==================================================================================================== Quick Installation Guide of Utsusemi4 for MacOS ==================================================================================================== :Author: Yasuhiro Inamura, Ryoichi Kajimoto :Last update: Jul. 3rd, 2019 :Utsusemi version: 4.0 or later .. contents:: Contents :depth: 3 Supported MacOS ============================ The following MacOS X's are supported - 10.15 (macOS Catalina) - 10.14 (macOS Mojave) - 10.13 (macOS High Sierra) - 10.12 (macOS Sierra) Installation ================== Utsusemi4 Installer for macOS is distributed as a installer package (.pkg) file for macOS. Users have only to double click this file to install the whole set of Utsusemi applications with Python3 into Application folder. 1. Double click the installer package file. |image00| If you see the dialog as below after double click, |image01err| you have a right-click, or ctrl + left-click, on the installer package file to show the short-cut menu as below, |image01menu| then click "Open". After this, you will see the confirmation dialog to open this file actually. Push "Open". |image01confirm| 2. In installation dialogs, you push "Continue". |image02| 3. If you are asked where you want to install Utsusemi, you choose the storage for installation and push "Continue". |image03| 4. Push "Install" to the default path ( /Application/Utsusemi ) |image04| 5. Input the password of your account for authorization to install. |image05| 6. Installation starts. |image06| 7. After installation finishes, push "Close". |image07| 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. |image08| +----------------------------+----------------------------------------------------------------+ |Application |Description | +============================+================================================================+ |D4MatSlicer |Launch D4MatSlicer | +----------------------------+----------------------------------------------------------------+ |D4Mat2Slicer |Launch D4Mat2Slicer | +----------------------------+----------------------------------------------------------------+ |M2PlotPlus |Launch M2PlotPlus | +----------------------------+----------------------------------------------------------------+ |MPlot |Launch MPlot | +----------------------------+----------------------------------------------------------------+ |SequenceEditorQ |Launch SequenceEditor | +----------------------------+----------------------------------------------------------------+ |Utsusemi Environment Setting|[Environment setting] Set the environment valuables for Utsusemi| +----------------------------+----------------------------------------------------------------+ |Utsusemi Shell |Launch "Terminal" with Utsusemi environment | +----------------------------+----------------------------------------------------------------+ 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_DIR) |Folder to include ana and tmp folders in which temporary files are stored (Same as "$HOME" in the Linux version)| +-------------------------------+----------------------------------------------------------------------------------------------------------------+ These two folders are automatically made at the location below by the launching of **Utsusemi Environment Setting** app. Of cause, you can choose the other location, but recent macOS security prohibits to read/write data files in the "Desktop", the "Documents" and some shared folders from **Utsusemi**. Home folder is OK for the present. +---------------+-----------------------------+ |Folder |Location to be made | +===============+=============================+ |Data folder |/Utsusemi/DATA | +---------------+-----------------------------+ |Analysis folder|/Utsusemi/HOME | +---------------+-----------------------------+ |image09| If you do not know how to open home folder, you select a "Home" item from "Go" menu. |image09r1| Environment setting and requirements --------------------------------------------- The initial setting of Utsusemi must be done by using **Utsusemi Environment Settings** . .. warning:: 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 - Swiching debug-mode on/off 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 ), like saved data file (.dmp or .mdb file), you need not. Launch Environment Setting ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Laounch **Utsusemi Environment Settings** in "Utsusemi" folder in "Application" folder, or from "LaunchPad". |image08| |image10| 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 .. warning:: All logs write in a file */tmp/mlfsoft.log*. If something wrong happens on using Utsusemi, you should check this file. 3. **Utsusemi_debugmode** Turn on/off the debug mode in Utsusemi ( Default is off ) 4. **Number of thread** Some analysis command are affected by this value. Normaly you set the number of CPUs in your Mac machine. 5. **DATA_DIR** and **USR_DIR** 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_DIR |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. |image11| 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 |image12| .. warning:: 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**, **M2PlotPlus** Launch Utsusemi Plotters. Same as ones in Linux version. +-------------+-------------------------------------+ |MPlot |1-dimentional data plotter | +-------------+-------------------------------------+ |M2PlotPlus |2-dimentional data plotter 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. For details of each application, please refer to Utsusemi Users' Manual. 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. .. code-block:: shell $ source /Applications/Utsusemi/.opt/bin/_loadenv 3. Then, any functions of Manyo-Library or Utsusemi can be called. .. code-block:: shell $ 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.nnnnnn | +=======+======================+ |X.Y.Z |Release number | +-------+----------------------+ |nnnnnn |Latest date for update| +-------+----------------------+ 2. Command of **Utsusemi Shell** Launch **Utsusemi Shell**, and run the following command. .. code-block:: python >>> import utsusemi >>> utsusemi.__version__ '4.0.0' Or, .. code-block:: python import UtsusemiInfo Then, the following information is displayed. .. code-block:: shell --------------------------------------------- Utsusemi Info --------------------------------------------- version : X.Y.Z (rev nnnnnn) Contact person : Yasuhiro Inamura e-mail : xxxxx.yyyyy@j-parc.jp --------------------------------------------- X.Y.Z, and nnnn are release number and the latest date for update, 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_DIR* 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. .. code-block:: shell $ cp /tmp/mlfsoft.log ~/Desktop .. |image00| image:: media/mac_Utsusemi4Installer00.png :width: 132px .. |image01err| image:: media/mac_Utsusemi4Installer01err.png :width: 400px .. |image01menu| image:: media/mac_Utsusemi4Installer01menu.png :width: 200px .. |image01confirm| image:: media/mac_Utsusemi4Installer01conf.png :width: 400px .. |image02| image:: media/mac_Utsusemi4Installer02.png :width: 400px .. |image03| image:: media/mac_Utsusemi4Installer03.png :width: 400px .. |image04| image:: media/mac_Utsusemi4Installer04.png :width: 400px .. |image05| image:: media/mac_Utsusemi4Installer05.png :width: 400px .. |image06| image:: media/mac_Utsusemi4Installer06.png :width: 400px .. |image07| image:: media/mac_Utsusemi4Installer07.png :width: 400px .. |image08| image:: media/mac_Utsusemi4Installer08.png :width: 300px .. |image09| image:: media/mac_Utsusemi4Installer09.png :width: 300px .. |image09r1| image:: media/mac_Utsusemi4Installer09r1.png :width: 300px .. |image10| image:: media/mac_Utsusemi4Installer10.png :width: 300px .. |image11| image:: media/mac_Utsusemi4Installer11.png :width: 300px .. |image12| image:: media/mac_Utsusemi4Installer12.png :width: 300px