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base: Commit

This repository is a base of Eos.


Commit MetaInfo

Revisioncd8fbe376638f4e3e96b8b599395c5932d4f85c7 (tree)
Time2015-02-28 14:09:21
AuthorTakuo Yasunaga <yasunaga@bio....>
CommiterTakuo Yasunaga

Log Message

rebuild

Change Summary

Incremental Difference

--- a/Makefile
+++ b/Makefile
@@ -104,11 +104,8 @@ git-add:: git-add-hostdepend
104104 git add -v --all .
105105
106106 git-add-hostdepend::
107- #echo tacyas@git.sourceforge.jp:/gitroot/eos/hostdependX86MAC64.git
108- #echo $${EOS_GITUSER}@$(EOS_GIT_REPOSITRY_HOSTDEPEND)$${EOS_HOSTDIR}.git
109107 cd hostdepend/$${EOS_HOSTDIR}/ ; git remote add hostdepend$${EOS_HOSTDIR} $${EOS_GITUSER}@$(EOS_GIT_REPOSITRY_HOSTDEPEND)$${EOS_HOSTDIR}.git | echo "Already exist"
110- #git subtree add --prefix=hostdepend/$${EOS_HOSTDIR}/ --squash hostdepend$${EOS_HOSTDIR} master
111- cd hostdepend/$${EOS_HOSTDIR}/ ; git add -v --all . ; git commit
108+ cd hostdepend/$${EOS_HOSTDIR}/ ; git add -v --all .
112109
113110 git-add-optional::
114111 cd optional; git add -v --all .
@@ -127,9 +124,12 @@ git-add-others2::
127124
128125 git-commit-all:: git-commit git-commit-data git-commit-optional git-commit-tutorial git-commit-others
129126
130-git-commit::
127+git-commit:: git-commit-hostdepend
131128 git commit
132129
130+git-commit-hostdepend::
131+ cd hostdepend/$${EOS_HOSTDIR}/ ; git commit
132+
133133 git-commit-optional::
134134 cd optional; git commit
135135
--- /dev/null
+++ b/bin/probabilityDensityFunction
@@ -0,0 +1 @@
1+../sbin/MachineIndependent
\ No newline at end of file
--- a/bin/wish/Display2/tclIndex
+++ b/bin/wish/Display2/tclIndex
@@ -6,38 +6,41 @@
66 # element name is the name of a command and the value is
77 # a script that loads the command.
88
9-set auto_index(roiAreaRotateStart) [list source [file join $dir RoiAreaRotate.wish]]
10-set auto_index(roiAreaRotateMotion) [list source [file join $dir RoiAreaRotate.wish]]
11-set auto_index(roiAreaRotateEnd) [list source [file join $dir RoiAreaRotate.wish]]
12-set auto_index(rectangleRotate) [list source [file join $dir RoiAreaRotate.wish]]
13-set auto_index(rectangleRotateCalc) [list source [file join $dir RoiAreaRotate.wish]]
14-set auto_index(lineRotate) [list source [file join $dir RoiAreaRotate.wish]]
15-set auto_index(lineRotateCalc) [list source [file join $dir RoiAreaRotate.wish]]
16-set auto_index(splineRotate) [list source [file join $dir RoiAreaRotate.wish]]
17-set auto_index(splineRotateCalc) [list source [file join $dir RoiAreaRotate.wish]]
18-set auto_index(roiAreaSelectStart) [list source [file join $dir RoiAreaSelect.wish]]
19-set auto_index(roiAreaSelectMotion) [list source [file join $dir RoiAreaSelect.wish]]
20-set auto_index(roiAreaSelectEnd) [list source [file join $dir RoiAreaSelect.wish]]
21-set auto_index(roiAreaSelectOK) [list source [file join $dir RoiAreaSelect.wish]]
9+set auto_index(display2BindingSet) [list source [file join $dir Display2Binding.wish]]
2210 set auto_index(colormapChange) [list source [file join $dir Display2Colormap.wish]]
11+set auto_index(display2DesktopSet) [list source [file join $dir Display2Desktop.wish]]
12+set auto_index(display2ETCSet) [list source [file join $dir Display2ETCSet.wish]]
13+set auto_index(fileOpenWinCreate) [list source [file join $dir Display2File.wish]]
14+set auto_index(fileNewWinCreate) [list source [file join $dir Display2File.wish]]
15+set auto_index(seqFileOpenWinCreate) [list source [file join $dir Display2File.wish]]
16+set auto_index(seqFileNewWinCreate) [list source [file join $dir Display2File.wish]]
17+set auto_index(fileOpen) [list source [file join $dir Display2Image.wish]]
18+set auto_index(mainImagePut) [list source [file join $dir Display2Image.wish]]
19+set auto_index(overviewImagePut) [list source [file join $dir Display2Image.wish]]
20+set auto_index(histgramGraphCreate) [list source [file join $dir Display2Info.wish]]
21+set auto_index(display2InformationWinCreate) [list source [file join $dir Display2Info.wish]]
22+set auto_index(fileReopen) [list source [file join $dir Display2Info.wish]]
23+set auto_index(mrcImageInformationWinCreate) [list source [file join $dir Display2Info.wish]]
24+set auto_index(imageInformationWinCreate) [list source [file join $dir Display2Info.wish]]
25+set auto_index(layerLineInformationWinCreate) [list source [file join $dir Display2Info.wish]]
26+set auto_index(projectionInformationWinCreate) [list source [file join $dir Display2Info.wish]]
27+set auto_index(sectionInformationWinCreate) [list source [file join $dir Display2Info.wish]]
28+set auto_index(ctfInformationWinCreate) [list source [file join $dir Display2Info.wish]]
29+set auto_index(unitCellInformationWinCreate) [list source [file join $dir Display2Info.wish]]
30+set auto_index(scaleInfoWinCreate) [list source [file join $dir Display2Info.wish]]
31+set auto_index(roiInformationWinCreate) [list source [file join $dir Display2InfoROI.wish]]
32+set auto_index(roiLineInfoFrameCreate) [list source [file join $dir Display2InfoROI.wish]]
33+set auto_index(roiSplineInfoFrameCreate) [list source [file join $dir Display2InfoROI.wish]]
34+set auto_index(roiRectangleInfoFrameCreate) [list source [file join $dir Display2InfoROI.wish]]
35+set auto_index(roiAnalysisFrameCreate) [list source [file join $dir Display2InfoROI.wish]]
36+set auto_index(display2Init) [list source [file join $dir Display2Init.wish]]
37+set auto_index(display2MenuSet) [list source [file join $dir Display2Menu.wish]]
38+set auto_index(menuFileCreate) [list source [file join $dir Display2Menu.wish]]
39+set auto_index(menuSeqFileCreate) [list source [file join $dir Display2Menu.wish]]
40+set auto_index(menuWindowCreate) [list source [file join $dir Display2Menu.wish]]
41+set auto_index(menuInfoCreate) [list source [file join $dir Display2Menu.wish]]
42+set auto_index(menuHelpCreate) [list source [file join $dir Display2Menu.wish]]
2343 set auto_index(display2MenuSet2) [list source [file join $dir Display2Menu2.wish]]
24-set auto_index(fft2dCmd) [list source [file join $dir fft2dCmd.wish]]
25-set auto_index(display2BindingSet) [list source [file join $dir Display2Binding.wish]]
26-set auto_index(roiMultiAreaInfoSave) [list source [file join $dir RoiAreaFile.wish]]
27-set auto_index(roiMultiAreaInfoLoad) [list source [file join $dir RoiAreaFile.wish]]
28-set auto_index(roiAreaFileSave) [list source [file join $dir RoiAreaFile.wish]]
29-set auto_index(roiAreaFFT) [list source [file join $dir RoiAreaUtil.wish]]
30-set auto_index(splineNearPoint) [list source [file join $dir RoiAreaUtil.wish]]
31-set auto_index(rectangleNearPoint) [list source [file join $dir RoiAreaUtil.wish]]
32-set auto_index(lineNearPoint) [list source [file join $dir RoiAreaUtil.wish]]
