Changeset 27323 in project

Timestamp:

08/29/12 04:37:25 (9 years ago)

Author:

Ivan Raikov

Message:

neurolucida: added --permute-coords option

File:

• release/4/neurolucida/trunk/neurolucida.scm (modified) (9 diffs)

release/4/neurolucida/trunk/neurolucida.scm

@@ -87 +87 @@
 (define opt-grammar
   `(
+    (permute-coords
+     "permute coordinates of node points in NG format according to the given list of 1-based indices"
+     (value (required INDICES)))
+
     (data-dir
      "set download directory (default is a randomly generated name in /tmp)"
@@ -270 +274 @@
 ;;
 
-(define (make-ng g)
+(define (make-ng g #!key (permute-coords #f))
 
   (define (sum lst) (fold + 0. lst))
@@ -411 +415 @@
                   (let ((ax1 (cons
                               (if next-node
-                                  `(Node (origin . ,cylinder-origin) 
+                                  `(Node (origin . ,(or (and permute-coords (permute-coords cylinder-origin) )
+                                                        cylinder-origin))
                                          (radius . ,cylinder-radius)
                                          (length . ,cylinder-length)
@@ -418 +423 @@
                                          ,@(if (null? spines) '() `((spine-density-linear . ,(/ (length spines) cylinder-length))))
                                          )
-                                  `(Terminal (origin . ,cylinder-origin) 
+                                  `(Terminal (origin . ,(or (and permute-coords (permute-coords cylinder-origin) )
+                                                            cylinder-origin))
                                              (radius . ,cylinder-radius)
                                              (branch-order-Soma . ,(s32vector-ref node-depths node))
@@ -436 +442 @@
                   
                   (cons
-                   `(Branch (origin . ,branch-origin) 
+                   `(Branch (origin . ,(or (and permute-coords (permute-coords branch-origin) )
+                                           branch-origin))
                             (radius . ,branch-radius)
                             (branch-order-Soma . ,(s32vector-ref node-depths node))
@@ -608 +615 @@
     (d "data directory is ~s~%" (get-data-dir))
 
-    (let* ((data-map
+    (let* ((format (string->symbol (or (opt 'format) (defopt 'format))))
+           (data-map
             (concatenate
              (map (lambda (p)
@@ -618 +626 @@
                                   (elms (append contours trees)) 
                                   (data-map '()))
+
                         (if (null? keys)
-                            (if (null? elms) data-map (error "elements with unknown color" elms))
+                            (if (null? elms) data-map (if (equal? format 'ng) data-map (error "elements with unknown color" elms)))
                             (let-values (((lst rest)  (partition-by-key elms (car keys) key=?)))
                               (recur (cdr keys) rest (cons (cons (car keys) (map cadr lst)) data-map)))))
@@ -627 +636 @@
            )
 
-      (let ((format (string->symbol (or (opt 'format) (defopt 'format)))))
 
         (case format
@@ -653 +661 @@
 
           ((ng)
-           (for-each (lambda (f x) 
-                       (with-output-to-file f
-                         (lambda () 
-                           (pp  (make-ng (make-tree-graph 'neurolucida x)) (current-output-port)))))
-                     (map (lambda (x) (make-pathname ddir (car (string-split (cadar x) "#")) "ng")) data-map)
-                     data-map))
-
+           (let* ((permute-coords (opt 'permute-coords))
+                  (permute-coords (and permute-coords
+                                       (let ((permute-coords (map string->number (string-split permute-coords ","))))
+                                         (if (not (and (list? permute-coords)
+                                                       (= (length permute-coords) 3)
+                                                       (every (lambda (x) (and (integer? x) (<= 1 x) (>= 3 x))) permute-coords)))
+                                             (error "invalid point coordinate permutation indices" permute-coords))
+                                         (let ((permute-coords (map (lambda (i) (- i 1)) permute-coords)))
+                                           (lambda (p) (map (lambda (i) (list-ref p i)) permute-coords))
+                                           ))
+                                       ))
+                  )
+                                           
+             (for-each (lambda (f x) 
+                         (with-output-to-file f
+                           (lambda () 
+                             (pp (make-ng (make-tree-graph 'neurolucida x) permute-coords: permute-coords)
+                                 (current-output-port)))))
+                       (map (lambda (x) (make-pathname ddir (car (string-split (cadar x) "#")) "ng")) data-map)
+                       data-map)
+             ))
           ))
-      )))
+      ))
 
 (main)