/* do not call externally; used to seek file pointer to start of file
*/
void _config_reset()
{
if(fseek(config_file, SEEK_SET, 0) != 0)
{
p_log_errorno("ERROR:\tconfig_reset: fseek(SEEK_SET,0)");
exit(0);
}
clearerr(config_file);
}
int ReceiveFCNum(char *argv, int portnum)
{
int sock; // socket descriptor
int bytesRcvd, totalBytesRcvd=0; // bytes read in single rcv() and total bytes read
char errorString[255];
char sendBuffer[] = "3"; //CODE OF 3 ASKS SENDER FOR FCNUM
char rcvbyte; // return arg
char log_string[255];
sock = GetSock(argv, portnum);
bytesRcvd = 0;
totalBytesRcvd = 0;
// tell server we're ready for the fcnum
if(send(sock, sendBuffer, 1, 0) != 1)
{
p_log_errorno((char*)"send() from client to request data failed");
exit(0);
}
// wait for full block to be received
while(totalBytesRcvd < 1)
{
if((bytesRcvd = recv(sock, &rcvbyte, 1, 0)) <= 0)
{
sprintf(errorString, "recv() failed or connection closed prematurely, %d bytes received",
totalBytesRcvd);
close(sock);
p_log_errorno(errorString);
exit(0);
}
totalBytesRcvd += bytesRcvd;
}
if(shutdown(sock, 2) < 0)
{
p_log_errorno((char*)"ERROR shutdown(sock)");
}//close(sock);
return (int) rcvbyte;
}
int main(int argc, char *argv[])
{
FILE *regfile;
FILE *posfile;
FILE *logfile;
FILE *dualfcoffsetfile;
fpos_t offsetval;
char regfilename[200];
char logfilename[200];
char log_string[255];
int i, j, k, l;
int curr_fc, curr_array, curr_img, curr_numobjs;
int num_fcs;
short unsigned int *curr_img_x;
short unsigned int *curr_img_y;
short unsigned int *regindices;
short unsigned int temp;
srand((unsigned)time(NULL) );
srandom((unsigned)time(NULL));
start_logger((char*)"initialize_processor-log", 1);
if(argc !=3 )
{
sprintf(log_string, "Usage: %s <Position file> <Number of flowcells>", argv[0]);
p_log(log_string);
exit(0);
}
num_fcs = atoi(argv[2]);
if( (dualfcoffsetfile = fopen("DUAL_FC_REGOFFSET.dat", "wb"))==NULL)
{
sprintf(log_string, "ERROR opening offset file DUAL_FC_REGOFFSET.dat for output");
p_log_errorno(log_string);
exit(0);
}
if((curr_img_x = (short unsigned int*) malloc(MAX_BEADS_PERFRAME * sizeof(short unsigned int))) == NULL)
{
p_log_errorno((char*)"ERROR allocating memory for curr_img_x");
exit(0);
}
if((curr_img_y = (short unsigned int*) malloc(MAX_BEADS_PERFRAME * sizeof(short unsigned int))) == NULL)
{
p_log_errorno((char*)"ERROR allocating memory for curr_img_y");
exit(0);
}
if((regindices = (short unsigned int*) malloc(REG_PIXELS * sizeof(short unsigned int))) == NULL)
{
p_log_errorno((char*)"ERROR allocating memory for regindices");
exit(0);
}
strcpy(regfilename, argv[1]);
strcat(regfilename, ".reg");
sprintf(log_string, "Generating .reg file %s from position file %s with %d beads per image (random)",
regfilename,
argv[1],
REG_PIXELS);
p_log(log_string);
strcpy(logfilename, argv[1]);
strcat(logfilename, ".reglog");
sprintf(log_string, "Logging positions used to file %s", logfilename);
p_log(log_string);
if( (posfile=fopen(argv[1], "rb")) == NULL)
{
sprintf(log_string, "ERROR opening position file %s for input", argv[1]);
p_log_errorno(log_string);
exit(0);
}
if( (regfile=fopen(regfilename, "wb")) == NULL)
{
sprintf(log_string, "ERROR opening reg file %s for output", argv[2]);
p_log_errorno(log_string);
exit(0);
}
if( (logfile=fopen(logfilename, "wb")) == NULL)
{
sprintf(log_string, "ERROR opening reglog file %s for output", argv[2]);
p_log_errorno(log_string);
exit(0);
}
// loop through FC, ARRAY, IMAGE:
for(i=0; i < num_fcs; i++)
{
for(j=0; j < ARRAYS_PER_FC; j++)
{
for(k=0; k < IMGS_PER_ARRAY; k++)
{
// load positions for current image
// ------
// each 'record' in the pos file is as follows:
// 4 bytes: -1
// 4 bytes: flowcell # ([0..num_fcs])
// 4 bytes: array # ([0..ARRAYS_PER_FC])
// 4 bytes: image # ([0..IMGS_PER_ARRAY])
// 4 bytes: # of beads
// 2 bytes: beadpos_xcol
// 2 bytes: beadpos_yrow
// ...
// 2 bytes: 0
//
// ------
if( (fread(&curr_fc, sizeof(int), 1, posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_fc(1) from posfile");
}
if( (fread(&curr_fc, sizeof(int), 1, posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_fc(2) from posfile");
}
if( (fread(&curr_array, sizeof(int), 1, posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_array from posfile");
}
if( (fread(&curr_img, sizeof(int), 1, posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_img from posfile");
}
if( (fread(&curr_numobjs, sizeof(int), 1, posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_numobjs from posfile");
}
// make sure we are where we think we are in the position file
if( (curr_fc != i) || (curr_array != j)|| (curr_img != k))
{
sprintf(log_string, "ERROR: expecting %d %d %d from position file, and read %d %d %d",
i, j, k,
curr_fc, curr_array, curr_img);
p_log(log_string);
exit(0);
}
sprintf(log_string, "Position %d %d %d... %d objects", i, j, k, curr_numobjs);
p_log(log_string);
for(l=0; l < curr_numobjs; l++)
{
if((fread(curr_img_x+l, sizeof(short unsigned int), 1, posfile)) < 1)
{
sprintf(log_string, "ERROR reading x from posfile at %d %d %d %d",
i, j, k, l);
p_log_errorno(log_string);
}
if((fread(curr_img_y+l, sizeof(short unsigned int), 1, posfile)) < 1)
{
sprintf(log_string, "ERROR reading y from posfile at %d %d %d %d",
i, j, k, l);
p_log_errorno(log_string);
}
}
// make sure we are where we think we are in the position file
if( (fread(&temp, sizeof(short unsigned int), 1, posfile)) < 1)
{
p_log_errorno((char*)"ERROR reading curr_img from posfile");
}
if(temp != 0)
{
sprintf(log_string, "ERROR: expecting delimiter value of 0, read %d", temp);
p_log(log_string);
exit(0);
}
// generate list of random coords and log to reglog, 2 bytes per position
// as we generate them, output corresponding position values to regfile
for(l = 0; l < REG_PIXELS; l++)
{
if(curr_numobjs < 100)
{
*(regindices + l) = randdist(0, NUM_XCOLS-1);
}
else
{
*(regindices + l) = randdist(0, curr_numobjs-1);
}
if((fwrite(regindices+l, sizeof(short unsigned int), 1, logfile)) < 1)
{
sprintf(log_string, "ERROR writing to reglog at %d %d %d %d", i, j, k, l);
p_log_errorno(log_string);
exit(0);
}
if((fwrite(curr_img_x+(*(regindices+l)), sizeof(short unsigned int), 1, regfile)) < 1)
{
sprintf(log_string, "ERROR writing x to regfile at %d %d %d %d: %d",
i,j,k,l,*(regindices+l));
p_log_errorno(log_string);
exit(0);
}
if((fwrite(curr_img_y+(*(regindices+l)), sizeof(short unsigned int), 1, regfile)) < 1)
{
sprintf(log_string, "ERROR writing y to regfile at %d %d %d %d: %d",
i,j,k,l,*(regindices+l));
p_log_errorno(log_string);
exit(0);
}
}
} // end for k
} // end for j
if( i == 0 )
{
fgetpos(regfile, &offsetval);
fwrite(&offsetval, sizeof(fpos_t), 1, dualfcoffsetfile);
fclose(dualfcoffsetfile);
}
} // end for i
fclose(posfile);
fclose(regfile);
}
int GetSock(char *argv,
int port) {
int sock; // socket descriptor
struct sockaddr_in servAddr; // server address
unsigned short servPort; // server port
char *servIP; // server IP address
char errorString[255];
struct hostent *h;
struct in_addr a;
int flag = 1;
int result;
int waiting_to_connect = 0;
servIP = argv;
servPort = port;
fprintf(stdout, "GetSock:\tConnecting to server %s on port %d\n", servIP, servPort);
if ((sock = socket(PF_INET, SOCK_STREAM, IPPROTO_TCP)) < 0) {
perror(NULL);
fprintf(stdout, "ERROR: socket() failed\n");
exit(1);
}
fprintf(stdout, "GetSock:\tResolving hostname...\n");
h=gethostbyname(servIP);
bcopy(*h->h_addr_list, (char*) &a, sizeof(a));
