EMAN2 Cmp Manual


Last modified on Thu, 09 Dec 2010 13:44:55 CST
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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)
ccc.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 (should be for normalized images). Default is true.
int searchx: The maximum range of the peak location in the x direction. Default is sizex/4
int searchy: The maximum range of the peak location in the y direction. Default is sizey/4
int searchz: The maximum range of the peak location in the z direction. Default is sizez/4
float zeroori: When using the ccc.tomo aligner, use the peak at origin (use only with refine3D aligner).
Ccc with consideration given for the missing wedge
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)
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).
lod emdata mask: image mask
int negative: If set (which is the default), returns Lod. (The smaller the better)
int normalize: If set, normalizes maps prior to computing the difference. Default=0 (no normalization)
L^1 normalized difference (positive by default)
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.