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Eos-Image Analysis Environment
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base: Commit

This repository is a base of Eos.

Commit MetaInfo

Revision	79b6b51b2d0ac0c467f883fd6aa98a5caedddd21 (tree)
Time	2015-11-11 19:37:52
Author	久永浩司 <hisanagakouji@hisa...>
Commiter	久永浩司

Log Message

Merge branch 'master' of git.sourceforge.jp:/gitroot/eos/base

Change Summary

modified: bin/wish/Display2/Display2Init.wish (diff)
modified: bin/wish/Display2/tclIndex (diff)
modified: env/Eos_env (diff)
modified: env/install-eos.sh (diff)
add: env/update-eos.sh (diff)
modified: include/lmrcImageCalcArea.h (diff)
modified: include/lmrcImageSymmetryFind.h (diff)
modified: src/Objects/DataManip/mrcImage/src/lmrcImageCalcArea.c (diff)
modified: src/Objects/DataManip/mrcImage/src/lmrcImageCalcArea.h (diff)
modified: src/Objects/DataManip/mrcImage/src/lmrcImageSymmetryFind.c (diff)
modified: src/Objects/DataManip/mrcImage/src/lmrcImageSymmetryFind.h (diff)
modified: src/Objects/DataManip/mrcImage/src/lmrcImageTransformDescartesIntoPolar.c (diff)
modified: src/Tools/Config/Define.inc (diff)
modified: src/Tools/Integration/Display2/Config/OptionControlFile (diff)
modified: src/Tools/Integration/Display2/inc/Display2.h (diff)
modified: src/Tools/Integration/Display2/src/Display2.c (diff)
modified: src/Tools/Integration/Display2/src/Display2.html (diff)
modified: src/Tools/Integration/Display2/src/Display2.pane (diff)
modified: src/Tools/Integration/Display2/src/argCheck.c (diff)
modified: src/Tools/Integration/Display2/src/init.c (diff)
modified: src/Tools/Integration/Display2/src/test/Makefile (diff)
modified: src/Tools/Integration/Display2/src/usage.c (diff)
modified: src/Tools/Integration/Display2/src/wish/Display2Init.wish (diff)
modified: src/Tools/mrcImage/mrcImageAreaCalc/Config/OptionControlFile (diff)
modified: src/Tools/mrcImage/mrcImageAreaCalc/inc/mrcImageAreaCalc.h (diff)
modified: src/Tools/mrcImage/mrcImageAreaCalc/src/argCheck.c (diff)
modified: src/Tools/mrcImage/mrcImageAreaCalc/src/init.c (diff)
modified: src/Tools/mrcImage/mrcImageAreaCalc/src/mrcImageAreaCalc.c (diff)
modified: src/Tools/mrcImage/mrcImageAreaCalc/src/mrcImageAreaCalc.html (diff)
modified: src/Tools/mrcImage/mrcImageAreaCalc/src/mrcImageAreaCalc.pane (diff)
modified: src/Tools/mrcImage/mrcImageAreaCalc/src/usage.c (diff)
modified: src/Tools/mrcImage/mrcImageSymmetryAverage/src/mrcImageSymmetryAverage.c (diff)
modified: src/Tools/mrcImage/mrcImageSymmetryAverage/src/mrcImageSymmetryAverage.html (diff)
add: src/Tools/mrcImage/mrcImageSymmetryAverage/src/test/Makefile (diff)
add: src/Tools/mrcImage/mrcImageSymmetryAverage/src/test/data (diff)
modified: src/Tools/mrcImage/mrcImageSymmetryCentreFind/src/mrcImageSymmetryCentreFind.c (diff)
modified: src/Tools/mrcImage/mrcImageSymmetryCentreFind/src/mrcImageSymmetryCentreFind.html (diff)
add: src/Tools/mrcImage/mrcImageSymmetryCentreFind/src/test/Makefile (diff)
add: src/Tools/mrcImage/mrcImageSymmetryCentreFind/src/test/data (diff)
modified: src/Tools/mrcImage/mrcImageSymmetryFind/Config/OptionControlFile (diff)
modified: src/Tools/mrcImage/mrcImageSymmetryFind/inc/mrcImageSymmetryFind.h (diff)
modified: src/Tools/mrcImage/mrcImageSymmetryFind/src/argCheck.c (diff)
modified: src/Tools/mrcImage/mrcImageSymmetryFind/src/init.c (diff)
modified: src/Tools/mrcImage/mrcImageSymmetryFind/src/mrcImageSymmetryFind.c (diff)
modified: src/Tools/mrcImage/mrcImageSymmetryFind/src/mrcImageSymmetryFind.html (diff)
modified: src/Tools/mrcImage/mrcImageSymmetryFind/src/mrcImageSymmetryFind.pane (diff)
add: src/Tools/mrcImage/mrcImageSymmetryFind/src/test/Makefile (diff)
add: src/Tools/mrcImage/mrcImageSymmetryFind/src/test/data (diff)
modified: src/Tools/mrcImage/mrcImageSymmetryFind/src/usage.c (diff)

Incremental Difference

--- a/bin/wish/Display2/Display2Init.wish

+++ b/bin/wish/Display2/Display2Init.wish

		@@ -1,5 +1,30 @@
1	1	#!../Display2.HP
2		-proc display2Init {} {
	2	+
	3	+# From Arguments
	4	+proc display2SetVar {} {
	5	+ global mainImage
	6	+ global Roi
	7	+ global thresHigh
	8	+ global thresLow
	9	+ global Inverse
	10	+ global Zoom
	11	+
	12	+ if [ info exists thresHigh ] {
	13	+ set mainImage(thresHigh) $thresHigh
	14	+ }
	15	+ if [ info exists thresLow ] {
	16	+ set mainImage(thresLow) $thresLow
	17	+ }
	18	+ if [ info exists Inverse ] {
	19	+ set mainImage(Inverse) Yes
	20	+ }
	21	+ if { [ info exists Zoom ] } {
	22	+ set Roi(Zoom) $Zoom
	23	+ }
	24	+}
	25	+
	26	+# Set
	27	+proc display2InitVar {} {
3	28	global mousePressed
4	29	global Roi
5	30	global Point

		@@ -16,6 +41,7 @@ proc display2Init {} {
16	41	global mainImage
17	42	global overviewImage
18	43	global UnitCell
	44	+ global Section
19	45
20	46	global roiInfoWin
21	47

		@@ -29,8 +55,6 @@ proc display2Init {} {
29	55
30	56	set tcl_precision 17
31	57
32		- #puts "in display2Init"
33		-
34	58	# Canvas Area Create
35	59	if [ info exists Desktop(mainCanvasX) ] {
36	60	set Desktop(mainCanvasX) $Desktop(mainCanvasX)

		@@ -42,9 +66,13 @@ proc display2Init {} {
42	66	} else {
43	67	set Desktop(mainCanvasY) 1999
44	68	}
	69	+
	70	+
45	71	Canvas .overview_canvas 128 128
46	72	Canvas .zoom_canvas 128 128
	73	+
47	74	scrolledCanvas .main_canvas 128 128 [ list 0 0 $Desktop(mainCanvasX) $Desktop(mainCanvasY) ]
	75	+
48	76	set Desktop(mainCanvas) .main_canvas
49	77	set Desktop(overviewCanvas) .overview_canvas
50	78	set Desktop(zoomCanvas) .zoom_canvas

		@@ -53,7 +81,8 @@ proc display2Init {} {
53	81	set mainImage(mainCanvas) .main_canvas
54	82	set mainImage(overviewCanvas) .overview_canvas
55	83	set mainImage(zoomCanvas) .zoom_canvas
56		-
	84	+
	85	+
57	86	set overviewImage(image) No
58	87
59	88	set mainImage(image) No

		@@ -66,21 +95,11 @@ proc display2Init {} {
66	95	set mainImage(lz) 0
67	96	set mainImage(max) 1.0
68	97	set mainImage(min) 0.0
69		- if [ info exists thresHigh ] {
70		- set mainImage(thresHigh) $thresHigh
71		- } else {
72		- set mainImage(thresHigh) No
73		- }
74		- if [ info exists thresLow ] {
75		- set mainImage(thresLow) $thresLow
76		- } else {
77		- set mainImage(thresLow) No
78		- }
79		- if [ info exists Inverse ] {
80		- set mainImage(Inverse) Yes
81		- } else {
82		- set mainImage(Inverse) No
83		- }
	98	+
	99	+ set mainImage(thresHigh) No
	100	+ set mainImage(thresLow) No
	101	+ set mainImage(Inverse) No
	102	+
84	103	set mainImage(Contrast) 2
85	104
86	105	set mainImage(region) No

		@@ -117,11 +136,12 @@ proc display2Init {} {
117	136	set Roi(Extract) foreground
118	137	set Roi(withScale) Off
119	138	set Roi(absTicks) 54.6
	139	+ set Roi(numFormat) "-%04d.roi"
120	140
121	141	if { [ info exists fileNameIn ] } {
122	142	set Roi(MontageFile) [ string trimright $fileNameIn ".mrc" ].mon
123	143	set Roi(InformationFile) [ string trimright $fileNameIn ".mrc" ].roiinfo
124		- set Roi(ROIFile) [ string trimright $fileNameIn ".mrc" ]-%04d.roi
	144	+ set Roi(ROIFile) [ string trimright $fileNameIn ".mrc" ]$Roi(numFormat)
125	145	set Roi(ShrinkOriginalFile) [ string trimright $fileNameIn ".shrink"].mrc
126	146	} else {
127	147	set Roi(MontageFile) No.mon

		@@ -131,11 +151,7 @@ proc display2Init {} {
131	151	set Roi(CurrentID) 0
132	152	set Roi(TotalN) 0
133	153	#
134		- if { [ info exists Zoom ] } {
135		- set Roi(Zoom) $Zoom
136		- } else {
137		- set Roi(Zoom) 1
138		- }
	154	+ set Roi(Zoom) 1
139	155	set Roi(ZoomX) 1
140	156	set Roi(ZoomY) 1
141	157