fprintf(stdout, "GetSock:\tHost address: %s\n", inet_ntoa(a));
memset(&servAddr, 0, sizeof(servAddr));
servAddr.sin_family = AF_INET;
servAddr.sin_addr.s_addr = inet_addr(inet_ntoa(a));
// servAddr.sin_addr.s_addr = inet_addr(servIP);
servAddr.sin_port = htons(servPort);
result = setsockopt(sock, IPPROTO_TCP, TCP_NODELAY, (char*)&flag, sizeof(int));
if(result<0) {
p_log_errorno((char*)"ERROR SETTING TCP_NODELAY ON SOCKET");
}
while(connect(sock, (struct sockaddr *) & servAddr, sizeof(servAddr)) < 0) {
if(waiting_to_connect) {
;
}
else
{
fprintf(stdout, "GetSock:\tWaiting to connect to server ...\n");
waiting_to_connect = 1;
}
}
/*
if(connect(sock, (struct sockaddr *) & servAddr, sizeof(servAddr)) < 0){
perror(NULL);
DieWithError("connect() failed");
}
*/
return sock;
}
void ReceiveData(char *argv, int portnum,
short unsigned int *reg_pix_list_xcols,
short unsigned int *reg_pix_list_yrows,
FILE *full_pixel_list,
short unsigned int *beadvals,
FILE *beadfile,
FILE *sumfile,
FILE *imgsumfile,
FILE *reglogfile,
int curr_fcnum)
{
int sock; // socket descriptor
unsigned int data_size; // length of data block to receive
int bytesRcvd, totalBytesRcvd=0; // bytes read in single rcv() and total bytes read
int imagesRcvd=0;
char errorString[255];
char log_string[255];
char sendBuffer[] = "18"; //CODE OF 1/8 ASKS SENDER FOR DATA
short unsigned int *inputBuffer;//
short unsigned int img_err_code;
int i, j, k;
int *offsetx_history, *offsety_history;
clock_t time1, time2;
int num_loops;
int connection_isok=1;
char command_buffer[255];
char image_dir[255];
sprintf(image_dir, "%s/polonator/G.007/acquisition/images", getenv("HOME"));
sprintf(command_buffer, "mkdir -p %s", image_dir);
system(command_buffer);
#ifdef SAVE_FL_IMAGES
char outputfilename[255];
FILE *imgfile;
#endif
sock = GetSock(argv, portnum);
data_size = ((NUM_XCOLS * NUM_YROWS)+4) * sizeof(short unsigned int);
if( (inputBuffer=(short unsigned int *)malloc(data_size)) == NULL)
{
p_log_errorno((char*)"malloc() failed");
}
//ALLOCATE MEMORY FOR OFFSET HISTORY ARRAYS (USED BY PROCESSIMAGE_REGISTER)
if((offsetx_history=(int*)malloc(OFFSET_HISTORY_LENGTH * sizeof(int))) == NULL)
{
p_log_errorno((char*)"malloc() offsetx_history failed");
exit(0);
}
if((offsety_history=(int*)malloc(OFFSET_HISTORY_LENGTH * sizeof(int))) == NULL)
{
p_log_errorno((char*)"malloc() offsety_history failed");
exit(0);
}
for(i=0; i < OFFSET_HISTORY_LENGTH; i++)
{
*(offsetx_history + i) = 0;
*(offsety_history + i) = 0;
}
//TELL SENDER WE WANT TO RECEIVE DATA
if(send(sock, sendBuffer, 1, 0)!=1)
{
if(errno = EPIPE)
{
p_log_errorno((char*)"ERROR:\tReceivData: send() failed because connection is broken");
connection_isok=0;
}
else
{
p_log_errorno((char*)"send() from client to request data failed");
exit(0);
}
}
if(send(sock, sendBuffer+1, 1, 0) !=1 )
{
if(errno = EPIPE)
{
p_log_errorno((char*)"ERROR:\tReceivData: send() failed because connection is broken");
connection_isok=0;
}
else
{
p_log_errorno((char*)"send() from client to request data failed");
exit(0);
}
}
//CONSUME 'PRIMIMG' DATA SINCE FIRST IMAGE XFER
//IS VERY SLOW
if(connection_isok)
{
bytesRcvd=0;
totalBytesRcvd=0;
while(totalBytesRcvd < data_size)
{
if((bytesRcvd=recv(sock, ((char*)inputBuffer)+totalBytesRcvd, data_size-totalBytesRcvd, 0)) < 0)
{
sprintf(errorString, "recv() failed or connection closed prematurely, %d bytes received (%d)", totalBytesRcvd, bytesRcvd);
close(sock);
p_log_errorno(errorString);
exit(0);
}
else if(bytesRcvd == 0)
{
p_log((char*)"ERROR:\tReceiveData: connection is broken");
connection_isok = 0;
totalBytesRcvd=data_size;
}
totalBytesRcvd += bytesRcvd;
}
}
#ifdef SAVE_FL_IMAGES
sprintf(outputfilename, "mkdir -p %s/%s", image_dir, CYCLE_NAME);
system(outputfilename);
#endif
// loop through all images, receiving blocks of data (1 image + header per block)
if(connection_isok)
{
for(i=curr_fcnum; i < curr_fcnum + 1; i++)
{
for(j=0; j < ARRAYS_PER_FC; j++)
{
for(k=0; k < IMGS_PER_ARRAY; k++)
{
bytesRcvd = 0;
totalBytesRcvd = 0;
// tell server we're ready for the next block
#ifdef DEBUG1
p_log((char*)"STATUS:\tReceiveData: request data from server");
p_log((char*)"STATUS:\tReceiveData: send first byte to request");
#endif
if(send(sock, sendBuffer, 1, 0) != 1)
{
if(errno = EPIPE)
{
p_log_errorno((char*)"ERROR:\tsend() failed because connection is broken");
connection_isok=0;
totalBytesRcvd=data_size;
}
else
{
p_log_errorno((char*)"ERROR:\tsend() from client to request data failed");
exit(0);
}
}
#ifdef DEBUG1
p_log((char*)"STATUS:\tReceiveData: send second byte to request");
#endif
if(send(sock, sendBuffer+1, 1, 0) !=1 )
{
if(errno = EPIPE)
{
p_log_errorno((char*)"ERROR:\tsend() failed because connection is broken");
connection_isok = 0;
totalBytesRcvd = data_size;
}
else
{
p_log_errorno((char*)"ERROR:\tsend() from client to request data failed");
exit(0);
}
}
#ifdef DEBUG1
p_log((char*)"STATUS:\tReceiveData: start receiving data");
p_log((char*)"STATUS:\tReceiveData: wait for data to arrive");
#endif
// wait for full block to be received
while(totalBytesRcvd < data_size)
{
// was there an error during the recv? if so, this is bad; crash
if((bytesRcvd = recv(sock, ((char*)inputBuffer) + totalBytesRcvd, data_size-totalBytesRcvd, 0)) < 0)
{
sprintf(errorString, "recv() failed, %d bytes received (%d)", totalBytesRcvd, bytesRcvd);
close(sock);
p_log_errorno(errorString);
// do a graceful restart here
connection_isok = 0;
totalBytesRcvd = data_size;
bytesRcvd = 0;
}
// was the connection broken? if so, the acq software was probably stopped prematurely; recover gracefully
else if(bytesRcvd == 0)
{
sprintf(log_string, "connection to acq appears to be broken while trying to receive image %d %d %d, received %d bytes so far", i, j, k, totalBytesRcvd);
p_log(log_string);
connection_isok = 0;
totalBytesRcvd = data_size;
}
/*
#ifdef DEBUG1
sprintf(log_string, "STATUS:\tReceiveData: received %d bytes of image data", bytesRcvd);
p_log(log_string);
#endif
*/
totalBytesRcvd += bytesRcvd;
num_loops++;
}
if(!connection_isok)
{
i = curr_fcnum + 1;
j = ARRAYS_PER_FC;
k = IMGS_PER_ARRAY;
p_log((char*)"ERROR:\tReceiveData: connection was broken; exiting");
break;
}
p_log((char*)"STATUS:\tReceiveData: all data received for current image");
imagesRcvd++;
num_loops = 0;
// NOW THAT WE HAVE THE IMAGE, DO SOMETHING WITH IT
#ifdef SAVE_FL_IMAGES
if( (k % 100) == 0)
{
sprintf(outputfilename, "%s/%s/%02d_%04d.raw",
image_dir, CYCLE_NAME, *(inputBuffer+1), *(inputBuffer+2));
sprintf(log_string, "STATUS:\tReceiveData: write received data to image file %s",
outputfilename);
p_log(log_string);
imgfile = fopen(outputfilename, "w");
fwrite(inputBuffer+4, sizeof(short unsigned int), 1000000, imgfile);
fclose(imgfile);
}
#endif
#ifdef DEBUG1
sprintf(log_string, "STATUS:\tReceiveData: calling ProcessImage for frame %d %d %d, expecting %d %d %d",
*(inputBuffer),
*(inputBuffer+1),
*(inputBuffer+2),
i, j, k);
p_log(log_string);
#endif
ProcessImage(reg_pix_list_xcols,
reg_pix_list_yrows,
full_pixel_list,
inputBuffer + 4,
inputBuffer,
beadvals,
beadfile,
sumfile,
imgsumfile,
reglogfile,
offsetx_history,
offsety_history);
} // end for k
} // end for j
} // end for i
} // end if connection_isok
// tell acq we're finished receiving all data (we don't want it to close the connection
// before the processor finishes receiving the last image)
if(connection_isok)
{
