diff --git a/Makefile b/Makefile
index 823665a0..c867a9a9 100644
--- a/Makefile
+++ b/Makefile
@@ -580,6 +580,7 @@ SOCFLAGS = -fPIC
SOLDFLAGS = -shared -Wl,-rpath,$(CBF_PREFIX)/lib
JAVAINCLUDES = -I$(JDKDIR)/include -I$(JDKDIR)/include/linux
LDPREFIX = LD_LIBRARY_PATH=$(SOLIB):$$LD_LIBRARY_PATH;export LD_LIBRARY_PATH;
+RUNLDPREFIX = LD_LIBRARY_PATH=$(CBF_PREFIX)/LIB:$$LD_LIBRARY_PATH;export LD_LIBRARY_PATH;
EXTRALIBS = -lm
M4FLAGS = -Dfcb_bytes_in_rec=131072
TIME = time
@@ -1028,6 +1029,11 @@ Makefile: $(M4)/Makefile.m4
m4 -P $(PYCIFRWDEF) -Dcbf_system=default $(M4)/Makefile.m4 > Makefile.tmp
mv Makefile.tmp Makefile
+cbflib.ini: $(M4)/Makefile.m4
+ echo "$(LDPREFIX)" > cbflib.ini
+ echo "HDF5_PLUGIN_PATH=$(SOLIB):$$HDF5_PLUGIN_PATH" >> cbflib.ini
+ echo "export HDF5_PLUGIN_PATH" >> cbflib.ini
+
symlinksdone:
chmod a+x .symlinks
chmod a+x .undosymlinks
@@ -1073,6 +1079,10 @@ baseinstall: all $(CBF_PREFIX) $(CBF_PREFIX)/lib $(CBF_PREFIX)/bin \
-cp $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/libfcb_old.so
cp $(SOLIB)/libfcb.so $(CBF_PREFIX)/lib/libfcb.so
$(LN) $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/lib_fcb.so
+ -cp $(CBF_PREFIX)/bin/cbflib.ini $(CBF_PREFIX)/bin/cbflib.ini_old
+ echo "$(RUNLDPREFIX)" > $(CBF_PREFIX)/bin/cbflib.ini
+ echo "HDF5_PLUGIN_PATH=$(CBF_PREFIX)/lib:$$HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini
+ echo "export HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini
-cp $(CBF_PREFIX)/bin/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf_old
cp $(BIN)/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf
-cp $(CBF_PREFIX)/bin/cbf2adscimg $(CBF_PREFIX)/bin/cbf2adscimg_old
@@ -1236,7 +1246,7 @@ $(TIFF): build_tiff config.guess config.sub
$(TIFF)_INSTALL: $(TIFF)
-rm -rf $(TIFF)_install
rsync -avz $(TIFF)/ $(TIFF)_install
- (cd $(TIFF_install); make distclean; ./configure --prefix=$(CBF_PREFIX); make install)
+ (cd $(TIFF)_install; make distclean; ./configure --prefix=$(CBF_PREFIX); make install)
ifneq ($(CBFLIB_DONT_USE_LOCAL_HDF5),yes)
@@ -2071,7 +2081,7 @@ restore_output: $(NEWTESTOUTPUT) $(DATADIRO) $(MINICBF_TEST)/minicbf.h5
cp test_fcb_read_testflatpackedout.out $(DATADIRO)/test_fcb_read_testflatpackedout_orig.out
cp XRD1621.cbf $(DATADIRO)/XRD1621_orig.cbf
cp XRD1621_I4encbC100.cbf $(DATADIRO)/XRD1621_I4encbC100_orig.cbf
- cp minicbf_orig.h5 $(DATADIRO)/minicbf_orig.h5
+ cp $(MINICBF_TEST)/minicbf.h5 $(DATADIRO)/minicbf_orig.h5
restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS)
$(SIGNATURE) < adscconverted_flat.cbf > $(DATADIRS)/adscconverted_flat_orig.cbf$(SEXT)
@@ -2089,7 +2099,7 @@ restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS)
$(SIGNATURE) < test_fcb_read_testflatpackedout.out > $(DATADIRS)/test_fcb_read_testflatpackedout_orig.out$(SEXT)
$(SIGNATURE) < XRD1621.cbf > $(DATADIRS)/XRD1621_orig.cbf$(SEXT)
$(SIGNATURE) < XRD1621_I4encbC100.cbf > $(DATADIRS)/XRD1621_I4encbC100_orig.cbf$(SEXT)
- $(SIGNATURE) < minicbf_orig.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT)
+ $(SIGNATURE) < $(MINICBF_TEST)/minicbf.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT)
restore_signatures: restore_output restore_sigs_only
#
@@ -2241,7 +2251,7 @@ endif
$(TIME) $(BIN)/cif2cbf -5 rn $(HDF5REGISTER) -en -cp -i insulin_pilatus6mconverted_enc2.cbf.h5 -o insulin_pilatus6mconverted_enc2.cbf.h5.cbf; \
$(BIN)/cif2cbf -eq -cI -i insulin_pilatus6mconverted_enc2.cbf.h5.cbf -o insulin_pilatus6mconverted_enc2.cbf.h5.eqcI.cbf)
-cmp insulin_pilatus6mconverted_enc2.cbf.h5.eqcI.cbf insulin_pilatus6mconverted_orig.cbf.h5.eqcI.cbf
- #-rm -f insulin_pilatus6mconverted*.cbf.h5.eqcI.cbf
+ -rm -f insulin_pilatus6mconverted*.cbf.h5.eqcI.cbf
$(LDPREFIX) $(TINE) $(BIN)/test_cbf_airy_disk
$(LDPREFIX) $(TIME) $(BIN)/cbf_testxfelread
$(LDPREFIX) $(TIME) $(BIN)/testalloc
@@ -2256,7 +2266,7 @@ endif
-cd $(MINICBF_TEST); $(DIFF) minicbf_original.dump minicbf.dump
$(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf_original.dump
$(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf.dump
- cd $(MINICBF_TEST); rm -f minicbf.h5
+ #cd $(MINICBF_TEST); rm -f minicbf.h5
$(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/cbf2nexus -c zlib \
--list -o i19-1.h5 ../1191_00005.cbf
$(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/nexus2cbf \
diff --git a/Makefile_AIX b/Makefile_AIX
index fb648aec..939457f4 100644
--- a/Makefile_AIX
+++ b/Makefile_AIX
@@ -577,6 +577,7 @@ F90FLAGS = -g -qsuffix=f=f90
F90LDFLAGS =
M4FLAGS = -Dfcb_bytes_in_rec=131072
LDPREFIX = LIBPATH=$(SOLIB):$$LIBPATH;export LIBPATH;
+RUNLDPREFIX = LIBPATH=$(CBF_PREFIX)/lib:$$LIBPATH;export LIBPATH;
EXTRALIBS = -lm
TIME = time
@@ -1024,6 +1025,11 @@ Makefile: $(M4)/Makefile.m4
m4 -P $(PYCIFRWDEF) -Dcbf_system=default $(M4)/Makefile.m4 > Makefile.tmp
mv Makefile.tmp Makefile
+cbflib.ini: $(M4)/Makefile.m4
+ echo "$(LDPREFIX)" > cbflib.ini
+ echo "HDF5_PLUGIN_PATH=$(SOLIB):$$HDF5_PLUGIN_PATH" >> cbflib.ini
+ echo "export HDF5_PLUGIN_PATH" >> cbflib.ini
+
symlinksdone:
chmod a+x .symlinks
chmod a+x .undosymlinks
@@ -1069,6 +1075,10 @@ baseinstall: all $(CBF_PREFIX) $(CBF_PREFIX)/lib $(CBF_PREFIX)/bin \
-cp $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/libfcb_old.so
cp $(SOLIB)/libfcb.so $(CBF_PREFIX)/lib/libfcb.so
$(LN) $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/lib_fcb.so
+ -cp $(CBF_PREFIX)/bin/cbflib.ini $(CBF_PREFIX)/bin/cbflib.ini_old
+ echo "$(RUNLDPREFIX)" > $(CBF_PREFIX)/bin/cbflib.ini
+ echo "HDF5_PLUGIN_PATH=$(CBF_PREFIX)/lib:$$HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini
+ echo "export HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini
-cp $(CBF_PREFIX)/bin/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf_old
cp $(BIN)/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf
-cp $(CBF_PREFIX)/bin/cbf2adscimg $(CBF_PREFIX)/bin/cbf2adscimg_old
@@ -1232,7 +1242,7 @@ $(TIFF): build_tiff config.guess config.sub
$(TIFF)_INSTALL: $(TIFF)
-rm -rf $(TIFF)_install
rsync -avz $(TIFF)/ $(TIFF)_install
- (cd $(TIFF_install); make distclean; ./configure --prefix=$(CBF_PREFIX); make install)
+ (cd $(TIFF)_install; make distclean; ./configure --prefix=$(CBF_PREFIX); make install)
ifneq ($(CBFLIB_DONT_USE_LOCAL_HDF5),yes)
@@ -2067,7 +2077,7 @@ restore_output: $(NEWTESTOUTPUT) $(DATADIRO) $(MINICBF_TEST)/minicbf.h5
cp test_fcb_read_testflatpackedout.out $(DATADIRO)/test_fcb_read_testflatpackedout_orig.out
cp XRD1621.cbf $(DATADIRO)/XRD1621_orig.cbf
cp XRD1621_I4encbC100.cbf $(DATADIRO)/XRD1621_I4encbC100_orig.cbf
- cp minicbf_orig.h5 $(DATADIRO)/minicbf_orig.h5
+ cp $(MINICBF_TEST)/minicbf.h5 $(DATADIRO)/minicbf_orig.h5
restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS)
$(SIGNATURE) < adscconverted_flat.cbf > $(DATADIRS)/adscconverted_flat_orig.cbf$(SEXT)
@@ -2085,7 +2095,7 @@ restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS)
$(SIGNATURE) < test_fcb_read_testflatpackedout.out > $(DATADIRS)/test_fcb_read_testflatpackedout_orig.out$(SEXT)
$(SIGNATURE) < XRD1621.cbf > $(DATADIRS)/XRD1621_orig.cbf$(SEXT)
$(SIGNATURE) < XRD1621_I4encbC100.cbf > $(DATADIRS)/XRD1621_I4encbC100_orig.cbf$(SEXT)
- $(SIGNATURE) < minicbf_orig.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT)
+ $(SIGNATURE) < $(MINICBF_TEST)/minicbf.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT)
restore_signatures: restore_output restore_sigs_only
#
@@ -2252,7 +2262,7 @@ endif
-cd $(MINICBF_TEST); $(DIFF) minicbf_original.dump minicbf.dump
