NDPluginStats

author:

Mark Rivers, University of Chicago

Overview

NDPluginStats computes the following.

1. Basic statistics: minimum, maximum, mean, sigma, total, and net (background subtracted).

2. Centroid, sigma, skewness and kurtosis values in the X and Y dimensions.

3. Profiles of the array in the X and Y dimensions. A total of 8 profiles are calculated:

   • The average profiles in the X and Y directions.

   • The average profiles in the X and Y directions, for array elements greater than the centroid threshold.

   • The profiles in the X and Y directions at the X and Y centroid position.

   • The profiles in the X and Y directions at a user-defined X and Y cursor position.

4. A histogram of the values (e.g. number of pixels versus intensity per pixel).

Each calculcation can be independently enabled and disabled. Calculations 1 and 4 can be perfomed on arrays of any dimension. Calculations 2 and 3 are restricted to 2-D arrays.

Time-series arrays of the basic statistics, centroid and sigma statistics can also be collected. This is very useful for on-the-fly data acquisition, where the NDStats plugin computes the net or total counts in the detector or an ROI. It can also be used to quickly plot a time-history of beam position or width, etc. The time series can also be used in a circular buffer mode where is continuously displays the last N values of the statistic.

NDPluginStats inherits from NDPluginDriver. The NDPluginStats class documentation describes this class in detail.

NDPluginStats.h defines the following parameters. It also implements all of the standard plugin parameters from NDPluginDriver. The EPICS database NDStats.template provide access to these parameters, listed in the following table. Note that to reduce the width of this table the parameter index variable names have been split into 2 lines, but these are just a single name, for example NDPluginStatsComputeStatistics.

