Quick Installation Guide of Utsusemi for MacOS

Author

Yasuhiro Inamura, Ryoichi Kajimoto

Last update

Feb. 9th, 2018

Utsusemi version

0.3.5.1 or later

Contents

• Quick Installation Guide of Utsusemi for MacOS

  • Supported MacOS

  • Installation

    • 1. Preparation ( Setting for MacOS Security )

    • 2. Installation

  • Applications to be installed

  • Set up

    • Creation of necessary folders

    • Environment setting and requirements

    • Rule for data location

  • Data analysis

    • On macOS Sierra, High Sierra

  • Running Utsusemi on a terminal

  • Version number confirmation

  • Uninstall

  • Troubles

    • What must be reported

    • About log file

Supported MacOS

The following MacOS X's are supported

• 10.10 (Yosemite)

• 10.11 (El Capitan)

• 10.12 (macOS Sierra), 10.13 (macOS High Sierra) Notice : A part of installation steps is different before.

Installation

1. Preparation ( Setting for MacOS Security )

Utsusemi software is not reliable from a point of view of MacOS security policy because Apple does not guarantee that Utsusemi is secure as applications delivered in AppStore. So we must do setting of security of MacOS to use Utsusemi.

1. Open "System Setting" panel on MacOS

2. Select "General" tab in "Security & Privacy" setting

3. Turn on "Anywhere" checkbox in "Allow apps downloaded from:"

   

If not this setting, a dialog as below will open on launching Utsusemi.

For macOS Sierra or later

If you use Sierra or High Sierra , "Anywhere" checkbox, as shown above, is disappeared. In this case, please try following steps.

1. Launch "Terminal" App in "Utilities" folder in "Applications" folder.

2. Type commands as below in the terminal and type your account password.

$ sudo spctl --master-disable

3. Reboot Mac machine. Then you find "Anywhere" checkbox and turn on it.

4. If you've already installed Utsusemi folder before, you must move the Utsusemi folder to the trash and copy it again from dmg file.

2. Installation

Installation package is distributed as a disk image (.dmg) file for MacOS X. Users have only to double click this file to mount, and then, drag and drop the folder that includes the whole set of applications into Application folder.

1. Double click the disk image file.

   

2. In the opened folder, drag and drop "Utsusemi" folder into "Application" folder.

   

Applications to be installed

You will find a set of Utsusemi software in "Utsusemi" folder in "Application" folder. You can also access them via LaunchPad. The following programs will be prepared.

Application	Description
Utsusemi Environment Setting	[Environment setting] Set the environment valuables for Utsusemi
SequenceEditor	Launch SequenceEditor
MPlot	Launch MPlot
M2Plot	Launch M2Plot
SliceViewer	Launch SliceViewer3D
D4MatSlicer	Launch D4MatSlicer
uGao	Launch uGao plotter (under testing)
Utsusemi Shell	Launch "Terminal" with Utsusemi environment
MethodAssistant2	Launch MethodAssistant2

The details will be described later.

Set up

Creation of necessary folders

The following two folders must be prepared. These folders store raw data and temporary files.

Folder (Environment valuable)	Description
Data folder (DATA_DIR)	Folder to store raw data (Same as "/data" in the Linux version.)
Analysis folder (USR_PRIV_HOME)	Folder to include ana and tmp folders in which temporary files are stored (Same as "$HOME" in the Linux version)

The above two folders can be prepared in arbitrary places. For example,

Folder	Example
Data folder	Documents/Utsusemi/DATA
Analysis folder	Documents/Utsusemi/HOME

Environment setting and requirements

The initial setting of Utsusemi must be done by using Utsusemi Environment Setting .

警告

This setting must be done at least once after the installation.

Setting items are below.

• The instrument environment

• Two folders to store raw data and analysis temporal information.

• Logging

• The number of processers for high performance on analysis

If you analyze raw data set obtained from other instrument, you must change the instrument environment in this setting. However, you treat 2nd data ( after histogram creations ), you need not.

Launch Environment Setting

Laounch Utsusemi Environment Setting in "Utsusemi" folder in "Application" folder, or from "LaunchPad".

If you meet the dialog as below, you choose "Open".

Setting Items

1. Instrument

   Choose the instrument for data analysis. Raw data folder and executable commands are changed to suitable ones.

2. Log quiet

   Turn on to decrease logs of analysis commands

警告

All logs write in a file /tmp/mlfsoft.log. If something wrong happens on using Utsusemi, you should check this file.

3. Number of thread

   Some analysis command are affected by this value. Normaly you set the number of CPUs in your Mac machine.

4. DATA_DIR and USR_PRIV_HOME

   modify or confirm the initial setting for two folders (setting of the environment valuables) described in previous section. Push Brows button opens small dialog to choose a folder for each.

   Environment valuable	Purpose	Example
   DATA_DIR	Folder to store raw data (Same as "/data" in the Linux version)	Documents/Utsusemi/DATA
   USR_PRIV_HOME	Place to locate "ana" and "tmp" folders for temporary files are stored (Same as "$HOME" in the Linux version)	Documents/Utsusmei/HOME

Finishing Setting

After setting, push OK button. Then you see confirmation dialog as below.

If you meet an error dialog instead of this, check whether the given path to two folders are existed or not.