$(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf_original.dump
$(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf.dump
- cd $(MINICBF_TEST); rm -f minicbf.h5
+ #cd $(MINICBF_TEST); rm -f minicbf.h5
$(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/cbf2nexus -c zlib \
--list -o i19-1.h5 ../1191_00005.cbf
$(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/nexus2cbf \
diff --git a/Makefile_IRIX_gcc b/Makefile_IRIX_gcc
index 56a4a2c2..5ad7f138 100644
--- a/Makefile_IRIX_gcc
+++ b/Makefile_IRIX_gcc
@@ -578,6 +578,9 @@ LDFLAGS =
F90C =
F90FLAGS =
M4FLAGS = -Dfcb_bytes_in_rec=4096
+JAVAINCLUDES = -I$(JDKDIR)/include -I$(JDKDIR)/include/linux
+LDPREFIX = LD_LIBRARY_PATH=$(SOLIB):$$LD_LIBRARY_PATH;export LD_LIBRARY_PATH;
+RUNLDPREFIX = LD_LIBRARY_PATH=$(CBF_PREFIX)/LIB:$$LD_LIBRARY_PATH;export LD_LIBRARY_PATH;
EXTRALIBS = -lm
TIME =
SHAR = shar
@@ -1028,6 +1031,11 @@ Makefile: $(M4)/Makefile.m4
m4 -P $(PYCIFRWDEF) -Dcbf_system=default $(M4)/Makefile.m4 > Makefile.tmp
mv Makefile.tmp Makefile
+cbflib.ini: $(M4)/Makefile.m4
+ echo "$(LDPREFIX)" > cbflib.ini
+ echo "HDF5_PLUGIN_PATH=$(SOLIB):$$HDF5_PLUGIN_PATH" >> cbflib.ini
+ echo "export HDF5_PLUGIN_PATH" >> cbflib.ini
+
symlinksdone:
chmod a+x .symlinks
chmod a+x .undosymlinks
@@ -1073,6 +1081,10 @@ baseinstall: all $(CBF_PREFIX) $(CBF_PREFIX)/lib $(CBF_PREFIX)/bin \
-cp $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/libfcb_old.so
cp $(SOLIB)/libfcb.so $(CBF_PREFIX)/lib/libfcb.so
$(LN) $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/lib_fcb.so
+ -cp $(CBF_PREFIX)/bin/cbflib.ini $(CBF_PREFIX)/bin/cbflib.ini_old
+ echo "$(RUNLDPREFIX)" > $(CBF_PREFIX)/bin/cbflib.ini
+ echo "HDF5_PLUGIN_PATH=$(CBF_PREFIX)/lib:$$HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini
+ echo "export HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini
-cp $(CBF_PREFIX)/bin/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf_old
cp $(BIN)/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf
-cp $(CBF_PREFIX)/bin/cbf2adscimg $(CBF_PREFIX)/bin/cbf2adscimg_old
@@ -1236,7 +1248,7 @@ $(TIFF): build_tiff config.guess config.sub
$(TIFF)_INSTALL: $(TIFF)
-rm -rf $(TIFF)_install
rsync -avz $(TIFF)/ $(TIFF)_install
- (cd $(TIFF_install); make distclean; ./configure --prefix=$(CBF_PREFIX); make install)
+ (cd $(TIFF)_install; make distclean; ./configure --prefix=$(CBF_PREFIX); make install)
ifneq ($(CBFLIB_DONT_USE_LOCAL_HDF5),yes)
@@ -2071,7 +2083,7 @@ restore_output: $(NEWTESTOUTPUT) $(DATADIRO) $(MINICBF_TEST)/minicbf.h5
cp test_fcb_read_testflatpackedout.out $(DATADIRO)/test_fcb_read_testflatpackedout_orig.out
cp XRD1621.cbf $(DATADIRO)/XRD1621_orig.cbf
cp XRD1621_I4encbC100.cbf $(DATADIRO)/XRD1621_I4encbC100_orig.cbf
- cp minicbf_orig.h5 $(DATADIRO)/minicbf_orig.h5
+ cp $(MINICBF_TEST)/minicbf.h5 $(DATADIRO)/minicbf_orig.h5
restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS)
$(SIGNATURE) < adscconverted_flat.cbf > $(DATADIRS)/adscconverted_flat_orig.cbf$(SEXT)
@@ -2089,7 +2101,7 @@ restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS)
$(SIGNATURE) < test_fcb_read_testflatpackedout.out > $(DATADIRS)/test_fcb_read_testflatpackedout_orig.out$(SEXT)
$(SIGNATURE) < XRD1621.cbf > $(DATADIRS)/XRD1621_orig.cbf$(SEXT)
$(SIGNATURE) < XRD1621_I4encbC100.cbf > $(DATADIRS)/XRD1621_I4encbC100_orig.cbf$(SEXT)
- $(SIGNATURE) < minicbf_orig.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT)
+ $(SIGNATURE) < $(MINICBF_TEST)/minicbf.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT)
restore_signatures: restore_output restore_sigs_only
#
@@ -2256,7 +2268,7 @@ endif
-cd $(MINICBF_TEST); $(DIFF) minicbf_original.dump minicbf.dump
$(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf_original.dump
$(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf.dump
- cd $(MINICBF_TEST); rm -f minicbf.h5
+ #cd $(MINICBF_TEST); rm -f minicbf.h5
$(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/cbf2nexus -c zlib \
--list -o i19-1.h5 ../1191_00005.cbf
$(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/nexus2cbf \
diff --git a/Makefile_LINUX b/Makefile_LINUX
index fce7061e..36222068 100644
--- a/Makefile_LINUX
+++ b/Makefile_LINUX
@@ -579,6 +579,7 @@ SOCFLAGS = -fPIC
SOLDFLAGS = -shared -Wl,-rpath,$(CBF_PREFIX)/lib
JAVAINCLUDES = -I$(JDKDIR)/include -I$(JDKDIR)/include/linux
LDPREFIX = LD_LIBRARY_PATH=$(SOLIB):$$LD_LIBRARY_PATH;export LD_LIBRARY_PATH;
+RUNLDPREFIX = LD_LIBRARY_PATH=$(CBF_PREFIX)/lib:$$LD_LIBRARY_PATH;export LD_LIBRARY_PATH;
EXTRALIBS = -lm
M4FLAGS = -Dfcb_bytes_in_rec=131072
TIME = time
@@ -1027,6 +1028,11 @@ Makefile: $(M4)/Makefile.m4
m4 -P $(PYCIFRWDEF) -Dcbf_system=default $(M4)/Makefile.m4 > Makefile.tmp
mv Makefile.tmp Makefile
+cbflib.ini: $(M4)/Makefile.m4
+ echo "$(LDPREFIX)" > cbflib.ini
+ echo "HDF5_PLUGIN_PATH=$(SOLIB):$$HDF5_PLUGIN_PATH" >> cbflib.ini
+ echo "export HDF5_PLUGIN_PATH" >> cbflib.ini
+
symlinksdone:
chmod a+x .symlinks
chmod a+x .undosymlinks
@@ -1072,6 +1078,10 @@ baseinstall: all $(CBF_PREFIX) $(CBF_PREFIX)/lib $(CBF_PREFIX)/bin \
-cp $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/libfcb_old.so
cp $(SOLIB)/libfcb.so $(CBF_PREFIX)/lib/libfcb.so
$(LN) $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/lib_fcb.so
+ -cp $(CBF_PREFIX)/bin/cbflib.ini $(CBF_PREFIX)/bin/cbflib.ini_old
+ echo "$(RUNLDPREFIX)" > $(CBF_PREFIX)/bin/cbflib.ini
+ echo "HDF5_PLUGIN_PATH=$(CBF_PREFIX)/lib:$$HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini
+ echo "export HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini
-cp $(CBF_PREFIX)/bin/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf_old
cp $(BIN)/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf
-cp $(CBF_PREFIX)/bin/cbf2adscimg $(CBF_PREFIX)/bin/cbf2adscimg_old
@@ -1235,7 +1245,7 @@ $(TIFF): build_tiff config.guess config.sub
$(TIFF)_INSTALL: $(TIFF)
-rm -rf $(TIFF)_install
rsync -avz $(TIFF)/ $(TIFF)_install
- (cd $(TIFF_install); make distclean; ./configure --prefix=$(CBF_PREFIX); make install)
+ (cd $(TIFF)_install; make distclean; ./configure --prefix=$(CBF_PREFIX); make install)
ifneq ($(CBFLIB_DONT_USE_LOCAL_HDF5),yes)
@@ -2070,7 +2080,7 @@ restore_output: $(NEWTESTOUTPUT) $(DATADIRO) $(MINICBF_TEST)/minicbf.h5
cp test_fcb_read_testflatpackedout.out $(DATADIRO)/test_fcb_read_testflatpackedout_orig.out
cp XRD1621.cbf $(DATADIRO)/XRD1621_orig.cbf
cp XRD1621_I4encbC100.cbf $(DATADIRO)/XRD1621_I4encbC100_orig.cbf
- cp minicbf_orig.h5 $(DATADIRO)/minicbf_orig.h5
+ cp $(MINICBF_TEST)/minicbf.h5 $(DATADIRO)/minicbf_orig.h5
restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS)
$(SIGNATURE) < adscconverted_flat.cbf > $(DATADIRS)/adscconverted_flat_orig.cbf$(SEXT)
@@ -2088,7 +2098,7 @@ restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS)
$(SIGNATURE) < test_fcb_read_testflatpackedout.out > $(DATADIRS)/test_fcb_read_testflatpackedout_orig.out$(SEXT)
$(SIGNATURE) < XRD1621.cbf > $(DATADIRS)/XRD1621_orig.cbf$(SEXT)
$(SIGNATURE) < XRD1621_I4encbC100.cbf > $(DATADIRS)/XRD1621_I4encbC100_orig.cbf$(SEXT)
- $(SIGNATURE) < minicbf_orig.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT)
+ $(SIGNATURE) < $(MINICBF_TEST)/minicbf.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT)
restore_signatures: restore_output restore_sigs_only
#
@@ -2255,7 +2265,7 @@ endif
-cd $(MINICBF_TEST); $(DIFF) minicbf_original.dump minicbf.dump
$(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf_original.dump
