;---------------------------------------------------------------------------
; cas.spi 
; PURPOSE: Automates running of "CA S" command to run CORAN (CA)
;          with circular mask
; OUTPUT :
;   CA S : cor_EIG, cor_IMC, cor_PIX, cor_SEQ (where 'cor' is template)
;
;---------------------------------------------------------------------------

[n1] = 1.	; First number of image/micrograph to analyze
[n2] = 80.      ; Final number
[nf] = 8 	; Number of factors to search for 

[x]  = 64       ; X size of mask
[y]  = 64       ; Y size of mask
[cx] = 33	; X center of circular mask
[cy] = 33       ; Y center of circular mask
[r]  = 30	; Radius of mask, take into account center and size of mask

; ----- INPUT FILES ------

FR G
[ma]data/sma         ; Input images file template

; ----- OUTPUT FILES -----

FR G
[mask]data/mask01    ; Mask file

FR G
[cor]data/control    ; Prefix for SEQ, IMC, PIX, and EIG files from CA S

FR G
[doc]data/eigendoc   ; Lists coords. for each image, from _IMC

; ----- END BATCH HEADER ----------------------------------------

VM
echo " Creating mask file xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx"

DE
[mask]

PT             ; Create mask
[mask]
[x],[y]        ; Size
C
[cx],[cy]
[r]            ; Radius
N

VM
echo " Running correspondence analysis xxxxxxxxxxxxxxxxxxxxxx"

CA S
[ma]***        ; Input image template
[n1]-[n2]      ; File numbers
[mask]         ; Mask
[nf]           ; Number of factors
C              ; Coran or PCA
0.0            ; Additive constant
[cor]          ; Output prefix

DE
[doc]
  
SD C            ; Transfer image coordinates along factors from _IMC00
[cor]           ; Input prefix for IMC file
1-2             ; Factors
[doc]           ; Doc file   (output)

VM
echo " Displaying factors 1 & 2  doc. file xxxxxxxxxxxxxxxxxx" ; echo " "
VM
gedit [doc].$DATEXT &

EN