From 93e6e4621a8da674ac2b91fbb22ca006985a42ef Mon Sep 17 00:00:00 2001
From: Erik Diers <erik.diers@ruhr-uni-bochum.de>
Date: Sun, 2 Feb 2025 23:07:44 +0100
Subject: [PATCH] Added creation by xlsx file
---
src/main/Main.java | 99 +++++++++++++++++++++++++++++++++------
src/utils/CSV_Reader.java | 40 ++++++++++++++++
2 files changed, 125 insertions(+), 14 deletions(-)
diff --git a/src/main/Main.java b/src/main/Main.java
index f70c89c..c1c5d8d 100644
--- a/src/main/Main.java
+++ b/src/main/Main.java
@@ -13,9 +13,16 @@ import uiutils.InputFieldPanel;
import uiutils.LabelPanel;
import uiutils.SimpleFrame;
import uiutils.SpinnerINTPanel;
+import utils.CSV_Reader;
+import utils.SFB_JSON_Util;
+import utils.SFB_Util;
public class Main {
+ private static final String XLSX_SESSION_PREFIX = "SessionDate";
+ private static final String SFB_SUBJID = "subjectID";
+ private static final String SFB_RECORD_DATE = "Record Date";
+ private static int xlsx_subjIdHeaderIndex = -1;
public static void main(String[] args) {
SimpleFrame frame = new SimpleFrame("Create Study", 600, 400);
@@ -30,6 +37,12 @@ public class Main {
ComboSelectionPanel modalities = new ComboSelectionPanel("Modalities:", "Select", ComboSelectionPanel.SFB_MODALITIES);
InputFieldPanel customeModalities = new InputFieldPanel("Modality Folder", "EDA, fMRI, ...").setTextFieldprefWidth(300);
ConditionedPanel useCustomModalityFolders = new ConditionedPanel("Enter own modality folder names:", false, customeModalities);
+
+
+ FileChooserPanel baseMetaJson = new FileChooserPanel("Base Meta.json").switchToFileSelect("meta.json");
+ FileChooserPanel xlsxImportFile = new FileChooserPanel("Excel import file").switchToFileSelect(".xlsx");
+ ConditionedPanel importFromXlsx = new ConditionedPanel("Import from Excel", false, baseMetaJson, xlsxImportFile);
+
ButtonPanel submit = new ButtonPanel("Create", new ActionListener() {
@Override
@@ -52,25 +65,56 @@ public class Main {
return;
}
String[] codes;
+ CSV_Reader xlsxReader = null;
- if (useCustomSubjectCodes.getOutput()) {
- String codesSTR = sfbCodes.getOutput();
- if (codesSTR.trim().isEmpty()) {
- SimpleFrame.promt("Please enter patient identifiers");
+ int sessions = sessionAmount.getOutput();
+
+ if (importFromXlsx.getOutput()) {
+ if (baseMetaJson.getOutput() == null || !baseMetaJson.getOutput().exists()) {
+ SimpleFrame.promt("Please specify a valid base meta.json file");
return;
}
- codesSTR = codesSTR.replaceAll(" ", "");
- codes = codesSTR.split(",");
+
+ if (xlsxImportFile.getOutput() == null || !xlsxImportFile.getOutput().exists()) {
+ SimpleFrame.promt("Please specify a valid excel import file");
+ return;
+ }
+
+ xlsxReader = CSV_Reader.fromXLSX(xlsxImportFile.getOutput(), null);
+
+ for (int i = 0; i < sessions; i++) {
+ if (xlsxReader.getColumn(XLSX_SESSION_PREFIX + " " + i) == -1) {
+ SimpleFrame.promt("Excel file has not specifed Session date " + i + " [" + XLSX_SESSION_PREFIX + " " + i + "]");
+ return;
+ }
+ }
+
+
+ xlsx_subjIdHeaderIndex = xlsxReader.getColumnUncased(SFB_SUBJID); //
+ codes = xlsxReader.getCompleteColumn(xlsx_subjIdHeaderIndex);
+
} else {
- int subj = numberOfConsecutiveSubjects.getOutput();
- codes = new String[subj];
- for(int i = 0; i < subj; i++) {
- codes[i] = "sub-" + (i + 1);
+
+ //Does not generate codes when a xlsx file is given!
