EosPedia - User contributions [en]

Main Page

2014-07-19T20:13:44Z

Tacyas: /* Installation */

== '''Welcome to Eospedia''' ==

We started the new manual site of Eos for only few people at 05 Nov. 2010. And we started the operation of Eospedia closed β version of the laboratory.
In August 2012, we opened as the head family of the home page of the electron microscope image processing system Eos here.

We would like to summarize extensive knowledges as description and algorithm of the command about [[Eos]]. Also We will summarize here in the same way for the [[PIONE]] (developing since 2012) and [[VEM/WITs]] (developing since 2013).
In addition, we would like to operate as a site that is possible to learn including an electron microscope image processing, the basics of the various image processing here.

We are developing [[Eos]] on [https://sourceforge.jp/projects/eos/ Eos@sourceforge], [[PIONE]] on [https://github.com/pione PIONE@github]. We would like to expand the information that summarizes them here. In the future, we are considering also be independent of the university. Try and take a look at this related sites If you are interested in any of the development and use of these. The philosophy of wiki is not "how do us prevent mistakes" but "how do us improve it". Therefore we are glad, if you write freely your know-how and knowledge without afraid to make mistakes (Of course, incoherence is out of the question.).

Old Eos pages are [http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos_old here].

Now this Eospedia is under construction. Eospedia.ja has also opend [http://www.yasunaga-lab.bio.kyutech.ac.jp/EosJ/ here]. Japanese version of Eospedia has more information than this Eospedia in English.

In addition, there is a forum and mailing list for Eos.
If you want to know how to use the Eos: eos-users@
If you are interested in the development of in Eos: eos-developers@
If you are able to help write the document of Eos: eos-document@
If you can cooperate, we are glad.

We opened "Eos User Group"[https://www.facebook.com/EosUserGroup] on the facebook futher. We would like to spread using this.

Please contact Yasunaga[mailto:yasunaga@bio.kyutech.ac.jp] for more information.

=='''Beginner's Guid''' ==
=== [[Eos|What is Eos ?]]===
We here describe what is Eos.

=== [[Command|How to use Eos Commands]] ===
We here describe commands of Eos by CUI.

===[[Makefile|How to use Eos by Makefile]] ===
We here describe how to integrate commands using [[make]]

=== [[List of command|List of command]] ===
We here show all of commands Eos supplies.

===[[Functional Order of Commands|Functional order of Eos command list]] ===
We here show functional order of Eos commands.

== '''Installation'''==
=== [[Required Environment]] ===

=== [[Download|Download]] ===
We here describe how to download Eos. We are currently developing a Eos at SourceForge.

=== [[Installation|How to install Eos]] ===
We here describe how to install Eos.

=== [[Installation of PIONE]]===
We here describe how to install a new process flow control system, PIONE. PIONE has been developed on "github".

== '''Eos reference''' ==

=== [[Integration Commands | Integration commands supplied by Eos]] ===
We here describe integration commands supplied by Eos, one of the '''support''' Eos supplies.

=== Integration comannd : [[PIONE]]===
We here describe PIONE that is provided as an integrated environment that corresponds to the cloud environment and distributed environment by Eos.

== '''Eos tutorial'''　==
=== How to set Eos environment　===
At first, we explain how to install Eos simplily. The details are described in [[Eos installation|Eos Installation]].

* [[Eos installation|Eos Installation]]

=== How to use commands of Eos　===
We explain how to use Eos commands. In details, please refer to the [[Commands|Eos Commands]]. Eos perform image processing and analysis with CUI, normally, although some interactive tools have GUI. In the near-future, each command has GUI on a browser by javascript.

* [[Commands |Eos Commands]]

=== [[Image format on Eos]]　===
Image formats in Eos and how to transform image format from other general image formats are explained here.
* [[Image Format|Image Format]]
* [[Image format transform|Image format transform]]

=== Simple image processing using Eos　===
Simple image processing and analysis can be performed here.
* [[Simple Image Processing|Simple Image Processing]]

=== CTF Correction ===
Electron micrographs were greatly modified in contrast due to how to take them. Here we show the correction methods of CTF.
* [[CTF Correction|CTF Correction]]

=== Single particle analysis　===
This is a tutorial section of single particle analysis. Here we show the single particle analysis with reference. Actually, we must choose the 3D reconstruction methods considering the situations.

==== Concept of [[Single particle analysis]] ====

==== [[Particle picking|Particle picking]] ====
At first, we pick particles from electron micrographs. Here, the manual picking method is shown, although automatic methods are also proposed.

==== [[Classification of 2D images|Classification of 2D images]] ====
Next, we classify 2D-images following their shape and so average them per cluster to improve the ratio of signal to noise.

==== [[Estimation of projection angle using reference|Estimation of projection angle using reference]] ====
Third, we determine the projection angle of each particle in the case of the presence of reference images, although the determination methods of projection angles are also proposed without reference.

==== [[Estimation of projection angle without using reference]] ====
As another way, we show the method of determining the projection angle of each particle in the case of not using reference images.

==== [[3D Reconstruction: Backprojection|3D Reconstruction: Backprojecdtion]] ====
Forth, we reconstruct 3D objects from 2D images, especially backprojection.

==== [[Visualization tools|Visualization tools]] ====
FInally, we interpret 3D objects reconstructed from 2D images using visualization tools.

=== [[Electron tomography]] ===
Electron tomography is one of the powerful techniques to solive 3D objects such as whole cell, cytoskeleton in cell, and protein structure with polymorphism. It reconstruct 3D objects from tilt-series images of the same photo field.

==== The overview of [[Electron tomography]] ====
Electron tomography can supply us 3D objects from tilt-series of 2D images of the same field. Here we explain the overview.

==== [[Image Correction]] ====
Fist, we must correct [[CTF]] (contrast transfer function) becuase the 2D images are taken with larger defocusing values.

==== Rough Alignment ====
Nest, we align 2D images roughly using correlation between each image.

==== Alignment ====
Third, we estimate the tilt-axis position and angles.

==== 3D reconstruction ====
Forth, we reconstruct 3D image from a set of tilt-series images.

==== Problems of 3D reconstruction ====
We must pay attention of misleading blurring due to missing area, which is generated from the limitation of projection angles.

==== Interpretation of 3D reconstruction ====
Last, we must perform segmentation of 3D objects to interpret them. Thus we must use computer-aided visualization tools.

==== Averaging of Subtomograms ====
Tomogram images of cryo-microscopy include a lot of noise, thus it is required the averaging of the particles have the same structure.

=== Notes ===
　This tutorial pages were created with refer to the documents used single particle workshop on 2012/09/10-11.

== '''Developers' Guide of Eos''' ==
=== [[Eos System Architecture]] ===

=== [[For Eos System Developers]] ===

=== [[Eos System Commands]] ===

=== [[Eos development under Sourceforge|Eos development under Sourceforge]]===
We here show a flow of development of Eos under Sourceforge: 1. create clone from Sourceforge, develop a new tool or object and finally register them into Sourceforge.

=== [[Development of small tools]] ===
==== [[How to create a small tool]] ====
How to create [[Small Tools]]([[Command Group]]) is described.

==== [[Introduction of small tools]] ====
We introduce some simple examples of [[Small Tools]]([[Command Group]]).

=== [[How to create API]]===
How to carete [[Object-oriented library]] ([[API]]) is described。

=== [[API list]]===
We show a list of [[Object-oriented library]] ([[API]]).

=== [[Functional order of API]]===
We here show functionl oder of API ([[Object-oriented libraries]]) supplied by Eos.

=== [[How to create integration commands]]===
We describe how to develop integration commands.

==== [[Integration by Makefile]] ====
Here how to integrate commands using [[Makefile]] are shown。Furthreore, [[Visualmake]] supply simple and easy GUI (Graphical User Interface).

==== [[Integration by PIONE]] ====
We here show how to integrate commands using [[PIONE]], which is a rule-based process definition and work under distributed computing system.

==== [[Integration by bash]] ====
bash etc.

==== [[Integration by integration commands]] ====
We here describe how to integrate commands by [[Display2]], [[smolet]], [[Eos]] etc. programed with Tcl/Tk, [[ctfDisplay]] etc. programed with Ruby/Tk，[[molvie]] etc. programmed by C-language.

== [[Image Processing]] and [[Image Analysis]] ==
=== [[General Image Processing]] ===
Summarizing about the general image processing here.

==== [[Simple Image Processing]]====
Tutorial on simple image processing using the Eos has been published.

==== [[Input of image]] and [[Lens]] ====
Before performing image processing using a computer, you should keep in mind about the input device that digitize images.

==== [[CTF]], [[PSF]] and [[MTF]] ====
True image: f(x,y) is degraded due to the method of [[Input of image]] and performance of the [[Lens]].

==== [[Sampling]] ====
To convert analog images to digital images, it is important that discretize the space by decomposing. This step is called Sampling.

==== [[Quantization]] ====
First, in digital image process the operation that expresses density values within certain number of bits (Optical density) is required. This operation is called quantization(AD convert).

==== [[Noise reduction]] ====
In order to deal the image including a lot of noise, knowing well the nature of the noise is important.

===== [[Smoothing]] =====
This is an image processing method with the primary purpose of eliminating the noise in the image. By understanding well the nature of the noise, the noise can be reduced properly.

==== [[Edge extraction]] ====
This is an important step in order to understand the shape of the object, but it is also a very difficult step.

==== [[Binarization]] ====
This is the process of isolating the background and the signal, and extracting the representative point and the skeletal.
And it is the start process of the analysis and image processing.

==== Image processing using the [[Fourier space]] ====

==== Image processing using the [[Kernel]] of the Real space ====

==== Image processing using the [[Mathematical morphology]] ====

=== [[EM Image Processing]] ===
Summarizing about the EM image processing here.

==== [[Montage]] and [[Panorama]] image ====
This is how to combine multiple images obtained by photographing the different regions (However, the set of image overlapping portion thereof ), to create an image of a large area.

==== [[CTF Collection]] ====
EM image has received the image modulation in principle. It is the image processing to correct the image modulation.

==== [[Alignment of 3D objects]] ====
It is a method for removing noise by averaging the three-dimensional image with each other.

==== [[Alignment of a series of images]] ====
It is a method for reconstructing a three-dimensional image by combining the position of the image between the serial sections.

=== [[3D Reconstruction]] ===
3D Reconstruction is a technique of reconstructing a three-dimensional image from a two-dimensional image.

==== [[Central slice theorem]]====
　Why can the internal structure be proved by the projected image? It is Central slice theorem that proves it.

==== [[Fourier method]]====
==== [[Backprojection]]====
==== [[SIRT]]====

== [[Electron Microscopy]] ==
We here describe electron microscopy.

=== [[Electron source]]===
We here describe an electron source of electron microscope, a gun.

=== [[Lens]]===
We here explain the mechanism of lens and optics, especially TEM (Transmission Electron Microscopy).

=== [[Contrast of TEM]]===
We here explain what is [[contrast]] of TEM.

=== [[Contrast of SEM]]===
We here explain what is [[contrast]] of SEM.

=== [[Contrast of STEM]] ===
We here explain what is [[contrast]] of STEM.

=== [[Electron cryo-microscopy]] ===
We here explain what is electron cryo-microscopy

=== [[FAQ of electron microscopy]] ===
We here answer the FAQ.

=== [[TIPS of electron microscopy]] ===
We here collect EM TIPS.

== [[Loadmap|The future of Eos]] ==
　The future of Eos ([[Loadmap]]) is shown here.

== FAQ and TIPS ==
=== [[EosFAQ | FAQ]] ===
We here plan to collenct FAQ(Frequenty asked question).

=== [[Eos TIPS| Eos TIPS]] ===
We here plan to collect TIPS in using Eos and processing/analyzing/intepreting images.

=== [[TIPS around software related to Eos]] ===
We here plan to collect useful TIPs around Eos. If you have some comments, please send me.

=== [[TIPS around software related to LINUX]] ===

== Why we have been developing Eos/PIONE ? ==
Comparing the date when Eos was born, 1996, many types of software for electron micrographs have been developed and used for more users and biologist. Nonetheless, we also ask ourselves the reason why we have been developing and maintenance '''Eos'''. We will note [[Why Eos by Yasunaga]].

== Eos User Group ==
We plan to create '''Eos User Group''' and discuss the current and the future of Eos on the sourceforge or facebook. Please access them.

== '''About a symbol mark of Eos''' ==
Now we plan to make a symbol mark of Eos. If you have some ideas about Eos symbol, please send us yours.

If you want to know how to use mediawiki, please refer to [http://meta.wikimedia.org/wiki/Main_Page User's Guid]

== Tools and Sites related to Eos ==
=== Programming languages ===
*[[C]]
*[[C++]]
*[[Ruby]]
*[[Tcl]]
*[[Tk]]

=== Related workflow(PIONE) ===
==== Petri Net ====
*[[PNML]]
*[[WoPeD]]
==== Action description ====
*[[markdown]]

==== Log file ====
*[[ProM]]:
*[[XES]]:

=== Documentation tools ===
*[[Pandoc]]
*[[html]]
*[[mediawiki]]

== '''External link''' ==
* [http://www.yasunaga-lab.bio.kyutech.ac.jp/EosJ/ Eospedia.jp]
* [http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos/ Eospedia.en]
* [http://sourceforge.jp/projects/eos/ Eos SourceForge]
* [http://www.yasunaga-lab.bio.kyutech.ac.jp/ Yasunaga Lab.]
* [http://www.bio.kyutech.ac.jp/ Kyutech, Dept. of Bioscience and Bioinformatics]
* [http://www.iizuka.kyutech.ac.jp/ Kyutech. School of Computer Science and Systems Engineering]
* [http://www.kyutech.ac.jp/ Kyushu Institute of Technology(Kyutech)]

* [http://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy Software Tools For Molecular Microscopy]
* [http://emdatabank.org/emsoftware.html EM Software on EMDataBank]

== '''How to use mediawiki''' ==

* [http://www.mediawiki.org/wiki/Manual:Configuration_settings/ Configuration Settings]
* [http://www.mediawiki.org/wiki/Manual:FAQ/ FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce/ mediawiki-announce]

Download

2014-04-30T17:00:51Z

Tacyas:

Download

2014-04-30T17:00:26Z

Tacyas:

1. tarball [http://www.yasunaga-lab.bio.kyutech.ac.jp/ja/reserach/eos/eos-download-sites/]

2. git from SourceFoge [http://sourceforge.jp/projects/eos/]
$ git clone git://git.sourceforge.jp/gitroot/eos/base.git
or
$ git clone git://git.code.sf.net/p/eosforemimageprocessing/code eosforemimageprocessing-code

3. (PIONE) github or gem

3.1 gem (ruby)
$ gem install pione

3.2 git from github
$ git clone https://github.com/pione/pione.git

<script type="text/javascript">
var sfjp_widget_width = null;
var sfjp_widget_customcss = null;
</script>
<script src="http://sourceforge.jp/projects/eos/files/compact.js" type="text/javascript" charset="utf-8"></script>

Download

2014-02-27T20:57:45Z

Tacyas:

Main Page

2013-05-29T14:01:11Z

Tacyas: /* CTF Correction */

== '''Welcome to Eospedia''' ==

We started the new manual site of Eos for only few people at 05 Nov. 2010.
We would like to summarize knowledges about [[Eos]].