33-set auto_index(pointDistance) [list source [file join $dir RoiAreaUtil.wish]]
34-set auto_index(pointDistance2) [list source [file join $dir RoiAreaUtil.wish]]
35-set auto_index(vectorAngle) [list source [file join $dir RoiAreaUtil.wish]]
36-set auto_index(coordGetInMainImageToReal) [list source [file join $dir RoiAreaUtil.wish]]
37-set auto_index(coordGetInMainImageToCanvas) [list source [file join $dir RoiAreaUtil.wish]]
38-set auto_index(dataGetInMainImageToReal) [list source [file join $dir RoiAreaUtil.wish]]
39-set auto_index(dataGetInMainImageToCanvas) [list source [file join $dir RoiAreaUtil.wish]]
40-set auto_index(pointSet) [list source [file join $dir RoiAreaUtil.wish]]
4144 set auto_index(roiRelatedObjectRecreate) [list source [file join $dir Display2MenuROI.wish]]
4245 set auto_index(menuRoiCreate) [list source [file join $dir Display2MenuROI.wish]]
4346 set auto_index(menuRoiCancelCommand) [list source [file join $dir Display2MenuROI.wish]]
@@ -46,42 +49,14 @@ set auto_index(menuMultiRoiOKCommand) [list source [file join $dir Display2MenuR
4649 set auto_index(menuMultiRoiAllDeleteCommand) [list source [file join $dir Display2MenuROI.wish]]
4750 set auto_index(menuMultiRoiDeleteCommand) [list source [file join $dir Display2MenuROI.wish]]
4851 set auto_index(menuEditCreate) [list source [file join $dir Display2MenuROI.wish]]
49-<<<<<<< HEAD
50-set auto_index(display2Init) [list source [file join $dir Display2Init.wish]]
51-set auto_index(display2MenuSet) [list source [file join $dir Display2Menu.wish]]
52-set auto_index(menuFileCreate) [list source [file join $dir Display2Menu.wish]]
53-set auto_index(menuSeqFileCreate) [list source [file join $dir Display2Menu.wish]]
54-set auto_index(menuWindowCreate) [list source [file join $dir Display2Menu.wish]]
55-set auto_index(menuInfoCreate) [list source [file join $dir Display2Menu.wish]]
56-set auto_index(menuHelpCreate) [list source [file join $dir Display2Menu.wish]]
57-set auto_index(roiAreaResizeStart) [list source [file join $dir RoiAreaResize.wish]]
58-set auto_index(roiAreaResizeMotion) [list source [file join $dir RoiAreaResize.wish]]
59-set auto_index(roiAreaResizeEnd) [list source [file join $dir RoiAreaResize.wish]]
60-set auto_index(rectangleResize) [list source [file join $dir RoiAreaResize.wish]]
61-set auto_index(rectangleResizeCalc) [list source [file join $dir RoiAreaResize.wish]]
62-set auto_index(lineResize) [list source [file join $dir RoiAreaResize.wish]]
63-set auto_index(splineResize) [list source [file join $dir RoiAreaResize.wish]]
64-=======
65-set auto_index(fft2dCmd) [list source [file join $dir fft2dCmd.wish]]
66->>>>>>> FETCH_HEAD
6752 set auto_index(layerLineRecreate) [list source [file join $dir LayerLineUtil.wish]]
6853 set auto_index(layerLineCreate) [list source [file join $dir LayerLineUtil.wish]]
6954 set auto_index(layerLineClear) [list source [file join $dir LayerLineUtil.wish]]
7055 set auto_index(layerLineChange) [list source [file join $dir LayerLineUtil.wish]]
71-set auto_index(histgramGraphCreate) [list source [file join $dir Display2Info.wish]]
72-set auto_index(display2InformationWinCreate) [list source [file join $dir Display2Info.wish]]
73-set auto_index(fileReopen) [list source [file join $dir Display2Info.wish]]
74-set auto_index(mrcImageInformationWinCreate) [list source [file join $dir Display2Info.wish]]
75-set auto_index(imageInformationWinCreate) [list source [file join $dir Display2Info.wish]]
76-set auto_index(layerLineInformationWinCreate) [list source [file join $dir Display2Info.wish]]
77-set auto_index(projectionInformationWinCreate) [list source [file join $dir Display2Info.wish]]
78-set auto_index(sectionInformationWinCreate) [list source [file join $dir Display2Info.wish]]
79-set auto_index(ctfInformationWinCreate) [list source [file join $dir Display2Info.wish]]
80-set auto_index(unitCellInformationWinCreate) [list source [file join $dir Display2Info.wish]]
81-set auto_index(scaleInfoWinCreate) [list source [file join $dir Display2Info.wish]]
82-set auto_index(roiAreaZoomIn) [list source [file join $dir RoiAreaZoom.wish]]
83-set auto_index(roiAreaZoomOut) [list source [file join $dir RoiAreaZoom.wish]]
84-set auto_index(roiAreaZoom) [list source [file join $dir RoiAreaZoom.wish]]
56+set auto_index(projectionRecreate) [list source [file join $dir ProjectionUtil.wish]]
57+set auto_index(projectionCreate) [list source [file join $dir ProjectionUtil.wish]]
58+set auto_index(projectionClear) [list source [file join $dir ProjectionUtil.wish]]
59+set auto_index(projectionChange) [list source [file join $dir ProjectionUtil.wish]]
8560 set auto_index(roiAreaCreateStart) [list source [file join $dir RoiAreaCreate.wish]]
8661 set auto_index(roiAreaCreateMotion) [list source [file join $dir RoiAreaCreate.wish]]
8762 set auto_index(roiAreaCreateEnd) [list source [file join $dir RoiAreaCreate.wish]]
@@ -99,29 +74,54 @@ set auto_index(roiSplineEnd) [list source [file join $dir RoiAreaCreate.wish]]
9974 set auto_index(splineCreate) [list source [file join $dir RoiAreaCreate.wish]]
10075 set auto_index(knobShow) [list source [file join $dir RoiAreaCreate.wish]]
10176 set auto_index(knobHide) [list source [file join $dir RoiAreaCreate.wish]]
102-set auto_index(fileOpenWinCreate) [list source [file join $dir Display2File.wish]]
103-set auto_index(fileNewWinCreate) [list source [file join $dir Display2File.wish]]
104-set auto_index(seqFileOpenWinCreate) [list source [file join $dir Display2File.wish]]
105-set auto_index(seqFileNewWinCreate) [list source [file join $dir Display2File.wish]]
106-set auto_index(ScaleRecreate) [list source [file join $dir ScaleUtil.wish]]
107-set auto_index(ScaleCreate) [list source [file join $dir ScaleUtil.wish]]
108-set auto_index(ScaleClear) [list source [file join $dir ScaleUtil.wish]]
109-set auto_index(ScaleChange) [list source [file join $dir ScaleUtil.wish]]
110-set auto_index(unitCellRecreate) [list source [file join $dir UnitCell.wish]]
111-set auto_index(fileOpen) [list source [file join $dir Display2Image.wish]]
112-set auto_index(mainImagePut) [list source [file join $dir Display2Image.wish]]
113-set auto_index(overviewImagePut) [list source [file join $dir Display2Image.wish]]
77+set auto_index(roiMultiAreaInfoSave) [list source [file join $dir RoiAreaFile.wish]]
78+set auto_index(roiMultiAreaInfoLoad) [list source [file join $dir RoiAreaFile.wish]]
79+set auto_index(roiAreaFileSave) [list source [file join $dir RoiAreaFile.wish]]
11480 set auto_index(roiAreaMoveStart) [list source [file join $dir RoiAreaMove.wish]]
11581 set auto_index(roiAreaMoveMotion) [list source [file join $dir RoiAreaMove.wish]]
11682 set auto_index(roiAreaMoveEnd) [list source [file join $dir RoiAreaMove.wish]]
