Nodes¶
Data¶
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class
mesmerize.pyqtgraphCore.flowchart.library.Data.
DropNa
(*args, **kwargs)[source]¶ Drop NaNs from the DataFrame
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class
mesmerize.pyqtgraphCore.flowchart.library.Data.
LoadFile
(name)[source]¶ Load Transmission data object from pickled file
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class
mesmerize.pyqtgraphCore.flowchart.library.Data.
LoadProjDF
(name)[source]¶ Load raw project DataFrames as Transmission
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class
mesmerize.pyqtgraphCore.flowchart.library.Data.
NormRaw
(name, ui=None, terminals=None, **kwargs)[source]¶ Normalize between raw min and max values.
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class
mesmerize.pyqtgraphCore.flowchart.library.Data.
PadArrays
(name, ui=None, terminals=None, **kwargs)[source]¶ Pad 1-D numpy arrays in a particular column
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class
mesmerize.pyqtgraphCore.flowchart.library.Data.
Save
(name)[source]¶ Save Transmission data object
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class
mesmerize.pyqtgraphCore.flowchart.library.Data.
SelectColumns
(name, ui=None, terminals=None, **kwargs)[source]¶
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class
mesmerize.pyqtgraphCore.flowchart.library.Data.
SelectRows
(name, ui=None, terminals=None, **kwargs)[source]¶
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class
mesmerize.pyqtgraphCore.flowchart.library.Data.
SpliceArrays
(name, ui=None, terminals=None, **kwargs)[source]¶ Splice 1-D numpy arrays in a particular column.
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class
mesmerize.pyqtgraphCore.flowchart.library.Data.
TextFilter
(name, ui=None, terminals=None, **kwargs)[source]¶ Simple string filtering in a specified column
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class
mesmerize.pyqtgraphCore.flowchart.library.Data.
ViewHistory
(*args, **kwargs)[source]¶ View History Trace of the input Transmission
Display¶
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class
mesmerize.pyqtgraphCore.flowchart.library.Display.
AnalysisGraph
(name)[source]¶ Graph of the analysis log
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class
mesmerize.pyqtgraphCore.flowchart.library.Display.
BeeswarmPlots
(name)[source]¶ Beeswarm and Violin plots
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class
mesmerize.pyqtgraphCore.flowchart.library.Display.
FrequencyDomainMagnitude
(name, ui=None, terminals=None, **kwargs)[source]¶ Plot Frequency vs. Frequency Domain Magnitude
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class
mesmerize.pyqtgraphCore.flowchart.library.Display.
Heatmap
(name)[source]¶ Stack 1-D arrays and plot visually like a heatmap
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class
mesmerize.pyqtgraphCore.flowchart.library.Display.
Plot
(name)[source]¶ Plot curves and/or scatter points
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class
mesmerize.pyqtgraphCore.flowchart.library.Display.
Proportions
(name)[source]¶ Plot proportions of one categorical column vs another
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class
mesmerize.pyqtgraphCore.flowchart.library.Display.
ScatterPlot
(name)[source]¶ Scatter Plot, useful for visualizing transformed data and clusters
Signal¶
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class
mesmerize.pyqtgraphCore.flowchart.library.Signal.
ButterWorth
(name, ui=None, terminals=None, **kwargs)[source]¶ Butterworth Filter
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class
mesmerize.pyqtgraphCore.flowchart.library.Signal.
Normalize
(name, ui=None, terminals=None, **kwargs)[source]¶ Normalize a column containing 1-D arrays such that values in each array are normalized between 0 and 1
Output Column -> Input Column
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class
mesmerize.pyqtgraphCore.flowchart.library.Signal.
PeakDetect
(name, **kwargs)[source]¶ Detect peaks & bases by finding local maxima & minima. Use this after the Derivative Filter
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class
mesmerize.pyqtgraphCore.flowchart.library.Signal.
PeakFeatures
(*args, **kwargs)[source]¶ Extract peak features after peak detection
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class
mesmerize.pyqtgraphCore.flowchart.library.Signal.
PowerSpectralDensity
(name, ui=None, terminals=None, **kwargs)[source]¶ Return the Power Spectral Density of a curve.
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class
mesmerize.pyqtgraphCore.flowchart.library.Signal.
RFFT
(name, ui=None, terminals=None, **kwargs)[source]¶ Uses fftpack.rfft, ‘Discrete Fourier transform of a real sequence.
https://docs.scipy.org/doc/scipy/reference/generated/scipy.fftpack.rfft.html#scipy.fftpack.rfft
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class
mesmerize.pyqtgraphCore.flowchart.library.Signal.
Resample
(name, ui=None, terminals=None, **kwargs)[source]¶ Resample 1D data, uses scipy.signal.resample. “Rs” is the new sampling rate in “Tu” units of time. If “Tu” = 1, then Rs is the new sampling rate in Hertz.
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class
mesmerize.pyqtgraphCore.flowchart.library.Signal.
SavitzkyGolay
(name, ui=None, terminals=None, **kwargs)[source]¶ Savitzky-Golay filter.
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class
mesmerize.pyqtgraphCore.flowchart.library.Signal.
ScalerMeanVariance
(name, ui=None, terminals=None, **kwargs)[source]¶ Scaler for time series. Scales time series so that their mean (resp. standard deviation) in each dimension is mu (resp. std).