Old Eos pages are [http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos_old here].

Now this Eospedia is under construction. Eospedia.ja has also opend [http://www.yasunaga-lab.bio.kyutech.ac.jp/EosJ/ here]. Japanese version of Eospedia has more information than this Eospedia in English.

=='''Beginner's Guid''' ==
=== [[Eos|What is Eos ?]]===
We here describe what is Eos.

=== [[Command|How to use Eos Commands]]
We here describe commands of Eos by CUI.

===[[Makefile|How to use Eos by Makefile]]
We here describe how to integrate commands using [[make]]

=== [[List of command|List of command]] ===
We here show all of commands Eos supplies.

===[[Functional Order of Commands]Functional order of Eos command list]
We here show functional order of Eos commands.

== '''Installation'''==
=== [[Download|Download]] ===
1. tarball [http://www.yasunaga-lab.bio.kyutech.ac.jp/ja/reserach/eos/eos-download-sites/]
2. git from SourceFoge [http://sourceforge.jp/projects/eos/]
3. (PIONE) github or gem
3.1 gem (ruby)
$ gem install pione

3.2 git from github
$ git clone https://github.com/pione/pione.git

=== [[Installation|How to install Eos]] ===
We here describe how to install Eos.

=== [[Installation of PIONE]]===
We here describe how to install a new process flow control system, PIONE. PIONE has been developed on "github".

== '''Eos reference''' ==

=== [Integration Commands|Integration commands supplied by Eos]] ===
We here describe integration commands supplied by Eos, one of the '''support''' Eos supplies.

=== Integration comannd : [[PIONE]]===
We here describe PIONE.

== '''Eos tutorial'''　==
=== How to set Eos environment　===
At first, we explain how to install Eos simplily. The details are described in [[Eos installation|Eos Installation]].

* [[Eos installation|Eos Installation]]

=== How to use commands of Eos　===
Eosのコマンドの簡単な使い方を説明します。詳細は、[[コマンド|コマンドの詳細]]をご覧下さい。Eosでは、基本はCUIを使ったコマンドの実行により画像処理を進めます。その結果は、ファイルとして保存され、その内容を確認することが出来ます。

* [[Commands |Eos Commands]]

=== Image format in Eos　===
Eosで取り扱うことのできる画像フォーマットと一般的な画像フォーマットからの変換方法を示します。
* [[画像フォーマット変換|画像フォーマットの変換]]

=== Simple image processing using Eos　===
Eosを使った簡単な画像処理を実行してもらいます。
* [[Simple Image Processing|Simple Image Processing]]

=== CTF Correction ===
Electron micrographs were greatly modified in contrast due to how to take them. Here we show the correction methods of CTF.
* [[CTF Correction|CTF Correction]]

=== Single particle analysis　===
　ここでは、単粒子解析の基礎を行います。実際の単粒子解析は、粒子の形やその対称性などを使って探索方法や3次元再構成法を切り替えることができます。

==== Concept of [[Single particle analysi]] ====
　単粒子解析の概要を示します。

==== [[Particle picking|Particle picking]] ====
　まず、単粒子を抽出します。ここでは、手動で切り出す方法を示します。自動で切り出す方法も各種提案されています。

==== [[Classification of 2D images|Classification of 2D images]] ====
　２次元画像を分類して、ＳＮ比を上げます。

==== [[Estimation of projection angle using reference|Estimation of projection angle using reference]] ====
　参照像があるときの投影角の決定方法を説明します。参照像としては、単なる球や楕円体などとすることもあり得ます。参照像がない場合の構造解析法も別途存在しています。

==== [[3D Reconstruction: Backprojection|3D Reconstruction: Backprojecdtion]] ====
　3次元再構成自身を解説します。

==== [[Visualization tools|Visualization tools]] ====
　できあがった三次元像を可視化するためのツールを紹介します。

=== [[Electron tomography]] ===
　電子線トモグラフィーとは、同一視野の連続傾斜像から、その視野の３次元画像を再構成する方法です。細胞内の構造や構造多型性をもつタンパク質の構造解析に有効な方法です。

==== [[Electron tomography]]の概要 ====
　電子線トモグラフィー法は、同一視野の傾斜シリーズ画像のセットから３次元像を再構成する方法です。ここではその概要を述べます。

==== [[Image Correction]] ====
　傾斜画像では、視野全体がアンダーフォーカスとなるように、通常の電子顕微鏡撮影よりも大きなデフォカース値をとる場合が多いです。その場合、LaB6などの電子銃では第一トーンリングより外側の情報がほとんど無いために、CTF補正等は必要ありませんが、電界放出銃を利用した場合には、場合によっては間違った情報を与える場合があるので注意が必要です。

==== Rough Alignment ====
　傾斜画像の中心付近の画像の相関から、それぞれの傾斜画像の大まかな位置を合わせます。

==== Alignment ====
　傾斜画像の軸の位置、角度を出来る限り一致させます。

==== 3D reconstruction ====
　２次元画像のセットから３次元画像を再構成します。

==== Problems of 3D reconstruction ====
　全方位からの投影像を得られないために、ミッシングエリアとよばれる情報がない領域があります。そのため、方向依存でのボケを生じます。

==== Interpretation of 3D reconstruction ====
　また、多様な構造を含むため、３次元画像から興味あるセグメントを切り出すなどの作業が必要です。そのための支援ソフトウェアが必要です。

=== Notes ===
　This tutorial pages were created with refer to the documents used single particle workshop on 2012/09/10-11.

== '''Developers' Guide of Eos''' ==
=== [[Eos System Architecture]] ===

=== [[For Eos System Developers]] ===

=== [[Eos System Commands]] ===

=== [[Eos development under Sourceforge|Eos development under Sourceforge]]===
We here show a flow of development of Eos under Sourceforge: 1. create clone from Sourceforge, develop a new tool or object and finally register them into Sourceforge.

=== [[Development of small tools]] ===
==== [[How to create a small tool]] ====
How to create [[Small Tools]]([[Command Group]]) is described.

==== [[Introduction of small tools]] ====
We introduce some simple examples of [[Small Tools]]([[Command Group]]).

=== [[How to create API]]===
How to carete [[Object-oriented library]] ([[API]]) is described。

=== [[API list]]===
We show a list of [[Object-oriented library]] ([[API]]).

=== [[Functional oder of API]]===
We here show functionl oder of API ([[Object-oriented libraries]]) supplied by Eos.

=== [[How to create integration commands]]===
We describe how to develop integration commands.

==== [[Integration by Makefile]] ====
Here how to integrate commands using [[Makefile]] are shown。Furthreore, [[Visualmake]] supply simple and easy GUI (Graphical User Interface).

==== [[Integration by PIONE]] ====
We here show how to integrate commands using [[PIONE]], which is a rule-based process definition and work under distributed computing system.

==== [[Integration by bash]] ====
bash etc.

==== [[Integration by integration commands]] ====
We here describe how to integrate commands by [[Display2]], [[smolet]], [[Eos]] etc. programed with Tcl/Tk, [[ctfDisplay]] etc. programed with Ruby/Tk，[[molvie]] etc. programmed by C-language.

== [[Image Processing]] and [[Image Analysis]] ==
=== [[General Image Processing]] ===

=== [[EM Image Processing]] ===

==== [[Montage]] ====

==== [[CTF Collection]] ====

==== [[Alignment of 3D objects]] ====

==== [[Alignment of a series of images]] ====

== [[Electron Microscopy]] ==
We here describe electron microscopy.

=== [[Electron source]]===
We here describe an electron source of electron microscope, a gun.

=== [[Lens]]===
We here explain the mechanism of lens and optics, especially TEM (Transmission Electron Microscopy).

=== [[Contrast of TEM]]===
We here explain what is [[contrast]] of TEM.

=== [[Contrast of SEM]]===
We here explain what is [[contrast]] of SEM.

=== [[Contrast of STEM]] ===
We here explain what is [[contrast]] of STEM.

=== [[Electron cryo-microscopy]] ===
We here explain what is electron cryo-microscopy

=== [[FAQ of electron microscopy]] ===
We here answer the FAQ.

=== [[TIPS of electron microscopy]] ===
We here collect EM TIPS.

== [[ロードマップ|Eosの今後の発展（ロードマップ）について]] ==
　Eosの今後の開発方針([[ロードマップ]])について述べます。

== FAQ and TIPS ==
=== [[EosFAQ | FAQ]] ===
We here plan to collenct FAQ(Frequenty asked question).

=== [[Eos TIPS| Eos TIPS]] ===
We here plan to collect TIPS in using Eos and processing/analyzing/intepreting images.

=== [[Eos around TIPS| Eos around TIPS]] ===
We here plan to collect useful TIPs around Eos. If you have some comments, please send me.

== Why we have been developing Eos/PIONE ? ==
Comparing the date when Eos was born, 1996, many types of software for electron micrographs have been developed and used for more users and biologist. Nonetheless, we also ask ourselves the reason why we have been developing and maintenance '''Eos'''. We will note [[Why Eos by Yasunaga]].

== Eos User Group ==
We plan to create '''Eos User Group''' and discuss the current and the future of Eos on the sourceforge or facebook. Please access them.

== '''About a symbol mark of Eos''' ==
Now we plan to make a symbol mark of Eos. If you have some ideas about Eos symbol, please send us yours.

If you want to know how to use mediawiki, please refer to [http://meta.wikimedia.org/wiki/Main_Page User's Guid]

== '''External link''' ==
* [http://www.yasunaga-lab.bio.kyutech.ac.jp/EosJ/ Eospedia.jp]
* [http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos/ Eospedia.en]
* [http://sourceforge.jp/projects/eos/ Eos SourceForge]
* [http://www.yasunaga-lab.bio.kyutech.ac.jp/ Yasunaga Lab.]
* [http://www.bio.kyutech.ac.jp/ Kyutech, Dept. of Bioscience and Bioinformatics]
* [http://www.iizuka.kyutech.ac.jp/ Kyutech. School of Computer Science and Systems Engineering]
* [http://www.kyutech.ac.jp/ Kyushu Institute of Technology(Kyutech)]

* [http://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy Software Tools For Molecular Microscopy]
* [http://emdatabank.org/emsoftware.html EM Software on EMDataBank]

== '''How to use mediawiki''' ==

* [http://www.mediawiki.org/wiki/Manual:Configuration_settings/ Configuration Settings]
* [http://www.mediawiki.org/wiki/Manual:FAQ/ FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce/ mediawiki-announce]

Main Page

2013-05-29T13:57:48Z

Tacyas: /* How to set Eos environment　 */

== '''Welcome to Eospedia''' ==

We started the new manual site of Eos for only few people at 05 Nov. 2010.
We would like to summarize knowledges about [[Eos]].

Old Eos pages are [http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos_old here].

Now this Eospedia is under construction. Eospedia.ja has also opend [http://www.yasunaga-lab.bio.kyutech.ac.jp/EosJ/ here]. Japanese version of Eospedia has more information than this Eospedia in English.

=='''Beginner's Guid''' ==
=== [[Eos|What is Eos ?]]===
We here describe what is Eos.

=== [[Command|How to use Eos Commands]]
We here describe commands of Eos by CUI.

===[[Makefile|How to use Eos by Makefile]]
We here describe how to integrate commands using [[make]]

=== [[List of command|List of command]] ===
We here show all of commands Eos supplies.

===[[Functional Order of Commands]Functional order of Eos command list]
We here show functional order of Eos commands.

== '''Installation'''==
=== [[Download|Download]] ===
1. tarball [http://www.yasunaga-lab.bio.kyutech.ac.jp/ja/reserach/eos/eos-download-sites/]
2. git from SourceFoge [http://sourceforge.jp/projects/eos/]
3. (PIONE) github or gem
3.1 gem (ruby)
$ gem install pione

3.2 git from github
$ git clone https://github.com/pione/pione.git

=== [[Installation|How to install Eos]] ===
We here describe how to install Eos.

=== [[Installation of PIONE]]===
We here describe how to install a new process flow control system, PIONE. PIONE has been developed on "github".

== '''Eos reference''' ==

=== [Integration Commands|Integration commands supplied by Eos]] ===
We here describe integration commands supplied by Eos, one of the '''support''' Eos supplies.

=== Integration comannd : [[PIONE]]===
We here describe PIONE.

== '''Eos tutorial'''　==
=== How to set Eos environment　===
At first, we explain how to install Eos simplily. The details are described in [[Eos installation|Eos Installation]].