if(send(sock, sendBuffer, 1, 0) != 1)
{
p_log_errorno((char*)"send() from client to signal all data received failed");
//exit(0);
}
if(shutdown(sock, 2) < 0)
{
p_log_errorno((char*)"ERROR on shutdown(sock)");
//exit(0);
}//close(sock);
}
free(offsetx_history);
free(offsety_history);
free(inputBuffer);
}
int run_autoexp(char *argv, int cell_num) {
FILE *full_pix_list;
FILE *regpixfile;
FILE *beadfile;
FILE *sumfile;
FILE *imgsumfile;
FILE *reglogfile;
FILE *bead_value_file;
FILE *bead_sum_file;
short unsigned int *reg_pix_list_xcols;
short unsigned int *reg_pix_list_yrows;
short unsigned int *beadvals;
int fcnum =0;
fpos_t pix_list_offset;
int reg_X_pointer_offset;
int reg_Y_pointer_offset;
int portnum;// = atoi(argv[2]);
char filename[255];
char autoefilename[255];
char autoefilename2[255];
char rcvfilename[255];
char posfilename[200];
char reglogfilename[200];
char temp_string[255];
char log_string[255];
char outputfilename[500];
int num_regs_skipped;
int num_fcs;
int i;
int h =0;
start_logger((char*)DEFAULT_PROCESSOR_LOGFILENAME, 1);
strcpy(posfilename, "autoexp_pos");
portnum = PORTNUM;
num_fcs = cell_num;
p_log((char*)"processor:\tAllocating memory for arrays ...");
if( (reg_pix_list_xcols=(short unsigned int*)malloc(REG_PIXELS*ARRAYS_PER_FC*15*sizeof(short unsigned int))) == NULL) {
p_log((char*)"malloc() for reg_pixel_list_xcols failed...");
}
if( (reg_pix_list_yrows=(short unsigned int*)malloc(REG_PIXELS*ARRAYS_PER_FC*15*sizeof(short unsigned int))) == NULL) {
p_log((char*)"malloc() for reg_pixel_list_yrows failed...");
}
if((beadvals=(short unsigned int*)malloc(MAX_BEADS_PERFRAME*sizeof(short unsigned int))) == NULL) {
p_log((char*)"malloc() for beadvals failed...");
}
memset(&pix_list_offset, 0, sizeof(pix_list_offset));
if( (full_pix_list = fopen(posfilename, "r")) == NULL) {
sprintf(log_string, "ERROR opening pixel list file %s", posfilename);
p_log(log_string);
perror(NULL);
return 1;
}
strcat(posfilename, ".reg");
if( (regpixfile = fopen(posfilename, "r")) == NULL) {
sprintf(log_string, "ERROR opening reg pixel list file %s", posfilename);
p_log(log_string);
exit(0);
}
//LOAD REGISTRATION PIXEL LIST INTO MEMORY
//IF A SET OF COORDS IS WITHIN THE BORDER
//OF THE IMAGE (SIZE SPECIFIED BY SEARCH_XCOLS
//AND SEARCH_YROWS, DO NOT USE THAT POINT -- INSTEAD,
//USE THE PREVIOUS POINT
num_regs_skipped=0;
sprintf(log_string, "processor:\tLoading regpix file %s ...", posfilename);
p_log(log_string);
sprintf(log_string, "processor:\tautoe %s ...", posfilename);
p_log(log_string);
for(i=0; i<(REG_PIXELS*ARRAYS_PER_FC*15); i++) {
if((fread(reg_pix_list_xcols+i, 2, 1, regpixfile)) < 1) {
sprintf(log_string, "ERROR reading from file regpix_list at data element %d", i);
p_log_errorno(log_string);
exit(0);
}
if((fread(reg_pix_list_yrows+i, 2, 1, regpixfile)) < 1) {
sprintf(log_string, "ERROR reading from file regpix_list at data element %d", i);
p_log_errorno(log_string);
exit(0);
}
if( (*(reg_pix_list_xcols+i) <= (SEARCH_XCOLS+MAX_ADDITIONAL_OFFSET+1)) ||
(*(reg_pix_list_yrows+i) <= (SEARCH_YROWS+MAX_ADDITIONAL_OFFSET+1)) ||
((NUM_XCOLS - *(reg_pix_list_xcols+i)) <= (SEARCH_XCOLS+MAX_ADDITIONAL_OFFSET+1)) ||
((NUM_YROWS - *(reg_pix_list_yrows+i)) <= (SEARCH_YROWS+MAX_ADDITIONAL_OFFSET+1)))
{
num_regs_skipped++;
if(i==0) {
*(reg_pix_list_xcols + i) = (int)(NUM_XCOLS/2);
*(reg_pix_list_yrows + i) = (int)(NUM_YROWS/2);
}
else {
*(reg_pix_list_xcols + i) = *(reg_pix_list_xcols + i - 1);
*(reg_pix_list_yrows + i) = *(reg_pix_list_yrows + i - 1);
}
} // end if
} // end for
fclose(regpixfile);
/* int percentage_skipped = (int)( ((float)(num_regs_skipped) / (REG_PIXELS)) * 100);*/
int percentage_skipped = num_regs_skipped*100.0 / (15*ARRAYS_PER_FC*REG_PIXELS);
int avg_regpix_perframe = REG_PIXELS - (int)( ((float)(percentage_skipped)/100) * REG_PIXELS);
sprintf(log_string, "processor:\tSkipped %d reg coords (%d%%), using avg of %d/%d reg pixels at window size %d/%d ...",
num_regs_skipped,
percentage_skipped,
avg_regpix_perframe,
REG_PIXELS,
SEARCH_XCOLS,
SEARCH_YROWS);
p_log(log_string);
ReceiveFilename(argv, portnum, rcvfilename);
/* p_log((char*)"processor:\tRequesting flowcell number from server ...");
fcnum = ReceiveFCNum(argv[1], portnum); */
strcpy(filename, "autoexp_images/beads/");
sprintf(temp_string, "%d_", fcnum);
strcat(filename, temp_string);
strcat(filename, rcvfilename);
#ifdef SAVE_FL_IMAGES
strcpy(CYCLE_NAME, temp_string);
strcpy(CYCLE_NAME, rcvfilename);
#endif
sprintf(log_string, "processor:\tReceived filename %s from server ...", rcvfilename);
p_log(log_string);
sprintf(temp_string, "autoexp_images/logs/%s.processorlog", rcvfilename);
change_logfile(temp_string);
p_log(log_string);
strcat(filename, ".beads");
if( (beadfile = fopen(filename, "wb")) == NULL) {
sprintf(log_string, "ERROR opening output bead file %s", filename);
p_log_errorno(log_string);
exit(0);
}
strcpy(autoefilename, "autoexp_images/");
strcat(autoefilename,CYCLE_NAME);
strcat(autoefilename,"_bead_value_file.txt");
if( (bead_value_file = fopen(autoefilename, "w")) == NULL) {
sprintf(log_string, "ERROR opening output bead file %s", filename);
p_log_errorno(log_string);
exit(0);
}
strcpy(autoefilename2, "autoexp_images/");
strcat(autoefilename2,CYCLE_NAME);
strcat(autoefilename2,"_bead_sum_file.txt");
if( (bead_sum_file = fopen(autoefilename2, "w")) == NULL) {
sprintf(log_string, "ERROR opening output bead file %s", filename);
p_log_errorno(log_string);
exit(0);
}
sprintf(temp_string, "autoexp_images/logs/%d_", fcnum);
strcpy(reglogfilename, temp_string);
strcat(reglogfilename, rcvfilename);
strcat(reglogfilename, ".register-log");
if( (reglogfile = fopen(reglogfilename, "wb")) == NULL) {
sprintf(log_string, "ERROR opening output reglog file %s", reglogfilename);
p_log_errorno(log_string);
exit(0);
}
sprintf(log_string, "processor:\tRequesting data from server for file %s ...", filename);
p_log(log_string);
strcat(filename, "ums");
if( (sumfile = fopen(filename, "wb")) == NULL) {
sprintf(log_string, "ERROR opening output sum file %s", filename);
p_log_errorno(log_string);
exit(0);
}
strcat(filename, "_full");
if( (imgsumfile = fopen(filename, "wb")) == NULL) {
sprintf(log_string, "ERROR opening output imgsum file %s", filename);
p_log_errorno(log_string);
exit(0);
}
// seek to correct place in object table, and advance pointer to
// correct place in reg object table
if(fcnum == 0) { // fcnum is either 0 or 1
// seek to start of object table file
if(fseek(full_pix_list, 0, SEEK_SET)!=0) {
p_log_errorno((char*)"ERROR ");
}
// set reg pointer offsets
reg_X_pointer_offset = 0;
reg_Y_pointer_offset = 0;
}
else {
// seek to position in object table where the current flowcell starts
// we know where to go because the last time through the loop when we
// were on FC0, we recorded the position after ReceiveData finished
fsetpos(full_pix_list, &pix_list_offset);
// set reg pointer offsets
reg_X_pointer_offset = 0;
reg_Y_pointer_offset = 0;
}
p_log((char*)"READY TO RECEIVE IMAGE DATA");
ReceiveData_new(argv, portnum, reg_pix_list_xcols + reg_X_pointer_offset,
reg_pix_list_yrows + reg_Y_pointer_offset, full_pix_list, beadvals, beadfile, sumfile, imgsumfile, reglogfile,bead_value_file,bead_sum_file, fcnum, pix_list_offset);
// remember position in object table so we can get back later
if(fcnum == 0) {
fgetpos(full_pix_list, &pix_list_offset);
}
fclose(beadfile);
fclose(sumfile);
fclose(imgsumfile);