11783 set auto_index(rectangleMove) [list source [file join $dir RoiAreaMove.wish]]
11884 set auto_index(lineMove) [list source [file join $dir RoiAreaMove.wish]]
11985 set auto_index(splineMove) [list source [file join $dir RoiAreaMove.wish]]
120-set auto_index(roiInformationWinCreate) [list source [file join $dir Display2InfoROI.wish]]
121-set auto_index(roiLineInfoFrameCreate) [list source [file join $dir Display2InfoROI.wish]]
122-set auto_index(roiSplineInfoFrameCreate) [list source [file join $dir Display2InfoROI.wish]]
123-set auto_index(roiRectangleInfoFrameCreate) [list source [file join $dir Display2InfoROI.wish]]
124-set auto_index(roiAnalysisFrameCreate) [list source [file join $dir Display2InfoROI.wish]]
86+set auto_index(roiAreaResizeStart) [list source [file join $dir RoiAreaResize.wish]]
87+set auto_index(roiAreaResizeMotion) [list source [file join $dir RoiAreaResize.wish]]
88+set auto_index(roiAreaResizeEnd) [list source [file join $dir RoiAreaResize.wish]]
89+set auto_index(rectangleResize) [list source [file join $dir RoiAreaResize.wish]]
90+set auto_index(rectangleResizeCalc) [list source [file join $dir RoiAreaResize.wish]]
91+set auto_index(lineResize) [list source [file join $dir RoiAreaResize.wish]]
92+set auto_index(splineResize) [list source [file join $dir RoiAreaResize.wish]]
93+set auto_index(roiAreaRotateStart) [list source [file join $dir RoiAreaRotate.wish]]
94+set auto_index(roiAreaRotateMotion) [list source [file join $dir RoiAreaRotate.wish]]
95+set auto_index(roiAreaRotateEnd) [list source [file join $dir RoiAreaRotate.wish]]
96+set auto_index(rectangleRotate) [list source [file join $dir RoiAreaRotate.wish]]
97+set auto_index(rectangleRotateCalc) [list source [file join $dir RoiAreaRotate.wish]]
98+set auto_index(lineRotate) [list source [file join $dir RoiAreaRotate.wish]]
99+set auto_index(lineRotateCalc) [list source [file join $dir RoiAreaRotate.wish]]
100+set auto_index(splineRotate) [list source [file join $dir RoiAreaRotate.wish]]
101+set auto_index(splineRotateCalc) [list source [file join $dir RoiAreaRotate.wish]]
102+set auto_index(roiAreaSelectStart) [list source [file join $dir RoiAreaSelect.wish]]
103+set auto_index(roiAreaSelectMotion) [list source [file join $dir RoiAreaSelect.wish]]
104+set auto_index(roiAreaSelectEnd) [list source [file join $dir RoiAreaSelect.wish]]
105+set auto_index(roiAreaSelectOK) [list source [file join $dir RoiAreaSelect.wish]]
106+set auto_index(roiAreaFFT) [list source [file join $dir RoiAreaUtil.wish]]
107+set auto_index(splineNearPoint) [list source [file join $dir RoiAreaUtil.wish]]
108+set auto_index(rectangleNearPoint) [list source [file join $dir RoiAreaUtil.wish]]
109+set auto_index(lineNearPoint) [list source [file join $dir RoiAreaUtil.wish]]
110+set auto_index(pointDistance) [list source [file join $dir RoiAreaUtil.wish]]
111+set auto_index(pointDistance2) [list source [file join $dir RoiAreaUtil.wish]]
112+set auto_index(vectorAngle) [list source [file join $dir RoiAreaUtil.wish]]
113+set auto_index(coordGetInMainImageToReal) [list source [file join $dir RoiAreaUtil.wish]]
114+set auto_index(coordGetInMainImageToCanvas) [list source [file join $dir RoiAreaUtil.wish]]
115+set auto_index(dataGetInMainImageToReal) [list source [file join $dir RoiAreaUtil.wish]]
116+set auto_index(dataGetInMainImageToCanvas) [list source [file join $dir RoiAreaUtil.wish]]
117+set auto_index(pointSet) [list source [file join $dir RoiAreaUtil.wish]]
118+set auto_index(roiAreaZoomIn) [list source [file join $dir RoiAreaZoom.wish]]
119+set auto_index(roiAreaZoomOut) [list source [file join $dir RoiAreaZoom.wish]]
120+set auto_index(roiAreaZoom) [list source [file join $dir RoiAreaZoom.wish]]
121+set auto_index(ScaleRecreate) [list source [file join $dir ScaleUtil.wish]]
122+set auto_index(ScaleCreate) [list source [file join $dir ScaleUtil.wish]]
123+set auto_index(ScaleClear) [list source [file join $dir ScaleUtil.wish]]
124+set auto_index(ScaleChange) [list source [file join $dir ScaleUtil.wish]]
125125 set auto_index(sectionInit) [list source [file join $dir SectionUtil.wish]]
126126 set auto_index(sectionRecreateAll) [list source [file join $dir SectionUtil.wish]]
127127 set auto_index(sectionRecreate) [list source [file join $dir SectionUtil.wish]]
@@ -130,13 +130,5 @@ set auto_index(sectionCreate) [list source [file join $dir SectionUtil.wish]]
130130 set auto_index(sectionClearAll) [list source [file join $dir SectionUtil.wish]]
131131 set auto_index(sectionClear) [list source [file join $dir SectionUtil.wish]]
132132 set auto_index(sectionChange) [list source [file join $dir SectionUtil.wish]]
133-<<<<<<< HEAD
134-set auto_index(display2DesktopSet) [list source [file join $dir Display2Desktop.wish]]
135-set auto_index(display2ETCSet) [list source [file join $dir Display2ETCSet.wish]]
136-set auto_index(projectionRecreate) [list source [file join $dir ProjectionUtil.wish]]
137-set auto_index(projectionCreate) [list source [file join $dir ProjectionUtil.wish]]
138-set auto_index(projectionClear) [list source [file join $dir ProjectionUtil.wish]]
139-set auto_index(projectionChange) [list source [file join $dir ProjectionUtil.wish]]
140-=======
141133 set auto_index(unitCellRecreate) [list source [file join $dir UnitCell.wish]]
142->>>>>>> FETCH_HEAD
134+set auto_index(fft2dCmd) [list source [file join $dir fft2dCmd.wish]]
--- /dev/null
+++ b/src/Objects/Config/Target.inc
@@ -0,0 +1,109 @@
1+all:
2+ for i in $(SOURCE); \
3+ do \
4+ echo $$i; \
5+ $(CD) $$i; \
6+ $(MAKE) all; \
7+ $(CD) ..; \
8+ done
9+
10+install:
11+ for i in $(SOURCE);\
12+ do \
13+ $(CD) $$i; $(MAKE) install; $(CD) ..; \
14+ done
15+
16+debug:
17+ for i in $(SOURCE); \
18+ do \
19+ echo $$i; \
20+ $(CD) $$i; \
21+ $(MAKE) debug; \
22+ $(CD) ..; \
23+ done
24+
25+install-debug:
26+ for i in $(SOURCE);\
27+ do \
28+ $(CD) $$i; $(MAKE) install-debug; $(CD) ..; \
29+ done
30+
31+clean:
32+ for i in $(SOURCE);\
33+ do \
34+ $(CD) $$i; $(MAKE) clean; $(CD) ..; \
35+ done
36+
37+put:
38+ for i in $(SOURCE);\
39+ do \
40+ $(CD) $$i; $(MAKE) put; $(CD) ..; \
41+ done
42+
43+depend: check
44+ for i in $(SOURCE);\
45+ do \
46+ $(CD) $$i; $(MAKE) depend; $(CD) ..; \
47+ done
48+
49+check::
50+ @if [ ! -d $(EOS_HOME)/lib ] ; then \
51+ mkdir $(EOS_HOME)/lib ; \
52+ fi
53+ @if [ ! -d $(EOS_HOME)/include ] ; then \
54+ mkdir $(EOS_HOME)/include ; \
55+ fi
56+ @for i in $(SOURCE);\
57+ do \
58+ $(CD) $$i; \
59+ dotSourceInMakefileCreate ./ $$i $(WORLDNAME); \
60+ $(RM) -f Makefile; \
61+ $(CP) ../../Config/Template/$(WORLDNAME)ClassTemplate.Dir/Makefile Makefile; \
62+ $(CD) Config; \
63+ $(RM) -f Target.inc; \
64+ $(CP) ../../../Config/Template/$(WORLDNAME)ClassTemplate.Dir/Config/Target.inc Target.inc; \
65+ $(CD) ..; \