* [[Eos installation|Eos Installation]]

=== How to use commands of Eos　===
Eosのコマンドの簡単な使い方を説明します。詳細は、[[コマンド|コマンドの詳細]]をご覧下さい。Eosでは、基本はCUIを使ったコマンドの実行により画像処理を進めます。その結果は、ファイルとして保存され、その内容を確認することが出来ます。

* [[Commands |Eos Commands]]

=== Image format in Eos　===
Eosで取り扱うことのできる画像フォーマットと一般的な画像フォーマットからの変換方法を示します。
* [[画像フォーマット変換|画像フォーマットの変換]]

=== Simple image processing using Eos　===
Eosを使った簡単な画像処理を実行してもらいます。
* [[Simple Image Processing|Simple Image Processing]]

=== CTF Correction ===
電子顕微鏡画像では、その撮影方法に由来して、コントラストが大きく変調を受けています。ここでは、その画像のコントラストの変調を補正する方法を示します。
* [[CTF Correction|CTF Correction]]

=== Single particle analysis　===
　ここでは、単粒子解析の基礎を行います。実際の単粒子解析は、粒子の形やその対称性などを使って探索方法や3次元再構成法を切り替えることができます。

==== Concept of [[Single particle analysi]] ====
　単粒子解析の概要を示します。

==== [[Particle picking|Particle picking]] ====
　まず、単粒子を抽出します。ここでは、手動で切り出す方法を示します。自動で切り出す方法も各種提案されています。

==== [[Classification of 2D images|Classification of 2D images]] ====
　２次元画像を分類して、ＳＮ比を上げます。

==== [[Estimation of projection angle using reference|Estimation of projection angle using reference]] ====
　参照像があるときの投影角の決定方法を説明します。参照像としては、単なる球や楕円体などとすることもあり得ます。参照像がない場合の構造解析法も別途存在しています。

==== [[3D Reconstruction: Backprojection|3D Reconstruction: Backprojecdtion]] ====
　3次元再構成自身を解説します。

==== [[Visualization tools|Visualization tools]] ====
　できあがった三次元像を可視化するためのツールを紹介します。

=== [[Electron tomography]] ===
　電子線トモグラフィーとは、同一視野の連続傾斜像から、その視野の３次元画像を再構成する方法です。細胞内の構造や構造多型性をもつタンパク質の構造解析に有効な方法です。

==== [[Electron tomography]]の概要 ====
　電子線トモグラフィー法は、同一視野の傾斜シリーズ画像のセットから３次元像を再構成する方法です。ここではその概要を述べます。

==== [[Image Correction]] ====
　傾斜画像では、視野全体がアンダーフォーカスとなるように、通常の電子顕微鏡撮影よりも大きなデフォカース値をとる場合が多いです。その場合、LaB6などの電子銃では第一トーンリングより外側の情報がほとんど無いために、CTF補正等は必要ありませんが、電界放出銃を利用した場合には、場合によっては間違った情報を与える場合があるので注意が必要です。

==== Rough Alignment ====
　傾斜画像の中心付近の画像の相関から、それぞれの傾斜画像の大まかな位置を合わせます。

==== Alignment ====
　傾斜画像の軸の位置、角度を出来る限り一致させます。

==== 3D reconstruction ====
　２次元画像のセットから３次元画像を再構成します。

==== Problems of 3D reconstruction ====
　全方位からの投影像を得られないために、ミッシングエリアとよばれる情報がない領域があります。そのため、方向依存でのボケを生じます。

==== Interpretation of 3D reconstruction ====
　また、多様な構造を含むため、３次元画像から興味あるセグメントを切り出すなどの作業が必要です。そのための支援ソフトウェアが必要です。

=== Notes ===
　This tutorial pages were created with refer to the documents used single particle workshop on 2012/09/10-11.

== '''Developers' Guide of Eos''' ==
=== [[Eos System Architecture]] ===

=== [[For Eos System Developers]] ===

=== [[Eos System Commands]] ===

=== [[Eos development under Sourceforge|Eos development under Sourceforge]]===
We here show a flow of development of Eos under Sourceforge: 1. create clone from Sourceforge, develop a new tool or object and finally register them into Sourceforge.

=== [[Development of small tools]] ===
==== [[How to create a small tool]] ====
How to create [[Small Tools]]([[Command Group]]) is described.

==== [[Introduction of small tools]] ====
We introduce some simple examples of [[Small Tools]]([[Command Group]]).

=== [[How to create API]]===
How to carete [[Object-oriented library]] ([[API]]) is described。

=== [[API list]]===
We show a list of [[Object-oriented library]] ([[API]]).

=== [[Functional oder of API]]===
We here show functionl oder of API ([[Object-oriented libraries]]) supplied by Eos.

=== [[How to create integration commands]]===
We describe how to develop integration commands.

==== [[Integration by Makefile]] ====
Here how to integrate commands using [[Makefile]] are shown。Furthreore, [[Visualmake]] supply simple and easy GUI (Graphical User Interface).

==== [[Integration by PIONE]] ====
We here show how to integrate commands using [[PIONE]], which is a rule-based process definition and work under distributed computing system.

==== [[Integration by bash]] ====
bash etc.

==== [[Integration by integration commands]] ====
We here describe how to integrate commands by [[Display2]], [[smolet]], [[Eos]] etc. programed with Tcl/Tk, [[ctfDisplay]] etc. programed with Ruby/Tk，[[molvie]] etc. programmed by C-language.

== [[Image Processing]] and [[Image Analysis]] ==
=== [[General Image Processing]] ===

=== [[EM Image Processing]] ===

==== [[Montage]] ====

==== [[CTF Collection]] ====

==== [[Alignment of 3D objects]] ====

==== [[Alignment of a series of images]] ====

== [[Electron Microscopy]] ==
We here describe electron microscopy.

=== [[Electron source]]===
We here describe an electron source of electron microscope, a gun.

=== [[Lens]]===
We here explain the mechanism of lens and optics, especially TEM (Transmission Electron Microscopy).

=== [[Contrast of TEM]]===
We here explain what is [[contrast]] of TEM.

=== [[Contrast of SEM]]===
We here explain what is [[contrast]] of SEM.

=== [[Contrast of STEM]] ===
We here explain what is [[contrast]] of STEM.

=== [[Electron cryo-microscopy]] ===
We here explain what is electron cryo-microscopy

=== [[FAQ of electron microscopy]] ===
We here answer the FAQ.

=== [[TIPS of electron microscopy]] ===
We here collect EM TIPS.

== [[ロードマップ|Eosの今後の発展（ロードマップ）について]] ==
　Eosの今後の開発方針([[ロードマップ]])について述べます。

== FAQ and TIPS ==
=== [[EosFAQ | FAQ]] ===
We here plan to collenct FAQ(Frequenty asked question).

=== [[Eos TIPS| Eos TIPS]] ===
We here plan to collect TIPS in using Eos and processing/analyzing/intepreting images.

=== [[Eos around TIPS| Eos around TIPS]] ===
We here plan to collect useful TIPs around Eos. If you have some comments, please send me.

== Why we have been developing Eos/PIONE ? ==
Comparing the date when Eos was born, 1996, many types of software for electron micrographs have been developed and used for more users and biologist. Nonetheless, we also ask ourselves the reason why we have been developing and maintenance '''Eos'''. We will note [[Why Eos by Yasunaga]].

== Eos User Group ==
We plan to create '''Eos User Group''' and discuss the current and the future of Eos on the sourceforge or facebook. Please access them.

== '''About a symbol mark of Eos''' ==
Now we plan to make a symbol mark of Eos. If you have some ideas about Eos symbol, please send us yours.

If you want to know how to use mediawiki, please refer to [http://meta.wikimedia.org/wiki/Main_Page User's Guid]

== '''External link''' ==
* [http://www.yasunaga-lab.bio.kyutech.ac.jp/EosJ/ Eospedia.jp]
* [http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos/ Eospedia.en]
* [http://sourceforge.jp/projects/eos/ Eos SourceForge]
* [http://www.yasunaga-lab.bio.kyutech.ac.jp/ Yasunaga Lab.]
* [http://www.bio.kyutech.ac.jp/ Kyutech, Dept. of Bioscience and Bioinformatics]
* [http://www.iizuka.kyutech.ac.jp/ Kyutech. School of Computer Science and Systems Engineering]
* [http://www.kyutech.ac.jp/ Kyushu Institute of Technology(Kyutech)]

* [http://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy Software Tools For Molecular Microscopy]
* [http://emdatabank.org/emsoftware.html EM Software on EMDataBank]

== '''How to use mediawiki''' ==

* [http://www.mediawiki.org/wiki/Manual:Configuration_settings/ Configuration Settings]
* [http://www.mediawiki.org/wiki/Manual:FAQ/ FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce/ mediawiki-announce]

Main Page

2013-05-29T13:56:17Z

Tacyas: /* Eos tutorial　 */

== '''Welcome to Eospedia''' ==

We started the new manual site of Eos for only few people at 05 Nov. 2010.
We would like to summarize knowledges about [[Eos]].

Old Eos pages are [http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos_old here].

Now this Eospedia is under construction. Eospedia.ja has also opend [http://www.yasunaga-lab.bio.kyutech.ac.jp/EosJ/ here]. Japanese version of Eospedia has more information than this Eospedia in English.

=='''Beginner's Guid''' ==
=== [[Eos|What is Eos ?]]===
We here describe what is Eos.

=== [[Command|How to use Eos Commands]]
We here describe commands of Eos by CUI.

===[[Makefile|How to use Eos by Makefile]]
We here describe how to integrate commands using [[make]]

=== [[List of command|List of command]] ===
We here show all of commands Eos supplies.

===[[Functional Order of Commands]Functional order of Eos command list]
We here show functional order of Eos commands.

== '''Installation'''==
=== [[Download|Download]] ===
1. tarball [http://www.yasunaga-lab.bio.kyutech.ac.jp/ja/reserach/eos/eos-download-sites/]
2. git from SourceFoge [http://sourceforge.jp/projects/eos/]
3. (PIONE) github or gem
3.1 gem (ruby)
$ gem install pione

3.2 git from github
$ git clone https://github.com/pione/pione.git

=== [[Installation|How to install Eos]] ===
We here describe how to install Eos.

=== [[Installation of PIONE]]===
We here describe how to install a new process flow control system, PIONE. PIONE has been developed on "github".

== '''Eos reference''' ==

=== [Integration Commands|Integration commands supplied by Eos]] ===
We here describe integration commands supplied by Eos, one of the '''support''' Eos supplies.

=== Integration comannd : [[PIONE]]===
We here describe PIONE.

== '''Eos tutorial'''　==
=== How to set Eos environment　===
最初にEosのインストール方法を簡単に説明します。詳細は、[[インストール方法|Eosのインストール方法の詳細]]をご覧下さい。

* [[Eos installation|Eos Installation]]

=== How to use commands of Eos　===
Eosのコマンドの簡単な使い方を説明します。詳細は、[[コマンド|コマンドの詳細]]をご覧下さい。Eosでは、基本はCUIを使ったコマンドの実行により画像処理を進めます。その結果は、ファイルとして保存され、その内容を確認することが出来ます。

* [[Commands |Eos Commands]]

=== Image format in Eos　===
Eosで取り扱うことのできる画像フォーマットと一般的な画像フォーマットからの変換方法を示します。
* [[画像フォーマット変換|画像フォーマットの変換]]

=== Simple image processing using Eos　===
Eosを使った簡単な画像処理を実行してもらいます。
* [[Simple Image Processing|Simple Image Processing]]

=== CTF Correction ===
電子顕微鏡画像では、その撮影方法に由来して、コントラストが大きく変調を受けています。ここでは、その画像のコントラストの変調を補正する方法を示します。
* [[CTF Correction|CTF Correction]]

=== Single particle analysis　===
　ここでは、単粒子解析の基礎を行います。実際の単粒子解析は、粒子の形やその対称性などを使って探索方法や3次元再構成法を切り替えることができます。

==== Concept of [[Single particle analysi]] ====
　単粒子解析の概要を示します。

==== [[Particle picking|Particle picking]] ====
　まず、単粒子を抽出します。ここでは、手動で切り出す方法を示します。自動で切り出す方法も各種提案されています。

==== [[Classification of 2D images|Classification of 2D images]] ====
　２次元画像を分類して、ＳＮ比を上げます。

==== [[Estimation of projection angle using reference|Estimation of projection angle using reference]] ====
　参照像があるときの投影角の決定方法を説明します。参照像としては、単なる球や楕円体などとすることもあり得ます。参照像がない場合の構造解析法も別途存在しています。

==== [[3D Reconstruction: Backprojection|3D Reconstruction: Backprojecdtion]] ====
　3次元再構成自身を解説します。

==== [[Visualization tools|Visualization tools]] ====
　できあがった三次元像を可視化するためのツールを紹介します。

=== [[Electron tomography]] ===
　電子線トモグラフィーとは、同一視野の連続傾斜像から、その視野の３次元画像を再構成する方法です。細胞内の構造や構造多型性をもつタンパク質の構造解析に有効な方法です。

==== [[Electron tomography]]の概要 ====
　電子線トモグラフィー法は、同一視野の傾斜シリーズ画像のセットから３次元像を再構成する方法です。ここではその概要を述べます。

==== [[Image Correction]] ====
　傾斜画像では、視野全体がアンダーフォーカスとなるように、通常の電子顕微鏡撮影よりも大きなデフォカース値をとる場合が多いです。その場合、LaB6などの電子銃では第一トーンリングより外側の情報がほとんど無いために、CTF補正等は必要ありませんが、電界放出銃を利用した場合には、場合によっては間違った情報を与える場合があるので注意が必要です。

==== Rough Alignment ====
　傾斜画像の中心付近の画像の相関から、それぞれの傾斜画像の大まかな位置を合わせます。

==== Alignment ====
　傾斜画像の軸の位置、角度を出来る限り一致させます。

==== 3D reconstruction ====
　２次元画像のセットから３次元画像を再構成します。

==== Problems of 3D reconstruction ====
　全方位からの投影像を得られないために、ミッシングエリアとよばれる情報がない領域があります。そのため、方向依存でのボケを生じます。

==== Interpretation of 3D reconstruction ====
　また、多様な構造を含むため、３次元画像から興味あるセグメントを切り出すなどの作業が必要です。そのための支援ソフトウェアが必要です。

=== Notes ===
　This tutorial pages were created with refer to the documents used single particle workshop on 2012/09/10-11.

== '''Developers' Guide of Eos''' ==
=== [[Eos System Architecture]] ===

=== [[For Eos System Developers]] ===

=== [[Eos System Commands]] ===

=== [[Eos development under Sourceforge|Eos development under Sourceforge]]===
We here show a flow of development of Eos under Sourceforge: 1. create clone from Sourceforge, develop a new tool or object and finally register them into Sourceforge.

=== [[Development of small tools]] ===
==== [[How to create a small tool]] ====
How to create [[Small Tools]]([[Command Group]]) is described.

==== [[Introduction of small tools]] ====
We introduce some simple examples of [[Small Tools]]([[Command Group]]).

=== [[How to create API]]===
How to carete [[Object-oriented library]] ([[API]]) is described。

=== [[API list]]===
We show a list of [[Object-oriented library]] ([[API]]).

=== [[Functional oder of API]]===
We here show functionl oder of API ([[Object-oriented libraries]]) supplied by Eos.

=== [[How to create integration commands]]===
We describe how to develop integration commands.

==== [[Integration by Makefile]] ====
Here how to integrate commands using [[Makefile]] are shown。Furthreore, [[Visualmake]] supply simple and easy GUI (Graphical User Interface).

==== [[Integration by PIONE]] ====
We here show how to integrate commands using [[PIONE]], which is a rule-based process definition and work under distributed computing system.

==== [[Integration by bash]] ====
bash etc.

==== [[Integration by integration commands]] ====
We here describe how to integrate commands by [[Display2]], [[smolet]], [[Eos]] etc. programed with Tcl/Tk, [[ctfDisplay]] etc. programed with Ruby/Tk，[[molvie]] etc. programmed by C-language.

== [[Image Processing]] and [[Image Analysis]] ==
=== [[General Image Processing]] ===

=== [[EM Image Processing]] ===

==== [[Montage]] ====

==== [[CTF Collection]] ====

==== [[Alignment of 3D objects]] ====

==== [[Alignment of a series of images]] ====

== [[Electron Microscopy]] ==
We here describe electron microscopy.

