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base: Commit

This repository is a base of Eos.


Commit MetaInfo

Revisionaf3a7360ff82a4644aeae59fdba69879806134c2 (tree)
Time2014-10-01 20:09:10
AuthorTakuo Yasunaga <yasunaga@bio....>
CommiterTakuo Yasunaga

Log Message

Create a new tool of mrcImageAutoRotationAverage:
new file: mrcImageAutoRotationAverage
modified: src/Objects/DataManip/mrcImage/src/lmrcImageCorrelation.h
Input/Output separation of struct

Change Summary

Incremental Difference

--- /dev/null
+++ b/bin/mrcImageAutoRotationAverage
@@ -0,0 +1 @@
1+../sbin/MachineIndependent
\ No newline at end of file
Binary files /dev/null and b/hostdepend/X86MAC64/bin/X86MAC64/mrcImageAutoRotationAverage differ
Binary files a/hostdepend/X86MAC64/lib/X86MAC64/libEosObjects.a and b/hostdepend/X86MAC64/lib/X86MAC64/libEosObjects.a differ
Binary files a/hostdepend/X86MAC64/lib/X86MAC64/libmrcImage.a and b/hostdepend/X86MAC64/lib/X86MAC64/libmrcImage.a differ
Binary files a/hostdepend/X86MAC64/lib/X86MAC64/shared/lmrcImageCorrelation.sharedo and b/hostdepend/X86MAC64/lib/X86MAC64/shared/lmrcImageCorrelation.sharedo differ
Binary files a/hostdepend/X86MAC64/src/Objects/DataManip/mrcImage/src/X86MAC64/libmrcImage.a and b/hostdepend/X86MAC64/src/Objects/DataManip/mrcImage/src/X86MAC64/libmrcImage.a differ
Binary files a/hostdepend/X86MAC64/src/Objects/DataManip/mrcImage/src/X86MAC64/libmrcImage.debug.a and b/hostdepend/X86MAC64/src/Objects/DataManip/mrcImage/src/X86MAC64/libmrcImage.debug.a differ
Binary files a/hostdepend/X86MAC64/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageCorrelation.sharedo and b/hostdepend/X86MAC64/src/Objects/DataManip/mrcImage/src/X86MAC64/lmrcImageCorrelation.sharedo differ
--- /dev/null
+++ b/hostdepend/X86MAC64/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/X86MAC64/.Depend
@@ -0,0 +1,209 @@
1+argCheck.o: argCheck.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
2+ /usr/include/sys/_symbol_aliasing.h \
3+ /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
4+ /usr/include/AvailabilityInternal.h /usr/include/_types.h \
5+ /usr/include/sys/_types.h /usr/include/machine/_types.h \
6+ /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
7+ /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
8+ /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
9+ /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
10+ /usr/include/stdlib.h /usr/include/sys/wait.h \
11+ /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
12+ /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
13+ /usr/include/machine/signal.h /usr/include/i386/signal.h \
14+ /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
15+ /usr/include/mach/i386/_structs.h \
16+ /usr/include/sys/_types/_sigaltstack.h \
17+ /usr/include/sys/_types/_ucontext.h \
18+ /usr/include/sys/_types/_pthread_attr_t.h \
19+ /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
20+ /usr/include/sys/resource.h \
21+ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/6.0/include/stdint.h \
22+ /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
23+ /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
24+ /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
25+ /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
26+ /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
27+ /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
28+ /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
29+ /usr/include/machine/endian.h /usr/include/i386/endian.h \
30+ /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
31+ /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
32+ /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
33+ /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
34+ /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
35+ /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
36+ /Users/tacyas/Eos/include/string.h /usr/include/math.h ../inc/config.h \
37+ ../inc/../inc/mrcImageAutoRotationAverage.h \
38+ /Users/tacyas/Eos/include/genUtil.h /Users/tacyas/Eos/include/File.h \
39+ /Users/tacyas/Eos/include/Memory.h \
40+ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/6.0/include/limits.h \
41+ /usr/include/limits.h /usr/include/machine/limits.h \
42+ /usr/include/i386/limits.h /usr/include/i386/_limits.h \
43+ /usr/include/sys/syslimits.h
44+init.o: init.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
45+ /usr/include/sys/_symbol_aliasing.h \
46+ /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
47+ /usr/include/AvailabilityInternal.h /usr/include/_types.h \
48+ /usr/include/sys/_types.h /usr/include/machine/_types.h \
49+ /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
50+ /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
51+ /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
52+ /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
53+ /usr/include/stdlib.h /usr/include/sys/wait.h \
54+ /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
55+ /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
56+ /usr/include/machine/signal.h /usr/include/i386/signal.h \
57+ /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
58+ /usr/include/mach/i386/_structs.h \
59+ /usr/include/sys/_types/_sigaltstack.h \
60+ /usr/include/sys/_types/_ucontext.h \
61+ /usr/include/sys/_types/_pthread_attr_t.h \
62+ /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
63+ /usr/include/sys/resource.h \
64+ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/6.0/include/stdint.h \
65+ /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
66+ /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
67+ /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
68+ /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
69+ /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
70+ /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
71+ /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
72+ /usr/include/machine/endian.h /usr/include/i386/endian.h \
73+ /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
74+ /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
75+ /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
76+ /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
77+ /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
78+ /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
79+ /Users/tacyas/Eos/include/string.h /usr/include/math.h ../inc/config.h \
80+ ../inc/../inc/mrcImageAutoRotationAverage.h \
81+ /Users/tacyas/Eos/include/genUtil.h /Users/tacyas/Eos/include/File.h \
82+ /Users/tacyas/Eos/include/Memory.h \
83+ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/6.0/include/limits.h \
84+ /usr/include/limits.h /usr/include/machine/limits.h \
85+ /usr/include/i386/limits.h /usr/include/i386/_limits.h \
86+ /usr/include/sys/syslimits.h
87+mrcImageAutoRotationAverage.o: mrcImageAutoRotationAverage.c \
88+ /usr/include/stdio.h /usr/include/sys/cdefs.h \
89+ /usr/include/sys/_symbol_aliasing.h \
