# mystic scripts documentation¶

## mystic_collapse_plotter script¶

generate cost convergence rate plots from file written with `write_support_file`

Available from the command shell as:

```
mystic_collapse_plotter filename [options]
```

or as a function call:

```
mystic.collapse_plotter(filename, **options)
```

- Parameters
**filename**(*str*) – name of the convergence logfile (e.g`paramlog.py`

).- returns
None

Notes

The option

*dots*takes a boolean, and will show data points in the plot.The option

*linear*takes a boolean, and will plot in a linear scale.The option

*out*takes a string of the filepath for the generated plot. If`out = True`

, return the Figure object instead of generating a plot.The option

*iter*takes an integer of the largest iteration to plot.The option

*label*takes a label string. For example,`label = "y"`

will label the plot with a ‘y’, while`label = " log-cost, $ log_{10}(\hat{P} - \hat{P}_{max})$"`

will label the y-axis with standard LaTeX math formatting. Note that the leading space is required, and that the text is aligned along the axis.The option

*col*takes a string of comma-separated integers indicating iteration numbers where parameter collapse has occurred. If a second set of integers is provided (delineated by a semicolon), the additional set of integers will be plotted with a different linestyle (to indicate a different type of collapse).

## mystic_log_reader script¶

plot parameter convergence from file written with `LoggingMonitor`

Available from the command shell as:

```
mystic_log_reader filename [options]
```

or as a function call:

```
mystic.log_reader(filename, **options)
```

- Parameters
**filename**(*str*) – name of the convergence logfile (e.g`log.txt`

).- returns
None

Notes

The option

*out*takes a string of the filepath for the generated plot. If`out = True`

, return the Figure object instead of generating a plot.The option

*dots*takes a boolean, and will show data points in the plot.The option

*line*takes a boolean, and will connect the data with a line.The option

*iter*takes an integer of the largest iteration to plot.The option

*legend*takes a boolean, and will display the legend.The option

*nid*takes an integer of the nth simultaneous points to plot.The option

*param*takes an indicator string. The indicator string is built from comma-separated array slices. For example,`param = ":"`

will plot all parameters. Alternatively,`param = ":2, 3:"`

will plot all parameters except for the third parameter, while`param = "0"`

will only plot the first parameter.

## mystic_model_plotter script¶

generate surface contour plots for model, specified by full import path; and generate model trajectory from logfile (or solver restart file), if provided

Available from the command shell as:

```
mystic_model_plotter model (logfile) [options]
```

or as a function call:

```
mystic.model_plotter(model, logfile=None, **options)
```

- Parameters
**model**(*str*) – full import path for the model (e.g.`mystic.models.rosen`

)**logfile**(*str, default=None*) – name of convergence logfile (e.g.`log.txt`

)

- returns
None

Notes

The option

*out*takes a string of the filepath for the generated plot. If`out = True`

, return the Figure object instead of generating a plot.The option

*bounds*takes an indicator string, where bounds are given as comma-separated slices. For example, using`bounds = "-1:10, 0:20"`

will set lower and upper bounds for x to be (-1,10) and y to be (0,20). The “step” can also be given, to control the number of lines plotted in the grid. Thus`"-1:10:.1, 0:20"`

sets the bounds as above, but uses increments of .1 along x and the default step along y. For models > 2D, the bounds can be used to specify 2 dimensions plus fixed values for remaining dimensions. Thus,`"-1:10, 0:20, 1.0"`

plots the 2D surface where the z-axis is fixed at z=1.0. When called from a script, slice objects can be used instead of a string, thus`"-1:10:.1, 0:20, 1.0"`

becomes`(slice(-1,10,.1), slice(20), 1.0)`

.The option

*label*takes comma-separated strings. For example,`label = "x,y,"`

will place ‘x’ on the x-axis, ‘y’ on the y-axis, and nothing on the z-axis. LaTeX is also accepted. For example,`label = "$ h $, $ {\alpha}$, $ v$"`

will label the axes with standard LaTeX math formatting. Note that the leading space is required, while a trailing space aligns the text with the axis instead of the plot frame.The option

*nid*takes an integer of the nth simultaneous points to plot.The option

*iter*takes an integer of the largest iteration to plot.The option

*reduce*can be given to reduce the output of a model to a scalar, thus converting`model(params)`

to`reduce(model(params))`

. A reducer is given by the import path (e.g.`numpy.add`

).The option

*scale*will convert the plot to log-scale, and scale the cost by`z=log(4*z*scale+1)+2`

