisAssignmentImagePath}[1]{\Dipl@ThesisAssignmentImagePath={#1}}
\newcommand{\AuthorDeclarationImageFile}[1]{\Dipl@AuthorDeclarationImageFile={#1}}
\newcommand{\ThesisAccessRestriction}[1]{\Dipl@ThesisAccessRestriction={#1}}
\newcommand{\CooperatingPersonsDeclarationImageFile}[1]{\Dipl@CooperatingPersonsDeclarationImageFile={#1}}
\newcommand{\Thanks}[1]{\Dipl@Thanks={#1}}
\newcommand{\CzechAbstract}[1]{\Dipl@CzechAbstract={#1}}
\newcommand{\CzechKeywords}[1]{\Dipl@CzechKeywords={#1}}
\newcommand{\EnglishAbstract}[1]{\Dipl@EnglishAbstract={#1}}
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{
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\tableofcontents\cleardoublepage
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{\theorembodyfont{\itshape}\newtheorem{definition}{\Dipl@IfEnglish{Definition}{Definice}}}
{\theorembodyfont{\itshape}\newtheorem{theorem}{\Dipl@IfEnglish{Theorem}{Věta}}}
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{\par\noindent\textbf{\proofname}}
{\mbox{}\hspace*{5pt}\hfill\hbox{\vrule height5pt depth0pt width5pt}\par\medskip}
{\theorembodyfont{\rmfamily}\newtheorem{remark}{\Dipl@IfEnglish{Remark}{Poznámka}}}
{\theoremstyle{break}\theorembodyfont{\rmfamily}\newtheorem{Dipl@examplebody}{\Dipl@IfEnglish{Example}{Příklad}}}
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\nopagebreak\mbox{}\hspace*{5pt}\hfill\hbox{\vrule height5pt depth0pt width5pt}
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\begin{figure}
\centering
\includegraphics[width=#2]{#1}
\caption{#3}
\label{#4}
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\sffamily
{\Large\the\Dipl@UniversityName\par
\the\Dipl@FacultyName\par
\the\Dipl@DepartmentName\par}
\vspace{26mm}
{\Huge\bfseries\Dipl@IfEnglish{\the\Dipl@EnglishThesisTitle}{\the\Dipl@CzechThesisTitle}\par}
\bigskip
{\Huge\bfseries\Dipl@IfEnglish{\the\Dipl@CzechThesisTitle}{\the\Dipl@EnglishThesisTitle}\par}
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{
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{\huge\Dipl@IfEnglish{Non-public part/Neveřejná část}{Neveřejná část/Non-public part}\par}
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{
\begin{center}
\Large\sffamily\bfseries
\Dipl@IfEnglish{This page will be replaced by official thesis assignment in printed and electronic version of the submitted thesis.}%
{Tuto stránku nahradíte v tištěné verzi práce oficiálním zadáním Vaší diplomové či bakalářské práce.}
\end{center}
}
{
\setcounter{Dipl@ThesisAssignmentImageCounter}{1}
\whiledo{\value{Dipl@ThesisAssignmentImageCounter}>0}
{
\IfFileExists{\the\Dipl@ThesisAssignmentImagePath\theDipl@ThesisAssignmentImageCounter.jpg}
{
\Dipl@InsertFullPageImage{\the\Dipl@ThesisAssignmentImagePath\theDipl@ThesisAssignmentImageCounter.jpg}