90+ /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
91+ /usr/include/AvailabilityInternal.h /usr/include/_types.h \
92+ /usr/include/sys/_types.h /usr/include/machine/_types.h \
93+ /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
94+ /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
95+ /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
96+ /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
97+ /usr/include/stdlib.h /usr/include/sys/wait.h \
98+ /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
99+ /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
100+ /usr/include/machine/signal.h /usr/include/i386/signal.h \
101+ /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
102+ /usr/include/mach/i386/_structs.h \
103+ /usr/include/sys/_types/_sigaltstack.h \
104+ /usr/include/sys/_types/_ucontext.h \
105+ /usr/include/sys/_types/_pthread_attr_t.h \
106+ /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
107+ /usr/include/sys/resource.h \
108+ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/6.0/include/stdint.h \
109+ /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
110+ /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
111+ /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
112+ /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
113+ /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
114+ /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
115+ /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
116+ /usr/include/machine/endian.h /usr/include/i386/endian.h \
117+ /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
118+ /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
119+ /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
120+ /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
121+ /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
122+ /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
123+ /Users/tacyas/Eos/include/string.h /usr/include/math.h ../inc/config.h \
124+ ../inc/../inc/mrcImageAutoRotationAverage.h \
125+ /Users/tacyas/Eos/include/genUtil.h \
126+ /Users/tacyas/Eos/include/mrcImage.h \
127+ /Users/tacyas/Eos/include/Matrix3D.h \
128+ /Users/tacyas/Eos/include/Vector.h /Users/tacyas/Eos/include/Array.h \
129+ /Users/tacyas/Eos/include/ctfInfo.h /Users/tacyas/Eos/include/Memory.h \
130+ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/6.0/include/limits.h \
131+ /usr/include/limits.h /usr/include/machine/limits.h \
132+ /usr/include/i386/limits.h /usr/include/i386/_limits.h \
133+ /usr/include/sys/syslimits.h \
134+ /Users/tacyas/Eos/include/lmrcImageAverage.h \
135+ /Users/tacyas/Eos/include/lmrcImageCorrelation.h \
136+ /Users/tacyas/Eos/include/PVM.h \
137+ /Users/tacyas/Eos/include/lmrcImageSSDA.h
138+usage.o: usage.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
139+ /usr/include/sys/_symbol_aliasing.h \
140+ /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
141+ /usr/include/AvailabilityInternal.h /usr/include/_types.h \
142+ /usr/include/sys/_types.h /usr/include/machine/_types.h \
143+ /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
144+ /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
145+ /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
146+ /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
147+ /usr/include/stdlib.h /usr/include/sys/wait.h \
148+ /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
149+ /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
150+ /usr/include/machine/signal.h /usr/include/i386/signal.h \
151+ /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
152+ /usr/include/mach/i386/_structs.h \
153+ /usr/include/sys/_types/_sigaltstack.h \
154+ /usr/include/sys/_types/_ucontext.h \
155+ /usr/include/sys/_types/_pthread_attr_t.h \
156+ /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
157+ /usr/include/sys/resource.h \
158+ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/6.0/include/stdint.h \
159+ /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
160+ /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
161+ /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
162+ /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
163+ /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
164+ /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
165+ /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
166+ /usr/include/machine/endian.h /usr/include/i386/endian.h \
167+ /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
168+ /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
169+ /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
170+ /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
171+ /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
172+ /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
173+ ../inc/config.h ../inc/../inc/mrcImageAutoRotationAverage.h
174+util.o: util.c /usr/include/stdio.h /usr/include/sys/cdefs.h \
175+ /usr/include/sys/_symbol_aliasing.h \
176+ /usr/include/sys/_posix_availability.h /usr/include/Availability.h \
177+ /usr/include/AvailabilityInternal.h /usr/include/_types.h \
178+ /usr/include/sys/_types.h /usr/include/machine/_types.h \
179+ /usr/include/i386/_types.h /usr/include/sys/_types/_va_list.h \
180+ /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h \
181+ /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h \
182+ /usr/include/secure/_stdio.h /usr/include/secure/_common.h \
183+ /usr/include/stdlib.h /usr/include/sys/wait.h \
184+ /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h \
185+ /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
186+ /usr/include/machine/signal.h /usr/include/i386/signal.h \
187+ /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h \
188+ /usr/include/mach/i386/_structs.h \
189+ /usr/include/sys/_types/_sigaltstack.h \
190+ /usr/include/sys/_types/_ucontext.h \
191+ /usr/include/sys/_types/_pthread_attr_t.h \
192+ /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h \
193+ /usr/include/sys/resource.h \
194+ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/6.0/include/stdint.h \
195+ /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h \
196+ /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h \
197+ /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h \
198+ /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h \
199+ /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h \
200+ /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h \
201+ /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h \
202+ /usr/include/machine/endian.h /usr/include/i386/endian.h \
203+ /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
204+ /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
205+ /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h \
206+ /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h \
207+ /usr/include/i386/types.h /usr/include/sys/_types/___offsetof.h \
208+ /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h \