$(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf.dump
- cd $(MINICBF_TEST); rm -f minicbf.h5
+ #cd $(MINICBF_TEST); rm -f minicbf.h5
$(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/cbf2nexus -c zlib \
--list -o i19-1.h5 ../1191_00005.cbf
$(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/nexus2cbf \
diff --git a/Makefile_LINUX_64 b/Makefile_LINUX_64
index 60f2bd1e..3b38b55c 100644
--- a/Makefile_LINUX_64
+++ b/Makefile_LINUX_64
@@ -580,6 +580,7 @@ SOCFLAGS = -fPIC
SOLDFLAGS = -shared -Wl,-rpath,$(CBF_PREFIX)/lib
JAVAINCLUDES = -I$(JDKDIR)/include -I$(JDKDIR)/include/linux
LDPREFIX = LD_LIBRARY_PATH=$(SOLIB):$$LD_LIBRARY_PATH;export LD_LIBRARY_PATH;
+RUNLDPREFIX = LD_LIBRARY_PATH=$(CBF_PREFIX)/lib:$$LD_LIBRARY_PATH;export LD_LIBRARY_PATH;
EXTRALIBS = -lm
M4FLAGS = -Dfcb_bytes_in_rec=131072
TIME = time
@@ -1028,6 +1029,11 @@ Makefile: $(M4)/Makefile.m4
m4 -P $(PYCIFRWDEF) -Dcbf_system=default $(M4)/Makefile.m4 > Makefile.tmp
mv Makefile.tmp Makefile
+cbflib.ini: $(M4)/Makefile.m4
+ echo "$(LDPREFIX)" > cbflib.ini
+ echo "HDF5_PLUGIN_PATH=$(SOLIB):$$HDF5_PLUGIN_PATH" >> cbflib.ini
+ echo "export HDF5_PLUGIN_PATH" >> cbflib.ini
+
symlinksdone:
chmod a+x .symlinks
chmod a+x .undosymlinks
@@ -1073,6 +1079,10 @@ baseinstall: all $(CBF_PREFIX) $(CBF_PREFIX)/lib $(CBF_PREFIX)/bin \
-cp $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/libfcb_old.so
cp $(SOLIB)/libfcb.so $(CBF_PREFIX)/lib/libfcb.so
$(LN) $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/lib_fcb.so
+ -cp $(CBF_PREFIX)/bin/cbflib.ini $(CBF_PREFIX)/bin/cbflib.ini_old
+ echo "$(RUNLDPREFIX)" > $(CBF_PREFIX)/bin/cbflib.ini
+ echo "HDF5_PLUGIN_PATH=$(CBF_PREFIX)/lib:$$HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini
+ echo "export HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini
-cp $(CBF_PREFIX)/bin/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf_old
cp $(BIN)/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf
-cp $(CBF_PREFIX)/bin/cbf2adscimg $(CBF_PREFIX)/bin/cbf2adscimg_old
@@ -1236,7 +1246,7 @@ $(TIFF): build_tiff config.guess config.sub
$(TIFF)_INSTALL: $(TIFF)
-rm -rf $(TIFF)_install
rsync -avz $(TIFF)/ $(TIFF)_install
- (cd $(TIFF_install); make distclean; ./configure --prefix=$(CBF_PREFIX); make install)
+ (cd $(TIFF)_install; make distclean; ./configure --prefix=$(CBF_PREFIX); make install)
ifneq ($(CBFLIB_DONT_USE_LOCAL_HDF5),yes)
@@ -2071,7 +2081,7 @@ restore_output: $(NEWTESTOUTPUT) $(DATADIRO) $(MINICBF_TEST)/minicbf.h5
cp test_fcb_read_testflatpackedout.out $(DATADIRO)/test_fcb_read_testflatpackedout_orig.out
cp XRD1621.cbf $(DATADIRO)/XRD1621_orig.cbf
cp XRD1621_I4encbC100.cbf $(DATADIRO)/XRD1621_I4encbC100_orig.cbf
- cp minicbf_orig.h5 $(DATADIRO)/minicbf_orig.h5
+ cp $(MINICBF_TEST)/minicbf.h5 $(DATADIRO)/minicbf_orig.h5
restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS)
$(SIGNATURE) < adscconverted_flat.cbf > $(DATADIRS)/adscconverted_flat_orig.cbf$(SEXT)
@@ -2089,7 +2099,7 @@ restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS)
$(SIGNATURE) < test_fcb_read_testflatpackedout.out > $(DATADIRS)/test_fcb_read_testflatpackedout_orig.out$(SEXT)
$(SIGNATURE) < XRD1621.cbf > $(DATADIRS)/XRD1621_orig.cbf$(SEXT)
$(SIGNATURE) < XRD1621_I4encbC100.cbf > $(DATADIRS)/XRD1621_I4encbC100_orig.cbf$(SEXT)
- $(SIGNATURE) < minicbf_orig.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT)
+ $(SIGNATURE) < $(MINICBF_TEST)/minicbf.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT)
restore_signatures: restore_output restore_sigs_only
#
@@ -2256,7 +2266,7 @@ endif
-cd $(MINICBF_TEST); $(DIFF) minicbf_original.dump minicbf.dump
$(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf_original.dump
$(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf.dump
- cd $(MINICBF_TEST); rm -f minicbf.h5
+ #cd $(MINICBF_TEST); rm -f minicbf.h5
$(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/cbf2nexus -c zlib \
--list -o i19-1.h5 ../1191_00005.cbf
$(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/nexus2cbf \
diff --git a/Makefile_LINUX_DMALLOC b/Makefile_LINUX_DMALLOC
index cfca6839..e1569b6a 100644
--- a/Makefile_LINUX_DMALLOC
+++ b/Makefile_LINUX_DMALLOC
@@ -579,6 +579,7 @@ SOCFLAGS = -fPIC
SOLDFLAGS = -shared -Wl,-rpath,$(CBF_PREFIX)/lib
JAVAINCLUDES = -I$(JDKDIR)/include -I$(JDKDIR)/include/linux
LDPREFIX = LD_LIBRARY_PATH=$(SOLIB):$$LD_LIBRARY_PATH;export LD_LIBRARY_PATH;
+RUNLDPREFIX = LD_LIBRARY_PATH=$(CBF_PREFIX)/lib:$$LD_LIBRARY_PATH;export LD_LIBRARY_PATH;
EXTRALIBS = -lm -L$(HOME)/lib -ldmalloc
M4FLAGS = -Dfcb_bytes_in_rec=131072
TIME = time
@@ -1027,6 +1028,11 @@ Makefile: $(M4)/Makefile.m4
m4 -P $(PYCIFRWDEF) -Dcbf_system=default $(M4)/Makefile.m4 > Makefile.tmp
mv Makefile.tmp Makefile
+cbflib.ini: $(M4)/Makefile.m4
+ echo "$(LDPREFIX)" > cbflib.ini
+ echo "HDF5_PLUGIN_PATH=$(SOLIB):$$HDF5_PLUGIN_PATH" >> cbflib.ini
+ echo "export HDF5_PLUGIN_PATH" >> cbflib.ini
+
symlinksdone:
chmod a+x .symlinks
chmod a+x .undosymlinks
@@ -1072,6 +1078,10 @@ baseinstall: all $(CBF_PREFIX) $(CBF_PREFIX)/lib $(CBF_PREFIX)/bin \
-cp $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/libfcb_old.so
cp $(SOLIB)/libfcb.so $(CBF_PREFIX)/lib/libfcb.so
$(LN) $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/lib_fcb.so
+ -cp $(CBF_PREFIX)/bin/cbflib.ini $(CBF_PREFIX)/bin/cbflib.ini_old
+ echo "$(RUNLDPREFIX)" > $(CBF_PREFIX)/bin/cbflib.ini
+ echo "HDF5_PLUGIN_PATH=$(CBF_PREFIX)/lib:$$HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini
+ echo "export HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini
-cp $(CBF_PREFIX)/bin/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf_old
cp $(BIN)/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf
-cp $(CBF_PREFIX)/bin/cbf2adscimg $(CBF_PREFIX)/bin/cbf2adscimg_old
@@ -1235,7 +1245,7 @@ $(TIFF): build_tiff config.guess config.sub
$(TIFF)_INSTALL: $(TIFF)
-rm -rf $(TIFF)_install
rsync -avz $(TIFF)/ $(TIFF)_install
- (cd $(TIFF_install); make distclean; ./configure --prefix=$(CBF_PREFIX); make install)
+ (cd $(TIFF)_install; make distclean; ./configure --prefix=$(CBF_PREFIX); make install)
ifneq ($(CBFLIB_DONT_USE_LOCAL_HDF5),yes)
@@ -2070,7 +2080,7 @@ restore_output: $(NEWTESTOUTPUT) $(DATADIRO) $(MINICBF_TEST)/minicbf.h5
cp test_fcb_read_testflatpackedout.out $(DATADIRO)/test_fcb_read_testflatpackedout_orig.out
cp XRD1621.cbf $(DATADIRO)/XRD1621_orig.cbf
cp XRD1621_I4encbC100.cbf $(DATADIRO)/XRD1621_I4encbC100_orig.cbf
- cp minicbf_orig.h5 $(DATADIRO)/minicbf_orig.h5
+ cp $(MINICBF_TEST)/minicbf.h5 $(DATADIRO)/minicbf_orig.h5
restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS)
$(SIGNATURE) < adscconverted_flat.cbf > $(DATADIRS)/adscconverted_flat_orig.cbf$(SEXT)
@@ -2088,7 +2098,7 @@ restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS)
$(SIGNATURE) < test_fcb_read_testflatpackedout.out > $(DATADIRS)/test_fcb_read_testflatpackedout_orig.out$(SEXT)
$(SIGNATURE) < XRD1621.cbf > $(DATADIRS)/XRD1621_orig.cbf$(SEXT)
$(SIGNATURE) < XRD1621_I4encbC100.cbf > $(DATADIRS)/XRD1621_I4encbC100_orig.cbf$(SEXT)
- $(SIGNATURE) < minicbf_orig.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT)
+ $(SIGNATURE) < $(MINICBF_TEST)/minicbf.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT)
restore_signatures: restore_output restore_sigs_only
#
@@ -2255,7 +2265,7 @@ endif
-cd $(MINICBF_TEST); $(DIFF) minicbf_original.dump minicbf.dump
$(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf_original.dump
