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Eos-Image Analysis Environment
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base: Commit

This repository is a base of Eos.

Commit MetaInfo

Revisión	10da2e95c5b15654dd70b8dafaf4f382ed1a92ae (tree)
Tiempo	2015-11-14 14:04:52
Autor	Takuo Yasunaga <yasunaga@bio....>
Commiter	Takuo Yasunaga

Log Message

mrcImageFeatureCalc: modified
modified: include/lmrcImageFeatureCalc.h
modified: src/Objects/DataManip/mrcImage/src/lmrcImageFeatureCalc.c
modified: src/Objects/DataManip/mrcImage/src/lmrcImageFeatureCalc.h
modified: src/Objects/DataManip/mrcImage/src/lmrcImageSurfaceAreaCalc.c

Cambiar Resumen

modified: include/lmrcImageFeatureCalc.h (diff)
modified: src/Objects/DataManip/mrcImage/src/lmrcImageFeatureCalc.c (diff)
modified: src/Objects/DataManip/mrcImage/src/lmrcImageFeatureCalc.h (diff)
modified: src/Objects/DataManip/mrcImage/src/lmrcImageSurfaceAreaCalc.c (diff)

Diferencia incremental

--- a/include/lmrcImageFeatureCalc.h

+++ b/include/lmrcImageFeatureCalc.h

		@@ -77,6 +77,14 @@ typedef struct lmrcImageFeatureEach {
77	77	int flagCircularity;
78	78	double circularity;
79	79
	80	+ // Complexity
	81	+ int flagComplexity;
	82	+ double complexity;
	83	+
	84	+ // Complexity
	85	+ int flagDiameter;
	86	+ double diameter;
	87	+
80	88	// PCA
81	89	float lamda[3];
82	90

		@@ -116,6 +124,8 @@ extern void lmrcImageSurfaceAreaCalcUsage(FILE* fpt);
116	124
117	125
118	126	extern void lmrcImageCircularityCalc(lmrcImageFeatureList* linfo, int mode);
	127	+extern void lmrcImageComplexityCalc(lmrcImageFeatureList* linfo, int mode);
	128	+extern void lmrcImageDiameterCalc(lmrcImageFeatureList* linfo, int mode);
119	129
120	130	extern int lmrcImageChainCodeSearch(int* chain, mrcImageParaTypeRealCoord* next, double* dL, mrcImage* in, mrcImageParaTypeRealCoord ori, int chainCodeStart, int mode);
121	131

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

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

		@@ -35,6 +35,18 @@ lmrcImageFeaturePrint(FILE* fpt, lmrcImageFeatureList* linfo, int mode)
35	35	if(linfo->each[0].flagCircularity) {
36	36	fprintf(fpt, " %12s", "circularity");
37	37	}
	38	+ if(!linfo->each[0].flagComplexity) {
	39	+ lmrcImageComplexityCalc(linfo, 0);
	40	+ }
	41	+ if(linfo->each[0].flagComplexity) {
	42	+ fprintf(fpt, " %12s", "complexity");
	43	+ }
	44	+ if(!linfo->each[0].flagDiameter) {
	45	+ lmrcImageDiameterCalc(linfo, 0);
	46	+ }
	47	+ if(linfo->each[0].flagDiameter) {
	48	+ fprintf(fpt, " %12s", "diameter");
	49	+ }
38	50	fprintf(fpt, "\n");
39	51	for(i=0; i<=linfo->Number; i++) {
40	52	fprintf(fpt, "%06d %10.4f %10.4f %10.4f %12.4f %6d %6d %6d",

		@@ -55,6 +67,12 @@ lmrcImageFeaturePrint(FILE* fpt, lmrcImageFeatureList* linfo, int mode)
55	67	if(linfo->each[i].flagCircularity) {
56	68	fprintf(fpt, " %12.4f", linfo->each[i].circularity);
57	69	}
	70	+ if(linfo->each[i].flagComplexity) {
	71	+ fprintf(fpt, " %12.4f", linfo->each[i].complexity);
	72	+ }
	73	+ if(linfo->each[i].flagDiameter) {
	74	+ fprintf(fpt, " %12.4f", linfo->each[i].diameter);
	75	+ }
58	76	fprintf(fpt, "\n");
59	77	}
60	78	}

