From 02e91a145a1e6a1de74130e5dad8d5e3ba85fbe2 Mon Sep 17 00:00:00 2001
From: Mark Jenkinson <mark@fmrib.ox.ac.uk>
Date: Sat, 22 Feb 2003 18:40:19 +0000
Subject: [PATCH] Fixed include paths for headers

---
 AutoCorrEstimator.cc  |  2 ++
 AutoCorrEstimator.h   |  2 ++
 BandPassOptions.cc    |  4 ++++
 BandPassOptions.h     |  6 ++++++
 ContrastMgr.cc        |  2 ++
 ContrastMgr.h         |  2 ++
 ContrastMgrOptions.cc |  4 ++++
 ContrastMgrOptions.h  |  6 ++++++
 FilmGlsOptions.cc     |  4 ++++
 FilmGlsOptions.h      |  6 ++++++
 FilmGlsOptionsRes.cc  |  4 ++++
 FilmGlsOptionsRes.h   |  6 ++++++
 FilmOlsOptions.cc     |  4 ++++
 FilmOlsOptions.h      |  6 ++++++
 Log.h                 |  5 +++++
 Logbak.h              |  5 +++++
 Volume.cc             |  3 +++
 Volume.h              |  3 +++
 VolumeSeries.cc       |  3 +++
 VolumeSeries.h        |  3 +++
 band_pass.cc          |  4 ++++
 contrast_mgr.cc       |  4 ++++
 film_gls.cc           |  5 +++++
 film_gls_res.cc       |  5 +++++
 film_ols.cc           |  4 ++++
 ftoz.cc               |  3 +++
 gaussComparer.h       |  2 ++
 glim.cc               |  1 +
 glim.h                |  2 ++
 glimGls.cc            |  1 +
 glimGls.h             |  2 ++
 glm.h                 |  2 ++
 glmrand.cc            |  2 ++
 glmrand.h             |  2 ++
 paradigm.cc           |  4 ++--
 paradigm.h            |  4 ++--
 quick.cc              | 14 +++++++-------
 ttologp.cc            |  8 ++++----
 ttoz.cc               |  8 ++++----
 39 files changed, 138 insertions(+), 19 deletions(-)

diff --git a/AutoCorrEstimator.cc b/AutoCorrEstimator.cc
index 6e6dab7..68cf93f 100644
--- a/AutoCorrEstimator.cc
+++ b/AutoCorrEstimator.cc
@@ -32,6 +32,8 @@
     Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
     USA */
 
+#include <iostream>
+#include <strstream>
 #define WANT_STREAM
 
 #include "AutoCorrEstimator.h"
diff --git a/AutoCorrEstimator.h b/AutoCorrEstimator.h
index 2e5cb13..9e9887a 100644
--- a/AutoCorrEstimator.h
+++ b/AutoCorrEstimator.h
@@ -9,6 +9,8 @@
 #if !defined(__AutoCorrEstimator_h)
 #define __AutoCorrEstimator_h
 
+#include <iostream>
+#include <fstream>
 #define WANT_STREAM
 #define WANT_MATH
 
diff --git a/BandPassOptions.cc b/BandPassOptions.cc
index ed13a9b..1d773f6 100644
--- a/BandPassOptions.cc
+++ b/BandPassOptions.cc
@@ -9,6 +9,10 @@
 #define WANT_STREAM
 #define WANT_MATH
 
+#include <iostream.h>
+#include <fstream.h>
+#include <stdlib.h>
+#include <stdio.h>
 #include "newmat/newmatap.h"
 #include "newmat/newmatio.h"
 #include "BandPassOptions.h"
diff --git a/BandPassOptions.h b/BandPassOptions.h
index 7f4d3eb..88fd9f4 100644
--- a/BandPassOptions.h
+++ b/BandPassOptions.h
@@ -9,6 +9,12 @@
 #if !defined(__BandPassOptions_h)
 #define __BandPassOptions_h
 
+#include <string>
+#include <math.h>
+#include <iostream.h>
+#include <fstream.h>
+#include <stdlib.h>
+#include <stdio.h>
 
 namespace FILM {
 
diff --git a/ContrastMgr.cc b/ContrastMgr.cc
index 9834694..cc9b21f 100644
--- a/ContrastMgr.cc
+++ b/ContrastMgr.cc
@@ -6,6 +6,8 @@
 