+ if (useCustomSubjectCodes.getOutput()) {
+ String codesSTR = sfbCodes.getOutput();
+ if (codesSTR.trim().isEmpty()) {
+ SimpleFrame.promt("Please enter patient identifiers");
+ return;
+ }
+ codesSTR = codesSTR.replaceAll(" ", "");
+ codes = codesSTR.split(",");
+ } else {
+ int subj = numberOfConsecutiveSubjects.getOutput();
+ codes = new String[subj];
+ for(int i = 0; i < subj; i++) {
+ codes[i] = "sub-" + (i + 1);
+ }
}
}
- int sessions = sessionAmount.getOutput();
+
String[] modalityFolders = modalities.getOutput();
@@ -94,7 +138,7 @@ public class Main {
}
try {
- createStudy(dest, codes, sessions, modalityFolders);
+ createStudy(dest, codes, sessions, modalityFolders, xlsxReader, baseMetaJson.getOutput());
} catch (IOException e1) {
e1.printStackTrace();
}
@@ -112,14 +156,15 @@ public class Main {
frame.addCenter(sessionAmount);
frame.addCenter(modalities);
frame.addCenter(useCustomModalityFolders);
+ frame.addCenter(importFromXlsx);
frame.addCenterNoLeftalignment(submit);
frame.submit();
}
- private static void createStudy(File studyFile, String[] sfbCodes, int sessionAmount, String[] modalities) throws IOException {
+ private static void createStudy(File studyFile, String[] sfbCodes, int sessionAmount, String[] modalities, CSV_Reader xlsxReader, File baseMeta) throws IOException {
studyFile.mkdir();
- for(String code:sfbCodes) {
+ for(String code : sfbCodes) {
File subjFolder = new File(studyFile.getAbsolutePath() + "\\" + code);
subjFolder.mkdir();
@@ -127,14 +172,40 @@ public class Main {
File sessionFolder = new File(subjFolder.getAbsolutePath() + "\\ses-" + i);
sessionFolder.mkdir();
+ if (xlsxReader != null)
+ createMetaFile(sessionFolder, xlsxReader, baseMeta, code, i);
+
for(String modality : modalities) {
File modFolder = new File(sessionFolder.getAbsolutePath() + "\\" + modality);
modFolder.mkdir();
+ if (xlsxReader != null)
+ createMetaFile(modFolder, xlsxReader, baseMeta, code, i);
}
}
}
+ }
+
+ @SuppressWarnings("unchecked")
+ private static void createMetaFile(File dir, CSV_Reader xlsxReader, File baseMeta, String sfbSubjCode ,int currentSession) throws IOException {
+ File metaJson = new File(dir.getAbsolutePath() + File.separator + "meta.json");
+ SFB_Util.copy(baseMeta, metaJson);
+ SFB_JSON_Util.performOnJson(metaJson, (obj) -> {
+ String[] currentRow = xlsxReader.getCompleteRow(xlsxReader.findRow(sfbSubjCode, xlsx_subjIdHeaderIndex));
+
+ for(int i = 0; i < currentRow.length; i++) {
+ String header = xlsxReader.getColumnHead(i);
+ if (header.startsWith(XLSX_SESSION_PREFIX)) {
+ if (header.endsWith("" + currentSession)) //Identifies the current session. This breaks in case of more than 9 sessions. But this wont happen.
+ header = SFB_RECORD_DATE;
+ else
+ continue;
+ }
+ obj.put(header, currentRow[i]);
+
+ }
+ });
}
}
diff --git a/src/utils/CSV_Reader.java b/src/utils/CSV_Reader.java
index 108581a..00cf110 100644
--- a/src/utils/CSV_Reader.java
+++ b/src/utils/CSV_Reader.java
@@ -5,6 +5,7 @@ import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.Calendar;
+import java.util.Iterator;
import java.util.LinkedList;
import java.util.Scanner;
import java.util.zip.ZipEntry;
@@ -87,11 +88,41 @@ public class CSV_Reader {
return -1;
}
+ public String getColumnHead(int indx) {
+ return headers[indx];
+ }
+
+ public int getColumnUncased(String header) {
+ header = header.toLowerCase();
+ for(int i = 0; i < headers.length; i++) {
+ if (headers[i].toLowerCase().equals(header)) return i;
+ }
+ return -1;
+ }
+
+ public String[] getCompleteColumn(int col) {
+ String[] column = new String[getMaxRows()];
+
+ for(int i = 0; i < column.length; i++) {
+ column[i] = entries[i][col];
+ }
+ return column;
+ }
+
+ public String[] getCompleteRow(int row) {
+ return entries[row];
+ }
+
public int getMaxRows() {
if (entries == null) return 0;
return entries.length;
}
+ public int getMaxColumns() {
+ if (headers == null) return 0;
+ return headers.length;
+ }
+
public String get(int column, int row) {
return entries[row][column];
}
@@ -108,6 +139,15 @@ public class CSV_Reader {
}
}
+ public int findRow(String searchFor, int inColumn) {
+ for (int row = 0; row < getMaxRows(); row++) {
+ if (entries[row][inColumn].equals(searchFor))
+ return row;
+ }
+ return -1;
+ }
+
+
public void printInlineVersion() {
StringBuilder b = new StringBuilder();
b.append("private static CSV_Reader csv = new CSV_Reader(new String[] {");
--
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