\addtocounter{Dipl@ThesisAssignmentImageCounter}{1}
}
{
\setcounter{Dipl@ThesisAssignmentImageCounter}{-1}
}
}
}
\cleardoublepage
}
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{
\ifthenelse{\equal{\the\Dipl@AuthorDeclarationImageFile}{\empty}}
{
\mbox{}
\vfill
\noindent
\the\Dipl@AuthorDeclaration
\par
\vspace{15mm}
\noindent\Dipl@IfEnglish{Ostrava,}{V Ostravě}~\the\Dipl@SubmissionDate\hfill\hbox to50mm{\dotfill}
}
{
\Dipl@InsertFullPageImage{\the\Dipl@AuthorDeclarationImageFile}
}
\cleardoublepage
}
\newcommand{\Dipl@CooperatingPersonsDeclarationPage}
{
\ifthenelse{\boolean{Dipl@PrintCooperatingPersonsDeclaration}}
{
\ifthenelse{\equal{\the\Dipl@CooperatingPersonsDeclarationImageFile}{\empty}}
{
\mbox{}
\vfill
\ifthenelse{\equal{\the\Dipl@ThesisAccessRestriction}{\empty}}
{\relax}
{\noindent\the\Dipl@ThesisAccessRestriction\par\bigskip}
\noindent
\the\Dipl@CooperatingPersonsDeclaration
\par
\vspace{15mm}
\noindent\Dipl@IfEnglish{Ostrava,}{V Ostravě}~\the\Dipl@SubmissionDate\hfill\hbox to50mm{\dotfill}
}
{
\Dipl@InsertFullPageImage{\the\Dipl@CooperatingPersonsDeclarationImageFile}
}
\cleardoublepage
}
{\relax}
}
\newcommand{\Dipl@WriteThanksPage}
{
\ifthenelse{\equal{\the\Dipl@Thanks}{\empty}}
{\relax}
{
\mbox{}
\vfill
\noindent\the\Dipl@Thanks
\cleardoublepage
}
}
\newcommand{\Dipl@AbstractsKeywordsPage}
{
\vspace*{20mm plus 0mm minus 25mm}
\ifthenelse{\value{Dipl@CurrentThesisLanguage}=\Dipl@SlovakLanguage}
{
\begin{otherlanguage}{slovak}
\noindent\textbf{Abstrakt}
\medbreak
\noindent\the\Dipl@CzechAbstract
\bigbreak
\noindent\textbf{Kľúčové slová}:~\the\Dipl@CzechKeywords\par
\end{otherlanguage}
}
{
\begin{otherlanguage}{czech}
\noindent\textbf{Abstrakt}
\medbreak
\noindent\the\Dipl@CzechAbstract
\bigbreak
\noindent\textbf{Klíčová slova}:~\the\Dipl@CzechKeywords\par
\end{otherlanguage}
}
\vspace{30mm plus 0mm minus 30mm}
\begin{otherlanguage}{english}
\noindent\textbf{Abstract}
\medbreak
\noindent\the\Dipl@EnglishAbstract
\bigbreak
\noindent\textbf{Key Words}:~\the\Dipl@EnglishKeywords\par
\end{otherlanguage}
\cleardoublepage
}
\newcommand{\Dipl@WriteAcronymsPage}
{
\ifthenelse{\equal{\the\Dipl@Acronyms}{\empty}}
{\relax}
{
\section*{\Dipl@IfEnglish{List of symbols and abbreviations}{Seznam použitých zkratek a symbolů}}
\ifthenelse{\value{Dipl@CurrentThesisLanguage}=\Dipl@EnglishLanguage}
{
\addcontentsline{toc}{section}{List of symbols and abbreviations}
}
{
\addcontentsline{toc}{section}{Seznam použitých zkratek a symbolů}
}
\begin{longtable*}[l]{p{0.2\textwidth}cp{0.7\textwidth}}
\the\Dipl@Acronyms
\end{longtable*}
\cleardoublepage
}
}
\newcommand{\Dipl@PrintRestriction}
{
\noindent\the\Dipl@PublicationAgreement\par
\ifthenelse{\equal{\the\Dipl@AccessRestriction}{\empty}}
{\relax}
{\bigskip\noindent\the\Dipl@AccessRestriction\par}
\vspace{15mm}
