# BIDS-ing sub-01, ses-02; collected 09/16/2017
# written by Jo Etzel (jetzel@wustl.edu), 9 October 2018
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rm(list=ls());    # clear R's memory

in.path <- "d:/temp/DMCC_box/Raw_Data/999008/999008_test2017/caseforge2_16Sept2017/scans/";       # path to source dicoms
ds.path <- "d:/temp/DMCC_box/Raw_Data/999008/999008_test2017/multibandCFtests/sub-01/ses-02/";   # new BIDS dataset
dcm.path <- "c:/Program Files/mricrogl/dcm2niix";   # dcm2niix.exe location

do.rename <- function(idb.num, new.fname) {  # idb.num <- 11; new.fname <- "sub-01_ses-03_T1w"
  file.rename(from=list.files(out.path, pattern=paste0("_", idb.num, ".json"), full.names=TRUE), to=paste0(out.path, new.fname, ".json"));
  file.rename(from=list.files(out.path, pattern=paste0("_", idb.num, ".nii.gz"), full.names=TRUE), to=paste0(out.path, new.fname, ".nii.gz"));
}

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# anat
# no anatomy collected during caseforge testing sessions; here's an anatomy of the same person, same scanner and headcoil, collected 17 July 2018

ds.path <- "d:/temp/DMCC_box/Raw_Data/999008/999008_test2017/multibandCFtests/sub-01/ses-03/";   # new BIDS dataset
out.path <- paste0(ds.path, "anat/");
if (!dir.exists(out.path)) { dir.create(out.path); }

system2(dcm.path, args=paste0("-b y -z y -v y -o ", out.path, ' -f "%t_%p_%s" "', in.path, '12_T1w"'), stdout=TRUE);
do.rename(12, "sub-01_ses-03_T1w");
system2(dcm.path, args=paste0("-b y -z y -v y -o ", out.path, ' -f "%t_%p_%s" "', in.path, '14_T2w"'), stdout=TRUE);
do.rename(14, "sub-01_ses-03_T2w");

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# func: bold and sbref

out.path <- paste0(ds.path, "func/");
if (!dir.exists(out.path)) { dir.create(out.path); }


system2(dcm.path, args=paste0("-b y -z y -v y -o ", out.path, ' -f "%t_%p_%s" "', in.path, '17_tfMRI_SBRef"'), stdout=TRUE);
do.rename(17, "sub-01_ses-02_task-Stroop_acq-cf2AP_run-01_sbref");
system2(dcm.path, args=paste0("-b y -z y -v y -o ", out.path, ' -f "%t_%p_%s" "', in.path, '18_tfMRI"'), stdout=TRUE);
do.rename(18, "sub-01_ses-02_task-Stroop_acq-cf2AP_run-01_bold");

system2(dcm.path, args=paste0("-b y -z y -v y -o ", out.path, ' -f "%t_%p_%s" "', in.path, '20_tfMRI_SBRef"'), stdout=TRUE);
do.rename(20, "sub-01_ses-02_task-Stroop_acq-cf2PA_run-02_sbref");
system2(dcm.path, args=paste0("-b y -z y -v y -o ", out.path, ' -f "%t_%p_%s" "', in.path, '21_tfMRI"'), stdout=TRUE);
do.rename(21, "sub-01_ses-02_task-Stroop_acq-cf2PA_run-02_bold");

system2(dcm.path, args=paste0("-b y -z y -v y -o ", out.path, ' -f "%t_%p_%s" "', in.path, '32_tfMRI_SBRef"'), stdout=TRUE);
do.rename(32, "sub-01_ses-02_task-notStroop_acq-cf2AP_run-03_sbref");
system2(dcm.path, args=paste0("-b y -z y -v y -o ", out.path, ' -f "%t_%p_%s" "', in.path, '33_tfMRI"'), stdout=TRUE);
do.rename(33, "sub-01_ses-02_task-notStroop_acq-cf2AP_run-03_bold");

system2(dcm.path, args=paste0("-b y -z y -v y -o ", out.path, ' -f "%t_%p_%s" "', in.path, '35_tfMRI_SBRef"'), stdout=TRUE);
do.rename(35, "sub-01_ses-02_task-notStroop_acq-cf2PA_run-04_sbref");
system2(dcm.path, args=paste0("-b y -z y -v y -o ", out.path, ' -f "%t_%p_%s" "', in.path, '36_tfMRI"'), stdout=TRUE);
do.rename(36, "sub-01_ses-02_task-notStroop_acq-cf2PA_run-04_bold");

system2(dcm.path, args=paste0("-b y -z y -v y -o ", out.path, ' -f "%t_%p_%s" "', in.path, '48_tfMRI_SBRef"'), stdout=TRUE);
do.rename(48, "sub-01_ses-02_task-notStroop_acq-cf0AP_run-05_sbref");
system2(dcm.path, args=paste0("-b y -z y -v y -o ", out.path, ' -f "%t_%p_%s" "', in.path, '49_tfMRI"'), stdout=TRUE);
do.rename(49, "sub-01_ses-02_task-notStroop_acq-cf0AP_run-05_bold");

system2(dcm.path, args=paste0("-b y -z y -v y -o ", out.path, ' -f "%t_%p_%s" "', in.path, '51_tfMRI_SBRef"'), stdout=TRUE);
do.rename(51, "sub-01_ses-02_task-Stroop_acq-cf0PA_run-06_sbref");
system2(dcm.path, args=paste0("-b y -z y -v y -o ", out.path, ' -f "%t_%p_%s" "', in.path, '52_tfMRI"'), stdout=TRUE);
do.rename(52, "sub-01_ses-02_task-Stroop_acq-cf0PA_run-06_bold");



