515 lines
25 KiB
ReStructuredText
515 lines
25 KiB
ReStructuredText
.. include:: <isogrk1.txt>
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.. index:: musredit
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.. _musredit-sec:
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``musredit``: the GUI Based Interface to ``musrfit``
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====================================================
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Introduction
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------------
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.. _Qt: https://qt.io
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``musredit`` is an editor which also provide a graphical user interface to the programs contained in the ``musrfit`` suite and are intended
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to help the user handle ``musrfit`` msr files. It is implemented in ``C++`` and use the `Qt`_ framework. ``musredit`` is based on Qt 4.6 or Qt 5.6 (or above).
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The Qt 5.6 version of ``musredit`` will be actively developed, whereas the Qt 4.x version will only get bug fixing and eventually will be dropped.
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On this documentation page only the features related to ``musrfit`` are described — the basic editor functions which should be self-explanatory are *not*.
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``musrgui`` is an outdated early version of ``musredit`` and will not described anymore. If still in use, the user is urged to switch to ``musredit``.
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.. note::
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Before going on using ``musredit`` it is strongly recommended to read the :ref:`manual of musrfit <user-manual>` first!
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Available Executable, Configuration Files and their Basic Usage
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----------------------------------------------------------------
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musredit (musrgui)
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++++++++++++++++++
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``musredit`` (``musrgui``) is the editor executable. If called from within a shell it accepts a few optional parameters:
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**<msr-files>**
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File names of the msr files that should be opened in separate editor tabs on startup of ``musredit``.
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**- -help**
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Displays a small help notice in the shell explaining the basic usage of the program.
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**- -version**
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Prints the version number of ``musredit``.
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If called without any parameters an empty editor window opens.
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.. index:: musredit_startup
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musredit_startup.xml
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++++++++++++++++++++
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``musredit_startup.xml`` is the configuration file located under ``$HOME\.musrfit\musredit``. It is also possible to have another version
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of this file in the working directory which then will be used!
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In this file the following ``XML`` tags are allowed to define settings and might proof useful for all users of ``musredit``:
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**<general></general>**
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set the default paths to executable and files in this environment
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**<exec_path>PATH_TO_EXEC</exec_path>**
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set the path ``PATH_TO_EXEC`` where the executable ``musrfit``, ``musrview``, ``musrt0``, etc. can be found (inside the ``<general>`` environment)
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**<default_save_path>SAVE_PATH</default_save_path>**
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specify the path ``SAVE_PATH`` where ``musredit`` point by default when opening and saving msr files (inside the ``<general>`` environment). Default is the current directory.
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**<msr_default_file_path>MSR_DEF_PATH</msr_default_file_path>**
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set the path ``MSR_DEF_PATH`` where the default msr files provided by ``musredit`` are stored (inside the ``<general>`` environment)
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**<timeout>3600</timeout>**
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timeout in seconds after which :ref:`musrview <musrview>` canvas will automatically quit. A value of 0 or
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a negative number will keep the ``musrview`` canvas open without self-determination.
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**<keep_minuit2_output>y/n</keep_minuit2_output>**
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flag indicating if the ``MINUIT2`` output shall be kept per msr-file ('y') or only for the current msr-file ('n').
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**<dump_ascii>y/n</dump_ascii>**
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flag indicating if ``musrfit`` shall dump fit data into ascii format. See help of :ref:`musrfit <musrfit>`.
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**<dump_root>y/n</dump_root>**
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flag indicating if ``musrfit`` shall dump fit data into root format. See help of :ref:`musrfit <musrfit>`.
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**<title_from_data_file>y/n</title_from_data_file>**
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specify if ``musrfit`` should be called with the ``-t`` option by default (inside the ``<general>`` environment)
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**<chisq_pre_run_block>y/n</chisq_pre_run_block>**
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flag indicating if per-run chisq shall be written into the msr-output-file.
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**<estimate_n0>y/n</estimate_n0>**
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flag indicating if for a single histogram fit :math:`N_0` shall be estimated before the fit procedure starts.
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**<musrview_show_fourier>y/n</musrview_show_fourier>**
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flag indicating if ``musrview`` will directly present the Fourier transform rather than the time domain data.
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**<musrview_show_avg>y/n</musrview_show_avg>**
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flag indicating if ``musrview`` will directly present averaged data, typically used for Fourier power spectra.