=== [[Electron source]]===
We here describe an electron source of electron microscope, a gun.

=== [[Lens]]===
We here explain the mechanism of lens and optics, especially TEM (Transmission Electron Microscopy).

=== [[Contrast of TEM]]===
We here explain what is [[contrast]] of TEM.

=== [[Contrast of SEM]]===
We here explain what is [[contrast]] of SEM.

=== [[Contrast of STEM]] ===
We here explain what is [[contrast]] of STEM.

=== [[Electron cryo-microscopy]] ===
We here explain what is electron cryo-microscopy

=== [[FAQ of electron microscopy]] ===
We here answer the FAQ.

=== [[TIPS of electron microscopy]] ===
We here collect EM TIPS.

== [[ロードマップ|Eosの今後の発展（ロードマップ）について]] ==
　Eosの今後の開発方針([[ロードマップ]])について述べます。

== FAQ and TIPS ==
=== [[EosFAQ | FAQ]] ===
We here plan to collenct FAQ(Frequenty asked question).

=== [[Eos TIPS| Eos TIPS]] ===
We here plan to collect TIPS in using Eos and processing/analyzing/intepreting images.

=== [[Eos around TIPS| Eos around TIPS]] ===
We here plan to collect useful TIPs around Eos. If you have some comments, please send me.

== Why we have been developing Eos/PIONE ? ==
Comparing the date when Eos was born, 1996, many types of software for electron micrographs have been developed and used for more users and biologist. Nonetheless, we also ask ourselves the reason why we have been developing and maintenance '''Eos'''. We will note [[Why Eos by Yasunaga]].

== Eos User Group ==
We plan to create '''Eos User Group''' and discuss the current and the future of Eos on the sourceforge or facebook. Please access them.

== '''About a symbol mark of Eos''' ==
Now we plan to make a symbol mark of Eos. If you have some ideas about Eos symbol, please send us yours.

If you want to know how to use mediawiki, please refer to [http://meta.wikimedia.org/wiki/Main_Page User's Guid]

== '''External link''' ==
* [http://www.yasunaga-lab.bio.kyutech.ac.jp/EosJ/ Eospedia.jp]
* [http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos/ Eospedia.en]
* [http://sourceforge.jp/projects/eos/ Eos SourceForge]
* [http://www.yasunaga-lab.bio.kyutech.ac.jp/ Yasunaga Lab.]
* [http://www.bio.kyutech.ac.jp/ Kyutech, Dept. of Bioscience and Bioinformatics]
* [http://www.iizuka.kyutech.ac.jp/ Kyutech. School of Computer Science and Systems Engineering]
* [http://www.kyutech.ac.jp/ Kyushu Institute of Technology(Kyutech)]

* [http://en.wikibooks.org/wiki/Software_Tools_For_Molecular_Microscopy Software Tools For Molecular Microscopy]
* [http://emdatabank.org/emsoftware.html EM Software on EMDataBank]

== '''How to use mediawiki''' ==

* [http://www.mediawiki.org/wiki/Manual:Configuration_settings/ Configuration Settings]
* [http://www.mediawiki.org/wiki/Manual:FAQ/ FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce/ mediawiki-announce]

Main Page

2013-03-07T00:05:32Z

Tacyas:

Main Page

2012-09-24T09:02:13Z

Tacyas: /* Welcome to Eospedia */

File:CtfDisplay-startup.png

2012-09-24T02:00:57Z

Tacyas:

List of command

2012-09-24T01:58:58Z

Tacyas: Created page with "== Alphabetical Command List == *CheckCommonLineData *CheckOfOrientation *CheckOrientationByDegree *CommonLineCalculation *CommonLineRankCalc_k *[[Descart..."

== Alphabetical Command List ==

*[[CheckCommonLineData]]
*[[CheckOfOrientation]]
*[[CheckOrientationByDegree]]
*[[CommonLineCalculation]]
*[[CommonLineRankCalc_k]]
*[[Descartes2Polar]]
*[[Display2]]
*[[Display3]]
*[[Eos]]
*[[EvaluateCorrelationMapwithCommonLine]]
*[[FETOrientationSearchByAnnealing]]
*[[FETOrientationSearchByFeatureAlignment]]
*[[FETmapOrientationSearchBySimultaneousFitting]]
*[[FETsmallMapSetCreate_forSimultaneousMinimization]]
*[[LCalculationForOrientationSearch]]
*[[Polar2Descartes]]
*[[ProjectionDirectionMapCreate]]
*[[StereoDisplay]]
*[[TestForLcalculationOfOrientationSearchBySimultaneousMinimization]]
*[[Visualmake]]
*[[WeightCalculationOfCommonLineSearch]]
*[[WeightCalculationOfCommonLineSearchByAllSinogram]]
*[[WeigthCaluculationOfCommonLineCalculation]]
*[[angleMatchTest_k]]
*[[anglediffcalc]]
*[[anglediffchk]]
*[[array2mrc]]
*[[bin2mrc]]
*[[calcCommonLine]]
*[[clusterLog2ToLog]]
*[[clusterLogASCII2Binary]]
*[[clusterShow]]
*[[commonLinesSearchByVoting]]
*[[coordRotation]]
*[[ctfDeterminationFromMultiImage]]
*[[ctfDeterminationFromPhaseComparison]]
*[[ctfDeterminationFromThonRing]]
*[[ctfDetermine]]
*[[ctfDisplay]]
*[[ctfEnvelopFunction]]
*[[ctfFunction]]
*[[ctfFunctionServer]]
*[[ctfInfoSet]]
*[[ctfMultiFunction]]
*[[ctfWeightMapCreation]]
*[[ctfZeroPoint]]
*[[cufft]]
*[[dataAnalysis_kayabuki]]
*[[dcdAtomChangeDistanceFromAtom]]
*[[dcdAtomDistanceDistribution]]
*[[dcdCompareCA]]
*[[dcdDistanceAtomBetweenAtom]]
*[[dcdFilePrint]]
*[[dcdInfo]]
*[[dcdSelectAtoms]]
*[[dcdSerectAtom]]
*[[dcdTest]]
*[[dcdTimeSeriesBehavior]]
*[[defocusDeterminationFromThonRing]]
*[[dos2unix]]
*[[electronWaveLength]]
*[[emData2mrc]]
*[[energyTransferModelCheck]]
*[[energyTransferModelResultCheck]]
*[[fft2d]]
*[[gmolvie]]
*[[hf2000Init]]
*[[hf2000LenzCurrent]]
*[[hf2000SpecimenPosition]]
*[[homology2PG]]
*[[hostCondition]]
*[[imageView]]
*[[imagesClustering]]
*[[imagesView]]
*[[imodst2mrc]]
*[[ip2mrc]]
*[[khorosFilterGenerate]]
*[[largeIPInfo]]
*[[ll2ltlg]]
*[[llDataAverage]]
*[[llDataAxisSearch]]
*[[llDataCTFCompensate]]
*[[llDataCompare]]
*[[llDataContributionCalcDifferentN]]
*[[llDataDump]]
*[[llDataEquatorAdd]]
*[[llDataExtract]]
*[[llDataFit]]
*[[llDataFitServer]]
*[[llDataInfo]]
*[[llDataLowPassFiltering]]
*[[llDataMultiCTFCompensation]]
*[[llDataNEstimation]]
*[[llDataNormalization]]
*[[llDataPrint]]
*[[llDataRescaling]]
*[[llDataResolutionCheck]]
*[[llDataRotation]]
*[[llDataSelectionEstimation]]
*[[llDataSeparate]]
*[[llDataWeightSet]]
*[[llDatarMaxLimit]]
*[[llExtract]]
*[[llExtractCtfinfFileCreate]]
*[[llExtractCtrlFileCreate]]
*[[llExtractWithLayerSeparation]]
*[[llExtractWithLayerSeparationCtrlFileCreate]]
*[[llExtractWithLayerSeparationCtrlFileCreateMyosin]]
*[[llExtractWithLayerSeparationFilamentInfo]]
*[[llExtractWithLayerSeparationServer]]
*[[llExtractWithLayerSeparationSingle]]
*[[ltlg2mrc]]
*[[ltlg2ps]]
*[[ltlgDataInfo]]
*[[mallocCheck]]
*[[matrix3DEulerAngleTransform]]
*[[matrix3DFromEulerAngle]]
*[[matrix3DInverse]]
*[[matrix3DToEulerAngle]]
*[[moi2mrc]]
*[[molecularEnvelopeResampling]]
*[[molecularWeightCalc]]
*[[molvie]]
*[[molvieDock]]
*[[molvieFlight]]
*[[molvieMrcViewer]]
*[[molvieProjection]]
*[[molvieViewer]]
*[[mrc2Dto3D]]
*[[mrc2Dto3DforVariation]]
*[[mrc2dsn6]]
*[[mrc2fld]]
*[[mrc2gif]]
*[[mrc2hdf]]
*[[mrc2lattice]]
*[[mrc2map]]
*[[mrc2pov]]
*[[mrc2tiff]]
*[[mrc2viff]]
*[[mrc3DExtractZ]]
*[[mrc3Dto2D]]
*[[mrcFETnormalizeBySD]]
*[[mrcFFTBandPassFilter]]
*[[mrcFFTCTFCompensation]]
*[[mrcFFTDigitize]]
*[[mrcFFTExpression]]
*[[mrcFFTFibreDiagram]]
*[[mrcFFTFiltering]]
*[[mrcFFTIQEstimation]]
*[[mrcFFTInfo]]
*[[mrcFFTLayerLineCheck]]
*[[mrcFFTMedianFilter]]
*[[mrcFFTProjection]]
*[[mrcFFTResampling]]
*[[mrcFFTShellInfo]]
*[[mrcFFTSizeChange]]
*[[mrcFFTSpectrum]]
*[[mrcFFTXFiltering]]
*[[mrcFFTplainreduce]]
*[[mrcFTMeridianEquatorRedece]]
*[[mrcImage1DProjectionfrom2D]]
*[[mrcImage1dAverageByCorrelation]]
*[[mrcImage1dCutAverage]]
*[[mrcImage1dShiftAverageByAnnealing]]
*[[mrcImage1dShiftByCorrelation]]
*[[mrcImage2DBackProjection]]
*[[mrcImage2DProjection]]
*[[mrcImage2pdb]]
*[[mrcImage3DHighResoEmphasis]]
*[[mrcImage3DPad]]
*[[mrcImage3DPad2]]
*[[mrcImage3DSymmetryFind]]
*[[mrcImage3DWindowing]]
*[[mrcImageAbnormalValueRemove]]
*[[mrcImageActinSingleParticleAnalysis]]
*[[mrcImageAdaptiveBinalization]]
*[[mrcImageAdd]]
*[[mrcImageAddValue]]
*[[mrcImageAreaCalc]]
*[[mrcImageAssignedToTFofPDB]]
*[[mrcImageAutoCorrelationWithWindowing]]
*[[mrcImageAutoFilamentExtract]]
*[[mrcImageAutoFilamentExtractResultAnalysis]]
*[[mrcImageAutoRotationCorrelation]]
*[[mrcImageAutoRotationCorrelation3D]]
*[[mrcImageAutoRotationCorrelationResultPrint]]
*[[mrcImageAverage]]
*[[mrcImageBandPassFilter]]
*[[mrcImageBinalization]]
*[[mrcImageBlockMerge]]
*[[mrcImageBoundaryInfo]]
*[[mrcImageBtest]]
*[[mrcImageCCDNoiseRemove]]
*[[mrcImageCTFCompensation]]
*[[mrcImageCTFCompensationForTiltImage]]
*[[mrcImageCTFDetermination]]
*[[mrcImageCTFObservation]]
*[[mrcImageCTFSN]]
*[[mrcImageCVE]]
*[[mrcImageCenterDensityChange]]
*[[mrcImageCenterGet]]
*[[mrcImageCenterOfMassCalculate]]
*[[mrcImageCircumferentialProjection]]
*[[mrcImageClusterAnalysis]]
*[[mrcImageColoring]]
*[[mrcImageCommonLineSearch]]
*[[mrcImageConnection]]
*[[mrcImageConnectivityNumberCalc]]
*[[mrcImageContourSurfaceCreate]]
*[[mrcImageCoordinateChange]]
*[[mrcImageCoreImageCalc]]
*[[mrcImageCorrelation]]
*[[mrcImageCorrelationInFourierSpace]]
*[[mrcImageCorrelationServer]]
*[[mrcImageCorrelationWithCTFCompensation]]
*[[mrcImageCrystalCreate]]
*[[mrcImageCutAndSetInArray]]
*[[mrcImageCylinderSection]]
*[[mrcImageDeadPixelCorrection]]
*[[mrcImageDensityChangeEstimation]]
*[[mrcImageDensityInfo]]
*[[mrcImageDensityNormalization]]
*[[mrcImageDensityNormalizationByImage]]
*[[mrcImageDisplayDensityAsTempFactor]]
*[[mrcImageDistanceConversion]]
*[[mrcImageDivideInfoForTomography]]
*[[mrcImageDivideIntoTwoImages]]
*[[mrcImageEdgeImageGet]]
*[[mrcImageEnhancementWithFuzzySets]]
*[[mrcImageEstimateTiltImage]]
*[[mrcImageExpression]]
*[[mrcImageFFT]]
*[[mrcImageFFTLayerLineExtraction]]
*[[mrcImageFOMCalc]]
*[[mrcImageFTest]]
*[[mrcImageFeatureExtraction]]
*[[mrcImageFilamentSearch]]
*[[mrcImageFilterCreate]]
*[[mrcImageFilteringbyFile]]
*[[mrcImageFilteringbyFileForVariance]]
*[[mrcImageFourierPowerSpectrum]]
*[[mrcImageFourierShellCorrelation]]
*[[mrcImageFractalFourierShellCorrelation]]
*[[mrcImageFractalFrourierShellCorrelation]]
*[[mrcImageGaussDisc]]
*[[mrcImageGaussSphere]]
*[[mrcImageHeaderChange]]
*[[mrcImageHelicalAveraging]]
*[[mrcImageHelicalConvolution]]
*[[mrcImageHelicalMappingFrom2DImage]]
*[[mrcImageHelicalMasking]]
*[[mrcImageHelicalMaskingBy2DImage]]
*[[mrcImageHelicalProjection]]
*[[mrcImageHighPassFilter]]
*[[mrcImageHighlighting]]
*[[mrcImageInfo]]
*[[mrcImageInverseRadonTransform]]
*[[mrcImageLabeling]]
*[[mrcImageLowPassFilter]]
*[[mrcImageMagnificationChange]]
*[[mrcImageMake2DArrayImage]]
*[[mrcImageMakeCylinder]]
*[[mrcImageMakeDump]]
*[[mrcImageMakeFromTextFile]]
*[[mrcImageMakeSphere]]
*[[mrcImageMappingtoPdb]]
*[[mrcImageMasking]]
*[[mrcImageMaskingByImage]]
*[[mrcImageMergebyside]]
*[[mrcImageMirroring]]
*[[mrcImageModeChange]]
*[[mrcImageModelCreate]]
*[[mrcImageModelSubfilamentsCreate]]
*[[mrcImageMontageCreate]]
*[[mrcImageMove]]
*[[mrcImageMultiCTFCompensation]]
*[[mrcImageMultiCTFDetermination]]
*[[mrcImageMultiplying]]
*[[mrcImageMultiplyingbyFile]]
*[[mrcImageNLMeansFilter]]
*[[mrcImageNeuralNetParticleExtraction]]
*[[mrcImageNeuralNetParticleLearning]]
*[[mrcImageNfoldAxisSearch]]
*[[mrcImageNoiseAdd]]
*[[mrcImageNoiseCreate]]
*[[mrcImageNoiseReductionByRelaxation]]
*[[mrcImageNormalDistributionTest]]
*[[mrcImageNormalizedSubtraction]]
*[[mrcImageNormalizing]]
*[[mrcImageNullImageCreate]]
*[[mrcImageOddBoxel]]
*[[mrcImageOneLineSimilarityCalc]]
*[[mrcImageOrientationSearch]]
*[[mrcImageOrientationSearchByHigherSelection]]
*[[mrcImageOrientationSearchByHybridization]]
*[[mrcImageOrientationSearchBySimultaneousMinimization]]
*[[mrcImagePCA]]
*[[mrcImagePad]]
*[[mrcImageParticleCandidateExtract]]
*[[mrcImagePeakSearch]]
*[[mrcImagePhaseCTFCompensationFromCTFINFO]]
*[[mrcImagePixelDataGet]]
*[[mrcImagePolyROI]]
*[[mrcImagePosterization]]
*[[mrcImagePrint]]
*[[mrcImagePrint3D]]
*[[mrcImageProjection]]
*[[mrcImagePut3D]]
*[[mrcImageROI]]
*[[mrcImageROI3D]]
*[[mrcImageROIs]]
*[[mrcImageROItoPCAoutputImage]]
*[[mrcImageRadialDistribution]]
*[[mrcImageRadonTransform]]
*[[mrcImageRealValueAdd]]
*[[mrcImageRectangleGet]]
*[[mrcImageRectangleGetByCorrelation]]
*[[mrcImageRefConv2D]]
*[[mrcImageRefCreate]]
*[[mrcImageRefFFTConv2D]]
*[[mrcImageRefScaleChangeWithPad]]
*[[mrcImageResolutionEstimateForFilaments]]
*[[mrcImageReverse]]
*[[mrcImageRotation]]
*[[mrcImageRotation3D]]
*[[mrcImageSN]]
*[[mrcImageSamplingUnitChange]]
*[[mrcImageScalarAdd]]
*[[mrcImageSectionGet]]
*[[mrcImageSetFunction]]
*[[mrcImageShapePCA]]
*[[mrcImageShift]]
*[[mrcImageShiftFollowingGC]]
*[[mrcImageShrink]]
*[[mrcImageSiemensStar]]
*[[mrcImageSimilarImageSearch]]
*[[mrcImageSimilarityEstimate]]
*[[mrcImageSinogramCorrelation]]
*[[mrcImageSinogramCreate]]
*[[mrcImageSinogramFFT]]
*[[mrcImageSmoothing]]
*[[mrcImageSolventFlattening]]
*[[mrcImageSphere]]
*[[mrcImageSplit]]
*[[mrcImageSquare]]
*[[mrcImageStack]]
*[[mrcImageStandardDeviation]]
*[[mrcImageSubtraction]]
*[[mrcImageSuperResolution]]
*[[mrcImageSymmetryAverage]]
*[[mrcImageSymmetryCentreFind]]
*[[mrcImageSymmetryFind]]
*[[mrcImageTTest]]
*[[mrcImageTfunction]]
*[[mrcImageTiltAxisSearch]]
*[[mrcImageTiltAxisSearchHelp]]
*[[mrcImageToNAMDConstantForces]]
*[[mrcImageTrans]]
*[[mrcImageTransformDescartesIntoPolar]]
*[[mrcImageTransformSign]]
*[[mrcImageTranspose]]
*[[mrcImageTwoImageTest]]
*[[mrcImageUnbentROI]]
*[[mrcImageUnexpectedMassFromPDB]]
*[[mrcImageUntwist]]
*[[mrcImageVarianceAnalysis]]
*[[mrcImageVarianceMap]]
*[[mrcImageVolumeCalc]]
*[[mrcImageWindowing]]
*[[mrcImageZPad]]
*[[mrcImagepdbFileReduce]]
*[[mrcImagesSinogramCorrelation]]
*[[mrcImagestoRef]]
*[[mrcInfo]]
*[[mrcInfoSet]]
*[[mrcManipulate_kaya]]
*[[mrcMask]]
*[[mrcMeanYlinePos]]
*[[mrcMirrorImageCreate]]
*[[mrcRadon2Dto3D]]
*[[mrcRefCorEstimate]]
*[[mrcRefCorModify]]
*[[mrcRefCoreGet]]
*[[mrcRefCorrelation]]
*[[mrcRefCorrelationConv]]
*[[mrcRefEstimate]]
*[[mrcRefFFTConvert]]
*[[mrcRefHeaderCreate]]
*[[mrcRefHighPassFilter]]
*[[mrcRefImageCorrelation]]
*[[mrcRefImageOmegaCorrelation]]
*[[mrcRefImagepwzCorEstimate]]
*[[mrcRefImagepwzCorModify]]
*[[mrcRefImagepwzCorPeakFind]]
*[[mrcRefImagepwzCorSmoothing]]
*[[mrcRefImagepwzCorrelation]]
*[[mrcRefImagepwzCorrelationByFFT]]
*[[mrcRefImagexaFit]]
*[[mrcRefLowPassFilter]]
*[[mrcRefNoiseAdd]]
*[[mrcRefNormalizing]]
*[[mrcRefPhaseImageCreate]]
*[[mrcRefSmoothing]]
*[[mrcRefz1ImageCorrelation]]
*[[mrcSinogramFET]]
*[[mrcSinogramFETcalcSDforNormalize]]
*[[mrcSinogramFETcalcWeight]]
*[[mrcSinogramFETcorrelationMap]]
*[[mrcSinogramFETnormalizedMap]]
*[[mrcSinogramFETreferredCorrelation]]
*[[mrcSinogramFETsmoothParameterMatching]]
*[[mrcView]]
*[[muscleSimulation]]
*[[obj3Don2DImageView]]
*[[openGLTest]]
*[[pdb2SketchMacro]]
*[[pdb2bender]]
*[[pdb2mrc]]
*[[pdb2mrc2d]]
*[[pdb2mrc2dWithCTF]]
*[[pdb2ucd]]
*[[pdbAtomSection]]
*[[pdbCAOnly]]
*[[pdbChargeFit]]
*[[pdbCoordAdd]]
*[[pdbCrystalCreate]]
*[[pdbDisplay]]
*[[pdbFileMerge]]
*[[pdbHelix]]
*[[pdbHomologySearch]]
*[[pdbInfo]]
*[[pdbListRMSDCalc]]
*[[pdbMatrixCreate]]
*[[pdbMolecularInterfaceFind]]
*[[pdbMove]]
*[[pdbNAMDRestraintCreate]]
*[[pdbNearAtomListShow]]
*[[pdbOneProteinGet]]
*[[pdbPCA]]
*[[pdbProteinIDSet]]
*[[pdbRhoFit]]
*[[pdbRhoFitCoiledCoil]]
*[[pdbRhoFitTm]]
*[[pdbRotation]]
*[[pdbSecondaryStructurePrint]]
*[[pdbShapeFit]]
*[[pdbSurface]]
*[[pdbTempFactorSet]]
*[[pdbTrans]]
*[[pdbTwoProteinFit]]
*[[pdbView]]
*[[pdbWaterAdd]]
*[[pgDataBaseSelectServer]]
*[[pgJournalSelect]]
*[[pgJournalSelectCORBAClient]]
*[[pgJournalSelectCORBAServer]]
*[[pgMemoSelectCORBAServer]]
*[[pgSelect]]
*[[pointAffineTransform]]
*[[psFileMerge]]
*[[psFilePageMerge]]
*[[randomNormalGet]]
*[[randomUniformGet]]
*[[rasmonyo]]
*[[smolet]]
*[[tgaInfo]]
*[[tiff2mrc]]
*[[tiltInfoDetermine]]
*[[vector2pdb]]
*[[vectorImageNearestNeighborMethod]]

