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CA SRI - Correspondence Analysis - Reconstitute Importance images

(08/21/96)

PURPOSE

Compute importance image for a selected factor. The suboption '/C' refers to a cluster coordinate file. In this case, the center of gravity coordinates of stable clusters found by 'CA CLA' or other classification operations are used.

SEE ALSO

CA MAP [Correspondence Analysis - nonlinear mapping]
CA S [Correspondence Analysis - find solution]
CA SI [Correspondence AnalysiS - initialize]
CA SM [Correspondence Analysis - factor map]
CA SME [Correspondence Analysis - factor map and Eigen Values]
CA SR [Correspondence Analysis - full reconstitution of images]
CA SRD [Correspondence Analysis - reconstitute differential images]
CA SRP [Correspondence Analysis - PCA reconstitution]
CA VIS [Correspondence Analysis - Create visual map]

USAGE

.OPERATION: CA SRI [optional: /C]

.ENTER FILE TEMPLATE (EG. PIC****): TST***
[Enter the template forthe file or file series to be created.]

.ENTER FILE NUMBERS (EG. 1-8,12-22,55): 1-80,90-95
[Numbers are consecutive, and refer to the sequence of files specified in 'CA S'. However, in the case of the cluster option (/C), the numbers refer to the cluster numbers, and are restricted to the range of these numbers]

For the /C option, specify a cluster file:

.CLUST FILE: CLU003
[Enter cluster coordinate file created by previous 'CA CLA' run or other classification operations.]

.COORDINATE FILE CODE: 2
[Enter the number identifying the three files used to store the output from the previous 'CA S' run: IMC#, PIX#, EIG#.]

The following factor selection is NOT supported for /C option:

.ENTER FACTORS TO BE USED: 2-4
[Enter the factors to be used for image reconstitution. Note that the numbers have to be less that the number of images and less than or equal to the number of factors originally specified in 'CA S'.]

If there is no existing image with the number given above, in response to ".ENTER FILE NUMBERS", then coordinates are solicited for each of the factors specified:

.ENTER COORDINATES FOR EACH FACTOR SELECTED: 0.0013, -0.0011,
0.0004 [Enter coordinates related to the scales of the factorial axes in the Results file from 'CA S' or from factorial maps produced by 'CA SM' or 'CA SME'.]

NOTES

  1. The "importance image" obtained by using 'CA SRI' has both positive and negative values. To obtain the more familiar pair of complementary positive-definite importance images used in the earlier literature (e.g. Frank et al., 1982), follow this operation by 'TH' (threshold), specifying '0' as the lower or upper threshold, respectively. Then invert contrast of the latter thresholded image.

  2. For a detailed explanation of concepts used here see: J.P. Bretaudiere and J. Frank (1986) J. Microscopy 144:1-14. Importance images are defined in J. Frank and M. van Heel (1982) J. Mol. Biol. 161:133-137.

SUBROUTINES

JPMSK2, RECDUM, RECONS, SRIPE, MSKDEC

CALLER

UTIL1

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