		@@ -195,6 +211,174 @@ proc display2Init {} {
195	211	set UnitCell(beta) 90
196	212	set UnitCell(gamma) 90
197	213
	214	+ set Section(Initialize) 1
	215	+ set Section(flag) OFF
	216	+ set Section(which) Y
	217	+ set Section(scale) 1
	218	+ set Section(scaleDelta) 0.1
	219	+ set Section(at) 0
	220	+ set Section(atDelta) 1
	221	+ set Section(mode) normal
	222	+ set Section(Num) 0
	223	+ set Section(Current) -1
	224	+ set Section(Win,Title) "Section Information"
	225	+}
	226	+
	227	+proc display2InitVarSet { filename } {
	228	+ if [ file isdirectory "~/.Eos/ ] {
	229	+ #
	230	+ } else {
	231	+ file mkdir "~/.Eos"
	232	+ }
	233	+ set fpt [ open $filename a ]
	234	+
	235	+puts $fpt {
	236	+#
	237	+# Default
	238	+#
	239	+
	240	+# Precision
	241	+set tcl_precision 17
	242	+
	243	+# Image
	244	+set mainImage(thresHigh) No
	245	+set mainImage(thresLow) No
	246	+set mainImage(Inverse) No
	247	+set mainImage(Contrast) 2
	248	+set mainImage(flagLog) 0
	249	+set mainImage(flagPow) 0
	250	+set mainImage(HistNum) 256
	251	+
	252	+# Roi
	253	+set Roi(OKColor) #118866
	254	+set Roi(SelectColor) #0000ff
	255	+set Roi(LineWidth) 3
	256	+set Roi(CurrentColor) $Roi(OKColor)
	257	+set Roi(Shape) Rectangle
	258	+set Roi(Shrink) 1
	259	+set Roi(MultiShape) Off
	260	+set Roi(MultiNumber) Off
	261	+set Roi(SizeLock) Off
	262	+set Roi(Analysis) Off
	263	+set Roi(View) off
	264	+set Roi(Extract) foreground
	265	+set Roi(withScale) Off
	266	+set Roi(absTicks) 54.6
	267	+set Roi(numFormat) "-%04d.roi"
	268	+
	269	+# Zooming
	270	+set Roi(Zoom) 1
	271	+set Roi(ZoomX) 1
	272	+set Roi(ZoomY) 1
	273	+
	274	+# Point
	275	+set Point(x) 0
	276	+set Point(y) 0
	277	+set Point(dat) 0
	278	+set Point(cx) 0
	279	+set Point(cy) 0
	280	+set Point(cdat) 0
	281	+
	282	+# Roi Rectangle
	283	+set rectanglePoints(width) 128.0
	284	+set rectanglePoints(height) 128.0
	285	+set rectanglePoints(angle) 0.0
	286	+
	287	+# spline
	288	+set splinePoints(Width) 80
	289	+
	290	+# LayerLine
	291	+set LayerLine(flag) OFF
	292	+set LayerLine(pointRadius) 3
	293	+
	294	+# Projection Line
	295	+set Projection(flag) OFF
	296	+set Projection(which) Y
	297	+set Projection(scale) 1
	298	+
	299	+# Unit Cell
	300	+set UnitCell(n) 0
	301	+set UnitCell(dimension) 2
	302	+set UnitCell(axis1,n) 5
	303	+set UnitCell(axis2,n) 5
	304	+set UnitCell(axis3,n) 0
	305	+set UnitCell(axis1,x) 1
	306	+set UnitCell(axis1,y) 0
	307	+set UnitCell(axis1,z) 0
	308	+set UnitCell(axis2,x) 0
	309	+set UnitCell(axis2,y) 1
	310	+set UnitCell(axis2,z) 0
	311	+set UnitCell(axis3,x) 0
	312	+set UnitCell(axis3,y) 0
	313	+set UnitCell(axis3,z) 1
	314	+
	315	+set UnitCell(box,x) 5
	316	+set UnitCell(box,y) 5
	317	+set UnitCell(box,z) 0
	318	+
	319	+set UnitCell(alpha) 90
	320	+set UnitCell(beta) 90
	321	+set UnitCell(gamma) 90
	322	+
	323	+# Section
	324	+set Section(flag) OFF
	325	+set Section(which) Y
	326	+set Section(scale) 1
	327	+set Section(scaleDelta) 0.1
	328	+set Section(at) 0
	329	+set Section(atDelta) 1
	330	+set Section(mode) normal
	331	+}
	332	+ close $fpt
	333	+}
	334	+
	335	+proc display2Init {} {
	336	+ global mousePressed
	337	+ global Roi
	338	+ global Point
	339	+ global rectanglePoints
	340	+ global linePoints
	341	+ global splinePoints
	342	+ global LayerLine
	343	+ global Projection
	344	+ global ctfInfo
	345	+ global LogFile
	346	+
	347	+ global Desktop
	348	+ global CommandPut
	349	+ global mainImage
	350	+ global overviewImage
	351	+ global UnitCell
	352	+
	353	+ global roiInfoWin
	354	+
	355	+ # Global Variables from Display2
	356	+ global fileNameIn
	357	+ global LogFile
	358	+ global thresHigh
	359	+ global thresLow
	360	+ global Inverse
	361	+ global Zoom
	362	+
	363	+ global defaultFile
	364	+
	365	+ display2InitVar
	366	+
	367	+ if [ info exists defaultFile ] {
	368	+ #
	369	+ } else {
	370	+ set defaultFile "~/.Eos/Display2"
	371	+ }
	372	+ if [ file exists $defaultFile ] {
	373	+ #
	374	+ } else {
	375	+ display2InitVarSet $defaultFile
	376	+ }
	377	+ source $defaultFile
	378	+
	379	+ # from arguments
	380	+ display2SetVar
	381	+
198	382	display2MenuSet
199	383	display2MenuSet2
200	384	display2BindingSet .main_canvas.canvas

--- a/bin/wish/Display2/tclIndex

+++ b/bin/wish/Display2/tclIndex

		@@ -33,6 +33,9 @@ set auto_index(roiLineInfoFrameCreate) [list source [file join $dir Display2Info
33	33	set auto_index(roiSplineInfoFrameCreate) [list source [file join $dir Display2InfoROI.wish]]
34	34	set auto_index(roiRectangleInfoFrameCreate) [list source [file join $dir Display2InfoROI.wish]]
35	35	set auto_index(roiAnalysisFrameCreate) [list source [file join $dir Display2InfoROI.wish]]
	36	+set auto_index(display2SetVar) [list source [file join $dir Display2Init.wish]]
	37	+set auto_index(display2InitVar) [list source [file join $dir Display2Init.wish]]
	38	+set auto_index(display2InitVarSet) [list source [file join $dir Display2Init.wish]]
36	39	set auto_index(display2Init) [list source [file join $dir Display2Init.wish]]
37	40	set auto_index(display2MenuSet) [list source [file join $dir Display2Menu.wish]]
38	41	set auto_index(menuFileCreate) [list source [file join $dir Display2Menu.wish]]

--- a/env/Eos_env

+++ b/env/Eos_env

		@@ -5,11 +5,15 @@
5	5	if [ -z "$EOS_HOME0" ] ; then
6	6	export EOS_HOME=$HOME/Eos
7	7	export EOS_MIRROR_SITE=$HOME/EosMirror
8		- export EOS_GITUSER=$USER
9	8	else
10	9	# For Personal(by install-eos.sh)
11	10	export EOS_HOME=$EOS_HOME0
12	11	export EOS_MIRROR_SITE=$EOS_HOME0/EosMirror
	12	+fi
	13	+
	14	+#
	15	+# Eos
	16	+if [ -z $EOS_GITUSER ] ; then
13	17	export EOS_GITUSER=$USER
14	18	fi
15	19

--- a/env/install-eos.sh

+++ b/env/install-eos.sh

		@@ -1,6 +1,12 @@
1	1	#!/bin/bash
2	2	####
3		-EOS_HOME0=$HOME/Eos
	3	+WD=`pwd`
	4	+
	5	+
	6	+if [ -z $EOS_HOME0 ] ; then
	7	+ EOS_HOME0=$HOME/Eos
	8	+fi
	9	+
4	10	echo "Set the directroy to be installed [$EOS_HOME0]: "; read ANS
5	11	if [ ! -z $ANS ] ; then
6	12	EOS_HOME0=$ANS;

		@@ -11,14 +17,37 @@ unset ANS
11	17	echo "Directory: $EOS_HOME0";
12	18
13	19	#### No Change
14		-ROOT_EOS_SOURCEFORGE=https://sourceforge.jp/projects/eos/scm/git/base/blobs/master/
	20	+#ROOT_EOS_SOURCEFORGE=https://sourceforge.jp/projects/eos/scm/git/base/blobs/master/
	21	+ROOT_EOS_OSDN_GIT=git://git.osdn.jp/gitroot/eos/base.git
	22	+ROOT_EOS_OSDN_HTTP=http://scm.osdn.jp/gitroot/eos/base.git
	23	+ROOT_EOS_OSDN_SSH=${EOS_GITUSER}@git.osdn.jp:/gitroot/eos/base.git
	24	+ROOT_EOS_OSDN_HTTPS=https://scm.osdn.jp/gitroot/eos/base.git
	25	+
15	26	if [ ! -d $EOS_HOME0 ] ; then
16	27	mkdir $EOS_HOME0
17	28	fi
18	29
19	30	#curl -L $ROOT_EOS_SOURCEFORGE/env/Eos_env?export=raw \| sh - ;
20	31
21		-git clone --depth 1 git://git.sourceforge.jp/gitroot/eos/base.git $EOS_HOME0 \|\| echo "Already installed on $EOS_HOME0 or there are something wrong."
	32	+if [ -d $EOS_HOME0/.git ] ; then
	33	+ echo "Already installed"
	34	+ echo "Use update-eos.sh for updating or set a new directory for installation"
	35	+else
	36	+ if [ -z $EOS_GITUSER ] ; then
	37	+ INSTALL_FLAG=
	38	+ else
	39	+ git clone --depth 1 $ROOT_EOS_OSDN_SSH $EOS_HOME0 \|\| \
	40	+ git clone --depth 1 $ROOT_EOS_OSDN_HTTPS $EOS_HOME0 \|\| \
	41	+ echo "A port for SSH or HTTPS is not open, or something wrong for $EOS_GITUSER."
	42	+ INSTALL_FLAG=INSTALL
	43	+ fi
	44	+ if [ -z $INSTALL_FLAG ] ; then
	45	+ git clone --depth 1 $ROOT_EOS_OSDN_GIT $EOS_HOME0 \|\| \
	46	+ git clone --depth 1 $ROOT_EOS_OSDN_HTTP $EOS_HOME0 \|\| \
	47	+ echo "A port for git (9418) or HTTP is not open, or something wrong."
	48	+ fi
	49	+fi
	50	+
22	51
23	52	if [ -z $EOS_HOME0 ] ; then
24	53	export EOS_HOME0=$HOME/Eos

		@@ -39,6 +68,10 @@ test -r $HOME/.Eos_env && . $HOME/.Eos_env
39	68
40	69	EOF
41	70
	71	+#
	72	+# hostdepend
	73	+#
	74	+
42	75	if [ ! -f $HOME/.Eos_env ] ; then
43	76	echo "No .Eos_env"
44	77	ln -sf $EOS_HOME0/env/Eos_env $HOME/.Eos_env

		@@ -47,13 +80,37 @@ fi
47	80	source ~/.Eos_env \|\| echo "Prepare environment"
48	81	echo "hostdepend for ${EOS_HOSTDIR}"
49	82
	83	+HOSTDEPEND_EOS_OSDN_GIT=git://git.osdn.jp/gitroot/eos/hostdepend${EOS_HOSTDIR}.git
	84	+HOSTDEPEND_EOS_OSDN_HTTP=http://scm.osdn.jp/gitroot/eos/hostdepend${EOS_HOSTDIR}.git
	85	+HOSTDEPEND_EOS_OSDN_SSH=${EOS_GITUSER}@git.osdn.jp:/gitroot/eos/hostdepend${EOS_HOSTDIR}.git
	86	+HOSTDEPEND_EOS_OSDN_HTTPS=https://scm.osdn.jp/gitroot/eos/hostdepend${EOS_HOSTDIR}.git
	87	+
50	88	if [ ! -d $EOS_HOME0/hostdepend ] ; then
51	89	mkdir $EOS_HOME0/hostdepend
52	90	fi
53	91
54	92	if [ -d $EOS_HOME0/hostdepend ] ; then
55	93	cd $EOS_HOME0/hostdepend/;
56		- git clone --depth 1 git://git.sourceforge.jp/gitroot/eos/hostdepend${EOS_HOSTDIR}.git ${EOS_HOSTDIR} \|\| echo "Already installed hostdepend/${EOS_HOSTDIR} or there are something wrong.";
	94	+ if [ -d ${EOS_HOSTDIR}/.git ] ; then
	95	+ echo "Already installed hostdepend/${EOS_HOSTDIR}";
	96	+ echo "Use update-eos.sh for updating or set a new directory for installation"
	97	+ else
	98	+ if [ -z $EOS_GITUSER ] ; then
	99	+ INSTALL_FLAG=
	100	+ else
	101	+ git clone --depth 1 ${HOSTDEPEND_EOS_OSDN_SSH} ${EOS_HOSTDIR} \|\| \
	102	+ git clone --depth 1 ${HOSTDEPEND_EOS_OSDN_HTTPS} ${EOS_HOSTDIR} \|\| \
	103	+ echo "A port for SSH or HTTPS is not open, or something wrong."
	104	+ INSTALL_FLAG=INSTALL
	105	+ fi
	106	+ if [ -z $INSTALL_FLAG ] ; then
	107	+ git clone --depth 1 ${HOSTDEPEND_EOS_OSDN_GIT} ${EOS_HOSTDIR} \|\| \
	108	+ git clone --depth 1 ${HOSTDEPEND_EOS_OSDN_HTTP} ${EOS_HOSTDIR} \|\| \
	109	+ echo "A port for git (9418) or HTTP is not open, or something wrong."
	110	+ fi
	111	+ fi
57	112	else
58	113	echo "Cannot make hostdepend"
59	114	fi
	115	+
	116	+cd $WD