After closing this dialog, following folders are automatically created in the folder specified by USR_PRIV_HOME.

• ana folder

• tmp folder and xml folder under ana folder

  

警告

If you cannot find these folders, you must make them by yourself to avoid the failure of Utsusemi launch.

On the other hand, you make folders to store raw data DATA_DIR according to a rule described in next section.

Rule for data location

Raw data should be stored in the folder specified by DATA_DIR according to the following rule.

1. Create a folder who has the same name as the instrument code.

   For example, "SIK" for 4SEASONS (BL01) and "AMR" for AMATERAS (BL14).

2. Place the data folder of corresponding instrument in this folder. The name of the data folder must include each Run No.

   For example, "SIK012345_20150301" for 4SEASONS.

   BL	Instrument code|Example of data folder
   BL01 4SEASONS	SIK	DATA/SIK/SIK012345_20160401
   BL11 PLANET	HPN	DATA/HPN/HPN012345_20160401
   BL14 AMATERAS	AMR	DATA/AMR/AMR012345_20160401
   BL15 TAIKAN	SAS	DATA/SAS/SAS012345_20160401
   BL19 TAKUMI	ENG	DATA/ENG/ENG012345_20160401

Data analysis

After completing the environment setting and preparing raw data, you can perform data analysis.

The following applications are available from Application/Utsusemi folder.

Utsusemi Environment Setting

[Environment setting] Set and confirm the environment valuables for Utsusemi. Refer to "Launch Environment Setting" section.

MPlot, M2Plot, SliceViewer

Launch Utsusemi Plotters. Same as ones in Linux version.

MPlot	1-dimentional data plotter
M2Plot	2-dimentional data plotter and slicer
SliceViewer3D	3-dimentional data viewer and slicer

D4MatSlicer

Launch D4MatSlicer, same as one in Linux version.

SequenceEditor

Launch SequenceEditor, same as one in Linux version.

Utsusemi Shell

Launch "Terminal" App under Utsusemi environment. In this terminal, you can execute commands defined on the selected instrument environment and any script made by yourself.

Notices launching at the first time

When you launch Utsusemi Shell at the first time, a warning dialog appears and Utsusemi Shell app does not launch though pushing "Open" or "OK" buttons. In this case, try launching again.

uGao

[icon_uGao]

Launch uGao, which is new 2-dimentional plotter for testing.

MethodAssistant2

Launch MethodAssistant2, same as one in Linux version.

For details of each application, please refer to Utsusemi Users' Manual.

On macOS Sierra, High Sierra

On macOS SIerra and High Sierra, sometimes the dialog as below opens on launching applications.

In this case, you select "Install" to install automatically required software from the internet.

Running Utsusemi on a terminal

Python scripts including Utsusemi commands can be run without utilizing the above applications. In particular, if you try any new idea of data analysis, you need to utilize the Utsusemi environment on a terminal of MacOS. The following is the procedure.

1. Launch a terminal.

2. Run the following command.

   $ source /Applications/Utsusemi/.opt/bin/_loadenv
   

3. Then, any functions of Manyo-Library or Utsusemi can be called.

   $ python
   Python 2.7.10 (default, Oct 23 2015, 19:19:21)
   [GCC 4.2.1 Compatible Apple LLVM 7.0.0 (clang-700.0.59.5)] on darwin
   Type "help", "copyright", "credits" or "license" for more information.
   >>> import Manyo
   Manyo>>>
   

Version number confirmation

Utusemi version can be seen in the following ways. It is useful when you report bugs or update Utsusemi.

1. Installer file name

   Installer file name consists of two sets of numbers.

   Example	MLFSOFT.X.Y.Z.nnnn
   X.Y.Z	Release number
   nnnn	Revision number

2. Command of Utsusemi Python

   Launch Utsusemi Python, and run the following command.

   import UtsusemiInfo
   

   Then, the following information is displayed.

   ---------------------------------------------
                  Utsusemi Info
   ---------------------------------------------
            version :  X.Y.Z (rev nnnn)
     Contact person : Yasuhiro Inamura
             e-mail : xxxxx.yyyyy@j-parc.jp
   ---------------------------------------------
   

   X.Y.Z, and nnnn are release number and revision number, respectively.

Uninstall

Just move Utsusemi folder in Application folder to trash box.

However, this does not completely all the relevant files, and some folders show below are remained. Delete them manually is you want.

DATA_DIR folder

USR_PRIV_HOME folder

In addition, several configuration files are remained. Although these files will be used when you re-install Utsusemi, you may delete them.

Home folder/Library/Utsusemi folder

Note that these are invisible folders.

Troubles

If you feel something wrong on Utsusemi works, for example no progress of commands steps, please send a report about your situations and a log file "/tmp/mlfsoft.log" .

What must be reported

To report your trouble, you tell us the information as below :

• Which software or command you are using

• What you are going to

• What you did

• What happened

About log file

All logs under Utsusemi working are recorded in a file /tmp/mlfsoft.log . So you copy this file to send with report. In order to copy this file, do this command from command line in "Terminal" App to copy a log file to Desktop.

$ cp /tmp/mlfsoft.log ~/Desktop

For trouble shooting, you shuld remove the check of "Log quiet" on the "Utsusemi Environment Settings" to get more information in log file.