Testing and Bugfixing

README.md

@@ -2,7 +2,7 @@
 
 
 ### Purpose
-This application will create _SFB_-conform meta data (_meta.json_ files) for all participants in the _participants.tsv_ file of you your study. The _meta.json files_ will include the subjects _ID_, _sex_ and _age_. Moreover it is possible to register a template _meta.json_ file, which values will be adopted into the newly created meta-files.
+This application will create _SFB_-conform meta data (_meta.json_ files) for all participants in the _participants.tsv_ file of you your study. The _meta.json files_ will include the subjects _ID_, _sex_, _age_ and _record-date_. Moreover it is possible to register a template _meta.json_ file, which values will be adopted into the newly created meta-files.
 ### Requirements
 It is required to have a Java version greater or equal to 1.8.0 installed. You can download the current Java Corretto here: https://docs.aws.amazon.com/de_de/corretto/latest/corretto-11-ug/downloads-list.html
 
@@ -11,6 +11,7 @@ The _participants.tsv_ has to follow the this [standard](https://bids-specificat
 - `participant_id`: The exact name of the subject folder. Usually this is composed of two parts: "sub-" and the _SFB code_. The _SFB code_ will be extracted and used as _Subject ID_. The _SFB code_ cannot contain hyphens.  
 - `sex`: Sex of the subject (_m\[ale] or f\[emale])_.
 - `age`: Age of the subject (in years).
+- if one also wants to transfer the record date to the meta.json files. Then this information has to be included in the participants.tsv file. For each existing session a column should appear. The naming scheme of the columns must be consistent. The SFB suggests the following pattern: `day-1`, `day-2`, ..., `day-n`
 
 ### GUI Usage
 Input fields top down:
@@ -21,7 +22,13 @@ Input fields top down:
    If not used, meta-files will be empty besides subject-_ID_, _sex_, _age_ and the name of the Study.
    1. _meta.json - File selector:_
       Select the template _meta.json_ file.
-3. _Convert:_
+      
+3. _Include record date from participants.tsv_
+	If checked then the application tries to transfer the record date from the participants.tsv to the corresponding meta.json file. This only works when:
+	- the session prefix is defined. This is done with the first input field. This prefix should be "ses-" but may vary if the session are named differently.
+	- the participants.tsv coloumn name prefix is defined. This is done with the second input field. This is the prefix of column names in the participants.tsv file. This is optimally `day-`.
+	- the date is in format YYYY-mm-dd[T HH:MM] 
+4. _Convert:_
    Starts _meta.json_ creation process. Once finished, a pop-up message will inform the user. If subjects defined in the _participants.tsv_ are non existing, a warning message will be displayed. 
 
 **Please keep in mind that this application overwrites any already created _meta.json_ files in the subjects modality folders** 

src/main/Main.java

@@ -73,7 +73,7 @@ public class Main {
 					SimpleFrame.promt("Please select a valid Session Prefix");
 					return;
 				}
-				tsvPrefix = sessionPrefixPanel.getOutput();
+				tsvPrefix = pTsvPrefixPanel.getOutput();
 				if (tsvPrefix.equals("")) {
 					SimpleFrame.promt("Please select a valid Participants TSV RecordDate Column Prefix");
 					return;
@@ -105,7 +105,7 @@ public class Main {
 		final int maxRows = pTsv.getMaxRows();
 		
 		if (useRecordDate) {
-			int sesAmount = pTsv.getColumnByPrefixAmount(sessionTSVPrefix);
+			int sesAmount = pTsv.getColumnByPrefixAmount(sessionTSVPrefix); // This might produce more sessions than exits, but this is normally no drama
 			sessionsIndexesInTSV = new int[sesAmount];
 			for(int i = 0; i < sesAmount; i++) {
 				sessionsIndexesInTSV[i] = pTsv.getColumnByPrefix(sessionTSVPrefix + (i + 1));
@@ -186,12 +186,12 @@ public class Main {
 				
 			}
 		}
-		System.out.println("Subj Sex: " + sex);
+		
 		final String DEFAULT_RECORD_DATE = "1970-1-1";
 		String recordDate = DEFAULT_RECORD_DATE;
 		
 		if (sessionsIndexesInTSV != null) {
-			int session = SFB_Util.extractIntegerFromString(metaJSON.getAbsolutePath(), metaJSON.getAbsolutePath().indexOf(sessionFolderPrefix));
+			int session = SFB_Util.extractIntegerFromString(metaJSON.getAbsolutePath(), metaJSON.getAbsolutePath().indexOf(sessionFolderPrefix) + sessionFolderPrefix.length());
 			if (session != Integer.MIN_VALUE) {
 				String pTsvDate = pTsv.get(sessionsIndexesInTSV[session - 1], row);
 				int clockIndex = pTsvDate.indexOf('T');
@@ -199,6 +199,7 @@ public class Main {
 					pTsvDate = pTsvDate.substring(0, clockIndex);
 				}
 				recordDate = pTsvDate;
+				System.out.println("Session: " + session + " Data: " + recordDate);
 			}
 		}
 		
@@ -218,8 +219,10 @@ public class Main {
 				obj.put("Subject age", age);
 				obj.put("Subject ID", subjID);
 				
-				if(!recordDateCpy.equals(DEFAULT_RECORD_DATE))
+				if(!recordDateCpy.equals(DEFAULT_RECORD_DATE)) {
 					SFB_JSON_Util.setRecordDate(recordDateCpy, obj);
+					System.out.println("Data: " + recordDateCpy);
+				}
 			});
 		}