--- /dev/null

+++ b/env/update-eos.sh

		@@ -0,0 +1,72 @@
	1	+#!/bin/sh
	2	+WD=`pwd`
	3	+
	4	+if [ -z $EOS_HOME ] ; then
	5	+ echo "Please set an environment for Eos using $source env/Eos_env."
	6	+ exit
	7	+fi
	8	+
	9	+ROOT_EOS_OSDN_GIT=git://git.osdn.jp/gitroot/eos/base.git
	10	+ROOT_EOS_OSDN_HTTP=http://scm.osdn.jp/gitroot/eos/base.git
	11	+ROOT_EOS_OSDN_SSH=${EOS_GITUSER}@git.osdn.jp:/gitroot/eos/base.git
	12	+ROOT_EOS_OSDN_HTTPS=https://scm.osdn.jp/gitroot/eos/base.git
	13	+
	14	+if [ ! -d $EOS_HOME/.git ] ; then
	15	+ echo "Not installed"
	16	+ echo "Use install-eos.sh for updating or make concern env of EOS_HOME. Current var is $EOS_HOME."
	17	+else
	18	+ if [ -z $EOS_GITUSER ] ; then
	19	+ INSTALL_FLAG=
	20	+ else
	21	+ cd $EOS_HOME; echo "$EOS_GITUSER as EOS_GITUSER";
	22	+ git pull $ROOT_EOS_OSDN_SSH \|\| \
	23	+ git pull --depth 1 $ROOT_EOS_OSDN_HTTPS \|\| \
	24	+ echo "A port for SSH or HTTPS is not open, or something wrong for $EOS_GITUSER."
	25	+ INSTALL_FLAG=INSTALL
	26	+ fi
	27	+ if [ -z $NOT_INSTALL ] ; then
	28	+ cd $EOS_HOME; echo "No EOS_GITUSER.";
	29	+ git pull $ROOT_EOS_OSDN_GIT \|\| \
	30	+ git pull $ROOT_EOS_OSDN_HTTP \|\| \
	31	+ echo "A port for git (9418) or HTTP is not open, or something wrong."
	32	+ fi
	33	+fi
	34	+
	35	+if [ -z ${EOS_HOSTDIR} ] ; then
	36	+ echo "Set EOS_HOSTDIR. Current is $EOS_HOSTDIR";
	37	+ exit;
	38	+else
	39	+ echo "hostdepend for ${EOS_HOSTDIR}"
	40	+fi
	41	+
	42	+HOSTDEPEND_EOS_OSDN_GIT=git://git.osdn.jp/gitroot/eos/hostdepend${EOS_HOSTDIR}.git
	43	+HOSTDEPEND_EOS_OSDN_HTTP=http://scm.osdn.jp/gitroot/eos/hostdepend${EOS_HOSTDIR}.git
	44	+HOSTDEPEND_EOS_OSDN_SSH=${EOS_GITUSER}@git.osdn.jp:/gitroot/eos/hostdepend${EOS_HOSTDIR}.git
	45	+HOSTDEPEND_EOS_OSDN_HTTPS=https://scm.osdn.jp/gitroot/eos/hostdepend${EOS_HOSTDIR}.git
	46	+
	47	+if [ -d $EOS_HOME/hostdepend ] ; then
	48	+ cd $EOS_HOME/hostdepend/;
	49	+ if [ ! -d ${EOS_HOSTDIR}/.git ] ; then
	50	+ echo "Not installed hostdepend/${EOS_HOSTDIR}";
	51	+ echo "Use install-eos.sh for updating or set a new directory for update"
	52	+ else
	53	+ if [ -z $EOS_GITUSER ] ; then
	54	+ INSTALL_FLAG=
	55	+ else
	56	+ cd ${EOS_HOSTDIR}
	57	+ git pull ${HOSTDEPEND_EOS_OSDN_SSH} \|\| \
	58	+ git pull ${HOSTDEPEND_EOS_OSDN_HTTPS} \|\| \
	59	+ echo "A port for SSH or HTTPS is not open, or something wrong."
	60	+ INSTALL_FLAG=INSTALL
	61	+ fi
	62	+ if [ -z $NOT_INSTALL ] ; then
	63	+ git pull ${HOSTDEPEND_EOS_OSDN_GIT} \|\| \
	64	+ git pull ${HOSTDEPEND_EOS_OSDN_HTTP} \|\| \
	65	+ echo "A port for git (9418) or HTTP is not open, or something wrong."
	66	+ fi
	67	+ fi
	68	+else
	69	+ echo "No hostdepend dir"
	70	+fi
	71	+
	72	+cd $WD

--- a/include/lmrcImageCalcArea.h

+++ b/include/lmrcImageCalcArea.h

		@@ -10,4 +10,4 @@
10	10	*/
11	11
12	12	#include "mrcImage.h"
13		-void lmrcImageCalcArea(mrcImage* area, mrcImage* label, mrcImage* in, int mode);
	13	+void lmrcImageCalcArea(mrcImage* area, mrcImage* label, mrcImage* in, int neighbor, int mode);

--- a/include/lmrcImageSymmetryFind.h

+++ b/include/lmrcImageSymmetryFind.h

		@@ -36,7 +36,9 @@ typedef enum lmrcImageSymmetryFindCheckType {
36	36
37	37	typedef enum lmrcImageSymmetryFindCentreType {
38	38	lmrcImageSymmetryFindCheckTypeCentreGC = 0,
39		- lmrcImageSymmetryFindCheckTypeCentreSymmetry = 1
	39	+ lmrcImageSymmetryFindCheckTypeCentreSymmetry = 1,
	40	+ lmrcImageSymmetryFindCheckTypeCentreCentre = 2,
	41	+ lmrcImageSymmetryFindCheckTypeCentreOrigin = 3
40	42	} lmrcImageSymmetryFindCentreType;
41	43
42	44	typedef enum lmrcImageSymmetryFindSubtractionType {

		@@ -120,7 +122,17 @@ extern void
120	122	lmrcImageSymmetryFindModePrint(FILE* fpt);
121	123
122	124	extern void
	125	+lmrcImageSymmetryFindAlgorythmPrint(FILE* fpt);
	126	+
	127	+extern void
123	128	lmrcImageSymmetryCentreFind(mrcImage* in, DescartesCoord* centre, int mode);
	129	+
	130	+extern void
	131	+lmrcImageSymmetryCentreFindGC(mrcImage* in, DescartesCoord* centre, int mode);
	132	+
	133	+extern void
	134	+lmrcImageSymmetryCentreFindSymmetry(mrcImage* in, DescartesCoord* centre, int mode);
	135	+
124	136	/* prototype end */
125	137
126	138	#endif

--- a/src/Objects/DataManip/mrcImage/src/lmrcImageCalcArea.c

+++ b/src/Objects/DataManip/mrcImage/src/lmrcImageCalcArea.c

		@@ -16,7 +16,7 @@
16	16	#include "./lmrcImageCalcArea.h"
17	17
18	18	void
19		-lmrcImageCalcArea(mrcImage* area, mrcImage* label, mrcImage* in, int mode)
	19	+lmrcImageCalcArea(mrcImage* area, mrcImage* label, mrcImage* in, int neighbor, int mode)
20	20	{
21	21	mrcImageParaTypeReal x, y, z;
22	22	double data, data0, data1;

		@@ -25,7 +25,7 @@ lmrcImageCalcArea(mrcImage* area, mrcImage* label, mrcImage* in, int mode)
25	25	int total;
26	26
27	27	DEBUGPRINT("lmrcImageCalcArea Start\n");
28		- lmrcImageLabeling(label, in, 0);
	28	+ lmrcImageLabeling(label, in, neighbor, 0);
29	29	mrcStatDataSet(label, 0);
30	30
31	31	maxLabel = (int)(label->HeaderAMax+0.5);

--- a/src/Objects/DataManip/mrcImage/src/lmrcImageCalcArea.h

+++ b/src/Objects/DataManip/mrcImage/src/lmrcImageCalcArea.h

		@@ -10,4 +10,4 @@
10	10	*/
11	11
12	12	#include "mrcImage.h"
13		-void lmrcImageCalcArea(mrcImage* area, mrcImage* label, mrcImage* in, int mode);
	13	+void lmrcImageCalcArea(mrcImage* area, mrcImage* label, mrcImage* in, int neighbor, int mode);

--- a/src/Objects/DataManip/mrcImage/src/lmrcImageSymmetryFind.c

+++ b/src/Objects/DataManip/mrcImage/src/lmrcImageSymmetryFind.c

		@@ -30,7 +30,22 @@ static char __sccs_id[] = "%Z%lmrcImageSymmetryFind ver%I%; Date:%D% %Z%";
30	30	#include "lmrcImagesStatDataGet.h"
31	31	#include "lmrcFFTExpression.h"
32	32
33		-extern void
	33	+void
	34	+lmrcImageSymmetryFindAlgorythmPrint(FILE* fpt)
	35	+{
	36	+ fprintf(fpt, ">> Add\n");
	37	+ fprintf(fpt, " Image: Descartes coordinates (2D) -> Polar coordinates (2D) : PolarImage \n");
	38	+ fprintf(fpt, " Shift: Polar coordinates (2D) + Shift(360/n) -> Polar coordinates (2D) : ShiftImage \n");
	39	+ fprintf(fpt, " Add: AddImage(data2) := PolarImage(data1) + ShiftImage(data1_1)\n");
	40	+ fprintf(fpt, " Count: If 0<data1 && 0<data2 && data1threshold1 <= data2 <= 2data1 \n");
	41	+ fprintf(fpt, " (threshodl1 - 1)*data1_1 <= data1 <= data1_1 \n");
	42	+ fprintf(fpt, ">> Correalation\n");
	43	+ fprintf(fpt, " Image: Descartes coordinates (2D) -> Polar coordinates (2D) : PolarImage \n");
	44	+ fprintf(fpt, " Correlation: Polar coordinates (2D) -> Polar coordinates (2D) : Correlation\n");
	45	+ fprintf(fpt, " Average: each 360/n\n");
	46	+}
	47	+
	48	+void
34	49	lmrcImageSymmetryFindModePrint(FILE* fpt)
35	50	{
36	51	fprintf(fpt, ">>>> check type mode\n");

		@@ -43,6 +58,8 @@ lmrcImageSymmetryFindModePrint(FILE* fpt)
43	58	fprintf(fpt, ">>>> centre type mode\n");
44	59	fprintf(fpt, " %d : Centre is GC (gravity of centre)\n", lmrcImageSymmetryFindCheckTypeCentreGC);
45	60	fprintf(fpt, " %d : Centre is Rotational Symmetry\n", lmrcImageSymmetryFindCheckTypeCentreSymmetry);
	61	+ fprintf(fpt, " %d : Centre is at Image Centre \n", lmrcImageSymmetryFindCheckTypeCentreCentre);
	62	+ fprintf(fpt, " %d : Centre is at Image Origin\n", lmrcImageSymmetryFindCheckTypeCentreOrigin);
46	63
47	64
48	65	fprintf(fpt, ">>>> subtrcation type mode\n");

		@@ -51,9 +68,47 @@ lmrcImageSymmetryFindModePrint(FILE* fpt)
51	68	fprintf(fpt, " %d : Min Subtraction\n", lmrcImageSymmetryFindCheckTypeMinSubtraction);
52	69	}
53	70
54		-extern void
	71	+void
55	72	lmrcImageSymmetryCentreFind(mrcImage* in, DescartesCoord* centre, int mode)
56	73	{
	74	+ switch(mode) {
	75	+ case lmrcImageSymmetryFindCheckTypeCentreGC: {
	76	+ lmrcImageSymmetryCentreFindGC(in, centre, mode);
	77	+ break;
	78	+ }
	79	+ case lmrcImageSymmetryFindCheckTypeCentreSymmetry: {
	80	+ lmrcImageSymmetryCentreFindSymmetry(in, centre, mode);
	81	+ break;
	82	+ }
	83	+ case lmrcImageSymmetryFindCheckTypeCentreCentre: {
	84	+ centre->x = in->HeaderN.x/2+1;
	85	+ centre->y = in->HeaderN.y/2+1;
	86	+ centre->z = in->HeaderN.z/2+1;
	87	+ break;
	88	+ }
	89	+ case lmrcImageSymmetryFindCheckTypeCentreOrigin: {
	90	+ centre->x = 0;
	91	+ centre->y = 0;
	92	+ centre->z = 0;
	93	+ break;
	94	+ }
	95	+ default: {
	96	+ fprintf(stderr, "Not supported mode in lmrcImageSymmetryCentreFind: %d\n", mode);
	97	+ exit(EXIT_FAILURE);
	98	+ }
	99	+ }
	100	+}
	101	+
	102	+void
	103	+
	104	+lmrcImageSymmetryCentreFindSymmetry(mrcImage* in, DescartesCoord* centre, int mode)
	105	+{
	106	+ fprintf(stderr, "Not supported: pre\n");
	107	+}
	108	+
	109	+void
	110	+lmrcImageSymmetryCentreFindGC(mrcImage* in, DescartesCoord* centre, int mode)
	111	+{
57	112	DescartesCoord d, c, cMin, cMax, optimum;
58	113	double est, tmp;
59	114	mrcImageParaTypeReal x, y, z;