fclose(reglogfile);
fclose(bead_value_file);
fclose(bead_sum_file);
change_logfile((char*)DEFAULT_PROCESSOR_LOGFILENAME);
p_log_simple((char*)"processor:\tAutoexposure exited; waiting before attempting to reconnect...");
sleep(10);
fclose(full_pix_list);
} // end function
// RETURN 1 ON SUCCESS,
// -1 ON MISSING IMAGE
int ProcessImage(short unsigned int *reg_pix_list_xcols,
short unsigned int *reg_pix_list_yrows,
FILE *full_pixel_list,
short unsigned int *image,
short unsigned int *image_info,
short unsigned int *beadvals,
FILE *beadfile,
FILE *sumfile,
FILE *imgsumfile,
FILE *reglogfile,
int *offsetx_history,
int *offsety_history){
// IMAGE INFO VARIABLES
int curr_imgnum;
int curr_arraynum;
int curr_fcnum;
// REGISTRATION VARIABLES
int reg_pointer_offset;
int offset_xcols;
int offset_yrows;
int score;
// BEAD VARIABLES
short unsigned int num_beads; // number of beads in current frame
int i;
double *temp_img; //gets sorted to find median pixel val
short unsigned int *temp_img2; //bg subtracted image passed to register
int percentile_val;
int temp_val;
unsigned long long int beadsum;
unsigned long long int imgsum;
int index;
char log_string[255];
// ALLOCATE MEMORY
if((temp_img = (double*)malloc((NUM_XCOLS*NUM_YROWS) * sizeof(double)))==NULL){
p_log_errorno((char*)"ERROR:\tProcessImage memory allocation failed (double *temp_img)");
exit(1);
}
if((temp_img2 = (short unsigned int*)malloc((NUM_XCOLS*NUM_YROWS) * sizeof(short unsigned int)))==NULL){
p_log_errorno((char*)"ERROR:\tProcessImage memory allocation failed (short unsigned int *temp_img2)");
exit(1);
}
// PARSE IMAGE INFO FIELDS
curr_imgnum = (int)(*(image_info + 2));
curr_arraynum = (int)(*(image_info + 1));
curr_fcnum = (int)(*(image_info + 0));
// ERROR WITH CURRENT IMAGE; PROBABLY FAILURE TO ACQUIRE
if(*(image_info + 3) == 1){
sprintf(log_string, "ERROR:\tProcessImage: image header indicates problem with image %d %d %d",
curr_fcnum, curr_arraynum, curr_imgnum);
p_log(log_string);
}
// UPDATE POINTER TO CURRENT POSITION IN REG_PIXEL_LIST
reg_pointer_offset = ((curr_fcnum * ARRAYS_PER_FC * IMGS_PER_ARRAY) +
(curr_arraynum * IMGS_PER_ARRAY) +
curr_imgnum);
reg_pointer_offset = reg_pointer_offset * REG_PIXELS;
sprintf(log_string, "STATUS:\tProcessImage: started operating on image %d, array %d, fc %d",
curr_imgnum,
curr_arraynum,
curr_fcnum);
p_log_simple(log_string);
#ifdef DEBUG1
p_log((char*)"STATUS:\tProcessImage: calling ProcessImage_register");
//sprintf(log_string, "STATUS:\tProcessImage: seek to position %ld", reg_pointer_offset);
sprintf(log_string, "STATUS:\tProcessImage: seek to position %d", reg_pointer_offset);
p_log(log_string);
#endif
// BACKGROUND SUBTRACT IMAGE FOR REGISTRATION
index=0;
for(i=0; i<1000000; i+=135){
temp_img[index] = (double)*(image + i);
index++;
}
quickSort(temp_img, index);
percentile_val = (int)temp_img[index-(int)((double)index*0.9)];
for(i=0; i<1000000; i++){
temp_val = (int)*(image+i) - percentile_val;
if(temp_val<0){
temp_img2[i]=0;
}
else{
temp_img2[i] = (short unsigned int)temp_val;
}
}
// Added to correct offset history for discontinuous image tracking.
if((curr_imgnum)%218==0){
p_log((char*)"STATUS:\tProcessImage: RESET HISTORY");
for(i=0; i<OFFSET_HISTORY_LENGTH; i++){
*(offsetx_history + i) = 0;
*(offsety_history + i) = 0;
}
}
// REGISTER IMAGE WITH 'BEAD PIXELS' FROM MASK IMAGE
ProcessImage_register(reg_pix_list_xcols,
reg_pix_list_yrows,
//image,
temp_img2,
reg_pointer_offset,
REG_PIXELS,
SEARCH_XCOLS,
SEARCH_YROWS,
&offset_xcols,
&offset_yrows,
&score,
*(image_info+3),
reglogfile,
offsetx_history,
offsety_history);
//fprintf(reglogfile, "=%d\t%d\t%d\t%d\t%d\n", curr_arraynum, curr_imgnum, offset_xcols, offset_yrows, score);
#ifdef DEBUG1
sprintf(log_string, "STATUS:\tProcessImage: calling ProcessImage_extract w/ offsets %d %d",
offset_xcols, offset_yrows);
p_log(log_string);
#endif
// PULL 'BEAD PIXELS' FROM IMAGE USING FULL MASK ON DISK
ProcessImage_extract(image,
offset_xcols,
offset_yrows,
*(image_info+3),
full_pixel_list,
curr_imgnum,
curr_arraynum,
curr_fcnum,
&num_beads,
beadvals,
&beadsum);
#ifdef DEBUG1
p_log((char*)"STATUS:\tProcessImage: writing output to files");
#endif
if(fwrite(beadvals, sizeof(short unsigned int), num_beads, beadfile) < num_beads){
p_log_errorno((char*)"ERROR:\tProcessImage: write to bead file failed");
exit(1);
}
if(fwrite(&beadsum, sizeof(long long int), 1, sumfile) < 1){
p_log_errorno((char*)"ERROR:\tProcessImage: write to sum file failed");
exit(1);
}
imgsum=0;
for(i=0; i<100000; i+=100){
imgsum+=*(image+i);
}
if(fwrite(&imgsum, sizeof(long long int), 1, imgsumfile) < 1){
p_log_errorno((char*)"ERROR:\tProcessImage: write to imgsum file failed");
exit(1);
}
free(temp_img);
free(temp_img2);
#ifdef DEBUG1
p_log_simple((char*)"STATUS:\tProcessImage: finished image");
#endif
} // end function
int main(int argc, char *argv[])
{
FILE *posfile;
FILE *infofile;
char log_string[255];
#ifdef SAVE_IMAGES
char img_fcnum[255];
#endif
int portnum;// = atoi(argv[2]);
char filename[12];
int fcnum;
int dual_flowcell = 0;
start_logger((char*)"initialize_processor-log", 1);
if(argc != 2 )
{
sprintf(log_string, "Usage: %s <Server hostname>", argv[0]);
p_log(log_string);
exit(0);
}
portnum = PORTNUM;
p_log((char*)"processor:\tRequesting position filename from server ...");
strcpy(filename, "");
ReceiveFilename(argv[1], portnum, filename);
sprintf(log_string, "processor:\treceived filename %s", filename);
p_log(log_string);
fcnum = ReceiveFCNum(argv[1], portnum);
sprintf(log_string, "processor:\treceived fcnum %d", fcnum);
p_log(log_string);
if(fcnum > 1)
{
dual_flowcell = 1;
}
#ifdef SAVE_IMAGES
sprintf(img_fcnum, "%d", fcnum);
strcat(CYCLE_NAME, img_fcnum);
strcat(CYCLE_NAME, "_");
strcat(CYCLE_NAME, filename);
#endif
if( (posfile = fopen(filename, "wb")) == NULL)
{
sprintf(log_string, "ERROR opening output pos file %s", filename);
p_log_errorno(log_string);
exit(0);
}
sprintf(log_string, "processor:\tRequesting data from server for file %s ", filename);
p_log(log_string);
strcat(filename, ".info");
if( (infofile = fopen(filename, "wb")) == NULL)
{
sprintf(log_string, "ERROR opening output info file %s", filename);
p_log_errorno(log_string);
exit(0);
}
/* fcnum will be == 2 if we're doing both flowcells; in this case,
the next set of images will be the second half of the data necessary
to generate the object table; re-request the filename, fcnum, and get
the second half of the brightfield images
*/
if (fcnum > 1)
{
p_log((char*)"RECEIVE_INIT_DATA...");
ReceiveInitData(argv[1], portnum, posfile, infofile, fcnum-2);
p_log((char*)"wait before attempting to reconnect");
sleep(2);
p_log((char*)"RECEIVE_FILENAME...");
ReceiveFilename(argv[1], portnum, filename);
p_log((char*)"RECEIVE_FCNUM...");
fcnum = ReceiveFCNum(argv[1], portnum);
p_log((char*)"RECEIVE_INIT_DATA...");
ReceiveInitData(argv[1], portnum, posfile, infofile, fcnum-2);
}
else
{
ReceiveInitData(argv[1], portnum, posfile, infofile, fcnum);
}
fclose(posfile);
fclose(infofile);
return dual_flowcell + 1;
}
int main(int argc, char *argv[]){
FILE *posfile;
FILE *cy3_posfile;
FILE *fam_posfile;
FILE *txred_posfile;
FILE *final_posfile;
FILE *obj_logfile;
FILE *infofile;
fpos_t offsetval;
char regfilename[200];
char logfilename[200];
char log_string[500];
char info_filename[200];
int i, j, k, l,m,n,o,convert,sconvert, object_count;
int curr_fc, curr_array, curr_img;
