Data

This page describes the main data object that are used by ClusterKinG. If you do not need to include errors in your analysis, use Data, else DataWithErrors (which inherits from Data but adds additional methods to it).

Both classes inherit from a very basic class, DFMD, which provides basic input and output methods.

DFMD

class clusterking.data.DFMD(path: Optional[Union[str, pathlib.PurePath]] = None, log: Optional[Union[str, logging.Logger]] = None)[source]

Bases: object

DFMD = DataFrame with MetaData. This class bundles a pandas dataframe together with metadata and provides methods to save and load such an object.

__init__(path: Optional[Union[str, pathlib.PurePath]] = None, log: Optional[Union[str, logging.Logger]] = None)[source]

Initialize a DFMD object.

Parameters
  • path – Optional: load from this file (specified as string or pathlib.PurePath)

  • log – Optional: instance of logging.Logger or name of logger to be created

md

This will hold all the configuration that we will write out

df

pandas.DataFrame to hold all of the results

log

Instance of logging.Logger

write(path: Union[str, pathlib.PurePath], overwrite='ask')[source]

Write output files.

Parameters
  • path – Path to output file

  • overwrite – How to proceed if output file already exists: ‘ask’ (ask interactively for approval if we have to overwrite), ‘overwrite’ (overwrite without asking), ‘raise’ (raise Exception if file exists). Default is ‘ask’.

Returns

None

copy(deep=True, data=True, memo=None)[source]

Make a copy of this object.

Parameters
  • deep – Make a deep copy (default True). If this is disabled, any change to the copy will also affect the original.

  • data – Also copy data

  • memo

Returns

New object.

Data

class clusterking.data.Data(*args, **kwargs)[source]

Bases: clusterking.data.dfmd.DFMD

This class inherits from the DFMD class and adds additional methods to it. It is the basic container, that contains

  • The distributions to cluster

  • The cluster numbers after clustering

  • The benchmark points after they are selected.

__init__(*args, **kwargs)[source]
property bin_cols: List[str]

All columns that correspond to the bins of the distribution. This is automatically read from the metadata as set in e.g. clusterking.scan.Scanner.run().

property par_cols: List[str]

All columns that correspond to the parameters (e.g. Wilson parameters). This is automatically read from the metadata as set in e.g. the clusterking.scan.Scanner.run().

property n: int

Number of points in parameter space that were sampled.

property nbins: int

Number of bins of the distribution.

property npars: int

Number of parameters that were sampled (i.e. number of dimensions of the sampled parameter space.

data(normalize=False) numpy.ndarray[source]

Returns all histograms as a large matrix.

Parameters

normalize – Normalize all histograms

Returns

numpy.ndarray of shape self.n x self.nbins

norms() numpy.ndarray[source]

Returns a vector of all normalizations of all histograms (where each histogram corresponds to one sampled point in parameter space).

Returns

numpy.ndarray of shape self.n

clusters(cluster_column='cluster') List[Any][source]

Return list of all cluster names (unique)

Parameters

cluster_column – Column that contains the cluster names

get_param_values(param: Union[None, str] = None)[source]

Return all unique values of this parameter

Parameters

param – Name of parameter. If none is given, instead return a dictionary mapping of parameters to their values.

Returns:

only_bpoints(bpoint_column='bpoint', inplace=False)[source]

Keep only the benchmark points as sample points.

Parameters
  • bpoint_column – benchmark point column (boolean)

  • inplace – If True, the current Data object is modified, if False, a new copy of the Data object is returned.

Returns

None or Data

fix_param(inplace=False, bpoints=False, bpoint_slices=False, bpoint_column='bpoint', **kwargs)[source]

Fix some parameter values to get a subset of sample points.

Parameters
  • inplace – Modify this Data object instead of returning a new one

  • bpoints – Keep bpoints (no matter if they are selected by the other selection or not)

  • bpoint_slices – Keep all parameter values that are attained by benchmark points.

  • bpoint_column – Column with benchmark points (default ‘bpoints’) (for use with the bpoints option)

  • **kwargs – Specify parameter values: Use <parameter name>=<value> or <parameter name>=[<value1>, ..., <valuen>].

Returns

If inplace == False, return new Data with subset of sample points.

