update of the docu for version 1.6.0
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@ -13,6 +13,11 @@ Also a collection of ``msr``-files can be invoked. ``mupp`` is heavily inspired
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``mupp`` can be operated from within as graphical user interface or via a command line scripting interface.
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The ``mupp`` GUI can be invoked either directly from the command line or from within :ref:`musredit <musredit-sec>`.
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Each collection bundles a number of runs, where a run is a single |mgr|\SR measurement.
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A run is analyzed by a number of parameters (defined in the msr-files), and complemented by
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additional physical parameters as the temperature, magnetic field, implantation energy, etc.
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Hence parameters can be seen as vectors and can be plot against each other.
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.. index:: mupp-gui
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The Graphical User Interface
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@ -52,10 +57,30 @@ A typical setting could look like this
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11. ``Remove Collection``: will remove the selected collection
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12. ``Refresh Collection``: will reload the collection (``db``- or ``dat``-file). This is often useful
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during beamtime where the collection is growing run-by-run.
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13. This is the script command line. Currently it allows to perform the tasks without mouse gambling.
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13. Command history window.
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14. This is the script command line. Currently it allows to perform the tasks without mouse gambling.
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In the future much more commands are planed. See the ``Help / Cmd's`` for the currently available
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commands.
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Define Variable Dialog
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++++++++++++++++++++++
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.. image:: ../images/mupp-add-var.*
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1. Variable text edit window.
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2. Collection link window.
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3. Shows the parameters of the selected collection.
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4. Check if the variable/error variable from the edit window is valid.
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5. Add the variable to the selected collection(s) if the parsing is successful.
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A variable defined here is a mathematical expression defined by parameters of loaded collections.
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Since a parameter also has an associated error, also newly defined variables **always** need
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to be defined together with a corresponding error variable. If the name of a variable is defined
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as ``SigmaSC_10`` (see the above snapshot), the error variable need to be named as ``SigmaSC_10Err``.
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Currently the following mathematical functions are defined: ``max``, ``min``, ``abs``, ``sin``, ``cos``,
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``tan``, ``exp``, ``log``, ``ln``, ``pow``.
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.. index:: mupp-scripting
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The Scripting Interface
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@ -78,11 +103,14 @@ or web-based interaction which requests figures. A script is invoked by the comm
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selects collection ``<nn>``, where ``<nn>`` is either the *number* of the collections, or its *name*, *e.g.*
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select YBCO-40nm-T5K-FC150mT-Escan.db.
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**addX <label>**
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**x <label>**
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add ``<label>`` as a *x*-variable. Only *one* is allowed.
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**addY <label(s)>**
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add ``<label(s)>`` as *y*-variable. *Multiple* labels are possible.
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**y <label(s)>**
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add ``<label(s)>`` as *y*-variable. *Multiple* labels are possible.
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**norm**
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this will normalize all the *y*-variables by their maximum.
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**savePath <dir>**
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set the save path to ``<dir>``. The place where the macros, and/or the plot output will be saved.
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@ -93,32 +121,71 @@ or web-based interaction which requests figures. A script is invoked by the comm
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**macro <fln>**
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where ``<fln>`` is the file name under which the root macro should be saved.
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An example script file ``field-vs-energy.txt`` might look like this:
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**var <var_name> = <expr>**
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defines a variable.
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<expr> is a mathematical expression where collection variables are addressed
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via the '$', e.g. ``dataT`` is addressed by ``$dataT``, etc. An example:
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``var invT = 1000.0 / $dataT``
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Each variable has to be accompanied by its error variable. An error variable
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is defined by the ``<var_name>`` followed by ``Err``
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For the above example the error variable is
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``var invTErr = $invT * $dataTErr / $dataT``
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**col <nn> : <var_name>**
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links <var_name> to the collection <nn>, where <nn> is the number of the
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collection as defined by the order of load, starting with 0.
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An example script file ``sigmaSC-vs-temp.txt`` might look like this:
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::
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# This is a comment
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# Script: sigmaSC-vs-temp.txt
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loadPath ./
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load YBCO-40nm-T5K-FC150mT-Escan.db
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load YBCO-40nm-T30K-FC150mT-Escan.db
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load YBCO-40nm-T60K-FC150mT-Escan.db
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load YBCO-40nm-T120K-FC150mT-Escan.db
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load YBCO-40nm-FC-E3p8keV-B10mT-Tscan.db # collection 0
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load YBCO-40nm-FC-E3p8keV-B150mT-Tscan.db # collection 1
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selectAll
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# define variables: for each variable an associated error variable is needed.
