use strict;
use Win32::SerialPort;

# user control
######
#  STILL TO DO
#####
# PROMPT USER FOR INPUT

#   Z axis is Velmex Bislide E01
#   E01 -  1 step = 0.00025"
#   X, Y axis is Velmex Bislide E04
#   E04 - 1 step = 0.001"

my $number_of_plates = 0;
my $number_of_filters = 0;
my $replicate_spots_per_filter = 0;
my $replicate_hits_per_spot = 0;
my $pause_every_plate = 0;
my $temp_pause = '';
my $z_speed_liquid = 0;
my $ready_to_go = 0;
#  need to be 4 cm higher 
#  4 cm = 1.57480315" devided by 0.00025 (inches per step)
#  = 6299.213  steps
my $y_adjust = 5300 - 6250;#jg changed from 6000 to 6250 Nov07,2005
while ($ready_to_go == 0){

print "INPUT:  Number of Source Plates\n";
$number_of_plates = <STDIN>;
chomp $number_of_plates;
print "INPUT:  Number of Destination Filters\n";
$number_of_filters = <STDIN>;
chomp $number_of_filters;
print "INPUT:  Number of Replicate Spots per Filter\n";
$replicate_spots_per_filter = <STDIN>;
chomp $replicate_spots_per_filter;
print "INPUT:  Number of Replicate Hits per Spot\n";
$replicate_hits_per_spot = <STDIN>;
chomp $replicate_hits_per_spot;

#  print "INPUT:  Speed coming in and out of plates and filters\n";
#  $z_speed_liquid = <STDIN>;
#  chomp $z_speed_liquid;
$z_speed_liquid = 2000;

print "INPUT:  Pause After Every OTHER Plate (1=yes, 0=no)\n";
$pause_every_plate = <STDIN>;
chomp $pause_every_plate;
my $temp_pause = "";
if($pause_every_plate == 0){
	$temp_pause = "NOT";
	}

print "It appears that you plan to print from $number_of_plates source plates\n";
print "to $number_of_filters destination filters.  You wish each sample\n";
print "to be replicate spotted $replicate_spots_per_filter times\n";
print "and each spot to be hit $replicate_hits_per_spot times.\n";
print "You do $temp_pause wish to pause after every OTHER plate (to remove a lid, etc.).\n\n";
my $temp_product = $number_of_plates * $replicate_spots_per_filter;
print "$number_of_plates times $replicate_spots_per_filter equals $temp_product total spots per filter\n\n";
print "Is the above information all correct (1=yes, 0=no)???\n";
$ready_to_go = <STDIN>;
if($temp_product > 12){
	$ready_to_go = 0;
	print "You want to print too many spots\n";
	}
}


####
#  STILL TO DO
####
# files of positions and offsets
# these are hardwired at the moment
my $filter_definition_file = "filters.in";

# ideally I would like to read these in
my @x_filter_offset_positions = (0, 53, 106, 27, 80, 133, 0, 53, 106, 27, 80, 133);
my @y_filter_offset_positions = (0, 0, 0, 39, 39, 39, 79, 79, 79, 118, 118, 118);

my @x_wash_positions = (0,0,0,0);
my @y_wash_positions = (1500,5250,9000,12750);
my @x_plate_positions = (6000, 6030, 6004, 6004, 12010, 12000);
my @y_plate_positions = (20, 3997, 8015, 12015, 5, 3990);
my @x_filter_positions = (18000, 18000, 18000, 18000, 23000, 23000, 23000, 23000, 28000, 28000, 28000, 28000, 33000, 33000, 33000, 33000, 38000, 38000, 38000, 38000, 43000, 43000, 43000, 43000, 48000, 48000, 48000, 48000);
my @y_filter_positions = (0, 3850, 7700, 11550, 0, 3850, 7700, 11550, 0, 3850, 7700, 11550, 0, 3850, 7700, 11550, 0, 3850, 7700, 11550, 0, 3850, 7700, 11550, 0, 3850, 7700, 11550);

# speeds and heights
my $x_speed = 3000;
my $y_speed = 3000;
my $z_speed = 2000;
#  speed in plates and touching membrane
#  my $z_speed_liquid = 2000;
my $time_of_pause = 30;
$time_of_pause = $time_of_pause*10;

