;;
;; A model of the projections between Golgi and granule cells in
;; cerebellar granular layer.
;;
;; Copyright 2012-2014 Ivan Raikov and the Okinawa Institute of Science and Technology
;;
;; This program is free software: you can redistribute it and/or
;; modify it under the terms of the GNU General Public License as
;; published by the Free Software Foundation, either version 3 of the
;; License, or (at your option) any later version.
;;
;; This program is distributed in the hope that it will be useful, but
;; WITHOUT ANY WARRANTY; without even the implied warranty of
;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
;; General Public License for more details.
;;
;; A full copy of the GPL license can be found at
;; <http://www.gnu.org/licenses/>.
;;

(picnic-model GL

      (

       (config PFlength)

       (config PCLdepth)

       (config numAxonGolgi)  ;; GoC axonal dimensions
       (config GoC_Axon_Xmin)
       (config GoC_Axon_Xmax)
       (config GoC_Axon_Ymin)
       (config GoC_Axon_Ymax)
       (config GoC_Axon_Zmin)
       (config GoC_Axon_Zmax)

       (config GoC_nDendML) ;; GoC # of apical dendrites
       (config GoC_nDendGL) ;; GoC # of basolateral dendrites

       (config GoC_Ad_nseg) ;; GoC apical dendrites number of segments
       (config GoC_Ad_nsegpts) ;; GoC apical dendrites number of points per segment

       (config GoC_Bd_nseg)
       (config GoC_Bd_nsegpts)

       (config GoC_PhysApicalDendH)
       (config GoC_PhysApicalDendR)
       (config GoC_Atheta_min )
       (config GoC_Atheta_max )
       (config GoC_Atheta_stdev)

       (config GoC_PhysBasolateralDendH)
       (config GoC_PhysBasolateralDendR)
       (config GoC_Btheta_min )
       (config GoC_Btheta_max )
       (config GoC_Btheta_stdev)

       (config AAtoGoCzone)
       (config PFtoGoCzone)
       (config GoCtoGoCzone)
       (config GoCtoGoCgapzone)

       (config GoCxrange)
       (config GoCyrange)

       (const xExtent = GoCxrange)
       (const yExtent = GoCyrange)


       (component (type local-cell-forest) (name GC)


         (component (type layout) (name GranuleTcoordinates)

                    (s = (PointsFromFile ("GCTcoordinates.dat")))
		  
                    (output s)
            )

         (component (type section) (name AscendingAxons)
                    
                    (defun f (gid origin)
                      (let ((dX 0)
                            (dY 0)
                            (dZ (neg (PCLdepth))))
                        LineSegment (origin dX dY dZ)
                        ))

                    (const n = 1)

                    (p (u) = (generator f) (npts 4))
                    
                    (output u n)

                    )
         
         
         (component (type section) (name ParallelFibers)

                    (defun f (gid origin)
                      (let ((dX (PFlength / 2))
                            (dY 0)
                            (dZ 0))
                        LineSegment (origin dX dY dZ)))

                    (defun g (gid origin)
                      (let ((dX (PFlength / 2))
                            (dY 0)
                            (dZ 0))
                        LineSegment (origin ~ (neg (dX)) ~ dY ~ dZ)))
                    
                    (const n = 1)

                    ;; process u grows in the positive X direction
                    ;; process v grows in the negative X direction
                    (p (u) = (generator f) (npts 200))
                    (p (v) = (generator g) (npts 200))
                    
                    (output u n v n)

                    )
         
         

         )
         

       (component (type cell-forest) (name GoC)

         (component (type layout) (name GolgiCoordinates)

                    (s = (PointsFromFile ("GoCcoordinates.dat")))
		  
                    (output s)
            )
         
         (component (type section) (name BasolateralDendrites)


                    (defun f (gid origin init)
                      (let (
                            (thetaDeg (randomNormal (GoC_Btheta_min GoC_Btheta_stdev init)))
                            (theta    ((PI / 180.) * thetaDeg))

                            (dX (GoC_PhysBasolateralDendR * cos (theta)))
                            (dY (GoC_PhysBasolateralDendR * sin (theta)))
                            (dZ GoC_PhysBasolateralDendH)
                            )
                    
                        LineSegment (origin dX dY dZ)))

