EMAN2 Cmp Manual


Last modified on Tue, 25 May 2010 17:13:23 CDT
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Cmp Name Parameters Description
ccc emdata mask: image mask
int negative: If set, returns -1 * ccc product. Set by default so smaller is better
Cross-correlation coefficient (default -1 * ccc)
dot emdata mask: image mask
int negative: If set, returns -1 * dot product. Set by default so smaller is better
int normalize: If set, returns normalized dot product (cosine of the angle) -1.0 - 1.0.
Dot product (default -1 * dot product)
dot.tomo emdata ccf: The ccf image, can be provided if it already exists to avoid recalculating it
bool norm: Whether the cross correlation image should be normalized. Default is false.
float threshold: Threshold applied to the Fourier amplitudes of the ccf image - helps to correct for the missing wedge.
int tx: The x location of the maximum in the ccf image. May be negative. Useful thing to supply if you know the maximum is not at the phase origin
int ty: The y location of the maximum in the ccf image. May be negative. Useful thing to supply if you know the maximum is not at the phase origin
int tz: The z location of the maximum in the ccf image. May be negative. Useful thing to supply if you know the maximum is not at the phase origin
straight dot product with consideration given for the missing wedge - normalization is applied by detecting significantly large Fourier amplitudes in the cross correlation image
frc int ampweight: If set, the amplitude of 'this' will be used to weight the result (default=0)
float maxres: Highest resolution to use in comparison (soft cutoff). Requires accurate A/pix in image. <0 disables. Default=10
float minres: Lowest resolution to use in comparison (soft cutoff). Requires accurate A/pix in image. <0 disables. Default=500
int nweight: Downweight similarity based on number of particles in reference (default=0)
int snrweight: If set, the SNR of 'this' will be used to weight the result. If 'this' lacks CTF info, it will check 'with'. (default=0)
int sweight: If set, weight the (1-D) average by the number of pixels in each ring (default=1)
int zeromask: Treat regions in either image that are zero as a mask
Computes the mean Fourier Ring Correlation between the image and reference (with optional weighting factors).
optvariance int debug: Performs various debugging actions if set.
int invert: If set, 'with' is rescaled rather than 'this'. 'this' should still be the noisier image. (default=0)
int keepzero: If set, zero pixels will not be adjusted in the linear density optimization. (default=1)
int matchamp: Takes per-pixel Fourier amplitudes from self and imposes them on the target, but leaves the phases alone. (default=0)
int matchfilt: If set, with will be filtered so its radial power spectrum matches 'this' before density optimization of this. (default=1)
int radweight: Upweight variances closer to the edge of the image. (default=0)
Real-space variance after density optimization, self should be noisy and target less noisy. Linear transform applied to density to minimize variance.
phase int ampweight: If set, the amplitude of 'with' will be used as a weight in the averaging'. (default=0)
float maxres: Highest resolution to use in comparison (soft cutoff). Requires accurate A/pix in image. <0 disables. Default=10
float minres: Lowest resolution to use in comparison (soft cutoff). Requires accurate A/pix in image. <0 disables. Default=500
int snrfn: If nonzero, an empirical function will be used as a radial weight rather than the true SNR. (1 - exp decay)'. (default=0)
int snrweight: If set, the SNR of 'this' will be used to weight the result. If 'this' lacks CTF info, it will check 'with'. (default=0)
int zeromask: Treat regions in either image that are zero as a mask
Mean phase difference
quadmindot int negative: If set, returns -1 * dot product. Default = true (smaller is better)
int normalize: If set, returns normalized dot product -1.0 - 1.0.
Caclultes dot product for each quadrant and returns worst value (default -1 * dot product)
sqeuclidean emdata mask: image mask
int normto: If set, 'with' is normalized to 'this' before computing the distance
int zeromask: If set, zero pixels in either image will be excluded from the statistics
Squared Euclidean distance (sum(a - b)^2)/n.