		@@ -168,6 +223,8 @@ lmrcImageSymmetryCentreFind(mrcImage* in, DescartesCoord* centre, int mode)
168	223	void
169	224	lmrcImageSymmetryFind(mrcImage* in, lmrcImageSymmetryFindInfo* linfo, int mode)
170	225	{
	226	+ //lmrcImageSymmetryCentreFind(in, &linfo->centre, linfo->centreMode);
	227	+
171	228	floatVectorInit(&(linfo->Value), linfo->maxNfold+1);
172	229	floatVectorInit(&(linfo->Point), linfo->maxNfold+1);
173	230

		@@ -215,8 +272,10 @@ lmrcImageSymmetryFindResultOut(FILE* fpt, mrcImage* in, lmrcImageSymmetryFindInf
215	272	}
216	273	}
217	274
218		- if(max<=min) {
	275	+
	276	+ if(max<min) {
219	277	fprintf(stderr, "Something wrong in lmrcImageSymmetryFindCheckResultOut: max <= min\n");
	278	+ exit(EXIT_FAILURE);
220	279	}
221	280
222	281	for(i=linfo->minNfold; i<=linfo->maxNfold; i++) {

		@@ -248,6 +307,7 @@ lmrcImageSymmetryFindResultOut(FILE* fpt, mrcImage* in, lmrcImageSymmetryFindInf
248	307	}
249	308	}
250	309	fprintf(fpt, ")\n");
	310	+ fprintf(fpt, "Centre: %f %f %f\n", linfo->centre.x, linfo->centre.y, linfo->centre.z);
251	311	if(linfo->flagAvg) {
252	312	lmrcImageSymmetryAverage(&(linfo->avg), in, symn, linfo->centre, 0);
253	313	mrcFileWrite(&(linfo->avg), linfo->avgName, "in lmrcImageSymmetryFindResultOut", 0);

		@@ -528,10 +588,39 @@ lmrcImageSymmetryFindCheckByFourier(mrcImage* in, lmrcImageSymmetryFindInfo* inf
528	588	/* Transform Descartes Coordinates Into Polar Coordinates */
529	589	linfo.dr = info->dr;
530	590	linfo.dphi = info->dtheta;
531		- linfo.flagDescartesIntoPolarInfo = 0;
532	591	linfo.flagrWeight = 0;
533	592	linfo.axisInfo = info->centreInfo;
534	593
	594	+ linfo.flagRotationalSymmetry = 0;
	595	+ linfo.flagImageCentreIsGravityCentre = 0;
	596	+ linfo.flagCentre = 0;
	597	+
	598	+ switch(info->centreMode) {
	599	+ case lmrcImageSymmetryFindCheckTypeCentreGC: {
	600	+ lmrcImageSymmetryCentreFind(in, &info->centre, info->centreMode);
	601	+ linfo.flagCentre = 1;
	602	+ linfo.Centre.x = info->centre.x;
	603	+ linfo.Centre.y = info->centre.y;
	604	+ linfo.Centre.z = info->centre.z;
	605	+ break;
	606	+ }
	607	+ case lmrcImageSymmetryFindCheckTypeCentreSymmetry: {
	608	+ linfo.flagRotationalSymmetry = 1;
	609	+ break;
	610	+ }
	611	+ default: {
	612	+ lmrcImageSymmetryCentreFind(in, &info->centre, info->centreMode);
	613	+ linfo.flagCentre = 1;
	614	+ linfo.Centre.x = info->centre.x;
	615	+ linfo.Centre.y = info->centre.y;
	616	+ linfo.Centre.z = info->centre.z;
	617	+ break;
	618	+ }
	619	+ }
	620	+ linfo.flagDescartesIntoPolarInfo = 0;
	621	+ linfo.flagrWeight = 1;
	622	+
	623	+
535	624	/* Fourier Component */
536	625	for(i=info->minNfold; i<=info->maxNfold; i++) {
537	626	DEBUGPRINT1("%d-fold Start\n", i)

		@@ -540,10 +629,6 @@ lmrcImageSymmetryFindCheckByFourier(mrcImage* in, lmrcImageSymmetryFindInfo* inf
540	629	linfo.flagImageCentreIsGravityCentre = 0;
541	630	linfo.flagRotationalSymmetry = 1;
542	631	linfo.flagCentre = 0;
543		- } else {
544		- linfo.flagImageCentreIsGravityCentre = 1;
545		- linfo.flagRotationalSymmetry = 0;
546		- linfo.flagCentre = 0;
547	632	}
548	633	lmrcImageTransformDescartesIntoPolar(&polarout, &subout, &linfo, &linfo2, 0);
549	634	DEBUGPRINT3("%d %d %d\n", polarout.HeaderN.x, polarout.HeaderN.y, polarout.HeaderN.z);

		@@ -568,7 +653,7 @@ lmrcImageSymmetryFindCheckByAdd(mrcImage* in, lmrcImageSymmetryFindInfo* info, i
568	653	mrcImageParaTypeRealCoord shift;
569	654	int x,y;
570	655	int i;
571		- double data1,data2;
	656	+ double data1,data2, ave;
572	657	lmrcImageTransformDescartesIntoPolarInfo linfo;
573	658	lDescartesIntoPolarInfo linfo2;
574	659

		@@ -577,21 +662,45 @@ lmrcImageSymmetryFindCheckByAdd(mrcImage* in, lmrcImageSymmetryFindInfo* info, i
577	662
578	663	/* Subtraction */
579	664	lmrcImageSymmetryFindSubtraction(&subout, in, info, mode);
580		-
581	665	shift.y=0;
582	666	shift.z=0;
583	667	linfo.dr = info->dr;
584	668	linfo.dphi = info->dtheta;
585		- linfo.flagImageCentreIsGravityCentre = 1;
	669	+
	670	+ linfo.flagRotationalSymmetry = 0;
	671	+ linfo.flagImageCentreIsGravityCentre = 0;
	672	+ linfo.flagCentre = 0;
	673	+
	674	+ switch(info->centreMode) {
	675	+ case lmrcImageSymmetryFindCheckTypeCentreGC: {
	676	+ lmrcImageSymmetryCentreFind(in, &info->centre, info->centreMode);
	677	+ linfo.flagCentre = 1;
	678	+ linfo.Centre.x = info->centre.x;
	679	+ linfo.Centre.y = info->centre.y;
	680	+ linfo.Centre.z = info->centre.z;
	681	+ break;
	682	+ }
	683	+ case lmrcImageSymmetryFindCheckTypeCentreSymmetry: {
	684	+ linfo.flagRotationalSymmetry = 1;
	685	+ break;
	686	+ }
	687	+ default: {
	688	+ lmrcImageSymmetryCentreFind(in, &info->centre, info->centreMode);
	689	+ linfo.flagCentre = 1;
	690	+ linfo.Centre.x = info->centre.x;
	691	+ linfo.Centre.y = info->centre.y;
	692	+ linfo.Centre.z = info->centre.z;
	693	+ break;
	694	+ }
	695	+ }
586	696	linfo.flagDescartesIntoPolarInfo = 0;
587	697	linfo.flagrWeight = 1;
588		- linfo.flagRotationalSymmetry = 0;
589	698
590	699	lmrcImageTransformDescartesIntoPolar(&polarout, &subout, &linfo, &linfo2, 0);
591	700
592	701	for(i=info->minNfold; i<=info->maxNfold; i++) {
593	702	info->Value.data[i]=0;
594		- shift.x=360/i;
	703	+ shift.x=360.0/info->dtheta/i+0.5;
595	704	shift.y=0;
596	705	shift.z=0;
597	706	lmrcImageShift(&shiftout,&polarout,shift,mrcPixelHowLinear);

		@@ -599,15 +708,19 @@ lmrcImageSymmetryFindCheckByAdd(mrcImage* in, lmrcImageSymmetryFindInfo* info, i
599	708
600	709	for(x=0;x<=subout.HeaderN.x;x++){
601	710	for(y=0;y<=subout.HeaderN.y;y++){
602		- mrcPixelDataGet(&polarout, x,y,0,&data1,mrcPixelRePart,mrcPixelHowNearest);
603		- mrcPixelDataGet(&shiftout,x,y,0,&data2,mrcPixelRePart,mrcPixelHowNearest);
604		- if(data1>0 && data2>0 && data1info->threshold1<=data2 && data2<=data12) {
	711	+ mrcPixelDataGet(&polarout, x,y,0,&data1,mrcPixelRePart,mrcPixelHowNearest);
	712	+ mrcPixelDataGet(&shiftout, x,y,0,&data2,mrcPixelRePart,mrcPixelHowNearest);
	713	+ ave = data2/2.0;
	714	+ if(0<data1 && 0<data2 && data1info->threshold1 <= data2 && data2<= data12) {
605	715	info->Value.data[i]++;
606	716	}
607	717	}
608	718	}
609	719	DEBUGPRINT1("Finish until %2d.\n",i);
610	720	}
	721	+ info->centre.x = linfo.Centre.x;
	722	+ info->centre.y = linfo.Centre.y;
	723	+ info->centre.z = linfo.Centre.z;
611	724	}
612	725
613	726

		@@ -631,13 +744,49 @@ lmrcImageSymmetryFindCheckByCorrelation(mrcImage* in, lmrcImageSymmetryFindInfo*
631	744	/* Transform Descartes coordinates into Polar coordinates */
632	745	linfo.dr = info->dr;
633	746	linfo.dphi = info->dtheta;
634		- linfo.flagImageCentreIsGravityCentre = 1;
	747	+
	748	+ linfo.flagRotationalSymmetry = 0;
	749	+ linfo.flagImageCentreIsGravityCentre = 0;
	750	+ linfo.flagCentre = 0;
	751	+
	752	+ switch(info->centreMode) {
	753	+ case lmrcImageSymmetryFindCheckTypeCentreGC: {
	754	+ lmrcImageSymmetryCentreFind(in, &info->centre, info->centreMode);
	755	+ linfo.flagCentre = 1;
	756	+ linfo.Centre.x = info->centre.x;
	757	+ linfo.Centre.y = info->centre.y;
	758	+ linfo.Centre.z = info->centre.z;
	759	+ break;
	760	+ }
	761	+ case lmrcImageSymmetryFindCheckTypeCentreSymmetry: {
	762	+ fprintf(stderr, "Not supported for this algorythm.\n");
	763	+ exit(EXIT_FAILURE);
	764	+ break;
	765	+ }
	766	+ default: {
	767	+ lmrcImageSymmetryCentreFind(in, &info->centre, info->centreMode);
	768	+ linfo.flagCentre = 1;
	769	+ linfo.Centre.x = info->centre.x;
	770	+ linfo.Centre.y = info->centre.y;
	771	+ linfo.Centre.z = info->centre.z;
	772	+ break;
	773	+ }
	774	+ }
635	775	linfo.flagDescartesIntoPolarInfo = 0;
636	776	linfo.flagrWeight = 1;
637		- linfo.flagRotationalSymmetry = 0;
638	777
639	778	lmrcImageTransformDescartesIntoPolar(&polarout, &subout, &linfo, &linfo2, 0);
640	779
	780	+ switch(info->centreMode) {
	781	+ case lmrcImageSymmetryFindCheckTypeCentreSymmetry: {
	782	+ linfo.Centre.x = linfo2.centre.x;
	783	+ linfo.Centre.y = linfo2.centre.y;
	784	+ linfo.Centre.z = linfo2.centre.z;
	785	+ break;
	786	+ }
	787	+ default:
	788	+ break;
	789	+ }
641	790	/* Projection along radial axis */
642	791	onedimout.Header=polarout.Header;
643	792	onedimout.HeaderN.y=1;

		@@ -668,7 +817,7 @@ lmrcImageSymmetryFindCheckByCorrelation(mrcImage* in, lmrcImageSymmetryFindInfo*
668	817
669	818	for(i=info->minNfold;i<=info->maxNfold;i++) {
670	819	sum.data[i]=0;
671		- delta=360/i;
	820	+ delta=(int)(360.0/info->dtheta/i+0.5);
672	821	for(j=1;j<i;j++){
673	822	mrcPixelDataGet(&(info->correlation),delta*j,0,0,&data1,mrcPixelRePart,mrcPixelHowNearest);
674	823	sum.data[i]+=data1;