66+ $(MAKE) check; \
67+ $(CD) ..; \
68+ done
69+
70+backup::
71+ @cd ../..; \
72+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/Config ; \
73+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/Makefile ; \
74+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/.[A-z]*
75+ @for i in $(SOURCE);\
76+ do \
77+ $(CD) $$i; $(MAKE) backup; $(CD) ..; \
78+ done
79+
80+backup-all::
81+ @cd ../..; \
82+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/Config ; \
83+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/Makefile ; \
84+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/.[A-z]*
85+ @for i in $(SOURCE);\
86+ do \
87+ $(CD) $$i; $(MAKE) backup-all; $(CD) ..; \
88+ done
89+
90+distribute::
91+ @cd ../..; \
92+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/Config ; \
93+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/Makefile ; \
94+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/.[A-z]*
95+ @for i in $(SOURCE);\
96+ do \
97+ $(CD) $$i; $(MAKE) distribute; $(CD) ..; \
98+ done
99+
100+distribute-all::
101+ @cd ../..; \
102+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/Config ; \
103+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/Makefile ; \
104+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/.[A-z]*
105+ @for i in $(SOURCE);\
106+ do \
107+ $(CD) $$i; $(MAKE) distribute-all; $(CD) ..; \
108+ done
109+
--- a/src/Objects/DataManip/ctfInfo/doc/ctfInfo.html
+++ b/src/Objects/DataManip/ctfInfo/doc/ctfInfo.html
@@ -0,0 +1,231 @@
1+<HTML>
2+<HEAD>
3+<TITLE>
4+ctfInfo
5+</TITLE>
6+</HEAD>
7+<BODY bgcolor="#ffffcc">
8+<H1> ctfInfo Object </H1>
9+
10+<H2> <A HREF="#information"> information from souce codes</A></H2>
11+<H2> <A HREF="#include"> include file </A></H2>
12+<HR>
13+<A NAME="Information">
14+<H2>Information from source codes</H2>
15+</A>
16+<PRE>
17+../src/ctfDeterminationFromPhaseComparison.c:
18+
19+../src/ctfFunction.c:
20+
21+../src/ctfInfoPVM.c:
22+
23+../src/ctfInfoRead.c:
24+
25+../src/ctfInfoWrite.c:
26+
27+../src/ctfInfoWrite2.c:
28+
29+../src/ctfWeight.c:
30+
31+../src/ctfZeroPoint.c:
32+
33+../src/lastigmatismDetection.c:
34+
35+../src/lctfDetermination.c:
36+
37+../src/lctfDetermine.c:
38+
39+../src/lmolecularEnvelope.c:
40+
41+../src/lmrcFSInfoScatteringAngularDistributionAverageSection.c:
42+
43+../src/powerspectraTangentLine.c:
44+
45+../src/thonRing.c:
46+</PRE>
47+<HR>
48+<A NAME="include">
49+<H2>ctfInfo.h</H2>
50+</A>
51+<PRE>
52+#ifndef CTF_INFO_H
53+#define CTF_INFO_H
54+#include <stdio.h>
55+
56+/* constant begin */
57+#define ctfInfoModeWithAmplitudeContrast 0x0f
58+#define ctfInfoModeWithMTF 0x10
59+#define ctfInfoModeWithIlluminationAngle 0x20
60+#define ctfInfoModeWithEnergySpread 0x40
61+#define ctfInfoModeAbsoluteValue 0x100
62+
63+typedef enum ctfInfoMode {
64+ ctfInfoModePhaseCTFOnly = 0,
65+ ctfInfoModePhaseAndAmpCTF = 1
66+} ctfInfoMode;
67+
68+typedef enum ctfInfoMTFMode {
69+ ctfInfoMTFModeSingleExp = 0,
70+ ctfInfoMTFModeSingleLorentzian = 1,
71+ ctfInfoMTFModeBoth = 2,
72+ ctfInfoMTFModeLinear = 3,
73+ ctfInfoMTFModeBothSum = 4,
74+ ctfInfoMTFModePolynomial = 5
75+} ctfInfoMTFMode;
76+/* constant end */
77+
78+/* struct begin */
79+typedef struct moleculrEnvelope {
80+ char* filename;
81+ int nR;
82+ float* R;
83+ float* Envelope;
84+ int mode;
85+} molecularEnvelope;
86+
87+typedef struct ctfInfo {
88+ float kV; /* kV */
89+ float defocus; /* A : Underfocus is plus, while overfocus is minus*/
90+ float Cc; /* mm */
91+ float dE;
92+ float Cs; /* mm */
93+ float Ain; /* mrad : Illumination Angle */
94+ long flagWin; /* Windowing */
95+ float CutLow; /* Windowing: CutLow A-1 */
96+ float CutHigh; /* Windowing: CutHigh A-1 */
97+
98+ float I0; /* Intensity */
99+ float Isignal; /* Intensity of signal */
100+
101+ float ratioOfAmpToPhase; /* The ratio of amp to phase */
102+
103+ float Inoise; /* Intensity of noise : Isignal*/
104+ long flagWhiteNoise;
105+ float WhiteNoise; /* Affected by MTF(R) */
106+
107+ long flagWhiteNoiseRaising;
108+ float WhiteNoiseRaising; /* WhiteNoise Raising depending upon R */
109+
110+ long flagMaxWhiteNoise;
111+ float MaxWhiteNoise; /* max White Noise*/
112+
113+ long flagNdependentWhiteNoise;
114+ float NdependentWhiteNoise; /* max White Noise*/
115+
116+ float Inoise2; /* Intensity of noise */
117+ long flagWhiteNoise2;
118+ float WhiteNoise2; /* Not Affected by MTF(R)*/
119+
120+ int flagAstigmatism;
121+ float defocus2D[2]; /* A : Normally [0]: Max [1]: Min */
122+ float defocus0axis; /* radian : angle of the defocus2D[0]-axis */
123+
124+ long mode;
125+
126+ long flagMagnification;
127+ float Magnification;
128+
129+ /* MTF(R): Modulation Transfer Function */
130+ ctfInfoMTFMode MTFMode;
131+ float BofMTF; /* Exponential: exp(-B R) */
132+ float BofMTF2; /* Lorentzian : 1/(B*B+R*R) */
133+ float WeightOfSecondTermForMTF; /* 0 <-> 1 */
134+ /*for PolynomialExpNoise*//*d = degree*/
135+ float BofMTFd2;
136+ float BofMTFd3;
137+ float BofMTFd4;
138+ float BofMTFd5;
139+ float BofMTFd6;
140+
141+ /* Molecular Envelope: Scattering Factor */
142+ /* For Gaussian */
143+ float MolecEnv; /* A : */
144+ /* For Table */
145+ long flagMolecEnvTable;
146+ molecularEnvelope MolecEnvTable;
147+ /* For Lorentzian */
148+ float flagElastic;
149+ float Elastic;
150+ float ElasticShift;
151+ float ElasticWidth;
152+ float ElasticRing;
153+ float ElasticRingPosition;
154+ float ElasticRingWidth;
155+
156+ /* Stage Vibration */
157+ long flagVibration;
158+ long VibrationMode;
159+ float BofVibration;
160+
161+ /* Aliasing and Sampling */
162+ long flagAliasing;
163+ float NyquistFrequency;
164+ long flagSampling;
165+
166+ /* Inelastic Signal */
167+ /* For Gaussian */
168+ long flagWithInElastic;
169+ float InElasticGaussian;
170+ /* For Table */
171+ long flagWithInElasticTable;
172+ molecularEnvelope InElasticEnvTable;
173+ /* Lorentzian */
174+ long flagInElastic;
175+ float InElastic;
176+ float InElasticShift;
177+ float InElasticWidth;
178+ float InElasticRing;
179+ float InElasticRingPosition;
180+ float InElasticRingWidth;
181+} ctfInfo;
182+/* struct end */
183+
184+
185+#ifdef __cplusplus
186+extern "C" {
187+#endif
188+
189+/* prototype begin */
190+
191+extern void ctfInfoSendByPVM(ctfInfo* info, int tid, long mode);
192+extern void ctfInfoRecieveByPVM(ctfInfo* info, int tid, long mode);
193+extern float ctfSignalFunction(ctfInfo* info, float R, long mode);
194+extern float ctfNoiseFunction(ctfInfo* info, float R, long mode);
195+extern float ctfNoise2Function(ctfInfo* info, float R, long mode);
196+extern float ctfSignalPowerFunction(ctfInfo* info, float R, long mode);
197+extern float ctfNoisePowerFunction(ctfInfo* info, float R, long mode);
198+extern float ctfNoise2PowerFunction(ctfInfo* info, float R, long mode);
