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base: コミット

This repository is a base of Eos.

コミットメタ情報

リビジョン	8bfe92901b5284d94760603d9736da69c929525c (tree)
日時	2015-03-23 19:09:23
作者	Takuo Yasunaga <yasunaga@bio....>
コミッター	Takuo Yasunaga

ログメッセージ

new:
mrcImageAutoTriming
modified:
mrcImage.h

変更サマリ

add: bin/mrcImageAutoTriming (diff)
modified: include/mrcImage.h (diff)
modified: src/Objects/DataManip/mrcImage/doc/mrcImage.html (diff)
modified: src/Objects/DataManip/mrcImage/inc/mrcImage.h (diff)
modified: src/Objects/DataManip/mrcImage/src/mrcImageCopy.c (diff)
modified: src/Objects/DataManip/mrcImage/src/mrcImageInfo.c (diff)
modified: src/Tools/Config/Define.inc (diff)
modified: src/Tools/mrcImage/.Source (diff)
add: src/Tools/mrcImage/mrcImageAreaCalc/src/test/Makefile (diff)
add: src/Tools/mrcImage/mrcImageAreaCalc/src/test/data (diff)
add: src/Tools/mrcImage/mrcImageAutoTriming/Config/Define.inc (diff)
add: src/Tools/mrcImage/mrcImageAutoTriming/Config/OptionControlFile (diff)
add: src/Tools/mrcImage/mrcImageAutoTriming/Config/Target.inc (diff)
add: src/Tools/mrcImage/mrcImageAutoTriming/Makefile (diff)
add: src/Tools/mrcImage/mrcImageAutoTriming/doc/Makefile (diff)
add: src/Tools/mrcImage/mrcImageAutoTriming/inc/config.h (diff)
add: src/Tools/mrcImage/mrcImageAutoTriming/inc/mrcImageAutoTriming.h (diff)
add: src/Tools/mrcImage/mrcImageAutoTriming/src/.Depend (diff)
add: src/Tools/mrcImage/mrcImageAutoTriming/src/.Source (diff)
add: src/Tools/mrcImage/mrcImageAutoTriming/src/Makefile (diff)
add: src/Tools/mrcImage/mrcImageAutoTriming/src/X86MAC64 (diff)
add: src/Tools/mrcImage/mrcImageAutoTriming/src/argCheck.c (diff)
add: src/Tools/mrcImage/mrcImageAutoTriming/src/init.c (diff)
add: src/Tools/mrcImage/mrcImageAutoTriming/src/mrcImageAutoTriming.c (diff)
add: src/Tools/mrcImage/mrcImageAutoTriming/src/mrcImageAutoTriming.html (diff)
add: src/Tools/mrcImage/mrcImageAutoTriming/src/mrcImageAutoTriming.pane (diff)
add: src/Tools/mrcImage/mrcImageAutoTriming/src/test/Makefile (diff)
add: src/Tools/mrcImage/mrcImageAutoTriming/src/test/data (diff)
add: src/Tools/mrcImage/mrcImageAutoTriming/src/usage.c (diff)
add: src/Tools/mrcImage/mrcImageAutoTriming/src/util.c (diff)
modified: src/Tools/mrcImage/mrcImageInfo/src/mrcImageInfo.c (diff)
modified: src/Tools/mrcImage/mrcImageInfo/src/mrcImageInfo.html (diff)
modified: src/Tools/mrcImage/mrcImageInfo/src/test/Makefile (diff)
modified: src/Tools/mrcImage/mrcImageMeanFreePathCalc/Config/OptionControlFile (diff)
modified: src/Tools/mrcImage/mrcImageMeanFreePathCalc/inc/mrcImageMeanFreePathCalc.h (diff)
modified: src/Tools/mrcImage/mrcImageMeanFreePathCalc/src/argCheck.c (diff)
modified: src/Tools/mrcImage/mrcImageMeanFreePathCalc/src/init.c (diff)
modified: src/Tools/mrcImage/mrcImageMeanFreePathCalc/src/mrcImageMeanFreePathCalc.c (diff)
modified: src/Tools/mrcImage/mrcImageMeanFreePathCalc/src/mrcImageMeanFreePathCalc.html (diff)
modified: src/Tools/mrcImage/mrcImageMeanFreePathCalc/src/mrcImageMeanFreePathCalc.pane (diff)
modified: src/Tools/mrcImage/mrcImageMeanFreePathCalc/src/test/Makefile (diff)
modified: src/Tools/mrcImage/mrcImageMeanFreePathCalc/src/usage.c (diff)

差分

--- /dev/null

+++ b/bin/mrcImageAutoTriming

		@@ -0,0 +1 @@
	1	+../sbin/MachineIndependent
		\ No newline at end of file

--- a/include/mrcImage.h

+++ b/include/mrcImage.h

		@@ -412,6 +412,8 @@ typedef struct mrcImageInformation {
412	412	long flagrmax;
413	413	double RMS; /* Root mean square */
414	414	int mode;
	415	+ mrcImageParaTypeRealCoord sdOfAllAxis;
	416	+ mrcImageParaTypeRealCoord aveOfAllAxis;
415	417
416	418	/* For Search Area */
417	419	int flagXrange;

		@@ -441,7 +443,8 @@ typedef enum mrcImageInformationMode {
441	443	meanOfCentre = 4,
442	444	meanOfSparse = 5,
443	445	meanOf2DEdgeY = 6,
444		- RMSofAllPixels = 7
	446	+ RMSofAllPixels = 7,
	447	+ sdOfAllAxis = 8
445	448	} mrcImageInformationMode;
446	449
447	450	/*

--- a/src/Objects/DataManip/mrcImage/doc/mrcImage.html

+++ b/src/Objects/DataManip/mrcImage/doc/mrcImage.html

		@@ -103,343 +103,6 @@
103	103	<H2>Information from source codes</H2>
104	104	</A>
105	105	<PRE>
106		-../src/fftn.c:
107		-
108		-../src/lmrcFETnormalizeBySD.c:
109		-
110		-../src/lmrcFFTExpression.c:
111		-
112		-../src/lmrcFFTFGconj.c:
113		-
114		-../src/lmrcFFTFxG.c:
115		-
116		-../src/lmrcFFTInfo.c:
117		-
118		-../src/lmrcImage3DPad.c:
119		-
120		-../src/lmrcImage3DWindowing.c:
121		-
122		-../src/lmrcImageAddValue.c:
123		-
124		-../src/lmrcImageAsProbability.c:
125		-
126		-../src/lmrcImageAverage.c:
127		-
128		-../src/lmrcImageBandPassFilter.c:
129		-
130		-../src/lmrcImageBilateralFilter.c:
131		-
132		-../src/lmrcImageBinarization.c:
133		-
134		-../src/lmrcImageBottomHatTransform.c:
135		-
136		-../src/lmrcImageBoundaryInfo.c:
137		-
138		-../src/lmrcImageCTFCompensation.c:
139		-
140		-../src/lmrcImageCTFDetermination.c:
141		-
142		-../src/lmrcImageCTFObservation.c:
143		-
144		-../src/lmrcImageCTFSN.c:
145		-
146		-../src/lmrcImageCVE.c:
147		-
148		-../src/lmrcImageCalcArea.c:
149		-
150		-../src/lmrcImageCenterGet.c:
151		-
152		-../src/lmrcImageCentre.c:
153		-
154		-../src/lmrcImageClosing.c:
155		-
156		-../src/lmrcImageClusterAnalysis.c:
157		-
158		-../src/lmrcImageCommonLine.c:
159		-
160		-../src/lmrcImageConnection.c:
161		-
162		-../src/lmrcImageConnectivityNumberCalc.c:
163		-
164		-../src/lmrcImageContourSurface.c:
165		-
166		-../src/lmrcImageContraction.c:
167		-
168		-../src/lmrcImageCorrelation.c:
169		- $lmrcImageEuclidDistanceCalc: Calculate Euclid distance between two images $
170		- $arg: in1: input mrcImage1 $
171		- $arg: in2: input mrcImage2 $
172		- $arg: mode: input int $
173		- $mode: 0 Sum of SQR $
174		- $mode: 1 Distance $
175		- $return: EuclidDistance $
176		-
177		-../src/lmrcImageCorrelationPVM.c:
178		-
179		-../src/lmrcImageCorrelationWithCTFCompensation.c:
180		-
181		-../src/lmrcImageCorrelationinSpace.c:
182		-
183		-../src/lmrcImageCrystalCreate.c:
184		-
185		-../src/lmrcImageDataMaxAndMinGetByImage.c:
186		-
187		-../src/lmrcImageDataStraightCopy.c:
188		-
189		-../src/lmrcImageDeconvolution.c:
190		-
191		-../src/lmrcImageDensity.c:
192		-
193		-../src/lmrcImageDensityInverse.c:
194		-
195		-../src/lmrcImageDensityNormalizationByImage.c:
196		-
197		-../src/lmrcImageDifferential.c:
198		-
199		-../src/lmrcImageDilation.c:
200		-
201		-../src/lmrcImageDistanceConversion.c:
202		-
203		-../src/lmrcImageEdge.c:
204		-
205		-../src/lmrcImageEdgeAverage.c:
206		-
207		-../src/lmrcImageEdgeEnhancement.c:
208		-
209		-../src/lmrcImageErosion.c:
210		-
211		-../src/lmrcImageFFT.c:
212		-
213		-../src/lmrcImageFOMCalc.c:
214		-
215		-../src/lmrcImageFeatureExtraction.c:
216		-
217		-../src/lmrcImageFeatureExtractionCoOccurrence.c:
218		-
219		-../src/lmrcImageFeatureExtractionRunLength.c:
220		-
221		-../src/lmrcImageFilterCreate.c:
222		-
223		-../src/lmrcImageFirstNoiseReductionByRelaxation.c:
224		-
225		-../src/lmrcImageFloating.c:
226		-
227		-../src/lmrcImageFourierNeighborCorrelation.c:
228		-
229		-../src/lmrcImageFourierPowerSpectrum.c:
230		-
231		-../src/lmrcImageFourierShellCorrelation.c:
232		-
233		-../src/lmrcImageHighPassFilter.c:
234		-
235		-../src/lmrcImageHighlighting.c:
236		-
237		-../src/lmrcImageHoughTransform.c:
238		-
239		-../src/lmrcImageLabeling.c:
240		-
241		-../src/lmrcImageLogicalOperation.c:
242		-
243		-../src/lmrcImageLowPassFilter.c:
244		-
245		-../src/lmrcImageMasking.c:
246		-
247		-../src/lmrcImageMaxDataGet.c:
248		-
249		-../src/lmrcImageMirroring.c:
250		- $lmrcImageMirroring: (mrcImage* out, mrcImage* in, lmrcImageMirroring mode) $
251		-
252		-../src/lmrcImageModeChange.c:
253		-
254		-../src/lmrcImageModelCreate.c:
255		-
256		-../src/lmrcImageMontageCreate.c:
257		-
258		-../src/lmrcImageMorphology.c:
259		-
260		-../src/lmrcImageMove.c:
261		-
262		-../src/lmrcImageMultiCTFCompensation.c:
263		-
264		-../src/lmrcImageMultiplying.c:
265		-
266		-../src/lmrcImageNegativeLaplacian.c:
267		-
268		-../src/lmrcImageNoiseCreate.c:
269		-
270		-../src/lmrcImageNormalizing.c:
271		-
272		-../src/lmrcImageOneLineSimilarityCalc.c:
273		-
274		-../src/lmrcImageOpening.c:
275		-
276		-../src/lmrcImagePad.c:
277		-
278		-../src/lmrcImagePartImageSegmentation.c:
279		-
280		-../src/lmrcImagePixelSummationOfProbabilityGetByImage.c:
281		-
282		-../src/lmrcImagePosterization.c:
283		-
284		-../src/lmrcImagePrewitt.c:
285		-
286		-../src/lmrcImageProjection.c:
287		-
288		-../src/lmrcImageProportionalDensityLevelSetByImage.c:
289		-
290		-../src/lmrcImageROI2D.c:
291		-
292		-../src/lmrcImageROI3D.c:
293		-
294		-../src/lmrcImageROInotChangeHeaderLength.c:
295		-
296		-../src/lmrcImageRadialDistribution.c:
297		-
298		-../src/lmrcImageRhoFiltering.c:
299		-
300		-../src/lmrcImageRoberts.c:
301		-
302		-../src/lmrcImageRotation.c:
303		-
304		-../src/lmrcImageSSDA.c:
305		-
306		-../src/lmrcImageSamplingUnitChange.c:
307		-
308		-../src/lmrcImageSecondNoiseReductionByRelaxation.c:
309		-
310		-../src/lmrcImageSecondNoiseReductionByRelaxationDijDimensionSet.c:
311		-
312		-../src/lmrcImageSecondNoiseReductionByRelaxationDijValueCalculate.c:
313		-
314		-../src/lmrcImageSecondNoiseReductionByRelaxationDijValueSet.c:
315		-
316		-../src/lmrcImageSecondNoiseReductionByRelaxationQValueSet.c:
317		-
318		-../src/lmrcImageSecondNoiseReductionByRelaxationRValueSet.c:
319		-
320		-../src/lmrcImageShapePCA.c:
321		-
322		-../src/lmrcImageShift.c:
323		-
324		-../src/lmrcImageShrink.c:
325		-
326		-../src/lmrcImageSigmaCalculate.c:
327		-
328		-../src/lmrcImageSinogram.c:
329		-
330		-../src/lmrcImageSinogramCorrelation.c:
331		-
332		-../src/lmrcImageSinogramFFT.c:
333		-
334		-../src/lmrcImageSmoothing.c:
335		-
336		-../src/lmrcImageSobel.c:
337		-
338		-../src/lmrcImageSolventFlattening.c:
339		-
340		-../src/lmrcImageSpatialFrequencyFilter.c:
341		-
342		-../src/lmrcImageSphere.c:
343		-
344		-../src/lmrcImageSplit.c:
345		-
346		-../src/lmrcImageStack.c:
347		-
348		-../src/lmrcImageStudentCalculate.c:
349		-
350		-../src/lmrcImageSubtractionCalc.c:
351		-
352		-../src/lmrcImageSummationCalculate.c:
353		-
354		-../src/lmrcImageSymmetryFind.c:
355		-
356		-../src/lmrcImageTfunction.c:
357		-
358		-../src/lmrcImageToneReversal.c:
359		-
360		-../src/lmrcImageTopHatTransform.c:
361		-
362		-../src/lmrcImageTrans.c:
363		-
364		-../src/lmrcImageTransformDescartesIntoPolar.c:
365		-
366		-../src/lmrcImageTriming.c:
367		-
368		-../src/lmrcImageVolumeCalc.c:
369		-
370		-../src/lmrcImageWindowing.c:
371		-
372		-../src/lmrcImagesFTest.c:
373		-
374		-../src/lmrcImagesStatDataGet.c:
375		-
376		-../src/lmrcImagesTTest.c:
377		-
378		-../src/lmrcImagesVarianceAnalysis.c:
379		-
380		-../src/lmrcImagesVarianceMap.c:
381		-
382		-../src/lmrcSinogramFET.c:
383		-
384		-../src/lmrcSinogramFETPCA.c:
385		-
386		-../src/lmrcSinogramFETcalcWeight.c:
387		-
388		-../src/lmrcSinogramFETcorrelationMap.c:
389		-
390		-../src/lmrcSinogramFETnormalizedMap.c:
391		-
392		-../src/lmrcSinogramFETreferredCorrelation.c:
393		-
394		-../src/lmrcSinogramFETsmoothParameterMatching.c:
395		-
396		-../src/mrcImageCheckFFT.c:
397		-
398		-../src/mrcImageCheckSameSize.c:
399		-
400		-../src/mrcImageCopy.c:
401		-
402		-../src/mrcImageDataSet.c:
403		-
404		-../src/mrcImageError.c:
405		-
406		-../src/mrcImageGet.c:
407		-
408		-../src/mrcImageGetPixels.c:
409		-
410		-../src/mrcImageInfo.c:
411		-
412		-../src/mrcImageInit.c:
413		-
414		-../src/mrcImageOperation.c:
415		-
416		-../src/mrcImagePVM.c:
417		-
418		-../src/mrcImagePrint.c:
419		-
420		-../src/mrcImageRead.c:
421		-
422		-../src/mrcImageSectionGet.c:
423		-
424		-../src/mrcImageSectionSet.c:
425		-
426		-../src/mrcImageSet.c:
427		-
428		-../src/mrcImageTailer.c:
429		-
430		-../src/mrcImageToIntImage.c:
431		-
432		-../src/mrcImageUtil.c:
433		-
434		-../src/mrcImageUtilityforVariance.c:
435		-
436		-../src/mrcImageWrite.c:
437		-
438		-../src/mrcImageWrite2.c:
439		-
440		-../src/mrcImagefuncmin.c:
441		-
442		-../src/mrcRefUtil.c:
443	106	</PRE>
444	107	<HR>
445	108	<A NAME="include">