		Parameter Definitions in NDPluginStats.h and EPICS Record Definitions in NDStats.template
Parameter index variable	asyn interface	Access	Description	drvInfo string	EPICS record name	EPICS record type
		Basic statistics
NDPluginStats ComputeStatistics	asynInt32	r/w	Flag to control whether to compute statistics for this array (0=No, 1=Yes). Not computing statistics reduces CPU load. Basic statistics computations are quite fast, since they involve mostly double precision addition, with 1 multiply to compute sigma, per array element.	COMPUTE_STATISTICS	$(P)$(R)ComputeStatistics, $(P)$(R)ComputeStatistics_RBV	bo, bi
NDPluginStats BgdWidth	asynInt32	r/w	Width of the background in pixels to use when computing net counts. 0=no background subtraction, so the net counts is the same as the total counts.	BGD_WIDTH	$(P)$(R)BgdWidth, $(P)$(R)BgdWidth_RBV	longout, longin
NDPluginStats MinValue	asynFloat64	r/o	Minimum value in any element in the array	MIN_VALUE	$(P)$(R)MinValue_RBV	ai
NDPluginStats MinX	asynFloat64	r/o	X pixel location of minimum value in the array. This is only valid for 2-D monochromatic arrays.	MIN_X	$(P)$(R)MinX_RBV	ai
NDPluginStats MinY	asynFloat64	r/o	Y pixel location of minimum value in the array. This is only valid for 2-D monochromatic arrays.	MIN_Y	$(P)$(R)MinY_RBV	ai
NDPluginStats MaxValue	asynFloat64	r/o	Maximum value in any element in the array	MAX_VALUE	$(P)$(R)MaxValue_RBV	ai
NDPluginStats MaxX	asynFloat64	r/o	X pixel location of maximum value in the array. This is only valid for 2-D monochromatic arrays.	MAX_X	$(P)$(R)MaxX_RBV	ai
NDPluginStats MaxY	asynFloat64	r/o	Y pixel location of maximum value in the array. This is only valid for 2-D monochromatic arrays.	MAX_Y	$(P)$(R)MaxY_RBV	ai
NDPluginStats MeanValue	asynFloat64	r/o	Mean value in the array	MEAN_VALUE	$(P)$(R)MeanValue_RBV	ai
NDPluginStats Total	asynFloat64	r/o	Sum (total) of all elements in the array. This is available as an ai record. The total counts are also available as epicsInt32 values in an mca record via callbacks to the drvFastSweep driver. The mca record is very useful for on-the-fly data acquisition of the total counts in the detector or in an ROI.	TOTAL	$(P)$(R)Total_RBV, $(P)$(R)TotalArray	ai, mca
NDPluginStats Net	asynFloat64	r/o	Net (background subtracted) total of all elements in the array. The background is calculated by determining the average counts per array element in a border around the array of width NDPluginStatsBgdWidth. This average background counts per element is then subtracted from all elements inside the array. If NDPluginStatsBgdWidth is ≤ 0 then no background is computed. The net counts is available as an ai record. The net counts is also available as epicsInt32 values in an mca record via callbacks to the drvFastSweep driver. The mca record is very useful for on-the-fly data acquisition of the net counts in the detector or in an ROI.	NET	$(P)$(R)Net_RBV, $(P)$(R)NetArray	ai, mca
NDPluginStats SigmaValue	asynFloat64	r/o	Sigma (standard deviation) of all elements in the array	SIGMA_VALUE	$(P)$(R)Sigma_RBV	ai
		Centroid statistics
NDPluginStats ComputeCentroid	asynInt32	r/w	Flag to control whether to compute the centroid statistics (0=No, 1=Yes). The centroids are computed from the average row and column profiles above the centroid threshold. These calculations are also quite fast, since they just involve addition operations for each array element.	COMPUTE_CENTROID	$(P)$(R)ComputeCentroid, $(P)$(R)ComputeCentroid_RBV	bo, bi
NDPluginStats CentroidThreshold	asynFloat64	r/w	Threshold used when computing the centroid statistics. All array elements less than this value are set to 0 for computing the centroid statistics. It is important to set this value to ignore the “background” when computing the position and size of a “beam” image, for example.	CENTROID_THRESHOLD	$(P)$(R)CentroidThreshold, $(P)$(R)CentroidThreshold_RBV	ao, ai
NDPluginStats CentroidTotal	asynFloat64	r/o	Total mass, sum of all elements above the threshold.	CENTROID_TOTAL	$(P)$(R)CentroidTotal_RBV	ai
NDPluginStats CentroidX	asynFloat64	r/o	X centroid of the array above the centroid threshold.	CENTROIDX_VALUE	$(P)$(R)CentroidX_RBV	ai
NDPluginStats CentroidY	asynFloat64	r/o	Y centroid of the array above the centroid threshold.	CENTROIDY_VALUE	$(P)$(R)CentroidY_RBV	ai
NDPluginStats SigmaX	asynFloat64	r/o	Sigma X (width) of the distribution above the centroid threshold.	SIGMAX_VALUE	$(P)$(R)SigmaX_RBV	ai
NDPluginStats SigmaY	asynFloat64	r/o	Sigma Y (height) of the distribution above the centroid threshold.	SIGMAY_VALUE	$(P)$(R)SigmaY_RBV	ai
NDPluginStats SigmaXY	asynFloat64	r/o	This is the normalized value of sigmaXY, i.e. sigmaXY/(sigmaX * sigmaY). This is often called the correlation coefficient, r. It is zero if the X and Y profiles are not correlated, meaning that the distribution is not tilted with respect to the X and Y axes.	SIGMAXY_VALUE	$(P)$(R)SigmaXY_RBV	ai
NDPluginStats SkewX	asynFloat64	r/o	Skewness X (symmetry) of the distribution above the centroid threshold, in relation to the center of mass. == 0, symmetric distribution < 0, distribution assymetric to the left > 0, distribution assymetric to the right	SKEWX_VALUE	$(P)$(R)SkewX_RBV	ai
NDPluginStats SkewY	asynFloat64	r/o	Skewness Y (symmetry) of the distribution above the centroid threshold, in relation to the center of mass. == 0, symmetric distribution < 0, distribution assymetric to the top > 0, distribution assymetric to the bottom	SKEWY_VALUE	$(P)$(R)SkewY_RBV	ai
NDPluginStats KurtosisX	asynFloat64	r/o	Excess Kurtosis X (flatness) of the distribution above the centroid threshold == 0, Gaussian (normal) distribution < 0, distribution flatter than normal > 0, distribution more peaky than normal	KURTOSISX_VALUE	$(P)$(R)KurtosisX_RBV	ai
NDPluginStats KurtosisY	asynFloat64	r/o	Excess Kurtosis Y (flatness) of the distribution above the centroid threshold. == 0, Gaussian (normal) distribution < 0, distribution flatter than normal > 0, distribution more peaky than normal	KURTOSISY_VALUE	$(P)$(R)KurtosisY_RBV	ai