199+extern float ctfScatteringFunction(ctfInfo* info, float R, long mode);
200+extern float ctfMolecularEnvelopeFunction(ctfInfo* info, float R, long mode);
201+extern float ctfMolecularEnvelopeInElasticFunction(ctfInfo* info, float R, long mode);
202+extern float ctfVibrationFunction(ctfInfo* info, float R, long mode);
203+extern float ctfFunction(ctfInfo* info, float R, long mode);
204+extern float ctfFunctionSampling(float R, float Nyquist, long mode);
205+extern void ctfFunctionPVMStart(ctfInfo* info, float R, int tid, long mode);
206+extern float ctfFunctionPVMEnd(ctfInfo* info, float R, int tid, long mode);
207+extern void ctfFunctionPVMServer();
208+extern float ctfEnvelopFunction(ctfInfo* info, float R, long mode);
209+extern float ctfMTFFunction(ctfInfo* info, float R, long mode);
210+extern float ctfFunction2D(ctfInfo* info, float X, float Y, long mode);
211+extern float wavelengthOfElectron(float E);
212+extern float defocusDeterminationFromThonRing(ctfInfo* info, float R, long n, long mode);
213+extern void ctfWeightForCorrectionUsage(FILE* fpt);
214+extern float ctfWeightForCorrection2D(ctfInfo* info, float X, float Y, long mode);
215+extern float ctfWeightForCorrection(ctfInfo* info, float R, long mode);
216+extern void lmolecularEnvelopeFileRead(FILE* fpt, molecularEnvelope* mol, int mode);
217+extern void lmolecularEnvelopeFileWrite(FILE* fpt, molecularEnvelope* mol, int mode);
218+extern void lmolecularEnvelopeResampling(molecularEnvelope* dst, molecularEnvelope* src, float dR, float RMax, int mode);
219+extern float lmolecularEnvelopeDataGet(molecularEnvelope* src, float R, int mode);
220+extern void ctfInfoRead(FILE* fpt, ctfInfo* ctf, char* pre, int mode);
221+extern void ctfInfoWrite(FILE* fpt, ctfInfo ctf, char* pre, int mode);
222+/* prototype end */
223+
224+#ifdef __cplusplus
225+};
226+#endif
227+
228+#endif
229+</PRE>
230+</BODY>
231+</HTML>
--- a/src/Objects/DataManip/mrcImage/doc/mrcImage.html
+++ b/src/Objects/DataManip/mrcImage/doc/mrcImage.html
@@ -103,6 +103,343 @@
103103 <H2>Information from source codes</H2>
104104 </A>
105105 <PRE>
106+../src/fftn.c:
107+
108+../src/lmrcFETnormalizeBySD.c:
109+
110+../src/lmrcFFTExpression.c:
111+
112+../src/lmrcFFTFGconj.c:
113+
114+../src/lmrcFFTFxG.c:
115+
116+../src/lmrcFFTInfo.c:
117+
118+../src/lmrcImage3DPad.c:
119+
120+../src/lmrcImage3DWindowing.c:
121+
122+../src/lmrcImageAddValue.c:
123+
124+../src/lmrcImageAsProbability.c:
125+
126+../src/lmrcImageAverage.c:
127+
128+../src/lmrcImageBandPassFilter.c:
129+
130+../src/lmrcImageBilateralFilter.c:
131+
132+../src/lmrcImageBinarization.c:
133+
134+../src/lmrcImageBottomHatTransform.c:
135+
136+../src/lmrcImageBoundaryInfo.c:
137+
138+../src/lmrcImageCTFCompensation.c:
139+
140+../src/lmrcImageCTFDetermination.c:
141+
142+../src/lmrcImageCTFObservation.c:
143+
144+../src/lmrcImageCTFSN.c:
145+
146+../src/lmrcImageCVE.c:
147+
148+../src/lmrcImageCalcArea.c:
149+
150+../src/lmrcImageCenterGet.c:
151+
152+../src/lmrcImageCentre.c:
153+
154+../src/lmrcImageClosing.c:
155+
156+../src/lmrcImageClusterAnalysis.c:
157+
158+../src/lmrcImageCommonLine.c:
159+
160+../src/lmrcImageConnection.c:
161+
162+../src/lmrcImageConnectivityNumberCalc.c:
163+
164+../src/lmrcImageContourSurface.c:
165+
166+../src/lmrcImageContraction.c:
167+
168+../src/lmrcImageCorrelation.c:
169+ $lmrcImageEuclidDistanceCalc: Calculate Euclid distance between two images $
170+ $arg: in1: input mrcImage1 $
171+ $arg: in2: input mrcImage2 $
172+ $arg: mode: input int $
173+ $mode: 0 Sum of SQR $
174+ $mode: 1 Distance $
175+ $return: EuclidDistance $
176+
177+../src/lmrcImageCorrelationPVM.c:
178+
179+../src/lmrcImageCorrelationWithCTFCompensation.c:
180+
181+../src/lmrcImageCorrelationinSpace.c:
182+
183+../src/lmrcImageCrystalCreate.c:
184+
185+../src/lmrcImageDataMaxAndMinGetByImage.c:
186+
187+../src/lmrcImageDataStraightCopy.c:
188+
189+../src/lmrcImageDeconvolution.c:
190+
191+../src/lmrcImageDensity.c:
192+
193+../src/lmrcImageDensityInverse.c:
194+
195+../src/lmrcImageDensityNormalizationByImage.c:
196+
197+../src/lmrcImageDifferential.c:
198+
199+../src/lmrcImageDilation.c:
200+
201+../src/lmrcImageDistanceConversion.c:
202+
203+../src/lmrcImageEdge.c:
204+
205+../src/lmrcImageEdgeAverage.c:
206+
207+../src/lmrcImageEdgeEnhancement.c:
208+
209+../src/lmrcImageErosion.c:
210+
211+../src/lmrcImageFFT.c:
212+
213+../src/lmrcImageFOMCalc.c:
214+
215+../src/lmrcImageFeatureExtraction.c:
216+
217+../src/lmrcImageFeatureExtractionCoOccurrence.c:
218+
219+../src/lmrcImageFeatureExtractionRunLength.c:
220+
221+../src/lmrcImageFilterCreate.c:
222+
223+../src/lmrcImageFirstNoiseReductionByRelaxation.c:
224+
225+../src/lmrcImageFloating.c:
226+
227+../src/lmrcImageFourierNeighborCorrelation.c:
228+
229+../src/lmrcImageFourierPowerSpectrum.c:
230+
231+../src/lmrcImageFourierShellCorrelation.c:
232+
233+../src/lmrcImageHighPassFilter.c:
234+
235+../src/lmrcImageHighlighting.c:
236+
237+../src/lmrcImageHoughTransform.c:
238+
239+../src/lmrcImageLabeling.c:
240+
241+../src/lmrcImageLogicalOperation.c:
242+
243+../src/lmrcImageLowPassFilter.c:
244+
245+../src/lmrcImageMasking.c:
246+
247+../src/lmrcImageMaxDataGet.c:
248+
249+../src/lmrcImageMirroring.c:
250+ $lmrcImageMirroring: (mrcImage* out, mrcImage* in, lmrcImageMirroring mode) $
251+
252+../src/lmrcImageModeChange.c:
253+
254+../src/lmrcImageModelCreate.c:
255+
256+../src/lmrcImageMontageCreate.c:
257+
258+../src/lmrcImageMorphology.c:
259+
260+../src/lmrcImageMove.c:
261+
262+../src/lmrcImageMultiCTFCompensation.c:
263+
264+../src/lmrcImageMultiplying.c:
265+
266+../src/lmrcImageNegativeLaplacian.c:
267+
268+../src/lmrcImageNoiseCreate.c:
269+
270+../src/lmrcImageNormalizing.c:
271+
272+../src/lmrcImageOneLineSimilarityCalc.c:
273+
274+../src/lmrcImageOpening.c:
275+
276+../src/lmrcImagePad.c:
277+
278+../src/lmrcImagePartImageSegmentation.c:
279+
280+../src/lmrcImagePixelSummationOfProbabilityGetByImage.c:
281+
282+../src/lmrcImagePosterization.c:
283+
284+../src/lmrcImagePrewitt.c:
285+
286+../src/lmrcImageProjection.c:
287+
288+../src/lmrcImageProportionalDensityLevelSetByImage.c:
289+
290+../src/lmrcImageROI2D.c:
291+
292+../src/lmrcImageROI3D.c:
293+
294+../src/lmrcImageROInotChangeHeaderLength.c:
295+
296+../src/lmrcImageRadialDistribution.c:
297+
298+../src/lmrcImageRhoFiltering.c:
299+
300+../src/lmrcImageRoberts.c:
301+
302+../src/lmrcImageRotation.c:
303+
304+../src/lmrcImageSSDA.c:
305+
306+../src/lmrcImageSamplingUnitChange.c:
307+
308+../src/lmrcImageSecondNoiseReductionByRelaxation.c:
309+
310+../src/lmrcImageSecondNoiseReductionByRelaxationDijDimensionSet.c:
311+
312+../src/lmrcImageSecondNoiseReductionByRelaxationDijValueCalculate.c:
313+
314+../src/lmrcImageSecondNoiseReductionByRelaxationDijValueSet.c:
315+
316+../src/lmrcImageSecondNoiseReductionByRelaxationQValueSet.c:
317+
318+../src/lmrcImageSecondNoiseReductionByRelaxationRValueSet.c:
319+
320+../src/lmrcImageShapePCA.c:
321+
322+../src/lmrcImageShift.c:
323+
324+../src/lmrcImageShrink.c:
325+
326+../src/lmrcImageSigmaCalculate.c:
327+
328+../src/lmrcImageSinogram.c:
329+
330+../src/lmrcImageSinogramCorrelation.c:
331+
332+../src/lmrcImageSinogramFFT.c:
333+
334+../src/lmrcImageSmoothing.c:
335+
336+../src/lmrcImageSobel.c:
337+
338+../src/lmrcImageSolventFlattening.c:
339+
340+../src/lmrcImageSpatialFrequencyFilter.c:
341+
342+../src/lmrcImageSphere.c:
343+
344+../src/lmrcImageSplit.c:
345+
346+../src/lmrcImageStack.c:
347+
348+../src/lmrcImageStudentCalculate.c:
349+
350+../src/lmrcImageSubtractionCalc.c:
351+
352+../src/lmrcImageSummationCalculate.c:
353+
354+../src/lmrcImageSymmetryFind.c:
355+
356+../src/lmrcImageTfunction.c:
357+
358+../src/lmrcImageToneReversal.c:
359+
360+../src/lmrcImageTopHatTransform.c:
361+
362+../src/lmrcImageTrans.c:
363+
364+../src/lmrcImageTransformDescartesIntoPolar.c:
365+
366+../src/lmrcImageTriming.c:
367+
368+../src/lmrcImageVolumeCalc.c:
369+
370+../src/lmrcImageWindowing.c:
371+
372+../src/lmrcImagesFTest.c:
373+
374+../src/lmrcImagesStatDataGet.c:
375+
376+../src/lmrcImagesTTest.c:
377+
378+../src/lmrcImagesVarianceAnalysis.c:
379+
380+../src/lmrcImagesVarianceMap.c:
381+
382+../src/lmrcSinogramFET.c:
383+
384+../src/lmrcSinogramFETPCA.c:
385+
386+../src/lmrcSinogramFETcalcWeight.c:
387+
388+../src/lmrcSinogramFETcorrelationMap.c:
389+
390+../src/lmrcSinogramFETnormalizedMap.c:
391+
392+../src/lmrcSinogramFETreferredCorrelation.c:
393+
394+../src/lmrcSinogramFETsmoothParameterMatching.c:
395+
396+../src/mrcImageCheckFFT.c:
397+
398+../src/mrcImageCheckSameSize.c:
399+
400+../src/mrcImageCopy.c:
401+
402+../src/mrcImageDataSet.c:
403+
404+../src/mrcImageError.c:
405+
406+../src/mrcImageGet.c:
407+
408+../src/mrcImageGetPixels.c:
409+
410+../src/mrcImageInfo.c:
411+
412+../src/mrcImageInit.c:
413+
414+../src/mrcImageOperation.c:
415+
416+../src/mrcImagePVM.c:
417+
418+../src/mrcImagePrint.c:
419+
420+../src/mrcImageRead.c:
421+
422+../src/mrcImageSectionGet.c:
423+
424+../src/mrcImageSectionSet.c:
425+
426+../src/mrcImageSet.c:
427+
428+../src/mrcImageTailer.c:
429+
430+../src/mrcImageToIntImage.c:
431+
432+../src/mrcImageUtil.c:
433+
434+../src/mrcImageUtilityforVariance.c:
435+
436+../src/mrcImageWrite.c:
437+
438+../src/mrcImageWrite2.c:
439+
440+../src/mrcImagefuncmin.c:
441+
442+../src/mrcRefUtil.c:
106443 </PRE>
107444 <HR>
108445 <A NAME="include">
--- a/src/Objects/General/.Source.org
+++ b/src/Objects/General/.Source.org
@@ -16,7 +16,6 @@ Socket \
1616 SpecialNumber \
1717 String \
1818 Vector \
19-X86MAC64 \
2019 dummy \
2120 eosCuda \
2221 eosFunc \
--- a/src/Objects/General/Cluster/doc/Cluster.html
+++ b/src/Objects/General/Cluster/doc/Cluster.html
@@ -3,6 +3,15 @@
33 <H2>Information from source codes</H2>
44 </A>
55 <PRE>
6+../src/clusterLogAnalysis.c:
7+
8+../src/clusterLogInit.c:
9+
10+../src/clusterLogRead.c:
11+
12+../src/clusterLogUtil.c:
13+
14+../src/clusterLogWrite.c:
615 </PRE>
716 <HR>
817 <A NAME="include">
--- /dev/null
+++ b/src/Objects/General/Matrix3D/doc/Makefile
@@ -0,0 +1,41 @@
1+include ../../../../Config/Define.inc
2+include ../../../Config/Define.inc
3+include ../../Config/Define.inc
4+include ../Config/Define.inc
5+
6+SOURCEDOC = $(OBJECTNAME).html
7+DOCDSTDIR = $(EOS_HOME)/doc/Objects
8+TARGETDOC = $(DOCDSTDIR)/$(SOURCEDOC)
9+
10+all: $(SOURCEDOC)
11+
12+install : $(TARGETDOC)
13+
14+$(TARGETDOC):$(SOURCEDOC)
15+ $(INSTALL) -m 444 *.html $(DOCDSTDIR)
16+ @cd $(DOCDSTDIR); make
17+
18+$(SOURCEDOC) : .$(SOURCEDOC) .header .footer ../inc/$(OBJECTNAME).h Makefile ../src/*.c
19+ @echo Creating $(OBJECTNAME).html
20+ @cat .header > $(SOURCEDOC)
21+ @#htmlUpdateTime >> $(SOURCEDOC)
22+ @cat .$(SOURCEDOC) >> $(SOURCEDOC)
23+ @echo \<HR\> >> $(SOURCEDOC)
24+ @echo "<A NAME=\"Information\">" >> $(SOURCEDOC)
25+ @echo "<H2>Information from source codes</H2>" >> $(SOURCEDOC)
26+ @echo "</A>" >> $(SOURCEDOC)
27+ @echo "<PRE>" >> $(SOURCEDOC)
28+ -@ident ../src/*.c >> $(SOURCEDOC)
29+ @echo "</PRE>" >> $(SOURCEDOC)
30+ @echo \<HR\> >> $(SOURCEDOC)
31+ @echo \<A NAME=\"include\"\>>> $(SOURCEDOC)
32+ @echo "<H2>$(OBJECTNAME).h</H2>">> $(SOURCEDOC)
33+ @echo \</A\> >>$(SOURCEDOC)
34+ @echo \<PRE\> >> $(SOURCEDOC)
35+ @cat ../inc/$(OBJECTNAME).h >> $(SOURCEDOC)
36+ @echo \</PRE\> >> $(SOURCEDOC)
37+ @cat .footer >> $(SOURCEDOC)
38+
39+clean:
40+
41+depend:
--- a/src/Tools/DCDFile/dcdAtomChangeDistanceFromAtom/src/dcdAtomChangeDistanceFromAtom.html
+++ b/src/Tools/DCDFile/dcdAtomChangeDistanceFromAtom/src/dcdAtomChangeDistanceFromAtom.html
@@ -1 +1,18 @@
1-/bin/bash: dcdAtomChangeDistanceFromAtom: No such file or directory
1+<HTML>
2+<HEAD>
3+<TITLE>dcdAtomChangeDistanceFromAtom</TITLE>
4+</HEAD>
5+<BODY>
6+<H1>dcdAtomChangeDistanceFromAtom</H1>
7+<H2>Usage</H2>
8+<PRE>
9+Usage: dcdAtomChangeDistanceFromAtom
10+Options:
11+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
12+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
13+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
14+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
15+----- Additional Usage -----
16+</PRE>
17+</BODY>
18+</HTML>
--- a/src/Tools/DCDFile/dcdAtomDistanceDistribution/src/dcdAtomDistanceDistribution.html
+++ b/src/Tools/DCDFile/dcdAtomDistanceDistribution/src/dcdAtomDistanceDistribution.html
@@ -1 +1,19 @@
1-/bin/bash: dcdAtomDistanceDistribution: No such file or directory
1+<HTML>
2+<HEAD>
3+<TITLE>dcdAtomDistanceDistribution</TITLE>
4+</HEAD>
5+<BODY>
6+<H1>dcdAtomDistanceDistribution</H1>
7+<H2>Usage</H2>
8+<PRE>
9+Usage: dcdAtomDistanceDistribution
10+Options:
11+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
12+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
13+ [-o[utput]mrc OutMRC (NULL ).as(outFile ) ] :Optional :Output: MRCFile
14+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
15+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
16+----- Additional Usage -----
17+</PRE>
18+</BODY>
19+</HTML>
--- a/src/Tools/DCDFile/dcdFilePrint/src/dcdFilePrint.html
+++ b/src/Tools/DCDFile/dcdFilePrint/src/dcdFilePrint.html
@@ -1 +1,26 @@
1-/bin/bash: dcdFilePrint: No such file or directory
1+<HTML>
2+<HEAD>
3+<TITLE>dcdFilePrint</TITLE>
4+</HEAD>
5+<BODY>
6+<H1>dcdFilePrint</H1>
7+<H2>Usage</H2>
8+<PRE>
9+Usage: dcdFilePrint
10+Options:
11+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: DCD
12+ [-i[nput]p[db] InPDB (NULL ).as(inFile ) ] :Optional :Input: PDB
13+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output: ASCII
14+ [-o[utput]p[db] OutPDB (NULL ).as(outFile ) ] :Optional :Output: PDB