		@@ -860,6 +523,8 @@ typedef struct mrcImageInformation {
860	523	long flagrmax;
861	524	double RMS; /* Root mean square */
862	525	int mode;
	526	+ mrcImageParaTypeRealCoord sdOfAllAxis;
	527	+ mrcImageParaTypeRealCoord aveOfAllAxis;
863	528
864	529	/* For Search Area */
865	530	int flagXrange;

		@@ -889,7 +554,8 @@ typedef enum mrcImageInformationMode {
889	554	meanOfCentre = 4,
890	555	meanOfSparse = 5,
891	556	meanOf2DEdgeY = 6,
892		- RMSofAllPixels = 7
	557	+ RMSofAllPixels = 7,
	558	+ sdOfAllAxis = 8
893	559	} mrcImageInformationMode;
894	560
895	561	/*

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

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

		@@ -412,6 +412,8 @@ typedef struct mrcImageInformation {
412	412	long flagrmax;
413	413	double RMS; /* Root mean square */
414	414	int mode;
	415	+ mrcImageParaTypeRealCoord sdOfAllAxis;
	416	+ mrcImageParaTypeRealCoord aveOfAllAxis;
415	417
416	418	/* For Search Area */
417	419	int flagXrange;

		@@ -441,7 +443,8 @@ typedef enum mrcImageInformationMode {
441	443	meanOfCentre = 4,
442	444	meanOfSparse = 5,
443	445	meanOf2DEdgeY = 6,
444		- RMSofAllPixels = 7
	446	+ RMSofAllPixels = 7,
	447	+ sdOfAllAxis = 8
445	448	} mrcImageInformationMode;
446	449
447	450	/*

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

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

		@@ -17,14 +17,19 @@ static char __sccs_id[] = "@(#)mrcImageCopy ver1.1; Date:96/05/08 @(#)";
17	17	void
18	18	lmrcImageCopy(mrcImage* dst, mrcImage* src, mrcImageParaTypeRealCoord to)
19	19	{
20		- mrcImageParaTypeReal ix, iy, iz;
	20	+ mrcImageParaTypeInteger ix, iy, iz;
21	21	double data;
	22	+ mrcImageParaTypeInteger x, y, z;
	23	+ int k;
22	24
23		- for(iz=0; iz<src->HeaderN.z; iz++) {
24		- for(iy=0; iy<src->HeaderN.y; iy++) {
25		- for(ix=0; ix<src->HeaderN.x; ix++) {
26		- mrcPixelDataGet(src, (mrcImageParaTypeReal)ix, (mrcImageParaTypeReal)iy, (mrcImageParaTypeReal)iz, &data, mrcPixelRePart, mrcPixelHowNearest);
27		- mrcPixelDataSet(dst, (mrcImageParaTypeReal)to.x + ix, (mrcImageParaTypeReal)to.y + iy, (mrcImageParaTypeReal)to.z + iz, data, mrcPixelRePart);
	25	+ for(iz=0; iz<dst->HeaderN.z; iz++) {
	26	+ for(iy=0; iy<dst->HeaderN.y; iy++) {
	27	+ for(ix=0; ix<dst->HeaderN.x; ix++) {
	28	+ x = (int)(ix - to.x + 0.5);
	29	+ y = (int)(iy - to.y + 0.5);
	30	+ z = (int)(iz - to.z + 0.5);
	31	+ mrcPixelDataGet(src, x, y, z, &data, mrcPixelRePart, mrcPixelHowNearest);
	32	+ mrcPixelDataSet(dst, ix, iy, iz, data, mrcPixelRePart);
28	33	}
29	34	}
30	35	}

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

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

		@@ -938,6 +938,65 @@ lmrcImageInformation(mrcImageInformation* info, mrcImage* img)
938	938
939	939	break;
940	940	}
	941	+ case sdOfAllAxis: {
	942	+ DEBUGPRINT("SDofAllAxis\n");
	943	+ double weight, weight2;
	944	+ double sumx, sumy, sumz;
	945	+ double avex, avey, avez;
	946	+ double dat2;
	947	+
	948	+ sumx = 0;
	949	+ sumy = 0;
	950	+ sumz = 0;
	951	+ weight = 0;
	952	+ count = img->HeaderN.ximg->HeaderN.yimg->HeaderN.z;
	953	+ for(iz=0; iz<img->HeaderN.z; iz++) {
	954	+ for(iy=0; iy<img->HeaderN.y; iy++) {
	955	+ for(ix=0; ix<img->HeaderN.x; ix++) {
	956	+ mrcPixelDataGet(img,
	957	+ (mrcImageParaTypeReal)ix,
	958	+ (mrcImageParaTypeReal)iy,
	959	+ (mrcImageParaTypeReal)iz,
	960	+ &data, mrcPixelRePart, mrcPixelHowNearest);
	961	+ sumx += ix*data;
	962	+ sumy += iy*data;
	963	+ sumz += iz*data;
	964	+ weight += data;
	965	+ }
	966	+ }
	967	+ }
	968	+
	969	+ avex = sumx/weight;
	970	+ avey = sumy/weight;
	971	+ avez = sumz/weight;
	972	+
	973	+ sumx = 0;
	974	+ sumy = 0;
	975	+ sumz = 0;
	976	+ weight2 = 0;
	977	+ for(iz=0; iz<img->HeaderN.z; iz++) {
	978	+ for(iy=0; iy<img->HeaderN.y; iy++) {
	979	+ for(ix=0; ix<img->HeaderN.x; ix++) {
	980	+ mrcPixelDataGet(img,
	981	+ (mrcImageParaTypeReal)ix,
	982	+ (mrcImageParaTypeReal)iy,
	983	+ (mrcImageParaTypeReal)iz,
	984	+ &data, mrcPixelRePart, mrcPixelHowNearest);
	985	+ sumx += SQR((ix - avex)*data);
	986	+ sumy += SQR((iy - avey)*data);
	987	+ sumz += SQR((iz - avez)*data);
	988	+ }
	989	+ }
	990	+ }
	991	+
	992	+ info->sdOfAllAxis.x = sqrt(sumx/weight);
	993	+ info->sdOfAllAxis.y = sqrt(sumy/weight);
	994	+ info->sdOfAllAxis.z = sqrt(sumz/weight);
	995	+ info->aveOfAllAxis.x = avex;
	996	+ info->aveOfAllAxis.y = avey;
	997	+ info->aveOfAllAxis.z = avez;
	998	+ break;
	999	+ }
941	1000	default:{
942	1001	fprintf(stderr, "Not supported mode :%d", info->mode);
943	1002	exit(EXIT_FAILURE);

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

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

		@@ -568,3 +568,11 @@ WORLDNAME=Tools
568	568	WORLDNAME=Tools
569	569	WORLDNAME=Tools
570	570	WORLDNAME=Tools
	571	+WORLDNAME=Tools
	572	+WORLDNAME=Tools
	573	+WORLDNAME=Tools
	574	+WORLDNAME=Tools
	575	+WORLDNAME=Tools
	576	+WORLDNAME=Tools
	577	+WORLDNAME=Tools
	578	+WORLDNAME=Tools

--- a/src/Tools/mrcImage/.Source

+++ b/src/Tools/mrcImage/.Source

		@@ -51,6 +51,7 @@ mrcImageAutoRotationAverage \
51	51	mrcImageAutoRotationCorrelation \
52	52	mrcImageAutoRotationCorrelation3D \
53	53	mrcImageAutoRotationCorrelationResultPrint \
	54	+mrcImageAutoTriming \
54	55	mrcImageAverage \
55	56	mrcImageBandPassFilter \
56	57	mrcImageBilateralFilter \

