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 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
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.

../_images/NDStats.png

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

../_images/NDStats_AverageX.png

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

../_images/NDStats_CursorY.png

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

../_images/NDStats_Histogram.png

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

../_images/NDStats5.png

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

../_images/NDStatsTimeSeriesTotal.png

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

../_images/NDStatsTimeSeriesCentroidY.png

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

../_images/NDStatsTimeSeriesBasicAll.png

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

../_images/NDStatsTimeSeriesCentroidAll.png