209+ ../inc/config.h ../inc/../inc/mrcImageAutoRotationAverage.h
--- /dev/null
+++ b/hostdepend/X86MAC64/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/X86MAC64/Makefile
@@ -0,0 +1,114 @@
1+include $(EOS_HOME)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config/Define.inc
2+include $(EOS_HOME)/src/$(WORLDNAME)/$(CLASSNAME)/Config/Define.inc
3+include $(EOS_HOME)/src/$(WORLDNAME)/Config/Define.inc
4+include $(EOS_HOME)/src/Config/DefineTool.inc
5+
6+LIBFILES = \
7+ $(LIBPREFIX)EosObjects$(LIBSUFFIX)
8+
9+LIBFILESDEBUG = \
10+ $(LIBPREFIX)EosObjects.debug$(LIBSUFFIX)
11+
12+SRCC = \
13+ $(OBJECTNAME).c \
14+ init.c \
15+ argCheck.c \
16+ usage.c \
17+ util.c
18+
19+SRCCXX = \
20+ $(OBJECTNAME).cc \
21+ init.cc \
22+ argCheck.cc \
23+ usage.cc \
24+ util.cc
25+
26+MODULES = \
27+ $(OBJECTNAME).o \
28+ init.o \
29+ argCheck.o \
30+ usage.o \
31+ util.o
32+
33+REALMODULES = \
34+ $(OSTYPE)/$(OBJECTNAME).o \
35+ $(OSTYPE)/init.o \
36+ $(OSTYPE)/argCheck.o \
37+ $(OSTYPE)/usage.o \
38+ $(OSTYPE)/util.o
39+
40+MODULESDEBUG = \
41+ $(OBJECTNAME).debugo \
42+ init.debugo \
43+ argCheck.debugo \
44+ usage.debugo \
45+ util.debugo
46+
47+MODULESCUDAGDB = \
48+ $(OBJECTNAME).cudagdb.o \
49+ init.cudagdb.o \
50+ argCheck.cudagdb.o \
51+ usage.cudagdb.o \
52+ util.cudagdb.o
53+
54+REALMODULESDEBUG = \
55+ $(OSTYPE)/$(OBJECTNAME).debugo \
56+ $(OSTYPE)/init.debugo \
57+ $(OSTYPE)/argCheck.debugo \
58+ $(OSTYPE)/usage.debugo \
59+ $(OSTYPE)/util.debugo
60+
61+
62+$(OBJECTNAME): $(MODULES) $(LIBFILES)
63+ @if [ -f $(VPATH)/$(OBJECTNAME).c ] ; \
64+ then \
65+ echo $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ; \
66+ $(CC) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ; \
67+ fi
68+ @if [ -f $(VPATH)/$(OBJECTNAME).cc ] ; \
69+ then \
70+ echo $(CXX) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ; \
71+ $(CXX) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ; \
72+ fi
73+ @if [ -f $(VPATH)/$(OBJECTNAME).ccm ] ; \
74+ then \
75+ echo "MICO"; \
76+ echo $(MICOLD) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ; \
77+ $(MICOLD) $(CCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ; \
78+ fi
79+ @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
80+ then \
81+ echo $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ; \
82+ $(NVCC) $(NVCCOPTS) $(MODULES) $(LIBFILES) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) $(CUDALIB) $(CUDAINC) -o $@ ; \
83+ fi
84+
85+
86+$(OBJECTNAME).debug: $(MODULESDEBUG) $(LIBFILESDEBUG)
87+ @if [ -f $(VPATH)/$(OBJECTNAME).c ] ; \
88+ then \
89+ echo $(CC) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ; \
90+ $(CC) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ; \
91+ fi
92+ @if [ -f $(VPATH)/$(OBJECTNAME).cc ] ; \
93+ then \
94+ echo $(CXX) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ; \
95+ $(CXX) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ; \
96+ fi
97+ @if [ -f $(VPATH)/$(OBJECTNAME).ccm ] ; \
98+ then \
99+ echo "MICO"; \
100+ echo $(MICOLD) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ; \
101+ $(MICOLD) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ; \
102+ fi
103+ @if [ -f $(VPATH)/$(OBJECTNAME).cu ] ; \
104+ then \
105+ echo $(CC) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ; \
106+ $(CC) $(CCOPTSDEBUG) $(MODULESDEBUG) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@ ; \
107+ fi
108+
109+$(OBJECTNAME).cudagdb: $(MODULESCUDAGDB) $(LIBFILESDEBUG)
110+ echo $(NVCC) "$(NVCCOPTSCUDAGDB) $(MODULESCUDAGDB) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@"
111+ $(NVCC) $(NVCCOPTSCUDAGDB) $(MODULESCUDAGDB) $(LIBFILESDEBUG) $(EXTRA_LIB) $(KHOROS_LIBS) $(LIBPVM) $(STANDARDLIB) $(HOSTDEPENDENTLIB) -o $@
112+
113+include ./.Depend
114+include $(EOS_HOME)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config/Target.inc
--- /dev/null
+++ b/hostdepend/X86MAC64/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/X86MAC64/X86MAC64
@@ -0,0 +1 @@
1+../../../../../hostdepend/X86MAC64/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/X86MAC64
\ No newline at end of file
Binary files /dev/null and b/hostdepend/X86MAC64/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/X86MAC64/mrcImageAutoRotationAverage differ
--- a/include/lmrcImageCorrelation.h
+++ b/include/lmrcImageCorrelation.h
@@ -26,19 +26,12 @@ typedef enum lmrcImageAutoRotationCorrelationMethod {
2626 } lmrcImageAutoRotationCorrelationMethod;
2727
2828 typedef struct lmrcImageAutoRotationCorrelationInfo {
29+/* Input */
2930 int iter; /* iteration */
3031 int nRot; /* Rotation */
31- lmrcImageAutoRotationCorrelationMethod Method;
32- float max;
33- float maxTheta;
34- mrcImageParaTypeRealCoord maxP;
35- mrcImageInformation corInfo;
36- lmrcImageSSDAInfo SSDAInfo;
37- float EuclidDistance;
38- float LinearCorrelation;
32+ lmrcImageAutoRotationCorrelationMethod Method; /* Correlation Method */
3933
40- /* Restriction Rotation Area */
41- int flagRestrictionArea;
34+ int flagRestrictionArea;
4235 float thetaMin;
4336 float thetaMax;
4437
@@ -51,6 +44,15 @@ typedef struct lmrcImageAutoRotationCorrelationInfo {
5144 int flagXshiftOnly;
5245 int flagNoShift;
5346
47+/* Output */
48+ float max; //
49+ float maxTheta; //
50+ mrcImageParaTypeRealCoord maxP;
51+ mrcImageInformation corInfo;
52+ lmrcImageSSDAInfo SSDAInfo;
53+ float EuclidDistance;
54+ float LinearCorrelation;
55+
5456 } lmrcImageAutoRotationCorrelationInfo;
5557
5658 typedef struct lmrcImageCorrelationRefinementInfo {
--- a/src/Objects/DataManip/mrcImage/src/lmrcImageCorrelation.h
+++ b/src/Objects/DataManip/mrcImage/src/lmrcImageCorrelation.h
@@ -26,19 +26,12 @@ typedef enum lmrcImageAutoRotationCorrelationMethod {
2626 } lmrcImageAutoRotationCorrelationMethod;
2727
2828 typedef struct lmrcImageAutoRotationCorrelationInfo {
29+/* Input */
2930 int iter; /* iteration */
3031 int nRot; /* Rotation */
31- lmrcImageAutoRotationCorrelationMethod Method;
32- float max;
33- float maxTheta;
34- mrcImageParaTypeRealCoord maxP;
35- mrcImageInformation corInfo;
36- lmrcImageSSDAInfo SSDAInfo;
37- float EuclidDistance;
38- float LinearCorrelation;
32+ lmrcImageAutoRotationCorrelationMethod Method; /* Correlation Method */
3933
40- /* Restriction Rotation Area */
41- int flagRestrictionArea;
34+ int flagRestrictionArea;
4235 float thetaMin;
4336 float thetaMax;
4437
@@ -51,6 +44,15 @@ typedef struct lmrcImageAutoRotationCorrelationInfo {
5144 int flagXshiftOnly;
5245 int flagNoShift;
5346
47+/* Output */
48+ float max; //
49+ float maxTheta; //
50+ mrcImageParaTypeRealCoord maxP;
51+ mrcImageInformation corInfo;
52+ lmrcImageSSDAInfo SSDAInfo;
53+ float EuclidDistance;
54+ float LinearCorrelation;
55+
5456 } lmrcImageAutoRotationCorrelationInfo;
5557
5658 typedef struct lmrcImageCorrelationRefinementInfo {
--- a/src/Tools/Config/Define.inc
+++ b/src/Tools/Config/Define.inc
@@ -172,3 +172,11 @@ WORLDNAME=Tools
172172 WORLDNAME=Tools
173173 WORLDNAME=Tools
174174 WORLDNAME=Tools
175+WORLDNAME=Tools
176+WORLDNAME=Tools
177+WORLDNAME=Tools
178+WORLDNAME=Tools