Examples:

d = Data("/path/to/tutorial/csv/folder", "tutorial_basics")

Return a new Data object, keeping the two values CT_bctaunutau closest to -0.75 or 0.5

d.fix_param(CT_bctaunutau=[-.75, 0.5])

Return a new Data object, where we also fix CSL_bctaunutau to the value closest to -1.0:

d.fix_param(CT_bctaunutau=[-.75, 0.5], CSL_bctaunutau=-1.0)

Return a new Data object, keeping the two values CT_bctaunutau closest to -0.75 or 0.5, but make sure we do not discard any benchmark points in that process:

d.fix_param(CT_bctaunutau=[-.75, 0.5], bpoints=True)

Return a new Data object, keeping the two values CT_bctaunutau closest to -0.75 or 0.5, but keep all values of CT_bctaunutau that are attained by at least one benchmark point:

d.fix_param(CT_bctaunutau=[-.75, 0.5], bpoint_slices=True)

Return a new Data object, keeping only those values of CT_bctaunutau, that are attained by at least one benchmark point:

d.fix_param(CT_bctaunutau=[], bpoint_slice=True)
sample_param(bpoints=False, bpoint_slices=False, bpoint_column='bpoint', inplace=False, **kwargs)[source]

Return a Data object that contains a subset of the sample points (points in parameter space). Similar to Data.fix_param.

Parameters
  • inplace – Modify this Data object instead of returning a new one

  • bpoints – Keep bpoints (no matter if they are selected by the other selection or not)

  • bpoint_slices – Keep all parameter values that are attained by benchmark points

  • bpoint_column – Column with benchmark points (default ‘bpoints’) (for use with the bpoints option)

  • **kwargs – Specify parameter ranges: <coeff name>=(min, max, npoints) or <coeff name>=npoints For each coeff (identified by <coeff name>), select (at most) npoints points between min and max. In total this will therefore result in npoints_{coeff_1} x … x npoints_{coeff_npar} sample points (provided that there are enough sample points available). If a coefficient isn’t contained in the dictionary, this dimension of the sample remains untouched.

Returns

If inplace == False, return new Data with subset of sample points.

Examples:

d = Data("/path/to/tutorial/csv/folder", "tutorial_basics")

Return a new Data object, keeping subsampling CT_bctaunutau closest to 5 values between -1 and 1:

d.sample_param(CT_bctaunutau=(-1, 1, 10))

The same in shorter syntax (because -1 and 1 are the minimum and maximum of the parameter)

d.sample_param(CT_bctaunutau=10)

For the bpoints and bpoint_slices syntax, see the documentation of clusterking.data.Data.fix_param().

sample_param_random(inplace=False, bpoints=False, bpoint_column='bpoint', **kwargs)[source]

Random subsampling in parameter space.

Parameters
  • inplace – Modify this Data object instead of returning a new one

  • bpoints – Keep bpoints (no matter if they are selected by the other selection or not)

  • bpoint_column – Column with benchmark points (default ‘bpoints’) (for use with the bpoints option)

  • **kwargs – Arguments for pandas.DataFrame.sample()

Returns

If inplace == False, return new Data with subset of sample points.

find_closest_spoints(point: Dict[str, float], n=10) clusterking.data.data.Data[source]

Given a point in parameter space, find the closest sampling points to it and return them as a Data object with the corresponding subset of spoints. The order of the rows in the dataframe Data.df will be in order of increasing parameter space distance from the given point.

Parameters
  • point – Dictionary of parameter name to value

  • n – Maximal number of rows to return

Returns

Data object with subset of rows of dataframe corresponding to the closest points in parameter space.

find_closest_bpoints(point: Dict[str, float], n=10, bpoint_column='bpoint')[source]

Given a point in parameter space, find the closest benchmark points to it and return them as a Data object with the corresponding subset of benchmark points. The order of the rows in the dataframe Data.df will be in order of increasing parameter space distance from the given point.

Parameters
  • point – Dictionary of parameter name to value

  • n – Maximal number of rows to return

  • bpoint_column – Column name of the benchmark column

Returns

Data object with subset of rows of dataframe corresponding to the closest points in parameter space.

configure_variable(variable, axis_label=None)[source]

Set additional information for variables, e.g. the variable on the x axis of the plots of the distribution or the parameters.

Parameters
  • variable – Name of the variable

  • axis_label – An alternate name which will be used on the axes of plots.

rename_clusters(arg=None, column='cluster', new_column=None)[source]

Rename clusters based on either

  1. A dictionary of the form {<old cluster name>: <new cluster name>}

  2. A function that maps the old cluster name to the new cluster name

Example for 2: Say our Data object d contains clusters 1 to 10 in the default column cluster. The following method call will instead use the numbers 0 to 9:

d.rename_clusters(lambda x: x-1)
Parameters
  • arg – Dictionary or function as described above.