--- /dev/null

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

		@@ -0,0 +1,34 @@
	1	+include ../../Config/Define.inc
	2	+include ../../../Config/Define.inc
	3	+include ../../../../Config/Define.inc
	4	+include ../../../../../Config/Define.inc
	5	+
	6	+all: help exec exec2 exec3
	7	+
	8	+help:
	9	+ @echo "----- Help Message Check -----"
	10	+ @../$(OSTYPE)/$(OBJECTNAME) -h
	11	+
	12	+exec:
	13	+ @echo "----- Execution Check -----"
	14	+ ../$(OSTYPE)/$(OBJECTNAME) -i data/test.bin -o data/test.area -l data/test.label
	15	+ @echo "----- Calc check -----"
	16	+
	17	+exec2:
	18	+ @echo "----- Execution Check -----"
	19	+ ../$(OSTYPE)/$(OBJECTNAME) -i data/test2.bin -o data/test2.area -l data/test2.label
	20	+ @echo "----- Calc check -----"
	21	+
	22	+exec3:
	23	+ @echo "----- Execution Check -----"
	24	+ ../$(OSTYPE)/$(OBJECTNAME) -i data/test3.bin -o data/test3.area -l data/test3.label
	25	+ @echo "----- Calc check -----"
	26	+
	27	+clean:
	28	+
	29	+init:
	30	+ pdb2mrc -i data/121p.pdb2 -o data/test.mrc -nx 32 -ny 32 -nz 32 -dx 2 -dy 2 -dz 2 -Sx -32 -Sy -32 -Sz -32 -sig 1.6 -w 1.0
	31	+ mrcImageBinalization -i data/test.mrc -o data/test.bin -m 32
	32	+ mrcImageBinalization -i data/test2.mrc -o data/test2.bin -m 33
	33	+ mrcImageErosion -i data/test2.bin -o data/test3.bin
	34	+

--- /dev/null

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

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

--- /dev/null

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

		@@ -0,0 +1,4 @@
	1	+OBJECTNAME = mrcImageAutoTriming
	2	+EXTRA_LIB =
	3	+EXTRA_CCOPTS =
	4	+EXTRA_INC =

--- /dev/null

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

		@@ -0,0 +1,12 @@
	1	+# OptionControlFile
	2	+# FileFormat
	3	+"-i","-i[nput]","Input:mrcImage","Essential","1","1","In","inFile::mrcImage","NULL"
	4	+"-o","-o[utput]","Output:mrcImage","Essential","1","1","Out","outFile::mrcImage","NULL"
	5	+"-O","-O[utput]","OutputParams:YAML","Optional","1","1","OutParam","outFile::YAML","stdout"
	6	+"-EAMode","-E[uler]A[ngle]Mode","EulerAngle","Optional","1","1","EAMode","String","ZONS"
	7	+"-Rot1","-Rot[ation]1","Rot1","Optional","3","1","Rot1Min","Real","-5","1","Rot1Max","Real","5","3","Rot1Delta","Real","1"
	8	+"-Rot2","-Rot[ation]2","Rot2","Optional","3","1","Rot2Min","Real","-5","1","Rot2Max","Real","5","3","Rot2Delta","Real","1"
	9	+"-Rot3","-Rot[ation]3","Rot3","Optional","3","1","Rot3Min","Real","-5","1","Rot3Max","Real","5","3","Rot3Delta","Real","1"
	10	+"-M","-M[ode]","Iterpolation Mode","Optional","1","1","InterpolationMode","Integer","0"
	11	+"-c","-c[onfig]","ConfigurationFile","Optional","1","1","configFile","inFile","NULL"
	12	+"-m","-m[ode]","Mode","Optional","1","1","mode","Integer","0"

--- /dev/null

+++ b/src/Tools/mrcImage/mrcImageAutoTriming/Makefile

		@@ -0,0 +1,115 @@
	1	+include ../../../Config/Define.inc
	2	+include ../../Config/Define.inc
	3	+include ../Config/Define.inc
	4	+include Config/Define.inc
	5	+
	6	+all:
	7	+ cd src; make all; cd ..
	8	+
	9	+install:
	10	+ cd src; make install; cd ..
	11	+
	12	+
	13	+putSF:
	14	+ if [ -f private ] ; \
	15	+ then \
	16	+ echo "$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME) is private"; \
	17	+ else \
	18	+ cvs -z4 -d:ext:$$USER@$$EOS_SOURCEFORGE commit \|\| cvs -z4 -d:ext:$$USER@$$EOS_SOURCEFORGE import src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME); \
	19	+ fi
	20	+
	21	+put:
	22	+ cd src; make put; cd ..
	23	+
	24	+clean:
	25	+ cd src; make clean; cd ..
	26	+
	27	+depend:
	28	+ cd src; make depend; cd ..
	29	+
	30	+check:
	31	+ @if [ ! -d $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) ] ; then \
	32	+ echo making directory; \
	33	+ mkdir -p $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE); \
	34	+ fi
	35	+ ln -sf ../../../../../hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) src/$(OSTYPE);
	36	+ @$(RM) src/Makefile
	37	+ @echo "New src/Makefile"
	38	+ @$(CP) ../../../Config/Template/$(WORLDNAME)Template.Dir/src/Makefile src/Makefile
	39	+ @cd src; touch $(OSTYPE)/.Depend; make depend
	40	+
	41	+update:
	42	+ @if [ ! -d $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) ] ; then \
	43	+ echo making directory; \
	44	+ mkdir -p $(EOS_HOME)/hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE); \
	45	+ fi
	46	+ ln -sf ../../../../../hostdepend/$(OSTYPE)/src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE) src/$(OSTYPE);
	47	+ @$(RM) src/Makefile
	48	+ @echo "New src/Makefile"
	49	+ @$(CP) ../../../Config/Template/$(WORLDNAME)Template.Dir/src/Makefile src/Makefile
	50	+ @cd src; touch $(OSTYPE)/.Depend; echo "Y" \| make update
	51	+
	52	+cvsupdate::
	53	+ cvs -d $(EOS_CVSROOT) update -d
	54	+
	55	+cvscommit::
	56	+ cvs -d $(EOS_CVSROOT) commit
	57	+
	58	+backup:
	59	+ @cd ../../../..; \
	60	+ echo $(OBJECTNAME) ; \
	61	+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config ; \
	62	+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
	63	+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
	64	+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
	65	+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
	66	+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
	67	+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z].[A-z]; \
	68	+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
	69	+ tar uvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile
	70	+
	71	+backup-all:
	72	+ @cd ../../../..; \
	73	+ echo $(OBJECTNAME) ; \
	74	+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config ; \
	75	+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
	76	+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
	77	+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
	78	+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
	79	+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
	80	+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z].[A-z]; \
	81	+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
	82	+ tar rvf ${EOS_HOME}/backup/EosBase.tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile
	83	+
	84	+distribute:
	85	+ cd ../../../..; \
	86	+ echo $(OBJECTNAME) ; \
	87	+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config ; \
	88	+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
	89	+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
	90	+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
	91	+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
	92	+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
	93	+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z].[A-z]; \
	94	+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
	95	+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile ; \
	96	+ tar uvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE)
	97	+
	98	+distribute-all:
	99	+ @cd ../../../..; \
	100	+ echo $(OBJECTNAME) ; \
	101	+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Config ; \
	102	+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/Makefile ;\
	103	+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/.[A-z]* ; \
	104	+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/inc ; \
	105	+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/doc; \
	106	+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/wish; \
	107	+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/[A-z].[A-z]; \
	108	+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/.[A-z]*; \
	109	+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/Makefile ; \
	110	+ tar rvf ${EOS_HOME}/distribute/src.$(OSTYPE).tar src/$(WORLDNAME)/$(CLASSNAME)/$(OBJECTNAME)/src/$(OSTYPE)
	111	+
	112	+eosintroduce:
	113	+ ${EOS_HOME}/sbin/eosintroduce ${WORLDNAME} ${CLASSNAME} ${OBJECTNAME} ./
	114	+
	115	+include Config/Target.inc

--- /dev/null

+++ b/src/Tools/mrcImage/mrcImageAutoTriming/doc/Makefile

		@@ -0,0 +1,2 @@
	1	+install:
	2	+ cd ../src; make install-doc; cd ../doc

--- /dev/null

+++ b/src/Tools/mrcImage/mrcImageAutoTriming/inc/config.h

		@@ -0,0 +1,6 @@
	1	+#ifndef CONFIG_H
	2	+#define CONFIG_H
	3	+
	4	+#include "../inc/mrcImageAutoTriming.h"
	5	+
	6	+#endif /* CONFIG_H */

--- /dev/null

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

		@@ -0,0 +1,83 @@
	1	+#ifndef MRCIMAGEAUTOTRIMING_H
	2	+#define MRCIMAGEAUTOTRIMING_H
	3	+#include <stdio.h>
	4	+#include <stdlib.h>
	5	+
	6	+#define OPTION_FLAG '-'
	7	+#define OPTION_FLAG_POS (0)
	8	+#define OPTION_POS (1)
	9	+
	10	+
	11	+
	12	+
	13	+typedef struct mrcImageAutoTrimingInfo {
	14	+ long flagRedirect;
	15	+
	16	+ long flagIn;
	17	+ char* In;
	18	+ FILE* fptIn;
	19	+
	20	+ long flagOut;
	21	+ char* Out;
	22	+ FILE* fptOut;
	23	+
	24	+ long flagOutParam;
	25	+ char* OutParam;
	26	+ FILE* fptOutParam;
	27	+
	28	+ long flagEAMode;
	29	+ char* EAMode;
	30	+
	31	+ long flagRot1Min;
	32	+ float Rot1Min;
	33	+
	34	+ long flagRot1Max;
	35	+ float Rot1Max;
	36	+
	37	+ long flagRot1Delta;
	38	+ float Rot1Delta;
	39	+
	40	+ long flagRot2Min;
	41	+ float Rot2Min;
	42	+
	43	+ long flagRot2Max;
	44	+ float Rot2Max;
	45	+
	46	+ long flagRot2Delta;
	47	+ float Rot2Delta;
	48	+
	49	+ long flagRot3Min;
	50	+ float Rot3Min;
	51	+
	52	+ long flagRot3Max;
	53	+ float Rot3Max;
	54	+
	55	+ long flagRot3Delta;
	56	+ float Rot3Delta;
	57	+
	58	+ long flagInterpolationMode;
	59	+ long InterpolationMode;
	60	+
	61	+ long flagconfigFile;
	62	+ char* configFile;
	63	+ FILE* fptconfigFile;
	64	+
	65	+ long flagmode;
	66	+ long mode;
	67	+
	68	+} mrcImageAutoTrimingInfo;
	69	+#ifdef __cplusplus
	70	+extern "C" {
	71	+#endif
	72	+extern void argCheck(mrcImageAutoTrimingInfo* info, int argc, char* avgv[]);
	73	+extern void khorosInit(int argc, char* avgv[]);
	74	+extern void init0(mrcImageAutoTrimingInfo* info);
	75	+extern void init1(mrcImageAutoTrimingInfo* info);
	76	+extern void usage(char* usage);
	77	+extern void additionalUsage(void);
	78	+extern void htmlBeforeUsage(char* usage);
	79	+extern void htmlAfterUsage(char* usage);
	80	+#ifdef __cplusplus
	81	+};
	82	+#endif
	83	+#endif /* MRCIMAGEAUTOTRIMING_H */