Eos System Commands

2012-09-17T17:23:31Z

Tacyas:

== maketool ==
=== Function ===
This shell program prepares a new tool for developers.
Usage
$ maketool ClassName ToolName [Action]
ClassName: Name of the class where a new tool belongs.
ToolName: Name of a new tool
Action:
All
All files and environments will be set up. A new default control file will be supplied.
AllFollowingControlFile
All files and environments will be supplied following the control file you once prepared
except for a main-source file.
EnvironmentOnly
You will use this argument when you want to use Eos environments and create a new tool which belongs to Eos.

== makeobj ==
=== Function ===
This shell program prepares a new object for developers.
Usage
$ maketool ClassName ObjectName [Action]
ClassName: Name of the class where a new tool belongs.
ObjcectName: Name of a new object
Action:
All
All files and environments will be set up. A new default control file will be supplied.
AllFollowingControlFile
All files and environments will be supplied following the control file you once prepared
except for a main-source file.
EnvironmentOnly
You will use this argument when you want to use Eos environments and create a new tool which belongs to Eos.

== makegeneral ==
=== Function ===
This shell program is used in maketool and makeobj.
Usage
$ makegeneral [World] [ClassName] [ObjectName] [Action]
World
Tools
You will use this argument when you create a new tool following Eos.
Objects
You will use this argument when you create a new object-oriented library
ClassName : Class Name to which a new object is attributted
ObjectName : Name of object
Action
All
All files and environment will be set up. A new default control file will be supplied.
AllFollowingControlFile
All files and environment will be supplied following a control file you prepared except for a main-source file.
EnvironmentOnly
You will use this argument when you want to use Eos environment and create a new tool which belongs to Eos.

=== Source Code Structure ===
Enviroment Varilabls
Predefined variables

EOS_HOME
Eos Top pathname

Used variables inside

WorldHomeDir
${EOS_HOME}/src
ObjectClassHomeDir
${WorldHomeDir}/Objects
ToolClassHomeDir
${WorldHomeDir}/Tools
World
Tools | Objects
ClassName
Class Name of an implemented object/tool
ObjectName
Name of an implemented object
Action
Action
Name
return temporary value of NameRead fucntion

Function
General
usage
print usage this tool
NameList
Show directories except for a directory named Config
arg1: Name of a directory including named one.
Full: arg1
NameShow
Show a list of implemented tools/objects/classes. Create ${Full}/Config/Source.lst
arg1: full pathname including inplemented
arg2: Tools | Objects | Class
Full: arg1
Target: arg2
NameRead
Get a name of a implemented tool/object/class
arg1: Full pathname including a implemented tool/object/class
arg2: Tools | Objects | Class
Name: Wanted name
Full: arg1
Target: arg2
ans: Y|y
DirCheckAndMake
Check and Create new directories, i.e., ${Full}/${Name} and ${Full}/${Name}
arg1: full pathname of a directory including a implemented directory
arg2: a directory name to be implemented
arg3: Tools | Objects | Class
Full: arg1
Name: arg2
World: arg3
ans: Y|y
NewNameAddToMakefile
Add a new name in Makefile.
arg1: Full pathname of Makefile.
arg2: name of an implemented tool/class/object.
arg3: Class| Objects | Tools
Full: arg1
Name: arg2
World: arg3
World : Tools | Objects

WorldNameShow
WorldNameRead
World: Tools | Objects
WorldDirCheckAndMake

Object :
ObjectClassNameShow
ObjectClassNameRead
ObjectClassName
ObjectClassDirCheckAndMake
ObjectNameShow
ObjectNameRead
ObjectName
ObjectDirCheckAndMake
ObjectActionRead
Action:
ObjectClassDirModifyFollowingAction
ObjectDirModifyFollowingAction

Tool :
ToolClassNameShow
ToolClassNameRead
ToolClassName
ToolClassDirCheckAndMake
ToolNameShow
ToolNameRead
ToolName
ToolDirCheckAndMake
ToolActionRead
Action:
ToolClassDirModifyFollowingAction
Create src, bin, doc, sccs, src/Tools, src/Config.
Create Makefile in Tools
ToolDirModifyFollowingAction
Create a new tool directory.
Register a new tool name in Makefile.
Set Eos environment files and directories.
Create directories, tool, tool/src etc..
Create Config/Define.inc and Config/Define.inc
Set Makefile
Set src/Makefile, src/.Depend, and src/.Source
Set a option control file.
Create prototype source codes.

Template Directory:
${EOS_HOME}/src/Config/Template/ToolTemplate.Dir
${EOS_HOME}/src/Config/Template/ToolClassTemplate.Dir
${EOS_HOME}/src/Config/Template/ToolHomeTemplate.Dir
${EOS_HOME}/src/Config/Template/ObjectTemplate.Dir
${EOS_HOME}/src/Config/Template/ObjectClassTemplate.Dir
${EOS_HOME}/src/Config/Template/ObjectHomeTemplate.Dir

Eos System Commands

2012-09-17T17:13:36Z

Tacyas: Created page with " == makegeneral == === Function === This shell program will be used in maketool and makeobj. Usage $ makegeneral [World] [ClassName] [ObjectName] [Action] World T..."

== makegeneral ==
=== Function ===
This shell program will be used in maketool and makeobj.
Usage

$ makegeneral [World] [ClassName] [ObjectName] [Action]
World
Tools
You will use this argument when you create a new tool following Eos.
Objects
You will use this argument when you create a new object-oriented library
ClassName : Class Name to which a new object is attributted
ObjectName : Name of object
Action
All
All files and environment will be set up. A new default control file will be supplied.
AllFollowingControlFile
All files and environment will be supplied following a control file you prepared except for a main-source file.
EnvironmentOnly
You will use this argument when you want to use Eos environment and create a new tool which belongs to Eos.