                    (defun g (gid origin init)
                      (let (
                            (thetaDeg (randomNormal (GoC_Btheta_max GoC_Btheta_stdev init)))
                            (theta    ((PI / 180.) * thetaDeg))

                            (dX (GoC_PhysBasolateralDendR * cos (theta)))
                            (dY (GoC_PhysBasolateralDendR * sin (theta)))
                            (dZ GoC_PhysBasolateralDendH)
                            )
                    
                        LineSegment (origin dX dY dZ)))

                    (const n = 1)

                    (segp (u) = (generator f) (initial (randomInit (13))) 
                                (nsegs GoC_Bd_nseg) (nsegpts GoC_Bd_nsegpts))

                    (segp (v) = (generator g) (initial (randomInit (13))) 
                                (nsegs GoC_Bd_nseg) (nsegpts GoC_Bd_nsegpts))
                    
                    (output u n v n)

                    )

         (component (type section) (name ApicalDendrites)

                    (defun f (gid origin init)
                      (let (
                            (thetaDeg (randomNormal (GoC_Atheta_min GoC_Atheta_stdev init)))
                            (theta    ((PI / 180.) * thetaDeg))

                            (dX (GoC_PhysApicalDendR * cos (theta)))
                            (dY (GoC_PhysApicalDendR * sin (theta)))
                            (dZ GoC_PhysApicalDendH)
                            )
                    
                        LineSegment (origin dX dY dZ)))
                    
                    (defun g (gid origin init)
                      (let (
                            (thetaDeg (randomNormal (GoC_Atheta_max GoC_Atheta_stdev init)))
                            (theta    ((PI / 180.) * thetaDeg))

                            (dX (GoC_PhysApicalDendR * cos (theta)))
                            (dY (GoC_PhysApicalDendR * sin (theta)))
                            (dZ GoC_PhysApicalDendH)
                            )
                    
                        LineSegment (origin dX dY dZ)))
                    
                    (const n = 1)

                    (segp (u) = (generator f) (initial (randomInit (17)))
                                (nsegs GoC_Ad_nseg) (nsegpts GoC_Ad_nsegpts))
                    
                    (segp (v) = (generator g) (initial (randomInit (17)))
                                (nsegs GoC_Ad_nseg) (nsegpts GoC_Ad_nsegpts))
                    
                    (output u n v n)

                    )

         (component (type section) (name Axons)
                    
                    (const n = numAxonGolgi)

                    (defun f (gid origin init)
                      (let ((dX (randomUniform (GoC_Axon_Xmin GoC_Axon_Xmax init)))
                            (dY (randomUniform (GoC_Axon_Ymin GoC_Axon_Ymax init)))
                            (dZ (randomUniform (GoC_Axon_Zmin GoC_Axon_Zmax init))))
                        LineSegment (origin dX dY dZ)))

                    (p (u) = (generator f) (initial (randomInit (23))))
                    
                    (output u n)

                    )

         )

       (component (type projection) 

            (input (GC from cell-forests)
                   (GoC from cell-forests))

            (r = PFtoGoCzone)

            (set source = (section GC ParallelFibers))
            (set target = (section GoC ApicalDendrites))

            (PFtoGoC = (SegmentProjection (r source target)))

            (output PFtoGoC)
            )


       (component (type projection) 

            (input (GC from cell-forests)
                   (GoC from cell-forests))

            (r = AAtoGoCzone)

            (set source = (section GC AscendingAxons))
            (set target = (union
                           (section GoC ApicalDendrites)
                           (section GoC BasolateralDendrites)
                           ))

            (AAtoGoC = (SegmentProjection (r source target)))

            (output AAtoGoC)
            )

       (component (type projection) 

            (input (GoC from cell-forests))

            (r = GoCtoGoCzone)

            (set source = (section GoC Axons))
            (set target = (population GoC))

            (GoCtoGoC = (Projection (r source target)))

            (output GoCtoGoC)
            )

       (component (type projection) 

            (input (GoC from cell-forests))

            (r = GoCtoGoCgapzone)

            (set source = (population GoC))
            (set target = (population GoC))

            (GoCtoGoCgap = (Projection (r source target)))

            (output GoCtoGoCgap)
            )

       
       ))