--- /dev/null

+++ b/src/Tools/mrcImage/mrcImageAutoTriming/src/Makefile

		@@ -0,0 +1,427 @@
	1	+include ../Config/Define.inc
	2	+include ../../Config/Define.inc
	3	+include ../../../Config/Define.inc
	4	+include ../../../../Config/Define.inc
	5	+
	6	+EOSHOME=../../../../../
	7	+DSTDIR=$(EOSHOME)/bin
	8	+DSTDOC=$(EOSHOME)/doc
	9	+DSTTAR=$(EOSHOME)/tar
	10	+
	11	+INCFILES =
	12	+
	13	+LIBFILES = \
	14	+ $(LIBPREFIX)EosObjects$(LIBSUFFIX)
	15	+
	16	+LIBFILESDEBUG = \
	17	+ $(LIBPREFIX)EosObjects.debug$(LIBSUFFIX)
	18	+
	19	+SRCC = \
	20	+ $(OBJECTNAME).c \
	21	+ init.c \
	22	+ argCheck.c \
	23	+ usage.c \
	24	+ util.c \
	25	+
	26	+SRCCXX = \
	27	+ $(OBJECTNAME).cc \
	28	+ init.cc \
	29	+ argCheck.cc \
	30	+ usage.cc \
	31	+ util.cc \
	32	+
	33	+MODULES = \
	34	+ $(OBJECTNAME).o \
	35	+ init.o \
	36	+ argCheck.o \
	37	+ usage.o \
	38	+ util.o \
	39	+
	40	+REALMODULES = \
	41	+ $(OSTYPE)/$(OBJECTNAME).o \
	42	+ $(OSTYPE)/init.o \
	43	+ $(OSTYPE)/argCheck.o \
	44	+ $(OSTYPE)/usage.o \
	45	+ $(OSTYPE)/util.o
	46	+
	47	+MODULESDEBUG = \
	48	+ $(OBJECTNAME).debugo \
	49	+ init.debugo \
	50	+ argCheck.debugo \
	51	+ usage.debugo \
	52	+ util.debugo \
	53	+
	54	+REALMODULESDEBUG = \
	55	+ $(OSTYPE)/$(OBJECTNAME).debugo \
	56	+ $(OSTYPE)/init.debugo \
	57	+ $(OSTYPE)/argCheck.debugo \
	58	+ $(OSTYPE)/usage.debugo \
	59	+ $(OSTYPE)/util.debugo
	60	+
	61	+
	62	+all: $(OSTYPE)/$(OBJECTNAME)
	63	+ if [ ! -L $(OSTYPE) ] ; then \
	64	+ moveHostdependent; \
	65	+ fi
	66	+
	67	+debug: $(OSTYPE)/$(OBJECTNAME).debug
	68	+
	69	+cudagdb: $(OSTYPE)/$(OBJECTNAME).cudagdb
	70	+
	71	+
	72	+$(OSTYPE)/$(OBJECTNAME)::
	73	+ @$(RM) -f $(OSTYPE)/Makefile ; \
	74	+ $(CP) $(EOS_HOME)/src/Config/Template/$(WORLDNAME)Template.Dir/src/ARCH/Makefile $(OSTYPE)/Makefile ; \
	75	+ cd $(OSTYPE); \
	76	+ $(MAKE) $(OBJECTNAME) WORLDNAME=$(WORLDNAME) CLASSNAME=$(CLASSNAME) OBJECTNAME=$(OBJECTNAME)
	77	+
	78	+$(OSTYPE)/$(OBJECTNAME).debug::
	79	+ @$(RM) -f $(OSTYPE)/Makefile ; \
	80	+ $(CP) $(EOS_HOME)/src/Config/Template/$(WORLDNAME)Template.Dir/src/ARCH/Makefile $(OSTYPE)/Makefile ; \
	81	+ cd $(OSTYPE); \
	82	+ $(MAKE) $(OBJECTNAME).debug WORLDNAME=$(WORLDNAME) CLASSNAME=$(CLASSNAME) OBJECTNAME=$(OBJECTNAME)
	83	+
	84	+$(OSTYPE)/$(OBJECTNAME).cudagdb::
	85	+ @$(RM) -f $(OSTYPE)/Makefile ; \
	86	+ $(CP) $(EOS_HOME)/src/Config/Template/$(WORLDNAME)Template.Dir/src/ARCH/Makefile $(OSTYPE)/Makefile ; \
	87	+ cd $(OSTYPE); \
	88	+ $(MAKE) $(OBJECTNAME).cudagdb WORLDNAME=$(WORLDNAME) CLASSNAME=$(CLASSNAME) OBJECTNAME=$(OBJECTNAME)
	89	+
	90	+cvsupdate::
	91	+ cvs -d $(EOS_CVSROOT) update -d
	92	+
	93	+cvscommit::
	94	+ cvs -d $(EOS_CVSROOT) commit
	95	+
	96	+edit:
	97	+ @if [ -r $(OBJECTNAME).c ]; \
	98	+ then \
	99	+ sccsEdit $(OBJECTNAME).c; \
	100	+ else \
	101	+ echo "Source files are already editable"; \
	102	+ fi
	103	+ @if [ -r wish/$(OBJECTNAME).wish ]; \
	104	+ then \
	105	+ cd wish; sccsEdit $(OBJECTNAME).wish; \
	106	+ else \
	107	+ echo "Source files (wish) are already editable."; \
	108	+ fi
	109	+ @if [ -r ruby/$(OBJECTNAME).rb ]; \
	110	+ then \
	111	+ cd ruby; sccsEdit $(OBJECTNAME).rb; \
	112	+ else \
	113	+ echo "Source files (ruby) are already editable."; \
	114	+ fi
	115	+ @if [ -r perl/$(OBJECTNAME).pl ]; \
	116	+ then \
	117	+ cd perl; sccsEdit $(OBJECTNAME).pl ; \
	118	+ else \
	119	+ echo "Source files (perl) are already editable."; \
	120	+ fi
	121	+ @if [ -r ../Config/OptionControlFile ]; \
	122	+ then \
	123	+ cd ../Config; sccsEdit OptionControlFile; \
	124	+ else \
	125	+ echo "OptionControlFile are already editable."; \
	126	+ fi
	127	+
	128	+unedit:
	129	+ @if [ -w $(OBJECTNAME).c ]; \
	130	+ then \
	131	+ sccsUnedit $(OBJECTNAME).c; \
	132	+ else \
	133	+ echo "Source files are not editable"; \
	134	+ fi
	135	+ @if [ -w wish/$(OBJECTNAME).wish ]; \
	136	+ then \
	137	+ cd wish; sccsUnedit $(OBJECTNAME).wish; \
	138	+ else \
	139	+ echo "Source files (wish) are not editable."; \
	140	+ fi
	141	+ @if [ -w ruby/$(OBJECTNAME).rb]; \
	142	+ then \
	143	+ cd ruby; sccsUnedit $(OBJECTNAME).rb; \
	144	+ else \
	145	+ echo "Source files (ruby) are not editable."; \
	146	+ fi
	147	+ @if [ -w perl/$(OBJECTNAME).pl ]; \
	148	+ then \
	149	+ cd perl; sccsUnedit $(OBJECTNAME).pl ; \
	150	+ else \
	151	+ echo "Source files (ruby) are not editable."; \
	152	+ fi
	153	+ @if [ -w ../Config/OptionControlFile ]; \
	154	+ then \
	155	+ cd ../Config; sccsUnedit OptionControlFile; \
	156	+ else \
	157	+ echo "OptionControlFile are not editable."; \
	158	+ fi
	159	+
	160	+report:
	161	+ @if [ -r $(OBJECTNAME).c ]; \
	162	+ then \
	163	+ sccsReport $(OBJECTNAME).c; \
	164	+ else \
	165	+ echo "Source files are already editable"; \
	166	+ fi
	167	+ @if [ -r wish/$(OBJECTNAME).wish ]; \
	168	+ then \
	169	+ cd wish; sccsReport $(OBJECTNAME).wish; \
	170	+ else \
	171	+ echo "Source files (wish) are already editable."; \
	172	+ fi
	173	+ @if [ -r ruby/$(OBJECTNAME).rb ]; \
	174	+ then \
	175	+ cd ruby; sccsReport $(OBJECTNAME).rb; \
	176	+ else \
	177	+ echo "Source files (ruby) are already editable."; \
	178	+ fi
	179	+ @if [ -r perl/$(OBJECTNAME).pl ] ; \
	180	+ then \
	181	+ cd perl; sccsReport $(OBJECTNAME).pl ; \
	182	+ else \
	183	+ echo "Source files (perl) are already editable."; \
	184	+ fi
	185	+ @if [ -r ../Config/OptionControlFile ]; \
	186	+ then \
	187	+ cd ../Config; sccsReport OptionControlFile; \
	188	+ else \
	189	+ echo "OptionControlFile are already editable."; \
	190	+ fi
	191	+
	192	+clean :
	193	+ rm -f .debugo $(OSTYPE)/.debugo .cudagdbo $(OSTYPE)/.cudagdbo .o $(OSTYPE)/.o .linkinfo $(OSTYPE)/.linkinfo \
	194	+ $(OSTYPE)/$(OBJECTNAME) $(OSTYPE)/*.$(OSTYPE) \
	195	+ $(OSTYPE)/$(OBJECTNAME).debug $(OSTYPE)/*.$(OSTYPE).debug \
	196	+ $(OSTYPE)/$(OBJECTNAME).cudagdb $(OSTYPE)/*.$(OSTYPE).cudagdb \
	197	+ $(OSTYPE)/$(OBJECTNAME).linkinfo $(OSTYPE)/*.$(OSTYPE).linkinfo \
	198	+ .bak .$(OSTYPE) core
	199	+
	200	+install: install-bin install-doc install-wish install-ruby install-shell install-perl
	201	+ @if [ dummy$(KHOROS_KENGOBJ) != dummy ] ; \
	202	+ then \
	203	+ if [ -x $(KHOROS_KGENOBJ) ] ; \
	204	+ then \
	205	+ make install-khoros ; \
	206	+ fi; \
	207	+ fi
	208	+
	209	+install-bin:$(DSTDIR)/$(OSTYPE)/$(OBJECTNAME)
	210	+
	211	+$(DSTDIR)/$(OSTYPE)/$(OBJECTNAME):$(OSTYPE)/$(OBJECTNAME) $(DSTDIR)/$(OBJECTNAME)
	212	+ @echo ---- Installing to bin
	213	+ @echo $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME)
	214	+ @if [ ! -d $(DSTDIR)/$(OSTYPE) ]; \
	215	+ then \
	216	+ mkdir $(DSTDIR)/$(OSTYPE); \
	217	+ fi
	218	+ @if [ -x $(OSTYPE)/$(OBJECTNAME) ]; \
	219	+ then \
	220	+ echo "Compilation is complete"; \
	221	+ $(RM) -f $(DSTDIR)/$(OSTYPE)/$(OBJECTNAME); \
	222	+ $(CD) $(OSTYPE); $(INSTALL) -m 555 $(OBJECTNAME) ../$(DSTDIR)/$(OSTYPE); \
	223	+ $(CHMOD) 555 ../$(DSTDIR)/$(OSTYPE)/$(OBJECTNAME); \
	224	+ else \
	225	+ echo "Compilation is incomplete. $(OBJECTNAME)"; \
	226	+ fi
	227	+ @echo ---- end of bin
	228	+
	229	+install-wish:
	230	+ @if [ -d wish ]; \
	231	+ then \
	232	+ echo "---- Tcl/Tk file Install"; \
	233	+ if [ ! -d $(DSTDIR)/wish/$(OBJECTNAME) ]; \
	234	+ then \
	235	+ mkdir $(DSTDIR)/wish/$(OBJECTNAME) ; \
	236	+ fi ; \
	237	+ $(CP) -f wish/* $(DSTDIR)/wish/$(OBJECTNAME); \
	238	+ $(CHMOD) 555 $(DSTDIR)/wish/$(OBJECTNAME)/* ;\
	239	+ touch $(DSTDIR)/wish/$(OBJECTNAME)/tclIndex;\
	240	+ $(CHMOD) 666 $(DSTDIR)/wish/$(OBJECTNAME)/tclIndex;\
	241	+ echo "---- Tcl/Tk file Installed";\
	242	+ fi
	243	+
	244	+install-ruby:
	245	+ @if [ -d ruby ]; \
	246	+ then \
	247	+ echo "---- Ruby/Tk file Install"; \
	248	+ if [ ! -d $(DSTDIR)/ruby/$(OBJECTNAME) ]; \
	249	+ then \
	250	+ mkdir $(DSTDIR)/ruby/$(OBJECTNAME) ; \
	251	+ fi ; \
	252	+ $(CP) -f ruby/* $(DSTDIR)/ruby/$(OBJECTNAME); \
	253	+ $(CHMOD) 555 $(DSTDIR)/ruby/$(OBJECTNAME)/* ; \
	254	+ echo "---- Ruby/Tk file Installed"; \
	255	+ fi
	256	+
	257	+install-perl:
	258	+ @if [ -d perl ]; \
	259	+ then \
	260	+ echo "---- Perl/Tk file Install"; \
	261	+ if [ ! -d $(DSTDIR)/perl/$(OBJECTNAME) ]; \
	262	+ then \
	263	+ mkdir $(DSTDIR)/perl/$(OBJECTNAME) ; \
	264	+ fi; \
	265	+ $(CP) -f perl/* $(DSTDIR)/perl/$(OBJECTNAME); \
	266	+ $(CHMOD) 555 $(DSTDIR)/perl/$(OBJECTNAME)/* ; \
	267	+ echo "---- Perl/Tk file Installed"; \
	268	+ fi
	269	+
	270	+install-shell:
	271	+ @if [ ! -d $(DSTDIR)/shell/$(OBJECTNAME) ]; \
	272	+ then \
	273	+ mkdir $(DSTDIR)/shell/$(OBJECTNAME) ; \
	274	+ fi
	275	+ @if [ -d shell ]; \
	276	+ then \
	277	+ echo "---- Shell file Install"; \
	278	+ if [ ! -d $(DSTDIR)/shell/$(OBJECTNAME) ]; \
	279	+ then \
	280	+ mkdir $(DSTDIR)/shell/$(OBJECTNAME) ; \
	281	+ fi ; \
	282	+ $(CP) -f shell/* $(DSTDIR)/shell/$(OBJECTNAME); \
	283	+ $(CHMOD) 555 $(DSTDIR)/shell/$(OBJECTNAME)/*; \
	284	+ echo "---- Shell file Installed"; \
	285	+ fi
	286	+
	287	+install-khoros:
	288	+ @echo Installing to khoros
	289	+ @if [ ! -d ../../../../../objects/script/$(OBJECTNAME) -a -f $(KHOROS_KGENOBJ) ]; \
	290	+ then \
	291	+ echo kgenobj;\
	292	+ $(KHOROS_KGENOBJ) -tb Eos -oname $(OBJECTNAME) -type script -pane -cantata true -cat Eos -subcat $(CLASSNAME) -description $(OBJECTNAME) -bname $(OBJECTNAME) -form -lang ksh ; \
	293	+ fi
	294	+ @if [ ! -d ../../../../../objects/script/$(OBJECTNAME) -a -f $(KHOROS_KSET) ]; \
	295	+ then \
	296	+ $(KHOROS_KSET) -tb Eos -oname $(OBJECTNAME) -icon $(OBJECTNAME) ; \
	297	+ fi
	298	+ @if [ -d ../../../../../objects/script/$(OBJECTNAME) -a -f $(KHOROS_KSET) ]; \
	299	+ then \
	300	+ $(CHMOD) -R 775 ../../../../../objects/script/$(OBJECTNAME) ; \
	301	+ if [ $? ] ; \
	302	+ then \
	303	+ echo "-- setting khoros ---" ; \
	304	+ if [ -d ../../../../../objects/script/$(OBJECTNAME)/uis/ ] ; \
	305	+ then \
	306	+ $(CD) ../../../../../objects/script/$(OBJECTNAME)/uis/ ; \
	307	+ $(RM) -f $(OBJECTNAME).pane ; \
	308	+ $(LN) -s ../../../../src/Tools/$(CLASSNAME)/$(OBJECTNAME)/src/$(OBJECTNAME).pane $(OBJECTNAME).pane; \
	309	+ $(CD) ../../ ; \
	310	+ $(CHMOD) -R 555 $(OBJECTNAME); \
	311	+ else \
	312	+ echo "../../../../../objects/script/$(OBJECTNAME)/uis/ does not exist."; \
	313	+ fi ; \
	314	+ else \
	315	+ echo "Failed !!: Cannot chage mode in installing $(OBJECTNAME) to khoros system"; \
	316	+ fi ; \
	317	+ echo "-- end of khoros-installing"; \
	318	+ fi
	319	+
	320	+install-doc: html
	321	+ @if [ ! -d $(DSTDOC)/SmallTools ]; \
	322	+ then \
	323	+ mkdir $(DSTDOC)/SmallTools ;\
	324	+ fi
	325	+ @if [ -f $(DSTDOC)/SmallTools/$(OBJECTNAME).html ]; \
	326	+ then \
	327	+ $(RM) -f $(DSTDOC)/SmallTools/$(OBJECTNAME).html ;\
	328	+ fi
	329	+ @$(CP) $(OBJECTNAME).html $(DSTDOC)/SmallTools/$(OBJECTNAME).html
	330	+ @$(CHMOD) 444 $(DSTDOC)/SmallTools/$(OBJECTNAME).html
	331	+ @if [ -f ../doc/*.html ]; \
	332	+ then \
	333	+ $(CP) ../doc/*.html $(DSTDOC)/SmallTools/ ;\
	334	+ fi
	335	+ @$(CHMOD) 444 $(DSTDOC)/SmallTools/$(OBJECTNAME).html
	336	+ @if [ -f $(DSTDOC)/SmallTools/Makefile ]; \
	337	+ then \
	338	+ cd $(DSTDOC)/SmallTools; $(MAKE); \
	339	+ fi
	340	+
	341	+html: $(OBJECTNAME).html
	342	+
	343	+configFileRead:
	344	+ @ctrl2configFileRead $(CLASSNAME) $(OBJECTNAME) ../Config/OptionControlFile
	345	+
	346	+$(OBJECTNAME).html: $(OSTYPE)/$(OBJECTNAME)
	347	+ @echo creating html
	348	+ @$(OSTYPE)/$(OBJECTNAME) -html 2> $(OBJECTNAME).html.tmp
	349	+ @sed -e s/$(OSTYPE)\\/// $(OBJECTNAME).html.tmp > $(OBJECTNAME).html
	350	+ @$(RM) $(OBJECTNAME).html.tmp
	351	+
	352	+$(DSTDIR)/$(OBJECTNAME): $(OSTYPE)/$(OBJECTNAME)
	353	+ @ln -s -f ../sbin/MachineIndependent $@
	354	+
	355	+depend::
	356	+ @echo dependency checking now
	357	+ @if [ ! -L $(OSTYPE) ] ; then \
	358	+ moveHostdependent; \
	359	+ fi
	360	+ rm -f $(OSTYPE)/.Depend
	361	+ #echo C
	362	+ @if [ -f $(OBJECTNAME).c ] ; \
	363	+ then \
	364	+ echo "dependency: *.c"; \
	365	+ echo $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) *.c ; \
	366	+ $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) *.c >> $(OSTYPE)/.Depend ; \
	367	+ fi
	368	+ #echo CC
	369	+ @if [ -f $(OBJECTNAME).cc ] ; \
	370	+ then \
	371	+ echo "dependency: *.cc"; \
	372	+ echo $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.cc ; \
	373	+ $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.cc >> $(OSTYPE)/.Depend ; \
	374	+ fi
	375	+ @if [ -f $(OBJECTNAME).ccm ] ; \
	376	+ then \
	377	+ echo "dependency: *.ccm"; \
	378	+ echo $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.ccm ; \
	379	+ $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.ccm >> $(OSTYPE)/.Depend ; \
	380	+ fi
	381	+ @if [ -f $(OBJECTNAME).cu ] ; \
	382	+ then \
	383	+ echo "dependency: *.cu"; \
	384	+ echo $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.cu ; \
	385	+ $(DEPENDCOMMAND) $(INCLUDEDIR) $(EXTRA_INC) $(EXTRA_DEFINE) $(EXTRA_CCOPTS) *.cu >> $(OSTYPE)/.Depend ; \
	386	+ fi
	387	+
	388	+update:../Config/OptionControlFile
	389	+ maketool $(CLASSNAME) $(OBJECTNAME) update
	390	+
	391	+changeName::
	392	+
	393	+Test:$(OSTYPE)/$(OBJECTNAME) TestDir
	394	+ @if [ -f test/Makefile ] ; \
	395	+ then \
	396	+ cd test; make ; \
	397	+ else \
	398	+ echo "No test Makefile"; \
	399	+ fi
	400	+
	401	+TestDir::
	402	+ @if [ ! -d test ] ; \
	403	+ then \
	404	+ echo "Creating test dir"; \
	405	+ mkdir test; \
	406	+ fi
	407	+ @if [ ! -f test/Makefile ] ; \
	408	+ then \
	409	+ echo "Creating Makefile"; \
	410	+ cd test; \
	411	+ protoTestMakefileCreate; \
	412	+ fi
	413	+ @if [ ! -d test/data ]; \
	414	+ then \
	415	+ mkdir $(EOSHOME)/data/$(OBJECTNAME); \
	416	+ cd test; \
	417	+ ln -sf ../$(EOSHOME)/data/$(OBJECTNAME) data; \
	418	+ fi
	419	+
	420	+tar::
	421	+ cd $(DSTTAR); tar cvf Tools.$(CLASSNAME).$(OBJECTNAME).tar ../bin/$(OBJECTNAME) \
	422	+ ../bin//$(OBJECTNAME). \
	423	+ ../src/Tools/$(CLASSNAME)/$(OBJECTNAME) \
	424	+ ; gzip Tools.$(CLASSNAME).$(OBJECTNAME).tar
	425	+
	426	+-include $(OSTYPE)/.Depend
	427	+-include ../Config/Target.inc