  • column – Column that contains the cluster names

  • new_column – New column to write to (default None, i.e. rename in place)

Returns

None

plot_dist(cluster_column='cluster', bpoint_column='bpoint', title: Union[None, str] = None, clusters: Optional[List[int]] = None, nlines=None, bpoints=True, legend=True, ax=None, hist_kwargs: Optional[Dict[str, Any]] = None, hist_kwargs_bp: Optional[Dict[str, Any]] = None)[source]

Plot several examples of distributions for each cluster specified.

Parameters
  • cluster_column – Column with the cluster names (default ‘cluster’)

  • bpoint_column – Column with bpoints (default ‘bpoint’)

  • title – Plot title (None: automatic)

  • clusters – List of clusters to selected or single cluster. If None (default), all clusters are chosen.

  • nlines – Number of example distributions of each cluster to be plotted (default 0)

  • bpoints – Draw benchmark points (default True)

  • legend – Draw legend? (default True)

  • ax – Instance of matplotlib.axes.Axes to plot on. If None, a new one is instantiated.

  • hist_kwargs – Keyword arguments passed on to plot_histogram()

  • hist_kwargs_bp – Like hist_kwargs but used for benchmark points. If None, hist_kwargs is used.

Note: To customize these kind of plots further, check the BundlePlot class and the plot_bundles() method thereof.

Returns

Figure

plot_dist_minmax(cluster_column='cluster', bpoint_column='bpoint', title: Union[None, str] = None, clusters: Optional[List[int]] = None, bpoints=True, legend=True, ax=None, hist_kwargs: Optional[Dict[str, Any]] = None, fill_kwargs: Optional[Dict[str, Any]] = None)[source]

Plot the minimum and maximum of each bin for the specified clusters.

Parameters
  • cluster_column – Column with the cluster names (default ‘cluster’)

  • bpoint_column – Column with bpoints (default ‘bpoint’)

  • title – Plot title (None: automatic)

  • clusters – List of clusters to selected or single cluster. If None (default), all clusters are chosen.

  • bpoints – Draw benchmark points (default True)

  • legend – Draw legend? (default True)

  • ax – Instance of matplotlib.axes.Axes to plot on. If None, a new one is instantiated.

  • hist_kwargs – Keyword arguments to plot_histogram()

  • fill_kwargs – Keyword arguments to`matplotlib.pyplot.fill_between`

Note: To customize these kind of plots further, check the BundlePlot class and the plot_minmax() method thereof.

Returns

Figure

plot_dist_box(cluster_column='cluster', bpoint_column='bpoint', title: Union[None, str] = None, clusters: Optional[List[int]] = None, bpoints=True, whiskers=2.5, legend=True, ax=None, boxplot_kwargs: Optional[Dict[str, Any]] = None, hist_kwargs: Optional[Dict[str, Any]] = None)[source]

Box plot of the bin contents of the distributions corresponding to selected clusters.

Parameters
  • cluster_column – Column with the cluster names (default ‘cluster’)

  • bpoint_column – Column with bpoints (default ‘bpoint’)

  • title – Plot title (None: automatic)

  • clusters – List of clusters to selected or single cluster. If None (default), all clusters are chosen.

  • bpoints – Draw benchmark points (default True)

  • whiskers – Length of the whiskers of the box plot in units of IQR (interquartile range, containing 50% of all values). Default 2.5.

  • legend – Draw legend? (default True)

  • boxplot_kwargs – Arguments to matplotlib.pyplot.boxplot

  • ax – Instance of matplotlib.axes.Axes to plot on. If None, a new one is instantiated.

  • boxplot_kwargs – Keyword arguments to matplotlib.pyplot.boxplot

  • hist_kwargs – Keyword arguments to plot_histogram()

Note: To customize these kind of plots further, check the BundlePlot class and the box_plot() method thereof.

Returns

Figure

plot_clusters_scatter(params=None, clusters=None, cluster_column='cluster', bpoint_column='bpoint', legend=True, max_subplots=16, max_cols=4, markers=('o', 'v', '^', 'v', '<', '>'), figsize=4, aspect_ratio=None)[source]

Create scatter plot, specifying the columns to be on the axes of the plot. If 3 column are specified, 3D scatter plots are presented, else 2D plots. If the dataframe contains more columns, such that each row is not only specified by the columns on the axes, a selection of subplots is created, showing ‘cuts’. Benchmark points are marked by enlarged plot markers.