# heights
my $z_safe_up = 9921 - $y_adjust;
my $z_filter_down = 15000 - $y_adjust;
my $z_plate_down = 14200 - $y_adjust;
my $z_wash_down = 13780 - $y_adjust;
my $z_plate_and_filter_up = 11000 - $y_adjust;             #safe for plates and filters BUT NOT WASH
#  11750 safe for 384 thermocycle
my $z_plate_change_speed = 12800 - $y_adjust;              #change speed pulling out of plates
my $z_filter_change_speed = 14200 - $y_adjust;             #change speed pulling out of filters

# mapping of motors
# changing these would be VERY VERY BAD
# do not ever change these unless you REALLY REALLY know what you are doing
my $x_motor = 1;
my $y_motor = 3;
my $z_motor = 2;

########################
#  MAIN PROGRAM STARTS HERE
########################

my $wait_for_it = '';

# start talking to COM
my $ob = Win32::SerialPort->new ('COM1') || die;
$ob->user_msg(1); 	# misc. warnings
$ob->error_msg(1); 	# hardware and data errors
#initialize COM1
$ob->baudrate(9600);
$ob->parity("none");
#   $ob->parity_enable(1); 	  # for any parity except "none"
$ob->databits(8);
$ob->stopbits(1);
$ob->handshake('none');
#write settings
$ob->write_settings;
$ob->save("tpj4.cfg");
print "wrote configuration file tpj4.cfg\n";

#open port for talking
$ob -> write("F");
home_machine();

my $current_offset = 0;
for(my $nop = 0; $nop < $number_of_plates; $nop++){
	print "WASHING TOOL\n";
        wash_pin_tool();
	
	my $platewait = '';
        if ($nop%6 == 0){
			# GO HIGH, pause and wait for user to load six more plates
			send_to_velmex( "C, IA".$z_motor."M500, R");
			send_to_velmex( "C,(IA".$y_motor."M200,IA".$x_motor."M23000,)R");
			print "PLEASE LOAD SIX NEW PLATES\n";
			print "After loading plates press return to continue\n";
			$platewait = <STDIN>;
			}
	#  n_pause is normally equal to 2 (pause after every other plate
	#  by it may be useful to set it to other numbers for testing
	#  for example setting it equal to 1 would pause after EVERY plate	

	my $n_pause = 2;

        if($pause_every_plate & $nop%$n_pause ==  0){
        	# pause and wait for user to remove lid etc.
        	send_to_velmex( "C, IA".$z_motor."M500, R");
			send_to_velmex( "C,(IA".$y_motor."M200,IA".$x_motor."M23000,)R");
            print "PLEASE REMOVE LID OF PLATE NUMBERS  ".($nop+1)." AND ".($nop+2)."\n";
        	print "After removing lid press return to continue\n";
            $platewait = <STDIN>;
            }
          for(my $rhps = 0; $rhps < $replicate_hits_per_spot; $rhps++){
        	for(my $rspf = 0; $rspf < $replicate_spots_per_filter; $rspf++){
               for(my $nof = 0; $nof < $number_of_filters; $nof++){
				print "Source Plate = ".($nop+1).", Replicate Spot = ".($rspf+1).", Hit Number = ".($rhps+1).", Filter number = ".($nof+1)."\n";
                     get_sample($nop%6);
                     put_sample($nof,$current_offset);
                     } #nof
                # if doing replicate spots up offset
                $current_offset++;
                } #rspf

#Note:  this seems funny but it is better to loop through
#       all spots and filters before re-hitting in order
#       to maximize print yield

			$current_offset = $current_offset - $replicate_spots_per_filter;
            } #rhps
		$current_offset = $current_offset + $replicate_spots_per_filter;
        } #nop

# final wash and home
wash_pin_tool();
send_to_velmex( "C, IA".$z_motor."M200, R");
send_to_velmex( "C,(IA".$y_motor."M200,IA".$x_motor."M200,)R");
$ob -> write("Q");
undef $ob;

exit;

############functions#########


###################
#  get sample from plate
###################
sub get_sample{
        my ($plate_number) = @_;