int num_fcs;
int cy5_proceed, cy3_proceed, txred_proceed,fam_proceed;
long long int found_object = 0;
long long int total_object = 0;
int curr_numobjs,cy3_curr_numobjs,txred_curr_numobjs,fam_curr_numobjs, max_curr_numobjs = 0;
int **objects_array;
int p,q;
short unsigned int cy5_x,cy3_x,cy3_y,txred_x,txred_y,fam_x,fam_y,cy5_y;
short unsigned int *curr_img_x;
short unsigned int *curr_img_y;
short unsigned int *regindices;
short unsigned int temp;
start_logger((char*)"initialize_processor-log", 1);
system("rm 00_*.info");
system("rm autoexp_pos.info");
objects_array = (int**) malloc(sizeof(int) * 4000);
for (i = 0; i < 2000; i++)
{
objects_array[i] = (int*) malloc(sizeof(int) * 2000);
}
for(p=0;p<2000;p++){
for(q=0;q<2000;q++){
objects_array[p][q] = -1;
}
}
if((curr_img_x = (short unsigned int*) malloc(MAX_BEADS_PERFRAME * sizeof(short unsigned int))) == NULL){
p_log_errorno((char*)"ERROR allocating memory for curr_img_x");
exit(0);
}
if((curr_img_y = (short unsigned int*) malloc(MAX_BEADS_PERFRAME * sizeof(short unsigned int))) == NULL){
p_log_errorno((char*)"ERROR allocating memory for curr_img_y");
exit(0);
}
if( (obj_logfile=fopen("merge.log", "w")) == NULL){
sprintf(log_string, "ERROR opening reglog file %s for output", argv[2]);
p_log_errorno(log_string);
exit(0);
}
if((cy3_posfile=fopen("00_cy3", "rb")) == NULL){
sprintf(log_string, "ERROR opening position file %s for input", "cy3");
p_log_errorno(log_string);
exit(0);
}
if( (txred_posfile=fopen("00_txr", "rb")) == NULL){
sprintf(log_string, "ERROR opening position file %s for input", "txred");
p_log_errorno(log_string);
exit(0);
}
if( (fam_posfile=fopen("00_fam", "rb")) == NULL){
sprintf(log_string, "ERROR opening position file %s for input", "fam");
p_log_errorno(log_string);
exit(0);
}
if( (posfile=fopen("00_cy5", "rb")) == NULL){
sprintf(log_string, "ERROR opening position file %s for input", "cy5");
p_log_errorno(log_string);
exit(0);
}
if( (final_posfile=fopen(argv[1], "wb")) == NULL){
sprintf(log_string, "ERROR opening position file %s for input", argv[1]);
p_log_errorno(log_string);
exit(0);
}
strcpy(info_filename,argv[1]);
strcat(info_filename,".info");
if( (infofile=fopen(info_filename, "wb")) == NULL){
sprintf(log_string, "ERROR opening reg file %s for output", info_filename);
p_log_errorno(log_string);
exit(0);
}
// loop through FC, ARRAY, IMAGE:
for(i=0; i<1; i++){
for(j=0; j<ARRAYS_PER_FC; j++){
for(k=0; k<IMGS_PER_ARRAY; k++){
// load positions for current image
// ------
// each 'record' in the pos file is as follows:
// 4 bytes: -1
// 4 bytes: flowcell # ([0..num_fcs])
// 4 bytes: array # ([0..ARRAYS_PER_FC])
// 4 bytes: image # ([0..IMGS_PER_ARRAY])
// 4 bytes: # of beads
// 2 bytes: beadpos_xcol
// 2 bytes: beadpos_yrow
// ...
// 2 bytes: 0
//
// ------
if( (fread(&curr_fc, sizeof(int), 1, posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_fc(1) from posfile");
}
if( (fread(&curr_fc, sizeof(int), 1, posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_fc(2) from posfile");
}
if( (fread(&curr_array, sizeof(int), 1, posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_array from posfile");
}
if( (fread(&curr_img, sizeof(int), 1, posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_img from posfile");
}
if( (fread(&curr_numobjs, sizeof(int), 1, posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_numobjs from posfile");
}
/* sprintf(log_string, "flowcell %d, curr_array %d, curr_img %d",curr_fc, curr_array, curr_img);
p_log(log_string);
*/
if( (fread(&curr_fc, sizeof(int), 1, cy3_posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_fc(1) from posfile");
}
if( (fread(&curr_fc, sizeof(int), 1, cy3_posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_fc(2) from posfile");
}
if( (fread(&curr_array, sizeof(int), 1, cy3_posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_array from posfile");
}
if( (fread(&curr_img, sizeof(int), 1, cy3_posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_img from posfile");
}
if( (fread(&curr_fc, sizeof(int), 1, txred_posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_fc(1) from posfile");
}
if( (fread(&curr_fc, sizeof(int), 1, txred_posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_fc(2) from posfile");
}
if( (fread(&curr_array, sizeof(int), 1, txred_posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_array from posfile");
}
if( (fread(&curr_img, sizeof(int), 1, txred_posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_img from posfile");
}
if( (fread(&curr_fc, sizeof(int), 1, fam_posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_fc(1) from posfile");
}
if( (fread(&curr_fc, sizeof(int), 1, fam_posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_fc(2) from posfile");
}
if( (fread(&curr_array, sizeof(int), 1, fam_posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_array from posfile");
}
if( (fread(&curr_img, sizeof(int), 1, fam_posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_img from posfile");
}
max_curr_numobjs = 0;
if(max_curr_numobjs<curr_numobjs) max_curr_numobjs=curr_numobjs;
if( (fread(&cy3_curr_numobjs, sizeof(int), 1, cy3_posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_numobjs from posfile");
}
if(max_curr_numobjs<cy3_curr_numobjs) max_curr_numobjs=cy3_curr_numobjs;
if( (fread(&txred_curr_numobjs, sizeof(int), 1, txred_posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_numobjs from posfile");
}
if(max_curr_numobjs<txred_curr_numobjs) max_curr_numobjs=txred_curr_numobjs;
if( (fread(&fam_curr_numobjs, sizeof(int), 1, fam_posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_numobjs from posfile");
}
if(max_curr_numobjs<fam_curr_numobjs) max_curr_numobjs=fam_curr_numobjs;
l = 0;
m = 0;
n = 0;
o = 0;
p = 0;
q = 0;
cy5_proceed = 1;
cy3_proceed = 1;
txred_proceed = 1;
fam_proceed = 1;
found_object = 0;
total_object = 0;
for(p=0;p<2000;p++){
for(q=0;q<2000;q++){
objects_array[p][q] = -1;
}
}
while(l<max_curr_numobjs)
{
if(l<curr_numobjs)
{
if((fread(&cy5_x, sizeof(short unsigned int), 1, posfile)) < 1){
sprintf(log_string, "ERROR reading x from posfile at %d %d %d %d",
i, j, k, l);
p_log_errorno(log_string);
}
if((fread(&cy5_y, sizeof(short unsigned int), 1, posfile)) < 1){
sprintf(log_string, "ERROR reading y from posfile at %d %d %d %d",
i, j, k, l);
p_log_errorno(log_string);
}
if ((objects_array[(int)cy5_x][(int)cy5_y] == -1)&&((int)cy5_y!=1000 && (int)cy5_x!=1000)){
objects_array[(int)cy5_x][(int)cy5_y] = 1;
total_object++;
}
}
if(l<cy3_curr_numobjs)
{
if((fread(&cy3_x, sizeof(short unsigned int), 1, cy3_posfile)) < 1){
sprintf(log_string, "ERROR reading x from posfile at %d %d %d %d",
i, j, k, l);
p_log_errorno(log_string);
}
if((fread(&cy3_y, sizeof(short unsigned int), 1, cy3_posfile)) < 1){
sprintf(log_string, "ERROR reading y from posfile at %d %d %d %d",
i, j, k, l);
p_log_errorno(log_string);
}
if ((objects_array[(int)cy3_x][(int)cy3_y] == -1)&&((int)cy3_y!=1000 && (int)cy3_x!=1000)){
objects_array[(int)cy3_x][(int)cy3_y] = 1;
total_object++;
}
}
if(l<txred_curr_numobjs)
{
if((fread(&txred_x, sizeof(short unsigned int), 1, txred_posfile)) < 1){
sprintf(log_string, "ERROR reading x from posfile at %d %d %d %d",
i, j, k, l);
p_log_errorno(log_string);
}
if((fread(&txred_y, sizeof(short unsigned int), 1, txred_posfile)) < 1){
sprintf(log_string, "ERROR reading y from posfile at %d %d %d %d",
i, j, k, l);
p_log_errorno(log_string);