Parameters
  • params – The names of the columns to be shown on the x, (y, (z)) axis of the plots.

  • clusters – The get_clusters to be plotted (default: all)

  • cluster_column – Column with the cluster names (default ‘cluster’)

  • bpoint_column – Column with bpoints (default ‘bpoint’)

  • legend – Draw legend? (default True)

  • max_subplots – Maximal number of subplots

  • max_cols – Maximal number of columns of the subplot grid

  • markers – List of markers of the get_clusters

  • figsize – Base size of each subplot

  • aspect_ratio – Aspect ratio of 2D plots. If None, will be chosen automatically based on data ranges.

Returns

Figure

plot_clusters_fill(params=None, cluster_column='cluster', bpoint_column='bpoint', legend=True, max_subplots=16, max_cols=4, figsize=4, aspect_ratio=None)[source]

Call this method with two column names, x and y. The results are similar to those of 2D scatter plots as created by the scatter method, except that the coloring is expanded to the whole xy plane. Note: This method only works with uniformly sampled NP!

Parameters
  • params – The names of the columns to be shown on the x, y (and z) axis of the plots.

  • cluster_column – Column with the cluster names (default ‘cluster’)

  • bpoint_column – Column with bpoints (default ‘bpoint’)

  • legend – Draw legend? (default True)

  • max_subplots – Maximal number of subplots

  • max_cols – Maximal number of columns of the subplot grid

  • figsize – Base size of each subplot

  • aspect_ratio – Aspect ratio of 2D plots. If None, will be chosen automatically based on data ranges.

Returns

Figure

plot_bpoint_distance_matrix(cluster_column='cluster', bpoint_column='bpoint', metric='euclidean', ax=None)[source]

Plot the pairwise distances of all benchmark points.

Parameters
  • cluster_column – Column with the cluster names (default ‘cluster’)

  • bpoint_column – Column with bpoints (default ‘bpoint’)

  • metric – String or function. See clusterking.maths.metric.metric_selection(). Default: Euclidean distance.

  • ax – Matplotlib axes or None (automatic)

Returns

Figure

DataWithErrors

class clusterking.data.DataWithErrors(*args, **kwargs)[source]

Bases: clusterking.data.data.Data

This class extends the Data class by convenient and performant ways to add errors to the distributions.

See the description of the Data class for more information about the data structure itself.

There are three basic ways to add errors:

  1. Add relative errors (with correlation) relative to the bin content of each bin in the distribution: add_rel_err_... (\(\mathrm{Cov}^{(k)}_{\text{rel}}(i, j)\))

  2. Add absolute errors (with correlation): add_err_... (\(\mathrm{Cov}^{(k)}_{\text{abs}}(i, j)\))

  3. Add poisson errors: add_err_poisson()

The covariance matrix for bin i and j of distribution n (with contents \(d^{(n)}_i\)) will then be

\[\begin{split}\mathrm{Cov}(d^{(n)}_i, d^{(n)}_j) = &\sum_{k}\mathrm{Cov}_{\text{rel}}^{(k)}(i, j) \cdot d^{(n)}_i d^{(n)}_j + \\ + &\sum_k\mathrm{Cov}_{\text{abs}}^{(k)}(i, j) + \\ + &\delta_{ij} \sqrt{d^{(n)}_i d^{(n)}_j} / \sqrt{s}\end{split}\]

Note

All of these methods add the errors in a consistent way for all sample points/distributions, i.e. it is impossible to add a certain error specifically to one sample point only!

Afterwards, you can get errors, correlation and covariance matrices for every data point by using one of the methods such as cov(), corr(), err().

Note

When saving your dataset, your error configuration is saved as well, so you can reload it like any other Data or DFMD object.

Warning

The appendix of our paper mistakenly hinted at the unit of the relative uncertainties being in percent. This is not the case. That means that d.add_rel_err_uncorr(0.1) adds a 10% relative uncertainty, not 0.1%.

Parameters

data – n x nbins matrix

__init__(*args, **kwargs)[source]
property rel_cov

Relative covariance matrix that will be later applied to the data (see class documentation).

\[\mathrm{Cov}_{\text{rel}}(i, j) = \sum_k\mathrm{Cov}_{\text{rel}}^{(k)}(i, j)\]

If no errors have been added, this is defined to be a zero matrix.