		@@ -695,7 +844,8 @@ lmrcImageSymmetryAverage(mrcImage* out, mrcImage* in, int num, DescartesCoord ce
695	844	for(z=0; z<out->HeaderN.z; z++) {
696	845	for(y=0; y<out->HeaderN.y; y++) {
697	846	for(x=0; x<out->HeaderN.x; x++) {
698		- r = sqrt(SQR(x - centre.x) + SQR(y - centre.y));
	847	+ r = sqrt(SQR(MIN(fabs(x - centre.x), fabs(x - out->HeaderN.x - centre.x)))
	848	+ + SQR(MIN(fabs(y - centre.y), fabs(y - out->HeaderN.y - centre.y))));
699	849	angle = atan2(y-centre.y, x-centre.x);
700	850	for(i=0; i<num; i++) {
701	851	sx = centre.x + rcos(angle+i2*M_PI/num);

--- a/src/Objects/DataManip/mrcImage/src/lmrcImageSymmetryFind.h

+++ b/src/Objects/DataManip/mrcImage/src/lmrcImageSymmetryFind.h

		@@ -36,7 +36,9 @@ typedef enum lmrcImageSymmetryFindCheckType {
36	36
37	37	typedef enum lmrcImageSymmetryFindCentreType {
38	38	lmrcImageSymmetryFindCheckTypeCentreGC = 0,
39		- lmrcImageSymmetryFindCheckTypeCentreSymmetry = 1
	39	+ lmrcImageSymmetryFindCheckTypeCentreSymmetry = 1,
	40	+ lmrcImageSymmetryFindCheckTypeCentreCentre = 2,
	41	+ lmrcImageSymmetryFindCheckTypeCentreOrigin = 3
40	42	} lmrcImageSymmetryFindCentreType;
41	43
42	44	typedef enum lmrcImageSymmetryFindSubtractionType {

		@@ -120,7 +122,17 @@ extern void
120	122	lmrcImageSymmetryFindModePrint(FILE* fpt);
121	123
122	124	extern void
	125	+lmrcImageSymmetryFindAlgorythmPrint(FILE* fpt);
	126	+
	127	+extern void
123	128	lmrcImageSymmetryCentreFind(mrcImage* in, DescartesCoord* centre, int mode);
	129	+
	130	+extern void
	131	+lmrcImageSymmetryCentreFindGC(mrcImage* in, DescartesCoord* centre, int mode);
	132	+
	133	+extern void
	134	+lmrcImageSymmetryCentreFindSymmetry(mrcImage* in, DescartesCoord* centre, int mode);
	135	+
124	136	/* prototype end */
125	137
126	138	#endif

--- a/src/Objects/DataManip/mrcImage/src/lmrcImageTransformDescartesIntoPolar.c

+++ b/src/Objects/DataManip/mrcImage/src/lmrcImageTransformDescartesIntoPolar.c

		@@ -17,7 +17,7 @@ static char __sccs_id[] = "%Z%lmrcImageSymmetryFind ver%I%; Date:%D% %Z%";
17	17	#include <math.h>
18	18	#define GLOBAL_DECLARATION
19	19
20		-#undef DEBUG
	20	+#define DEBUG
21	21	#undef DEBUG2
22	22	#include "genUtil.h"
23	23	#include "../inc/mrcImage.h"

--- a/src/Tools/Config/Define.inc

+++ b/src/Tools/Config/Define.inc

		@@ -688,3 +688,11 @@ WORLDNAME=Tools
688	688	WORLDNAME=Tools
689	689	WORLDNAME=Tools
690	690	WORLDNAME=Tools
	691	+WORLDNAME=Tools
	692	+WORLDNAME=Tools
	693	+WORLDNAME=Tools
	694	+WORLDNAME=Tools
	695	+WORLDNAME=Tools
	696	+WORLDNAME=Tools
	697	+WORLDNAME=Tools
	698	+WORLDNAME=Tools

--- a/src/Tools/Integration/Display2/Config/OptionControlFile

+++ b/src/Tools/Integration/Display2/Config/OptionControlFile

		@@ -1,12 +1,13 @@
1	1	# OptionControlFile
2	2	# FileFormat
3		-"-i","-i[nput]","InputDataFile","Optional","1","1","In","inFile","NULL"
	3	+"-i","-i[nput]","Input:mrcImage","Optional","1","1","In","inFile::mrcImage","NULL"
4	4	"-t","-t[epmlate]","Template for InputFile ","Optional","1","1","Template","String","%d.roi"
5		-"-H","-H[ighForThres]","Template for InputFile ","Optional","1","1","ThresHigh","Real","0.0"
6		-"-L","-L[owForThres]","Template for InputFile ","Optional","1","1","ThresLow","Real","0.0"
	5	+"-H","-H[ighForThres]","HighThres","Optional","1","1","ThresHigh","Real","0.0"
	6	+"-L","-L[owForThres]","LowThres","Optional","1","1","ThresLow","Real","0.0"
7	7	"-Zoom","-Zoom","Zoom for InputFile ","Optional","1","1","Zoom","Real","1.0"
8	8	"-Inverse","-Inverse","Inverse (HighValue(dark)<->LowValue(bright)) for InputFile ","Optional","0"
9	9	"-o","-o[utput]","OutputLogFile","Optional","1","1","Out","String",".EosLog"
	10	+"-def","-def[ault]","OutputLogFile","Optional","1","1","Default","String","~/.Eos/Display2"
10	11	"-display","-display","OutputLogFile","Optional","1","1","geometry","String",":0.0"
11	12	"-geometry","-geometry","OutputLogFile","Optional","1","1","display","String","1024x1024+0+0"
12	13	"-c","-c[onfig]","ConfigurationFile","Optional","1","1","configFile","inFile","NULL"

--- a/src/Tools/Integration/Display2/inc/Display2.h

+++ b/src/Tools/Integration/Display2/inc/Display2.h

		@@ -34,6 +34,9 @@ typedef struct Display2Info {
34	34	long flagOut;
35	35	char* Out;
36	36
	37	+ long flagDefault;
	38	+ char* Default;
	39	+
37	40	long flaggeometry;
38	41	char* geometry;
39	42

--- a/src/Tools/Integration/Display2/src/Display2.c

+++ b/src/Tools/Integration/Display2/src/Display2.c

		@@ -87,6 +87,7 @@ Tcl_AppInit(Tcl_Interp *interp)
87	87	sprintf(s, "%ld", info.Inverse);
88	88	Tcl_SetVar(interp, "Inverse", s, 0);
89	89	}
	90	+ Tcl_SetVar(interp, "defaultFile", info.Default, 0);
90	91	Tcl_SetVar(interp, "LogFile", info.Out, 0);
91	92	Tcl_SetVar(interp, "fileNameTemplate", info.Template, 0);
92	93

--- a/src/Tools/Integration/Display2/src/Display2.html

+++ b/src/Tools/Integration/Display2/src/Display2.html

		@@ -8,13 +8,14 @@
8	8	<PRE>
9	9	Usage: Display2
10	10	Options:
11		- [-i[nput] In (NULL ).as(inFile ) ] :Optional :InputDataFile
	11	+ [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Optional :Input:mrcImage
12	12	[-t[epmlate] Template (%d.roi ).as(String ) ] :Optional :Template for InputFile
13		- [-H[ighForThres] ThresHigh (0.0 ).as(Real ) ] :Optional :Template for InputFile
14		- [-L[owForThres] ThresLow (0.0 ).as(Real ) ] :Optional :Template for InputFile
	13	+ [-H[ighForThres] ThresHigh (0.0 ).as(Real ) ] :Optional :HighThres
	14	+ [-L[owForThres] ThresLow (0.0 ).as(Real ) ] :Optional :LowThres
15	15	[-Zoom Zoom (1.0 ).as(Real ) ] :Optional :Zoom for InputFile
16	16	[-Inverse ] :Optional :Inverse (HighValue(dark)<->LowValue(bright)) for InputFile
17	17	[-o[utput] Out (.EosLog ).as(String ) ] :Optional :OutputLogFile
	18	+ [-def[ault] Default (~/.Eos/Display2).as(String ) ] :Optional :OutputLogFile
18	19	[-display geometry (:0.0 ).as(String ) ] :Optional :OutputLogFile
19	20	[-geometry display (1024x1024+0+0).as(String ) ] :Optional :OutputLogFile
20	21	[-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile

--- a/src/Tools/Integration/Display2/src/Display2.pane

+++ b/src/Tools/Integration/Display2/src/Display2.pane

		@@ -7,17 +7,18 @@
7	7	-R 1 0 1 5x1+35+0 'Run' 'execute operation' $EOS/bin/Display2
8	8	-H 1 5x1+41+0 'Help' 'help page' $EOS/src/Tools/Integration/Display2/doc/Display2.doc help
9	9	-Q 1 0 5.25x1+47+0 'Close'
10		- -I 1 0 1 0 0 1 -1x1+1+1.500000 ' ' 'In' 'InputDataFile' i
	10	+ -I 1 0 1 0 0 1 -1x1+1+1.500000 ' ' 'In' 'Input:mrcImage' i
11	11	-s 1 0 1 0 0 -1x1+1+3.000000 0 0 0 0 0 'Template' 'Template for InputFile ' t
12		- -f 1 0 1 0 0 -1x1+1+4.500000 0 0 0.000000 0 0 0 'ThresHigh' 'Template for InputFile ' H
13		- -f 1 0 1 0 0 -1x1+1+6.000000 0 0 0.000000 0 0 0 'ThresLow' 'Template for InputFile ' L
	12	+ -f 1 0 1 0 0 -1x1+1+4.500000 0 0 0.000000 0 0 0 'ThresHigh' 'HighThres' H
	13	+ -f 1 0 1 0 0 -1x1+1+6.000000 0 0 0.000000 0 0 0 'ThresLow' 'LowThres' L
14	14	-f 1 0 1 0 0 -1x1+1+7.500000 0 0 1.000000 0 0 0 'Zoom' 'Zoom for InputFile ' Zoom
15	15	-t 1 0 1 0 0 6x1+1+9 'Inverse' 'Inverse (HighValue(dark)<->LowValue(bright)) for InputFile ' Inverse
16	16	-s 1 0 1 0 0 -1x1+1+10.500000 0 0 0 0 0 'Out' 'OutputLogFile' o
17		- -s 1 0 1 0 0 -1x1+1+12.000000 0 0 0 0 0 'geometry' 'OutputLogFile' display
18		- -s 1 0 1 0 0 -1x1+1+13.500000 0 0 1024 0 0 'display' 'OutputLogFile' geometry
19		- -I 1 0 1 0 0 1 -1x1+1+15.000000 ' ' 'configFile' 'ConfigurationFile' c
20		- -i 1 0 1 0 0 -1x1+1+16.500000 0 0 0 0 0 'mode' 'Mode' m
	17	+ -s 1 0 1 0 0 -1x1+1+12.000000 0 0 0 0 0 'Default' 'OutputLogFile' def
	18	+ -s 1 0 1 0 0 -1x1+1+13.500000 0 0 0 0 0 'geometry' 'OutputLogFile' display
	19	+ -s 1 0 1 0 0 -1x1+1+15.000000 0 0 1024 0 0 'display' 'OutputLogFile' geometry
	20	+ -I 1 0 1 0 0 1 -1x1+1+16.500000 ' ' 'configFile' 'ConfigurationFile' c
	21	+ -i 1 0 1 0 0 -1x1+1+18.000000 0 0 0 0 0 'mode' 'Mode' m
21	22	-E
22	23	-E
23	24	-E

--- a/src/Tools/Integration/Display2/src/argCheck.c

+++ b/src/Tools/Integration/Display2/src/argCheck.c

		@@ -103,6 +103,17 @@ argCheck(Display2Info* info, int argc, char* argv[])
103	103	}
104	104	SBREAK;
105	105	}
	106	+ SCASE("def") {
	107	+ if(i+1<argc) {
	108	+ info->Default = stringGetNthWord(argv[i+1], 1, " ,");
	109	+ i++;
	110	+ info->flagDefault++;
	111	+ } else {
	112	+ usage(argv[0]);
	113	+ exit(EXIT_FAILURE);
	114	+ }
	115	+ SBREAK;
	116	+ }
106	117	SCASE("display") {
107	118	if(i+1<argc) {
108	119	info->geometry = stringGetNthWord(argv[i+1], 1, " ,");