179+WORLDNAME=Tools
180+WORLDNAME=Tools
181+WORLDNAME=Tools
182+WORLDNAME=Tools
--- a/src/Tools/mrcImage/.Source
+++ b/src/Tools/mrcImage/.Source
@@ -47,6 +47,7 @@ mrcImageAssignedToTFofPDB \
4747 mrcImageAutoCorrelationWithWindowing \
4848 mrcImageAutoFilamentExtract \
4949 mrcImageAutoFilamentExtractResultAnalysis \
50+mrcImageAutoRotationAverage \
5051 mrcImageAutoRotationCorrelation \
5152 mrcImageAutoRotationCorrelation3D \
5253 mrcImageAutoRotationCorrelationResultPrint \
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageAutoRotationAverage/Config/Define.inc
@@ -0,0 +1,4 @@
1+OBJECTNAME = mrcImageAutoRotationAverage
2+EXTRA_LIB =
3+EXTRA_CCOPTS =
4+EXTRA_INC =
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageAutoRotationAverage/Config/OptionControlFile
@@ -0,0 +1,15 @@
1+# OptionControlFile
2+# FileFormat
3+"-i","-i[nput]","Input: Ins","Essential","1","1","In","inFileList::mrcImage","stdin"
4+"-r","-r[eferenc]","Input: Ref","Optional","1","1","Ref","inFile::mrcImage","NULL"
5+"-o","-o[utput]","Output:Average","Essential","1","1","Out","outFile::mrcImage","NULL"
6+"-range","-range","Mode","Optional","4","1","Min","Real","0.0","2","Max","Real","360.0","3","Delta","Real","5.0","4","Iter","Integer","2"
7+"-iter","-iter","iteration for rotation","Optional","1","1","iter","Integer","2"
8+"-M","-M[odeCorrelation]","Mode: Correlation","Optional","1","1","CorMode","Integer","16"
9+"-Method","-Method[Correlation]","Method: Correlation","Optional","1","1","Method","Integer","0"
10+"-Periodic","-Periodic","Periodic","Optional","0"
11+"-maxIter","-maxIter[aration]","MaxIteration","Optional","1","1","maxIter","Integer","10"
12+"-rmsd","-rmsd","rmsd","Optional","1","1","rmsd","Real","1e-2"
13+"-log","-log","logFile","Optional","1","1","Log","inFile::ASCII","stdout"
14+"-c","-c[onfig]","ConfigurationFile","Optional","1","1","configFile","inFile","NULL"
15+"-m","-m[ode]","Mode","Optional","1","1","mode","Integer","0"
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageAutoRotationAverage/Makefile
@@ -0,0 +1 @@
1+/Users/tacyas/Eos/src/Config/Template/ToolsTemplate.Dir/Makefile
\ No newline at end of file
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageAutoRotationAverage/doc/Makefile
@@ -0,0 +1 @@
1+/Users/tacyas/Eos/src/Config/Template/ToolsTemplate.Dir/doc/Makefile
\ No newline at end of file
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageAutoRotationAverage/inc/config.h
@@ -0,0 +1,6 @@
1+#ifndef CONFIG_H
2+#define CONFIG_H
3+
4+#include "../inc/mrcImageAutoRotationAverage.h"
5+
6+#endif /* CONFIG_H */
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageAutoRotationAverage/inc/mrcImageAutoRotationAverage.h
@@ -0,0 +1,85 @@
1+#ifndef MRCIMAGEAUTOROTATIONAVERAGE_H
2+#define MRCIMAGEAUTOROTATIONAVERAGE_H
3+#include <stdio.h>
4+#include <stdlib.h>
5+
6+#define OPTION_FLAG '-'
7+#define OPTION_FLAG_POS (0)
8+#define OPTION_POS (1)
9+
10+
11+
12+
13+typedef struct mrcImageAutoRotationAverageInfo {
14+ long flagRedirect;
15+
16+ long flagIn;
17+ char** In;
18+ char* InList;
19+ FILE** fptIn;
20+ FILE* fptInList;
21+
22+ long flagRef;
23+ char* Ref;
24+ FILE* fptRef;
25+
26+ long flagOut;
27+ char* Out;
28+ FILE* fptOut;
29+
30+ long flagMin;
31+ float Min;
32+
33+ long flagMax;
34+ float Max;
35+
36+ long flagDelta;
37+ float Delta;
38+
39+ long flagIter;
40+ long Iter;
41+
42+ long flagiter;
43+ long iter;
44+
45+ long flagCorMode;
46+ long CorMode;
47+
48+ long flagMethod;
49+ long Method;
50+
51+ long Periodic;
52+
53+ long flagmaxIter;
54+ long maxIter;
55+
56+ long flagrmsd;
57+ float rmsd;
58+
59+ long flagLog;
60+ char* Log;
61+ FILE* fptLog;
62+
63+ long flagconfigFile;
64+ char* configFile;
65+ FILE* fptconfigFile;
66+
67+ long flagmode;
68+ long mode;
69+
70+} mrcImageAutoRotationAverageInfo;
71+#ifdef __cplusplus
72+extern "C" {
73+#endif
74+extern void argCheck(mrcImageAutoRotationAverageInfo* info, int argc, char* avgv[]);
75+extern void khorosInit(int argc, char* avgv[]);
76+extern void init0(mrcImageAutoRotationAverageInfo* info);
77+extern void init1(mrcImageAutoRotationAverageInfo* info);
78+extern void usage(char* usage);
79+extern void additionalUsage(void);
80+extern void htmlBeforeUsage(char* usage);
81+extern void htmlAfterUsage(char* usage);
82+#ifdef __cplusplus
83+};
84+#endif
85+#endif /* MRCIMAGEAUTOROTATIONAVERAGE_H */
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/Makefile
@@ -0,0 +1,427 @@
1+include ../Config/Define.inc
2+include ../../Config/Define.inc
3+include ../../../Config/Define.inc
4+include ../../../../Config/Define.inc
5+
6+EOSHOME=../../../../../
7+DSTDIR=$(EOSHOME)/bin
8+DSTDOC=$(EOSHOME)/doc
9+DSTTAR=$(EOSHOME)/tar
10+
11+INCFILES =
12+
13+LIBFILES = \
14+ $(LIBPREFIX)EosObjects$(LIBSUFFIX)
15+
16+LIBFILESDEBUG = \
17+ $(LIBPREFIX)EosObjects.debug$(LIBSUFFIX)
18+
19+SRCC = \
20+ $(OBJECTNAME).c \
21+ init.c \
22+ argCheck.c \
23+ usage.c \
24+ util.c \
25+
26+SRCCXX = \
27+ $(OBJECTNAME).cc \
28+ init.cc \
29+ argCheck.cc \
30+ usage.cc \
31+ util.cc \
32+
33+MODULES = \
34+ $(OBJECTNAME).o \
35+ init.o \
36+ argCheck.o \
37+ usage.o \
38+ util.o \
39+
40+REALMODULES = \
41+ $(OSTYPE)/$(OBJECTNAME).o \
42+ $(OSTYPE)/init.o \
43+ $(OSTYPE)/argCheck.o \
44+ $(OSTYPE)/usage.o \
45+ $(OSTYPE)/util.o
46+
47+MODULESDEBUG = \
48+ $(OBJECTNAME).debugo \
49+ init.debugo \
50+ argCheck.debugo \
51+ usage.debugo \
52+ util.debugo \
53+
54+REALMODULESDEBUG = \
55+ $(OSTYPE)/$(OBJECTNAME).debugo \
56+ $(OSTYPE)/init.debugo \
57+ $(OSTYPE)/argCheck.debugo \
58+ $(OSTYPE)/usage.debugo \
59+ $(OSTYPE)/util.debugo
60+
61+
62+all: $(OSTYPE)/$(OBJECTNAME)
63+ if [ ! -L $(OSTYPE) ] ; then \
64+ moveHostdependent; \
65+ fi
66+
67+debug: $(OSTYPE)/$(OBJECTNAME).debug
68+
69+cudagdb: $(OSTYPE)/$(OBJECTNAME).cudagdb
70+
71+
72+$(OSTYPE)/$(OBJECTNAME)::
73+ @$(RM) -f $(OSTYPE)/Makefile ; \
74+ $(CP) $(EOS_HOME)/src/Config/Template/$(WORLDNAME)Template.Dir/src/ARCH/Makefile $(OSTYPE)/Makefile ; \
75+ cd $(OSTYPE); \
76+ $(MAKE) $(OBJECTNAME) WORLDNAME=$(WORLDNAME) CLASSNAME=$(CLASSNAME) OBJECTNAME=$(OBJECTNAME)
77+
78+$(OSTYPE)/$(OBJECTNAME).debug::
79+ @$(RM) -f $(OSTYPE)/Makefile ; \
80+ $(CP) $(EOS_HOME)/src/Config/Template/$(WORLDNAME)Template.Dir/src/ARCH/Makefile $(OSTYPE)/Makefile ; \
81+ cd $(OSTYPE); \
82+ $(MAKE) $(OBJECTNAME).debug WORLDNAME=$(WORLDNAME) CLASSNAME=$(CLASSNAME) OBJECTNAME=$(OBJECTNAME)
83+
84+$(OSTYPE)/$(OBJECTNAME).cudagdb::
85+ @$(RM) -f $(OSTYPE)/Makefile ; \
86+ $(CP) $(EOS_HOME)/src/Config/Template/$(WORLDNAME)Template.Dir/src/ARCH/Makefile $(OSTYPE)/Makefile ; \
87+ cd $(OSTYPE); \
88+ $(MAKE) $(OBJECTNAME).cudagdb WORLDNAME=$(WORLDNAME) CLASSNAME=$(CLASSNAME) OBJECTNAME=$(OBJECTNAME)
89+
90+cvsupdate::
91+ cvs -d $(EOS_CVSROOT) update -d
92+
93+cvscommit::
94+ cvs -d $(EOS_CVSROOT) commit
95+
96+edit:
97+ @if [ -r $(OBJECTNAME).c ]; \
98+ then \
99+ sccsEdit $(OBJECTNAME).c; \
100+ else \
101+ echo "Source files are already editable"; \
102+ fi
103+ @if [ -r wish/$(OBJECTNAME).wish ]; \