$(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf.dump
- cd $(MINICBF_TEST); rm -f minicbf.h5
+ #cd $(MINICBF_TEST); rm -f minicbf.h5
$(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/cbf2nexus -c zlib \
--list -o i19-1.h5 ../1191_00005.cbf
$(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/nexus2cbf \
diff --git a/Makefile_LINUX_gcc42 b/Makefile_LINUX_gcc42
index 3e4a6ac1..8ecfa85f 100644
--- a/Makefile_LINUX_gcc42
+++ b/Makefile_LINUX_gcc42
@@ -580,6 +580,7 @@ SOCFLAGS = -fPIC
SOLDFLAGS = -shared -Wl,-rpath,$(CBF_PREFIX)/lib
JAVAINCLUDES = -I$(JDKDIR)/include -I$(JDKDIR)/include/linux
LDPREFIX = LD_LIBRARY_PATH=$(SOLIB):$$LD_LIBRARY_PATH;export LD_LIBRARY_PATH;
+RUNLDPREFIX = LD_LIBRARY_PATH=$(CBF_PREFIX)/lib:$$LD_LIBRARY_PATH;export LD_LIBRARY_PATH;
EXTRALIBS = -lm
M4FLAGS = -Dfcb_bytes_in_rec=131072
TIME = time
@@ -1028,6 +1029,11 @@ Makefile: $(M4)/Makefile.m4
m4 -P $(PYCIFRWDEF) -Dcbf_system=default $(M4)/Makefile.m4 > Makefile.tmp
mv Makefile.tmp Makefile
+cbflib.ini: $(M4)/Makefile.m4
+ echo "$(LDPREFIX)" > cbflib.ini
+ echo "HDF5_PLUGIN_PATH=$(SOLIB):$$HDF5_PLUGIN_PATH" >> cbflib.ini
+ echo "export HDF5_PLUGIN_PATH" >> cbflib.ini
+
symlinksdone:
chmod a+x .symlinks
chmod a+x .undosymlinks
@@ -1073,6 +1079,10 @@ baseinstall: all $(CBF_PREFIX) $(CBF_PREFIX)/lib $(CBF_PREFIX)/bin \
-cp $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/libfcb_old.so
cp $(SOLIB)/libfcb.so $(CBF_PREFIX)/lib/libfcb.so
$(LN) $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/lib_fcb.so
+ -cp $(CBF_PREFIX)/bin/cbflib.ini $(CBF_PREFIX)/bin/cbflib.ini_old
+ echo "$(RUNLDPREFIX)" > $(CBF_PREFIX)/bin/cbflib.ini
+ echo "HDF5_PLUGIN_PATH=$(CBF_PREFIX)/lib:$$HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini
+ echo "export HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini
-cp $(CBF_PREFIX)/bin/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf_old
cp $(BIN)/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf
-cp $(CBF_PREFIX)/bin/cbf2adscimg $(CBF_PREFIX)/bin/cbf2adscimg_old
@@ -1236,7 +1246,7 @@ $(TIFF): build_tiff config.guess config.sub
$(TIFF)_INSTALL: $(TIFF)
-rm -rf $(TIFF)_install
rsync -avz $(TIFF)/ $(TIFF)_install
- (cd $(TIFF_install); make distclean; ./configure --prefix=$(CBF_PREFIX); make install)
+ (cd $(TIFF)_install; make distclean; ./configure --prefix=$(CBF_PREFIX); make install)
ifneq ($(CBFLIB_DONT_USE_LOCAL_HDF5),yes)
@@ -2071,7 +2081,7 @@ restore_output: $(NEWTESTOUTPUT) $(DATADIRO) $(MINICBF_TEST)/minicbf.h5
cp test_fcb_read_testflatpackedout.out $(DATADIRO)/test_fcb_read_testflatpackedout_orig.out
cp XRD1621.cbf $(DATADIRO)/XRD1621_orig.cbf
cp XRD1621_I4encbC100.cbf $(DATADIRO)/XRD1621_I4encbC100_orig.cbf
- cp minicbf_orig.h5 $(DATADIRO)/minicbf_orig.h5
+ cp $(MINICBF_TEST)/minicbf.h5 $(DATADIRO)/minicbf_orig.h5
restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS)
$(SIGNATURE) < adscconverted_flat.cbf > $(DATADIRS)/adscconverted_flat_orig.cbf$(SEXT)
@@ -2089,7 +2099,7 @@ restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS)
$(SIGNATURE) < test_fcb_read_testflatpackedout.out > $(DATADIRS)/test_fcb_read_testflatpackedout_orig.out$(SEXT)
$(SIGNATURE) < XRD1621.cbf > $(DATADIRS)/XRD1621_orig.cbf$(SEXT)
$(SIGNATURE) < XRD1621_I4encbC100.cbf > $(DATADIRS)/XRD1621_I4encbC100_orig.cbf$(SEXT)
- $(SIGNATURE) < minicbf_orig.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT)
+ $(SIGNATURE) < $(MINICBF_TEST)/minicbf.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT)
restore_signatures: restore_output restore_sigs_only
#
@@ -2256,7 +2266,7 @@ endif
-cd $(MINICBF_TEST); $(DIFF) minicbf_original.dump minicbf.dump
$(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf_original.dump
$(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf.dump
- cd $(MINICBF_TEST); rm -f minicbf.h5
+ #cd $(MINICBF_TEST); rm -f minicbf.h5
$(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/cbf2nexus -c zlib \
--list -o i19-1.h5 ../1191_00005.cbf
$(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/nexus2cbf \
diff --git a/Makefile_LINUX_gcc42_DMALLOC b/Makefile_LINUX_gcc42_DMALLOC
index 99fa3d5f..02078c35 100644
--- a/Makefile_LINUX_gcc42_DMALLOC
+++ b/Makefile_LINUX_gcc42_DMALLOC
@@ -580,6 +580,7 @@ SOCFLAGS = -fPIC
SOLDFLAGS = -shared -Wl,-rpath,$(CBF_PREFIX)/lib
JAVAINCLUDES = -I$(JDKDIR)/include -I$(JDKDIR)/include/linux
LDPREFIX = LD_LIBRARY_PATH=$(SOLIB):$$LD_LIBRARY_PATH;export LD_LIBRARY_PATH;
+RUNLDPREFIX = LD_LIBRARY_PATH=$(CBF_PREFIX)/lib:$$LD_LIBRARY_PATH;export LD_LIBRARY_PATH;
EXTRALIBS = -lm -L$(HOME)/lib -ldmalloc
M4FLAGS = -Dfcb_bytes_in_rec=131072
TIME = time
@@ -1028,6 +1029,11 @@ Makefile: $(M4)/Makefile.m4
m4 -P $(PYCIFRWDEF) -Dcbf_system=default $(M4)/Makefile.m4 > Makefile.tmp
mv Makefile.tmp Makefile
+cbflib.ini: $(M4)/Makefile.m4
+ echo "$(LDPREFIX)" > cbflib.ini
+ echo "HDF5_PLUGIN_PATH=$(SOLIB):$$HDF5_PLUGIN_PATH" >> cbflib.ini
+ echo "export HDF5_PLUGIN_PATH" >> cbflib.ini
+
symlinksdone:
chmod a+x .symlinks
chmod a+x .undosymlinks
@@ -1073,6 +1079,10 @@ baseinstall: all $(CBF_PREFIX) $(CBF_PREFIX)/lib $(CBF_PREFIX)/bin \
-cp $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/libfcb_old.so
cp $(SOLIB)/libfcb.so $(CBF_PREFIX)/lib/libfcb.so
$(LN) $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/lib_fcb.so
+ -cp $(CBF_PREFIX)/bin/cbflib.ini $(CBF_PREFIX)/bin/cbflib.ini_old
+ echo "$(RUNLDPREFIX)" > $(CBF_PREFIX)/bin/cbflib.ini
+ echo "HDF5_PLUGIN_PATH=$(CBF_PREFIX)/lib:$$HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini
+ echo "export HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini
-cp $(CBF_PREFIX)/bin/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf_old
cp $(BIN)/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf
-cp $(CBF_PREFIX)/bin/cbf2adscimg $(CBF_PREFIX)/bin/cbf2adscimg_old
@@ -1236,7 +1246,7 @@ $(TIFF): build_tiff config.guess config.sub
$(TIFF)_INSTALL: $(TIFF)
-rm -rf $(TIFF)_install
rsync -avz $(TIFF)/ $(TIFF)_install
- (cd $(TIFF_install); make distclean; ./configure --prefix=$(CBF_PREFIX); make install)
+ (cd $(TIFF)_install; make distclean; ./configure --prefix=$(CBF_PREFIX); make install)
ifneq ($(CBFLIB_DONT_USE_LOCAL_HDF5),yes)
@@ -2071,7 +2081,7 @@ restore_output: $(NEWTESTOUTPUT) $(DATADIRO) $(MINICBF_TEST)/minicbf.h5
cp test_fcb_read_testflatpackedout.out $(DATADIRO)/test_fcb_read_testflatpackedout_orig.out
cp XRD1621.cbf $(DATADIRO)/XRD1621_orig.cbf
cp XRD1621_I4encbC100.cbf $(DATADIRO)/XRD1621_I4encbC100_orig.cbf
- cp minicbf_orig.h5 $(DATADIRO)/minicbf_orig.h5
+ cp $(MINICBF_TEST)/minicbf.h5 $(DATADIRO)/minicbf_orig.h5
restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS)
$(SIGNATURE) < adscconverted_flat.cbf > $(DATADIRS)/adscconverted_flat_orig.cbf$(SEXT)
@@ -2089,7 +2099,7 @@ restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS)
$(SIGNATURE) < test_fcb_read_testflatpackedout.out > $(DATADIRS)/test_fcb_read_testflatpackedout_orig.out$(SEXT)
$(SIGNATURE) < XRD1621.cbf > $(DATADIRS)/XRD1621_orig.cbf$(SEXT)
$(SIGNATURE) < XRD1621_I4encbC100.cbf > $(DATADIRS)/XRD1621_I4encbC100_orig.cbf$(SEXT)
- $(SIGNATURE) < minicbf_orig.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT)
+ $(SIGNATURE) < $(MINICBF_TEST)/minicbf.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT)
restore_signatures: restore_output restore_sigs_only
#
@@ -2256,7 +2266,7 @@ endif
-cd $(MINICBF_TEST); $(DIFF) minicbf_original.dump minicbf.dump