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**<enable_musrt0>y/n</enable_musrt0>**
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specify if :ref:`musrt0 <musrt0>` can be called from within ``musredit`` (inside the ``<general>`` environment)
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**<font_settings></font_settings>**
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set the default font in this environment
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**<font_name>FONT</font_name>**
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specify the name of the font ``FONT`` to be used by default in ``musredit`` (inside the ``<font_settings>`` environment)
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**<font_size>N</font_size>**
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specify the size ``N`` of the font to be used by default in ``musredit`` (inside the ``<font_settings>`` environment)
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**<msr_file_defaults></msr_file_defaults>**
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put the default settings for newly created msr files in this environment
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**<beamline>BL</beamline>**
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set the name of the muon beamline ``BL`` here (inside a ``<msr_file_defaults>`` environment)
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**<institute>INST</institute>**
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set the name of the facility ``INST`` where the beamline ``BL`` is located. Valid settings are ``PSI``, ``RAL``, ``JPARC``, and ``TRIUMF`` (inside a ``<msr_file_defaults>`` environment)
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**<file_format>FF</file_format>**
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specify the default data file format ``FF`` here. Valid formats are ``NEXUS``, ``MUSR-ROOT``, ``ROOT-NPP``, ``ROOT-PPC``, ``PSI-BIN``, ``PSI-MDU``, ``MDU-ASCII``, ``WKM``, ``MUD``, ``ASCII``, and ``DB`` (inside a ``<msr_file_defaults>`` environment)
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**<lifetime_correction>y/n</lifetime_correction>**
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choose if by default the ``lifetimecorrection`` option should be set (inside a ``<msr_file_defaults>`` environment)
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**<msr2data_defaults></msr2data_defaults>**
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define the default options for calling :ref:`msr2data <msr2data>` in this environment; the options set here are ticked by default in the graphical interface of ``musredit``.
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**<chain_fit>y/n</chain_fit>**
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(un)set the chain fit (!) option (inside a ``<msr2data_defaults>`` environment)
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**<write_data_header>y/n</write_data_header>**
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(un)set the noheader option (inside a ``<msr2data_defaults>`` environment)
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**<ignore_data_header_info>y/n</ignore_data_header_info>**
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(un)set the nosummary option (inside a ``<msr2data_defaults>`` environment)
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**<keep_minuit2_output>y/n</keep_minuit2_output>**
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(un)set the ``-k`` option (inside a ``<msr2data_defaults>`` environment)
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**<write_column_data>y/n</write_column_data>**
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(un)set the ``data`` option (inside a ``<msr2data_defaults>`` environment)
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**<create_msr_file_only>y/n</create_msr_file_only>**
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(un)set the ``msr`` option in case a template run is specified (inside a ``<msr2data_defaults>`` environment)
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**<fit_only>y/n</fit_only>**
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(un)set the ``fit`` option in case no template run is specified (inside a ``<msr2data_defaults>`` environment)
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**<global>y/n</global>**
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(un)set the ``global`` option (inside a ``<msr2data_defaults>`` environment)
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**<global_plus>y/n</global_plus>**
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(un)set the ``global+`` option (inside a ``<msr2data_defaults>`` environment)
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**<recreate_data_file>y/n</recreate_data_file>**
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(un)set the ``musredit`` option for recreating the output file (inside a ``<msr2data_defaults>`` environment)
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**<open_file_after_fitting>y/n</open_file_after_fitting>**
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(un)set the ``musredit`` option for opening msr files after fitting (inside a ``<msr2data_defaults>`` environment)
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Additionally, there are some settings defined in this XML file which should be only changed by experienced users who like to add new features to ``musredit``:
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**<help_section></help_section>**
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define various help messages in this environment
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**<musr_web_X>LINK</musr_web_X>**
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define the ``LINK`` to the help page ``musr_web_X``, where ``X`` is ``main``, ``title``, ``parameters``, ``theory``, ``functions``, ``run``,
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``command``, ``fourier``, ``plot``, ``statistics``, ``msr2data``, or ``musrFT`` (inside a ``<help_section>`` environment)
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**<func_pixmap_path>PIX_PATH</func_pixmap_path>**
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set the path ``PIX_PATH`` to LaTeX pixmaps visualizing the various supported theory functions
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**<theory_functions></theory_functions>**
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define the functions for a msr file's :ref:`THEORY block <msr-theory-block>` according to the correct syntax in this environment
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**<func></func>**
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specify a function here (inside a ``<theory_functions>`` environment)
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**<name>NAME</name>**
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the ``NAME`` of the function in the msr file (inside a ``<func>`` environment)
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**<comment>COMMENT</comment>**
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description of the used parameters (inside a ``<func>`` environment)
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**<label>LABEL</label>**
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``LABEL`` of the function in the ``musredit`` menu (inside a ``<func>`` environment)
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**<pixmap>PIXMAP</pixmap>**
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LaTeX picture used to describe the function and stored in the ``PIX_PATH`` (inside a ``<func>`` environment)
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**<params>N</params>**
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number of parameters ``N`` used by the function (inside a ``<func>`` environment)
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An example of the ``musredit_startup.xml`` looks like:
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.. code-block:: xml
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<?xml version="1.0" encoding="UTF-8"?>
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<musredit_startup xmlns="http://lmu.web.psi.ch/musrfit/user/MUSR/MusrGui.html">
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<comment>
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This is handling default setting parameters for the musredit.