--- /dev/null

+++ b/src/Tools/mrcImage/mrcImageAutoTriming/src/X86MAC64

		@@ -0,0 +1 @@
	1	+../../../../../hostdepend/X86MAC64/src/Tools/mrcImage/mrcImageAutoTriming/src/X86MAC64
		\ No newline at end of file

--- /dev/null

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

		@@ -0,0 +1,180 @@
	1	+#include <stdio.h>
	2	+#include <stdlib.h>
	3	+#include <string.h>
	4	+#include <math.h>
	5	+#include "../inc/config.h"
	6	+#include "genUtil.h"
	7	+#include "String.h"
	8	+#include "File.h"
	9	+#include "Memory.h"
	10	+
	11	+
	12	+void
	13	+argCheck(mrcImageAutoTrimingInfo* info, int argc, char* argv[])
	14	+{
	15	+ long i;
	16	+ char s[1024];
	17	+ FILE* fpt;
	18	+
	19	+ if(NULL==(fpt=fopen(".EosLog", "a+"))) {
	20	+
	21	+ } else {
	22	+ for(i=0; i<argc; i++) {
	23	+ fprintf(fpt, "%s ", argv[i]);
	24	+ }
	25	+ fprintf(fpt, "\n");
	26	+ fclose(fpt);
	27	+ }
	28	+ for(i=1; i<argc; i++) {
	29	+ if(OPTION_FLAG==argv[i][OPTION_FLAG_POS]) {
	30	+ SSWITCH(argv[i]+OPTION_POS)
	31	+ SCASE("i") {
	32	+ if(i+1<argc) {
	33	+ info->In = stringGetNthWord(argv[i+1], 1, " ,");
	34	+ i++;
	35	+ info->flagIn++;
	36	+ } else {
	37	+ usage(argv[0]);
	38	+ exit(EXIT_FAILURE);
	39	+ }
	40	+ SBREAK;
	41	+ }
	42	+ SCASE("o") {
	43	+ if(i+1<argc) {
	44	+ info->Out = stringGetNthWord(argv[i+1], 1, " ,");
	45	+ i++;
	46	+ info->flagOut++;
	47	+ } else {
	48	+ usage(argv[0]);
	49	+ exit(EXIT_FAILURE);
	50	+ }
	51	+ SBREAK;
	52	+ }
	53	+ SCASE("O") {
	54	+ if(i+1<argc) {
	55	+ info->OutParam = stringGetNthWord(argv[i+1], 1, " ,");
	56	+ i++;
	57	+ info->flagOutParam++;
	58	+ } else {
	59	+ usage(argv[0]);
	60	+ exit(EXIT_FAILURE);
	61	+ }
	62	+ SBREAK;
	63	+ }
	64	+ SCASE("EAMode") {
	65	+ if(i+1<argc) {
	66	+ info->EAMode = stringGetNthWord(argv[i+1], 1, " ,");
	67	+ i++;
	68	+ info->flagEAMode++;
	69	+ } else {
	70	+ usage(argv[0]);
	71	+ exit(EXIT_FAILURE);
	72	+ }
	73	+ SBREAK;
	74	+ }
	75	+ SCASE("Rot1") {
	76	+ if(i+3<argc) {
	77	+ info->Rot1Min = stringGetNthRealData(argv[i+1], 1, " ,");
	78	+ i++;
	79	+ info->flagRot1Min++;
	80	+ info->Rot1Max = stringGetNthRealData(argv[i+1], 1, " ,");
	81	+ i++;
	82	+ info->flagRot1Max++;
	83	+ info->Rot1Delta = stringGetNthRealData(argv[i+1], 1, " ,");
	84	+ i++;
	85	+ info->flagRot1Delta++;
	86	+ } else {
	87	+ usage(argv[0]);
	88	+ exit(EXIT_FAILURE);
	89	+ }
	90	+ SBREAK;
	91	+ }
	92	+ SCASE("Rot2") {
	93	+ if(i+3<argc) {
	94	+ info->Rot2Min = stringGetNthRealData(argv[i+1], 1, " ,");
	95	+ i++;
	96	+ info->flagRot2Min++;
	97	+ info->Rot2Max = stringGetNthRealData(argv[i+1], 1, " ,");
	98	+ i++;
	99	+ info->flagRot2Max++;
	100	+ info->Rot2Delta = stringGetNthRealData(argv[i+1], 1, " ,");
	101	+ i++;
	102	+ info->flagRot2Delta++;
	103	+ } else {
	104	+ usage(argv[0]);
	105	+ exit(EXIT_FAILURE);
	106	+ }
	107	+ SBREAK;
	108	+ }
	109	+ SCASE("Rot3") {
	110	+ if(i+3<argc) {
	111	+ info->Rot3Min = stringGetNthRealData(argv[i+1], 1, " ,");
	112	+ i++;
	113	+ info->flagRot3Min++;
	114	+ info->Rot3Max = stringGetNthRealData(argv[i+1], 1, " ,");
	115	+ i++;
	116	+ info->flagRot3Max++;
	117	+ info->Rot3Delta = stringGetNthRealData(argv[i+1], 1, " ,");
	118	+ i++;
	119	+ info->flagRot3Delta++;
	120	+ } else {
	121	+ usage(argv[0]);
	122	+ exit(EXIT_FAILURE);
	123	+ }
	124	+ SBREAK;
	125	+ }
	126	+ SCASE("M") {
	127	+ if(i+1<argc) {
	128	+ info->InterpolationMode = stringGetNthIntegerData(argv[i+1], 1, " ,");
	129	+ i++;
	130	+ info->flagInterpolationMode++;
	131	+ } else {
	132	+ usage(argv[0]);
	133	+ exit(EXIT_FAILURE);
	134	+ }
	135	+ SBREAK;
	136	+ }
	137	+ SCASE("c") {
	138	+ if(i+1<argc) {
	139	+ info->configFile = stringGetNthWord(argv[i+1], 1, " ,");
	140	+ i++;
	141	+ info->flagconfigFile++;
	142	+ } else {
	143	+ usage(argv[0]);
	144	+ exit(EXIT_FAILURE);
	145	+ }
	146	+ SBREAK;
	147	+ }
	148	+ SCASE("m") {
	149	+ if(i+1<argc) {
	150	+ info->mode = stringGetNthIntegerData(argv[i+1], 1, " ,");
	151	+ i++;
	152	+ info->flagmode++;
	153	+ } else {
	154	+ usage(argv[0]);
	155	+ exit(EXIT_FAILURE);
	156	+ }
	157	+ SBREAK;
	158	+ }
	159	+ SCASE("h") {
	160	+ usage(argv[0]);
	161	+ exit(EXIT_SUCCESS);
	162	+ break;
	163	+ }
	164	+ SCASE("html") {
	165	+ htmlBeforeUsage(argv[0]);
	166	+ usage(argv[0]);
	167	+ htmlAfterUsage(argv[0]);
	168	+ exit(EXIT_SUCCESS);
	169	+ break;
	170	+ }
	171	+ SDEFAULT {
	172	+ fprintf(stderr, "Not Supported Options: :%s\n", argv[i]);
	173	+ usage(argv[0]);
	174	+ exit(EXIT_FAILURE);
	175	+ break;
	176	+ }
	177	+ SSWITCHEND;
	178	+ }
	179	+ }
	180	+}