 /*  CCOPYRIGHT  */
 
+#include <strstream>
+#include <fstream>
 #include "ContrastMgr.h"
 #include "ContrastMgrOptions.h"
 #include "miscmaths/miscmaths.h"
diff --git a/ContrastMgr.h b/ContrastMgr.h
index 1dc3375..ce4b81d 100644
--- a/ContrastMgr.h
+++ b/ContrastMgr.h
@@ -9,6 +9,8 @@
 #if !defined(__ContrastMgr_h)
 #define __ContrastMgr_h
 
+#include <iostream>
+#include <fstream>
 #define WANT_STREAM
 #define WANT_MATH
 
diff --git a/ContrastMgrOptions.cc b/ContrastMgrOptions.cc
index 9ee34de..42c4119 100644
--- a/ContrastMgrOptions.cc
+++ b/ContrastMgrOptions.cc
@@ -9,6 +9,10 @@
 #define WANT_STREAM
 #define WANT_MATH
 
+#include <iostream.h>
+#include <fstream.h>
+#include <stdlib.h>
+#include <stdio.h>
 #include "newmat/newmatap.h"
 #include "newmat/newmatio.h"
 #include "ContrastMgrOptions.h"
diff --git a/ContrastMgrOptions.h b/ContrastMgrOptions.h
index 5cdc83e..0060795 100644
--- a/ContrastMgrOptions.h
+++ b/ContrastMgrOptions.h
@@ -9,6 +9,12 @@
 #if !defined(__ContrastMgrOptions_h)
 #define __ContrastMgrOptions_h
 
+#include <string>
+#include <math.h>
+#include <iostream.h>
+#include <fstream.h>
+#include <stdlib.h>
+#include <stdio.h>
 #include "utils/log.h"
 
 using namespace Utilities;
diff --git a/FilmGlsOptions.cc b/FilmGlsOptions.cc
index 49b7a81..fedbecb 100644
--- a/FilmGlsOptions.cc
+++ b/FilmGlsOptions.cc
@@ -9,6 +9,10 @@
 #define WANT_STREAM
 #define WANT_MATH
 
+#include <iostream.h>
+#include <fstream.h>
+#include <stdlib.h>
+#include <stdio.h>
 #include "FilmGlsOptions.h"
 #include "utils/log.h"
 
diff --git a/FilmGlsOptions.h b/FilmGlsOptions.h
index ded6249..165fef7 100644
--- a/FilmGlsOptions.h
+++ b/FilmGlsOptions.h
@@ -9,6 +9,12 @@
 #if !defined(__FilmGlsOptions_h)
 #define __FilmGlsOptions_h
 
+#include <string>
+#include <math.h>
+#include <iostream.h>
+#include <fstream.h>
+#include <stdlib.h>
+#include <stdio.h>
 #include "utils/log.h"
 
 using namespace Utilities;
diff --git a/FilmGlsOptionsRes.cc b/FilmGlsOptionsRes.cc
index 819736e..23fc9d5 100644
--- a/FilmGlsOptionsRes.cc
+++ b/FilmGlsOptionsRes.cc
@@ -9,6 +9,10 @@
 #define WANT_STREAM
 #define WANT_MATH
 
+#include <iostream.h>
+#include <fstream.h>
+#include <stdlib.h>
+#include <stdio.h>
 #include "newmat/newmatap.h"
 #include "newmat/newmatio.h"
 #include "FilmGlsOptionsRes.h"
diff --git a/FilmGlsOptionsRes.h b/FilmGlsOptionsRes.h
index 75a93f4..bb0f4a6 100644
--- a/FilmGlsOptionsRes.h
+++ b/FilmGlsOptionsRes.h
@@ -9,6 +9,12 @@
 #if !defined(__FilmGlsOptionsRes_h)
 #define __FilmGlsOptionsRes_h
 
+#include <string>
+#include <math.h>
+#include <iostream.h>
+#include <fstream.h>
+#include <stdlib.h>
+#include <stdio.h>
 
 namespace FILM {
 
diff --git a/FilmOlsOptions.cc b/FilmOlsOptions.cc
index 25b872e..6685e5c 100644
--- a/FilmOlsOptions.cc
+++ b/FilmOlsOptions.cc
@@ -10,6 +10,10 @@
 #define WANT_STREAM
 #define WANT_MATH
 