$(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf_original.dump
$(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf.dump
- cd $(MINICBF_TEST); rm -f minicbf.h5
+ #cd $(MINICBF_TEST); rm -f minicbf.h5
$(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/cbf2nexus -c zlib \
--list -o i19-1.h5 ../1191_00005.cbf
$(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/nexus2cbf \
diff --git a/Makefile_MINGW b/Makefile_MINGW
index a9158e0b..c44da345 100644
--- a/Makefile_MINGW
+++ b/Makefile_MINGW
@@ -578,7 +578,8 @@ F90C = g95
F90FLAGS = -g
F90LDFLAGS =
M4FLAGS = -Dfcb_bytes_in_rec=4096
-LDPREFIX = PATH=$(SOLIB);$$PATH;export PATH;
+LDPREFIX = PATH=$(SOLIB):$$PATH;export PATH;
+RUNLDPREFIX = PATH=$(CBF_PREFIX)/lib:$$PATH;export PATH;
SOCFLAGS = -D_JNI_IMPLEMENTATION_
SOLDFLAGS = -shared -Wl,--kill-at
JAVAINCLUDES = -I$(JDKDIR)/include -I$(JDKDIR)/include/win32
@@ -1041,6 +1042,11 @@ Makefile: $(M4)/Makefile.m4
m4 -P $(PYCIFRWDEF) -Dcbf_system=default $(M4)/Makefile.m4 > Makefile.tmp
mv Makefile.tmp Makefile
+cbflib.ini: $(M4)/Makefile.m4
+ echo "$(LDPREFIX)" > cbflib.ini
+ echo "HDF5_PLUGIN_PATH=$(SOLIB):$$HDF5_PLUGIN_PATH" >> cbflib.ini
+ echo "export HDF5_PLUGIN_PATH" >> cbflib.ini
+
symlinksdone:
chmod a+x .symlinks
chmod a+x .undosymlinks
@@ -1086,6 +1092,10 @@ baseinstall: all $(CBF_PREFIX) $(CBF_PREFIX)/lib $(CBF_PREFIX)/bin \
-cp $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/libfcb_old.so
cp $(SOLIB)/libfcb.so $(CBF_PREFIX)/lib/libfcb.so
$(LN) $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/lib_fcb.so
+ -cp $(CBF_PREFIX)/bin/cbflib.ini $(CBF_PREFIX)/bin/cbflib.ini_old
+ echo "$(RUNLDPREFIX)" > $(CBF_PREFIX)/bin/cbflib.ini
+ echo "HDF5_PLUGIN_PATH=$(CBF_PREFIX)/lib:$$HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini
+ echo "export HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini
-cp $(CBF_PREFIX)/bin/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf_old
cp $(BIN)/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf
-cp $(CBF_PREFIX)/bin/cbf2adscimg $(CBF_PREFIX)/bin/cbf2adscimg_old
@@ -1249,7 +1259,7 @@ $(TIFF): build_tiff config.guess config.sub
$(TIFF)_INSTALL: $(TIFF)
-rm -rf $(TIFF)_install
rsync -avz $(TIFF)/ $(TIFF)_install
- (cd $(TIFF_install); make distclean; ./configure --prefix=$(CBF_PREFIX); make install)
+ (cd $(TIFF)_install; make distclean; ./configure --prefix=$(CBF_PREFIX); make install)
ifneq ($(CBFLIB_DONT_USE_LOCAL_HDF5),yes)
@@ -2084,7 +2094,7 @@ restore_output: $(NEWTESTOUTPUT) $(DATADIRO) $(MINICBF_TEST)/minicbf.h5
cp test_fcb_read_testflatpackedout.out $(DATADIRO)/test_fcb_read_testflatpackedout_orig.out
cp XRD1621.cbf $(DATADIRO)/XRD1621_orig.cbf
cp XRD1621_I4encbC100.cbf $(DATADIRO)/XRD1621_I4encbC100_orig.cbf
- cp minicbf_orig.h5 $(DATADIRO)/minicbf_orig.h5
+ cp $(MINICBF_TEST)/minicbf.h5 $(DATADIRO)/minicbf_orig.h5
restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS)
$(SIGNATURE) < adscconverted_flat.cbf > $(DATADIRS)/adscconverted_flat_orig.cbf$(SEXT)
@@ -2102,7 +2112,7 @@ restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS)
$(SIGNATURE) < test_fcb_read_testflatpackedout.out > $(DATADIRS)/test_fcb_read_testflatpackedout_orig.out$(SEXT)
$(SIGNATURE) < XRD1621.cbf > $(DATADIRS)/XRD1621_orig.cbf$(SEXT)
$(SIGNATURE) < XRD1621_I4encbC100.cbf > $(DATADIRS)/XRD1621_I4encbC100_orig.cbf$(SEXT)
- $(SIGNATURE) < minicbf_orig.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT)
+ $(SIGNATURE) < $(MINICBF_TEST)/minicbf.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT)
restore_signatures: restore_output restore_sigs_only
#
@@ -2269,7 +2279,7 @@ endif
-cd $(MINICBF_TEST); $(DIFF) minicbf_original.dump minicbf.dump
$(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf_original.dump
$(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf.dump
- cd $(MINICBF_TEST); rm -f minicbf.h5
+ #cd $(MINICBF_TEST); rm -f minicbf.h5
$(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/cbf2nexus -c zlib \
--list -o i19-1.h5 ../1191_00005.cbf
$(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/nexus2cbf \
diff --git a/Makefile_MSYS2 b/Makefile_MSYS2
index a90e23bb..a67afcc0 100644
--- a/Makefile_MSYS2
+++ b/Makefile_MSYS2
@@ -579,6 +579,7 @@ SOCFLAGS = -fPIC
SOLDFLAGS = -shared -Wl,-rpath,$(CBF_PREFIX)/lib
JAVAINCLUDES = -I$(JDKDIR)/include -I$(JDKDIR)/include/linux
LDPREFIX = PATH=$(SOLIB);$$PATH;export PATH;
+RUNLDPREFIX = PATH=$(CBF_PREFIX)/lib:$$PATH;export PATH;
EXTRALIBS = -L/mingw64/bin -lm
M4FLAGS = -Dfcb_bytes_in_rec=131072
PYTHON = python2
@@ -1029,6 +1030,11 @@ Makefile: $(M4)/Makefile.m4
m4 -P $(PYCIFRWDEF) -Dcbf_system=default $(M4)/Makefile.m4 > Makefile.tmp
mv Makefile.tmp Makefile
+cbflib.ini: $(M4)/Makefile.m4
+ echo "$(LDPREFIX)" > cbflib.ini
+ echo "HDF5_PLUGIN_PATH=$(SOLIB):$$HDF5_PLUGIN_PATH" >> cbflib.ini
+ echo "export HDF5_PLUGIN_PATH" >> cbflib.ini
+
symlinksdone:
chmod a+x .symlinks
chmod a+x .undosymlinks
@@ -1074,6 +1080,10 @@ baseinstall: all $(CBF_PREFIX) $(CBF_PREFIX)/lib $(CBF_PREFIX)/bin \
-cp $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/libfcb_old.so
cp $(SOLIB)/libfcb.so $(CBF_PREFIX)/lib/libfcb.so
$(LN) $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/lib_fcb.so
+ -cp $(CBF_PREFIX)/bin/cbflib.ini $(CBF_PREFIX)/bin/cbflib.ini_old
+ echo "$(RUNLDPREFIX)" > $(CBF_PREFIX)/bin/cbflib.ini
+ echo "HDF5_PLUGIN_PATH=$(CBF_PREFIX)/lib:$$HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini
+ echo "export HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini
-cp $(CBF_PREFIX)/bin/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf_old
cp $(BIN)/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf
-cp $(CBF_PREFIX)/bin/cbf2adscimg $(CBF_PREFIX)/bin/cbf2adscimg_old
@@ -1237,7 +1247,7 @@ $(TIFF): build_tiff config.guess config.sub
$(TIFF)_INSTALL: $(TIFF)
-rm -rf $(TIFF)_install
rsync -avz $(TIFF)/ $(TIFF)_install
- (cd $(TIFF_install); make distclean; ./configure --prefix=$(CBF_PREFIX); make install)
+ (cd $(TIFF)_install; make distclean; ./configure --prefix=$(CBF_PREFIX); make install)
ifneq ($(CBFLIB_DONT_USE_LOCAL_HDF5),yes)
@@ -2072,7 +2082,7 @@ restore_output: $(NEWTESTOUTPUT) $(DATADIRO) $(MINICBF_TEST)/minicbf.h5
cp test_fcb_read_testflatpackedout.out $(DATADIRO)/test_fcb_read_testflatpackedout_orig.out
cp XRD1621.cbf $(DATADIRO)/XRD1621_orig.cbf
cp XRD1621_I4encbC100.cbf $(DATADIRO)/XRD1621_I4encbC100_orig.cbf
- cp minicbf_orig.h5 $(DATADIRO)/minicbf_orig.h5
+ cp $(MINICBF_TEST)/minicbf.h5 $(DATADIRO)/minicbf_orig.h5
restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS)
$(SIGNATURE) < adscconverted_flat.cbf > $(DATADIRS)/adscconverted_flat_orig.cbf$(SEXT)
@@ -2090,7 +2100,7 @@ restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS)
$(SIGNATURE) < test_fcb_read_testflatpackedout.out > $(DATADIRS)/test_fcb_read_testflatpackedout_orig.out$(SEXT)
$(SIGNATURE) < XRD1621.cbf > $(DATADIRS)/XRD1621_orig.cbf$(SEXT)
$(SIGNATURE) < XRD1621_I4encbC100.cbf > $(DATADIRS)/XRD1621_I4encbC100_orig.cbf$(SEXT)
- $(SIGNATURE) < minicbf_orig.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT)
+ $(SIGNATURE) < $(MINICBF_TEST)/minicbf.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT)
restore_signatures: restore_output restore_sigs_only
#
@@ -2257,7 +2267,7 @@ endif
-cd $(MINICBF_TEST); $(DIFF) minicbf_original.dump minicbf.dump
$(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf_original.dump