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class
mesmerize.pyqtgraphCore.flowchart.library.Signal.
SigmaMAD
(name, ui=None, terminals=None, **kwargs)[source]¶
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class
mesmerize.pyqtgraphCore.flowchart.library.Signal.
iRFFT
(name, ui=None, terminals=None, **kwargs)[source]¶ Uses fftpack.irfft, ‘Return inverse discrete Fourier transform of real sequence.’
https://docs.scipy.org/doc/scipy/reference/generated/scipy.fftpack.irfft.html#scipy.fftpack.irfft
Input must have an _RFFT column from the RFFT node.
Math¶
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class
mesmerize.pyqtgraphCore.flowchart.library.Math.
AbsoluteValue
(name, ui=None, terminals=None, **kwargs)[source]¶ Performs numpy.abs(<input>). Returns root-mean-square value if <input> is complex
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class
mesmerize.pyqtgraphCore.flowchart.library.Math.
ArgGroupStat
(name, ui=None, terminals=None, **kwargs)[source]¶ Group by a certain column and return value of another column based on a data column statistic
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class
mesmerize.pyqtgraphCore.flowchart.library.Math.
ArrayStats
(name, ui=None, terminals=None, **kwargs)[source]¶ Perform various statistical functions
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class
mesmerize.pyqtgraphCore.flowchart.library.Math.
Derivative
(name, ui=None, terminals=None, **kwargs)[source]¶ Return the Derivative of a curve.
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class
mesmerize.pyqtgraphCore.flowchart.library.Math.
Integrate
(name, ui=None, terminals=None, **kwargs)[source]¶
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class
mesmerize.pyqtgraphCore.flowchart.library.Math.
LinRegress
(name, ui=None, terminals=None, **kwargs)[source]¶ Linear Regression
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class
mesmerize.pyqtgraphCore.flowchart.library.Math.
LogTransform
(name, ui=None, terminals=None, **kwargs)[source]¶ Can perform various log transforms
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class
mesmerize.pyqtgraphCore.flowchart.library.Math.
TVDiff
(name, ui=None, terminals=None, **kwargs)[source]¶ Total Variation Regularized Numerical Differentiation, Chartrand 2011 method
Biology¶
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class
mesmerize.pyqtgraphCore.flowchart.library.Biology.
ExtractStim
(name, ui=None, terminals=None, **kwargs)[source]¶ Extract portions of curves according to stimulus maps
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class
mesmerize.pyqtgraphCore.flowchart.library.Biology.
ManualDFoF
(name, ui=None, terminals=None, **kwargs)[source]¶ Set Fo for dF/Fo using a particular time period. Useful for looking at stimulus responses
Clustering¶
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class
mesmerize.pyqtgraphCore.flowchart.library.Clustering.
KMeans
(name, ui=None, terminals=None, **kwargs)[source]¶ KMeans clustering https://scikit-learn.org/stable/modules/generated/sklearn.cluster.KMeans.html
Output column -> KMEANS_CLUSTER_<data_column>
Hierarchical¶
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class
mesmerize.pyqtgraphCore.flowchart.library.Hierarchical.
FCluster
(name, **kwargs)[source]¶ Basically scipy.cluster.hierarchy.fcluster. Form flat clusters from the hierarchical clustering defined by the given linkage matrix.
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class
mesmerize.pyqtgraphCore.flowchart.library.Hierarchical.
Inconsistent
(name)[source]¶ Calculate inconsistency statistics on a linkage matrix. Returns inconsistency matrix
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class
mesmerize.pyqtgraphCore.flowchart.library.Hierarchical.
Linkage
(name, ui=None, terminals=None, **kwargs)[source]¶ Basically scipy.cluster.hierarchy.linkage Compute a linkage matrix for Hierarchical clustering
Transform¶
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class
mesmerize.pyqtgraphCore.flowchart.library.Transform.
LDA
(name, **kwargs)[source]¶ Linear Discriminant Analysis, uses sklearn
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class
mesmerize.pyqtgraphCore.flowchart.library.Transform.
Manifold
(name, ui=None, terminals=None, **kwargs)[source]¶ Manifold learning
CtrlNode¶
Base for all nodes
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class
mesmerize.pyqtgraphCore.flowchart.library.common.
CtrlNode
(name, ui=None, terminals=None, **kwargs)[source]¶ Abstract class for nodes with auto-generated control UI
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ctrlWidget
()[source]¶ Return this Node’s control widget.
By default, Nodes have no control widget. Subclasses may reimplement this method to provide a custom widget. This method is called by Flowcharts when they are constructing their Node list.
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process
(**kwargs)[source]¶ Process data through this node. This method is called any time the flowchart wants the node to process data. It will be called with one keyword argument corresponding to each input terminal, and must return a dict mapping the name of each output terminal to its new value.
This method is also called with a ‘display’ keyword argument, which indicates whether the node should update its display (if it implements any) while processing this data. This is primarily used to disable expensive display operations during batch processing.
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saveState
()[source]¶ Return a dictionary representing the current state of this node (excluding input / output values). This is used for saving/reloading flowcharts. The default implementation returns this Node’s position, bypass state, and information about each of its terminals.
Subclasses may want to extend this method, adding extra keys to the returned dict.
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