+#include <iostream.h>
+#include <fstream.h>
+#include <stdlib.h>
+#include <stdio.h>
 #include "newmat/newmatap.h"
 #include "newmat/newmatio.h"
 #include "FilmOlsOptions.h"
diff --git a/FilmOlsOptions.h b/FilmOlsOptions.h
index 2b9c290..78ccfeb 100644
--- a/FilmOlsOptions.h
+++ b/FilmOlsOptions.h
@@ -9,6 +9,12 @@
 #if !defined(__FilmOlsOptions_h)
 #define __FilmOlsOptions_h
 
+#include <string>
+#include <math.h>
+#include <iostream.h>
+#include <fstream.h>
+#include <stdlib.h>
+#include <stdio.h>
 
 namespace FILM {
 
diff --git a/Log.h b/Log.h
index 9d81f20..a3a925f 100644
--- a/Log.h
+++ b/Log.h
@@ -6,6 +6,11 @@
 
 /*  CCOPYRIGHT  */
 
+#include <iostream>
+#include <fstream>
+#include <iomanip>
+#include <string>
+#include <math.h>
 #include "newmat/newmatap.h"
 #include "newmat/newmatio.h"
 
diff --git a/Logbak.h b/Logbak.h
index 9d81f20..a3a925f 100644
--- a/Logbak.h
+++ b/Logbak.h
@@ -6,6 +6,11 @@
 
 /*  CCOPYRIGHT  */
 
+#include <iostream>
+#include <fstream>
+#include <iomanip>
+#include <string>
+#include <math.h>
 #include "newmat/newmatap.h"
 #include "newmat/newmatio.h"
 
diff --git a/Volume.cc b/Volume.cc
index 96b0043..e0dce3e 100644
--- a/Volume.cc
+++ b/Volume.cc
@@ -6,6 +6,9 @@
 
 /*  CCOPYRIGHT  */
 
+#include <iostream>
+#include <cstdlib>
+#include <avwio.h>
 
 #include "newmat/newmatap.h"
 #include "newmat/newmatio.h"
diff --git a/Volume.h b/Volume.h
index da85e3f..7d89e6d 100644
--- a/Volume.h
+++ b/Volume.h
@@ -9,12 +9,15 @@
 #if !defined(__Volume_h)
 #define __Volume_h
 
+#include <iostream>
+#include <fstream>
 #define WANT_STREAM
 #define WANT_MATH
 
 #include "newmat/newmatap.h"
 #include "newmat/newmatio.h"
 #include "VolumeSeries.h"
+#include <string>
 
 using namespace NEWMAT;
 namespace FILM {
diff --git a/VolumeSeries.cc b/VolumeSeries.cc
index 52459ca..96de6d6 100644
--- a/VolumeSeries.cc
+++ b/VolumeSeries.cc
@@ -6,6 +6,9 @@
 
 /*  CCOPYRIGHT  */
 
+#include <iostream>
+#include <cstdlib>
+#include <avwio.h>
 
 #include "newmat/newmatap.h"
 #include "newmat/newmatio.h"
diff --git a/VolumeSeries.h b/VolumeSeries.h
index 5dd5939..52afe92 100644
--- a/VolumeSeries.h
+++ b/VolumeSeries.h
@@ -6,12 +6,15 @@
 
 /*  CCOPYRIGHT  */
 
+#include <iostream>
+#include <fstream>
 #define WANT_STREAM
 #define WANT_MATH
 
 #include "newmat/newmatap.h"
 #include "newmat/newmatio.h"
 
+#include <string>
 
 using namespace NEWMAT;
 
diff --git a/band_pass.cc b/band_pass.cc
index 6c0df8c..261225c 100644
--- a/band_pass.cc
+++ b/band_pass.cc
@@ -6,6 +6,9 @@
 
 /*  CCOPYRIGHT  */
 
+#include <iostream>
+#include <fstream>
+#include <strstream>
 #define WANT_STREAM
 #define WANT_MATH
 
@@ -15,6 +18,7 @@
 #include "Volume.h"
 #include "utils/log.h"
 #include "BandPassOptions.h"
+#include <string>
 
 #ifndef NO_NAMESPACE
 using namespace NEWMAT;
diff --git a/contrast_mgr.cc b/contrast_mgr.cc
index 000ae4b..5871ab3 100644
--- a/contrast_mgr.cc
+++ b/contrast_mgr.cc
@@ -6,6 +6,9 @@
 
 /*  CCOPYRIGHT  */
 
+#include <iostream>
+#include <fstream>
+#include <strstream>
 #define WANT_STREAM
 #define WANT_MATH
 