. This is useful for visualizing small contour changes around the minimium.If using log-scale produces negative numbers, the option

*shift*can be used to shift the cost by`z=z+shift`

. Both*shift*and*scale*are intended to help visualize contours.The option

*fill*takes a boolean, to plot using filled contours.The option

*depth*takes a boolean, to plot contours in 3D.The option

*dots*takes a boolean, to show trajectory points in the plot.The option

*join*takes a boolean, to connect trajectory points.The option

*verb*takes a boolean, to print the model documentation.The option

*kernel*can be given to transform the input of a model from nD to 2D, where`params' = model(params)`

with`params'`

being 2D. A kernel is given by the import path (e.g.`mymodule.kernel`

). Using kernel can be slow, as it may calcuate inverse transform at each point.The option

*tol*takes a float of max distance of dots from surface. For finer control, provide an array[float] the same length as`params`

.

## support_convergence script¶

generate parameter convergence plots from file written with `write_support_file`

Available from the command shell as:

```
support_convergence filename [options]
```

or as a function call:

```
mystic.support.convergence(filename, **options)
```

- Parameters
**filename**(*str*) – name of the convergence logfile (e.g`paramlog.py`

)- returns
None

Notes

*out*takes a string of the filepath for the generated plot. If`out = True`

, return the Figure object instead of generating a plot.The option

*iter*takes an integer of the largest iteration to plot.The option

*param*takes an indicator string. The indicator string is built from comma-separated array slices. For example,`param = ":"`

will plot all parameters in a single plot. Alternatively,`param = ":2, 2:"`

will split the parameters into two plots, and`param = "0"`

will only plot the first parameter.The option

*label*takes comma-separated strings. For example,`label = "x,y,"`

will label the y-axis of the first plot with ‘x’, a second plot with ‘y’, and not add a label to a third or subsequent plots. If more labels are given than plots, then the last label will be used for the y-axis of the ‘cost’ plot. LaTeX is also accepted. For example,`label = "$ h$, $ a$, $ v$"`

will label the axes with standard LaTeX math formatting. Note that the leading space is required, and the text is aligned along the axis.The option

*nid*takes an integer of the nth simultaneous points to plot.The option

*cost*takes a boolean, and will also plot the parameter cost.The option

*legend*takes a boolean, and will display the legend.

## support_hypercube script¶

generate parameter support plots from file written with `write_support_file`

Available from the command shell as:

```
support_hypercube filename [options]
```

or as a function call:

```
mystic.support.hypercube(filename, **options)
```

- Parameters
**filename**(*str*) – name of the convergence logfile (e.g`paramlog.py`

)- returns
None

Notes

*out*takes a string of the filepath for the generated plot. If`out = True`

, return the Figure object instead of generating a plot.The options

*bounds*,*axes*, and*iters*all take indicator strings. The bounds should be given as comma-separated slices. For example, using`bounds = "60:105, 0:30, 2.1:2.8"`

will set the lower and upper bounds for x to be (60,105), y to be (0,30), and z to be (2.1,2.8). Similarly, axes also accepts comma-separated groups of ints; however, for axes, each entry indicates which parameters are to be plotted along each axis – the first group for the x direction, the second for the y direction, and third for z. Thus,`axes = "2 3, 6 7, 10 11"`

would set 2nd and 3rd parameters along x. Iters also accepts strings built from comma-separated array slices. For example,`iters = ":"`

will plot all iters in a single plot. Alternatively,`iters = ":2, 2:"`

will split the iters into two plots, while`iters = "0"`

will only plot the first iteration.The option

*label*takes comma-separated strings. Thus`label = "x,y,"`

will place ‘x’ on the x-axis, ‘y’ on the y-axis, and nothing on the z-axis. LaTeX, such as`label = "$ h $, $ a$, $ v$"`

will label the axes with standard LaTeX math formatting. Note that the leading space is required, while a trailing space aligns the text with the axis instead of the plot frame.The option

*nid*takes an integer of the nth simultaneous points to plot.The option

*scale*takes an integer as a grayscale contrast multiplier.The option

*flat*takes a boolean, to plot results in a single plot.