--- a/src/Tools/Integration/Display2/src/init.c

+++ b/src/Tools/Integration/Display2/src/init.c

		@@ -19,6 +19,7 @@ init0(Display2Info* info)
19	19	info->Zoom = 1.0; info->flagZoom = 0;
20	20	info->Inverse=0;
21	21	info->Out = stringGetNthWord(".EosLog", 1, "\0"); info->flagOut = 0;
	22	+ info->Default = stringGetNthWord("~/.Eos/Display2", 1, "\0"); info->flagDefault = 0;
22	23	info->geometry = stringGetNthWord(":0.0", 1, "\0"); info->flaggeometry = 0;
23	24	info->display = stringGetNthWord("1024x1024+0+0", 1, "\0"); info->flagdisplay = 0;
24	25	info->fptconfigFile = NULL; info->flagconfigFile = 0;

		@@ -49,6 +50,9 @@ init1(Display2Info* info)
49	50	if(info->flagOut) {
50	51	}
51	52
	53	+ if(info->flagDefault) {
	54	+ }
	55	+
52	56	if(info->flaggeometry) {
53	57	}
54	58

--- a/src/Tools/Integration/Display2/src/test/Makefile

+++ b/src/Tools/Integration/Display2/src/test/Makefile

		@@ -11,7 +11,7 @@ help:
11	11
12	12	exec:
13	13	@echo "----- Execution Check -----"
14		- ../$(OSTYPE)/$(OBJECTNAME) -i data/test.mrc < ../wish/Display2.wish
	14	+ ../$(OSTYPE)/$(OBJECTNAME) -i data/FlagellaSection-0001.mrc < ../wish/Display2.wish
15	15	@echo "----- Calc check -----"
16	16
17	17	clean:

--- a/src/Tools/Integration/Display2/src/usage.c

+++ b/src/Tools/Integration/Display2/src/usage.c

		@@ -7,13 +7,14 @@ usage(char* thisProgram)
7	7	{
8	8	fprintf(stderr, "Usage: %s\n", thisProgram);
9	9	fprintf(stderr, "Options:\n");
10		- fprintf(stderr, " [-i[nput] In (NULL ).as(inFile ) ] :Optional :InputDataFile\n");
	10	+ fprintf(stderr, " [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Optional :Input:mrcImage\n");
11	11	fprintf(stderr, " [-t[epmlate] Template (%%d.roi ).as(String ) ] :Optional :Template for InputFile \n");
12		- fprintf(stderr, " [-H[ighForThres] ThresHigh (0.0 ).as(Real ) ] :Optional :Template for InputFile \n");
13		- fprintf(stderr, " [-L[owForThres] ThresLow (0.0 ).as(Real ) ] :Optional :Template for InputFile \n");
	12	+ fprintf(stderr, " [-H[ighForThres] ThresHigh (0.0 ).as(Real ) ] :Optional :HighThres\n");
	13	+ fprintf(stderr, " [-L[owForThres] ThresLow (0.0 ).as(Real ) ] :Optional :LowThres\n");
14	14	fprintf(stderr, " [-Zoom Zoom (1.0 ).as(Real ) ] :Optional :Zoom for InputFile \n");
15	15	fprintf(stderr, " [-Inverse ] :Optional :Inverse (HighValue(dark)<->LowValue(bright)) for InputFile \n");
16	16	fprintf(stderr, " [-o[utput] Out (.EosLog ).as(String ) ] :Optional :OutputLogFile\n");
	17	+ fprintf(stderr, " [-def[ault] Default (~/.Eos/Display2).as(String ) ] :Optional :OutputLogFile\n");
17	18	fprintf(stderr, " [-display geometry (:0.0 ).as(String ) ] :Optional :OutputLogFile\n");
18	19	fprintf(stderr, " [-geometry display (1024x1024+0+0).as(String ) ] :Optional :OutputLogFile\n");
19	20	fprintf(stderr, " [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile\n");

--- a/src/Tools/Integration/Display2/src/wish/Display2Init.wish

+++ b/src/Tools/Integration/Display2/src/wish/Display2Init.wish

		@@ -1,5 +1,30 @@
1	1	#!../Display2.HP
2		-proc display2Init {} {
	2	+
	3	+# From Arguments
	4	+proc display2SetVar {} {
	5	+ global mainImage
	6	+ global Roi
	7	+ global thresHigh
	8	+ global thresLow
	9	+ global Inverse
	10	+ global Zoom
	11	+
	12	+ if [ info exists thresHigh ] {
	13	+ set mainImage(thresHigh) $thresHigh
	14	+ }
	15	+ if [ info exists thresLow ] {
	16	+ set mainImage(thresLow) $thresLow
	17	+ }
	18	+ if [ info exists Inverse ] {
	19	+ set mainImage(Inverse) Yes
	20	+ }
	21	+ if { [ info exists Zoom ] } {
	22	+ set Roi(Zoom) $Zoom
	23	+ }
	24	+}
	25	+
	26	+# Set
	27	+proc display2InitVar {} {
3	28	global mousePressed
4	29	global Roi
5	30	global Point

		@@ -16,6 +41,7 @@ proc display2Init {} {
16	41	global mainImage
17	42	global overviewImage
18	43	global UnitCell
	44	+ global Section
19	45
20	46	global roiInfoWin
21	47

		@@ -29,8 +55,6 @@ proc display2Init {} {
29	55
30	56	set tcl_precision 17
31	57
32		- #puts "in display2Init"
33		-
34	58	# Canvas Area Create
35	59	if [ info exists Desktop(mainCanvasX) ] {
36	60	set Desktop(mainCanvasX) $Desktop(mainCanvasX)

		@@ -42,9 +66,13 @@ proc display2Init {} {
42	66	} else {
43	67	set Desktop(mainCanvasY) 1999
44	68	}
	69	+
	70	+
45	71	Canvas .overview_canvas 128 128
46	72	Canvas .zoom_canvas 128 128
	73	+
47	74	scrolledCanvas .main_canvas 128 128 [ list 0 0 $Desktop(mainCanvasX) $Desktop(mainCanvasY) ]
	75	+
48	76	set Desktop(mainCanvas) .main_canvas
49	77	set Desktop(overviewCanvas) .overview_canvas
50	78	set Desktop(zoomCanvas) .zoom_canvas

		@@ -53,7 +81,8 @@ proc display2Init {} {
53	81	set mainImage(mainCanvas) .main_canvas
54	82	set mainImage(overviewCanvas) .overview_canvas
55	83	set mainImage(zoomCanvas) .zoom_canvas
56		-
	84	+
	85	+
57	86	set overviewImage(image) No
58	87
59	88	set mainImage(image) No

		@@ -66,21 +95,11 @@ proc display2Init {} {
66	95	set mainImage(lz) 0
67	96	set mainImage(max) 1.0
68	97	set mainImage(min) 0.0
69		- if [ info exists thresHigh ] {
70		- set mainImage(thresHigh) $thresHigh
71		- } else {
72		- set mainImage(thresHigh) No
73		- }
74		- if [ info exists thresLow ] {
75		- set mainImage(thresLow) $thresLow
76		- } else {
77		- set mainImage(thresLow) No
78		- }
79		- if [ info exists Inverse ] {
80		- set mainImage(Inverse) Yes
81		- } else {
82		- set mainImage(Inverse) No
83		- }
	98	+
	99	+ set mainImage(thresHigh) No
	100	+ set mainImage(thresLow) No
	101	+ set mainImage(Inverse) No
	102	+
84	103	set mainImage(Contrast) 2
85	104
86	105	set mainImage(region) No

		@@ -117,11 +136,12 @@ proc display2Init {} {
117	136	set Roi(Extract) foreground
118	137	set Roi(withScale) Off
119	138	set Roi(absTicks) 54.6
	139	+ set Roi(numFormat) "-%04d.roi"
120	140
121	141	if { [ info exists fileNameIn ] } {
122	142	set Roi(MontageFile) [ string trimright $fileNameIn ".mrc" ].mon
123	143	set Roi(InformationFile) [ string trimright $fileNameIn ".mrc" ].roiinfo
124		- set Roi(ROIFile) [ string trimright $fileNameIn ".mrc" ]-%04d.roi
	144	+ set Roi(ROIFile) [ string trimright $fileNameIn ".mrc" ]$Roi(numFormat)
125	145	set Roi(ShrinkOriginalFile) [ string trimright $fileNameIn ".shrink"].mrc
126	146	} else {
127	147	set Roi(MontageFile) No.mon

		@@ -131,11 +151,7 @@ proc display2Init {} {
131	151	set Roi(CurrentID) 0
132	152	set Roi(TotalN) 0
133	153	#
134		- if { [ info exists Zoom ] } {
135		- set Roi(Zoom) $Zoom
136		- } else {
137		- set Roi(Zoom) 1
138		- }
	154	+ set Roi(Zoom) 1
139	155	set Roi(ZoomX) 1
140	156	set Roi(ZoomY) 1
141	157

		@@ -195,6 +211,174 @@ proc display2Init {} {
195	211	set UnitCell(beta) 90
196	212	set UnitCell(gamma) 90
197	213
	214	+ set Section(Initialize) 1
	215	+ set Section(flag) OFF
	216	+ set Section(which) Y
	217	+ set Section(scale) 1
	218	+ set Section(scaleDelta) 0.1
	219	+ set Section(at) 0
	220	+ set Section(atDelta) 1
	221	+ set Section(mode) normal
	222	+ set Section(Num) 0
	223	+ set Section(Current) -1
	224	+ set Section(Win,Title) "Section Information"
	225	+}
	226	+
	227	+proc display2InitVarSet { filename } {
	228	+ if [ file isdirectory "~/.Eos/ ] {
	229	+ #
	230	+ } else {
	231	+ file mkdir "~/.Eos"
	232	+ }
	233	+ set fpt [ open $filename a ]
	234	+
	235	+puts $fpt {
	236	+#
	237	+# Default
	238	+#
	239	+
	240	+# Precision
	241	+set tcl_precision 17
	242	+
	243	+# Image
	244	+set mainImage(thresHigh) No
	245	+set mainImage(thresLow) No
	246	+set mainImage(Inverse) No
	247	+set mainImage(Contrast) 2
	248	+set mainImage(flagLog) 0
	249	+set mainImage(flagPow) 0
	250	+set mainImage(HistNum) 256
	251	+
	252	+# Roi
	253	+set Roi(OKColor) #118866
	254	+set Roi(SelectColor) #0000ff
	255	+set Roi(LineWidth) 3
	256	+set Roi(CurrentColor) $Roi(OKColor)
	257	+set Roi(Shape) Rectangle
	258	+set Roi(Shrink) 1
	259	+set Roi(MultiShape) Off
	260	+set Roi(MultiNumber) Off
	261	+set Roi(SizeLock) Off
	262	+set Roi(Analysis) Off
	263	+set Roi(View) off
	264	+set Roi(Extract) foreground
	265	+set Roi(withScale) Off
	266	+set Roi(absTicks) 54.6
	267	+set Roi(numFormat) "-%04d.roi"
	268	+
	269	+# Zooming
	270	+set Roi(Zoom) 1
	271	+set Roi(ZoomX) 1
	272	+set Roi(ZoomY) 1
	273	+
	274	+# Point
	275	+set Point(x) 0
	276	+set Point(y) 0
	277	+set Point(dat) 0
	278	+set Point(cx) 0
	279	+set Point(cy) 0
	280	+set Point(cdat) 0
	281	+
	282	+# Roi Rectangle
	283	+set rectanglePoints(width) 128.0
	284	+set rectanglePoints(height) 128.0
	285	+set rectanglePoints(angle) 0.0
	286	+
	287	+# spline
	288	+set splinePoints(Width) 80
	289	+
	290	+# LayerLine
	291	+set LayerLine(flag) OFF
	292	+set LayerLine(pointRadius) 3
	293	+
	294	+# Projection Line
	295	+set Projection(flag) OFF
	296	+set Projection(which) Y
	297	+set Projection(scale) 1
	298	+
	299	+# Unit Cell
	300	+set UnitCell(n) 0
	301	+set UnitCell(dimension) 2
	302	+set UnitCell(axis1,n) 5
	303	+set UnitCell(axis2,n) 5
	304	+set UnitCell(axis3,n) 0
	305	+set UnitCell(axis1,x) 1
	306	+set UnitCell(axis1,y) 0
	307	+set UnitCell(axis1,z) 0
	308	+set UnitCell(axis2,x) 0
	309	+set UnitCell(axis2,y) 1
	310	+set UnitCell(axis2,z) 0
	311	+set UnitCell(axis3,x) 0
	312	+set UnitCell(axis3,y) 0
	313	+set UnitCell(axis3,z) 1
	314	+
	315	+set UnitCell(box,x) 5
	316	+set UnitCell(box,y) 5
	317	+set UnitCell(box,z) 0
	318	+
	319	+set UnitCell(alpha) 90
	320	+set UnitCell(beta) 90
	321	+set UnitCell(gamma) 90
	322	+
	323	+# Section
	324	+set Section(flag) OFF
	325	+set Section(which) Y
	326	+set Section(scale) 1
	327	+set Section(scaleDelta) 0.1
	328	+set Section(at) 0
	329	+set Section(atDelta) 1
	330	+set Section(mode) normal
	331	+}
	332	+ close $fpt
	333	+}
	334	+
	335	+proc display2Init {} {
	336	+ global mousePressed
	337	+ global Roi
	338	+ global Point
	339	+ global rectanglePoints
	340	+ global linePoints
	341	+ global splinePoints
	342	+ global LayerLine
	343	+ global Projection
	344	+ global ctfInfo
	345	+ global LogFile
	346	+
	347	+ global Desktop
	348	+ global CommandPut
	349	+ global mainImage
	350	+ global overviewImage
	351	+ global UnitCell
	352	+
	353	+ global roiInfoWin
	354	+
	355	+ # Global Variables from Display2
	356	+ global fileNameIn
	357	+ global LogFile
	358	+ global thresHigh
	359	+ global thresLow
	360	+ global Inverse
	361	+ global Zoom
	362	+
	363	+ global defaultFile
	364	+
	365	+ display2InitVar
	366	+
	367	+ if [ info exists defaultFile ] {
	368	+ #
	369	+ } else {
	370	+ set defaultFile "~/.Eos/Display2"
	371	+ }
	372	+ if [ file exists $defaultFile ] {
	373	+ #
	374	+ } else {
	375	+ display2InitVarSet $defaultFile
	376	+ }
	377	+ source $defaultFile
	378	+
	379	+ # from arguments
	380	+ display2SetVar
	381	+
198	382	display2MenuSet
199	383	display2MenuSet2
200	384	display2BindingSet .main_canvas.canvas