@@ -18,6 +21,7 @@
 #include "utils/log.h"
 #include "ContrastMgrOptions.h"
 #include "utils/tracer_plus.h"
+#include <string>
 
 using namespace NEWMAT;
 using namespace FILM;
diff --git a/film_gls.cc b/film_gls.cc
index ce6967d..9778e1e 100644
--- a/film_gls.cc
+++ b/film_gls.cc
@@ -6,6 +6,9 @@
 
 /*  CCOPYRIGHT  */
 
+#include <iostream>
+#include <fstream>
+#include <strstream>
 #define WANT_STREAM
 #define WANT_MATH
 
@@ -19,6 +22,8 @@
 #include "paradigm.h"
 #include "FilmGlsOptions.h"
 #include "glimGls.h"
+#include <vector>
+#include <string>
 
 using namespace NEWMAT;
 using namespace FILM;
diff --git a/film_gls_res.cc b/film_gls_res.cc
index 55eb1e7..92e1896 100644
--- a/film_gls_res.cc
+++ b/film_gls_res.cc
@@ -6,6 +6,9 @@
 
 /*  CCOPYRIGHT  */
 
+#include <iostream>
+#include <fstream>
+#include <strstream>
 #define WANT_STREAM
 #define WANT_MATH
 
@@ -20,6 +23,8 @@
 #include "paradigm.h"
 #include "FilmGlsOptionsRes.h"
 #include "glimGls.h"
+#include <vector>
+#include <string>
 
 using namespace NEWMAT;
 using namespace FILM;
diff --git a/film_ols.cc b/film_ols.cc
index 5d0a68b..efb019f 100644
--- a/film_ols.cc
+++ b/film_ols.cc
@@ -6,6 +6,9 @@
 
 /*  CCOPYRIGHT  */
 
+#include <iostream>
+#include <fstream>
+#include <strstream>
 #define WANT_STREAM
 #define WANT_MATH
 
@@ -20,6 +23,7 @@
 #include "AutoCorrEstimator.h"
 #include "paradigm.h"
 #include "FilmOlsOptions.h"
+#include <string>
 
 using namespace NEWMAT;
 using namespace FILM;
diff --git a/ftoz.cc b/ftoz.cc
index f38c1c8..b3c9c69 100644
--- a/ftoz.cc
+++ b/ftoz.cc
@@ -6,6 +6,8 @@
 
 /*  CCOPYRIGHT  */
 
+#include <iostream>
+#include <fstream>
 #define WANT_STREAM
 #define WANT_MATH
 
@@ -14,6 +16,7 @@
 
 #include "miscmaths/f2z.h"
 #include "Volume.h"
+#include <string>
 
 using namespace NEWMAT;
 using namespace FILM;
diff --git a/gaussComparer.h b/gaussComparer.h
index 263e47c..93e5c80 100644
--- a/gaussComparer.h
+++ b/gaussComparer.h
@@ -9,6 +9,8 @@
 #if !defined(__gaussComparer_h)
 #define __gaussComparer_h
 
+#include <iostream>
+#include <fstream>
 #define WANT_STREAM
 #define WANT_MATH
 
diff --git a/glim.cc b/glim.cc
index a326e76..c8bbaee 100644
--- a/glim.cc
+++ b/glim.cc
@@ -6,6 +6,7 @@
 
 /*  CCOPYRIGHT  */
 
+#include <strstream>
 
 #include "glim.h"
 #include "miscmaths/miscmaths.h"
diff --git a/glim.h b/glim.h
index fb07f5f..4cedf56 100644
--- a/glim.h
+++ b/glim.h
@@ -6,6 +6,8 @@
 
 /*  CCOPYRIGHT  */
 
+#include <iostream>
+#include <fstream>
 #define WANT_STREAM
 #define WANT_MATH
 
diff --git a/glimGls.cc b/glimGls.cc
index cea30d1..07b0c75 100644
--- a/glimGls.cc
+++ b/glimGls.cc
@@ -6,6 +6,7 @@
 
 /*  CCOPYRIGHT  */
 
+#include <strstream>
 
 #include "glimGls.h"
 #include "miscmaths/miscmaths.h"
diff --git a/glimGls.h b/glimGls.h
index adabc4b..8a8f3ba 100644
--- a/glimGls.h
+++ b/glimGls.h
@@ -9,6 +9,8 @@
 #if !defined(__glimgls_h)
 #define __glimgls_h
 