# add the TaskName field to the .json

#run.ids <- c("task-Stroop_acq-cf2AP_run-01", "task-Stroop_acq-cf2PA_run-02", "task-Stroop_acq-cf0PA_run-06"); 
run.ids <- c("task-notStroop_acq-cf2AP_run-03", "task-notStroop_acq-cf2PA_run-04", "task-notStroop_acq-cf0AP_run-05");
for (rid in 1:length(run.ids)) {   # rid <- 1;
  fname.in <- paste0(out.path, "sub-01_ses-02_", run.ids[rid], "_bold.json");
  if (file.exists(fname.in)) {  
    #file.copy(from=fname.in, to=paste0(fname.in, "2.txt"), overwrite=FALSE);
    tmp <- readLines(fname.in);    
    if (length(grep("TaskName", tmp)) == 0) {   # field not in, so add it.
      if (tmp[length(tmp)] != "}") { stop ('tmp[length(tmp)] != "}"'); } 
      move.to.last <- length(tmp) - 1;  # which entry will be copied to the (current) last spot, and replaced by the new field
      tmp <- c(tmp, "}");   # add a new element
      tmp[move.to.last+1] <- tmp[move.to.last];
      #tmp[move.to.last] <- '\t"TaskName": "Stroop",';
      tmp[move.to.last] <- '\t"TaskName": "notStroop",';
      cat(tmp, file=fname.in, sep="\n");   # OVERWRITE original file
    }
  }
}

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# fmap

out.path <- paste0(ds.path, "fmap/");
if (!dir.exists(out.path)) { dir.create(out.path); }

system2(dcm.path, args=paste0("-b y -z y -v y -o ", out.path, ' -f "%t_%p_%s" "', in.path, '9_FieldMap_SE_EPI"'), stdout=TRUE);
do.rename(9, "sub-01_ses-02_acq-cf2AP_run-01_epi");
system2(dcm.path, args=paste0("-b y -z y -v y -o ", out.path, ' -f "%t_%p_%s" "', in.path, '10_FieldMap_SE_EPI"'), stdout=TRUE);
do.rename(10, "sub-01_ses-02_acq-cf2PA_run-01_epi");

system2(dcm.path, args=paste0("-b y -z y -v y -o ", out.path, ' -f "%t_%p_%s" "', in.path, '46_FieldMap_SE_EPI"'), stdout=TRUE);
do.rename(46, "sub-01_ses-02_acq-cf0AP_run-05_epi");
system2(dcm.path, args=paste0("-b y -z y -v y -o ", out.path, ' -f "%t_%p_%s" "', in.path, '47_FieldMap_SE_EPI"'), stdout=TRUE);
do.rename(47, "sub-01_ses-02_acq-cf0PA_run-05_epi");


# add the IntendedFor field to the .jsons: fieldmap AP goes with task run PA (and the reverse)
top.path <- "d:/temp/DMCC_box/Raw_Data/999008/999008_test2017/multibandCFtests/sub-01/";
run.ids <- c("sub-01_ses-02_acq-cf2AP_run-01", "sub-01_ses-02_acq-cf2PA_run-01", 
             "sub-01_ses-02_acq-cf0AP_run-05", "sub-01_ses-02_acq-cf0PA_run-05");   # fieldmap names
for.ids <- c("task-Stroop_acq-cf2PA_run-02", "task-Stroop_acq-cf2AP_run-01", 
             "task-Stroop_acq-cf0PA_run-06", "task-notStroop_acq-cf0AP_run-05");    # corresponding task fmri run names

for (rid in 1:length(run.ids)) {   # rid <- 1;
  fname.in <- paste0(out.path, run.ids[rid], "_epi.json");
  fname.bold <- paste0("ses-02/func/sub-01_ses-02_", for.ids[rid], "_bold.nii.gz");
  if (file.exists(fname.in) & file.exists(paste0(top.path, fname.bold))) {  
    file.copy(from=fname.in, to=paste0(fname.in, "2.txt"), overwrite=FALSE);
    
    tmp <- readLines(fname.in);    
    if (length(grep("IntendedFor", tmp)) == 0) {   # field not in, so add it.
      if (tmp[length(tmp)] != "}") { stop ('tmp[length(tmp)] != "}"'); } 
      move.to.last <- length(tmp) - 1;  # which entry will be copied to the (current) last spot, and replaced by the new field
      tmp <- c(tmp, "}");   # add a new element
      tmp[move.to.last+1] <- tmp[move.to.last];
      tmp[move.to.last] <- paste0('\t"IntendedFor": "', fname.bold, '",');
      cat(tmp, file=fname.in, sep="\n");   # OVERWRITE original file
    }
  }
}