104+ then \
105+ cd wish; sccsEdit $(OBJECTNAME).wish; \
106+ else \
107+ echo "Source files (wish) are already editable."; \
108+ fi
109+ @if [ -r ruby/$(OBJECTNAME).rb ]; \
110+ then \
111+ cd ruby; sccsEdit $(OBJECTNAME).rb; \
112+ else \
113+ echo "Source files (ruby) are already editable."; \
114+ fi
115+ @if [ -r perl/$(OBJECTNAME).pl ]; \
116+ then \
117+ cd perl; sccsEdit $(OBJECTNAME).pl ; \
118+ else \
119+ echo "Source files (perl) are already editable."; \
120+ fi
121+ @if [ -r ../Config/OptionControlFile ]; \
122+ then \
123+ cd ../Config; sccsEdit OptionControlFile; \
124+ else \
125+ echo "OptionControlFile are already editable."; \
126+ fi
127+
128+unedit:
129+ @if [ -w $(OBJECTNAME).c ]; \
130+ then \
131+ sccsUnedit $(OBJECTNAME).c; \
132+ else \
133+ echo "Source files are not editable"; \
134+ fi
135+ @if [ -w wish/$(OBJECTNAME).wish ]; \
136+ then \
137+ cd wish; sccsUnedit $(OBJECTNAME).wish; \
138+ else \
139+ echo "Source files (wish) are not editable."; \
140+ fi
141+ @if [ -w ruby/$(OBJECTNAME).rb]; \
142+ then \
143+ cd ruby; sccsUnedit $(OBJECTNAME).rb; \
144+ else \
145+ echo "Source files (ruby) are not editable."; \
146+ fi
147+ @if [ -w perl/$(OBJECTNAME).pl ]; \
148+ then \
149+ cd perl; sccsUnedit $(OBJECTNAME).pl ; \
150+ else \
151+ echo "Source files (ruby) are not editable."; \
152+ fi
153+ @if [ -w ../Config/OptionControlFile ]; \
154+ then \
155+ cd ../Config; sccsUnedit OptionControlFile; \
156+ else \
157+ echo "OptionControlFile are not editable."; \
158+ fi
159+
160+report:
161+ @if [ -r $(OBJECTNAME).c ]; \
162+ then \
163+ sccsReport $(OBJECTNAME).c; \
164+ else \
165+ echo "Source files are already editable"; \
166+ fi
167+ @if [ -r wish/$(OBJECTNAME).wish ]; \
168+ then \
169+ cd wish; sccsReport $(OBJECTNAME).wish; \
170+ else \
171+ echo "Source files (wish) are already editable."; \
172+ fi
173+ @if [ -r ruby/$(OBJECTNAME).rb ]; \
174+ then \
175+ cd ruby; sccsReport $(OBJECTNAME).rb; \
176+ else \
177+ echo "Source files (ruby) are already editable."; \
178+ fi
179+ @if [ -r perl/$(OBJECTNAME).pl ] ; \
180+ then \
181+ cd perl; sccsReport $(OBJECTNAME).pl ; \
182+ else \
183+ echo "Source files (perl) are already editable."; \
184+ fi
185+ @if [ -r ../Config/OptionControlFile ]; \
186+ then \
187+ cd ../Config; sccsReport OptionControlFile; \
188+ else \
189+ echo "OptionControlFile are already editable."; \
190+ fi
191+
192+clean :
193+ rm -f *.debugo $(OSTYPE)/*.debugo *.cudagdbo $(OSTYPE)/*.cudagdbo *.o $(OSTYPE)/*.o *.linkinfo $(OSTYPE)/*.linkinfo \
194+ $(OSTYPE)/$(OBJECTNAME) $(OSTYPE)/*.$(OSTYPE) \
195+ $(OSTYPE)/$(OBJECTNAME).debug $(OSTYPE)/*.$(OSTYPE).debug \
196+ $(OSTYPE)/$(OBJECTNAME).cudagdb $(OSTYPE)/*.$(OSTYPE).cudagdb \
197+ $(OSTYPE)/$(OBJECTNAME).linkinfo $(OSTYPE)/*.$(OSTYPE).linkinfo \
198+ *.bak *.$(OSTYPE) core
199+
200+install: install-bin install-doc install-wish install-ruby install-shell install-perl
201+ @if [ dummy$(KHOROS_KENGOBJ) != dummy ] ; \
202+ then \
203+ if [ -x $(KHOROS_KGENOBJ) ] ; \
204+ then \
205+ make install-khoros ; \
206+ fi; \
207+ fi
208+
209+install-bin:$(DSTDIR)/$(OSTYPE)/$(OBJECTNAME)
210+
211+$(DSTDIR)/$(OSTYPE)/$(OBJECTNAME):$(OSTYPE)/$(OBJECTNAME) $(DSTDIR)/$(OBJECTNAME)
212+ @echo ---- Installing to bin
213+ @echo $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME)
214+ @if [ ! -d $(DSTDIR)/$(OSTYPE) ]; \
215+ then \
216+ mkdir $(DSTDIR)/$(OSTYPE); \
217+ fi
218+ @if [ -x $(OSTYPE)/$(OBJECTNAME) ]; \
219+ then \
220+ echo "Compilation is complete"; \
221+ $(RM) -f $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME); \
222+ $(CD) $(OSTYPE); $(INSTALL) -m 555 $(OBJECTNAME) ../$(DSTDIR)/$(OSTYPE); \
223+ $(CHMOD) 555 ../$(DSTDIR)/$(OSTYPE)/$(OBJECTNAME); \
224+ else \
225+ echo "Compilation is incomplete. $(OBJECTNAME)"; \
226+ fi
227+ @echo ---- end of bin
228+
229+install-wish:
230+ @if [ -d wish ]; \
231+ then \
232+ echo "---- Tcl/Tk file Install"; \
233+ if [ ! -d $(DSTDIR)/wish/$(OBJECTNAME) ]; \
234+ then \
235+ mkdir $(DSTDIR)/wish/$(OBJECTNAME) ; \
236+ fi ; \
237+ $(CP) -f wish/* $(DSTDIR)/wish/$(OBJECTNAME); \
238+ $(CHMOD) 555 $(DSTDIR)/wish/$(OBJECTNAME)/* ;\
239+ touch $(DSTDIR)/wish/$(OBJECTNAME)/tclIndex;\
240+ $(CHMOD) 666 $(DSTDIR)/wish/$(OBJECTNAME)/tclIndex;\
241+ echo "---- Tcl/Tk file Installed";\
242+ fi
243+
244+install-ruby:
245+ @if [ -d ruby ]; \
246+ then \
247+ echo "---- Ruby/Tk file Install"; \
248+ if [ ! -d $(DSTDIR)/ruby/$(OBJECTNAME) ]; \
249+ then \
250+ mkdir $(DSTDIR)/ruby/$(OBJECTNAME) ; \
251+ fi ; \
252+ $(CP) -f ruby/* $(DSTDIR)/ruby/$(OBJECTNAME); \
253+ $(CHMOD) 555 $(DSTDIR)/ruby/$(OBJECTNAME)/* ; \
254+ echo "---- Ruby/Tk file Installed"; \
255+ fi
256+
257+install-perl:
258+ @if [ -d perl ]; \
259+ then \
260+ echo "---- Perl/Tk file Install"; \
261+ if [ ! -d $(DSTDIR)/perl/$(OBJECTNAME) ]; \
262+ then \
263+ mkdir $(DSTDIR)/perl/$(OBJECTNAME) ; \
264+ fi; \
265+ $(CP) -f perl/* $(DSTDIR)/perl/$(OBJECTNAME); \
266+ $(CHMOD) 555 $(DSTDIR)/perl/$(OBJECTNAME)/* ; \
267+ echo "---- Perl/Tk file Installed"; \
268+ fi
269+
270+install-shell:
271+ @if [ ! -d $(DSTDIR)/shell/$(OBJECTNAME) ]; \
272+ then \
273+ mkdir $(DSTDIR)/shell/$(OBJECTNAME) ; \
274+ fi
275+ @if [ -d shell ]; \
276+ then \
277+ echo "---- Shell file Install"; \
278+ if [ ! -d $(DSTDIR)/shell/$(OBJECTNAME) ]; \
279+ then \
280+ mkdir $(DSTDIR)/shell/$(OBJECTNAME) ; \
281+ fi ; \
282+ $(CP) -f shell/* $(DSTDIR)/shell/$(OBJECTNAME); \
283+ $(CHMOD) 555 $(DSTDIR)/shell/$(OBJECTNAME)/*; \
284+ echo "---- Shell file Installed"; \
285+ fi
286+
287+install-khoros:
288+ @echo Installing to khoros
289+ @if [ ! -d ../../../../../objects/script/$(OBJECTNAME) -a -f $(KHOROS_KGENOBJ) ]; \
290+ then \
291+ echo kgenobj;\
292+ $(KHOROS_KGENOBJ) -tb Eos -oname $(OBJECTNAME) -type script -pane -cantata true -cat Eos -subcat $(CLASSNAME) -description $(OBJECTNAME) -bname $(OBJECTNAME) -form -lang ksh ; \
293+ fi
294+ @if [ ! -d ../../../../../objects/script/$(OBJECTNAME) -a -f $(KHOROS_KSET) ]; \
295+ then \
296+ $(KHOROS_KSET) -tb Eos -oname $(OBJECTNAME) -icon $(OBJECTNAME) ; \
297+ fi
298+ @if [ -d ../../../../../objects/script/$(OBJECTNAME) -a -f $(KHOROS_KSET) ]; \
299+ then \
300+ $(CHMOD) -R 775 ../../../../../objects/script/$(OBJECTNAME) ; \
301+ if [ $? ] ; \
302+ then \
303+ echo "-- setting khoros ---" ; \
304+ if [ -d ../../../../../objects/script/$(OBJECTNAME)/uis/ ] ; \
305+ then \
306+ $(CD) ../../../../../objects/script/$(OBJECTNAME)/uis/ ; \
307+ $(RM) -f $(OBJECTNAME).pane ; \
308+ $(LN) -s ../../../../src/Tools/$(CLASSNAME)/$(OBJECTNAME)/src/$(OBJECTNAME).pane $(OBJECTNAME).pane; \
309+ $(CD) ../../ ; \
310+ $(CHMOD) -R 555 $(OBJECTNAME); \
311+ else \
312+ echo "../../../../../objects/script/$(OBJECTNAME)/uis/ does not exist."; \
313+ fi ; \
314+ else \
315+ echo "Failed !!: Cannot chage mode in installing $(OBJECTNAME) to khoros system"; \
316+ fi ; \
317+ echo "-- end of khoros-installing"; \
318+ fi
319+
320+install-doc: html