=== Source Code Structure ===
Enviroment Varilabls
Predefined variables

EOS_HOME
Eos Top pathname

Used variables inside

WorldHomeDir
${EOS_HOME}/src
ObjectClassHomeDir
${WorldHomeDir}/Objects
ToolClassHomeDir
${WorldHomeDir}/Tools
World
Tools | Objects
ClassName
Class Name of an implemented object/tool
ObjectName
Name of an implemented object
Action
Action
Name
return temporary value of NameRead fucntion

Function
General
usage
print usage this tool
NameList
Show directories except for a directory named Config
arg1: Name of a directory including named one.
Full: arg1
NameShow
Show a list of implemented tools/objects/classes. Create ${Full}/Config/Source.lst
arg1: full pathname including inplemented
arg2: Tools | Objects | Class
Full: arg1
Target: arg2
NameRead
Get a name of a implemented tool/object/class
arg1: Full pathname including a implemented tool/object/class
arg2: Tools | Objects | Class
Name: Wanted name
Full: arg1
Target: arg2
ans: Y|y
DirCheckAndMake
Check and Create new directories, i.e., ${Full}/${Name} and ${Full}/${Name}
arg1: full pathname of a directory including a implemented directory
arg2: a directory name to be implemented
arg3: Tools | Objects | Class
Full: arg1
Name: arg2
World: arg3
ans: Y|y
NewNameAddToMakefile
Add a new name in Makefile.
arg1: Full pathname of Makefile.
arg2: name of an implemented tool/class/object.
arg3: Class| Objects | Tools
Full: arg1
Name: arg2
World: arg3
World : Tools | Objects

WorldNameShow
WorldNameRead
World: Tools | Objects
WorldDirCheckAndMake

Object :
ObjectClassNameShow
ObjectClassNameRead
ObjectClassName
ObjectClassDirCheckAndMake
ObjectNameShow
ObjectNameRead
ObjectName
ObjectDirCheckAndMake
ObjectActionRead
Action:
ObjectClassDirModifyFollowingAction
ObjectDirModifyFollowingAction

Tool :
ToolClassNameShow
ToolClassNameRead
ToolClassName
ToolClassDirCheckAndMake
ToolNameShow
ToolNameRead
ToolName
ToolDirCheckAndMake
ToolActionRead
Action:
ToolClassDirModifyFollowingAction
Create src, bin, doc, sccs, src/Tools, src/Config.
Create Makefile in Tools
ToolDirModifyFollowingAction
Create a new tool directory.
Register a new tool name in Makefile.
Set Eos environment files and directories.
Create directories, tool, tool/src etc..
Create Config/Define.inc and Config/Define.inc
Set Makefile
Set src/Makefile, src/.Depend, and src/.Source
Set a option control file.
Create prototype source codes.

Template Directory:
${EOS_HOME}/src/Config/Template/ToolTemplate.Dir
${EOS_HOME}/src/Config/Template/ToolClassTemplate.Dir
${EOS_HOME}/src/Config/Template/ToolHomeTemplate.Dir
${EOS_HOME}/src/Config/Template/ObjectTemplate.Dir
${EOS_HOME}/src/Config/Template/ObjectClassTemplate.Dir
${EOS_HOME}/src/Config/Template/ObjectHomeTemplate.Dir

Main Page

2012-09-17T17:07:41Z

Tacyas: /* Developers' Guide of Eos */

Eos

2012-09-17T02:10:54Z

Tacyas:

Eos is an environment for image analysis of electron micrographs. Eos system supplies four types of codes.

* [[Small Tools]]
* [[Object-oriented library]]
* [[Integration Tools]]
* [[Development Tools]]

Main Page

2012-09-17T02:06:04Z

Tacyas: /* Beginner's Guide of Eos */

For Eos System Developers

2012-09-17T02:05:22Z

Tacyas: /* DEBUGPRINT function */

= Eos System Developers =

== Eos Enviroment Setting ==

=== Eos default setting ===
EOS_HOME
Eos home directory
EOS_HOST
Eos working station type
When you want to create a new tool on another Eos,
EOS_ANOTHER_HOME
Anonther Eos home directory

== When you create a new tool, ==
=== Rule ===
create new directories and proto-type source codes

$ maketool classname toolname new

change a working directory.
$ cd $EOS_HOME/src/Tools/classname/toolname/src

When you want to add new arguments, you need to modify a file of ../Config/[[OptionControlFile]].
Now we are creating a interactive tool, [[makeOptionControlFile]]. Wait a moment please.
If you modify a file of OptionControlFile, you must update your new source codes.

$ make update

modify toolname.c (a main-source file)
This step is essential but cannot be auto-made.

Check file-dependency.
$ make depend

build a new tool
$ make

fix bugs in a main-source file.
This step is essential, too. It may take many hours to fix bugs. Eos supplies some techniques for the purpose of quick bug-fix, while the bug-fix step cannot be auto.

install a new tool
$ make install

== When you create a new object ==

$ protoObjectMethodCreate

== Control File Format ==
This control file is used to generate prototype-source code.

Main Source File

Main source file
Default: Tool.c
ToolInfo
This struct includes the information of argmunets (argv) of main function
init0 (init.c)
Assign default values to ToolInfo
argCheck (argCheck.c)
Assign values to ToolInfo using the information of arguments (argv)
init1 (init.c)
Initialize ToolInfo following the information of arguments (ToolInfo).

== Some Techiniques for Quick Bug-fix ==

=== DEBUGPRINT function ===
DEBUGPRINT is a print function for DEBUG. The tool is defined in 'genUtil.h'.

#include "genUtil.h"

If you begin to debug programs,

Example:
#define DEBUG
#include "genUtil.h"
................
DEBUGPRINT("This step is OK");
DEBUGPRINT1("This step is OK: %ld \n", mode);
................
DEBUGPRINT6("This step is OK: %ld %ld %ld %ld %ld %ld\n", mode1, mode2, mode3, mode4, mode5, mode6);
................

or

#define DEBUG2
#include "genUtil.h"
................
DEBUG2PRINT("This step is OK");
DEBUG2PRINT1("This step is OK: %ld \n", mode);
................
DEBUG2PRINT6("This step is OK: %ld %ld %ld %ld %ld %ld\n", mode1, mode2, mode3, mode4, mode5, mode6);
................

If you finish to debug programs,

Example:
#undef DEBUG or #undef DEBUG2
#include "genUtil.h"
................
DEBUGPRINT("This step is OK");
DEBUGPRINT1("This step is OK: %ld \n", mode);
................
DEBUGPRINT6("This step is OK: %ld %ld %ld %ld %ld %ld\n", mode1, mode2, mode3, mode4, mode5, mode6);
................

=== How to use gdb. ===
core analysis

Example:
OS: HP, Order: mrcImagePrint -i test -o test2

$ gdb ~/Eos/bin/HP/mrcImagePrint.HP core
or
$ gdb ~/Eos/bin/HP/mrcImagePrint.HP
$ gdb> run -i test -o test2

gdb command list
gdb> where
gdb> list
gdb> up, down
gdb> print
gdb> break
gdb> next

=== Log print ===
Print logs to both stdout and fpt for file
Example:
#define LOGPRINT4(fpt,ID,ID2,x,d1,d2,d3,d4) \
fprintf(fpt, "%-6s %-15s ",ID,ID2); \
fprintf(fpt, x, d1,d2,d3,d4); \
fprintf(fpt, "\n"); fflush(fpt); \
fprintf(stdout, "%-6s %-15s ",ID,ID2); \
fprintf(stdout, x, d1,d2,d3,d4); \
fprintf(stdout, "\n"); fflush(stdout);

For Eos System Developers

2012-09-17T02:01:55Z

Tacyas: /* Log print */

= Eos System Developers =

== Eos Enviroment Setting ==

=== Eos default setting ===
EOS_HOME
Eos home directory
EOS_HOST
Eos working station type
When you want to create a new tool on another Eos,
EOS_ANOTHER_HOME
Anonther Eos home directory

== When you create a new tool, ==
=== Rule ===
create new directories and proto-type source codes

$ maketool classname toolname new

change a working directory.
$ cd $EOS_HOME/src/Tools/classname/toolname/src

When you want to add new arguments, you need to modify a file of ../Config/[[OptionControlFile]].
Now we are creating a interactive tool, [[makeOptionControlFile]]. Wait a moment please.
If you modify a file of OptionControlFile, you must update your new source codes.

$ make update

modify toolname.c (a main-source file)
This step is essential but cannot be auto-made.

Check file-dependency.
$ make depend

build a new tool
$ make

fix bugs in a main-source file.
This step is essential, too. It may take many hours to fix bugs. Eos supplies some techniques for the purpose of quick bug-fix, while the bug-fix step cannot be auto.

install a new tool
$ make install

== When you create a new object ==

$ protoObjectMethodCreate

== Control File Format ==
This control file is used to generate prototype-source code.

Main Source File

Main source file
Default: Tool.c
ToolInfo
This struct includes the information of argmunets (argv) of main function
init0 (init.c)
Assign default values to ToolInfo
argCheck (argCheck.c)
Assign values to ToolInfo using the information of arguments (argv)
init1 (init.c)
Initialize ToolInfo following the information of arguments (ToolInfo).

== Some Techiniques for Quick Bug-fix ==

=== DEBUGPRINT function ===

#include "genUtil.h"

If you begin to debug programs,

Example:
#define DEBUG
#include "genUtil.h"
................
DEBUGPRINT("This step is OK");
DEBUGPRINT1("This step is OK: %ld \n", mode);
................
DEBUGPRINT6("This step is OK: %ld %ld %ld %ld %ld %ld\n", mode1, mode2, mode3, mode4, mode5, mode6);
................

or

#define DEBUG2
#include "genUtil.h"
................
DEBUG2PRINT("This step is OK");
DEBUG2PRINT1("This step is OK: %ld \n", mode);
................
DEBUG2PRINT6("This step is OK: %ld %ld %ld %ld %ld %ld\n", mode1, mode2, mode3, mode4, mode5, mode6);
................

If you finish to debug programs,

Example:
#undef DEBUG or #undef DEBUG2
#include "genUtil.h"
................
DEBUGPRINT("This step is OK");
DEBUGPRINT1("This step is OK: %ld \n", mode);
................
DEBUGPRINT6("This step is OK: %ld %ld %ld %ld %ld %ld\n", mode1, mode2, mode3, mode4, mode5, mode6);
................

=== How to use gdb. ===
core analysis

Example:
OS: HP, Order: mrcImagePrint -i test -o test2

$ gdb ~/Eos/bin/HP/mrcImagePrint.HP core
or
$ gdb ~/Eos/bin/HP/mrcImagePrint.HP
$ gdb> run -i test -o test2

gdb command list
gdb> where
gdb> list
gdb> up, down
gdb> print
gdb> break
gdb> next

=== Log print ===
Print logs to both stdout and fpt for file
Example:
#define LOGPRINT4(fpt,ID,ID2,x,d1,d2,d3,d4) \
fprintf(fpt, "%-6s %-15s ",ID,ID2); \
fprintf(fpt, x, d1,d2,d3,d4); \
fprintf(fpt, "\n"); fflush(fpt); \
fprintf(stdout, "%-6s %-15s ",ID,ID2); \
fprintf(stdout, x, d1,d2,d3,d4); \
fprintf(stdout, "\n"); fflush(stdout);

For Eos System Developers

2012-09-17T02:00:08Z

Tacyas: /* How to use gdb. */

= Eos System Developers =

== Eos Enviroment Setting ==

=== Eos default setting ===
EOS_HOME
Eos home directory
EOS_HOST
Eos working station type
When you want to create a new tool on another Eos,
EOS_ANOTHER_HOME
Anonther Eos home directory

== When you create a new tool, ==
=== Rule ===
create new directories and proto-type source codes

$ maketool classname toolname new

change a working directory.
$ cd $EOS_HOME/src/Tools/classname/toolname/src

When you want to add new arguments, you need to modify a file of ../Config/[[OptionControlFile]].
Now we are creating a interactive tool, [[makeOptionControlFile]]. Wait a moment please.
If you modify a file of OptionControlFile, you must update your new source codes.

$ make update

modify toolname.c (a main-source file)
This step is essential but cannot be auto-made.

Check file-dependency.
$ make depend

build a new tool
$ make

fix bugs in a main-source file.
This step is essential, too. It may take many hours to fix bugs. Eos supplies some techniques for the purpose of quick bug-fix, while the bug-fix step cannot be auto.

install a new tool
$ make install

== When you create a new object ==

$ protoObjectMethodCreate

== Control File Format ==
This control file is used to generate prototype-source code.

Main Source File

Main source file
Default: Tool.c
ToolInfo
This struct includes the information of argmunets (argv) of main function
init0 (init.c)
Assign default values to ToolInfo
argCheck (argCheck.c)
Assign values to ToolInfo using the information of arguments (argv)
init1 (init.c)
Initialize ToolInfo following the information of arguments (ToolInfo).

== Some Techiniques for Quick Bug-fix ==

=== DEBUGPRINT function ===

#include "genUtil.h"

If you begin to debug programs,

Example:
#define DEBUG
#include "genUtil.h"
................
DEBUGPRINT("This step is OK");
DEBUGPRINT1("This step is OK: %ld \n", mode);
................
DEBUGPRINT6("This step is OK: %ld %ld %ld %ld %ld %ld\n", mode1, mode2, mode3, mode4, mode5, mode6);
................

or

#define DEBUG2
#include "genUtil.h"
................
DEBUG2PRINT("This step is OK");
DEBUG2PRINT1("This step is OK: %ld \n", mode);
................
DEBUG2PRINT6("This step is OK: %ld %ld %ld %ld %ld %ld\n", mode1, mode2, mode3, mode4, mode5, mode6);
................

If you finish to debug programs,

Example:
#undef DEBUG or #undef DEBUG2
#include "genUtil.h"
................
DEBUGPRINT("This step is OK");
DEBUGPRINT1("This step is OK: %ld \n", mode);
................
DEBUGPRINT6("This step is OK: %ld %ld %ld %ld %ld %ld\n", mode1, mode2, mode3, mode4, mode5, mode6);
................

=== How to use gdb. ===
core analysis

Example:
OS: HP, Order: mrcImagePrint -i test -o test2

$ gdb ~/Eos/bin/HP/mrcImagePrint.HP core
or
$ gdb ~/Eos/bin/HP/mrcImagePrint.HP
$ gdb> run -i test -o test2

gdb command list
gdb> where
gdb> list
gdb> up, down
gdb> print
gdb> break
gdb> next

=== Log print ===
Example

#define LOGPRINT4(fpt,ID,ID2,x,d1,d2,d3,d4) \
fprintf(fpt, "%-6s %-15s ",ID,ID2); \
fprintf(fpt, x, d1,d2,d3,d4); \
fprintf(fpt, "\n"); fflush(fpt); \
fprintf(stdout, "%-6s %-15s ",ID,ID2); \
fprintf(stdout, x, d1,d2,d3,d4); \
fprintf(stdout, "\n"); fflush(stdout);

For Eos System Developers

2012-09-17T01:58:42Z

Tacyas: /* How to use gdb. */

= Eos System Developers =

== Eos Enviroment Setting ==

=== Eos default setting ===
EOS_HOME
Eos home directory
EOS_HOST
Eos working station type
When you want to create a new tool on another Eos,
EOS_ANOTHER_HOME
Anonther Eos home directory

== When you create a new tool, ==
=== Rule ===
create new directories and proto-type source codes

$ maketool classname toolname new

change a working directory.
$ cd $EOS_HOME/src/Tools/classname/toolname/src

When you want to add new arguments, you need to modify a file of ../Config/[[OptionControlFile]].
Now we are creating a interactive tool, [[makeOptionControlFile]]. Wait a moment please.
If you modify a file of OptionControlFile, you must update your new source codes.