15+ [-r[ange] rStart (10 ).as(Integer )
16+ rEnd (100 ).as(Integer )
17+ rDelta (10 ).as(Integer ) ] :Optional :Input: Start End Delta
18+ [-s[tart] Start (10 ).as(Integer ) ] :Optional :Input: Start
19+ [-e[nd] End (100 ).as(Integer ) ] :Optional :Input: End
20+ [-d[elta] Delta (10 ).as(Integer ) ] :Optional :Input: Delta(Interval)
21+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
22+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
23+----- Additional Usage -----
24+</PRE>
25+</BODY>
26+</HTML>
--- a/src/Tools/DCDFile/dcdInfo/src/dcdInfo.html
+++ b/src/Tools/DCDFile/dcdInfo/src/dcdInfo.html
@@ -1 +1,20 @@
1-/bin/bash: dcdInfo: No such file or directory
1+<HTML>
2+<HEAD>
3+<TITLE>dcdInfo</TITLE>
4+</HEAD>
5+<BODY>
6+<H1>dcdInfo</H1>
7+<H2>Usage</H2>
8+<PRE>
9+Usage: dcdInfo
10+Options:
11+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :Input: DCD
12+ [-i[nput]p[db] InPDB (NULL ).as(inFile ) ] :Optional :Input: PDB
13+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :Output: ASCII
14+ [-o[utput]p[db] OutPDB (NULL ).as(outFile ) ] :Optional :Output: PDB
15+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
16+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
17+----- Additional Usage -----
18+</PRE>
19+</BODY>
20+</HTML>
--- a/src/Tools/DCDFile/dcdSelectAtoms/src/dcdSelectAtoms.html
+++ b/src/Tools/DCDFile/dcdSelectAtoms/src/dcdSelectAtoms.html
@@ -1 +1,18 @@
1-/bin/bash: dcdSelectAtoms: No such file or directory
1+<HTML>
2+<HEAD>
3+<TITLE>dcdSelectAtoms</TITLE>
4+</HEAD>
5+<BODY>
6+<H1>dcdSelectAtoms</H1>
7+<H2>Usage</H2>
8+<PRE>
9+Usage: dcdSelectAtoms
10+Options:
11+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
12+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
13+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
14+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
15+----- Additional Usage -----
16+</PRE>
17+</BODY>
18+</HTML>
--- a/src/Tools/DCDFile/dcdSerectAtom/src/dcdSerectAtom.html
+++ b/src/Tools/DCDFile/dcdSerectAtom/src/dcdSerectAtom.html
@@ -1 +1,18 @@
1-/bin/bash: dcdSerectAtom: No such file or directory
1+<HTML>
2+<HEAD>
3+<TITLE>dcdSerectAtom</TITLE>
4+</HEAD>
5+<BODY>
6+<H1>dcdSerectAtom</H1>
7+<H2>Usage</H2>
8+<PRE>
9+Usage: dcdSerectAtom
10+Options:
11+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
12+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
13+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
14+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
15+----- Additional Usage -----
16+</PRE>
17+</BODY>
18+</HTML>
--- a/src/Tools/DCDFile/dcdTimeSeriesBehavior/src/dcdTimeSeriesBehavior.html
+++ b/src/Tools/DCDFile/dcdTimeSeriesBehavior/src/dcdTimeSeriesBehavior.html
@@ -1 +1,18 @@
1-/bin/bash: dcdTimeSeriesBehavior: No such file or directory
1+<HTML>
2+<HEAD>
3+<TITLE>dcdTimeSeriesBehavior</TITLE>
4+</HEAD>
5+<BODY>
6+<H1>dcdTimeSeriesBehavior</H1>
7+<H2>Usage</H2>
8+<PRE>
9+Usage: dcdTimeSeriesBehavior
10+Options:
11+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
12+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
13+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
14+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
15+----- Additional Usage -----
16+</PRE>
17+</BODY>
18+</HTML>
--- a/src/Tools/Integration/StereoDisplay/src/StereoDisplay.html
+++ b/src/Tools/Integration/StereoDisplay/src/StereoDisplay.html
@@ -1 +1 @@
1-/bin/bash: StereoDisplay: No such file or directory
1+/bin/bash: StereoDisplay: そのようなファイルやディレクトリはありません
--- a/src/Tools/Makefile
+++ /dev/null
@@ -1 +0,0 @@
1-/Users/tacyas/Eos/src/Config/Template/ToolsHomeTemplate.Dir/Makefile
\ No newline at end of file
--- /dev/null
+++ b/src/Tools/Makefile
@@ -0,0 +1,5 @@
1+include ../Config/Define.inc
2+include Config/Define.inc
3+include .Source
4+
5+include Config/Target.inc
--- a/src/Tools/ctfInfo/ctfEnvelopFunctionEstimate/src/ctfEnvelopFunctionEstimate.html
+++ b/src/Tools/ctfInfo/ctfEnvelopFunctionEstimate/src/ctfEnvelopFunctionEstimate.html
@@ -1 +1,21 @@
1-/bin/bash: ctfEnvelopFunctionEstimate: そのようなファイルやディレクトリはありません
1+<HTML>
2+<HEAD>
3+<TITLE>ctfEnvelopFunctionEstimate</TITLE>
4+</HEAD>
5+<BODY>
6+<H1>ctfEnvelopFunctionEstimate</H1>
7+<H2>Usage</H2>
8+<PRE>
9+Usage: ctfEnvelopFunctionEstimate
10+Options:
11+ [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :Input:
12+ [-o[utput] Out (stdout ).as(outFile::ASCII ) ] :Optional :Output:
13+ [-degree degree (6 ).as(Integer ) ] :Optional :[dim]
14+ [-Range CutLow (0.01 ).as(Real )
15+ CutHigh (0.2 ).as(Real ) ] :Optional :[/A]
16+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
17+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
18+----- Additional Usage -----
19+</PRE>
20+</BODY>
21+</HTML>
--- a/src/Tools/filter/mrc2gif/src/mrc2gif.html
+++ b/src/Tools/filter/mrc2gif/src/mrc2gif.html
@@ -1 +1 @@
1-/bin/bash: mrc2gif: No such file or directory
1+/bin/bash: mrc2gif: そのようなファイルやディレクトリはありません
--- a/src/Tools/mrcImage/mrcImageColoring/src/mrcImageColoring.html
+++ b/src/Tools/mrcImage/mrcImageColoring/src/mrcImageColoring.html
@@ -1 +1 @@
1-/bin/bash: mrcImageColoring: No such file or directory
1+/bin/bash: mrcImageColoring: そのようなファイルやディレクトリはありません
--- a/src/Tools/mrcImage/mrcImageDensityInfo/src/mrcImageDensityInfo.html
+++ b/src/Tools/mrcImage/mrcImageDensityInfo/src/mrcImageDensityInfo.html
@@ -10,7 +10,7 @@ Usage: mrcImageDensityInfo
1010 Options:
1111 [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
1212 [-o[utput] Out (stdout ).as(outFile ) ] :Optional :OutputDataFile
13- [-C[ontour] Contour (10 ).as(Real ) ] :Optional :ContourLevel: 10 5.533535e-322ach
13+ [-C[ontour] Contour (10 ).as(Real ) ] :Optional :ContourLevel: 10 6.899440e-310ach
1414 [-log Log (NULL ).as(appendFile ) ] :Optional :OutputDataFile
1515 [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
1616 [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
--- a/src/Tools/mrcImage/mrcImageSphereCheck/src/mrcImageSphereCheck.html
+++ b/src/Tools/mrcImage/mrcImageSphereCheck/src/mrcImageSphereCheck.html
@@ -1 +1,19 @@
1-/bin/bash: mrcImageSphereCheck: No such file or directory
1+<HTML>
2+<HEAD>
3+<TITLE>mrcImageSphereCheck</TITLE>
4+</HEAD>
5+<BODY>
6+<H1>mrcImageSphereCheck</H1>
7+<H2>Usage</H2>
8+<PRE>
9+Usage: mrcImageSphereCheck
10+Options:
11+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
12+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output:
13+ [-n[ormalized] OutNOr (NULL ).as(outFile ) ] :Optional :Output: NormalizedImage
14+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
15+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
16+----- Additional Usage -----
17+</PRE>
18+</BODY>
19+</HTML>
--- a/src/Tools/mrcImage/mrcImageSuperResolution/src/mrcImageSuperResolution.html
+++ b/src/Tools/mrcImage/mrcImageSuperResolution/src/mrcImageSuperResolution.html