$(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf.dump
- cd $(MINICBF_TEST); rm -f minicbf.h5
+ #cd $(MINICBF_TEST); rm -f minicbf.h5
$(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/cbf2nexus -c zlib \
--list -o i19-1.h5 ../1191_00005.cbf
$(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/nexus2cbf \
diff --git a/Makefile_OSX b/Makefile_OSX
index d0717372..1cde14b7 100644
--- a/Makefile_OSX
+++ b/Makefile_OSX
@@ -576,6 +576,11 @@ LDFLAGS =
F90C = gfortran
F90FLAGS = -g -fno-range-check
F90LDFLAGS = -bind_at_load
+SOCFLAGS = -fPIC
+SOLDFLAGS = -dynamiclib -Wl,-rpath,$(CBF_PREFIX)/lib
+JAVAINCLUDES = -I$(JDKDIR)/include -I$(JDKDIR)/include/linux
+LDPREFIX = DYLD_LIBRARY_PATH=$(SOLIB):$$DYLD_LIBRARY_PATH;export DYLD_LIBRARY_PATH;
+RUNLDPREFIX = DYLD_LIBRARY_PATH=$(CBF_PREFIX)/lib:$$DYLD_LIBRARY_PATH;export DYLD_LIBRARY_PATH;
EXTRALIBS = -lm
M4FLAGS = -Dfcb_bytes_in_rec=131072
TIME = time
@@ -1025,6 +1030,11 @@ Makefile: $(M4)/Makefile.m4
m4 -P $(PYCIFRWDEF) -Dcbf_system=default $(M4)/Makefile.m4 > Makefile.tmp
mv Makefile.tmp Makefile
+cbflib.ini: $(M4)/Makefile.m4
+ echo "$(LDPREFIX)" > cbflib.ini
+ echo "HDF5_PLUGIN_PATH=$(SOLIB):$$HDF5_PLUGIN_PATH" >> cbflib.ini
+ echo "export HDF5_PLUGIN_PATH" >> cbflib.ini
+
symlinksdone:
chmod a+x .symlinks
chmod a+x .undosymlinks
@@ -1070,6 +1080,10 @@ baseinstall: all $(CBF_PREFIX) $(CBF_PREFIX)/lib $(CBF_PREFIX)/bin \
-cp $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/libfcb_old.so
cp $(SOLIB)/libfcb.so $(CBF_PREFIX)/lib/libfcb.so
$(LN) $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/lib_fcb.so
+ -cp $(CBF_PREFIX)/bin/cbflib.ini $(CBF_PREFIX)/bin/cbflib.ini_old
+ echo "$(RUNLDPREFIX)" > $(CBF_PREFIX)/bin/cbflib.ini
+ echo "HDF5_PLUGIN_PATH=$(CBF_PREFIX)/lib:$$HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini
+ echo "export HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini
-cp $(CBF_PREFIX)/bin/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf_old
cp $(BIN)/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf
-cp $(CBF_PREFIX)/bin/cbf2adscimg $(CBF_PREFIX)/bin/cbf2adscimg_old
@@ -1233,7 +1247,7 @@ $(TIFF): build_tiff config.guess config.sub
$(TIFF)_INSTALL: $(TIFF)
-rm -rf $(TIFF)_install
rsync -avz $(TIFF)/ $(TIFF)_install
- (cd $(TIFF_install); make distclean; ./configure --prefix=$(CBF_PREFIX); make install)
+ (cd $(TIFF)_install; make distclean; ./configure --prefix=$(CBF_PREFIX); make install)
ifneq ($(CBFLIB_DONT_USE_LOCAL_HDF5),yes)
@@ -2068,7 +2082,7 @@ restore_output: $(NEWTESTOUTPUT) $(DATADIRO) $(MINICBF_TEST)/minicbf.h5
cp test_fcb_read_testflatpackedout.out $(DATADIRO)/test_fcb_read_testflatpackedout_orig.out
cp XRD1621.cbf $(DATADIRO)/XRD1621_orig.cbf
cp XRD1621_I4encbC100.cbf $(DATADIRO)/XRD1621_I4encbC100_orig.cbf
- cp minicbf_orig.h5 $(DATADIRO)/minicbf_orig.h5
+ cp $(MINICBF_TEST)/minicbf.h5 $(DATADIRO)/minicbf_orig.h5
restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS)
$(SIGNATURE) < adscconverted_flat.cbf > $(DATADIRS)/adscconverted_flat_orig.cbf$(SEXT)
@@ -2086,7 +2100,7 @@ restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS)
$(SIGNATURE) < test_fcb_read_testflatpackedout.out > $(DATADIRS)/test_fcb_read_testflatpackedout_orig.out$(SEXT)
$(SIGNATURE) < XRD1621.cbf > $(DATADIRS)/XRD1621_orig.cbf$(SEXT)
$(SIGNATURE) < XRD1621_I4encbC100.cbf > $(DATADIRS)/XRD1621_I4encbC100_orig.cbf$(SEXT)
- $(SIGNATURE) < minicbf_orig.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT)
+ $(SIGNATURE) < $(MINICBF_TEST)/minicbf.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT)
restore_signatures: restore_output restore_sigs_only
#
@@ -2253,7 +2267,7 @@ endif
-cd $(MINICBF_TEST); $(DIFF) minicbf_original.dump minicbf.dump
$(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf_original.dump
$(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf.dump
- cd $(MINICBF_TEST); rm -f minicbf.h5
+ #cd $(MINICBF_TEST); rm -f minicbf.h5
$(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/cbf2nexus -c zlib \
--list -o i19-1.h5 ../1191_00005.cbf
$(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/nexus2cbf \
diff --git a/Makefile_OSX_gcc42 b/Makefile_OSX_gcc42
index c41831d6..a04853fe 100644
--- a/Makefile_OSX_gcc42
+++ b/Makefile_OSX_gcc42
@@ -581,6 +581,7 @@ SOCFLAGS = -fPIC
SOLDFLAGS = -dynamiclib -Wl,-rpath,$(CBF_PREFIX)/lib
JAVAINCLUDES = -I$(JDKDIR)/include -I$(JDKDIR)/include/linux
LDPREFIX = DYLD_LIBRARY_PATH=$(SOLIB):$$DYLD_LIBRARY_PATH;export DYLD_LIBRARY_PATH;
+RUNLDPREFIX = DYLD_LIBRARY_PATH=$(CBF_PREFIX)/lib:$$DYLD_LIBRARY_PATH;export DYLD_LIBRARY_PATH;
EXTRALIBS = -lm
M4FLAGS = -Dfcb_bytes_in_rec=131072
TIME = time
@@ -1030,6 +1031,11 @@ Makefile: $(M4)/Makefile.m4
m4 -P $(PYCIFRWDEF) -Dcbf_system=default $(M4)/Makefile.m4 > Makefile.tmp
mv Makefile.tmp Makefile
+cbflib.ini: $(M4)/Makefile.m4
+ echo "$(LDPREFIX)" > cbflib.ini
+ echo "HDF5_PLUGIN_PATH=$(SOLIB):$$HDF5_PLUGIN_PATH" >> cbflib.ini
+ echo "export HDF5_PLUGIN_PATH" >> cbflib.ini
+
symlinksdone:
chmod a+x .symlinks
chmod a+x .undosymlinks
@@ -1075,6 +1081,10 @@ baseinstall: all $(CBF_PREFIX) $(CBF_PREFIX)/lib $(CBF_PREFIX)/bin \
-cp $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/libfcb_old.so
cp $(SOLIB)/libfcb.so $(CBF_PREFIX)/lib/libfcb.so
$(LN) $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/lib_fcb.so
+ -cp $(CBF_PREFIX)/bin/cbflib.ini $(CBF_PREFIX)/bin/cbflib.ini_old
+ echo "$(RUNLDPREFIX)" > $(CBF_PREFIX)/bin/cbflib.ini
+ echo "HDF5_PLUGIN_PATH=$(CBF_PREFIX)/lib:$$HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini
+ echo "export HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini
-cp $(CBF_PREFIX)/bin/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf_old
cp $(BIN)/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf
-cp $(CBF_PREFIX)/bin/cbf2adscimg $(CBF_PREFIX)/bin/cbf2adscimg_old
@@ -1238,7 +1248,7 @@ $(TIFF): build_tiff config.guess config.sub
$(TIFF)_INSTALL: $(TIFF)
-rm -rf $(TIFF)_install
rsync -avz $(TIFF)/ $(TIFF)_install
- (cd $(TIFF_install); make distclean; ./configure --prefix=$(CBF_PREFIX); make install)
+ (cd $(TIFF)_install; make distclean; ./configure --prefix=$(CBF_PREFIX); make install)
ifneq ($(CBFLIB_DONT_USE_LOCAL_HDF5),yes)
@@ -2073,7 +2083,7 @@ restore_output: $(NEWTESTOUTPUT) $(DATADIRO) $(MINICBF_TEST)/minicbf.h5
cp test_fcb_read_testflatpackedout.out $(DATADIRO)/test_fcb_read_testflatpackedout_orig.out
cp XRD1621.cbf $(DATADIRO)/XRD1621_orig.cbf
cp XRD1621_I4encbC100.cbf $(DATADIRO)/XRD1621_I4encbC100_orig.cbf
- cp minicbf_orig.h5 $(DATADIRO)/minicbf_orig.h5
+ cp $(MINICBF_TEST)/minicbf.h5 $(DATADIRO)/minicbf_orig.h5
restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS)
$(SIGNATURE) < adscconverted_flat.cbf > $(DATADIRS)/adscconverted_flat_orig.cbf$(SEXT)
@@ -2091,7 +2101,7 @@ restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS)
$(SIGNATURE) < test_fcb_read_testflatpackedout.out > $(DATADIRS)/test_fcb_read_testflatpackedout_orig.out$(SEXT)
$(SIGNATURE) < XRD1621.cbf > $(DATADIRS)/XRD1621_orig.cbf$(SEXT)
$(SIGNATURE) < XRD1621_I4encbC100.cbf > $(DATADIRS)/XRD1621_I4encbC100_orig.cbf$(SEXT)
- $(SIGNATURE) < minicbf_orig.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT)
+ $(SIGNATURE) < $(MINICBF_TEST)/minicbf.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT)
restore_signatures: restore_output restore_sigs_only
#
@@ -2258,7 +2268,7 @@ endif
-cd $(MINICBF_TEST); $(DIFF) minicbf_original.dump minicbf.dump
