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Eos-Image Analysis Environment
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base: Commit

This repository is a base of Eos.

Commit MetaInfo

Revision	8a11665b91e0933275245b31ae005a27cd6ba705 (tree)
Time	2015-11-06 02:38:14
Author	Takuo Yasunaga <yasunaga@bio....>
Commiter	Takuo Yasunaga

Log Message

install-env
modified: env/Eos_env
modified: env/install-eos.sh

mrcImageAreaCalc
modified: include/lmrcImageCalcArea.h
modified: src/Objects/DataManip/mrcImage/src/lmrcImageCalcArea.c
modified: src/Objects/DataManip/mrcImage/src/lmrcImageCalcArea.h

Change Summary

modified: env/Eos_env (diff)
modified: env/install-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/Tools/Config/Define.inc (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)
add: src/Tools/mrcImage/mrcImageSymmetryFind/src/test/Makefile (diff)
add: src/Tools/mrcImage/mrcImageSymmetryFind/src/test/data (diff)

Incremental Difference

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

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

		@@ -39,6 +66,10 @@ test -r $HOME/.Eos_env && . $HOME/.Eos_env
39	66
40	67	EOF
41	68
	69	+#
	70	+# hostdepend
	71	+#
	72	+
42	73	if [ ! -f $HOME/.Eos_env ] ; then
43	74	echo "No .Eos_env"
44	75	ln -sf $EOS_HOME0/env/Eos_env $HOME/.Eos_env

		@@ -47,13 +78,35 @@ fi
47	78	source ~/.Eos_env \|\| echo "Prepare environment"
48	79	echo "hostdepend for ${EOS_HOSTDIR}"
49	80
	81	+HOSTDEPEND_EOS_OSDN_GIT=git://git.osdn.jp/gitroot/eos/hostdepend${EOS_HOSTDIR}.git
	82	+HOSTDEPEND_EOS_OSDN_HTTP=http://scm.osdn.jp/gitroot/eos/hostdepend${EOS_HOSTDIR}.git
	83	+HOSTDEPEND_EOS_OSDN_SSH=${EOS_GITUSER}@git.osdn.jp:/gitroot/eos/hostdepend${EOS_HOSTDIR}.git
	84	+HOSTDEPEND_EOS_OSDN_HTTPS=https://scm.osdn.jp/gitroot/eos/hostdepend${EOS_HOSTDIR}.git
	85	+
50	86	if [ ! -d $EOS_HOME0/hostdepend ] ; then
51	87	mkdir $EOS_HOME0/hostdepend
52	88	fi
53	89
54	90	if [ -d $EOS_HOME0/hostdepend ] ; then
55	91	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.";
	92	+ if [ -d ${EOS_HOSTDIR}/.git ] ;
	93	+ echo "Already installed hostdepend/${EOS_HOSTDIR}";
	94	+ echo "Use update-eos.sh for updating or set a new directory for installation"
	95	+ else
	96	+ if [ -z $EOS_GITUSER ] ; then
	97	+ INSTALL_FLAG=
	98	+ else
	99	+ git clone --depth 1 ${HOSTDEPEND_EOS_OSDN_SSH} ${EOS_HOSTDIR} \|\| \
	100	+ git clone --depth 1 ${HOSTDEPEND_EOS_OSDN_HTTPS} ${EOS_HOSTDIR} \|\| \
	101	+ echo "A port for SSH or HTTPS is not open, or something wrong."
	102	+ INSTALL_FLAG=INSTALL
	103	+ fi
	104	+ if [ -z $NOT_INSTALL ] ; then
	105	+ git clone --depth 1 ${HOSTDEPEND_EOS_OSDN_GIT} ${EOS_HOSTDIR} \|\| \
	106	+ git clone --depth 1 ${HOSTDEPEND_EOS_OSDN_HTTP} ${EOS_HOSTDIR} \|\| \
	107	+ echo "A port for git (9418) or HTTP is not open, or something wrong."
	108	+ fi
	109	+ fi
57	110	else
58	111	echo "Cannot make hostdepend"
59	112	fi

--- 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 {

--- 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

		@@ -18,7 +18,7 @@ static char __sccs_id[] = "%Z%lmrcImageSymmetryFind ver%I%; Date:%D% %Z%";
18	18	#include <math.h>
19	19	#define GLOBAL_DECLARATION
20	20
21		-#undef DEBUG
	21	+#define DEBUG
22	22	#include "genUtil.h"
23	23	#include "Memory.h"
24	24	#include "mrcImage.h"

		@@ -43,6 +43,8 @@ lmrcImageSymmetryFindModePrint(FILE* fpt)
43	43	fprintf(fpt, ">>>> centre type mode\n");
44	44	fprintf(fpt, " %d : Centre is GC (gravity of centre)\n", lmrcImageSymmetryFindCheckTypeCentreGC);
45	45	fprintf(fpt, " %d : Centre is Rotational Symmetry\n", lmrcImageSymmetryFindCheckTypeCentreSymmetry);
	46	+ fprintf(fpt, " %d : Centre is at Image Centre \n", lmrcImageSymmetryFindCheckTypeCentreCentre);
	47	+ fprintf(fpt, " %d : Centre is at Image Origin\n", lmrcImageSymmetryFindCheckTypeCentreOrigin);
46	48
47	49
48	50	fprintf(fpt, ">>>> subtrcation type mode\n");

--- 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 {

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

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

		@@ -688,3 +688,5 @@ WORLDNAME=Tools
688	688	WORLDNAME=Tools
689	689	WORLDNAME=Tools
690	690	WORLDNAME=Tools
	691	+WORLDNAME=Tools
	692	+WORLDNAME=Tools

--- 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();

--- /dev/null

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

		@@ -0,0 +1,25 @@
	1	+include ../../Config/Define.inc
	2	+include ../../../Config/Define.inc
	3	+include ../../../../Config/Define.inc
	4	+include ../../../../../Config/Define.inc
	5	+
	6	+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.neg -O $(DATA)-0001.info -nRange 10 15 -A $(DATA)-0001.avg -centreMode 1 -m1 1 -m2 2
	17	+ @echo "----- Calc check -----"
	18	+
	19	+clean:
	20	+
	21	+init:
	22	+ mrcImagePad -i $(DATA)-0001.roi -o $(DATA)-0001.pad -m 3 -H 256 -W 256
	23	+ mrcImageWindowing -i $(DATA)-0001.pad -o $(DATA)-0001.win -m 18 -W 0.05 0 0.05 0
	24	+ mrcImageShift -i $(DATA)-0001.win -o $(DATA)-0001.shift -x 128 -y 128
	25	+ mrcImageToneReversal -i $(DATA)-0001.shift -o $(DATA)-0001.neg