; RUNS K-MEANS CLASSIFICATION

; -------------- Parameters --------------
x20 = 4   ; desired number of classes
x27 = 9   ; number of eigenfactors to use

; ---------------- Inputs ----------------
fr l
[cas_prefix]CA/cas                     ; correspondence-analysis output prefix
fr l
[particles]../Particles/flt/flt******  ; particle file-pattern

; --------------- Outputs --------------- 
fr l
[class_dir]KM                             ; output directory
fr l
[dendrogram_doc][class_dir]/docassign     ; particle-assignment doc
fr l
[class_doc][class_dir]/docclass           ; class-membership doc prefix, for each class
fr l
[class_avg][class_dir]/classaverage       ; class-average prefix, for each class
fr l
[class_var][class_dir]/classvariance      ; class-variance prefix, for each class
fr l
[class_stats_doc][class_dir]/listclasses  ; class-size document

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

vm
echo "if(! -d [class_dir]) mkdir [class_dir]"|csh

md
set mp
0

vm
echo "Running k-means classification"; date

; run k-means classification
cl km x21,x22,x23,x24,x25
[cas_prefix]_IMC
x20             ; number of classes
(1-x27)         ; eigenfactors to use
(0)             ; no factor weighting
(0)             ; no random seed
[class_doc]***  ; OUTPUT (temp): class-list doc
[dendrogram_doc]

sd -1,x21,x22,x23,x24,x25
dockm

; GENERATE CLASS AVERAGES
vm
echo "Generating class averages"; date

de
[class_stats_doc]

; loop through classes
do lb2 x16=1,x20
    ; calculate average
    as r
    [particles]
    [class_doc]{***x16}  ; INPUT: class list
    A                    ; _A_ll images
    [class_avg]{***x16}  ; OUTPUT: class average
    [class_var]{***x16}  ; OUTPUT: class variance

    ; get class size
    ud n,x15
    [class_doc]{***x16}

    ; write to doc file
    sd x16,x16,x15
    [class_stats_doc]
lb2
; end class-loop

sd e  ; close doc
[class_stats_doc]

vm
echo; echo "Done"; date

en d

; Modified 2008-04-06
;    2008-04-06 (trs) -- added doc file with class size
;    2005-08-24 (trs) -- adapted from classify.spi