## support_hypercube_measures script¶

generate measure support plots from file written with `write_support_file`

Available from the command shell as:

```
support_hypercube_measures filename [options]
```

or as a function call:

```
mystic.support.hypercube_measures(filename, **options)
```

- Parameters
**filename**(*str*) – name of the convergence logfile (e.g`paramlog.py`

)- returns
None

Notes

*out*takes a string of the filepath for the generated plot. If`out = True`

, return the Figure object instead of generating a plot.The options

*bounds*,*axes*,*weight*, and*iters*all take indicator strings. The bounds should be given as comma-separated slices. For example, using`bounds = "60:105, 0:30, 2.1:2.8"`

will set lower and upper bounds for x to be (60,105), y to be (0,30), and z to be (2.1,2.8). Similarly, axes also accepts comma-separated groups of ints; however, for axes, each entry indicates which parameters are to be plotted along each axis – the first group for the x direction, the second for the y direction, and third for z. Thus,`axes = "2 3, 6 7, 10 11"`

would set 2nd and 3rd parameters along x. The corresponding weights are used to color the measure points, where 1.0 is black and 0.0 is white. For example, using`weight = "0 1, 4 5, 8 9"`

would use the 0th and 1st parameters to weight x. Iters is also similar, however only accepts comma-separated ints. Hence,`iters = "-1"`

will plot the last iteration, while`iters = "0, 300, 700"`

will plot the 0th, 300th, and 700th in three plots.The option

*label*takes comma-separated strings. Thus`label = "x,y,"`

will place ‘x’ on the x-axis, ‘y’ on the y-axis, and nothing on the z-axis. LaTeX, such as`label = "$ h $, $ a$, $ v$"`

will label the axes with standard LaTeX math formatting. Note that the leading space is required, while a trailing space aligns the text with the axis instead of the plot frame.The option

*nid*takes an integer of the nth simultaneous points to plot.The option

*scale*takes an integer as a grayscale contrast multiplier.The option

*flat*takes a boolean, to plot results in a single plot.

Warning

This function is intended to visualize weighted measures (i.e. weights and positions), where the weights must be normalized (to 1) or an error will be thrown.

## support_hypercube_scenario script¶

generate scenario support plots from file written with `write_support_file`

;
and generate legacy data and cones from a dataset file, if provided

Available from the command shell as:

```
support_hypercube_scenario filename (datafile) [options]
```

or as a function call:

```
mystic.support.hypercube_scenario(filename, datafile=None, **options)
```

- Parameters
**filename**(*str*) – name of the convergence logfile (e.g.`paramlog.py`

)**datafile**(*str, default=None*) – name of the dataset file (e.g.`data.txt`

)

- returns
None

Notes

*out*takes a string of the filepath for the generated plot. If`out = True`

, return the Figure object instead of generating a plot.The options

*bounds*,*dim*, and*iters*all take indicator strings. The bounds should be given as comma-separated slices. For example, using`bounds = ".062:.125, 0:30, 2300:3200"`

will set lower and upper bounds for x to be (.062,.125), y to be (0,30), and z to be (2300,3200). If all bounds are to not be strictly enforced, append an asterisk`*`

to the string. The dim (dimensions of the scenario) should comma-separated ints. For example,`dim = "1, 1, 2"`

will convert the params to a two-member 3-D dataset. Iters accepts a string built from comma-separated array slices. Thus,`iters = ":"`

will plot all iters in a single plot. Alternatively,`iters = ":2, 2:"`

will split the iters into two plots, while`iters = "0"`

will only plot the first iteration.The option

*label*takes comma-separated strings. Thus`label = "x,y,"`

will place ‘x’ on the x-axis, ‘y’ on the y-axis, and nothing on the z-axis. LaTeX, such as`label = "$ h $, $ a$, $ v$"`

will label the axes with standard LaTeX math formatting. Note that the leading space is required, while a trailing space aligns the text with the axis instead of the plot frame.The option “filter” is used to select datapoints from a given dataset, and takes comma-separated ints.

A “mask” is given as comma-separated ints. When the mask has more than one int, the plot will be 2D.

The option “vertical” will plot the dataset values on the vertical axis; for 2D plots, cones are always plotted on the vertical axis.

The option

*nid*takes an integer of the nth simultaneous points to plot.The option

*scale*takes an integer as a grayscale contrast multiplier.The option

*gap*takes an integer distance from cone center to vertex.The option

*data*takes a boolean, to plot legacy data, if provided.The option

*cones*takes a boolean, to plot cones, if provided.The option

*flat*takes a boolean, to plot results in a single plot.