Quick Installation Guide of Utsusemi for MacOS ¶

Utsusemi version:
Author:	Yasuhiro Inamura, Ryoichi Kajimoto
Last update:	Feb. 9th, 2018
	0.3.5.1 or later

Contents

Quick Installation Guide of Utsusemi for MacOS

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 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.

Double click the disk image file.
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 ¶

Preparation 1 (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

Preparation 2 ( 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.

Open "System Setting" panel on MacOS
Select "General" tab in "Security & Privacy" setting
Turn on "Anywhere" checkbox in "Allow apps downloaded from:"

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

In case of macOS Sierra or later ¶

If MacOS version is Sierra or High Sierra , "Anywhere" checkbox, as shown above, is disappered. In this case, please try below steps.

Launch "Terminal" App in "Utilities" folder in "Applications" folder.
Type commands as below in the terminal and type your password.

$ sudo spctl --master-disable

Reboot Mac machine. Then you find "Anywhere" checkbox and turn on it.
If you've already installed Utsusemi folder before, you must move the Utsusemi folder to the trush and copy it again from dmg file.

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¶

Instrument

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

Number of thread

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

DATA_DIR and USR_PRIV_HOME

modify or confirm the initial setting for two folders (setting of the environment valuables) described in previous secion. 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 insteed 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 can not find these folders, you must make them by your self 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.

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

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

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. Reffer 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 apperes 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 automaticaly 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.

Launch a terminal.

Run the following command.

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

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.

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

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.

Trouble ¶

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" .

About situations of troubles ¶

To report your trouble, you collect informations as below :

What you are going to
Which software or command you are using
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