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</comment>
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<general>
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<exec_path>/usr/local/root/bin</exec_path>
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<default_save_path>./</default_save_path>
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<msr_default_file_path>/usr/local/root/share/doc/musrfit/templates</msr_default_file_path>
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<timeout>3600</timeout>
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<keep_minuit2_output>n</keep_minuit2_output>
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<dump_ascii>n</dump_ascii>
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<dump_root>n</dump_root>
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<title_from_data_file>y</title_from_data_file>
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<chisq_per_run_block>n</chisq_per_run_block>
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<estimate_n0>y</estimate_n0>
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<musrview_show_fourier>n</musrview_show_fourier>
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<musrview_show_avg>n</musrview_show_avg>
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<enable_musrt0>y</enable_musrt0>
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</general>
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<recent_files>
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<path_file_name>/usr/local/root/share/doc/musrfit/examples/test-histo-PSI-BIN.msr</path_file_name>
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</recent_files>
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<help_section>
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<musr_web_main>file:///usr/local/root/share/doc/musrfit/html/user/MUSR/MusrFit.html</musr_web_main>
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<musr_web_title>file:///usr/local/root/share/doc/musrfit/html/user/MUSR/MusrFit.html#TheTitle</musr_web_title>
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<musr_web_parameters>file:///usr/local/root/share/doc/musrfit/html/user/MUSR/MusrFit.html#TheFitparameterBlock</musr_web_parameters>
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<musr_web_theory>file:///usr/local/root/share/doc/musrfit/html/user/MUSR/MusrFit.html#TheTheoryBlock</musr_web_theory>
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<musr_web_functions>file:///usr/local/root/share/doc/musrfit/html/user/MUSR/MusrFit.html#TheFunctionsBlock</musr_web_functions>
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<musr_web_run>file:///usr/local/root/share/doc/musrfit/html/user/MUSR/MusrFit.html#TheRunBlock</musr_web_run>
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<musr_web_command>file:///usr/local/root/share/doc/musrfit/html/user/MUSR/MusrFit.html#TheCommandsBlock</musr_web_command>
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<musr_web_fourier>file:///usr/local/root/share/doc/musrfit/html/user/MUSR/MusrFit.html#TheFourierBlock</musr_web_fourier>
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<musr_web_plot>file:///usr/local/root/share/doc/musrfit/html/user/MUSR/MusrFit.html#ThePlotBlock</musr_web_plot>
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<musr_web_statistic>file:///usr/local/root/share/doc/musrfit/html/user/MUSR/MusrFit.html#TheStatisticBlock</musr_web_statistic>
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<musr_web_msr2data>file:///usr/local/root/share/doc/musrfit/html/user/MUSR/Msr2Data.html</musr_web_msr2data>
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<musr_web_musrFT>file:///usr/local/root/share/doc/musrfit/html/user/MUSR/MusrFit.html#A_2.3_musrFT</musr_web_musrFT>
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</help_section>
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<font_settings>
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<font_name>Monospace</font_name>
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<font_size>12</font_size>
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</font_settings>
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<msr_file_defaults>
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<beamline>mue4</beamline>
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<institute>psi</institute>
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<file_format>musr-root</file_format>
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<lifetime_correction>y</lifetime_correction>
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</msr_file_defaults>
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<msr2data_defaults>
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<chain_fit>y</chain_fit>
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<write_data_header>y</write_data_header>
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<ignore_data_header_info>n</ignore_data_header_info>
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<keep_minuit2_output>n</keep_minuit2_output>
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<write_column_data>n</write_column_data>
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<recreate_data_file>n</recreate_data_file>
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<open_file_after_fitting>y</open_file_after_fitting>
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<create_msr_file_only>n</create_msr_file_only>
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<fit_only>n</fit_only>
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<global>n</global>
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<global_plus>n</global_plus>
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</msr2data_defaults>
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<func_pixmap_path>/usr/local/root/share/doc/musrfit/latex_images</func_pixmap_path>
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<theory_functions>
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<func>
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<name>asymmetry</name>
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<comment></comment>
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<label>Asymmetry</label>