NDPluginStats Eccentricity	asynFloat64	r/o	Eccentricity, can take values from 0 to 1. 0 means a perfectly round object and 1 mean a line shaped object.	ECCENTRICITY_VALUE	$(P)$(R)Eccentricity_RBV	ai
NDPluginStats Orientation	asynFloat64	r/o	Orientation of the object, orientation of the “long” direction with respect to horizontal (x axis).	ORIENTATION_VALUE	$(P)$(R)Orientation_RBV	ai
		Time-Series data
The time series is implemented by loading an instance of the NDPluginTimeSeries plugin for each NDPluginStats plugin, and the time series control uses records in NDTimeSeries.template. That documentation should be consulted for an explanation of these records. The prefix and record name macro for the time-series plugin records from NDTimeSeries.template is $(P)$(R)TS:. NOTE: The time-series plugin is often used with drivers which sample at a fixed well-defined time interval. This cannot be guaranteed with the statistics plugin, so the averaging time records and time axis waveform record from NDPluginTimeSeries are typically not used, and the statistics data are plotted against time point #, rather than actual time. The time-series waveform records for each statistic are defined in NDStats.template.
NDPluginTimeSeries, TSTimeSeries	asynFloat64Array	r/o	The time series data arrays of the basic statistics and centroid and sigma statistics described above.	TS_TIME_SERIES	$(P)$(R)XXX, where XXX is: TSMinValue TSMinX TSMinY TSMaxValue TSMaxX TSMaxY TSMeanValue TSSigma TSTotal TSNet TSCentroidX TSCentroidY TSSigmaX TSSigmaY TSSigmaXY TSSkewX TSSkewY TSKurtosisX TSKurtosisY TSEccenticity TSOrientation TSTimestamp	waveform
		X and Y Profiles
NDPluginStats ComputeProfiles	asynInt32	r/w	Flag to control whether to compute the profiles for this array (0=No, 1=Yes).	COMPUTE_PROFILES	$(P)$(R)ComputeProfiles, $(P)$(R)ComputeProfiles_RBV	bo, bi
NDPluginStats ProfileSizeX	asynInt32	r/w	Number of array elements in the X profiles.	PROFILE_SIZE_X	$(P)$(R)ProfileSizeX_RBV	longin
NDPluginStats ProfileSizeY	asynInt32	r/w	Number of array elements in the Y profiles.	PROFILE_SIZE_Y	$(P)$(R)ProfileSizeY_RBV	longin
NDPluginStats CursorX	asynInt32	r/w	X position of a user-defined cursor for profiles.	CURSOR_X	$(P)$(R)CursorX, $(P)$(R)CursorX_RBV	longout, longin
NDPluginStats CursorY	asynInt32	r/w	Y position of a user-defined cursor for profiles.	CURSOR_Y	$(P)$(R)CursorY, $(P)$(R)CursorY_RBV	longout, longin
NDPluginStats CursorVal	asynFloat64	r/o	Value of the pixel at the current cursor position.	CURSOR_VAL	$(P)$(R)CursorVal	ai
NDPluginStats ProfileAverageX	asynFloat64Array	r/o	Profile of the average row in the array, i.e. the sum of all rows in the array divided by the number of rows.	PROFILE_AVERAGE_X	$(P)$(R)ProfileAverageX_RBV	waveform
NDPluginStats ProfileAverageY	asynFloat64Array	r/o	Profile of the average column in the array, i.e. the sum of all columns in the array divided by the number of columns.	PROFILE_AVERAGE_Y	$(P)$(R)ProfileAverageY_RBV	waveform
NDPluginStats ProfileThresholdX	asynFloat64Array	r/o	Same as ProfileAverageX except that all array elements less than CentroidThreshold are set to zero when computing the average.	PROFILE_THRESHOLD_X	$(P)$(R)ProfileThresholdX_RBV	waveform
NDPluginStats ProfileThresholdY	asynFloat64Array	r/o	Same as ProfileAverageY except that all array elements less than CentroidThreshold are set to zero when computing the average.	PROFILE_THRESHOLD_Y	$(P)$(R)ProfileThresholdY_RBV	waveform
NDPluginStats ProfileCentroidX	asynFloat64Array	r/o	X profile through the array in the row defined by CentroidY.	PROFILE_CENTROID_X	$(P)$(R)ProfileCentroidX_RBV	waveform
NDPluginStats ProfileCentroidY	asynFloat64Array	r/o	Y profile through the array in the column defined by CentroidX.	PROFILE_CENTROID_Y	$(P)$(R)ProfileCentroidY_RBV	waveform
NDPluginStats ProfileCursorX	asynFloat64Array	r/o	X profile through the array in the row defined by CursorY.	PROFILE_CURSOR_X	$(P)$(R)ProfileCursorX_RBV	waveform
NDPluginStats ProfileCursorY	asynFloat64Array	r/o	Y profile through the array in the row defined by CursorX.	PROFILE_CURSOR_Y	$(P)$(R)ProfileCursorY_RBV	waveform
		Array histogram
NDPluginStats ComputeHistogram	asynInt32	r/w	Flag to control whether to compute the histogram for this array (0=No, 1=Yes). Not computing the histogram reduces CPU load.	COMPUTE_HISTOGRAM	$(P)$(R)ComputeHistogram, $(P)$(R)ComputeHistogram_RBV	bo, bi
NDPluginStats HistSize	asynInt32	r/w	Number of elements (bins) in the histogram	HIST_SIZE	$(P)$(R)HistSize, $(P)$(R)HistSize_RBV	longout, longin
NDPluginStats HistMin	asynFloat64	r/w	Minimum value for the histogram. All values less than this will be counted in HistBelow.	HIST_MIN	$(P)$(R)HistMin, $(P)$(R)HistMin_RBV	ao, ai
NDPluginStats HistMax	asynFloat64	r/w	Maximum value for the histogram. All values greater than this will be counted in HistAbove.	HIST_MAX	$(P)$(R)HistMax, $(P)$(R)HistMax_RBV	ao, ai
NDPluginStats HistBelow	asynInt32	r/o	Count of all values less than HistMin.	HIST_BELOW	$(P)$(R)HistBelow_RBV	longin
NDPluginStats HistAbove	asynInt32	r/o	Count of all values greater than HistMax.	HIST_ABOVE	$(P)$(R)HistAbove_RBV	longin
NDPluginStats HistEntropy	asynFloat64	r/o	Entropy of the image. This is a measure of the sharpness of the histogram, and is often a useful figure of merit for determining sharpness of focus, etc. It is defined as -SUM(BIN[i]*log(BIN[i]), where the sum is over the number of bins in the histogram and BIN[i] is the number of elements in bin i.	HIST_ENTROPY	$(P)$(R)HistEntropy_RBV	ai
NDPluginStats HistArray	asynFloat64Array	r/o	Histogram array, i.e. counts in each histogram bin.	HIST_ARRAY	$(P)$(R)Histogram_RBV	waveform
NDPluginStats HistXArray	asynFloat64Array	r/o	Histogram X-axis array, i.e. minimum intensity in each histogram bin.	HIST_X_ARRAY	$(P)$(R)HistogramX_RBV	waveform

