From 48727138e88f056b67312603560e600362346462 Mon Sep 17 00:00:00 2001
From: tbaudier <thomas.baudier@creatis.insa-lyon.fr>
Date: Fri, 11 Jan 2019 11:58:58 +0100
Subject: [PATCH] Change paradigm to find files

When we find the files to sort them with itk::GDCMSeriesFileNames, I just have to remove the first ./ if present

Moreover, sliceIndex has to be the sorting vector (it was not correct before)
---
 tools/clitkDicom2Image.cxx | 19 +++++++++++++------
 1 file changed, 13 insertions(+), 6 deletions(-)

diff --git a/tools/clitkDicom2Image.cxx b/tools/clitkDicom2Image.cxx
index d32fbae..38e8aa3 100644
--- a/tools/clitkDicom2Image.cxx
+++ b/tools/clitkDicom2Image.cxx
@@ -155,22 +155,29 @@ int main(int argc, char * argv[])
     std::vector<double> locs = sliceLocations[*sn];
     std::vector<double> origin = theorigin[*sn];
     std::vector<std::string> files = seriesFiles[*sn];
-    std::vector<int> sliceIndex;
+    std::vector<int> sliceIndex(files.size());
     //clitk::GetSortedIndex(locs, sliceIndex);
     //Look for files into GDCMSeriesFileNames, because it sorts files correctly and take the order
     const std::vector<std::string> & temp = nameGenerator->GetFileNames(*sn);
     for(unsigned int i=0; i<files.size(); i++) {
       int j(0);
-      while (sliceIndex.size()==i && j<temp.size()) {
+      bool found(false);
+      while (!found && j<temp.size()) {
         const size_t last_slash_idx2 = temp[j].rfind('/');
         std::string tempFilename(temp[j]);
-        if (temp[j][0] == '.' && std::string::npos != last_slash_idx2)
-          tempFilename = temp[j].substr(last_slash_idx2+1, temp[j].size()-1);
-        if (tempFilename == files[i])
-          sliceIndex.push_back(j);
+        if (temp[j][0] == '.' && temp[j][1] == '/')
+          tempFilename = temp[j].substr(2, temp[j].size()-1);
+        if (tempFilename == files[i]) {
+          sliceIndex[j] = i;
+          found = true;
+        }
         ++j;
       }
     }
+    if (sliceIndex.size() == 0) { //ie. sn is not a serie present in files
+      sn++;
+      continue;
+    }
 
     if (args_info.verbose_flag) {
       std::cout << locs[sliceIndex[0]] << " -> "
-- 
2.47.1