+#include <iostream>
+#include <fstream>
 #define WANT_STREAM
 #define WANT_MATH
 
diff --git a/glm.h b/glm.h
index 5ebb5fc..8618036 100644
--- a/glm.h
+++ b/glm.h
@@ -9,6 +9,8 @@
 #if !defined(__glm_h)
 #define __glm_h
 
+#include <iostream>
+#include <fstream>
 #define WANT_STREAM
 #define WANT_MATH
 
diff --git a/glmrand.cc b/glmrand.cc
index bcfc147..96e535b 100644
--- a/glmrand.cc
+++ b/glmrand.cc
@@ -13,6 +13,8 @@
 #include "miscmaths/t2z.h"
 #define __STL_NO_DRAND48
 
+#include <vector.h>
+#include <algo.h>
 
 #ifndef NO_NAMESPACE
 using namespace MISCMATHS;
diff --git a/glmrand.h b/glmrand.h
index 0286f37..30fac52 100644
--- a/glmrand.h
+++ b/glmrand.h
@@ -9,6 +9,8 @@
 #if !defined(__glmRand_h)
 #define __glmRand_h
 
+#include <iostream>
+#include <fstream>
 #define WANT_STREAM
 #define WANT_MATH
 
diff --git a/paradigm.cc b/paradigm.cc
index 2ef814a..427ce6e 100644
--- a/paradigm.cc
+++ b/paradigm.cc
@@ -7,8 +7,8 @@
 /*  CCOPYRIGHT  */
 
 #include "paradigm.h"
-#include "log.h"
-#include "miscmaths.h"
+#include "utils/log.h"
+#include "miscmaths/miscmaths.h"
 #include <fstream>
 
 using namespace FILM;
diff --git a/paradigm.h b/paradigm.h
index 837dbfe..f813789 100644
--- a/paradigm.h
+++ b/paradigm.h
@@ -11,8 +11,8 @@
 
 #include <iostream>
 #include <fstream>
-#include "newmatap.h"
-#include "newmatio.h"
+#include "newmat/newmatap.h"
+#include "newmat/newmatio.h"
 #include <string>
 
 using namespace NEWMAT;
diff --git a/quick.cc b/quick.cc
index 6ceb93a..0c52e30 100644
--- a/quick.cc
+++ b/quick.cc
@@ -5,18 +5,18 @@
 #define WANT_STREAM
 #define WANT_MATH
 
-#include "newmatap.h"
-#include "newmatio.h"
+#include "newmat/newmatap.h"
+#include "newmat/newmatio.h"
 #include <string>
 #include <math.h>
 #include "glmrand.h"
 #include "Volume.h"
-#include "log.h"
+#include "utils/log.h"
 #include "histogram.h"
-#include "t2z.h"
-#include "f2z.h"
-#include "miscmaths.h"
-#include "libprob.h"
+#include "miscmaths/t2z.h"
+#include "miscmaths/f2z.h"
+#include "miscmaths/miscmaths.h"
+#include "libprob/libprob.h"
 #include <time.h>
 
 using namespace Utilities;
diff --git a/ttologp.cc b/ttologp.cc
index ea80c66..abe3421 100644
--- a/ttologp.cc
+++ b/ttologp.cc
@@ -11,13 +11,13 @@
 #define WANT_STREAM
 #define WANT_MATH
 
-#include "newmatap.h"
-#include "newmatio.h"
+#include "newmat/newmatap.h"
+#include "newmat/newmatio.h"
 
-#include "t2z.h"
+#include "miscmaths/t2z.h"
 #include "Volume.h"
 #include <string>
-#include "miscmaths.h"
+#include "miscmaths/miscmaths.h"
 
 using namespace NEWMAT;
 using namespace FILM;
diff --git a/ttoz.cc b/ttoz.cc
index 433e61e..cdf4869 100644
--- a/ttoz.cc
+++ b/ttoz.cc
@@ -11,11 +11,11 @@
 #define WANT_STREAM
 #define WANT_MATH
 
-#include "newmatap.h"
-#include "newmatio.h"
-#include "miscmaths.h"
+#include "newmat/newmatap.h"
+#include "newmat/newmatio.h"
+#include "miscmaths/miscmaths.h"
 
-#include "t2z.h"
+#include "miscmaths/t2z.h"
 #include "Volume.h"
 #include <string>
 
-- 
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