}
if ((objects_array[(int)txred_x][(int)txred_y] == -1)&&((int)txred_y!=1000 && (int)txred_x!=1000)){
objects_array[(int)txred_x][(int)txred_y] = 1;
total_object++;
}
}
if(l<fam_curr_numobjs)
{
if((fread(&fam_x, sizeof(short unsigned int), 1, fam_posfile)) < 1){
sprintf(log_string, "ERROR reading x from posfile at %d %d %d %d",
i, j, k, l);
p_log_errorno(log_string);
}
if((fread(&fam_y, sizeof(short unsigned int), 1, fam_posfile)) < 1){
sprintf(log_string, "ERROR reading y from posfile at %d %d %d %d",
i, j, k, l);
p_log_errorno(log_string);
}
if ((objects_array[(int)fam_x][(int)fam_y] == -1)&&((int)fam_y!=1000 && (int)fam_x!=1000)){
objects_array[(int)fam_x][(int)fam_y] = 1;
total_object++;
}
}
l++;
}
convert=-1;
// make sure we are where we think we are in the position file
if( (fread(&temp, sizeof(short unsigned int), 1, posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_img from posfile");
}
if(temp!=0){
sprintf(log_string, "ERROR: 1expecting delimiter value of 0, read %d", temp);
p_log(log_string);
exit(0);
}
// make sure we are where we think we are in the position file
if( (fread(&temp, sizeof(short unsigned int), 1, cy3_posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_img from posfile");
}
if(temp!=0){
sprintf(log_string, "ERROR: 2expecting delimiter value of 0, read %d", temp);
p_log(log_string);
exit(0);
}
// make sure we are where we think we are in the position file
if( (fread(&temp, sizeof(short unsigned int), 1, txred_posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_img from posfile");
}
if(temp!=0){
sprintf(log_string, "ERROR: 3expecting delimiter value of 0, read %d", temp);
p_log(log_string);
exit(0);
}
// make sure we are where we think we are in the position file
if( (fread(&temp, sizeof(short unsigned int), 1, fam_posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_img from posfile");
}
if(temp!=0){
sprintf(log_string, "ERROR: 4expecting delimiter value of 0, read %d", temp);
p_log(log_string);
exit(0);
}
//p_log((char*)"Write data to object table");
if(fwrite(&convert, sizeof(int), 1, final_posfile) < 1){
p_log_errorno((char*)"write of -1 to posfile failed");
exit(0);
}
if(fwrite(&i, sizeof(int), 1, final_posfile) < 1){
p_log_errorno((char*)"write of curr_fcnum to posfile failed");
exit(0);
}
if(fwrite(&j, sizeof(int), 1, final_posfile) < 1){
p_log_errorno((char*)"write of curr_arraynum to posfile failed");
exit(0);
}
if(fwrite(&k, sizeof(int), 1, final_posfile) < 1){
p_log_errorno((char*)"write of curr_imagenum to posfile failed");
exit(0);
}
convert = (int)total_object;
if(fwrite(&convert, sizeof(int), 1, final_posfile) < 1){
p_log_errorno((char*)"write of num_beads to posfile failed");
exit(0);
}
object_count=0;
for(q=0;q<1000;q++){
for(p=0;p<1000;p++){
if(objects_array[p][q] == 1){
if(fwrite(&p, sizeof(short unsigned int), 1, final_posfile) < 1){
p_log_errorno((char*)"write of beadpos_xcol to posfile failed");
exit(0);
}
if(fwrite(&q, sizeof(short unsigned int), 1, final_posfile) < 1){
p_log_errorno((char*)"write of beadpos_yrow to posfile failed");
exit(0);
}
object_count++;
}
}
}
//sprintf(log_string, "Position %d %d %d... %d cy5_objects, %d cy3_objects, %d txred_objects, %d fam_objects, total_object %d, total_object_count %d\n", i, j, k, curr_numobjs,cy3_curr_numobjs,txred_curr_numobjs,fam_curr_numobjs,total_object,object_count);
sprintf(log_string, "Position %d %d %d... %d cy5_objects, %d cy3_objects, %d txred_objects, %d fam_objects, total_object %lld, total_object_count %d\n", i, j, k, curr_numobjs,cy3_curr_numobjs,txred_curr_numobjs,fam_curr_numobjs,total_object,object_count);
p_log_simple(log_string);
fprintf(obj_logfile,log_string);
sconvert=0;
if(fwrite(&sconvert, sizeof(short unsigned int), 1, final_posfile) < 1){
p_log_errorno((char*)"write of 0 to posfile failed");
exit(0);
}
//write to the info file
sconvert = i;
if(fwrite(&sconvert, sizeof(short unsigned int), 1, infofile) < 1){
p_log_errorno((char*)"write of curr_fcnum to infofile failed");
exit(0);
}
sconvert = j;
if(fwrite(&sconvert, sizeof(short unsigned int), 1, infofile) < 1){
p_log_errorno((char*)"write of curr_arraynum to infofile failed");
exit(0);
}
sconvert = k;
if(fwrite(&sconvert, sizeof(short unsigned int), 1, infofile) < 1){
p_log_errorno((char*)"write of curr_imagenum to infofile failed");
exit(0);
}
sconvert = (int)total_object;
if(fwrite(&sconvert, sizeof(short unsigned int), 1, infofile) < 1){
p_log_errorno((char*)"write of num_beads to infofile failed");
exit(0);
}
}
}
}
fclose(posfile);
fclose(cy3_posfile);
fclose(fam_posfile);
fclose(txred_posfile);
fclose(final_posfile);
fclose(infofile);
fclose(obj_logfile);
//merge the autoexp object table
if((cy3_posfile=fopen("autoexp_pos_cy3", "rb")) == NULL){
sprintf(log_string, "ERROR opening position file %s for input", "autoexp_pos_cy3");
p_log_errorno(log_string);
exit(0);
}
if( (txred_posfile=fopen("autoexp_pos_txr", "rb")) == NULL){
sprintf(log_string, "ERROR opening position file %s for input", "autoexp_pos_txred");
p_log_errorno(log_string);
exit(0);
}
if( (fam_posfile=fopen("autoexp_pos_fam", "rb")) == NULL){
sprintf(log_string, "ERROR opening position file %s for input", "autoexp_pos_fam");
p_log_errorno(log_string);
exit(0);
}
if( (posfile=fopen("autoexp_pos_cy5", "rb")) == NULL){
sprintf(log_string, "ERROR opening position file %s for input", "autoexp_pos_cy5");
p_log_errorno(log_string);
exit(0);
}
if( (final_posfile=fopen("autoexp_pos", "wb")) == NULL){
sprintf(log_string, "ERROR opening position file %s for input", argv[1]);
p_log_errorno(log_string);
exit(0);
}
strcpy(info_filename,"autoexp_pos");
strcat(info_filename,".info");
if( (infofile=fopen(info_filename, "wb")) == NULL){
sprintf(log_string, "ERROR opening reg file %s for output", info_filename);
p_log_errorno(log_string);
exit(0);
}
i = 0;
j = 0;
k = 0;
for(j=0; j<ARRAYS_PER_FC; j++){
for(k = 0;k<15;k++){
if( (fread(&curr_fc, sizeof(int), 1, posfile)) < 1){
p_log_errorno((char*)"ERROR reading autoe curr_fc(1) from posfile");
}
if( (fread(&curr_fc, sizeof(int), 1, posfile)) < 1){
p_log_errorno((char*)"ERROR reading autoe curr_fc(2) from posfile");
}
if( (fread(&curr_array, sizeof(int), 1, posfile)) < 1){
p_log_errorno((char*)"ERROR reading autoe curr_array from posfile");
}
if( (fread(&curr_img, sizeof(int), 1, posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_img from posfile");
}
if( (fread(&curr_numobjs, sizeof(int), 1, posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_numobjs from posfile");
}
if( (fread(&curr_fc, sizeof(int), 1, cy3_posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_fc(1) from posfile");
}
if( (fread(&curr_fc, sizeof(int), 1, cy3_posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_fc(2) from posfile");
}
if( (fread(&curr_array, sizeof(int), 1, cy3_posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_array from posfile");
}
if( (fread(&curr_img, sizeof(int), 1, cy3_posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_img from posfile");
}
if( (fread(&curr_fc, sizeof(int), 1, txred_posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_fc(1) from posfile");
}
if( (fread(&curr_fc, sizeof(int), 1, txred_posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_fc(2) from posfile");
}
if( (fread(&curr_array, sizeof(int), 1, txred_posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_array from posfile");
}