$(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf_original.dump
$(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf.dump
- cd $(MINICBF_TEST); rm -f minicbf.h5
+ #cd $(MINICBF_TEST); rm -f minicbf.h5
$(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/cbf2nexus -c zlib \
--list -o i19-1.h5 ../1191_00005.cbf
$(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/nexus2cbf \
diff --git a/Makefile_OSX_gcc42_DMALLOC b/Makefile_OSX_gcc42_DMALLOC
index 5ab75ed6..a79db484 100644
--- a/Makefile_OSX_gcc42_DMALLOC
+++ b/Makefile_OSX_gcc42_DMALLOC
@@ -581,6 +581,7 @@ SOCFLAGS = -fPIC
SOLDFLAGS = -shared -Wl,-rpath,$(CBF_PREFIX)/lib
JAVAINCLUDES = -I$(JDKDIR)/include -I$(JDKDIR)/include/linux
LDPREFIX = DYLD_LIBRARY_PATH=$(SOLIB):$$DYLD_LIBRARY_PATH;export DYLD_LIBRARY_PATH;
+RUNLDPREFIX = DYLD_LIBRARY_PATH=$(CBF_PREFIX)/lib:$$DYLD_LIBRARY_PATH;export DYLD_LIBRARY_PATH;
EXTRALIBS = -lm -L$(HOME)/lib -ldmalloc
M4FLAGS = -Dfcb_bytes_in_rec=131072
TIME = time
@@ -1032,6 +1033,11 @@ Makefile: $(M4)/Makefile.m4
m4 -P $(PYCIFRWDEF) -Dcbf_system=default $(M4)/Makefile.m4 > Makefile.tmp
mv Makefile.tmp Makefile
+cbflib.ini: $(M4)/Makefile.m4
+ echo "$(LDPREFIX)" > cbflib.ini
+ echo "HDF5_PLUGIN_PATH=$(SOLIB):$$HDF5_PLUGIN_PATH" >> cbflib.ini
+ echo "export HDF5_PLUGIN_PATH" >> cbflib.ini
+
symlinksdone:
chmod a+x .symlinks
chmod a+x .undosymlinks
@@ -1077,6 +1083,10 @@ baseinstall: all $(CBF_PREFIX) $(CBF_PREFIX)/lib $(CBF_PREFIX)/bin \
-cp $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/libfcb_old.so
cp $(SOLIB)/libfcb.so $(CBF_PREFIX)/lib/libfcb.so
$(LN) $(CBF_PREFIX)/lib/libfcb.so $(CBF_PREFIX)/lib/lib_fcb.so
+ -cp $(CBF_PREFIX)/bin/cbflib.ini $(CBF_PREFIX)/bin/cbflib.ini_old
+ echo "$(RUNLDPREFIX)" > $(CBF_PREFIX)/bin/cbflib.ini
+ echo "HDF5_PLUGIN_PATH=$(CBF_PREFIX)/lib:$$HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini
+ echo "export HDF5_PLUGIN_PATH" >> $(CBF_PREFIX)/bin/cbflib.ini
-cp $(CBF_PREFIX)/bin/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf_old
cp $(BIN)/adscimg2cbf $(CBF_PREFIX)/bin/adscimg2cbf
-cp $(CBF_PREFIX)/bin/cbf2adscimg $(CBF_PREFIX)/bin/cbf2adscimg_old
@@ -1240,7 +1250,7 @@ $(TIFF): build_tiff config.guess config.sub
$(TIFF)_INSTALL: $(TIFF)
-rm -rf $(TIFF)_install
rsync -avz $(TIFF)/ $(TIFF)_install
- (cd $(TIFF_install); make distclean; ./configure --prefix=$(CBF_PREFIX); make install)
+ (cd $(TIFF)_install; make distclean; ./configure --prefix=$(CBF_PREFIX); make install)
ifneq ($(CBFLIB_DONT_USE_LOCAL_HDF5),yes)
@@ -2075,7 +2085,7 @@ restore_output: $(NEWTESTOUTPUT) $(DATADIRO) $(MINICBF_TEST)/minicbf.h5
cp test_fcb_read_testflatpackedout.out $(DATADIRO)/test_fcb_read_testflatpackedout_orig.out
cp XRD1621.cbf $(DATADIRO)/XRD1621_orig.cbf
cp XRD1621_I4encbC100.cbf $(DATADIRO)/XRD1621_I4encbC100_orig.cbf
- cp minicbf_orig.h5 $(DATADIRO)/minicbf_orig.h5
+ cp $(MINICBF_TEST)/minicbf.h5 $(DATADIRO)/minicbf_orig.h5
restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS)
$(SIGNATURE) < adscconverted_flat.cbf > $(DATADIRS)/adscconverted_flat_orig.cbf$(SEXT)
@@ -2093,7 +2103,7 @@ restore_sigs_only: $(NEWTESTOUTPUT) $(DATADIRS)
$(SIGNATURE) < test_fcb_read_testflatpackedout.out > $(DATADIRS)/test_fcb_read_testflatpackedout_orig.out$(SEXT)
$(SIGNATURE) < XRD1621.cbf > $(DATADIRS)/XRD1621_orig.cbf$(SEXT)
$(SIGNATURE) < XRD1621_I4encbC100.cbf > $(DATADIRS)/XRD1621_I4encbC100_orig.cbf$(SEXT)
- $(SIGNATURE) < minicbf_orig.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT)
+ $(SIGNATURE) < $(MINICBF_TEST)/minicbf.h5 > $(DATADIRS)/minicbf_orig.h5$(SEXT)
restore_signatures: restore_output restore_sigs_only
#
@@ -2260,7 +2270,7 @@ endif
-cd $(MINICBF_TEST); $(DIFF) minicbf_original.dump minicbf.dump
$(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf_original.dump
$(LDPREFIX) cd $(MINICBF_TEST); rm -f minicbf.dump
- cd $(MINICBF_TEST); rm -f minicbf.h5
+ #cd $(MINICBF_TEST); rm -f minicbf.h5
$(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/cbf2nexus -c zlib \
--list -o i19-1.h5 ../1191_00005.cbf
$(LDPREFIX) cd $(MINICBF_TEST); $(TIME) $(BIN)/nexus2cbf \
diff --git a/README b/README
index 4eda923c..20968c00 100644
--- a/README
+++ b/README
@@ -1,8 +1,21 @@
+ +------------------------------------------------------------------------+
+ | [IUCr | [CIF | | | Get CBFlib at |
+ | Home | Home | [CBF/imgCIF] | [CBFlib] | SourceForge.net. Fast, |
+ | Page] | Page] | | | secure and Free Open |
+ | | | | | Source software downloads |
+ +------------------------------------------------------------------------+
+
+ ----------------------------------------------------------------------
+
+ | IUCr Home Page | CIF Home Page | CBF/imgCIF | CBFlib |
+ | NOTICE | doc/GPL | doc/LGPL | imgCIF dictionary | SourceForge CBFlib site |
+ | Click Here to Make a Donation |
+
CBFlib
README
- Information for CBFlib 0.9.5 release of 27 April 2014
+ Information for CBFlib 0.9.6 release of 4 December 2018
by
Paul J. Ellis
@@ -13,7 +26,7 @@
Bernstein + Sons
yaya at bernstein-plus-sons dot com
- (c) Copyright 2006 -- 2014 Herbert J. Bernstein
+ © Copyright 2006 -- 2018 Herbert J. Bernstein
----------------------------------------------------------------------
@@ -22,9 +35,9 @@
ALTERNATIVELY YOU MAY REDISTRIBUTE THE CBFLIB API UNDER THE TERMS OF THE
LGPL.
- All functions in the src, include and examples directories are included
- in the term "API" unless explicitly placed under a diferent license in
- the header comments of that particular source code.
+ All functions in the src, include and examples directories are included in
+ the term "API" unless explicitly placed under a diferent license in the
+ header comments of that particular source code.
----------------------------------------------------------------------
@@ -39,13 +52,25 @@ for important disclaimers and the IUCr Policy on the Use of the Crystallographic
under grants DBI-0610407, DBI-0315281 and EF-0312612, the U. S. National
Institutes of Health (NIH) under grants 1R15GM078077 from NIGMS and
1R13RR023192 from NCRR and funding from the International Union for
- Crystallography (IUCr). The content is solely the responsibility of the
- authors and does not necessarily represent the official views of DOE, NSF,
- NIH, NIGMS, NCRR or IUCr. Recent work on integration among CBF, HDF5 and
- NeXus supported in part by Pandata ODI (EU 7th Framework Programme)
+ Crystallography (IUCr) and Dectris, Ltd. The content is solely the
+ responsibility of the authors and does not necessarily represent the
+ official views of DOE, NSF, NIH, NIGMS, NCRR, IUCr or Dectris. Recent work
+ on integration among CBF, HDF5 and NeXus supported in part by Pandata ODI
+ (EU 7th Framework Programme)
----------------------------------------------------------------------
+ CBFlib 0.9.6 is the full release supporting the integration of CBF and
+ NeXus, including support for the NeXus NXpdb embedding of CIF files in
+ NeXus files. *** IMPORTANT: Because of the requirements of dynamic loading
+ to support the compressions used by the Dectris NeXus/HDF5 format, all
+ applications require setting of library and plugin paths. See the
+ initialization file cbflib.ini, which should be sourced before running any
+ applications ***. The primary development source is at
+ https://github.com/yayahjb/cbflib. The branch pdb_in_nexus, which was used
+ for much of this development has been merged, is now deprecated, and will
+ be removed in the near future.