--- a/src/Tools/mrcImage/mrcImageAreaCalc/Config/OptionControlFile

+++ b/src/Tools/mrcImage/mrcImageAreaCalc/Config/OptionControlFile

		@@ -6,5 +6,6 @@
6	6	"-l","-l[abel]","Output: mrcImage:labeling","Optional","1","1","Label","outFile::mrcImage","NULL"
7	7	"-OH","-O[utput]H[istgram]","Output: ASCII: area info","Optional","1","1","OutHist","outFile::ASCII","NULL"
8	8	"-H","-H[istgram]","Delta","Optional","1","1","DelHist","Real","1"
	9	+"-N","-N[eighbor]","Neighbor","Optional","1","1","Neighbor","Real","0"
9	10	"-c","-c[onfig]","ConfigurationFile","Optional","1","1","configFile","inFile","NULL"
10	11	"-m","-m[ode]","Mode","Optional","1","1","mode","Integer","0"

--- a/src/Tools/mrcImage/mrcImageAreaCalc/inc/mrcImageAreaCalc.h

+++ b/src/Tools/mrcImage/mrcImageAreaCalc/inc/mrcImageAreaCalc.h

		@@ -36,6 +36,9 @@ typedef struct mrcImageAreaCalcInfo {
36	36	long flagDelHist;
37	37	float DelHist;
38	38
	39	+ long flagNeighbor;
	40	+ float Neighbor;
	41	+
39	42	long flagconfigFile;
40	43	char* configFile;
41	44	FILE* fptconfigFile;

--- a/src/Tools/mrcImage/mrcImageAreaCalc/src/argCheck.c

+++ b/src/Tools/mrcImage/mrcImageAreaCalc/src/argCheck.c

		@@ -94,6 +94,17 @@ argCheck(mrcImageAreaCalcInfo* info, int argc, char* argv[])
94	94	}
95	95	SBREAK;
96	96	}
	97	+ SCASE("N") {
	98	+ if(i+1<argc) {
	99	+ info->Neighbor = stringGetNthRealData(argv[i+1], 1, " ,");
	100	+ i++;
	101	+ info->flagNeighbor++;
	102	+ } else {
	103	+ usage(argv[0]);
	104	+ exit(EXIT_FAILURE);
	105	+ }
	106	+ SBREAK;
	107	+ }
97	108	SCASE("c") {
98	109	if(i+1<argc) {
99	110	info->configFile = stringGetNthWord(argv[i+1], 1, " ,");

--- a/src/Tools/mrcImage/mrcImageAreaCalc/src/init.c

+++ b/src/Tools/mrcImage/mrcImageAreaCalc/src/init.c

		@@ -18,6 +18,7 @@ init0(mrcImageAreaCalcInfo* info)
18	18	info->fptLabel = NULL; info->flagLabel = 0;
19	19	info->fptOutHist = NULL; info->flagOutHist = 0;
20	20	info->DelHist = 1; info->flagDelHist = 0;
	21	+ info->Neighbor = 0; info->flagNeighbor = 0;
21	22	info->fptconfigFile = NULL; info->flagconfigFile = 0;
22	23	info->mode = 0; info->flagmode = 0;
23	24	}

		@@ -60,6 +61,9 @@ init1(mrcImageAreaCalcInfo* info)
60	61	if(info->flagDelHist) {
61	62	}
62	63
	64	+ if(info->flagNeighbor) {
	65	+ }
	66	+
63	67	if(info->flagconfigFile) {
64	68	info->fptconfigFile = fileOpen(info->configFile, "r");
65	69	}

--- a/src/Tools/mrcImage/mrcImageAreaCalc/src/mrcImageAreaCalc.c

+++ b/src/Tools/mrcImage/mrcImageAreaCalc/src/mrcImageAreaCalc.c

		@@ -51,7 +51,7 @@ main(int argc, char* argv[])
51	51	DEBUGPRINT("Program Start\n");
52	52	mrcFileRead(&in, info.In, "mrcFileRead", 0);
53	53
54		- lmrcImageCalcArea(&out, &label, &in, 0);
	54	+ lmrcImageCalcArea(&out, &label, &in, info.Neighbor, 0);
55	55
56	56	mrcFileWrite(&out, info.Out, "mrcFileWrite", 0);
57	57	if(info.flagLabel) {

--- a/src/Tools/mrcImage/mrcImageAreaCalc/src/mrcImageAreaCalc.html

+++ b/src/Tools/mrcImage/mrcImageAreaCalc/src/mrcImageAreaCalc.html

		@@ -14,6 +14,7 @@ Options:
14	14	[-l[abel] Label (NULL ).as(outFile::mrcImage ) ] :Optional :Output: mrcImage:labeling
15	15	[-O[utput]H[istgram] OutHist (NULL ).as(outFile::ASCII ) ] :Optional :Output: ASCII: area info
16	16	[-H[istgram] DelHist (1 ).as(Real ) ] :Optional :Delta
	17	+ [-N[eighbor] Neighbor (0 ).as(Real ) ] :Optional :Neighbor
17	18	[-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
18	19	[-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
19	20	----- Additional Usage -----

--- a/src/Tools/mrcImage/mrcImageAreaCalc/src/mrcImageAreaCalc.pane

+++ b/src/Tools/mrcImage/mrcImageAreaCalc/src/mrcImageAreaCalc.pane

		@@ -13,8 +13,9 @@
13	13	-O 1 0 1 0 0 1 -1x1+1+6.000000 ' ' 'Label' 'Output: mrcImage:labeling' l
14	14	-O 1 0 1 0 0 1 -1x1+1+7.500000 ' ' 'OutHist' 'Output: ASCII: area info' OH
15	15	-f 1 0 1 0 0 -1x1+1+9.000000 0 0 1.000000 0 0 0 'DelHist' 'Delta' H
16		- -I 1 0 1 0 0 1 -1x1+1+10.500000 ' ' 'configFile' 'ConfigurationFile' c
17		- -i 1 0 1 0 0 -1x1+1+12.000000 0 0 0 0 0 'mode' 'Mode' m
	16	+ -f 1 0 1 0 0 -1x1+1+10.500000 0 0 0.000000 0 0 0 'Neighbor' 'Neighbor' N
	17	+ -I 1 0 1 0 0 1 -1x1+1+12.000000 ' ' 'configFile' 'ConfigurationFile' c
	18	+ -i 1 0 1 0 0 -1x1+1+13.500000 0 0 0 0 0 'mode' 'Mode' m
18	19	-E
19	20	-E
20	21	-E

--- a/src/Tools/mrcImage/mrcImageAreaCalc/src/usage.c

+++ b/src/Tools/mrcImage/mrcImageAreaCalc/src/usage.c

		@@ -13,6 +13,7 @@ usage(char* thisProgram)
13	13	fprintf(stderr, " [-l[abel] Label (NULL ).as(outFile::mrcImage ) ] :Optional :Output: mrcImage:labeling\n");
14	14	fprintf(stderr, " [-O[utput]H[istgram] OutHist (NULL ).as(outFile::ASCII ) ] :Optional :Output: ASCII: area info\n");
15	15	fprintf(stderr, " [-H[istgram] DelHist (1 ).as(Real ) ] :Optional :Delta\n");
	16	+ fprintf(stderr, " [-N[eighbor] Neighbor (0 ).as(Real ) ] :Optional :Neighbor\n");
16	17	fprintf(stderr, " [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile\n");
17	18	fprintf(stderr, " [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode\n");
18	19	additionalUsage();

--- a/src/Tools/mrcImage/mrcImageSymmetryAverage/src/mrcImageSymmetryAverage.c

+++ b/src/Tools/mrcImage/mrcImageSymmetryAverage/src/mrcImageSymmetryAverage.c

		@@ -61,4 +61,7 @@ void
61	61	additionalUsage()
62	62	{
63	63	fprintf(stderr, "----- Additional Usage -----\n");
	64	+ fprintf(stderr, "-centre : Set a defined centre\n");
	65	+ fprintf(stderr, " otherwise CentreOfGravity \n");
	66	+
64	67	}

--- a/src/Tools/mrcImage/mrcImageSymmetryAverage/src/mrcImageSymmetryAverage.html

+++ b/src/Tools/mrcImage/mrcImageSymmetryAverage/src/mrcImageSymmetryAverage.html

		@@ -17,6 +17,8 @@ Options:
17	17	[-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
18	18	[-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
19	19	----- Additional Usage -----
	20	+-centre : Set a defined centre
	21	+ otherwise CentreOfGravity
20	22	</PRE>
21	23	</BODY>
22	24	</HTML>

--- /dev/null

+++ b/src/Tools/mrcImage/mrcImageSymmetryAverage/src/test/Makefile

		@@ -0,0 +1,27 @@
	1	+include ../../Config/Define.inc
	2	+include ../../../Config/Define.inc
	3	+include ../../../../Config/Define.inc
	4	+include ../../../../../Config/Define.inc
	5	+
	6	+DATA=data/FlagellaSection-0001
	7	+
	8	+all: help exec
	9	+
	10	+help:
	11	+ @echo "----- Help Message Check -----"
	12	+ @../$(OSTYPE)/$(OBJECTNAME) -h
	13	+
	14	+exec:
	15	+ @echo "----- Execution Check -----"
	16	+ ../$(OSTYPE)/$(OBJECTNAME) -i $(DATA).cen -o $(DATA).rot12 -n 12 -centre 128 128 0
	17	+ ../$(OSTYPE)/$(OBJECTNAME) -i $(DATA).cen -o $(DATA).rot13 -n 13 -centre 128 128 0
	18	+ ../$(OSTYPE)/$(OBJECTNAME) -i $(DATA).cen -o $(DATA).rot14 -n 14 -centre 128 128 0
	19	+ ../$(OSTYPE)/$(OBJECTNAME) -i $(DATA).cen -o $(DATA).0.rot12 -n 12 -centre 0 0 0
	20	+ ../$(OSTYPE)/$(OBJECTNAME) -i $(DATA).cen -o $(DATA).0.rot13 -n 13 -centre 0 0 0
	21	+ ../$(OSTYPE)/$(OBJECTNAME) -i $(DATA).cen -o $(DATA).0.rot14 -n 14 -centre 0 0 0
	22	+ @echo "----- Calc check -----"
	23	+
	24	+clean:
	25	+
	26	+init:
	27	+ mrcImageSymmetryCentreFind -i $(DATA).roi -o $(DATA).cen -O $(DATA).info -m 0