\noindent\Dipl@IfEnglish{Ostrava,}{V Ostravě}~\the\Dipl@SubmissionDate\hfill\hbox to50mm{\dotfill}\par
\vspace{15mm}
}
\newcommand{\sectionbreak}
{
\cleardoublepage
\ifthenelse{\boolean{Dipl@IsAppendix}}{\relax}{\suppressfloats}
}
\let\Dipl@OldAppendix\appendix
\renewcommand{\appendix}
{
\Dipl@OldAppendix
\addcontentsline{toc}{section}{\appendixname}%
}
\newcommand{\Dipl@IfEnglish}[2]{\ifthenelse{\value{Dipl@CurrentThesisLanguage}=\Dipl@EnglishLanguage}{#1}{#2}}
\newcommand{\Dipl@AddTokens}[2]{\expandafter \global#1\expandafter{\the#1#2}}
\newcommand{\Dipl@InsertFullPageImage}[1]
{
\newgeometry{margin=1pt,nohead,nofoot,nomarginpar,centering}
\thispagestyle{empty}
\begin{center}
\includegraphics[width=0.99\textwidth,height=0.99\textheight]{#1}
\end{center}
\cleardoublepage
\restoregeometry
}
\newcommand{\Dipl@SetDefaultLanguage}
{
\ifthenelse{\equal{\the\Dipl@DefaultSourceCodeLanguage}{ansic}}{\lstset{language=[ANSI]C}}{}
\ifthenelse{\equal{\the\Dipl@DefaultSourceCodeLanguage}{bash}}{\lstset{language=bash}}{}
\ifthenelse{\equal{\the\Dipl@DefaultSourceCodeLanguage}{cil}}{\lstset{language=CIL}}{}
\ifthenelse{\equal{\the\Dipl@DefaultSourceCodeLanguage}{cpp}}{\lstset{language=C++}}{}
\ifthenelse{\equal{\the\Dipl@DefaultSourceCodeLanguage}{csharp}}{\lstset{language=[Sharp]C}}{}
\ifthenelse{\equal{\the\Dipl@DefaultSourceCodeLanguage}{delphi}}{\lstset{language=Delphi}}{}
\ifthenelse{\equal{\the\Dipl@DefaultSourceCodeLanguage}{gnuplot}}{\lstset{language=Gnuplot}}{}
\ifthenelse{\equal{\the\Dipl@DefaultSourceCodeLanguage}{html}}{\lstset{language=HTML}}{}
\ifthenelse{\equal{\the\Dipl@DefaultSourceCodeLanguage}{java}}{\lstset{language=Java}}{}
\ifthenelse{\equal{\the\Dipl@DefaultSourceCodeLanguage}{latex}}{\lstset{language=[LaTeX]TeX}}{}
\ifthenelse{\equal{\the\Dipl@DefaultSourceCodeLanguage}{lisp}}{\lstset{language=Lisp}}{}
\ifthenelse{\equal{\the\Dipl@DefaultSourceCodeLanguage}{lua}}{\lstset{language=Lua}}{}
\ifthenelse{\equal{\the\Dipl@DefaultSourceCodeLanguage}{make}}{\lstset{language=make}}{}
\ifthenelse{\equal{\the\Dipl@DefaultSourceCodeLanguage}{mathematica}}{\lstset{language=Mathematica}}{}
\ifthenelse{\equal{\the\Dipl@DefaultSourceCodeLanguage}{matlab}}{\lstset{language=Matlab}}{}
\ifthenelse{\equal{\the\Dipl@DefaultSourceCodeLanguage}{octave}}{\lstset{language=Octave}}{}
\ifthenelse{\equal{\the\Dipl@DefaultSourceCodeLanguage}{pascal}}{\lstset{language=Pascal}}{}
\ifthenelse{\equal{\the\Dipl@DefaultSourceCodeLanguage}{perl}}{\lstset{language=Perl}}{}
\ifthenelse{\equal{\the\Dipl@DefaultSourceCodeLanguage}{php}}{\lstset{language=PHP}}{}
\ifthenelse{\equal{\the\Dipl@DefaultSourceCodeLanguage}{pov}}{\lstset{language=POV}}{}
\ifthenelse{\equal{\the\Dipl@DefaultSourceCodeLanguage}{prolog}}{\lstset{language=Prolog}}{}