$ make update

modify toolname.c (a main-source file)
This step is essential but cannot be auto-made.

Check file-dependency.
$ make depend

build a new tool
$ make

fix bugs in a main-source file.
This step is essential, too. It may take many hours to fix bugs. Eos supplies some techniques for the purpose of quick bug-fix, while the bug-fix step cannot be auto.

install a new tool
$ make install

== When you create a new object ==

$ protoObjectMethodCreate

== Control File Format ==
This control file is used to generate prototype-source code.

Main Source File

Main source file
Default: Tool.c
ToolInfo
This struct includes the information of argmunets (argv) of main function
init0 (init.c)
Assign default values to ToolInfo
argCheck (argCheck.c)
Assign values to ToolInfo using the information of arguments (argv)
init1 (init.c)
Initialize ToolInfo following the information of arguments (ToolInfo).

== Some Techiniques for Quick Bug-fix ==

=== DEBUGPRINT function ===

#include "genUtil.h"

If you begin to debug programs,

Example:
#define DEBUG
#include "genUtil.h"
................
DEBUGPRINT("This step is OK");
DEBUGPRINT1("This step is OK: %ld \n", mode);
................
DEBUGPRINT6("This step is OK: %ld %ld %ld %ld %ld %ld\n", mode1, mode2, mode3, mode4, mode5, mode6);
................

or

#define DEBUG2
#include "genUtil.h"
................
DEBUG2PRINT("This step is OK");
DEBUG2PRINT1("This step is OK: %ld \n", mode);
................
DEBUG2PRINT6("This step is OK: %ld %ld %ld %ld %ld %ld\n", mode1, mode2, mode3, mode4, mode5, mode6);
................

If you finish to debug programs,

Example:
#undef DEBUG or #undef DEBUG2
#include "genUtil.h"
................
DEBUGPRINT("This step is OK");
DEBUGPRINT1("This step is OK: %ld \n", mode);
................
DEBUGPRINT6("This step is OK: %ld %ld %ld %ld %ld %ld\n", mode1, mode2, mode3, mode4, mode5, mode6);
................

=== How to use gdb. ===
core analysis

Example:
OS: HP, Order: mrcImagePrint -i test -o test2

gdb ~/Eos/bin/HP/mrcImagePrint.HP core
or
gdb ~/Eos/bin/HP/mrcImagePrint.HP
gdb> run -i test -o test2

gdb command list
where
list
up, down
print
break
next

=== Log print ===
Example

#define LOGPRINT4(fpt,ID,ID2,x,d1,d2,d3,d4) \
fprintf(fpt, "%-6s %-15s ",ID,ID2); \
fprintf(fpt, x, d1,d2,d3,d4); \
fprintf(fpt, "\n"); fflush(fpt); \
fprintf(stdout, "%-6s %-15s ",ID,ID2); \
fprintf(stdout, x, d1,d2,d3,d4); \
fprintf(stdout, "\n"); fflush(stdout);

For Eos System Developers

2012-09-17T01:56:10Z

Tacyas: /* DEBUGPRINT function */

= Eos System Developers =

== Eos Enviroment Setting ==

=== Eos default setting ===
EOS_HOME
Eos home directory
EOS_HOST
Eos working station type
When you want to create a new tool on another Eos,
EOS_ANOTHER_HOME
Anonther Eos home directory

== When you create a new tool, ==
=== Rule ===
create new directories and proto-type source codes

$ maketool classname toolname new

change a working directory.
$ cd $EOS_HOME/src/Tools/classname/toolname/src

When you want to add new arguments, you need to modify a file of ../Config/[[OptionControlFile]].
Now we are creating a interactive tool, [[makeOptionControlFile]]. Wait a moment please.
If you modify a file of OptionControlFile, you must update your new source codes.

$ make update

modify toolname.c (a main-source file)
This step is essential but cannot be auto-made.

Check file-dependency.
$ make depend

build a new tool
$ make

fix bugs in a main-source file.
This step is essential, too. It may take many hours to fix bugs. Eos supplies some techniques for the purpose of quick bug-fix, while the bug-fix step cannot be auto.

install a new tool
$ make install

== When you create a new object ==

$ protoObjectMethodCreate

== Control File Format ==
This control file is used to generate prototype-source code.

Main Source File

Main source file
Default: Tool.c
ToolInfo
This struct includes the information of argmunets (argv) of main function
init0 (init.c)
Assign default values to ToolInfo
argCheck (argCheck.c)
Assign values to ToolInfo using the information of arguments (argv)
init1 (init.c)
Initialize ToolInfo following the information of arguments (ToolInfo).

== Some Techiniques for Quick Bug-fix ==

=== DEBUGPRINT function ===

#include "genUtil.h"

If you begin to debug programs,

Example:
#define DEBUG
#include "genUtil.h"
................
DEBUGPRINT("This step is OK");
DEBUGPRINT1("This step is OK: %ld \n", mode);
................
DEBUGPRINT6("This step is OK: %ld %ld %ld %ld %ld %ld\n", mode1, mode2, mode3, mode4, mode5, mode6);
................

or

#define DEBUG2
#include "genUtil.h"
................
DEBUG2PRINT("This step is OK");
DEBUG2PRINT1("This step is OK: %ld \n", mode);
................
DEBUG2PRINT6("This step is OK: %ld %ld %ld %ld %ld %ld\n", mode1, mode2, mode3, mode4, mode5, mode6);
................

If you finish to debug programs,

Example:
#undef DEBUG or #undef DEBUG2
#include "genUtil.h"
................
DEBUGPRINT("This step is OK");
DEBUGPRINT1("This step is OK: %ld \n", mode);
................
DEBUGPRINT6("This step is OK: %ld %ld %ld %ld %ld %ld\n", mode1, mode2, mode3, mode4, mode5, mode6);
................

=== How to use gdb. ===
Example (core analysis)

OS: HP, Order: mrcImagePrint -i test -o test2

gdb ~/Eos/bin/HP/mrcImagePrint.HP core

or

gdb ~/Eos/bin/HP/mrcImagePrint.HP
run -i test -o test2

(command list)
where
list
up, down
print
break
next

=== Log print ===
Example

#define LOGPRINT4(fpt,ID,ID2,x,d1,d2,d3,d4) \
fprintf(fpt, "%-6s %-15s ",ID,ID2); \
fprintf(fpt, x, d1,d2,d3,d4); \
fprintf(fpt, "\n"); fflush(fpt); \
fprintf(stdout, "%-6s %-15s ",ID,ID2); \
fprintf(stdout, x, d1,d2,d3,d4); \
fprintf(stdout, "\n"); fflush(stdout);

For Eos System Developers

2012-09-17T01:55:46Z

Tacyas: /* DEBUGPRINT function */

= Eos System Developers =

== Eos Enviroment Setting ==

=== Eos default setting ===
EOS_HOME
Eos home directory
EOS_HOST
Eos working station type
When you want to create a new tool on another Eos,
EOS_ANOTHER_HOME
Anonther Eos home directory

== When you create a new tool, ==
=== Rule ===
create new directories and proto-type source codes

$ maketool classname toolname new

change a working directory.
$ cd $EOS_HOME/src/Tools/classname/toolname/src

When you want to add new arguments, you need to modify a file of ../Config/[[OptionControlFile]].
Now we are creating a interactive tool, [[makeOptionControlFile]]. Wait a moment please.
If you modify a file of OptionControlFile, you must update your new source codes.

$ make update

modify toolname.c (a main-source file)
This step is essential but cannot be auto-made.

Check file-dependency.
$ make depend

build a new tool
$ make

fix bugs in a main-source file.
This step is essential, too. It may take many hours to fix bugs. Eos supplies some techniques for the purpose of quick bug-fix, while the bug-fix step cannot be auto.

install a new tool
$ make install

== When you create a new object ==

$ protoObjectMethodCreate

== Control File Format ==
This control file is used to generate prototype-source code.

Main Source File

Main source file
Default: Tool.c
ToolInfo
This struct includes the information of argmunets (argv) of main function
init0 (init.c)
Assign default values to ToolInfo
argCheck (argCheck.c)
Assign values to ToolInfo using the information of arguments (argv)
init1 (init.c)
Initialize ToolInfo following the information of arguments (ToolInfo).

== Some Techiniques for Quick Bug-fix ==

=== DEBUGPRINT function ===

#include "genUtil.h"

If you begin to debug programs,

Example:
#define DEBUG
#include "genUtil.h"
................
DEBUGPRINT("This step is OK");
DEBUGPRINT1("This step is OK: %ld \n", mode);
................
DEBUGPRINT6("This step is OK: %ld %ld %ld %ld %ld %ld\n", mode1, mode2, mode3, mode4, mode5, mode6);
................

or

#define DEBUG2
#include "genUtil.h"
................
DEBUG2PRINT("This step is OK");
DEBUG2PRINT1("This step is OK: %ld \n", mode);
................
DEBUG2PRINT6("This step is OK: %ld %ld %ld %ld %ld %ld\n", mode1, mode2, mode3, mode4, mode5, mode6);
................

If you finish to debug programs,

#undef DEBUG or #undef DEBUG2
#include "genUtil.h"
................
DEBUGPRINT("This step is OK");
DEBUGPRINT1("This step is OK: %ld \n", mode);
................
DEBUGPRINT6("This step is OK: %ld %ld %ld %ld %ld %ld\n", mode1, mode2, mode3, mode4, mode5, mode6);
................

=== How to use gdb. ===
Example (core analysis)

OS: HP, Order: mrcImagePrint -i test -o test2

gdb ~/Eos/bin/HP/mrcImagePrint.HP core

or

gdb ~/Eos/bin/HP/mrcImagePrint.HP
run -i test -o test2

(command list)
where
list
up, down
print
break
next

=== Log print ===
Example

#define LOGPRINT4(fpt,ID,ID2,x,d1,d2,d3,d4) \
fprintf(fpt, "%-6s %-15s ",ID,ID2); \
fprintf(fpt, x, d1,d2,d3,d4); \
fprintf(fpt, "\n"); fflush(fpt); \
fprintf(stdout, "%-6s %-15s ",ID,ID2); \
fprintf(stdout, x, d1,d2,d3,d4); \
fprintf(stdout, "\n"); fflush(stdout);

For Eos System Developers

2012-09-17T01:55:28Z

Tacyas: /* DEBUGPRINT function */

= Eos System Developers =

== Eos Enviroment Setting ==

=== Eos default setting ===
EOS_HOME
Eos home directory
EOS_HOST
Eos working station type
When you want to create a new tool on another Eos,
EOS_ANOTHER_HOME
Anonther Eos home directory

== When you create a new tool, ==
=== Rule ===
create new directories and proto-type source codes

$ maketool classname toolname new

change a working directory.
$ cd $EOS_HOME/src/Tools/classname/toolname/src

When you want to add new arguments, you need to modify a file of ../Config/[[OptionControlFile]].
Now we are creating a interactive tool, [[makeOptionControlFile]]. Wait a moment please.
If you modify a file of OptionControlFile, you must update your new source codes.

$ make update

modify toolname.c (a main-source file)
This step is essential but cannot be auto-made.

Check file-dependency.
$ make depend

build a new tool
$ make

fix bugs in a main-source file.
This step is essential, too. It may take many hours to fix bugs. Eos supplies some techniques for the purpose of quick bug-fix, while the bug-fix step cannot be auto.

install a new tool
$ make install

== When you create a new object ==

$ protoObjectMethodCreate

== Control File Format ==
This control file is used to generate prototype-source code.

Main Source File

Main source file
Default: Tool.c
ToolInfo
This struct includes the information of argmunets (argv) of main function
init0 (init.c)
Assign default values to ToolInfo
argCheck (argCheck.c)
Assign values to ToolInfo using the information of arguments (argv)
init1 (init.c)
Initialize ToolInfo following the information of arguments (ToolInfo).

== Some Techiniques for Quick Bug-fix ==

=== DEBUGPRINT function ===

#include "genUtil.h"

If you begin to debug programs,

Example:
#define DEBUG
#include "genUtil.h"
................
DEBUGPRINT("This step is OK");
DEBUGPRINT1("This step is OK: %ld \n", mode);
................
DEBUGPRINT6("This step is OK: %ld %ld %ld %ld %ld %ld\n", mode1, mode2, mode3, mode4, mode5, mode6);
................

or

#define DEBUG2
#include "genUtil.h"
................
DEBUG2PRINT("This step is OK");
DEBUG2PRINT1("This step is OK: %ld \n", mode);
................

DEBUG2PRINT6("This step is OK: %ld %ld %ld %ld %ld %ld\n", mode1, mode2, mode3, mode4, mode5, mode6);
................

If you finish to debug programs,

#undef DEBUG or #undef DEBUG2
#include "genUtil.h"
................
DEBUGPRINT("This step is OK");
DEBUGPRINT1("This step is OK: %ld \n", mode);
................
DEBUGPRINT6("This step is OK: %ld %ld %ld %ld %ld %ld\n", mode1, mode2, mode3, mode4, mode5, mode6);
................

=== How to use gdb. ===
Example (core analysis)

OS: HP, Order: mrcImagePrint -i test -o test2

gdb ~/Eos/bin/HP/mrcImagePrint.HP core

or

gdb ~/Eos/bin/HP/mrcImagePrint.HP
run -i test -o test2

(command list)
where
list
up, down
print
break
next

=== Log print ===
Example

#define LOGPRINT4(fpt,ID,ID2,x,d1,d2,d3,d4) \
fprintf(fpt, "%-6s %-15s ",ID,ID2); \
fprintf(fpt, x, d1,d2,d3,d4); \
fprintf(fpt, "\n"); fflush(fpt); \
fprintf(stdout, "%-6s %-15s ",ID,ID2); \
fprintf(stdout, x, d1,d2,d3,d4); \
fprintf(stdout, "\n"); fflush(stdout);

For Eos System Developers

2012-09-17T01:55:05Z

Tacyas: /* DEBUGPRINT function */

= Eos System Developers =

== Eos Enviroment Setting ==

=== Eos default setting ===
EOS_HOME
Eos home directory
EOS_HOST
Eos working station type
When you want to create a new tool on another Eos,
EOS_ANOTHER_HOME
Anonther Eos home directory

== When you create a new tool, ==
=== Rule ===
create new directories and proto-type source codes

$ maketool classname toolname new

change a working directory.
$ cd $EOS_HOME/src/Tools/classname/toolname/src

When you want to add new arguments, you need to modify a file of ../Config/[[OptionControlFile]].
Now we are creating a interactive tool, [[makeOptionControlFile]]. Wait a moment please.
If you modify a file of OptionControlFile, you must update your new source codes.