--- /dev/null

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

		@@ -0,0 +1,140 @@
	1	+#include <stdio.h>
	2	+#include <stdlib.h>
	3	+#include <string.h>
	4	+#include <math.h>
	5	+#include "../inc/config.h"
	6	+#include "genUtil.h"
	7	+#include "String.h"
	8	+#include "File.h"
	9	+#include "Memory.h"
	10	+
	11	+
	12	+void
	13	+init0(mrcImageAutoTrimingInfo* info)
	14	+{
	15	+ info->fptIn = NULL; info->flagIn = 0;
	16	+ info->fptOut = NULL; info->flagOut = 0;
	17	+ info->fptOutParam = stdout; info->flagOutParam = 0;
	18	+ info->EAMode = stringGetNthWord("ZONS", 1, "\0"); info->flagEAMode = 0;
	19	+ info->Rot1Min = -5; info->flagRot1Min = 0;
	20	+ info->Rot1Max = 5; info->flagRot1Max = 0;
	21	+ info->Rot1Delta = 1; info->flagRot1Delta = 0;
	22	+ info->Rot2Min = -5; info->flagRot2Min = 0;
	23	+ info->Rot2Max = 5; info->flagRot2Max = 0;
	24	+ info->Rot2Delta = 1; info->flagRot2Delta = 0;
	25	+ info->Rot3Min = -5; info->flagRot3Min = 0;
	26	+ info->Rot3Max = 5; info->flagRot3Max = 0;
	27	+ info->Rot3Delta = 1; info->flagRot3Delta = 0;
	28	+ info->InterpolationMode = 0; info->flagInterpolationMode = 0;
	29	+ info->fptconfigFile = NULL; info->flagconfigFile = 0;
	30	+ info->mode = 0; info->flagmode = 0;
	31	+}
	32	+
	33	+void
	34	+init1(mrcImageAutoTrimingInfo* info)
	35	+{
	36	+ char s[1024];
	37	+ int i;
	38	+ if(!info->flagIn) {
	39	+ stringGetFromFile(s, "In", stdin, stdout, 0);
	40	+ info->In = stringGetNthWord(s, 1, " ,\t");
	41	+ info->flagIn++;
	42	+ }
	43	+ if(info->flagIn) {
	44	+ info->fptIn = fileOpen(info->In, "r");
	45	+ }
	46	+
	47	+ if(!info->flagOut) {
	48	+ stringGetFromFile(s, "Out", stdin, stdout, 0);
	49	+ info->Out = stringGetNthWord(s, 1, " ,\t");
	50	+ info->flagOut++;
	51	+ }
	52	+ if(info->flagOut) {
	53	+ info->fptOut = fileOpen(info->Out, "w");
	54	+ }
	55	+
	56	+ if(info->flagOutParam) {
	57	+ info->fptOutParam = fileOpen(info->OutParam, "w");
	58	+ }
	59	+
	60	+ if(info->flagEAMode) {
	61	+ }
	62	+
	63	+ if(info->flagRot1Min) {
	64	+ }
	65	+
	66	+ if(info->flagRot1Max) {
	67	+ }
	68	+
	69	+ if(info->flagRot1Delta) {
	70	+ }
	71	+
	72	+ if(info->flagRot2Min) {
	73	+ }
	74	+
	75	+ if(info->flagRot2Max) {
	76	+ }
	77	+
	78	+ if(info->flagRot2Delta) {
	79	+ }
	80	+
	81	+ if(info->flagRot3Min) {
	82	+ }
	83	+
	84	+ if(info->flagRot3Max) {
	85	+ }
	86	+
	87	+ if(info->flagRot3Delta) {
	88	+ }
	89	+
	90	+ if(info->flagInterpolationMode) {
	91	+ }
	92	+
	93	+ if(info->flagconfigFile) {
	94	+ info->fptconfigFile = fileOpen(info->configFile, "r");
	95	+ }
	96	+
	97	+ if(info->flagmode) {
	98	+ }
	99	+
	100	+}
	101	+#ifdef KHOROS
	102	+#include <stdio.h>
	103	+#include "bootstrap.h"
	104	+#include "dataserv.h"
	105	+#include "datamanip.h"
	106	+extern void func_usage_additions(void);
	107	+extern void func_free_args(kexit_status status, kaddr client_data);
	108	+extern void func_get_args(kform* pane);
	109	+
	110	+void
	111	+func_usage_additions(void)
	112	+{
	113	+}
	114	+void
	115	+func_free_args(kexit_status status, kaddr client_data)
	116	+{
	117	+}
	118	+void
	119	+func_get_args(kform* pane)
	120	+{
	121	+}
	122	+void
	123	+khorosInit(int argc, char* argv[])
	124	+{
	125	+ char* eospath;
	126	+ char panepath[1024];
	127	+ FILE* fpt;
	128	+
	129	+ eospath = getenv("EOS_HOME");
	130	+ sprintf(panepath, "%s/src/Tools/mrcImage/mrcImageAutoTriming/src/mrcImageAutoTriming.pane", eospath);
	131	+ khoros_initialize(argc, argv, "EOS");
	132	+ fpt = fopen(panepath, "r"); if(NULL!=fpt) {
	133	+ fclose(fpt);
	134	+ kclui_initialize(panepath, KGEN_NONE, "EOS", "mrcImageAutoTriming",
	135	+ func_usage_additions,
	136	+ func_get_args,
	137	+ func_free_args);
	138	+ }
	139	+}
	140	+#endif /* KHOROS */