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# B=10mT
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var SigmaSC_10 = pow(abs(pow($Sigma,2.0)-pow(0.11,2.0)), 0.5) # 0.11 (1/us) is the nuclear contribution (T>Tc)
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var SigmaSC_10Err = pow(pow($Sigma*$SigmaErr,2.0)+pow(0.11*0.0025,2.0), 0.5)/$SigmaSC_10
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# B=150mT
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var SigmaSC_150 = pow(abs(pow($Sigma,2.0)-pow(0.075,2.0)), 0.5) # 0.075 (1/us) is the nuclear contribution (T>Tc)
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var SigmaSC_150Err = pow(pow($Sigma*$SigmaErr,2.0)+pow(0.075*0.0025,2.0), 0.5)/$SigmaSC_150
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addX dataE
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addY Field
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# link variables to collections
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col 0 : SigmaSC_10 # error variable SigmaSC_10Err doesn't need to be given, it is automatically linked to SigmaSC_10
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col 1 : SigmaSC_150
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norm # normalize the plot to the maximum of each y-data-set
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# the next 3 cmds means the following: use collection 0, add dataT to the x-axis,
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# and SigmaSC_10 to the y-axis
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select 0
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x dataT
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y SigmaSC_10
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select 1
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x dataT
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y SigmaSC_150
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# where to save the output
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savePath ./
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plot FieldVsEnergy.pdf
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# create a pdf output file of the above defined xy-data sets. Currently also
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# other file formats are supported, like png, jpg, etc.
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plot SigmaSCVsTemp.pdf
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macro FieldVsEnergy.C
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# creates a ROOT macro which can be used for further refinement
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macro SigmaSCVsTemp.C
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# end
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.. index:: mupp-usage
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.. _mupp-usage:
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@ -137,30 +204,35 @@ The Usage Summary
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<fit-param-file-names>: list of file name(s) to be loaded.
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allowed formats are: db, dat, msr
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SCRIPT COMMANDS:
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Lines starting with '#', '%', or '//' are comments and will be ignored.
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The same is true for empty lines. Comments are also allowed at the end
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for a command, i.e. loadPath ./ # the best place ever.
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loadPath <dir> : set the load path to <dir>. Bash variables like
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$HOME are accepted.
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load <coll> : will load a collection <coll>. Currently *.db and *.dat
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are handled.
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selectAll : will select all loaded collections. Thie means every plot
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of variable x/y will be carried out to ALL collections.
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select <nn> : selects collection <nn>, where <nn> is either the number
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of the collections, or its name, e.g.
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select YBCO-40nm-T5K-FC150mT-Escan.db
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addX <label> : add <label> as a x-variable. Only one is allowed.
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addY <label(s)>: add <label(s)> as y-variable. Multiple labls are possible.
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savePath <dir> : set the save path to <dir>. The place where the macros,
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and/or the plot output will be saved.
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plot <fln> : where <fln> is the file name with extension under which
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the plot should be saved.
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macro <fln> : where <fln> is the file name under which the root macro
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should be saved.
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Lines starting with '#', '%', or '//' are comments and will be ignored.
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The same is true for empty lines. Comments are also allowed at the end
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for a command, i.e. loadPath ./ # the best place ever.
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load <coll> : load a collection. <coll> is the filename of the
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collection (*.db, *.dat)
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loadPath <path> : set the load path to <path>; accepting bash variables
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like $HOME, etc.
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x <var-name> : set a x-axis variable. <var-name> is a data tag of
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the db/dat-file.
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y <var-name> : set a y-axis variable. <var-name> is a data tag of
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the db/dat-file.
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select <nn> : select collection <nn>, where <nn> is the row-number
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or the name of the collection to be selected.
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selectAll : i.e. already set 'x', 'y' will apply to ALL collections
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present.
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savePath <path> : sets the save path to <path>; accepting bash variables
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like $HOME, etc.
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plot <fln> : where <fln> is the file name with extension under which
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the plot should be saved.
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macro <fln> : where <fln> is the file name under which the root macro
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should be saved.
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var <var_name> = <expr> : defines a variable.
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<expr> is a mathematical expression where
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collection variables are addressed via the '$',
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e.g. dataT is addressed by $dataT, etc.
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col <nn> : <var_name> : links <var_name> to the collection <nn>, where
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<nn> is the number of the collection as defined
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by the order of load, starting with 0.
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