if( (fread(&curr_img, sizeof(int), 1, txred_posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_img from posfile");
}
if( (fread(&curr_fc, sizeof(int), 1, fam_posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_fc(1) from posfile");
}
if( (fread(&curr_fc, sizeof(int), 1, fam_posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_fc(2) from posfile");
}
if( (fread(&curr_array, sizeof(int), 1, fam_posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_array from posfile");
}
if( (fread(&curr_img, sizeof(int), 1, fam_posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_img from posfile");
}
max_curr_numobjs = 0;
if(max_curr_numobjs<curr_numobjs) max_curr_numobjs=curr_numobjs;
if( (fread(&cy3_curr_numobjs, sizeof(int), 1, cy3_posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_numobjs from posfile");
}
if(max_curr_numobjs<cy3_curr_numobjs) max_curr_numobjs=cy3_curr_numobjs;
if( (fread(&txred_curr_numobjs, sizeof(int), 1, txred_posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_numobjs from posfile");
}
if(max_curr_numobjs<txred_curr_numobjs) max_curr_numobjs=txred_curr_numobjs;
if( (fread(&fam_curr_numobjs, sizeof(int), 1, fam_posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_numobjs from posfile");
}
if(max_curr_numobjs<fam_curr_numobjs) max_curr_numobjs=fam_curr_numobjs;
l = 0;
m = 0;
n = 0;
o = 0;
p = 0;
q = 0;
cy5_proceed = 1;
cy3_proceed = 1;
txred_proceed = 1;
fam_proceed = 1;
found_object = 0;
total_object = 0;
for(p=0;p<2000;p++){
for(q=0;q<2000;q++){
objects_array[p][q] = -1;
}
}
while(l<max_curr_numobjs)
{
if(l<curr_numobjs)
{
if((fread(&cy5_x, sizeof(short unsigned int), 1, posfile)) < 1){
sprintf(log_string, "ERROR reading x from autoe posfile at %d %d %d %d",
i, j, k, l);
p_log_errorno(log_string);
}
if((fread(&cy5_y, sizeof(short unsigned int), 1, posfile)) < 1){
sprintf(log_string, "ERROR reading y from autoe posfile at %d %d %d %d",
i, j, k, l);
p_log_errorno(log_string);
}
if ((objects_array[(int)cy5_x][(int)cy5_y] == -1)&&((int)cy5_y!=1000 && (int)cy5_x!=1000)){
objects_array[(int)cy5_x][(int)cy5_y] = 1;
total_object++;
}
}
if(l<cy3_curr_numobjs)
{
if((fread(&cy3_x, sizeof(short unsigned int), 1, cy3_posfile)) < 1){
sprintf(log_string, "ERROR reading x from autoe posfile at %d %d %d %d",
i, j, k, l);
p_log_errorno(log_string);
}
if((fread(&cy3_y, sizeof(short unsigned int), 1, cy3_posfile)) < 1){
sprintf(log_string, "ERROR reading y from autoe posfile at %d %d %d %d",
i, j, k, l);
p_log_errorno(log_string);
}
if ((objects_array[(int)cy3_x][(int)cy3_y] == -1)&&((int)cy3_y!=1000 && (int)cy3_x!=1000)){
objects_array[(int)cy3_x][(int)cy3_y] = 1;
total_object++;
}
}
if(l<txred_curr_numobjs)
{
if((fread(&txred_x, sizeof(short unsigned int), 1, txred_posfile)) < 1){
sprintf(log_string, "ERROR reading x from autoe posfile at %d %d %d %d",
i, j, k, l);
p_log_errorno(log_string);
}
if((fread(&txred_y, sizeof(short unsigned int), 1, txred_posfile)) < 1){
sprintf(log_string, "ERROR reading y from autoe posfile at %d %d %d %d",
i, j, k, l);
p_log_errorno(log_string);
}
if ((objects_array[(int)txred_x][(int)txred_y] == -1)&&((int)txred_y!=1000 && (int)txred_x!=1000)){
objects_array[(int)txred_x][(int)txred_y] = 1;
total_object++;
}
}
if(l<fam_curr_numobjs)
{
if((fread(&fam_x, sizeof(short unsigned int), 1, fam_posfile)) < 1){
sprintf(log_string, "ERROR reading x from autoe posfile at %d %d %d %d",
i, j, k, l);
p_log_errorno(log_string);
}
if((fread(&fam_y, sizeof(short unsigned int), 1, fam_posfile)) < 1){
sprintf(log_string, "ERROR reading y from autoe posfile at %d %d %d %d",
i, j, k, l);
p_log_errorno(log_string);
}
if ((objects_array[(int)fam_x][(int)fam_y] == -1)&&((int)fam_y!=1000 && (int)fam_x!=1000)){
objects_array[(int)fam_x][(int)fam_y] = 1;
total_object++;
}
}
l++;
}
// make sure we are where we think we are in the position file
if( (fread(&temp, sizeof(short unsigned int), 1, posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_img from autoe posfile");
}
if(temp!=0){
sprintf(log_string, "ERROR: 1expecting delimiter value of 0, read %d", temp);
p_log(log_string);
exit(0);
}
// make sure we are where we think we are in the position file
if( (fread(&temp, sizeof(short unsigned int), 1, cy3_posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_img from autoe posfile");
}
if(temp!=0){
sprintf(log_string, "ERROR: 2expecting delimiter value of 0, read %d", temp);
p_log(log_string);
exit(0);
}
// make sure we are where we think we are in the position file
if( (fread(&temp, sizeof(short unsigned int), 1, txred_posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_img from posfile");
}
if(temp!=0){
sprintf(log_string, "ERROR: 3expecting delimiter value of 0, read %d", temp);
p_log(log_string);
exit(0);
}
// make sure we are where we think we are in the position file
if( (fread(&temp, sizeof(short unsigned int), 1, fam_posfile)) < 1){
p_log_errorno((char*)"ERROR reading curr_img from posfile");
}
if(temp!=0){
sprintf(log_string, "ERROR: 4expecting delimiter value of 0, read %d", temp);
p_log(log_string);
exit(0);
}
convert=-1;
//p_log((char*)"Write data to object table");
if(fwrite(&convert, sizeof(int), 1, final_posfile) < 1){
p_log_errorno((char*)"write of -1 to posfile failed");
exit(0);
}
if(fwrite(&i, sizeof(int), 1, final_posfile) < 1){
p_log_errorno((char*)"write of curr_fcnum to posfile failed");
exit(0);
}
if(fwrite(&j, sizeof(int), 1, final_posfile) < 1){
p_log_errorno((char*)"write of curr_arraynum to posfile failed");
exit(0);
}
if(fwrite(&k, sizeof(int), 1, final_posfile) < 1){
p_log_errorno((char*)"write of curr_imagenum to posfile failed");
exit(0);
}
convert = (int)total_object;
if(fwrite(&convert, sizeof(int), 1, final_posfile) < 1){
p_log_errorno((char*)"write of num_beads to posfile failed");
exit(0);
}
object_count=0;
for(q=0;q<1000;q++){
for(p=0;p<1000;p++){
if(objects_array[p][q] == 1){
if(fwrite(&p, sizeof(short unsigned int), 1, final_posfile) < 1){
p_log_errorno((char*)"write of beadpos_xcol to posfile failed");
exit(0);
}
if(fwrite(&q, sizeof(short unsigned int), 1, final_posfile) < 1){
p_log_errorno((char*)"write of beadpos_yrow to posfile failed");
exit(0);
}
object_count++;
}
}
}
sprintf(log_string, "autoe1 Position %d %d %d... %d cy5_objects, %d cy3_objects, %d txred_objects, %d fam_objects, total_object %lld, total_object_count %d\n", curr_fc, curr_array, curr_img, curr_numobjs,cy3_curr_numobjs,txred_curr_numobjs,fam_curr_numobjs,total_object,object_count);
p_log_simple(log_string);
sconvert=0;
if(fwrite(&sconvert, sizeof(short unsigned int), 1, final_posfile) < 1){
p_log_errorno((char*)"write of 0 to posfile failed");
exit(0);
}
//write to the info file
sconvert = i;
if(fwrite(&sconvert, sizeof(short unsigned int), 1, infofile) < 1){
p_log_errorno((char*)"write of curr_fcnum to infofile failed");
exit(0);
}
sconvert = j;
if(fwrite(&sconvert, sizeof(short unsigned int), 1, infofile) < 1){
p_log_errorno((char*)"write of curr_arraynum to infofile failed");
exit(0);
}
sconvert = k;
if(fwrite(&sconvert, sizeof(short unsigned int), 1, infofile) < 1){
p_log_errorno((char*)"write of curr_imagenum to infofile failed");
exit(0);
}
sconvert = (int)total_object;
if(fwrite(&sconvert, sizeof(short unsigned int), 1, infofile) < 1){
p_log_errorno((char*)"write of num_beads to infofile failed");
exit(0);
}
}
}
fclose(posfile);
fclose(cy3_posfile);
fclose(fam_posfile);
fclose(txred_posfile);
fclose(final_posfile);