\ifthenelse{\equal{\the\Dipl@DefaultSourceCodeLanguage}{python}}{\lstset{language=Python}}{}
\ifthenelse{\equal{\the\Dipl@DefaultSourceCodeLanguage}{ruby}}{\lstset{language=Ruby}}{}
\ifthenelse{\equal{\the\Dipl@DefaultSourceCodeLanguage}{r}}{\lstset{language=R}}{}
\ifthenelse{\equal{\the\Dipl@DefaultSourceCodeLanguage}{sh}}{\lstset{language=sh}}{}
\ifthenelse{\equal{\the\Dipl@DefaultSourceCodeLanguage}{sql}}{\lstset{language=SQL}}{}
\ifthenelse{\equal{\the\Dipl@DefaultSourceCodeLanguage}{tcltk}}{\lstset{language=[tk]tcl}}{}
\ifthenelse{\equal{\the\Dipl@DefaultSourceCodeLanguage}{vb}}{\lstset{language=[Visual]Basic}}{}
\ifthenelse{\equal{\the\Dipl@DefaultSourceCodeLanguage}{vhdl}}{\lstset{language=VHDL}}{}
\ifthenelse{\equal{\the\Dipl@DefaultSourceCodeLanguage}{xml}}{\lstset{language=XML}}{}
\ifthenelse{\equal{\the\Dipl@DefaultSourceCodeLanguage}{xslt}}{\lstset{language=XSLT}}{}
}
\lstset
{
breaklines=true,
tabsize=3,
columns=flexible,
showstringspaces=false,
basicstyle=\ttfamily,
keywordstyle=\color{blue},
identifierstyle=\color[RGB]{43,145,175},
commentstyle=\slshape\color[RGB]{0,128,0},
stringstyle=\color[RGB]{163,21,21},
frame=lines,
captionpos=b,
inputencoding=utf8,
extendedchars=true,
literate={á}{{\'{a}}}1 {Á}{{\'{A}}}1 {ä}{{\"{a}}}1 {Ä}{{\"{A}}}1 {č}{{\v{c}}}1 {Č}{{\v{C}}}1 {ď}{{\v{d}}}1 {Ď}{{\v{D}}}1 {ě}{{\v{e}}}1 {Ě}{{\v{E}}}1 {é}{{\'{e}}}1 {É}{{\'{E}}}1 {í}{{\'{i}}}1 {Í}{{\'{I}}}1 {ĺ}{{\'{l}}}1 {Ĺ}{{\'{L}}}1 {ľ}{{\v{l}}}1 {Ľ}{{\v{L}}}1 {ň}{{\v{n}}}1 {Ň}{{\v{N}}}1 {ó}{{\'{o}}}1 {Ó}{{\'{O}}}1 {ô}{{\^{o}}}1 {Ô}{{\^{O}}}1 {ř}{{\v{r}}}1 {Ř}{{\v{R}}}1 {ŕ}{{\'{r}}}1 {Ŕ}{{\'{R}}}1 {š}{{\v{s}}}1 {Š}{{\v{S}}}1 {ť}{{\v{t}}}1 {Ť}{{\v{T}}}1 {ú}{{\'{u}}}1 {Ú}{{\'{U}}}1 {ů}{{\r{u}}}1 {Ů}{{\r{U}}}1 {ý}{{\'{y}}}1 {Ý}{{\'{Y}}}1 {ž}{{\v{z}}}1 {Ž}{{\v{Z}}}1
}
\onehalfspacing
\setcounter{tocdepth}{2}
\setcounter{secnumdepth}{5}
\widowpenalty=9000
\clubpenalty=9000
\regtotcounter{figure}
\regtotcounter{table}
\addto{\captionsczech}{\renewcommand{\refname}{Literatura}}
\addto{\captionsslovak}{\renewcommand{\refname}{Literatura}}
\addto{\captionsczech}{\renewcommand{\appendixname}{Přílohy}}
\addto{\captionsslovak}{\renewcommand{\appendixname}{Přílohy}}
\AtBeginDocument%
{
\ifthenelse{\value{Dipl@CurrentThesisLanguage}=\Dipl@CzechLanguage}
{
\selectlanguage{czech}
\def\lstlistlistingname{Seznam výpisů zdrojového kódu}
\def\lstlistingname{Výpis}
}{}
\ifthenelse{\value{Dipl@CurrentThesisLanguage}=\Dipl@EnglishLanguage}
{
\selectlanguage{english}
}{}
\ifthenelse{\value{Dipl@CurrentThesisLanguage}=\Dipl@SlovakLanguage}
{
\selectlanguage{slovak}
\def\lstlistlistingname{Seznam výpisů zdrojového kódu}
\def\lstlistingname{Výpis}
}{}
\renewcommand{\lstlistoflistings}{\begingroup\tocfile{\lstlistlistingname}{lol}\endgroup}
\Dipl@SetDefaultLanguage
}
\endinput
%%
%% End of file `diploma.cls'.