@@ -28,8 +28,8 @@ Options:
2828 [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
2929 [-m[ode] mode (0 ).as(Integer ) ] :Essential :RealSpaceCalculating
3030 [-LabelingMode labelingmode (0 ).as(Integer ) ] :Optional :LabelingMode
31- [-max[value] max (800 ).as(Integer ) ] :Optional :Density Max value:Support Constraint()
32- [-min[value] min (200 ).as(Integer ) ] :Optional :Density Min value:Support Constraint()
31+ [-max[value] max (800 ).as(Integer ) ] :Optional :Density Max value:Support Constraint(%)
32+ [-min[value] min (200 ).as(Integer ) ] :Optional :Density Min value:Support Constraint(%)
3333 [-sh[ape] shape (0 ).as(Integer ) ] :Optional :Shape:0(Rectangule),1(Globe)
3434 [-h[alf]v[alue]p[oint]hvp (0.0 ).as(Real ) ] :Optional :Half value point(/[A])
3535 [-Inverse ] :Optional :Inverse
--- a/src/Tools/mrcImage/mrcImageVolumeCalc/src/mrcImageVolumeCalc.html
+++ b/src/Tools/mrcImage/mrcImageVolumeCalc/src/mrcImageVolumeCalc.html
@@ -16,7 +16,7 @@ Options:
1616 [-D[elta] Delta (5.0 ).as(Real ) ] :Optional :Delta[A]
1717 [-R[ange] MinVol (0.0 ).as(Real )
1818 MaxVol (200.0 ).as(Real )
19- DeltaVol (10.0 ).as(Real ) ] :Optional :vol
19+ DeltaVol (10.0 ).as(Real ) ] :Optional :vol%
2020 [-I[nverse] ] :Optional :Inverse
2121 [-format Format (ContourLevel(%3g): %g %lu).as(StringAll ) ] :Optional :Format
2222 [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
--- a/src/Tools/openGL/molvieDock/src/molvieDock.html
+++ b/src/Tools/openGL/molvieDock/src/molvieDock.html
@@ -1 +1 @@
1-/bin/bash: molvieDock: No such file or directory
1+/bin/bash: molvieDock: そのようなファイルやディレクトリはありません
--- a/src/Tools/openGL/molvieProjection/src/molvieProjection.html
+++ b/src/Tools/openGL/molvieProjection/src/molvieProjection.html
@@ -1 +1 @@
1-/bin/bash: molvieProjection: No such file or directory
1+/bin/bash: molvieProjection: そのようなファイルやディレクトリはありません
--- a/src/Tools/openGL/molvieViewer/src/molvieViewer.html
+++ b/src/Tools/openGL/molvieViewer/src/molvieViewer.html
@@ -1 +1 @@
1-/bin/bash: molvieViewer: No such file or directory
1+/bin/bash: molvieViewer: そのようなファイルやディレクトリはありません
--- a/src/Tools/rec3d/calcCommonLine/src/calcCommonLine.html
+++ b/src/Tools/rec3d/calcCommonLine/src/calcCommonLine.html
@@ -1 +1,26 @@
1-/bin/bash: calcCommonLine: No such file or directory
1+<HTML>
2+<HEAD>
3+<TITLE>calcCommonLine</TITLE>
4+</HEAD>
5+<BODY>
6+<H1>calcCommonLine</H1>
7+<H2>Usage</H2>
8+<PRE>
9+Usage: calcCommonLine
10+Options:
11+ [-i[nput] In (NULL ).as(inFile ) ] :Optional :InputEulerAnglesList
12+ [-R[ot]1 EMode1 (YOYS ).as(String )
13+ Rot1_1 (0.0 ).as(Real )
14+ Rot1_2 (0.0 ).as(Real )
15+ Rot1_3 (0.0 ).as(Real ) ] :Optional :Input: RotAngle1[degree]
16+ [-R[ot]2 EMode2 (YOYS ).as(String )
17+ Rot2_1 (0.0 ).as(Real )
18+ Rot2_2 (0.0 ).as(Real )
19+ Rot2_3 (0.0 ).as(Real ) ] :Optional :Input: RotAngle2[degree]
20+ [-o[utput] Out (stdout ).as(outFile ) ] :Optional :Output:Degrees
21+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
22+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
23+----- Additional Usage -----
24+</PRE>
25+</BODY>
26+</HTML>
--- a/src/Tools/rec3d/commonLinesSearchByVoting/src/commonLinesSearchByVoting.html
+++ b/src/Tools/rec3d/commonLinesSearchByVoting/src/commonLinesSearchByVoting.html
@@ -1 +1,54 @@
1-/bin/bash: commonLinesSearchByVoting: No such file or directory
1+<HTML>
2+<HEAD>
3+<TITLE>commonLinesSearchByVoting</TITLE>
4+</HEAD>
5+<BODY>
6+<H1>commonLinesSearchByVoting</H1>
7+<H2>Usage</H2>
8+<PRE>
9+Usage: commonLinesSearchByVoting
10+Options:
11+ [-i[nput] In (NULL ).as(inFile ) ] :Optional :InputCorrelationMapList
12+ [-i[nput]c[ommonLines]InC (NULL ).as(inFile ) ] :Optional :InputCommonLinesList
13+ [-i[nput]c[orrect]c[ommonLines]InCC (NULL ).as(inFile ) ] :Optional :InputCorrectCommonLinesList
14+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputFilteredCommonLinesList
15+ [-o[utput]a[ll] OutA (NULL ).as(outFile ) ] :Optional :OutputAllCommonLinesList
16+ [-o[utput]d[etecting]r[ate]OutDR (NULL ).as(outFile ) ] :Optional :OutputDetectingRate
17+ [-o[utput]d[etecting]r[ate]a[ll]OutDRA (NULL ).as(outFile ) ] :Optional :OutputDetectingRateALL
18+ [-o[utput]p[eaks]h[istgram]OutPH (NULL ).as(outFile ) ] :Optional :OutputPeaksHistgram
19+ [-e[stimation]n[umber]en (1 ).as(Integer ) ] :Optional :EstimationNumber
20+ [-th[resholdLevel] th (1 ).as(Integer ) ] :Optional :ThresholdLevel
21+ [-histgramCreate[Flag] ] :Optional :HistgramCreateFlag
22+ [-extend[VotingFlag] ] :Optional :ExtendVotingFlag
23+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
24+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
25+----- Additional Usage -----
26+Common lines are filtered only top G*100/sqrt(N) %, where N is the number of projections.
27+-extend Option
28+ Execute extended voting.
29+-m Option
30+ 0: normal
31+ 1: self voting (each angle histgram peak is multiplyed by its correlation value)
32+-th Option
33+ :
34+ -1: G = 2^(-1)
35+ 0: G = 2^0
36+ 1: G = 2^1
37+ 2: G = 2^2
38+ :
39+-en Option
40+ Estimation number of common line in a map.
41+ Running time is proportional to this number.
42+ Default; 1: the largest value in a correlation map is detected as common line.
43+MapList Format
44+ numOfProjection1 numOfProjection2 mapFileName
45+ : : :
46+CLinesList Format
47+ numOfProjection1 numOfProjection2 [ degOfProjection1 degOfProjection2 degDiff cor ] mapFileName
48+ : : : : : : :
49+Voting Algorithm by Amit Singer et al (2010),
50+"Detecting consistent common lines in cryo-EM by voting " (doi:10.1016/j.jsb.2009.11.003)
51+----------------------------
52+</PRE>
53+</BODY>
54+</HTML>
--- a/src/Tools/simulation/.Source.org
+++ b/src/Tools/simulation/.Source.org
@@ -2,4 +2,5 @@ SOURCE=\
22 energyTransferModelCheck \
33 energyTransferModelResultCheck \
44 muscleSimulation \
5+probabilityDensityFunction \
56 #LastSource
--- /dev/null
+++ b/src/Tools/simulation/probabilityDensityFunction/src/X86LINUX64
@@ -0,0 +1 @@
1+../../../../../hostdepend/X86LINUX64/src/Tools/simulation/probabilityDensityFunction/src/X86LINUX64
\ No newline at end of file
--- /dev/null
+++ b/src/Tools/simulation/probabilityDensityFunction/src/probabilityDensityFunction.html
@@ -0,0 +1,18 @@
1+<HTML>
2+<HEAD>
3+<TITLE>probabilityDensityFunction</TITLE>
4+</HEAD>
5+<BODY>
6+<H1>probabilityDensityFunction</H1>
7+<H2>Usage</H2>
8+<PRE>
9+Usage: probabilityDensityFunction
10+Options:
11+ [-i[nput] In (NULL ).as(inFile ) ] :Essential :InputDataFile
12+ [-o[utput] Out (NULL ).as(outFile ) ] :Essential :OutputDataFile
13+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
14+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
15+----- Additional Usage -----
16+</PRE>
17+</BODY>
18+</HTML>
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