        #  position xy, z = speed change, slow, z = bottom, z = speed change, fast, z = filter&plate height
        send_to_velmex( "C,(IA".$y_motor."M".$y_plate_positions[$plate_number].",IA".$x_motor."M".$x_plate_positions[$plate_number].",)R");
#        send_to_velmex( "C, IA".$z_motor."M".$z_plate_change_speed.", R");
#        send_to_velmex( "C, S".$z_motor."M".$z_speed_liquid.", R");
        send_to_velmex( "C, IA".$z_motor."M".$z_plate_down.", R");


#  my $platewait = '';
#  print "After checking position press return to continue\n";
#  $platewait = <STDIN>;




#        send_to_velmex( "C, IA".$z_motor."M".$z_plate_change_speed.", R");
#        send_to_velmex( "C, S".$z_motor."M".$z_speed.", R");
        send_to_velmex( "C, IA".$z_motor."M".$z_plate_and_filter_up.", R");
        return;
        }


###################
#  print sample to filter
###################
sub put_sample{
        my ($filter_number,$offset_number) = @_;

        # filternumber + offset
        my $true_x = $x_filter_positions[$filter_number] + $x_filter_offset_positions[$offset_number];
        my $true_y = $y_filter_positions[$filter_number] + $y_filter_offset_positions[$offset_number];
        #  position xy, z = speed change, slow, z = bottom, z = speed change, fast, z = filter&plate height
        send_to_velmex( "C,(IA".$y_motor."M".$true_y.",IA".$x_motor."M".$true_x.",)R");
# 1/2 second pause as per sjm Oct 13/05
        send_to_velmex( "C, P5, R");
       
#        send_to_velmex( "C, IA".$z_motor."M".$z_filter_change_speed.", R");
#        send_to_velmex( "C, S".$z_motor."M".$z_speed_liquid.", R");
        send_to_velmex( "C, IA".$z_motor."M".$z_filter_down.", R");
#        send_to_velmex( "C, IA".$z_motor."M".$z_filter_change_speed.", R");
#        send_to_velmex( "C, S".$z_motor."M".$z_speed.", R");
        send_to_velmex( "C, IA".$z_motor."M".$z_plate_and_filter_up.", R");
        return;
        }


##################
#   wash pins and pause
##################
sub wash_pin_tool{

        for(my $ii = 0; $ii < 4; $ii++){
                #safe height, wash 1, down, shake-n-bake
                send_to_velmex( "C, IA".$z_motor."M".$z_safe_up.", R");
                send_to_velmex( "C,(IA".$y_motor."M".$y_wash_positions[$ii].",IA".$x_motor."M".$x_wash_positions[$ii].",)R");
                send_to_velmex( "C, IA".$z_motor."M".$z_wash_down.", R");
                send_to_velmex( "C, LM0, I1M100, I1M-100, L5, R");
                }
        # safe height, pause
        send_to_velmex( "C, IA".$z_motor."M".$z_safe_up.", R");
        send_to_velmex( "C, P".$time_of_pause.", R");
        return;
        }


###########
#  home all 3 axis
#  go to safe height
###########
sub home_machine{

        # slow speed
		send_to_velmex( "C, S2M200, R");
        send_to_velmex( "C, S1M200, R");
        send_to_velmex( "C, S3M200, R");
        # home
        send_to_velmex( "C, I2M-0, I2M200, IA2M-0,R");
        send_to_velmex( "C, I1M-0, I1M200, IA1M-0,R");
        send_to_velmex( "C, I3M-0, I3M200, IA3M-0,R");
        # return to fast speeds
        send_to_velmex( "C, S".$z_motor."M".$z_speed.", R");
        send_to_velmex( "C, S".$x_motor."M".$x_speed.", R");
        send_to_velmex( "C, S".$y_motor."M".$y_speed.", R");
        # go to safe height
        return;
        }
        
################
#   send commands to the arrayer
################
sub send_to_velmex{
    my ($print_command) = @_;
    
	#  print "Here is the command to send to Velmex   ".$print_command."\n";
	$ob -> write($print_command);
	my $result = '';
	do{
		$result = $ob->input;
		} until ($result eq '^');
	#  print "Command Has Now Run, Press Return to Continue\n";
	#  $wait_for_it = <STDIN>;
	return;       
    }