321+ @if [ ! -d $(DSTDOC)/SmallTools ]; \
322+ then \
323+ mkdir $(DSTDOC)/SmallTools ;\
324+ fi
325+ @if [ -f $(DSTDOC)/SmallTools/$(OBJECTNAME).html ]; \
326+ then \
327+ $(RM) -f $(DSTDOC)/SmallTools/$(OBJECTNAME).html ;\
328+ fi
329+ @$(CP) $(OBJECTNAME).html $(DSTDOC)/SmallTools/$(OBJECTNAME).html
330+ @$(CHMOD) 444 $(DSTDOC)/SmallTools/$(OBJECTNAME).html
331+ @if [ -f ../doc/*.html ]; \
332+ then \
333+ $(CP) ../doc/*.html $(DSTDOC)/SmallTools/ ;\
334+ fi
335+ @$(CHMOD) 444 $(DSTDOC)/SmallTools/$(OBJECTNAME).html
336+ @if [ -f $(DSTDOC)/SmallTools/Makefile ]; \
337+ then \
338+ cd $(DSTDOC)/SmallTools; $(MAKE); \
339+ fi
340+
341+html: $(OBJECTNAME).html
342+
343+configFileRead:
344+ @ctrl2configFileRead $(CLASSNAME) $(OBJECTNAME) ../Config/OptionControlFile
345+
346+$(OBJECTNAME).html: $(OSTYPE)/$(OBJECTNAME)
347+ @echo creating html
348+ @$(OSTYPE)/$(OBJECTNAME) -html 2> $(OBJECTNAME).html.tmp
349+ @sed -e s/$(OSTYPE)\\/// $(OBJECTNAME).html.tmp > $(OBJECTNAME).html
350+ @$(RM) $(OBJECTNAME).html.tmp
351+
352+$(DSTDIR)/$(OBJECTNAME): $(OSTYPE)/$(OBJECTNAME)
353+ @ln -s -f ../sbin/MachineIndependent $@
354+
355+depend::
356+ @echo dependency checking now
357+ @if [ ! -L $(OSTYPE) ] ; then \
358+ moveHostdependent; \
359+ fi
360+ rm -f $(OSTYPE)/.Depend
361+ #echo C
362+ @if [ -f $(OBJECTNAME).c ] ; \
363+ then \
364+ echo "dependency: *.c"; \
365+ echo $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) *.c ; \
366+ $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) *.c >> $(OSTYPE)/.Depend ; \
367+ fi
368+ #echo CC
369+ @if [ -f $(OBJECTNAME).cc ] ; \
370+ then \
371+ echo "dependency: *.cc"; \
372+ echo $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.cc ; \
373+ $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.cc >> $(OSTYPE)/.Depend ; \
374+ fi
375+ @if [ -f $(OBJECTNAME).ccm ] ; \
376+ then \
377+ echo "dependency: *.ccm"; \
378+ echo $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.ccm ; \
379+ $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.ccm >> $(OSTYPE)/.Depend ; \
380+ fi
381+ @if [ -f $(OBJECTNAME).cu ] ; \
382+ then \
383+ echo "dependency: *.cu"; \
384+ echo $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.cu ; \
385+ $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.cu >> $(OSTYPE)/.Depend ; \
386+ fi
387+
388+update:../Config/OptionControlFile
389+ maketool $(CLASSNAME) $(OBJECTNAME) update
390+
391+changeName::
392+
393+Test:$(OSTYPE)/$(OBJECTNAME) TestDir
394+ @if [ -f test/Makefile ] ; \
395+ then \
396+ cd test; make ; \
397+ else \
398+ echo "No test Makefile"; \
399+ fi
400+
401+TestDir::
402+ @if [ ! -d test ] ; \
403+ then \
404+ echo "Creating test dir"; \
405+ mkdir test; \
406+ fi
407+ @if [ ! -f test/Makefile ] ; \
408+ then \
409+ echo "Creating Makefile"; \
410+ cd test; \
411+ protoTestMakefileCreate; \
412+ fi
413+ @if [ ! -d test/data ]; \
414+ then \
415+ mkdir $(EOSHOME)/data/$(OBJECTNAME); \
416+ cd test; \
417+ ln -sf ../$(EOSHOME)/data/$(OBJECTNAME) data; \
418+ fi
419+
420+tar::
421+ cd $(DSTTAR); tar cvf Tools.$(CLASSNAME).$(OBJECTNAME).tar ../bin/$(OBJECTNAME) \
422+ ../bin/*/$(OBJECTNAME).* \
423+ ../src/Tools/$(CLASSNAME)/$(OBJECTNAME) \
424+ ; gzip Tools.$(CLASSNAME).$(OBJECTNAME).tar
425+
426+-include $(OSTYPE)/.Depend
427+-include ../Config/Target.inc
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/X86MAC64
@@ -0,0 +1 @@
1+../../../../../hostdepend/X86MAC64/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/X86MAC64
\ No newline at end of file
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/argCheck.c
@@ -0,0 +1,202 @@
1+#include <stdio.h>
2+#include <stdlib.h>
3+#include <string.h>
4+#include <math.h>
5+#include "../inc/config.h"
6+#include "genUtil.h"
7+#include "String.h"
8+#include "File.h"
9+#include "Memory.h"
10+
11+
12+void
13+argCheck(mrcImageAutoRotationAverageInfo* info, int argc, char* argv[])
14+{
15+ long i;
16+ char s[1024];
17+ FILE* fpt;
18+
19+ if(NULL==(fpt=fopen(".EosLog", "a+"))) {
20+
21+ } else {
22+ for(i=0; i<argc; i++) {
23+ fprintf(fpt, "%s ", argv[i]);
24+ }
25+ fprintf(fpt, "\n");
26+ fclose(fpt);
27+ }
28+ for(i=1; i<argc; i++) {
29+ if(OPTION_FLAG==argv[i][OPTION_FLAG_POS]) {
30+ SSWITCH(argv[i]+OPTION_POS)
31+ SCASE("i") {
32+ if(i+1<argc) {
33+ info->InList = stringGetNthWord(argv[i+1], 1, " ,");
34+ i++;
35+ info->flagIn++;
36+ } else {
37+ usage(argv[0]);
38+ exit(EXIT_FAILURE);
39+ }
40+ SBREAK;
41+ }
42+ SCASE("r") {
43+ if(i+1<argc) {
44+ info->Ref = stringGetNthWord(argv[i+1], 1, " ,");
45+ i++;
46+ info->flagRef++;
47+ } else {
48+ usage(argv[0]);
49+ exit(EXIT_FAILURE);
50+ }
51+ SBREAK;
52+ }
53+ SCASE("o") {
54+ if(i+1<argc) {
55+ info->Out = stringGetNthWord(argv[i+1], 1, " ,");
56+ i++;
57+ info->flagOut++;
58+ } else {
59+ usage(argv[0]);
60+ exit(EXIT_FAILURE);
61+ }
62+ SBREAK;
63+ }
64+ SCASE("range") {
65+ if(i+4<argc) {
66+ info->Min = stringGetNthRealData(argv[i+1], 1, " ,");
67+ i++;
68+ info->flagMin++;
69+ info->Max = stringGetNthRealData(argv[i+1], 1, " ,");
70+ i++;
71+ info->flagMax++;
72+ info->Delta = stringGetNthRealData(argv[i+1], 1, " ,");
73+ i++;
74+ info->flagDelta++;
75+ info->Iter = stringGetNthIntegerData(argv[i+1], 1, " ,");
76+ i++;
77+ info->flagIter++;
78+ } else {
79+ usage(argv[0]);
80+ exit(EXIT_FAILURE);
81+ }
82+ SBREAK;
83+ }
84+ SCASE("iter") {
85+ if(i+1<argc) {
86+ info->iter = stringGetNthIntegerData(argv[i+1], 1, " ,");
87+ i++;
88+ info->flagiter++;
89+ } else {
90+ usage(argv[0]);
91+ exit(EXIT_FAILURE);
92+ }
93+ SBREAK;
94+ }
95+ SCASE("M") {
96+ if(i+1<argc) {
97+ info->CorMode = stringGetNthIntegerData(argv[i+1], 1, " ,");
98+ i++;
99+ info->flagCorMode++;
100+ } else {
101+ usage(argv[0]);
102+ exit(EXIT_FAILURE);
103+ }
104+ SBREAK;
105+ }
106+ SCASE("Method") {
107+ if(i+1<argc) {
108+ info->Method = stringGetNthIntegerData(argv[i+1], 1, " ,");
109+ i++;
110+ info->flagMethod++;
111+ } else {
112+ usage(argv[0]);
113+ exit(EXIT_FAILURE);
114+ }
115+ SBREAK;
116+ }
117+ SCASE("Periodic") {
118+ if(i+0<argc) {
119+ info->Periodic++;
120+ } else {
121+ usage(argv[0]);
122+ exit(EXIT_FAILURE);
123+ }
124+ SBREAK;
125+ }
126+ SCASE("maxIter") {
127+ if(i+1<argc) {
128+ info->maxIter = stringGetNthIntegerData(argv[i+1], 1, " ,");
129+ i++;
130+ info->flagmaxIter++;
131+ } else {
132+ usage(argv[0]);
133+ exit(EXIT_FAILURE);
134+ }
135+ SBREAK;
136+ }
137+ SCASE("rmsd") {
138+ if(i+1<argc) {
139+ info->rmsd = stringGetNthRealData(argv[i+1], 1, " ,");
140+ i++;
141+ info->flagrmsd++;
142+ } else {
143+ usage(argv[0]);
144+ exit(EXIT_FAILURE);
145+ }
146+ SBREAK;
147+ }
148+ SCASE("log") {
149+ if(i+1<argc) {
150+ info->Log = stringGetNthWord(argv[i+1], 1, " ,");
151+ i++;
152+ info->flagLog++;
153+ } else {
154+ usage(argv[0]);
155+ exit(EXIT_FAILURE);
156+ }
157+ SBREAK;
158+ }
159+ SCASE("c") {
160+ if(i+1<argc) {
161+ info->configFile = stringGetNthWord(argv[i+1], 1, " ,");
162+ i++;
163+ info->flagconfigFile++;
164+ } else {
165+ usage(argv[0]);
166+ exit(EXIT_FAILURE);