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<pixmap>asymmetry.png</pixmap>
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<params>1</params>
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</func>
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<func>
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<name>statGssKT</name>
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<comment>(rate)</comment>
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<label>static Gauss KT</label>
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<pixmap>statGssKT.png</pixmap>
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<params>1</params>
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</func>
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</theory_functions>
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</musredit_startup>
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.. index:: musredit-features
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musredit Features
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-----------------
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The features of ``musrfit`` which can be accessed by the graphical front ends ``musredit`` will be described in the following. All functions
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can either be called by choosing them from the *MusrFit menu*, by clicking the respective button in the *MusrFit bar*, or by using a *keyboard shortcut*.
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**musrWiz**
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.. image:: ../images/musrWiz.*
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``musrWiz`` is a helper programs which allows to create a msr-file from scratch without too much a priori knowledge. For details see :ref:`musrWiz <musrWiz>`.
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.. index:: musrWiz
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.. _musrWiz:
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**Calculate Chisq**
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.. image:: ../images/musrchisq.*
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Calls ``musrfit`` with the option ``-c``, *i.e.* calculates the :math:`\chi^2` or log max-likelihood for the active msr file tab. Shortcut-key: ``Alt+C``.
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The equivalent call on the command line would be
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.. code-block:: bash
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$ musrfit -c <msr-file>
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**Fit**
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.. image:: ../images/musrfit.*
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Calls ``musrfit`` for fitting of the active msr file in the currently active tab. Shortcut-key: ``Alt+F``.
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The equivalent call on the command line could look like
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.. code-block:: bash
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$ musrfit <msr-file> [optional parameters]
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The optional parameters may be chosen under :ref:`Preferences <musredit-prefs>`. For further information refer to the manual of :ref:`musrfit <user-manual>`.
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**Swap Msr <-> Mlog**
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.. image:: ../images/musrswap.*
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Swap the msr and mlog files. *E.g.*, for a file called ``8472_zf.msr``, this is copied to ``8472_zf.mlog`` and vice versa. Shortcut-key: ``Alt+S``.
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**Set Steps**
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.. image:: ../images/musrStep.*
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``musrStep`` allows to adjust the step size, *i.e.* the initial steps for the fitter. Shortcut-key: ``Alt+P``.
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**Msr2Data**
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.. image:: ../images/msr2data.*
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Opens a graphical interface to the ``msr2data`` program described in detail in its :ref:`own manual <msr2data>`. Shortcut-key: ``Alt+2``.
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**mupp**
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.. image:: ../images/mupp.*
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Application which allows to plot ``*.db`` and ``*.dat`` parameter files. Shortcut-key: ``Alt+U``.
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For a detailed description see the :ref:`mupp docu <mupp>`.
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**View**
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.. image:: ../images/musrview.*
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Calls ``musrview`` from the active tab of ``musredit``. For more details see the :ref:`musrview <musrview>` docu. Shortcut-key: ``Alt+V``.
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The equivalent call on the command line could look like
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.. code-block:: bash
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$ musrview <msr-file> [optional parameters]
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**T0**
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.. image:: ../images/musrt0-icon.*
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Calls ``musrt0`` which allows to set the ``T0`` values for all the runs. For more details see the :ref:`musrt0 <musrt0>` docu.
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The equivalent call on the command line could look like
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.. code-block:: bash
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$ musrt0 <msr-file> [optional parameters]
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**Raw Fourier**
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.. image:: ../images/musrFT.*
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Calls ``musrFT`` which allows to perform a Fourier transform of the raw data. For more details see the :ref:`musrFT <musrFT>` docu.
