Classification and Clustering File Formats

Correspondence Analysis (CA) or Principal Component Analysis (PCA)

Description of 'CA S' Output Files (links lead to output from faces example).

• *_IMC is a text file that stores the coordinates of each IMAGE in the new vector space. The contents on the first line are:

  NUMIM	# of images included in analysis
  NFAC	# of factors requested, entry to "number of factors" question
  NX, NY	X and Y values of images, respectively
  NUMIM	# of images included in analysis
  PCA	1 if PCA analysis was used, 0 if CA used

  There is a line for each image included. The contents of this line are:

  IMAGE(#)...NFAC)	Coordinates for each image, in the vector space. The number of entries depend on how many factors were requested.
  WEIGHTP	Relative weight of each image, = # of pixels in this image/# of pixels in all images
  DOR	Distance from the image to the origin of the new vector space
  FIM	# of the image. The first, 32nd, etc.
  ACT	Active image flag.

• *_PIX is a text file that stores the coordinates of each PIXEL. Very similar to *_IMC. The contents on the first line are:

  NPIX	# of pixels included in each image, determined by the mask
  NFAC	# of factors requested
  NX,NY	X and Y values of images, respectively
  NUMIM	# of images included in analysis
  PCA	1 if PCA analysis was used, 0 if CA used

  There is a line for each pixel included. The outputs for this are:

  PIXEL(#)...NFAC)	Coordinates for each pixel, in the vector space. The number of entries depend on how many factors were requested.
  WEIGHTP	Relative weight of each pixel
  CO	Distance from the pixel to the origin of the new vector space
  FPIX	# of the pixel. The first, 32nd, etc.
  DUMMY	Unused

• *_EIG is a text file that stores the eigenvector values. The contents on the first line are:

  NFAC	# of factors requested
  TOTAL WEIGHT	Sum of all the pixels used. Not the # of them.
  TRACE	Sum of the diagonal of the eigenvector array
  PCA	1 if PCA analysis was used, 0 if CA used
  N	Number

  There is a line for each factor requested. The outputs for this are: variance is accounted for by eigenvalues

  EIGENVALUE	Eigenvalue, listed largest first.
  %	% of the total inter-image variance this eigenvalue is responsible for.
  CUMULATIVE %	Running tally of how much interimage

  If PCA was used there are additional lines. The outputs for these are:

  AVERAGE(#)...N )

  Average for this image or pixel

• *_SEQ is a binary file that stores all image pixel values within the mask from all the images. NOT SPIDER image. Only useful internally within other 'CA' & 'CL' operations.
• *_SET is a binary file with transposed data. NOT a SPIDER image. Only useful internally within other 'CA' & 'CL' operations.

Source: docs/techs/classif/cas_format.html     Last update: 04 Feb 2013