167+ }
168+ SBREAK;
169+ }
170+ SCASE("m") {
171+ if(i+1<argc) {
172+ info->mode = stringGetNthIntegerData(argv[i+1], 1, " ,");
173+ i++;
174+ info->flagmode++;
175+ } else {
176+ usage(argv[0]);
177+ exit(EXIT_FAILURE);
178+ }
179+ SBREAK;
180+ }
181+ SCASE("h") {
182+ usage(argv[0]);
183+ exit(EXIT_SUCCESS);
184+ break;
185+ }
186+ SCASE("html") {
187+ htmlBeforeUsage(argv[0]);
188+ usage(argv[0]);
189+ htmlAfterUsage(argv[0]);
190+ exit(EXIT_SUCCESS);
191+ break;
192+ }
193+ SDEFAULT {
194+ fprintf(stderr, "Not Supported Options: :%s\n", argv[i]);
195+ usage(argv[0]);
196+ exit(EXIT_FAILURE);
197+ break;
198+ }
199+ SSWITCHEND;
200+ }
201+ }
202+}
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/init.c
@@ -0,0 +1,153 @@
1+#include <stdio.h>
2+#include <stdlib.h>
3+#include <string.h>
4+#include <math.h>
5+#include "../inc/config.h"
6+#include "genUtil.h"
7+#include "String.h"
8+#include "File.h"
9+#include "Memory.h"
10+
11+
12+void
13+init0(mrcImageAutoRotationAverageInfo* info)
14+{
15+ info->fptIn = stdin; info->fptInList = stdin; info->flagIn = 0;
16+ info->fptRef = NULL; info->flagRef = 0;
17+ info->fptOut = NULL; info->flagOut = 0;
18+ info->Min = 0.0; info->flagMin = 0;
19+ info->Max = 360.0; info->flagMax = 0;
20+ info->Delta = 5.0; info->flagDelta = 0;
21+ info->Iter = 2; info->flagIter = 0;
22+ info->iter = 2; info->flagiter = 0;
23+ info->CorMode = 16; info->flagCorMode = 0;
24+ info->Method = 0; info->flagMethod = 0;
25+ info->Periodic=0;
26+ info->maxIter = 10; info->flagmaxIter = 0;
27+ info->rmsd = 1e-2; info->flagrmsd = 0;
28+ info->fptLog = stdout; info->flagLog = 0;
29+ info->fptconfigFile = NULL; info->flagconfigFile = 0;
30+ info->mode = 0; info->flagmode = 0;
31+}
32+
33+void
34+init1(mrcImageAutoRotationAverageInfo* info)
35+{
36+ char s[1024];
37+ int i;
38+ if(!info->flagIn) {
39+ stringGetFromFile(s, "In", stdin, stdout, 0);
40+ info->InList = stringGetNthWord(s, 1, " ,\t");
41+ info->flagIn++;
42+ }
43+ if(info->flagIn) {
44+ info->fptInList = fileOpen(info->InList, "r");
45+ fseek(info->fptInList, 0L, SEEK_SET);
46+ i=0;
47+ while(NULL!=stringGetFromFile(s, "", info->fptInList, stdout, 1)) {
48+ i++;
49+ }
50+ info->fptIn = (FILE**)memoryAllocate(i*sizeof(FILE*), "in init1");
51+ info->In = (char**)memoryAllocate(i*sizeof(char*), "in init1");
52+ info->flagIn = i;
53+ fseek(info->fptInList, 0L, SEEK_SET);
54+ i=0;
55+ while(NULL!=stringGetFromFile(s, "", info->fptInList, stdout, 1)) {
56+ info->In[i] = stringGetNthWord(s, 1, " ,\t");
57+ info->fptIn[i] = fileOpen(info->In[i],"r");
58+ i++;
59+ }
60+ }
61+
62+ if(info->flagRef) {
63+ info->fptRef = fileOpen(info->Ref, "r");
64+ }
65+
66+ if(!info->flagOut) {
67+ stringGetFromFile(s, "Out", stdin, stdout, 0);
68+ info->Out = stringGetNthWord(s, 1, " ,\t");
69+ info->flagOut++;
70+ }
71+ if(info->flagOut) {
72+ info->fptOut = fileOpen(info->Out, "w");
73+ }
74+
75+ if(info->flagMin) {
76+ }
77+
78+ if(info->flagMax) {
79+ }
80+
81+ if(info->flagDelta) {
82+ }
83+
84+ if(info->flagIter) {
85+ }
86+
87+ if(info->flagiter) {
88+ }
89+
90+ if(info->flagCorMode) {
91+ }
92+
93+ if(info->flagMethod) {
94+ }
95+
96+ if(info->flagmaxIter) {
97+ }
98+
99+ if(info->flagrmsd) {
100+ }
101+
102+ if(info->flagLog) {
103+ info->fptLog = fileOpen(info->Log, "r");
104+ }
105+
106+ if(info->flagconfigFile) {
107+ info->fptconfigFile = fileOpen(info->configFile, "r");
108+ }
109+
110+ if(info->flagmode) {
111+ }
112+
113+}
114+#ifdef KHOROS
115+#include <stdio.h>
116+#include "bootstrap.h"
117+#include "dataserv.h"
118+#include "datamanip.h"
119+extern void func_usage_additions(void);
120+extern void func_free_args(kexit_status status, kaddr client_data);
121+extern void func_get_args(kform* pane);
122+
123+void
124+func_usage_additions(void)
125+{
126+}
127+void
128+func_free_args(kexit_status status, kaddr client_data)
129+{
130+}
131+void
132+func_get_args(kform* pane)
133+{
134+}
135+void
136+khorosInit(int argc, char* argv[])
137+{
138+ char* eospath;
139+ char panepath[1024];
140+ FILE* fpt;
141+
142+ eospath = getenv("EOS_HOME");
143+ sprintf(panepath, "%s/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/mrcImageAutoRotationAverage.pane", eospath);
144+ khoros_initialize(argc, argv, "EOS");
145+ fpt = fopen(panepath, "r"); if(NULL!=fpt) {
146+ fclose(fpt);
147+ kclui_initialize(panepath, KGEN_NONE, "EOS", "mrcImageAutoRotationAverage",
148+ func_usage_additions,
149+ func_get_args,
150+ func_free_args);
151+ }
152+}
153+#endif /* KHOROS */
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/mrcImageAutoRotationAverage.c
@@ -0,0 +1,103 @@
1+/*
2+# mrcImageAutoRotationAverage : $Revision$
3+# $Date$
4+# Created by $Author$
5+# Usage : mrcImageAutoRotationAverage
6+# Attention
7+# $Loccker$
8+# $State$
9+#
10+*/
11+#include <stdio.h>
12+#include <stdlib.h>
13+#include <string.h>
14+#include <math.h>
15+#define GLOBAL_DECLARATION
16+#include "../inc/config.h"
17+
18+#define DEBUG
19+#include "genUtil.h"
20+#include "mrcImage.h"
21+#include "Memory.h"
22+#include "lmrcImageAverage.h"
23+#include "lmrcImageCorrelation.h"
24+
25+/*
26+Example:
27+typedef struct lmrcImageAutoRotationAverageInfo {
28+ float a;
29+ int b;
30+} lmrcImageAutoRotationAverageInfo;
31+
32+typedef enum lmrcImageAutoRotationAverageMode {
33+ a=0,
34+ b=1
35+} lmrcImageAutoRotationAverageMode;
36+*/
37+
38+int
39+main(int argc, char* argv[])
40+{
41+ mrcImage* in;
42+ mrcImage ref;
43+ mrcImage* fit;
44+ mrcImage* cor;
45+ mrcImage out;
46+ mrcImageAutoRotationAverageInfo info;
47+ lmrcImageAutoRotationCorrelationInfo* linfo;
48+ int i, k;
49+
50+ init0(&info);
51+ argCheck(&info, argc, argv);
52+ init1(&info);
53+
54+ DEBUGPRINT("Program Start\n");
55+ in = (mrcImage*)memoryAllocate(sizeof(mrcImage)*info.flagIn, "in main");
56+ fit = (mrcImage*)memoryAllocate(sizeof(mrcImage)*info.flagIn, "in main");
57+ cor = (mrcImage*)memoryAllocate(sizeof(mrcImage)*info.flagIn, "in main");
58+ linfo = (lmrcImageAutoRotationCorrelationInfo*)memoryAllocate(sizeof(lmrcImageAutoRotationCorrelationInfo)*info.flagIn, "in main");
59+ for(i=0; i<info.flagIn; i++) {
60+ mrcFileRead(&(in[i]), info.In[i], "in main", 0);
61+ }
62+ if(info.flagRef) {
63+ mrcFileRead(&ref, info.Ref, "in main", 0);
64+ } else {
65+ fprintf(stderr, "FileImage(%s) is used as a reference.\n", info.In[0]);
66+ mrcFileRead(&ref, info.In[0], "in main", 0);
67+ }
68+
69+ // linfo
70+ for(i=0; i<info.flagIn; i++) {
71+ linfo[i].iter = info.iter;
72+ linfo[i].nRot = (int)((info.Max - info.Min)/info.Delta)+1;
73+ linfo[i].Method = info.Method;
74+ linfo[i].flagRestrictionArea = 1;
75+ linfo[i].thetaMin = info.Min*RADIAN;
76+ linfo[i].thetaMax = info.Max*RADIAN;
77+ }
78+
79+ for(k=0; k<info.maxIter; k++) {
80+ for(i=0; i<info.flagIn; i++) {
81+ DEBUGPRINT2("%d: %d\n", k, i);
82+ lmrcImageAutoRotationCorrelation(&(fit[i]), &(cor[i]), &(in[i]), &ref, &(linfo[i]), info.CorMode);
83+ }
84+ }
85+
86+ lmrcImageAverage(&out, fit, info.flagIn, info.mode);
87+