Returns

self.nbins * self.nbins matrix

property abs_cov

Absolute covariance matrix that will be later applied to the data (see class documentation).

\[\mathrm{Cov}_{\text{abs}}(i, j) = \sum_k\mathrm{Cov}_{\text{abs}}^{(k)}(i, j)\]

If no errors have been added, this is defined to be a zero matrix.

Returns

self.nbins * self.nbins matrix

property poisson_errors: bool

Should poisson errors be added?

property poisson_errors_scale: float

Scale poisson errors. See documentation of add_err_poisson().

cov(relative=False) numpy.ndarray[source]

Return covariance matrix \(\mathrm{Cov}(d^{(n)}_i, d^{(n)}_j)\)

If no errors have been added, a zero matrix is returned.

Parameters

relative – “Relative to data”, i.e. \(\mathrm{Cov}(d^{(n)}_i, d^{(n)}_j) / (d^{(n)}_i \cdot d^{(n)}_j)\)

Returns

self.n x self.nbins x self.nbins array

corr() numpy.ndarray[source]

Return correlation matrix. If covariance matrix is empty (because no errors have been added), a unit matrix is returned.

Returns

self.n x self.nbins x self.nbins array

err(relative=False) numpy.ndarray[source]

Return errors per bin, i.e. \(e_i^{(n)} = \sqrt{\mathrm{Cov}(d^{(n)}_i, d^{(n)}_i)}\)

Parameters

relative – Relative errors, i.e. \(e_i^{(n)}/d_i^{(n)}\)

Returns

self.n x self.nbins array

reset_errors() None[source]

Set all errors back to 0.

Returns

None

add_err_cov(cov) None[source]

Add error from covariance matrix.

Parameters

covself.n x self.nbins x self.nbins array of covariance matrices or self.nbins x self.nbins covariance matrix (if equal for all data points)

add_err_corr(err, corr) None[source]

Add error from errors vector and correlation matrix.

Parameters
  • errself.n x self.nbins vector of errors for each data point and bin or self.nbins vector of uniform errors per data point or float (uniform error per bin and datapoint)

  • corrself.n x self.nbins x self.nbins correlation matrices or self.nbins x self.nbins correlation matrix

add_err_uncorr(err) None[source]

Add uncorrelated error.

Parameters

err – see argument of add_err_corr()

add_err_maxcorr(err) None[source]

Add maximally correlated error.

Parameters

err – see argument of add_err_corr()

add_rel_err_cov(cov) None[source]

Add error from “relative” covariance matrix

Parameters

cov – see argument of add_err_cov()

add_rel_err_corr(err, corr) None[source]

Add error from relative errors and correlation matrix. err=0.1 means 10% uncertainty.

Parameters
add_rel_err_uncorr(err) None[source]

Add uncorrelated relative uncertainty. err=0.1 means 10% uncertainty.

Parameters

err – see argument of add_err_corr()

add_rel_err_maxcorr(err) None[source]

Add maximally correlated relative error. err=0.1 means 10% uncertainty.

Parameters

err – see argument of add_err_corr()

add_err_poisson(normalization_scale=1) None[source]

Add poisson errors/statistical errors.

Parameters

normalization_scale – Apply poisson errors corresponding to data normalization scaled up by this factor. For example, if your data is normalized to 1 and you still want to apply Poisson errors that correspond to a yield of 200, you can call add_err_poisson(200). Your data will stay normalized, but the poisson errors are appropriate for a total yield of 200.

Returns

None

plot_dist_err(cluster_column='cluster', bpoint_column='bpoint', title: Union[None, str] = None, clusters: Optional[List[int]] = None, bpoints=True, legend=True, hist_kwargs: Optional[Dict[str, Any]] = None, hist_fill_kwargs: Optional[Dict[str, Any]] = None, ax=None)[source]

Plot distribution with errors.

Parameters
  • cluster_column – Column with the cluster names (default ‘cluster’)

  • bpoint_column – Column with bpoints (default ‘bpoint’)

  • title – Plot title (None: automatic)

  • clusters – List of clusters to selected or single cluster. If None (default), all clusters are chosen.

  • bpoints – Draw benchmark points if available (default True). If false or not benchmark points are available, pick a random sample point for each cluster.

  • legend – Draw legend? (default True)

  • hist_kwargs – Keyword arguments to plot_histogram()

  • hist_fill_kwargs – Keyword arguments to plot_histogram_fill()

  • ax – Instance of matplotlib.axes.Axes to plot on. If None, a new one is instantiated.

Note: To customize these kind of plots further, check the BundlePlot class and the err_plot() method thereof.

Returns

Figure