fclose(infofile);
//system("rm 00_*");
}
int main(int argc, char *argv[])
{
int m_sock,i,j, autoexp_gain;
char autoe_filename[500];
char autoe_dirname[500];
char command_buffer[255]; // buffer for commands to be executed
char image_dir[255];
sprintf(image_dir, "%s/polonator/G.007/acquisition", getenv("HOME"));
sprintf(command_buffer, "mkdir -p %s", image_dir);
system(command_buffer);
if(argc < 2)
{
fprintf(stdout, "%s must be called w/ one of the following arguments:\n", argv[0]);
fprintf(stdout, "\treset\t\t -- restart software on controller and home all axes\n");
fprintf(stdout, "\tunlock\t\t -- 'unlock' stage for manual movement\n");
fprintf(stdout, "\tlock\t\t -- 'lock' stage for servo movement\n");
fprintf(stdout, "\tlive\t\t -- display live darkfield image (%s live <integration in seconds> <EM gain>)\n", argv[0]);
fprintf(stdout, "\tsnap\t\t -- snap image and save to disk (%s snap <color[fam, cy5, cy3, txred, spare, or none]> <integration in seconds> <EM gain>)\n", argv[0]);
fprintf(stdout, "\tcolorsnap\t -- snap images in all 4 channels and save to disk (%s colorsnap <integration in seconds> <fam gain> <cy5 gain> <cy3 gain> <txred gain>)\n", argv[0]);
fprintf(stdout, "\tstatus\t\t -- get motion controller status and last errors, if any\n");
fprintf(stdout, "\tcomplete-scan\t -- if scanning was interrupted, and reset the controller software gracefully to its starting state\n");
fprintf(stdout, "\tdarkfield-off\t -- turn the darkfield ring illuminator off\n");
fprintf(stdout, "\tdarkfield-on\t -- turn the darkfield ring illuminator on\n");
fprintf(stdout, "\thometheta\t -- 'lock' theta (filter cube) axis and re-home\n");
fprintf(stdout, "\tunlocktheta\t -- 'unlock' theta (filter cube) axis\n");
fprintf(stdout, "\tpower-on\t -- turn camera and fluorescence light source on\n");
fprintf(stdout, "\tpower-off\t -- turn camera and fluorescence light source off\n");
fprintf(stdout, "\tgotostagealignpos\t -- goto position used for stage alignment (%s gotostagealignpos <flowcell> <lane>)\n", argv[0]);
fprintf(stdout, "\tgetfocus\t -- get current 'focus' value from Z axis (this is the offset applied to focus error signal)\n");
fprintf(stdout, "\tsetfocus\t -- set focus value for Z axis; note this DOES NOT write to non-volatile memory (%s setfocus <focus_value>)\n", argv[0]);
fprintf(stdout, "\twritefocus\t -- write current focus value to non-volatile memory; should be used after correct value is found with setfocus\n");
exit(1);
}
/* Reset the controller software and re-home the stage */
if(strcmp(argv[1], "reset") == 0) {
maestro_open(&m_sock);
maestro_reset(m_sock);
}
else if(strcmp(argv[1], "unlock") == 0) {
maestro_open(&m_sock);
maestro_unlock(m_sock);
}
else if(strcmp(argv[1], "lock") == 0) {
maestro_open(&m_sock);
maestro_lock(m_sock);
}
else if(strcmp(argv[1], "getfocus") == 0) {
maestro_open(&m_sock);
return maestro_getfocus(m_sock);
}
else if(strcmp(argv[1], "setfocus") == 0) {
maestro_open(&m_sock);
maestro_setfocus(m_sock, atoi(argv[2]));
}
else if(strcmp(argv[1], "writefocus") == 0) {
maestro_open(&m_sock);
maestro_writefocus(m_sock);
}
/* Display a live darkfield image */
else if((strcmp(argv[1], "live") == 0) && ((argc == 4)||(argc == 5))) {
maestro_open(&m_sock);
maestro_darkfield_on(m_sock);
maestro_setcolor(m_sock, "none");
if(argc == 4)
{
camera_live(argc, argv);
}
else {
camera_live(argc, argv);
}
maestro_darkfield_off(m_sock);
}
else if((strcmp(argv[1], "live_new") == 0) && ((argc == 5)||(argc == 6)))
{
maestro_open(&m_sock);
maestro_setcolor(m_sock, argv[4]);
if(strcmp(argv[4],"none") == 0)
{
maestro_darkfield_on(m_sock);
maestro_shutterclose(m_sock);
}
else
{
maestro_darkfield_off(m_sock);
maestro_shutteropen(m_sock);
}
fprintf(stdout, "Live view starting");
if(argc==5) {
fprintf(stdout, "Live view argc == 5");
camera_live(argc, argv);
}
else {
fprintf(stdout, "Live view argc != 5");
camera_live(argc, argv);
}
fprintf(stdout, "Live view done");
if(strcmp(argv[4],"none")==0) {
maestro_darkfield_off(m_sock);
}
else {
maestro_shutterclose(m_sock);
}
}
else if (strcmp(argv[1],"shutter_close")==0)
{
maestro_open(&m_sock);
maestro_shutterclose(m_sock);
}
/* Acquire an image at the current stage position */
else if((strcmp(argv[1], "snap") == 0) && (argc == 5)) {
sprintf(command_buffer, "%s/snap-image.raw", image_dir);
snap(atof(argv[3]), atof(argv[4]), argv[2], command_buffer);
}
else if((strcmp(argv[1], "snap1") == 0) && (argc == 6))
{
sprintf(command_buffer, "mkdir -p %s/autoexp_FL_images/cy3", image_dir);
system(command_buffer);
sprintf(command_buffer, "mkdir -p %s/autoexp_FL_images/fam", image_dir);
system(command_buffer);
sprintf(command_buffer, "mkdir -p %s/autoexp_FL_images/cy5", image_dir);
system(command_buffer);
sprintf(command_buffer, "mkdir -p %s/autoexp_FL_images/txred", image_dir);
system(command_buffer);
for(j = 0; j < atoi(argv[5]); j++)
{
maestro_open(&m_sock);
maestro_gotostagealign_position(m_sock, 0, j);
for(i = 0; i < 15; i++)
{
attempt_counter = 0;
autoexp_gain = atoi(argv[4])+i*10;
sprintf(autoe_filename, " ... start acquring FL image in lane %d, for %s with autoexposure gain of %d ... ",j, argv[2],autoexp_gain);
p_log_simple(autoe_filename);
sprintf(autoe_filename, "%s/autoexp_FL_images/%s/%d_image_%d.raw", image_dir,argv[2],j,autoexp_gain);
p_log_simple(autoe_filename);
wait_counter = 0;
snap(atof(argv[3]), autoexp_gain, argv[2], autoe_filename);
sprintf(autoe_filename, " ... acquired FL image in %d ms ...\n", wait_counter);
p_log_simple(autoe_filename);
while((attempt_counter < 4) && (attempt_counter > 0))
{
sprintf(autoe_filename, "... ACQUIRING FAILED !!! Re-acquring FL image in lane %d, for %s with autoexposure gain of %d ...\n",atoi(argv[5]), argv[2],atoi(argv[4]));
p_log_errorno(autoe_filename);
snap(atof(argv[3]), atof(argv[4]), argv[2], autoe_filename);
}
} // end for i
} // end for j
} // end else if
/* Acquire 4 fluorescence images */
else if((strcmp(argv[1], "colorsnap") == 0) && (argc == 7)) {
sprintf(command_buffer, "%s/colorsnap-fam.raw", image_dir);
snap(atof(argv[2]), atof(argv[3]), "fam", command_buffer);
sprintf(command_buffer, "%s/colorsnap-cy5.raw", image_dir);
snap(atof(argv[2]), atof(argv[4]), "cy5", command_buffer);
sprintf(command_buffer, "%s/colorsnap-cy3.raw", image_dir);
snap(atof(argv[2]), atof(argv[5]), "cy3", command_buffer);
sprintf(command_buffer, "%s/colorsnap-txr.raw", image_dir);
snap(atof(argv[2]), atof(argv[6]), "txred", command_buffer);
}
else if(strcmp(argv[1], "complete-scan") == 0) {
maestro_open(&m_sock);
maestro_stop(m_sock);
}
else if(strcmp(argv[1], "darkfield-off") == 0) {
maestro_open(&m_sock);
maestro_darkfield_off(m_sock);
}
else if(strcmp(argv[1], "darkfield-on") == 0) {
maestro_open(&m_sock);
maestro_darkfield_on(m_sock);
}
else if(strcmp(argv[1], "hometheta") == 0) {
maestro_open(&m_sock);
maestro_hometheta(m_sock);
}
else if(strcmp(argv[1], "unlocktheta") == 0) {
maestro_open(&m_sock);
maestro_unlocktheta(m_sock);
}
else if(strcmp(argv[1], "status") == 0) {
maestro_open(&m_sock);
maestro_getstatus(m_sock);
}
else if(strcmp(argv[1], "power-on") == 0) {
network_iboot_on(&m_sock);
}
else if(strcmp(argv[1], "power-off") == 0) {
network_iboot_off(&m_sock);
}
else if(strcmp(argv[1], "gotostagealignpos") == 0) {
maestro_open(&m_sock);
maestro_gotostagealign_position(m_sock, atoi(argv[2]), atoi(argv[3]));
}
else
{
main(1, argv);
}
} // end function