--- /dev/null

+++ b/src/Tools/mrcImage/mrcImageSymmetryAverage/src/test/data

		@@ -0,0 +1 @@
	1	+../../../../../..//data/mrcImageSymmetryAverage
		\ No newline at end of file

--- a/src/Tools/mrcImage/mrcImageSymmetryCentreFind/src/mrcImageSymmetryCentreFind.c

+++ b/src/Tools/mrcImage/mrcImageSymmetryCentreFind/src/mrcImageSymmetryCentreFind.c

		@@ -55,4 +55,5 @@ void
55	55	additionalUsage()
56	56	{
57	57	fprintf(stderr, "----- Additional Usage -----\n");
	58	+ lmrcImageSymmetryFindModePrint(stderr);
58	59	}

--- a/src/Tools/mrcImage/mrcImageSymmetryCentreFind/src/mrcImageSymmetryCentreFind.html

+++ b/src/Tools/mrcImage/mrcImageSymmetryCentreFind/src/mrcImageSymmetryCentreFind.html

		@@ -14,6 +14,21 @@ Options:
14	14	[-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
15	15	[-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
16	16	----- Additional Usage -----
	17	+>>>> check type mode
	18	+ 1 : Check by Add
	19	+ 2 : Check by Correlation
	20	+ 4 : Check by Fourier
	21	+ 8 : Check by TTest
	22	+ 16 : Check by SRP
	23	+>>>> centre type mode
	24	+ 0 : Centre is GC (gravity of centre)
	25	+ 1 : Centre is Rotational Symmetry
	26	+ 2 : Centre is at Image Centre
	27	+ 3 : Centre is at Image Origin
	28	+>>>> subtrcation type mode
	29	+ 0 : No Subtraction
	30	+ 1 : Mean Subtraction
	31	+ 2 : Min Subtraction
17	32	</PRE>
18	33	</BODY>
19	34	</HTML>

--- /dev/null

+++ b/src/Tools/mrcImage/mrcImageSymmetryCentreFind/src/test/Makefile

		@@ -0,0 +1,20 @@
	1	+include ../../Config/Define.inc
	2	+include ../../../Config/Define.inc
	3	+include ../../../../Config/Define.inc
	4	+include ../../../../../Config/Define.inc
	5	+
	6	+DATA=data/FlagellaSection-0001
	7	+
	8	+all: help exec
	9	+
	10	+help:
	11	+ @echo "----- Help Message Check -----"
	12	+ @../$(OSTYPE)/$(OBJECTNAME) -h
	13	+
	14	+exec:
	15	+ @echo "----- Execution Check -----"
	16	+ ../$(OSTYPE)/$(OBJECTNAME) -i $(DATA).roi -o $(DATA).out0 -O $(DATA).info0 -m 0
	17	+ ../$(OSTYPE)/$(OBJECTNAME) -i $(DATA).roi -o $(DATA).out1 -O $(DATA).info1 -m 1
	18	+ @echo "----- Calc check -----"
	19	+
	20	+clean:

--- /dev/null

+++ b/src/Tools/mrcImage/mrcImageSymmetryCentreFind/src/test/data

		@@ -0,0 +1 @@
	1	+../../../../../..//data/mrcImageSymmetryCentreFind
		\ No newline at end of file

--- a/src/Tools/mrcImage/mrcImageSymmetryFind/Config/OptionControlFile

+++ b/src/Tools/mrcImage/mrcImageSymmetryFind/Config/OptionControlFile

		@@ -17,4 +17,5 @@
17	17	"-rangex","-rangex","Input: ","Optional","3","1","minx","Real","-3","2","maxx","Real","3","3","delx","Real","1"
18	18	"-rangey","-rangey","Input: ","Optional","3","1","miny","Real","-3","2","maxy","Real","3","3","dely","Real","1"
19	19	"-rangez","-rangez","Input: ","Optional","3","1","minz","Real","0","2","maxz","Real","0","3","delz","Real","1"
	20	+"-Algorythm","-Algorythm","Algorythm","Optional","0"
20	21	"-c","-c[onfig]","ConfigurationFile","Optional","1","1","configFile","inFile","NULL"

--- a/src/Tools/mrcImage/mrcImageSymmetryFind/inc/mrcImageSymmetryFind.h

+++ b/src/Tools/mrcImage/mrcImageSymmetryFind/inc/mrcImageSymmetryFind.h

		@@ -98,6 +98,8 @@ typedef struct mrcImageSymmetryFindInfo {
98	98	long flagdelz;
99	99	float delz;
100	100
	101	+ long Algorythm;
	102	+
101	103	long flagconfigFile;
102	104	char* configFile;
103	105	FILE* fptconfigFile;

--- a/src/Tools/mrcImage/mrcImageSymmetryFind/src/argCheck.c

+++ b/src/Tools/mrcImage/mrcImageSymmetryFind/src/argCheck.c

		@@ -239,6 +239,15 @@ argCheck(mrcImageSymmetryFindInfo* info, int argc, char* argv[])
239	239	}
240	240	SBREAK;
241	241	}
	242	+ SCASE("Algorythm") {
	243	+ if(i+0<argc) {
	244	+ info->Algorythm++;
	245	+ } else {
	246	+ usage(argv[0]);
	247	+ exit(EXIT_FAILURE);
	248	+ }
	249	+ SBREAK;
	250	+ }
242	251	SCASE("c") {
243	252	if(i+1<argc) {
244	253	info->configFile = stringGetNthWord(argv[i+1], 1, " ,");

--- a/src/Tools/mrcImage/mrcImageSymmetryFind/src/init.c

+++ b/src/Tools/mrcImage/mrcImageSymmetryFind/src/init.c

		@@ -37,6 +37,7 @@ init0(mrcImageSymmetryFindInfo* info)
37	37	info->minz = 0; info->flagminz = 0;
38	38	info->maxz = 0; info->flagmaxz = 0;
39	39	info->delz = 1; info->flagdelz = 0;
	40	+ info->Algorythm=0;
40	41	info->fptconfigFile = NULL; info->flagconfigFile = 0;
41	42	}
42	43

--- a/src/Tools/mrcImage/mrcImageSymmetryFind/src/mrcImageSymmetryFind.c

+++ b/src/Tools/mrcImage/mrcImageSymmetryFind/src/mrcImageSymmetryFind.c

		@@ -35,6 +35,11 @@ main(int argc, char* argv[])
35	35	init0(&info);
36	36	argCheck(&info, argc, argv);
37	37	init1(&info);
	38	+ if(info.Algorythm) {
	39	+ lmrcImageSymmetryFindAlgorythmPrint(stderr);
	40	+ exit(EXIT_FAILURE);
	41	+ }
	42	+
38	43
39	44	DEBUGPRINT("#### Program Started\n");
40	45	mrcFileRead(&in, info.In, "in main", 0);

		@@ -81,7 +86,7 @@ main(int argc, char* argv[])
81	86	linfo.centreInfo.minz = info.minz;
82	87	linfo.centreInfo.maxz = info.maxz;
83	88	linfo.centreInfo.delz = info.delz;
84		- linfo.centreInfo.delPHI = linfo.dtheta;
	89	+ linfo.centreInfo.delPHI = linfo.dtheta*RADIAN;
85	90
86	91	lmrcImageSymmetryFind(&in, &linfo, info.mode1);
87	92

--- a/src/Tools/mrcImage/mrcImageSymmetryFind/src/mrcImageSymmetryFind.html

+++ b/src/Tools/mrcImage/mrcImageSymmetryFind/src/mrcImageSymmetryFind.html

		@@ -44,6 +44,8 @@ Options:
44	44	>>>> centre type mode
45	45	0 : Centre is GC (gravity of centre)
46	46	1 : Centre is Rotational Symmetry
	47	+ 2 : Centre is at Image Centre
	48	+ 3 : Centre is at Image Origin
47	49	>>>> subtrcation type mode
48	50	0 : No Subtraction
49	51	1 : Mean Subtraction

--- a/src/Tools/mrcImage/mrcImageSymmetryFind/src/mrcImageSymmetryFind.pane

+++ b/src/Tools/mrcImage/mrcImageSymmetryFind/src/mrcImageSymmetryFind.pane

		@@ -24,7 +24,8 @@
24	24	-I 1 0 0 1 0 1 -1x1+1+22 ' ' '-3' 'minx' Input:
25	25	-I 1 0 0 1 0 1 -1x1+1+24 ' ' '-3' 'miny' Input:
26	26	-I 1 0 0 1 0 1 -1x1+1+25 ' ' '0' 'minz' Input:
27		- -I 1 0 1 0 0 1 -1x1+1+27.000000 ' ' 'configFile' 'ConfigurationFile' c
	27	+ -t 1 0 1 0 0 6x1+1+27 'Algorythm' 'Algorythm' Algorythm
	28	+ -I 1 0 1 0 0 1 -1x1+1+28.500000 ' ' 'configFile' 'ConfigurationFile' c
28	29	-E
29	30	-E
30	31	-E

--- /dev/null

+++ b/src/Tools/mrcImage/mrcImageSymmetryFind/src/test/Makefile

		@@ -0,0 +1,35 @@
	1	+include ../../Config/Define.inc
	2	+include ../../../Config/Define.inc
	3	+include ../../../../Config/Define.inc
	4	+include ../../../../../Config/Define.inc
	5	+
	6	+DATA=data/FlagellaSection
	7	+
	8	+all: help exec
	9	+
	10	+help:
	11	+ @echo "----- Help Message Check -----"
	12	+ @../$(OSTYPE)/$(OBJECTNAME) -h
	13	+
	14	+exec:
	15	+ @echo "----- Execution Check -----"
	16	+ ../$(OSTYPE)/$(OBJECTNAME) -i $(DATA)-0001.roi -O $(DATA)-0001.info1 -nRange 10 16 -A $(DATA)-0001.avg1 -centreMode 0 -m1 1 -m2 1 -t1 1.5
	17	+
	18	+exec2:
	19	+ ../$(OSTYPE)/$(OBJECTNAME) -i $(DATA)-0001.roi -O $(DATA)-0001.info2 -nRange 10 16 -A $(DATA)-0001.avg2 -centreMode 0 -m1 2 -m2 0
	20	+
	21	+exec4:
	22	+ ../$(OSTYPE)/$(OBJECTNAME) -i $(DATA)-0001.roi -O $(DATA)-0001.info4 -nRange 10 16 -A $(DATA)-0001.avg4 -centreMode 0 -m1 4 -m2 0
	23	+
	24	+exec4_1:
	25	+ ../$(OSTYPE)/$(OBJECTNAME) -i $(DATA)-0001.roi -O $(DATA)-0001.info4_1 -nRange 10 16 -A $(DATA)-0001.avg4_1 -centreMode 1 -m1 4 -m2 0
	26	+
	27	+
	28	+
	29	+clean:
	30	+
	31	+init:
	32	+ mrcImagePad -i $(DATA)-0001.roi -o $(DATA)-0001.pad -m 3 -H 256 -W 256
	33	+ mrcImageWindowing -i $(DATA)-0001.pad -o $(DATA)-0001.win -m 18 -W 0.05 0 0.05 0
	34	+ mrcImageShift -i $(DATA)-0001.win -o $(DATA)-0001.shift -x 128 -y 128
	35	+ mrcImageToneReversal -i $(DATA)-0001.shift -o $(DATA)-0001.neg

--- /dev/null

+++ b/src/Tools/mrcImage/mrcImageSymmetryFind/src/test/data

		@@ -0,0 +1 @@
	1	+../../../../../..//data/mrcImageSymmetryFind
		\ No newline at end of file

--- a/src/Tools/mrcImage/mrcImageSymmetryFind/src/usage.c

+++ b/src/Tools/mrcImage/mrcImageSymmetryFind/src/usage.c

		@@ -24,6 +24,7 @@ usage(char* thisProgram)
24	24	fprintf(stderr, " [-rangex minx (-3 ).as(Real ) \n maxx (3 ).as(Real ) \n delx (1 ).as(Real ) ] :Optional :Input: \n");
25	25	fprintf(stderr, " [-rangey miny (-3 ).as(Real ) \n maxy (3 ).as(Real ) \n dely (1 ).as(Real ) ] :Optional :Input: \n");
26	26	fprintf(stderr, " [-rangez minz (0 ).as(Real ) \n maxz (0 ).as(Real ) \n delz (1 ).as(Real ) ] :Optional :Input: \n");
	27	+ fprintf(stderr, " [-Algorythm ] :Optional :Algorythm\n");
27	28	fprintf(stderr, " [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile\n");
28	29	additionalUsage();
29	30	}

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