NAME pkFindROI - Tcl/Tk Window Shell for Spectral Analysis DESCRIPTION The NMRWish peak detection command operates on any N- dimensional region of interest extracted from a spectrum. It can be used directly from a Tk script, or through an interactive interface such as the one provided in NMRDraw. Peak positions are estimated by multidimensional parabolic models. These models are also used to estimate the linewidth and extent of the peak in all dimensions. Peak overlap is characterized by a recursive method which identi- fies continuous collections of points above the detection threshold. Noise peaks are classified according to a Chi- square criterion. Truncation artifacts are also identified, based on analysis of Fourier transforms of the window func- tions used on the spectrum. PEAK DETECTION SETTINGS POP-UP Filter Command: The name of a command to execute after peak detection; when executed, the command will be given the name of the current peak table as its last argument. The intent of this option is to allow special filtering of the peak table. For example, using the command "pkFilter.tcl" will generate a "simple" version of the peak table from the original one. Chi2 Threshold: This is a probability threshold for noise peak rejec- tion by chi-square test. The chi-square test estimates the probability that the sum-of-squares intensity in the peak's neighborhood could be caused by random noise alone. To use this test, you must enter a reasonable "Noise:" value above. Increasing the chi2 threshold increase the rejection of peaks near the noise level. If the value is set to one or zero, no peaks will be rejected. Noise: Enter an estimate of the standard deviation of the spectral noise here. The default value comes from an automated estimate. This parameter is used in the Chi-squared test to classify random noise peaks. It is also used to estimate errors in peak position due to random noise (parameters DX DY DZ and DA in the peak table). Contour: Specifies the minimum number of contour levels which define the "High:" and "Low:" peak detection thres- holds. High: The detection threshold for positive peaks. By default, it is set to the height of the first positive contour level in use when the "Peak Detection" pop-up window appears. Low: The detection threshold for negative peaks. By default, it is set to the height of the first negative contour level in use when the "Peak Detection" pop-up window appears. If want want to detect positive peaks only, set this parameter to a large negative number. DDX: ... Size of the detection region in +/- points. A given point must be larger than all of the other points in this detection region in order to be detected as a peak. IDX: ... Size of the parabolic interpolation region in +/- points. IncX: ... Defines how much of the spectral data is read into memory for peak detection. Values of zero will cause the entire spectral region to be read at once. Since some spectral data may be too large for this, it is possible to perform peak detection on automatically on overlapping regions. For example, if 3D peak detection is performed with a setting of IncX=0, IncY=0, IncZ=16, the data will be read and analyzed in 16-plane slabs. This will not effect deter- mination of peak positions, widths, and heights, how- ever it can effect the volume (VOL) and bounding region values (X1/X3 etc). Local Noise: By default, the Chi-square noise classification scheme uses a uniform noise estimate for all parts of the spectrum. Selecting one of the X Y Z or A checkboxes will allow for an adaptive noise estimate with respect to the selected dimension. This can help compensate for noise ridges. Special Options Currently, these options select how noise peaks are identified and han- dled: Sinc Detect If this option is selected, the peak detec- tion module will attempt to identify peaks which are due to truncation noise (sinc artifacts). Reject Noise Peaks If this option is selected, any peak classified as noise (either random noise or truncation noise) will be automatically eliminated from the peak table. Sinc Detect Parameters The peak detection module attempts to identify trunca- tion artifacts based on the details of window function and zero filling which were applied to each dimension of the data. By taking this information into account, it is possible to estimate for a given peak how far truncation wiggles would extend in each dimension before falling below the detection threshold. XAdj: ... In the artifact detection procedure, the height and extent of the truncation peaks are modeled as a profile which decreases as 1/X, where X is the distance from the peak center, and in order for a small peak to be classified as the truncation artifact of a larger peak, the smaller peak must fall below the profile. This value is used as a multiplying factor to increase or decrease the overall profile height. XTol: ... In order for a small peak to be classified as the truncation artifact of a larger peak, the two peaks must align along a given dimension. This value specifies the tolerance in points for deciding whether two peaks are aligned. XLW: ... A rough estimate of the original linewidth in Hz in a given dimension before any window function was used. Save Script Selecting this command will save a new version of the peak detection script "pk.tcl" without executing it. Done Use this button to dismiss the "Peak Detection Set- tings" pop-up window. PEAK TABLE PARAMETERS INDEX the unique peak ID number. X_AXIS ... the position of the peak in points, by parabolic inter- polation. DX ... estimate of the error in peak position due to random noise, in points. X_PPM ... the position of the peak in PPM, by parabolic interpo- lation. X_HZ ... the position of the peak in Hz, by parabolic interpola- tion. XW ... the full width at half height in points, estimated by parabolic interpolation. XW_HZ ... the full width at half height in Hz, estimated by para- bolic interpolation. X1/X3 ... coords of the bounding region surrounding the peak or its cluster in points. HEIGHT the peak height, estimated by parabolic interpolation. DHEIGHT the error peak height due to random noise, estimated by parabolic interpolation. VOL the peak volume, estimated as the sum of intensities in the neighborhood (bounds given by X1/X3 etc) of the peak maximum. ASS location to hold assignment data. PCHI2 the chi-square probability for the peak (i.e. probabil- ity that the peak could be due to random noise alone). CLUSTID identifies the cluster of peaks that a given peak over- laps. Peaks with the same CLUSTID value are considered to be in one overlapped group. MEMCNT the total number of peaks which are in a given peak's cluster (i.e. peaks which have the same CLUSTID value). TYPE An integer describing the peak classification; currently 1 = Peak, 2 = Random Noise, 3 = Truncation artifact. pkFindROI: Peak Detection in a Region of Interest (ROI). Arguments for Peak Detection in a Region of Interest. -roi roiID ID of ROI for peak detec- tion; Default is current ROI. -out outName Peak table output name. -reject Reject peaks marked as noise or truncation artifacts. -parent Record results relative to the parent data of the ROI. -reset Erase current peaks and exit. -append Append to current peak table. -nopk Suppress peak detection, but keep previous settings. -verb Verbose mode ON. Peak Detection Settings: -dx dxList [1 1 ...] Detection limits +/- pts. -idx itList [1 1 ...] Interpolation limits +/- pts. -plus pThresh [0.0] Positive detection thres- hold. -minus mThresh [-1e16] Negative detection thres- hold. -clust [No] Adjust clusters after detect; used with multiple ROIs. -mask [No] Use binary mask to cluster peaks; replaces ROI data. Noise Detection Settings: -sigma noise [1.000] Standard deviation of noise. -pChi prob [0.001] P threshold for Chi2 test. -lnAdj aList [None] Axis list for local noise adjustment (use X Y Z A). Truncation Artifact (Sinc) Detection Setting: -sinc [No] Use sinc detection. -hiAdj adjList [1.2 ...] Height adjustment factors. -lw lwHz [1.0 ...] Intrinsic linewidths. -tol tolPts [2.0 ...] Postition tolerances. Out- put Printing Precision: -ppmPrec digits [3] Precision for values in ppm. -hzPrec digits [3] Precision for values in Hz. -ptsPrec digits [3] Precision for values in pts.