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The equivalent call on the command line could look like
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.. code-block:: bash
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$ musrFT <msr-file> [optional parameters]
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.. _musredit-prefs:
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**Preferences**
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.. image:: ../images/musrprefs.*
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Opens a window in which the optional parameters that should be passed to musrfit can be chosen.
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For further information refer to the manual of :ref:`musrfit <musrfit>`.
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**Dump Header**
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.. image:: ../images/musrdump.*
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Opens a file dialog which allows to select a |mgr|\SR data file. When this file can be read, the run header info is dumped into a dialog window.
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Essentially this calls ``dump_header`` internally.
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musrWiz
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-------
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``musrWiz`` is a helper program which allows to easily create the necessary msr-file needed as an input for ``musrfit``.
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``musrWiz`` is still in it's early stage; not all options are already implemented and here and there you will likely find some bugs.
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From ``musredit`` it can be accessed via the MusrFit menu or the wand
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.. image:: ../images/musredit-musrWiz.*
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The ``musrWiz`` GUI is organized in a couple of different dialogues which some information needs to be provided by the user.
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In the following these different dialogues will be discussed briefly.
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.. index:: musrWiz-Introduction
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musrWiz-Introduction
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++++++++++++++++++++
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The introduction dialogue
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.. image:: ../images/musrWiz-Intro.*
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#. an explicit msr-file name can be provided here. More often the msr-file name is generated out of the run number.
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#. year of the run data.
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#. run number. If no explicit msr-file is provided, the run number together with fit type and type of measurement will be used to generate the msr-file name.
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#. from the pull down menu the institute (for which a necessary ``xml``-file is provided) has to be choosen.
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#. from the pull down menu the the instrument can be chosen.
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#. the fit type has to be chosen. Possible fit types are: ``Single Histo`` / ``Single Histo RRF`` / ``Asymmetry`` / ``Asymmetry RRF`` / ``Mu Minus`` / ``None muSR``
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#. type of measurement is essentially needed for the grouping of the detectors. Possible are: ``ZF`` for zero field measurements / ``TF`` for transverse field measurements / ``LF`` for longitudinal field measurements.
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Depending on the choice and instrument some additional question might be asked, *e.g.* which magnet has been used.
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#. ``T0``'s: this last menu defines from where to get the t0's. The options are: ``from data file``, *i.e.* the t0 are assumed to be correctly set
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in the provided data file ``call musrT0``, *i.e.* after the msr-file is generated, ``musrt0`` will be called which allows the user to find the
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proper t0 from the prompt peak ``enter here`` will provide a pop-up menu where the t0 parameter can be given explicitly.
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If all this information have been provided ``Next>`` will lead you the the theory dialogue.
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.. index:: musrWiz-Theory
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musrWiz - Theory
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++++++++++++++++
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The theory dialogue is used to define the fitting function. There are two ways of using it:
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#. choose a template theory function. This option has the advantage that the next steps will be very easy because
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within the template almost everything is already pre-defined. The disadvantage is that you are not free in setting
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up your theory function as you would like to have.
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#. freely write your theory function. The advantage here is that you can customize your theory function at your needs.
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This will come at the cost that you also will need to define ``maps``, ``functions``, etc. yourself. The good thing
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though is that at the very end you can save this as a template for future re-use.
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First the template path will be described. The theory dialogue looks like this
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.. image:: ../images/musrWiz-Theory.*
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#. This is a text edit field were you can enter the theory fit function as you would like to have it. In the example
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given the theory reads :math:`p1 \exp(-p2\, t) \cos(2 \pi\, f1 + m1)`, where ``pX`` stands for parameter, ``fX`` for function,
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``mX`` for map, and ``X`` for the corresponding number.
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#. The ``Clear All`` button will clear whatever you entered in the text field above.
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#. This pull-down menu allows to select a theory function which will be added to the text field above by pressing
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the ``Add`` button. Pre defined theory function starting with a ``T`` are templates rather than only theory function strings.
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#. The ``Add`` button is used to add the chosen theory function / template from the pull-down menu to its left.
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#. The ``Check`` button is used to make a syntactical check of whatever is written in the text edit field.
