;-------------------------------------------------------------
; clhe.spi
; PURPOSE: Runs 'CL HD' and 'CL HE' operations
;-------------------------------------------------------------

; ------------ INPUT       -----------------------------------

[cutoff] = 64.0                     ; Cutoff percentage

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

FR G
[infile]data/clhc_dend_2            ; Name of dendrogram doc file 

FR G
[image_template]data/sma***         ; Template for images to be averaged 

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

FR G
[hdoutfile]data/clhc_dend_class    ; Class file 

FR G
[heoutfile]data/clhc_dend_class_   ; Class file template 

FR G
[avg]data/clhc_avg_                ; Class average files      
FR G
[var]data/clhc_var_                ; Class variance files   
FR G
[montage]data/clhc_class_montage   ; Class average montage file    

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

VM
echo " Running: 'CL HD' xxxxxxxxxxxxxxxxxxxxxxxxxxxx"

DE [hdoutfile]

CL HD              ; Calculate class assignments
[cutoff]           ; Threshold cutoff %
[infile]           ; Dendrogram doc file name         (input)
[hdoutfile]        ; Dendrogram doc file              (output)

vm
cat [hdoutfile]*

;UD MAX [nclass]    ; Find highest key
;[hdoutfile]        ; Dendrogram doc file              (input)
;0                  ; Key

[nclass]=4
VM
echo " Number of classes: {***[nclass]}  xxxxxxxxxxxxxxxxxxxxxxxxx"              

VM
echo " Running: 'CL HE' xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx"

VM
\rm -f [heoutfile]*

CL HE              ; Calculate class assignments
[cutoff]           ; Threshold cutoff %
[infile]           ; Dendrogram doc file name         (input)
[heoutfile]***     ; Dendrogram doc file template     (output)

VM
echo " Displaying class doc files  xxxxxxxxxxxxxxxxxxxxx"
VM                ; Show the output doc files
gedit  [heoutfile]*.$DATEXT &

VM
echo " Creating class average files  xxxxxxxxxxxxxxxxxxx"
DO [i]=1,[nclass]
   AS R
   [image_template]    ; Image file template          (input)
   [heoutfile]{***[i]} ; Image selection file
   All                 ; All images
   [avg]{***[i]}       ; Average files               (output)
   [var]{***[i]}       ; Variance files              (output)
ENDDO
 
MN                     ; Montage the averages
[avg]***               ; Average files               (input)
1-[nclass]             ; File numbers
[nclass],3             ; Images / row, margin
0                      ; Margin value
[montage]              ; Montage file                (output)

VM
echo " "

EN