$ make update

modify toolname.c (a main-source file)
This step is essential but cannot be auto-made.

Check file-dependency.
$ make depend

build a new tool
$ make

fix bugs in a main-source file.
This step is essential, too. It may take many hours to fix bugs. Eos supplies some techniques for the purpose of quick bug-fix, while the bug-fix step cannot be auto.

install a new tool
$ make install

== When you create a new object ==

$ protoObjectMethodCreate

== Control File Format ==
This control file is used to generate prototype-source code.

Main Source File

Main source file
Default: Tool.c
ToolInfo
This struct includes the information of argmunets (argv) of main function
init0 (init.c)
Assign default values to ToolInfo
argCheck (argCheck.c)
Assign values to ToolInfo using the information of arguments (argv)
init1 (init.c)
Initialize ToolInfo following the information of arguments (ToolInfo).

== Some Techiniques for Quick Bug-fix ==

=== DEBUGPRINT function ===

#include "genUtil.h"

If you begin to debug programs,

Example:
#define DEBUG
#include "genUtil.h"
................
DEBUGPRINT("This step is OK");
DEBUGPRINT1("This step is OK: %ld \n", mode);
................
DEBUGPRINT6("This step is OK: %ld %ld %ld %ld %ld %ld\n", mode1, mode2, mode3, mode4, mode5, mode6);
................

or

#define DEBUG2
#include "genUtil.h"
................
DEBUG2PRINT("This step is OK");
DEBUG2PRINT1("This step is OK: %ld \n", mode);
................

DEBUG2PRINT6("This step is OK: %ld %ld %ld %ld %ld %ld\n", mode1, mode2, mode3, mode4, mode5, mode6);
................

If you finish to debug programs,

#undef DEBUG or #undef DEBUG2
#include "genUtil.h"
................
DEBUGPRINT("This step is OK");
DEBUGPRINT1("This step is OK: %ld \n", mode);
................
DEBUGPRINT6("This step is OK: %ld %ld %ld %ld %ld %ld\n", mode1, mode2, mode3, mode4, mode5, mode6);
................

=== How to use gdb. ===
Example (core analysis)

OS: HP, Order: mrcImagePrint -i test -o test2

gdb ~/Eos/bin/HP/mrcImagePrint.HP core

or

gdb ~/Eos/bin/HP/mrcImagePrint.HP
run -i test -o test2

(command list)
where
list
up, down
print
break
next

=== Log print ===
Example

#define LOGPRINT4(fpt,ID,ID2,x,d1,d2,d3,d4) \
fprintf(fpt, "%-6s %-15s ",ID,ID2); \
fprintf(fpt, x, d1,d2,d3,d4); \
fprintf(fpt, "\n"); fflush(fpt); \
fprintf(stdout, "%-6s %-15s ",ID,ID2); \
fprintf(stdout, x, d1,d2,d3,d4); \
fprintf(stdout, "\n"); fflush(stdout);

For Eos System Developers

2012-09-17T01:53:23Z

Tacyas: Created page with "= Eos System Developers = == Eos Enviroment Setting == === Eos default setting === EOS_HOME Eos home directory EOS_HOST Eos working station type ..."

= Eos System Developers =

== Eos Enviroment Setting ==

=== Eos default setting ===
EOS_HOME
Eos home directory
EOS_HOST
Eos working station type
When you want to create a new tool on another Eos,
EOS_ANOTHER_HOME
Anonther Eos home directory

== When you create a new tool, ==
=== Rule ===
create new directories and proto-type source codes

$ maketool classname toolname new

change a working directory.
$ cd $EOS_HOME/src/Tools/classname/toolname/src

When you want to add new arguments, you need to modify a file of ../Config/[[OptionControlFile]].
Now we are creating a interactive tool, [[makeOptionControlFile]]. Wait a moment please.
If you modify a file of OptionControlFile, you must update your new source codes.

$ make update

modify toolname.c (a main-source file)
This step is essential but cannot be auto-made.

Check file-dependency.
$ make depend

build a new tool
$ make

fix bugs in a main-source file.
This step is essential, too. It may take many hours to fix bugs. Eos supplies some techniques for the purpose of quick bug-fix, while the bug-fix step cannot be auto.

install a new tool
$ make install

== When you create a new object ==

$ protoObjectMethodCreate

== Control File Format ==
This control file is used to generate prototype-source code.

Main Source File

Main source file
Default: Tool.c
ToolInfo
This struct includes the information of argmunets (argv) of main function
init0 (init.c)
Assign default values to ToolInfo
argCheck (argCheck.c)
Assign values to ToolInfo using the information of arguments (argv)
init1 (init.c)
Initialize ToolInfo following the information of arguments (ToolInfo).

== Some Techiniques for Quick Bug-fix ==

=== DEBUGPRINT function ===
#include "genUtil.h"

Example
If you begin to debug programs,

#define DEBUG
#include "genUtil.h"

................
DEBUGPRINT("This step is OK");
DEBUGPRINT1("This step is OK: %ld \n", mode);
................

DEBUGPRINT6("This step is OK: %ld %ld %ld %ld %ld %ld\n", mode1, mode2, mode3, mode4, mode5, mode6);
................

or

#define DEBUG2
#include "genUtil.h"

................
DEBUG2PRINT("This step is OK");
DEBUG2PRINT1("This step is OK: %ld \n", mode);
................

DEBUG2PRINT6("This step is OK: %ld %ld %ld %ld %ld %ld\n", mode1, mode2, mode3, mode4, mode5, mode6);
................

If you finish to debug programs,

#undef DEBUG or #undef DEBUG2
#include "genUtil.h"

................
DEBUGPRINT("This step is OK");
DEBUGPRINT1("This step is OK: %ld \n", mode);
................

DEBUGPRINT6("This step is OK: %ld %ld %ld %ld %ld %ld\n", mode1, mode2, mode3, mode4, mode5, mode6);
................

=== How to use gdb. ===
Example (core analysis)

OS: HP, Order: mrcImagePrint -i test -o test2

gdb ~/Eos/bin/HP/mrcImagePrint.HP core

or

gdb ~/Eos/bin/HP/mrcImagePrint.HP
run -i test -o test2

(command list)
where
list
up, down
print
break
next

=== Log print ===
Example

#define LOGPRINT4(fpt,ID,ID2,x,d1,d2,d3,d4) \
fprintf(fpt, "%-6s %-15s ",ID,ID2); \
fprintf(fpt, x, d1,d2,d3,d4); \
fprintf(fpt, "\n"); fflush(fpt); \
fprintf(stdout, "%-6s %-15s ",ID,ID2); \
fprintf(stdout, x, d1,d2,d3,d4); \
fprintf(stdout, "\n"); fflush(stdout);

Main Page

2012-09-17T01:45:25Z

Tacyas:

Eos

2012-09-17T01:23:22Z

Tacyas: Created page with "This Eos system supplies four types of codes. * Small Tools * Object-oriented library * Integration Tools * Development Tools"

This Eos system supplies four types of codes.

* [[Small Tools]]
* [[Object-oriented library]]
* [[Integration Tools]]
* [[Development Tools]]

EosFAQ

2012-09-17T01:19:52Z

Tacyas:

= FAQ =

== Concerning Display2 ==
=== How does NEW differ from OPEN under FILE? ===
NEW creates a new window (a new Display2 process) but OPEN does not create a new one because the same window are used to display a new image.

NEW has the function of NEW WINDOWN under WINDOW + OPEN under FILE.

=== How can I use ROI (region of interest) button ? ===
The ROI button on the menu bar (and/or the middle button of your mouse in the case of no draw of ROI) shows what type ROI we are interested in. The ROI types we now support are 'rectangle', 'line' and 'spline'. You cannot select a circle area because of mrc-File format. But you can mask images by circle, using a small tool of mrcImageMasking.

Using 'Extract ROI(Real)' under FILE and Extract(Real) button in RoiInfo under Information, mrcImageROI(rectangle) or mrcImageUnbentROI(spline) will start following ROI area information. In the case of Extract(Vertual), you can get the command of mrcImageROI/mrcImageUnbentROI with the argument information. But the command will be only displayed without performing the command.

=== How can I suggest the area of ROI ? ===
After decision of the ROI type, you can create the ROI using the left button of your mouse. In the case of 'line' and 'rectangle', you should push the left button and drag the mouse to create the ROI. In the case of 'spline', you should push the button and drag the mouse some times.

=== What is EDIT ? ===
After you created the first version area of ROI, you can cancel, move, resize and rotate the area by pushing the left button of mouse and drag your mouse, follwoing EDIT (and/or the middle button of your mouse).

=== How can I use WINDOW ? ===
The new window command creates a new window as the NEW command under FILE except for no open of the desired file. You can open the file using OPEN under FILE.
* OPERATION:FFT
I know the operation of FFT has some bug. This is a test-version operation. I now try to realize that small tools of Eos can be installed automatedly as OPERATION. Please wait for success of this trial (1997/9/15).

* Display2Info:Infomation
** HIGH/LOW
HIGH means the whitest density and LOW means the blackest density. Thus, you can get lighter display or darker display. If HIGH < LOW, you will get the nega-image.
** PREVZ/NEXTZ
In the case of three-dimensional images, you can get the 2D z-section images using PREVZ(Previous z)/NEXTZ(Next z).

== Concerning FFT Operations ==
=== Filtering (FFT space) ===
* mrcFFTFiltering: Filtering follwing space-group.
* mrcImageLowPassFilter: Low pass filtering
* mrcImageHighPassFilter: High pass filtering
* mrcFFTFiltering
-vx, -vy
These options indicate two vectors of crystal.
-sx, -sy
These options indicate the size of window size for filtering.
== Printing ==
=== How to print images and FFT. ===
You can use a small tool of mrcImagePrint in both cases.

== Small tools ==
mrcImageFourierPowerSpectrum
How to display a output
Eos does not have a general display tool of graph. We usually use gnuplot(free) or Splus(commercial) or Excel(commercial).

== MISCELLANEOUS ==
=== What is -c option ? ===
The "-c" option is one of reserved options. Some tools use this option, while others do not use it. The reserved options are -m, -h, -html and -c.

EosFAQ

2012-09-17T01:12:02Z

Tacyas: Created page with "== FAQ === Concerning Display2 How does NEW differ from OPEN under FILE? NEW creates a new window (a new Display2 process) but OPEN does not create a ..."

== FAQ ===

Concerning Display2
How does NEW differ from OPEN under FILE?
NEW creates a new window (a new Display2 process) but OPEN does not create a new one because the same window are used to display a new image.
NEW has the function of NEW WINDOWN under WINDOW + OPEN under FILE.
How can I use ROI (region of interest) button ?
The ROI button on the menu bar (and/or the middle button of your mouse in the case of no draw of ROI) shows what type ROI we are interested in. The ROI types we now support are 'rectangle', 'line' and 'spline'. You cannot select a circle area because of mrc-File format. But you can mask images by circle, using a small tool of mrcImageMasking.
Using 'Extract ROI(Real)' under FILE and Extract(Real) button in RoiInfo under Information, mrcImageROI(rectangle) or mrcImageUnbentROI(spline) will start following ROI area information. In the case of Extract(Vertual), you can get the command of mrcImageROI/mrcImageUnbentROI with the argument information. But the command will be only displayed without performing the command.
How can I suggest the area of ROI ?
After decision of the ROI type, you can create the ROI using the left button of your mouse. In the case of 'line' and 'rectangle', you should push the left button and drag the mouse to create the ROI. In the case of 'spline', you should push the button and drag the mouse some times.
What is EDIT ?
After you created the first version area of ROI, you can cancel, move, resize and rotate the area by pushing the left button of mouse and drag your mouse, follwoing EDIT (and/or the middle button of your mouse).
How can I use WINDOW ?
The new window command creates a new window as the NEW command under FILE except for no open of the desired file. You can open the file using OPEN under FILE.
OPERATION:FFT
I know the operation of FFT has some bug. This is a test-version operation. I now try to realize that small tools of Eos can be installed automatedly as OPERATION. Please wait for success of this trial (1997/9/15).
Display2Info:Infomation

HIGH/LOW
HIGH means the whitest density and LOW means the blackest density. Thus, you can get lighter display or darker display. If HIGH < LOW, you will get the nega-image.
PREVZ/NEXTZ
In the case of three-dimensional images, you can get the 2D z-section images using PREVZ(Previous z)/NEXTZ(Next z).

Concerning FFT Operations
Filtering (FFT space)
mrcFFTFiltering
Filtering follwing space-group.
mrcImageLowPassFilter
Low pass filtering
mrcImageHighPassFilter
High pass filtering
mrcFFTFiltering
-vx, -vy
These options indicate two vectors of crystal.
-sx, -sy
These options indicate the size of window size for filtering.
Printing
How to print images and FFT.
You can use a small tool of mrcImagePrint in both cases.
Small tools
mrcImageFourierPowerSpectrum
How to display a output
Eos does not have a general display tool of graph. We usually use gnuplot(free) or Splus(commercial) or Excel(commercial).
MISCELLANEOUS
What is -c option ?
The "-c" option is one of reserved options. Some tools use this option, while others do not use it.
The reserved options are -m -h and -c.

Main Page

2012-09-17T01:11:22Z

Tacyas:

Main Page

2012-09-16T22:15:44Z

Tacyas:

Main Page

2012-09-16T22:11:32Z

Tacyas:

== '''Welcome to Eospedia''' ==

We started the new manual site of Eos for only few people at 05 Nov. 2010.
We would like to summarize knowledges about [[Eos]].

== '''Beginner's Guide of Eos''' ==

* [[Eos|What is Eos]]
* [[Command|How to use CUI?]]
* [[Makefile|How to use Eos?]]
* [[List of command|List of command]]

User talk:Tacyas

2012-07-06T20:42:40Z

Tacyas: /* Download */ new section

== Download ==

We are building a download site for Eos.

Talk:Eos

2012-07-06T20:39:20Z

Tacyas: /* Download */ new section

== Download ==

We are now building a download site for Eos. Please wait a momnent.