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# func: events files. event times in seconds from run start.

in.path <- "d:/temp/DMCC_box/Raw_Data/999008/999008_test2017/caseforge2_16Sept2017/";     
out.path <- paste0(ds.path, "func/");   # where to write the tsv

# input and output filenames, same order
in.fnames <- c("999008_baseline_StroopBas_run1.txt_raw.csv", 
               "999008_baseline_StroopBas_run2.txt_raw.csv", 
               "999008_breath_baseline_StroopBas_run1.txt_raw.csv",
               "999008_breath_baseline_StroopBas_run2.txt_raw.csv",
               "999008_nocf_baseline_StroopBas_run1.txt_raw.csv",
               "999008_nocf_baseline_StroopBas_run2.txt_raw.csv"); 

out.fnames <- c("sub-01_ses-02_task-Stroop_acq-cf2AP_run-01_events.tsv", 
                "sub-01_ses-02_task-Stroop_acq-cf2PA_run-02_events.tsv",
                "sub-01_ses-02_task-notStroop_acq-cf2AP_run-03_events.tsv",
                "sub-01_ses-02_task-notStroop_acq-cf2PA_run-04_events.tsv",
                "sub-01_ses-02_task-notStroop_acq-cf0AP_run-05_events.tsv",
                "sub-01_ses-02_task-Stroop_acq-cf0PA_run-06_events.tsv");

for (i in 1:length(in.fnames)) {   # i <- 1;
  e.tbl <- read.csv(paste0(in.path, in.fnames[i]), stringsAsFactors=FALSE);
  onset <- (e.tbl$Flicker.OnsetTime - e.tbl$scanstart.RTTime[1])/1000;   # event onsets in seconds
  duration <- rep(1, length(onset));   # short events
  trial_type <- e.tbl$TrialType;    # congruent or incongruent
  out.tbl <- data.frame(onset, duration, trial_type);
  out.tbl <- out.tbl[which(!is.na(onset)),];   # NA onsets at block boundaries; all events are !is.na
  write.table(out.tbl, paste0(out.path, out.fnames[i]), sep='\t', row.names=FALSE, quote=FALSE);   # write as tsv
}


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# func: physio

in.path <- "d:/temp/DMCC_box/Raw_Data/999008/999008_test2017/caseforge2_16Sept2017/physio/";     
out.path <- paste0(ds.path, "func/");   # where to write the tsv

# input and output filenames, same order
in.fnames <- c("999008_scan52_physio.csv", "999008_scan18_physio.csv", 
               "999008_scan21_physio.csv", "999008_scan33_physio.csv", 
               "999008_scan36_physio.csv", "999008_scan49_physio.csv"); 

out.fnames <- c("sub-01_ses-02_task-Stroop_acq-cf2AP_run-01", "sub-01_ses-02_task-Stroop_acq-cf2PA_run-02",
                "sub-01_ses-02_task-notStroop_acq-cf2AP_run-03", "sub-01_ses-02_task-notStroop_acq-cf2PA_run-04",
                "sub-01_ses-02_task-notStroop_acq-cf0AP_run-05", "sub-01_ses-02_task-Stroop_acq-cf0PA_run-06");


for (i in 1:length(in.fnames)) {   # i <- 1;
  in.tbl <- read.csv(paste0(in.path, in.fnames[i]), stringsAsFactors=FALSE);  
  
  # save and rename columns for the output tsv
  out.tbl <- cbind(in.tbl$physio.PULS, in.tbl$physio.RESP, in.tbl$physio.ACQ);
  write.table(out.tbl, gzfile(paste0(out.path, out.fnames[i], "_physio.tsv.gz")), sep='\t',
              row.names=FALSE, col.names=FALSE, quote=FALSE);   # write as tsv

  # make the .json
  fout <- file(paste0(out.path, out.fnames[i], "_physio.json"), 'wt');
  cat("{\n", file=fout);
  cat('"SamplingFrequency": 400.0,', file=fout, sep="\n");  # all sampled at 2.5 msec/tic : 1000/2.5 = 400 HZ (samples/sec)

  start.tic <- min(which(in.tbl$physio.ACQ == 1));  # first acquisition time, in tics
  start.time <- start.tic * 2.5 / 1000;  # first acquisition time, in seconds
  cat(paste0('"StartTime": -', start.time, ','), file=fout, sep="\n");   # physio started -start.time before fMRI acquisitions
  cat('"Columns": ["cardiac", "respiratory", "trigger"]', file=fout, sep="\n");
  cat("}\n", file=fout);
  close(fout); unlink(fout);
}

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