If the values of CentroidThreshold, CursorX, or CursorY are changed then the centroid and profile calculations are performed again immediately on the last array collected. Thus updated centroid statistics and profiles can be displayed even when new arrays are not being acquired. These calculations are only performed when enabled by ComputeCentroid and ComputeProfiles.

Configuration

The NDPluginStats plugin is created with the NDStatsConfigure command, either from C/C++ or from the EPICS IOC shell.

NDStatsConfigure(const char *portName, int queueSize, int blockingCallbacks,
               const char *NDArrayPort, int NDArrayAddr,
               int maxBuffers, size_t maxMemory,
               int priority, int stackSize)

For details on the meaning of the parameters to this function refer to the detailed documentation on the NDStatsConfigure function in the NDPluginStats.cpp documentation and in the documentation for the constructor for the NDPluginStats class.

Screen shots

The following MEDM screen provides access to the parameters in NDPluginDriver.h and NDPluginStats.h through records in NDPluginBase.template and NDStats.template.

The following MEDM screen shows the average profile of an image in the X direction.

The following MEDM screen shows the profile of an image in the Y direction at the location of the user-defined cursor.

The following MEDM screen shows the histogram of intensities of an array.

The following MEDM screen combines many parameters for 5 NDPluginStats plugins on a single screen.

The following MEDM screen shows the the total counts from the Stats1 plugin. This is the total counts as a function of time.

The following MEDM screen shows the Y centroid as a function of time from the Stats1 plugin.

The following MEDM screen shows all of the basic statistics as a function of time from the Stats1 plugin.

The following MEDM screen shows all of the centroid statistics as a function of time from the Stats1 plugin.