fatfind-runner

Adipocyte filter for FatFind

FatFind is an application for adipocyte investigation using Diamond: Interactive Search of Non-Indexed Data.

This repository contains the filter executable that runs on the Diamond servers.

Building

This filter depends on LTI-Lib. If you get compile errors about undefined resize() functions revision 3360 in SVN seems to have the proper fixes.

If compilation still fails because of undefined libpng symbol errors, apply the following patch to ltilib.

--- ltilib/src/io/ltiPNGLibFunctor.cpp.orig     2017-05-30 19:32:21.600730711 +0000
+++ ltilib/src/io/ltiPNGLibFunctor.cpp  2017-05-30 19:36:30.351134377 +0000
@@ -350,7 +350,7 @@
              colorType == PNG_COLOR_TYPE_GRAY_ALPHA) {
       // convert 1, 2, 4 bit to 8 bit
       if (bitDepth < 8) {
-        png_set_gray_1_2_4_to_8(pngPtr);
+        png_set_expand_gray_1_2_4_to_8(pngPtr);
       }
       else if (!(bitDepth == 8 || bitDepth == 16)) {
         setStatusString("Invalid bit depth in grayscale image");
@@ -513,10 +513,7 @@
     png_read_info(pngPtr, infoPtr);
     png_get_IHDR(pngPtr, infoPtr, &width, &height, &bitDepth, &colorType,
                  NULL, NULL, NULL);
-
-    // get the palette of the image from the infoPtr directly
-    numPalette = infoPtr->num_palette;
-    pngPalette = infoPtr->palette;
+    png_get_PLTE(pngPtr, infoPtr, &pngPalette, &numPalette);
 
     // convert images and handle palette in 2 different cases below,
     // grayscale or palette data grayscale image convertion
@@ -526,7 +523,7 @@
 
         if (bitDepth < 8) {
           // convert 1, 2, 4 bit grayscale to 8 bit
-          png_set_gray_1_2_4_to_8(pngPtr);
+          png_set_expand_gray_1_2_4_to_8(pngPtr);
         }
         else if (bitDepth == 16) {
           // strip 16 bit grayscale to 8 bit

If binaries fail to link with the resulting library, with an undefined MAIN__ error. Use the following patch as a workaround. Apply patch, rerun configure and rebuild/reinstall lti-lib.

--- ltilib/linux/lti-config.in.orig  2017-06-01 17:40:07.202911793 +0000
+++ ltilib/linux/lti-config.in   2017-06-01 17:40:22.247308190 +0000
@@ -10,7 +10,7 @@
 # Check for LAPACK
 lapack_libs=@LAPACK_LIBS@
 if test -n "$lapack_libs" ; then
-LIBS="@LAPACK_LIBS@ @BLAS_LIBS@ @F2C_LIBS@ @LIBS@ @FLIBS@"
+LIBS="@LAPACK_LIBS@ @BLAS_LIBS@ -Wl,--undefined=MAIN__ @F2C_LIBS@ @LIBS@ @FLIBS@"
 else
 LIBS="@LIBS@" 
 fi
--- ltilib/linux/lti-local-config.in.orig    2017-06-01 18:08:51.785301013 +0000
+++ ltilib/linux/lti-local-config.in 2017-06-01 18:09:08.577750454 +0000
@@ -9,7 +9,7 @@
 # Check for LAPACK
 lapack_libs=@LAPACK_LIBS@
 if test -n "$lapack_libs" ; then
-LIBS="@LAPACK_LIBS@ @BLAS_LIBS@ @F2C_LIBS@ @LIBS@ @FLIBS@"
+LIBS="@LAPACK_LIBS@ @BLAS_LIBS@ -Wl,--undefined=MAIN__ @F2C_LIBS@ @LIBS@ @FLIBS@"
 lapack_include="-I${prefix}/misc/lamath"
 else
 LIBS="@LIBS@"