		@@ -91,6 +109,68 @@ lmrcImageCircularityCalc(lmrcImageFeatureList* linfo, int mode)
91	109	}
92	110
93	111	void
	112	+lmrcImageComplexityCalc(lmrcImageFeatureList* linfo, int mode)
	113	+{
	114	+ int i;
	115	+
	116	+ if(linfo->each[0].flagPerimeter) {
	117	+ for(i=0; i<=linfo->Number; i++) {
	118	+ if(0<linfo->each[i].perimeter) {
	119	+ linfo->each[i].complexity=SQR(linfo->each[i].perimeter)/linfo->each[i].area;
	120	+ } else {
	121	+ linfo->each[i].complexity=1e4;
	122	+ }
	123	+ linfo->each[i].flagComplexity=1;
	124	+ }
	125	+ } else if(linfo->each[0].flagSurfaceArea) {
	126	+ for(i=0; i<=linfo->Number; i++) {
	127	+ if(0<linfo->each[i].surfaceArea) {
	128	+ linfo->each[i].complexity=CUBIC(linfo->each[i].surfaceArea)/SQR(linfo->each[i].area);
	129	+ } else {
	130	+ linfo->each[i].complexity=1e4;
	131	+ }
	132	+ linfo->each[i].flagComplexity=1;
	133	+ }
	134	+ } else {
	135	+ fprintf(stderr, "Cannot calculate complexity because of no perimeter/surfaceArea\n");
	136	+ for(i=0; i<=linfo->Number; i++) {
	137	+ linfo->each[i].flagComplexity=0;
	138	+ }
	139	+ }
	140	+}
	141	+
	142	+void
	143	+lmrcImageDiameterCalc(lmrcImageFeatureList* linfo, int mode)
	144	+{
	145	+ int i;
	146	+
	147	+ if(linfo->each[0].flagPerimeter) {
	148	+ for(i=0; i<=linfo->Number; i++) {
	149	+ if(0<linfo->each[i].perimeter) {
	150	+ linfo->each[i].diameter=sqrt(linfo->each[i].area/M_PI);
	151	+ } else {
	152	+ linfo->each[i].diameter=1e4;
	153	+ }
	154	+ linfo->each[i].flagDiameter=1;
	155	+ }
	156	+ } else if(linfo->each[0].flagSurfaceArea) {
	157	+ for(i=0; i<=linfo->Number; i++) {
	158	+ if(0<linfo->each[i].surfaceArea) {
	159	+ linfo->each[i].diameter=pow(linfo->each[i].area/(4./3.*M_PI), 1.0/3.0);
	160	+ } else {
	161	+ linfo->each[i].diameter=1e4;
	162	+ }
	163	+ linfo->each[i].flagDiameter=1;
	164	+ }
	165	+ } else {
	166	+ fprintf(stderr, "Cannot calculate diameter because of no perimeter/surfaceArea\n");
	167	+ for(i=0; i<=linfo->Number; i++) {
	168	+ linfo->each[i].flagDiameter=0;
	169	+ }
	170	+ }
	171	+}
	172	+
	173	+void
94	174	lmrcImageBasicFeatureCalc(mrcImage* gc, lmrcImageFeatureList* linfo, mrcImage* label, int mode)
95	175	{
96	176	int x, y, z;

		@@ -229,7 +309,7 @@ lmrcImagePerimeterCalc(mrcImage* out, mrcImage* in, lmrcImagePerimeterCalcInfo*
229	309	linfo->flagArea = 1;
230	310	label = linfo->Label = memoryAllocate(sizeof(mrcImage), "in lmrcImagePerimeterCalc");
231	311	area = linfo->Area = memoryAllocate(sizeof(mrcImage), "in lmrcImagePerimeterCalc");
232		- lmrcImageCalcArea(area, label, in, 0);
	312	+ lmrcImageCalcArea(area, label, in, linfo->Neighbor, 0);
233	313	}
234	314	lmrcImageLabelingOrder(label, 1);
235	315

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

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

		@@ -77,6 +77,14 @@ typedef struct lmrcImageFeatureEach {
77	77	int flagCircularity;
78	78	double circularity;
79	79
	80	+ // Complexity
	81	+ int flagComplexity;
	82	+ double complexity;
	83	+
	84	+ // Complexity
	85	+ int flagDiameter;
	86	+ double diameter;
	87	+
80	88	// PCA
81	89	float lamda[3];
82	90

		@@ -116,6 +124,8 @@ extern void lmrcImageSurfaceAreaCalcUsage(FILE* fpt);
116	124
117	125
118	126	extern void lmrcImageCircularityCalc(lmrcImageFeatureList* linfo, int mode);
	127	+extern void lmrcImageComplexityCalc(lmrcImageFeatureList* linfo, int mode);
	128	+extern void lmrcImageDiameterCalc(lmrcImageFeatureList* linfo, int mode);
119	129
120	130	extern int lmrcImageChainCodeSearch(int* chain, mrcImageParaTypeRealCoord* next, double* dL, mrcImage* in, mrcImageParaTypeRealCoord ori, int chainCodeStart, int mode);
121	131

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

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

		@@ -54,7 +54,7 @@ lmrcImageSurfaceAreaCalc(mrcImage* out, mrcImage* bin, lmrcImageSurfaceAreaCalcI
54	54	} else {
55	55	area = linfo->Area = memoryAllocate(sizeof(mrcImage), "in lmrcImageSurfaceAreaCalc");
56	56	label = linfo->Label = memoryAllocate(sizeof(mrcImage), "in lmrcImageSurfaceAreaCalc");
57		- lmrcImageCalcArea(area, label, bin, 0);
	57	+ lmrcImageCalcArea(area, label, bin, linfo->Neighbor, 0);
58	58	DEBUGPRINT("lmrcImageLabelingOrder Start\n");
59	59	lmrcImageLabelingOrder(label, 0);
60	60	}

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