+
CBFlib 0.9.5 is the full release resulting from the interim effort on
0.9.4, reflecting significant and unfortunately somewhat disruptive
changes resulting from changes to the agreed CBF-NeXus mapping. Axis data
@@ -178,30 +203,32 @@ for important disclaimers and the IUCr Policy on the Use of the Crystallographic
space, for a full installation with complete tests. Read the instructions
below carefully, if space is a problem.
- A gizpped tarball of this release is available on sourceforge at
+ You may download clone the git repository with
+ git clone https://github.com/yayahjb/cbflib.git
+ or a gizpped tarball of this release is available on sourceforge at
- http://downloads.sf.net/cbflib/CBFlib-0.9.5.tar.gz
+ http://downloads.sf.net/cbflib/CBFlib-0.9.6.tar.gz
In addition,
- http://downloads.sf.net/cbflib/CBFlib_0.9.5_Data_Files_Input.tar.gz (13
+ http://downloads.sf.net/cbflib/CBFlib_0.9.6_Data_Files_Input.tar.gz (13
MB) is a "gzipped" tar of the input data files needed to test the API,
- http://downloads.sf.net/cbflib/CBFlib_0.9.5_Data_Files_Output.tar.gz (34
+ http://downloads.sf.net/cbflib/CBFlib_0.9.6_Data_Files_Output.tar.gz (34
MB) is a "gzipped" tar of the output data files needed to test the API,
and, if space is at a premium,
- http://downloads.sf.net/cbflib/CBFlib_0.9.5_Data_Files_Output_Sigs_Only.tar.gz
+ http://downloads.sf.net/cbflib/CBFlib_0.9.6_Data_Files_Output_Sigs_Only.tar.gz
(1KB) is a "gzipped" tar of only the MD5 signatures of the output data
- files needed to test the API. Place the CBFlib_0.9.5.tar.gz file in the
+ files needed to test the API. Place the CBFlib_0.9.6.tar.gz file in the
directory that is intended to contain up to 4 new directories, named
- CBFlib_0.9.5 (the "top-level" directory), CBFlib_0.9.5_Data_Files_Input
- and either CBFlib_0.9.5_Data_Files_Output or
- CBFlib_0.9.5_Data_Files_Output_Sigs_Only. If you have wget on your
+ CBFlib_0.9.6 (the "top-level" directory), CBFlib_0.9.6_Data_Files_Input
+ and either CBFlib_0.9.6_Data_Files_Output or
+ CBFlib_0.9.6_Data_Files_Output_Sigs_Only. If you have wget on your
machine, you only need to download the source tarball. If you do not have
wget, you will need to download all the tarballs into the same directory
- Uncompress CBFlib_0.9.5.tar.gz with gunzip and unpack it with tar:
+ Uncompress CBFlib_0.9.6.tar.gz with gunzip and unpack it with tar:
- gunzip CBFlib_0.9.5.tar.gz
- tar xvf CBFLIB_0.9.5.tar
+ gunzip CBFlib_0.9.6.tar.gz
+ tar xvf CBFLIB_0.9.6.tar
To run the test programs, you will also need Paul Ellis's sample MAR345
image, example.mar2300, Chris Nielsen's sample ADSC Quantum 315 image,
@@ -210,7 +237,7 @@ for important disclaimers and the IUCr Policy on the Use of the Crystallographic
file, 9ins.cif, and 3 special test files testflatin.cbf,
testflatpackedin.cbf and testrealin.cbf, and several files related to
NeXus and FEL testing. All these files will be dowloaded and extracted by
- the Makefile from CBFlib_0.9.5_Data_Files_Input. Do not download copies
+ the Makefile from CBFlib_0.9.6_Data_Files_Input. Do not download copies
into the top level directory.
After unpacking the archives, the top-level directory should contain a
@@ -278,18 +305,15 @@ for important disclaimers and the IUCr Policy on the Use of the Crystallographic
* To use the newer and more popular POSIX pcre regex. If neither
CBF_NO_REGEX nor CBF_REGEXLIB_REGEX is defined, pcreposix.h is used.
- The default in the supplied Makefiles is to use regex.h. The default in
- the CMakeLists.txt is to use pcreposix.h.
-
Cmake
A partial preliminary CMakeLists.txt has been included in this kit. It is
not yet complete, but on machines for which the Makefiles are not
appropriate, it is worth a try. To use in, create a directory named
- CBFlib-0.9.5-build on the same level as CBFlib-0.9.5, and in the new,
+ CBFlib-0.9.6-build on the same level as CBFlib-0.9.6, and in the new,
empty build directory, try
- cmake ../CBFlib-0.9.5
+ cmake ../CBFlib-0.9.6
make all
make test
@@ -302,10 +326,10 @@ for important disclaimers and the IUCr Policy on the Use of the Crystallographic
shared library or other shared libraries when tests are run prior to those
libraries having been installed in locations known to your system's
loader. This is handled automatically in the Makefiles, but we do not yet
- have a reliable way to do so for cmake ctest tests. Until this is
- resolved, you may need to set various system-dependent environment
- variables such as DYLD_LIBRARY_PATH, LD_LIBRARY_PATH or PATH. We hope to
- resolve this for an upcoming release.
+ have a reliable way to do so for cmake ctest tests. You may need to set
+ various system-dependent environment variables such as DYLD_LIBRARY_PATH,
+ LD_LIBRARY_PATH or PATH. The bash script in the kit cbflib.ini should be
+ sourced before testing.
Please refer to the manual doc/CBFlib.html for more detailed information.
@@ -313,4 +337,4 @@ for important disclaimers and the IUCr Policy on the Use of the Crystallographic
----------------------------------------------------------------------
- Updated 27 April 2014. yayahjb at gmail dot com
+ Updated 4 December 2018. yayahjb at gmail dot com
diff --git a/README.html b/README.html
index 2e65be00..3ace9f0b 100755
--- a/README.html
+++ b/README.html
@@ -42,7 +42,7 @@
README
-Information for CBFlib 0.9.5 release of 27 April 2014
+Information for CBFlib 0.9.6 release of 4 December 2018
-© Copyright 2006 -- 2014 Herbert J. Bernstein +© Copyright 2006 -- 2018 Herbert J. Bernstein
+CBFlib 0.9.6 is the full release supporting the integration of CBF and +NeXus, including support for the NeXus NXpdb embedding of CIF files +in NeXus files. *** IMPORTANT: Because of the requirements of dynamic +loading to support the compressions used by the Dectris NeXus/HDF5 format, all applications +require setting of library and plugin paths. See the initialization +file cbflib.ini, which should be sourced before running any applications ***. +The primary development source is at https://github.com/yayahjb/cbflib. +The branch pdb_in_nexus, which was used for much of this development has been +merged, is now deprecated, and will be removed in the near future. +
CBFlib 0.9.5 is the full release resulting from the interim effort on 0.9.4, reflecting significant and unfortunately somewhat disruptive changes resulting from changes to the agreed CBF-NeXus mapping. @@ -248,37 +258,39 @@
-A gizpped tarball of this release is available on sourceforge at
+You may download clone the git repository with
+git clone https://github.com/yayahjb/cbflib.git
+or a gizpped tarball of this release is available on sourceforge at
http://downloads.sf.net/cbflib/CBFlib-0.9.5.tar.gz +href="http://downloads.sf.net/cbflib/CBFlib-0.9.6.tar.gz">http://downloads.sf.net/cbflib/CBFlib-0.9.6.tar.gz
In addition, http://downloads.sf.net/cbflib/CBFlib_0.9.5_Data_Files_Input.tar.gz +href="http://downloads.sf.net/cbflib/CBFlib_0.9.6_Data_Files_Input.tar.gz">http://downloads.sf.net/cbflib/CBFlib_0.9.6_Data_Files_Input.tar.gz (13 MB) is a "gzipped" tar of the input data files needed to test the API, http://downloads.sf.net/cbflib/CBFlib_0.9.5_Data_Files_Output.tar.gz +href="http://downloads.sf.net/cbflib/CBFlib_0.9.6_Data_Files_Output.tar.gz">http://downloads.sf.net/cbflib/CBFlib_0.9.6_Data_Files_Output.tar.gz (34 MB) is a "gzipped" tar of the output data files needed to test the API, and, if space is at a premium, http://downloads.sf.net/cbflib/CBFlib_0.9.5_Data_Files_Output_Sigs_Only.tar.gz +href="http://downloads.sf.net/cbflib/CBFlib_0.9.6_Data_Files_Output_Sigs_Only.tar.gz">http://downloads.sf.net/cbflib/CBFlib_0.9.6_Data_Files_Output_Sigs_Only.tar.gz (1KB) is a "gzipped" tar of only the MD5 signatures of the output data files needed to test the API. -Place the CBFlib_0.9.5.tar.gz file in the directory +Place the CBFlib_0.9.6.tar.gz file in the directory that is intended to contain up to 4 new directories, named -CBFlib_0.9.5 (the "top-level" directory), -CBFlib_0.9.5_Data_Files_Input and either CBFlib_0.9.5_Data_Files_Output or -CBFlib_0.9.5_Data_Files_Output_Sigs_Only. +CBFlib_0.9.6 (the "top-level" directory), +CBFlib_0.9.6_Data_Files_Input and either CBFlib_0.9.6_Data_Files_Output or +CBFlib_0.9.6_Data_Files_Output_Sigs_Only. If you have wget on your machine, you only need to download the source tarball. If you do not have wget, you will need to download all the tarballs into the same directory
-Uncompress CBFlib_0.9.5.tar.gz with gunzip and unpack it with tar: +Uncompress CBFlib_0.9.6.tar.gz with gunzip and unpack it with tar:
- gunzip CBFlib_0.9.5.tar.gz - tar xvf CBFLIB_0.9.5.tar + gunzip CBFlib_0.9.6.tar.gz + tar xvf CBFLIB_0.9.6.tar
To run the test programs, you will also need @@ -291,7 +303,7 @@
After unpacking the archives, the top-level directory should contain @@ -372,21 +384,18 @@
-The default in the supplied Makefiles is to use regex.h. The default in the -CMakeLists.txt is to use pcreposix.h. -
- cmake ../CBFlib-0.9.5 + cmake ../CBFlib-0.9.6 make all make test@@ -399,17 +408,18 @@
Please refer to the manual doc/CBFlib.html for more detailed information.