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.. index:: musrWiz-Functions
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musrWiz - Functions
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+++++++++++++++++++
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In the Functions dialogue all the necessary functions can be entered. A function operates *only* on fitting parameters.
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This is different to the theory function which operates on the fitting parameters and the time. The dialogue looks like this
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.. image:: ../images/musrWiz-Functions.*
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#. a text edit field in which the various needed functions can be entered. In case a template theory is used, the appropriate function should be shown here and *no* editing will be needed here.
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#. pressing ``Show Theory`` button will pop-up a little window showing the previously entered theory function. This is handy when defining its own theory, *i.e.* not working with a template.
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.. image:: ../images/musrWiz-Functions-and-Theory.*
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.. index:: musrWiz-Maps
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musrWiz - Maps
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++++++++++++++
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.. image:: ../images/musrWiz-Maps.*
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The map dialogue will list the maps previously used in the theory and functions blocks/dialogues before. Again, if a template is used, nothing needs to be entered here.
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#. The ``Show Theory`` button allows to show the currently defined theory and the functions.
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.. index:: musrWiz-FitParam
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musrWiz - Fit Parameters
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++++++++++++++++++++++++
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.. image:: ../images/musrWiz-FitParam.*
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In the fit parameter dialogue all parameter names can be defined. Furthermore the starting values for the parameters, the step
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(initial step size for the parameter fit), and any boundaries can be defined here.
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#. The ``Show Theory`` button allows to show the currently defined theory and the functions.
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.. index:: musrWiz-FitInfo
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musrWiz - Fit Info
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++++++++++++++++++
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Collects all the ``musrfit`` and ``MINUIT2`` specific fit commands.
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.. image:: ../images/musrWiz-FitInfo.*
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#. allows to define the time fit range (start time, end time).
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#. packing defines how many bins of the original data shall be combined (added, also called re-binning).
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#. in this text field to fitting commands are given (see the ``MINUIT`` and :ref:`musrfit <msr-commands-block>` manual for details).
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.. index:: musrWiz-Create
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musrWiz - Create
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++++++++++++++++
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Collects the last necessary information before creating the msr-file.
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.. image:: ../images/musrWiz-Create.*
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#. shows the path where the msr-file will be saved. If you would like to save it somewhere else press the ``Save As (msr-file path)`` button.
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#. pressing this button will allow you to find the path where to save the msr-file.
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#. pressing this button will save to current configuration as a template for future re-use.
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.. index:: musrStep
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musrStep
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--------
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``musrStep`` is a little helper program which allows to reset the initial step size. This sometimes comes very handy if working on an instrument
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with many detectors after a fit slightly went wrong leaving you with a far too small initial step size for further iterations. To edit all the steps
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individually is tedious and error prone. Here ``musrStep`` can help.
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.. image:: ../images/musrStep-GUI.*
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When invoking ``musrStep`` the above dialogue will popup
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#. shows the relevant parts of the FITPARAMETER block. The only editable column is step.
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#. ``Check Specific`` will popup a dialogue where a template string can be entered, *e.g.* ``Asym``. As a result all fit parameters containing the template string will be selected.
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#. ``Check All`` will select all fit parameters.
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#. ``Uncheck All`` will unselect all fit parameters.
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#. ``Modify Automatic`` will change all the step values automatically. It basically sets all the step sizes to 1% of
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the corresponding fit parameter value, except the phases where the step will be set to a value of 5 degrees.
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#. ``Modify Selected`` will start the dialogue shown beneath. Follow the description there.
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#. ``Save&Quit`` will save the current step values, close the dialogue and reload the modified msr-file.
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#. ``Cancel`` will cancel the ``musrStep`` dialogue without modifying anything.
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.. image:: ../images/musrStep-Modify-Selected.*
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When clicking on ``Modify Selected`` the above dialogue will be presented. It allows to manipulate all selected fit parameter step values according to the following rules
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#. ``Scale by Factor`` will scale the step value by the factor given in the field (2). If the ``Absolute Value`` check box is selected, rather than scaling the factor value will be used to modify the step value.
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#. scaling factor or absolute value to modify the step values of the selected fit parameters.
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#. checking the ``Absolute Value`` check box will change the meaning from *Scale by Factor* to *Copy Factor Value*.
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#. ``Scale Automatically`` will modify the step values of the selected fit parameters according to the rules described before.
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#. ``Cancel`` will cancel the dialogue. |