; 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]Verify/../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 template, for each class
fr l
[class_avg][class_dir]/classaverage    ; class average template, for each class
fr l
[class_var][class_dir]/classvariance   ; class variance template, for each class

; ------ 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

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

vm
echo "\nDone"; date

en d