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......@@ -15,7 +15,9 @@
%\usepackage{titlesec}
%\newcommand{\sectionbreak}{\clearpage}
%\setlist{nosep}
\newcommand{\image}[3]{\begin{figure}[h!] \centering \includegraphics[width=#3\linewidth]{#1} \caption{#2} \end{figure}}
\newcommand{\image}[4]{\begin{figure}[h!] \centering \includegraphics[width=#1\linewidth]{figures/#2} \label{#3} \caption{#4} \end{figure}}
\newcommand{\bThreed}{B$^3$D}
\author{Moravec Vojtěch}
\title{Semestrální projekt}
......@@ -27,7 +29,7 @@
\section{ZISRAW (CZI) formát}
Vše co bude v této sekci uvedeno vychýzí z oficiální specifikace formátu CZI. \ref{czi_spec}.
Vše co bude v této sekci uvedeno vychýzí z oficiální specifikace formátu CZI. \cite{czi_spec}.
Formát CZI je určen pro uložení obrazků, samotné schéma uložení dat ale vychází z formátu ZISRAW, který je určen pro různé typy souborů.
Hlavním cílem formátu ZISRAW je umožnit streamování dat a metadat v binární podobě (metadata jsou buď binární nebo v XML). \textit{CZI formát je aktuálně jedinou implementací ZISRAW.}
......@@ -108,6 +110,27 @@ LZW je bezztrátová komprese, aktuálně se nepoužívá ve \say{widefield} mik
může být použita pouze pro 2D obrazy.
Jpeg-XR podporuje jak ztrátovou tak i bezztrátovou kompresi. Vychází z JPEG a nabízí menší velikost pro stejnou kvalitu obrazu, ale stejně jako JPEG, je omezen na 2D obrazy.
\bibliography{citations}
\section{Kompresní knihovna \bThreed}
\bThreed je Open Source knihovna, řešící problém komprese obrazů z mikroskopu. Je napsána v jazyce C++ a využívá CUDA architektury.
Slibovaná rychlost komprese je více než 1 GB/s \cite{Balazs164624}. Tato knihovna nabízí jak ztrátovou tak i bezztrátovou kompres, kde ztrátová zohledňuje fakt,
že se jedná o obrazy z mikroskopu a uživatel si může zvolit maximální chybu, kterou bude tolerovat. Definuji takzvaný WNL (\emph{within noise level}) mód
ztrátové komprese, kde kvantizační krok je roven šumu v obraze. V tomto módu je chyba vzniklá ztrátovou kompresí mnohem menší, než šum nacházející se v obraze.
Kompresní poměry bezztrátové a WNL komprese můžeme vídět na Obrázku \ref{img:compressionComp}.
\image{0.65}{compressionComparsionBars.pdf}{img:compressionComp}{Porovnání kompresních poměrů různých vzorků}
Vliv ztrátové komprese na obraz byl testován na datasetu ebrya octomilky obecné, metodou segmentačního překrývání. Testovalo se vzhledem k originálnímu
obrazu, a hodnota 1 znamená, že se obrazy dokonale překrývají. Na Obrázku \ref{img:segoverlap}, můžeme, že překryv klesá až při velkých komrpesních poměrech.
Překryv pro WNL je téměř dokonalý 0,996.
\image{0.65}{noise_overlap.pdf}{img:segoverlap}{Vliv ztrátové komprese na kvalitu obrazu}
Použitý bezztrátový algoritmus se skládá ze dvou částí. V první části se provede predikce hodnoty pixelu vzhledem k hodnotám jeho sousedů a v
druhé části jsou chyby predikce zakódovány pomocí RLE a Huffmana. Bezztrátová komprese dosáhla kompresního poměru 2,7 a pokud je použita WNL komprese
dostáváme se až na kompresní poměr 5, a chyba lokalizace jediné molekuly v obrazu vstoupla pouze o 4\%. (Bylo testováno na datasetu získaném pomocí
Single-Molecule Localization Microscopy, rozlišení 2-25 nm).
% \bibliography{citations}
% \bibliographystyle{ieeetr}
\end{document}
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