88+ mrcFileWrite(&out, info.Out, "in main", 0);
89+
90+ for(i=0; i<info.flagIn; i++) {
91+ fprintf(info.fptLog, "%d %f %f %f %f\n", i, linfo[i].max, linfo[i].maxTheta*DEGREE, linfo[i].maxP.x, linfo[i].maxP.y);
92+ }
93+ exit(EXIT_SUCCESS);
94+}
95+
96+void
97+additionalUsage()
98+{
99+ fprintf(stderr, "----- Additional Usage -----\n");
100+ fprintf(stderr, "----- -Mode -----\n");
101+ lmrcImageCorrelationModePrint(stderr);
102+
103+}
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/mrcImageAutoRotationAverage.html
@@ -0,0 +1,40 @@
1+<HTML>
2+<HEAD>
3+<TITLE>mrcImageAutoRotationAverage</TITLE>
4+</HEAD>
5+<BODY>
6+<H1>mrcImageAutoRotationAverage</H1>
7+<H2>Usage</H2>
8+<PRE>
9+Usage: mrcImageAutoRotationAverage
10+Options:
11+ [-i[nput] In (stdin ).as(inFileList::mrcImage) ] :Essential :Input: Ins
12+ [-r[eferenc] Ref (NULL ).as(inFile::mrcImage ) ] :Optional :Input: Ref
13+ [-o[utput] Out (NULL ).as(outFile::mrcImage ) ] :Essential :Output:Average
14+ [-range Min (0.0 ).as(Real )
15+ Max (360.0 ).as(Real )
16+ Delta (5.0 ).as(Real )
17+ Iter (2 ).as(Integer ) ] :Optional :Mode
18+ [-iter iter (2 ).as(Integer ) ] :Optional :iteration for rotation
19+ [-M[odeCorrelation] CorMode (16 ).as(Integer ) ] :Optional :Mode: Correlation
20+ [-Method[Correlation]Method (0 ).as(Integer ) ] :Optional :Method: Correlation
21+ [-Periodic ] :Optional :Periodic
22+ [-maxIter[aration] maxIter (10 ).as(Integer ) ] :Optional :MaxIteration
23+ [-rmsd rmsd (1e-2 ).as(Real ) ] :Optional :rmsd
24+ [-log Log (stdout ).as(inFile::ASCII ) ] :Optional :logFile
25+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
26+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
27+----- Additional Usage -----
28+----- -Mode -----
29+0: Normal Correlation FxG*
30+1: Phase Correlation FxG*/ |FxG*|
31+2: Phase Correlation FxG*/sqrt(|FxG*|)
32+3: Normalized Normal Correlation FxG*/|F||G|)
33+16: (0,0) = 0
34+Refinement Correlation Map
35+0: sqrt(Sum |Fi-Gi|^2 / Sum |Gi|^2)
36+1: Sum |Gi||phaseFi - phaseGi| / Sum |Gi|
37+2: sqrt(Sum |Gi||phaseFi - phaseGi|^2 / Sum |Gi| )
38+</PRE>
39+</BODY>
40+</HTML>
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/mrcImageAutoRotationAverage.pane
@@ -0,0 +1,25 @@
1+-F 4.3 1 0 52x1+0+0 +0+0 'Cantata' cantata
2+ -M 1 1 52x1+0+0 +1+0 ' ' subform
3+ -P 1 0 52x1+0+1 +0+0 ' ' mrcImageAutoRotationAverage
4+ -D 1 0 9x1+0+0 'Options' _gui_options
5+ -H 1 6x1+0+0 'License' 'license' $BOOTSTRAP/repos/license/License license
6+ -E
7+ -R 1 0 1 5x1+35+0 'Run' 'execute operation' $EOS/bin/mrcImageAutoRotationAverage
8+ -H 1 5x1+41+0 'Help' 'help page' $EOS/src/Tools/mrcImage/mrcImageAutoRotationAverage/doc/mrcImageAutoRotationAverage.doc help
9+ -Q 1 0 5.25x1+47+0 'Close'
10+ -I 1 0 1 1 0 1 -1x1+1+1.500000 ' ' 'In' 'Input: Ins' i
11+ -I 1 0 1 0 0 1 -1x1+1+3.000000 ' ' 'Ref' 'Input: Ref' r
12+ -O 1 0 1 1 0 1 -1x1+1+4.500000 ' ' 'Out' 'Output:Average' o
13+ -I 1 0 0 1 0 1 -1x1+1+6 ' ' '0.0' 'Min' Mode
14+ -i 1 0 1 0 0 -1x1+1+7.500000 0 0 2 0 0 'iter' 'iteration for rotation' iter
15+ -i 1 0 1 0 0 -1x1+1+9.000000 0 0 16 0 0 'CorMode' 'Mode: Correlation' M
16+ -i 1 0 1 0 0 -1x1+1+10.500000 0 0 0 0 0 'Method' 'Method: Correlation' Method
17+ -t 1 0 1 0 0 6x1+1+12 'Periodic' 'Periodic' Periodic
18+ -i 1 0 1 0 0 -1x1+1+13.500000 0 0 10 0 0 'maxIter' 'MaxIteration' maxIter
19+ -f 1 0 1 0 0 -1x1+1+15.000000 0 0 0.010000 0 0 0 'rmsd' 'rmsd' rmsd
20+ -I 1 0 1 0 0 1 -1x1+1+16.500000 ' ' 'Log' 'logFile' log
21+ -I 1 0 1 0 0 1 -1x1+1+18.000000 ' ' 'configFile' 'ConfigurationFile' c
22+ -i 1 0 1 0 0 -1x1+1+19.500000 0 0 0 0 0 'mode' 'Mode' m
23+ -E
24+ -E
25+-E
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/test/Makefile
@@ -0,0 +1,25 @@
1+include ../../Config/Define.inc
2+include ../../../Config/Define.inc
3+include ../../../../Config/Define.inc
4+include ../../../../../Config/Define.inc
5+
6+all: help exec
7+
8+help:
9+ @echo "----- Help Message Check -----"
10+ @../$(OSTYPE)/$(OBJECTNAME) -h
11+
12+exec:
13+ @echo "----- Execution Check -----"
14+ ../$(OSTYPE)/$(OBJECTNAME) -i data/in.lst -r data/test-000.mrc -o data/test.avg -Periodic -range 0 360 5 -M 18 -m 0 -maxIter 10 -iter 4;
15+ @echo "----- Calc check -----"
16+
17+init:
18+ pdb2mrc2d -i data/121p-GC.pdb -o data/test-000.mrc -d 2.5 2.5 -s -40 -40 -n 32 32 -sig 2.0 -w 1.0
19+ echo "data/test-000.mrc" > data/in.lst
20+ for i in 030 060 090 120 150 180 ; do \
21+ mrcImageRotation -i data/test-000.mrc -o data/test-$$i.mrc -a $$i -Periodic; \
22+ echo "data/test-$$i.mrc" >> data/in.lst; \
23+ done
24+
25+clean:
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/test/data
@@ -0,0 +1 @@
1+../../../../../..//data/mrcImageAutoRotationAverage
\ No newline at end of file
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/usage.c
@@ -0,0 +1,45 @@
1+#include <stdio.h>
2+#include <stdlib.h>
3+#include "../inc/config.h"
4+
5+void
6+usage(char* thisProgram)
7+{
8+ fprintf(stderr, "Usage: %s\n", thisProgram);
9+ fprintf(stderr, "Options:\n");
10+ fprintf(stderr, " [-i[nput] In (stdin ).as(inFileList::mrcImage) ] :Essential :Input: Ins\n");
11+ fprintf(stderr, " [-r[eferenc] Ref (NULL ).as(inFile::mrcImage ) ] :Optional :Input: Ref\n");
12+ fprintf(stderr, " [-o[utput] Out (NULL ).as(outFile::mrcImage ) ] :Essential :Output:Average\n");
13+ fprintf(stderr, " [-range Min (0.0 ).as(Real ) \n Max (360.0 ).as(Real ) \n Delta (5.0 ).as(Real ) \n Iter (2 ).as(Integer ) ] :Optional :Mode\n");
14+ fprintf(stderr, " [-iter iter (2 ).as(Integer ) ] :Optional :iteration for rotation\n");
15+ fprintf(stderr, " [-M[odeCorrelation] CorMode (16 ).as(Integer ) ] :Optional :Mode: Correlation\n");
16+ fprintf(stderr, " [-Method[Correlation]Method (0 ).as(Integer ) ] :Optional :Method: Correlation\n");
17+ fprintf(stderr, " [-Periodic ] :Optional :Periodic\n");
18+ fprintf(stderr, " [-maxIter[aration] maxIter (10 ).as(Integer ) ] :Optional :MaxIteration\n");
19+ fprintf(stderr, " [-rmsd rmsd (1e-2 ).as(Real ) ] :Optional :rmsd\n");
20+ fprintf(stderr, " [-log Log (stdout ).as(inFile::ASCII ) ] :Optional :logFile\n");
21+ fprintf(stderr, " [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile\n");
22+ fprintf(stderr, " [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode\n");
23+ additionalUsage();
24+}
25+
26+void
27+htmlBeforeUsage(char* thisProgram)
28+{
29+ fprintf(stderr, "<HTML>\n");
30+ fprintf(stderr, "<HEAD>\n");
31+ fprintf(stderr, "<TITLE>%s</TITLE>\n", thisProgram);
32+ fprintf(stderr, "</HEAD>\n");
33+ fprintf(stderr, "<BODY>\n");
34+ fprintf(stderr, "<H1>%s</H1>\n", thisProgram);
35+ fprintf(stderr, "<H2>Usage</H2>\n");
36+ fprintf(stderr, "<PRE>\n");
37+}
38+
39+void
40+htmlAfterUsage(char* thisProgram)
41+{
42+ fprintf(stderr, "</PRE>\n");
43+ fprintf(stderr, "</BODY>\n");
44+ fprintf(stderr, "</HTML>\n");
45+}
--- /dev/null
+++ b/src/Tools/mrcImage/mrcImageAutoRotationAverage/src/util.c
@@ -0,0 +1,4 @@
1+#include <stdio.h>
2+#include <stdlib.h>
3+#include "../inc/config.h"
4+
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