mystic scripts documentation

mystic_collapse_plotter script

generate convergence plots of | cost - cost_min | from convergence logfile

Available from the command shell as:

mystic_collapse_plotter filename [options]

or as a function call:

mystic.collapse_plotter(filename, **options)

param filename:: name of the convergence logfile (e.g paramlog.py).
type filename:: str
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 legend takes a boolean, and will display the legend.
The option nid takes an integer of the nth simultaneous points 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).

collapse_plotter(filename, **kwds)

generate convergence plots of | cost - cost_min | from convergence logfile

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 legend takes a boolean, and will display the legend.
The option nid takes an integer of the nth simultaneous points 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

generate parameter convergence plot from convergence logfile

Available from the command shell as:

mystic_log_reader filename [options]

or as a function call:

mystic.log_reader(filename, **options)

param filename:: name of the convergence logfile (e.g log.txt).
type filename:: str
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.

log_reader(filename, **kwds)

generate parameter convergence plot from convergence logfile

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_log_converter script

convert between cached archives, convergence logfiles, and support logfiles

Available from the command shell as:

mystic_log_converter readpath (writepath) [options]

or as a function call:

mystic.log_converter(readpath, writepath=None, **options)

param readpath:: path of the logfile (e.g paramlog.py).
type readpath:: str
param writepath:: path of converted file (e.g. log.txt).
type writepath:: str, default=None
returns:: None

Notes

If writepath is None, write file with derived name to current directory.
The option format takes a string name of the file format at writepath. Available formats are (‘logfile’, ‘support’, or a klepto.archive type).

log_converter(readpath, writepath=None, **kwds)

convert between cached archives, convergence logfiles, and support logfiles

Available from the command shell as:

mystic_log_converter readpath (writepath) [options]

or as a function call:

mystic.log_converter(readpath, writepath=None, **options)

Parameters:

readpath (str) – path of the logfile (e.g paramlog.py).
writepath (str, default=None) – path of converted file (e.g. log.txt).

Returns:

None

Notes

If writepath is None, write file with derived name to current directory.
The option format takes a string name of the file format at writepath. Available formats are (‘logfile’, ‘support’, or a klepto.archive type).

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)

param model:: full import path for the model (e.g. mystic.models.rosen)
type model:: str
param logfile:: name of convergence logfile (e.g. log.txt)
type logfile:: str, default=None
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.

model_plotter(model, logfile=None, **kwds)

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)

param filename:: name of the convergence logfile (e.g paramlog.py)
type filename:: str
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 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.

convergence(filename, **kwds)

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

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 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)

param filename:: name of the convergence logfile (e.g paramlog.py)
type filename:: str
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 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.

hypercube(filename, **kwds)

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

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 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)

param filename:: name of the convergence logfile (e.g paramlog.py)
type filename:: str
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 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.

hypercube_measures(filename, **kwds)

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

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 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)

param filename:: name of the convergence logfile (e.g. paramlog.py)
type filename:: str
param datafile:: name of the dataset file (e.g. data.txt)
type datafile:: str, default=None
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 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.

hypercube_scenario(filename, datafile=None, **kwds)

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

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 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.