--- /dev/null

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

		@@ -0,0 +1,219 @@
	1	+/*
	2	+# mrcImageAutoTriming : $Revision$
	3	+# $Date$
	4	+# Created by $Author$
	5	+# Usage : mrcImageAutoTriming
	6	+# Attention
	7	+# $Loccker$
	8	+# $State$
	9	+#
	10	+*/
	11	+#include <stdio.h>
	12	+#include <stdlib.h>
	13	+#include <string.h>
	14	+#include <math.h>
	15	+#define GLOBAL_DECLARATION
	16	+#include "../inc/config.h"
	17	+
	18	+#define DEBUG
	19	+#include "genUtil.h"
	20	+#include "Matrix3D.h"
	21	+#include "mrcImage.h"
	22	+
	23	+typedef struct lmrcImageAutoTrimingInfo {
	24	+ // Control
	25	+ EulerAngleInfo min;
	26	+ EulerAngleInfo max;
	27	+ EulerAngleInfo delta;
	28	+ int InterpolationMode;
	29	+
	30	+ // Temp
	31	+ EulerAngleInfo cur;
	32	+
	33	+ // Final
	34	+ EulerAngleInfo best;
	35	+ mrcImageParaTypeReal bestThickness;
	36	+ mrcImageParaTypeReal bestThicknessBottom;
	37	+ mrcImageParaTypeReal bestThicknessTop;
	38	+
	39	+} lmrcImageAutoTrimingInfo;
	40	+
	41	+typedef enum lmrcImageAutoTrimingMode {
	42	+ lmrcImageAutoTrimingModeZLayerMinCut=0,
	43	+ lmrcImageAutoTrimingModeZLayerSDCut=1
	44	+} lmrcImageAutoTrimingMode;
	45	+
	46	+extern char* stpncpy(char restrict dst, const char restrict src, size_t n);
	47	+extern void lmrcImageAutoTriming(mrcImage* out, mrcImage* in, lmrcImageAutoTrimingInfo* linfo, int mode);
	48	+extern void lmrcImageAutoTrimingOutput(FILE* fpt, lmrcImageAutoTrimingInfo* linfo, int mode);
	49	+extern void lmrcImageAutoTrimingUsage(FILE* fpt);
	50	+
	51	+int
	52	+main(int argc, char* argv[])
	53	+{
	54	+ mrcImageAutoTrimingInfo info;
	55	+ lmrcImageAutoTrimingInfo linfo;
	56	+ mrcImage in;
	57	+ mrcImage out;
	58	+
	59	+ init0(&info);
	60	+ argCheck(&info, argc, argv);
	61	+ init1(&info);
	62	+
	63	+ DEBUGPRINT("Program Start\n");
	64	+ strncpy(linfo.cur.EAMode, info.EAMode, 4);
	65	+ strncpy(linfo.min.EAMode, info.EAMode, 4);
	66	+ strncpy(linfo.max.EAMode, info.EAMode, 4);
	67	+ strncpy(linfo.delta.EAMode, info.EAMode, 4);
	68	+ linfo.min.Rot1 = info.Rot1Min*RADIAN;
	69	+ linfo.min.Rot2 = info.Rot2Min*RADIAN;
	70	+ linfo.min.Rot3 = info.Rot3Min*RADIAN;
	71	+ linfo.max.Rot1 = info.Rot1Max*RADIAN;
	72	+ linfo.max.Rot2 = info.Rot2Max*RADIAN;
	73	+ linfo.max.Rot3 = info.Rot3Max*RADIAN;
	74	+ linfo.delta.Rot1 = info.Rot1Delta*RADIAN;
	75	+ linfo.delta.Rot2 = info.Rot2Delta*RADIAN;
	76	+ linfo.delta.Rot3 = info.Rot3Delta*RADIAN;
	77	+ linfo.InterpolationMode = info.InterpolationMode;
	78	+
	79	+ mrcFileRead(&in, info.In, "in main", 0);
	80	+
	81	+ lmrcImageAutoTriming(&out, &in, &linfo, info.mode);
	82	+
	83	+ lmrcImageAutoTrimingOutput(info.fptOutParam, &linfo, info.mode);
	84	+
	85	+ mrcFileWrite(&out, info.Out, "in main", 0);
	86	+
	87	+ exit(EXIT_SUCCESS);
	88	+}
	89	+
	90	+void
	91	+additionalUsage()
	92	+{
	93	+ fprintf(stderr, "----- Additional Usage -----\n");
	94	+ lmrcImageAutoTrimingUsage(stderr);
	95	+}
	96	+
	97	+void
	98	+lmrcImageAutoTriming(mrcImage* out, mrcImage* in, lmrcImageAutoTrimingInfo* linfo, int mode)
	99	+{
	100	+ Matrix3D mat;
	101	+ mrcImage tmp;
	102	+ mrcImageParaTypeInteger ix, iy, iz, k, kz, ky, kx0;
	103	+ double data;
	104	+
	105	+ int flagBottom, izBottom;
	106	+ int flagTop, izTop;
	107	+ int thickness;
	108	+ double minSD;
	109	+ mrcImageParaTypeRealCoord to;
	110	+
	111	+ linfo->bestThickness = in->HeaderN.z;
	112	+ for(linfo->cur.Rot1=linfo->min.Rot1; linfo->cur.Rot1<=linfo->max.Rot1; linfo->cur.Rot1+=linfo->delta.Rot1) {
	113	+ for(linfo->cur.Rot2=linfo->min.Rot2; linfo->cur.Rot2<=linfo->max.Rot2; linfo->cur.Rot2+=linfo->delta.Rot2) {
	114	+ for(linfo->cur.Rot3=linfo->min.Rot3; linfo->cur.Rot3<=linfo->max.Rot3; linfo->cur.Rot3+=linfo->delta.Rot3) {
	115	+ lmrcImageRotation3DFollowingEulerAngle(&tmp, in, linfo->cur.EAMode, linfo->cur.Rot1, linfo->cur.Rot2, linfo->cur.Rot3, linfo->InterpolationMode, 0);
	116	+
	117	+ switch(mode) {
	118	+ case lmrcImageAutoTrimingModeZLayerMinCut: {
	119	+ flagBottom = 0;
	120	+ flagTop = 0;
	121	+ izBottom = 0;
	122	+ izTop = in->HeaderN.z - 1;
	123	+ for(iz=0; iz<in->HeaderN.z; iz++) {
	124	+ kz = izin->HeaderN.xin->HeaderN.y;
	125	+ for(iy=0; iy<in->HeaderN.y; iy++) {
	126	+ ky = iy*in->HeaderN.x;
	127	+ kx0 = ky + kz;
	128	+ for(ix=0; ix<in->HeaderN.x; ix++) {
	129	+ k = ix + kx0;
	130	+
	131	+ data = tmp.ImageFloatImage[k];
	132	+ if(0<data) {
	133	+ flagBottom = 1;
	134	+ izBottom = iz;
	135	+ }
	136	+ if(flagBottom) break;
	137	+ }
	138	+ if(flagBottom) break;
	139	+ }
	140	+ if(flagBottom) break;
	141	+ }
	142	+
	143	+ for(iz=in->HeaderN.z-1; 0<=iz; iz--) {
	144	+ kz = izin->HeaderN.xin->HeaderN.y;
	145	+ for(iy=0; iy<in->HeaderN.y; iy++) {
	146	+ ky = iy*in->HeaderN.x;
	147	+ kx0 = ky + kz;
	148	+ for(ix=0; ix<in->HeaderN.x; ix++) {
	149	+ k = ix + kx0;
	150	+
	151	+ data = tmp.ImageFloatImage[k];
	152	+ if(0<data) {
	153	+ flagTop = 1;
	154	+ izTop = iz;
	155	+ }
	156	+ if(flagTop) break;
	157	+ }
	158	+ if(flagTop) break;
	159	+ }
	160	+ if(flagTop) break;
	161	+ }
	162	+ thickness = izTop - izBottom + 1;
	163	+ if(thickness < linfo->bestThickness) {
	164	+ linfo->bestThickness = thickness;
	165	+ linfo->bestThicknessTop = izTop;
	166	+ linfo->bestThicknessBottom = izBottom;
	167	+ strncpy(linfo->best.EAMode, linfo->cur.EAMode, 4);
	168	+ linfo->best.Rot1 = linfo->cur.Rot1;
	169	+ linfo->best.Rot2 = linfo->cur.Rot2;
	170	+ linfo->best.Rot3 = linfo->cur.Rot3;
	171	+ }
	172	+ break;
	173	+ }
	174	+ case lmrcImageAutoTrimingModeZLayerSDCut: {
	175	+ minSD = in->HeaderN.z;
	176	+
	177	+ break;
	178	+ }
	179	+ default: {
	180	+ fprintf(stderr, "Not supported mode: %d\n", mode);
	181	+ break;
	182	+ }
	183	+ }
	184	+ mrcImageFree(&tmp, 0);
	185	+ }
	186	+ }
	187	+ }
	188	+ lmrcImageRotation3DFollowingEulerAngle(&tmp, in, linfo->best.EAMode, linfo->best.Rot1, linfo->best.Rot2, linfo->best.Rot3, linfo->InterpolationMode, 0);
	189	+ out->Header = tmp.Header;
	190	+ out->HeaderN.z = linfo->bestThickness;
	191	+ out->HeaderStartN.z = -out->HeaderN.z/2;
	192	+ mrcInit(out, NULL);
	193	+ to.x = to.y = 0;
	194	+ to.z = -linfo->bestThicknessBottom;
	195	+ DEBUGPRINT1("to.z: %f\n", to.z);
	196	+ lmrcImageCopy(out, &tmp, to);
	197	+}
	198	+
	199	+void
	200	+lmrcImageAutoTrimingOutput(FILE* fpt, lmrcImageAutoTrimingInfo* linfo, int mode)
	201	+{
	202	+ switch(mode) {
	203	+ case lmrcImageAutoTrimingModeZLayerMinCut:
	204	+ case lmrcImageAutoTrimingModeZLayerSDCut: {
	205	+ fprintf(fpt, "BestRotation: %4s %15.6g %15.6g %15.6g\n", linfo->best.EAMode, linfo->best.Rot1DEGREE, linfo->best.Rot2DEGREE, linfo->best.Rot3*DEGREE);
	206	+ fprintf(fpt, "Z-Thickness: %15.6g %15.6g %15.6g\n", linfo->bestThickness, linfo->bestThicknessBottom, linfo->bestThicknessTop);
	207	+ break;
	208	+ }
	209	+ }
	210	+}
	211	+
	212	+void
	213	+lmrcImageAutoTrimingUsage(FILE* fpt)
	214	+{
	215	+ fprintf(fpt, ">>> mode\n");
	216	+ fprintf(fpt, "%d: z-layer(minimum of z-axis by min)\n", lmrcImageAutoTrimingModeZLayerMinCut);
	217	+ fprintf(fpt, "%d: z-layer(minimum of z-axis by SD)\n", lmrcImageAutoTrimingModeZLayerSDCut);
	218	+}
	219	+

--- /dev/null

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

		@@ -0,0 +1,33 @@
	1	+<HTML>
	2	+<HEAD>
	3	+<TITLE>mrcImageAutoTriming</TITLE>
	4	+</HEAD>
	5	+<BODY>
	6	+<H1>mrcImageAutoTriming</H1>
	7	+<H2>Usage</H2>
	8	+<PRE>
	9	+Usage: mrcImageAutoTriming
	10	+Options:
	11	+ [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :Input:mrcImage
	12	+ [-o[utput] Out (NULL ).as(outFile::mrcImage ) ] :Essential :Output:mrcImage
	13	+ [-O[utput] OutParam (stdout ).as(outFile::YAML ) ] :Optional :OutputParams:YAML
	14	+ [-E[uler]A[ngle]Mode EAMode (ZONS ).as(String ) ] :Optional :EulerAngle
	15	+ [-Rot[ation]1 Rot1Min (-5 ).as(Real )
	16	+ Rot1Max (5 ).as(Real )
	17	+ Rot1Delta (1 ).as(Real ) ] :Optional :Rot1
	18	+ [-Rot[ation]2 Rot2Min (-5 ).as(Real )
	19	+ Rot2Max (5 ).as(Real )
	20	+ Rot2Delta (1 ).as(Real ) ] :Optional :Rot2
	21	+ [-Rot[ation]3 Rot3Min (-5 ).as(Real )
	22	+ Rot3Max (5 ).as(Real )
	23	+ Rot3Delta (1 ).as(Real ) ] :Optional :Rot3
	24	+ [-M[ode] InterpolationMode (0 ).as(Integer ) ] :Optional :Iterpolation Mode
	25	+ [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
	26	+ [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
	27	+----- Additional Usage -----
	28	+>>> mode
	29	+0: z-layer(minimum of z-axis by min)
	30	+1: z-layer(minimum of z-axis by SD)
	31	+</PRE>
	32	+</BODY>
	33	+</HTML>

--- /dev/null

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

		@@ -0,0 +1,22 @@
	1	+-F 4.3 1 0 52x1+0+0 +0+0 'Cantata' cantata
	2	+ -M 1 1 52x1+0+0 +1+0 ' ' subform
	3	+ -P 1 0 52x1+0+1 +0+0 ' ' mrcImageAutoTriming
	4	+ -D 1 0 9x1+0+0 'Options' _gui_options
	5	+ -H 1 6x1+0+0 'License' 'license' $BOOTSTRAP/repos/license/License license
	6	+ -E
	7	+ -R 1 0 1 5x1+35+0 'Run' 'execute operation' $EOS/bin/mrcImageAutoTriming
	8	+ -H 1 5x1+41+0 'Help' 'help page' $EOS/src/Tools/mrcImage/mrcImageAutoTriming/doc/mrcImageAutoTriming.doc help
	9	+ -Q 1 0 5.25x1+47+0 'Close'
	10	+ -I 1 0 1 1 0 1 -1x1+1+1.500000 ' ' 'In' 'Input:mrcImage' i
	11	+ -O 1 0 1 1 0 1 -1x1+1+3.000000 ' ' 'Out' 'Output:mrcImage' o
	12	+ -O 1 0 1 0 0 1 -1x1+1+4.500000 ' ' 'OutParam' 'OutputParams:YAML' O
	13	+ -s 1 0 1 0 0 -1x1+1+6.000000 0 0 0 0 0 'EAMode' 'EulerAngle' EAMode
	14	+ -I 1 0 0 1 0 1 -1x1+1+7 ' ' '-5' 'Rot1Min' Rot1
	15	+ -I 1 0 0 1 0 1 -1x1+1+9 ' ' '-5' 'Rot2Min' Rot2
	16	+ -I 1 0 0 1 0 1 -1x1+1+10 ' ' '-5' 'Rot3Min' Rot3
	17	+ -i 1 0 1 0 0 -1x1+1+12.000000 0 0 0 0 0 'InterpolationMode' 'Iterpolation Mode' M
	18	+ -I 1 0 1 0 0 1 -1x1+1+13.500000 ' ' 'configFile' 'ConfigurationFile' c
	19	+ -i 1 0 1 0 0 -1x1+1+15.000000 0 0 0 0 0 'mode' 'Mode' m
	20	+ -E
	21	+ -E
	22	+-E

--- /dev/null

+++ b/src/Tools/mrcImage/mrcImageAutoTriming/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	+all: help exec
	7	+
	8	+help:
	9	+ @echo "----- Help Message Check -----"
	10	+ @../$(OSTYPE)/$(OBJECTNAME) -h
	11	+
	12	+exec:
	13	+ @echo "----- Execution Check -----"
	14	+ ../$(OSTYPE)/$(OBJECTNAME) -i data/121p.bin -o data/121p.roi -O data/121p.param -m 0 -EAMode ZONS -Rot1 -10 10 1 -Rot2 0 0 1 -Rot3 0 0 1
	15	+ @echo "----- Calc check -----"
	16	+
	17	+init:
	18	+ mrcImageBinalization -i data/121p.in -o data/121p.bin -m 32
	19	+
	20	+clean:

--- /dev/null

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

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

--- /dev/null

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

		@@ -0,0 +1,42 @@
	1	+#include <stdio.h>
	2	+#include <stdlib.h>
	3	+#include "../inc/config.h"
	4	+
	5	+void
	6	+usage(char* thisProgram)
	7	+{
	8	+ fprintf(stderr, "Usage: %s\n", thisProgram);
	9	+ fprintf(stderr, "Options:\n");
	10	+ fprintf(stderr, " [-i[nput] In (NULL ).as(inFile::mrcImage ) ] :Essential :Input:mrcImage\n");
	11	+ fprintf(stderr, " [-o[utput] Out (NULL ).as(outFile::mrcImage ) ] :Essential :Output:mrcImage\n");
	12	+ fprintf(stderr, " [-O[utput] OutParam (stdout ).as(outFile::YAML ) ] :Optional :OutputParams:YAML\n");
	13	+ fprintf(stderr, " [-E[uler]A[ngle]Mode EAMode (ZONS ).as(String ) ] :Optional :EulerAngle\n");
	14	+ fprintf(stderr, " [-Rot[ation]1 Rot1Min (-5 ).as(Real ) \n Rot1Max (5 ).as(Real ) \n Rot1Delta (1 ).as(Real ) ] :Optional :Rot1\n");
	15	+ fprintf(stderr, " [-Rot[ation]2 Rot2Min (-5 ).as(Real ) \n Rot2Max (5 ).as(Real ) \n Rot2Delta (1 ).as(Real ) ] :Optional :Rot2\n");
	16	+ fprintf(stderr, " [-Rot[ation]3 Rot3Min (-5 ).as(Real ) \n Rot3Max (5 ).as(Real ) \n Rot3Delta (1 ).as(Real ) ] :Optional :Rot3\n");
	17	+ fprintf(stderr, " [-M[ode] InterpolationMode (0 ).as(Integer ) ] :Optional :Iterpolation Mode\n");
	18	+ fprintf(stderr, " [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile\n");
	19	+ fprintf(stderr, " [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode\n");
	20	+ additionalUsage();
	21	+}
	22	+
	23	+void
	24	+htmlBeforeUsage(char* thisProgram)
	25	+{
	26	+ fprintf(stderr, "<HTML>\n");
	27	+ fprintf(stderr, "<HEAD>\n");
	28	+ fprintf(stderr, "<TITLE>%s</TITLE>\n", thisProgram);
	29	+ fprintf(stderr, "</HEAD>\n");
	30	+ fprintf(stderr, "<BODY>\n");
	31	+ fprintf(stderr, "<H1>%s</H1>\n", thisProgram);
	32	+ fprintf(stderr, "<H2>Usage</H2>\n");
	33	+ fprintf(stderr, "<PRE>\n");
	34	+}
	35	+
	36	+void
	37	+htmlAfterUsage(char* thisProgram)
	38	+{
	39	+ fprintf(stderr, "</PRE>\n");
	40	+ fprintf(stderr, "</BODY>\n");
	41	+ fprintf(stderr, "</HTML>\n");
	42	+}

--- /dev/null

+++ b/src/Tools/mrcImage/mrcImageAutoTriming/src/util.c

		@@ -0,0 +1,4 @@
	1	+#include <stdio.h>
	2	+#include <stdlib.h>
	3	+#include "../inc/config.h"
	4	+

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

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

		@@ -54,6 +54,7 @@ additionalUsage()
54	54	fprintf(stderr, " 5: mean of Sparse \n");
55	55	fprintf(stderr, " 6: mean of 2DEdge\n");
56	56	fprintf(stderr, " 7: RMS of all pixels \n");
	57	+ fprintf(stderr, " 8: sd of all axes\n");
57	58	}
58	59
59	60	void

		@@ -265,6 +266,11 @@ outputMrcImageInfo(FILE* fpt, infoDataList* dat, mrcImage* img, mrcImageInfoInfo
265	266	fprintf(fpt, "RMS: %15.6g\n", dat->info.RMS);
266	267	break;
267	268	}
	269	+ case sdOfAllAxis:{
	270	+ fprintf(fpt, "aveOfAllAxis: %15.6g %15.6g %15.6g\n", dat->info.aveOfAllAxis.x , dat->info.aveOfAllAxis.y, dat->info.aveOfAllAxis.z);
	271	+ fprintf(fpt, "sdOfAllAxis: %15.6g %15.6g %15.6g\n", dat->info.sdOfAllAxis.x , dat->info.sdOfAllAxis.y, dat->info.sdOfAllAxis.z);
	272	+ break;
	273	+ }
268	274	default:{
269	275	fprintf(stderr, "Not supported mode :%ld", info->mode);
270	276	exit(EXIT_FAILURE);

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

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

		@@ -36,6 +36,7 @@ The -I option uses -rmax or -m options
36	36	5: mean of Sparse
37	37	6: mean of 2DEdge
38	38	7: RMS of all pixels
	39	+ 8: sd of all axes
39	40	</PRE>
40	41	</BODY>
41	42	</HTML>

--- a/src/Tools/mrcImage/mrcImageInfo/src/test/Makefile

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

		@@ -12,6 +12,18 @@ help:
12	12	exec:
13	13	@echo "----- Execution Check -----"
14	14	../$(OSTYPE)/$(OBJECTNAME) -i data/test.roi -I -rmax 100 -m 2
	15	+ ../$(OSTYPE)/$(OBJECTNAME) -i data/test.roi -I -m 0
	16	+ ../$(OSTYPE)/$(OBJECTNAME) -i data/test.roi -I -m 1
	17	+ ../$(OSTYPE)/$(OBJECTNAME) -i data/test.roi -I -m 2
	18	+ ../$(OSTYPE)/$(OBJECTNAME) -i data/test.roi -I -m 3
	19	+ ../$(OSTYPE)/$(OBJECTNAME) -i data/test.roi -I -m 4
	20	+ ../$(OSTYPE)/$(OBJECTNAME) -i data/test.roi -I -m 5
	21	+ ../$(OSTYPE)/$(OBJECTNAME) -i data/test.roi -I -m 6
	22	+ ../$(OSTYPE)/$(OBJECTNAME) -i data/test.roi -I -m 7
	23	+ @echo "----- Calc check -----"
	24	+
	25	+exec2:
	26	+ ../$(OSTYPE)/$(OBJECTNAME) -i data/121p.in -I -m 8
15	27	@echo "----- Calc check -----"
16	28
17	29	clean:

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

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

		@@ -7,5 +7,7 @@
7	7	"-Owe","-O[utput]w[hite]e[dge]","Output: whiteEdge","Optional","1","1","OutWhiteEdge","outFile::mrcImage","NULL"
8	8	"-Obe","-O[utput]b[lack]e[dge]","Output: blackEdge","Optional","1","1","OutBlackEdge","outFile::mrcImage","NULL"
9	9	"-lt","-l[ine]t[hickness]","[pixel]","Optional","2","1","LineThicknessX","Real","1","2","LineThicknessY","Real","1"
	10	+"-lm","-l[ine]m[ode]","LineMode","Optional","1","1","LineMode","Integer","0"
	11	+"-ls","-l[ine]s[hape]","LineShape","Optional","1","1","LineShape","Integer","0"
10	12	"-c","-c[onfig]","ConfigurationFile","Optional","1","1","configFile","inFile","NULL"
11	13	"-m","-m[ode]","Mode","Optional","1","1","mode","Integer","0"

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

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

		@@ -43,6 +43,12 @@ typedef struct mrcImageMeanFreePathCalcInfo {
43	43	long flagLineThicknessY;
44	44	float LineThicknessY;
45	45
	46	+ long flagLineMode;
	47	+ long LineMode;
	48	+
	49	+ long flagLineShape;
	50	+ long LineShape;
	51	+
46	52	long flagconfigFile;
47	53	char* configFile;
48	54	FILE* fptconfigFile;

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

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

		@@ -108,6 +108,28 @@ argCheck(mrcImageMeanFreePathCalcInfo* info, int argc, char* argv[])
108	108	}
109	109	SBREAK;
110	110	}
	111	+ SCASE("lm") {
	112	+ if(i+1<argc) {
	113	+ info->LineMode = stringGetNthIntegerData(argv[i+1], 1, " ,");
	114	+ i++;
	115	+ info->flagLineMode++;
	116	+ } else {
	117	+ usage(argv[0]);
	118	+ exit(EXIT_FAILURE);
	119	+ }
	120	+ SBREAK;
	121	+ }
	122	+ SCASE("ls") {
	123	+ if(i+1<argc) {
	124	+ info->LineShape = stringGetNthIntegerData(argv[i+1], 1, " ,");
	125	+ i++;
	126	+ info->flagLineShape++;
	127	+ } else {
	128	+ usage(argv[0]);
	129	+ exit(EXIT_FAILURE);
	130	+ }
	131	+ SBREAK;
	132	+ }
111	133	SCASE("c") {
112	134	if(i+1<argc) {
113	135	info->configFile = stringGetNthWord(argv[i+1], 1, " ,");

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

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

		@@ -20,6 +20,8 @@ init0(mrcImageMeanFreePathCalcInfo* info)
20	20	info->fptOutBlackEdge = NULL; info->flagOutBlackEdge = 0;
21	21	info->LineThicknessX = 1; info->flagLineThicknessX = 0;
22	22	info->LineThicknessY = 1; info->flagLineThicknessY = 0;
	23	+ info->LineMode = 0; info->flagLineMode = 0;
	24	+ info->LineShape = 0; info->flagLineShape = 0;
23	25	info->fptconfigFile = NULL; info->flagconfigFile = 0;
24	26	info->mode = 0; info->flagmode = 0;
25	27	}

		@@ -64,6 +66,12 @@ init1(mrcImageMeanFreePathCalcInfo* info)
64	66	if(info->flagLineThicknessY) {
65	67	}
66	68
	69	+ if(info->flagLineMode) {
	70	+ }
	71	+
	72	+ if(info->flagLineShape) {
	73	+ }
	74	+
67	75	if(info->flagconfigFile) {
68	76	info->fptconfigFile = fileOpen(info->configFile, "r");
69	77	}

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

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

		@@ -21,6 +21,17 @@
21	21	#include "mrcImage.h"
22	22	#include "lmrcImageMultiplying.h"
23	23
	24	+typedef enum lmrcImageMeanFreePathCalcLineMode {
	25	+ lmrcImageMeanFreePathCalcLineModeAnd = 0,
	26	+ lmrcImageMeanFreePathCalcLineModeOr = 1,
	27	+ lmrcImageMeanFreePathCalcLineModeGE = 2
	28	+} lmrcImageMeanFreePathCalcLineMode;
	29	+
	30	+typedef enum lmrcImageMeanFreePathCalcLineShape {
	31	+ lmrcImageMeanFreePathCalcLineShapeRectangle=0,
	32	+ lmrcImageMeanFreePathCalcLineShapeDisk=1
	33	+} lmrcImageMeanFreePathCalcLineShape;
	34	+
24	35	typedef struct lmrcImageMeanFreePathCalcInfo {
25	36	int N;
26	37	int* countWhite;

		@@ -45,7 +56,13 @@ typedef struct lmrcImageMeanFreePathCalcInfo {
45	56	// Control: Input
46	57	mrcImageParaTypeRealCoord Length;
47	58	mrcImageParaTypeRealCoord LineThickness;
	59	+ lmrcImageMeanFreePathCalcLineMode LineMode;
	60	+ lmrcImageMeanFreePathCalcLineShape LineShape;
48	61
	62	+ // TemporalVariables
	63	+ mrcImageParaTypeRealCoord min;
	64	+ mrcImageParaTypeRealCoord max;
	65	+ mrcImageParaTypeRealCoord cur;
49	66	} lmrcImageMeanFreePathCalcInfo;
50	67
51	68	typedef enum lmrcImageMeanFreePathCalcMode {

		@@ -57,6 +74,7 @@ typedef enum lmrcImageMeanFreePathCalcMode {
57	74	extern void lmrcImageMeanFreePathCalcPrint(FILE* fpt, lmrcImageMeanFreePathCalcInfo* linfo, lmrcImageMeanFreePathCalcMode mode);
58	75	extern void lmrcImageMeanFreePathCalc(mrcImage* in, lmrcImageMeanFreePathCalcInfo* linfo, lmrcImageMeanFreePathCalcMode mode);
59	76	extern void lmrcImageMeanFreePathCalcAlongZaxis(mrcImage* in, lmrcImageMeanFreePathCalcInfo* linfo, lmrcImageMeanFreePathCalcMode mode);
	77	+extern double lmrcImageMeanFreePathCalcBWEvaluation(mrcImage* in, lmrcImageMeanFreePathCalcInfo* linfo, lmrcImageMeanFreePathCalcMode mode);
60	78
61	79	extern void lmrcImageMeanFreePathCalcModePrint(FILE* fpt);
62	80

		@@ -80,6 +98,9 @@ main(int argc, char* argv[])
80	98	linfo.LineThickness.y = info.LineThicknessY;
81	99	linfo.LineThickness.z = 1;
82	100
	101	+ linfo.LineMode = info.LineMode;
	102	+ linfo.LineShape = info.LineShape;
	103	+
83	104	lmrcImageMeanFreePathCalc(&in, &linfo, info.mode);
84	105
85	106	lmrcImageMeanFreePathCalcPrint(info.fptOut, &linfo, info.mode);

		@@ -179,8 +200,8 @@ lmrcImageMeanFreePathCalcAlongZaxis(mrcImage* in, lmrcImageMeanFreePathCalcInfo*
179	200	int* countWhiteEdge;
180	201	int x, y, z;
181	202	int srcx, srcy;
182		- int minx, miny;
183		- int maxx, maxy;
	203	+ //int minx, miny;
	204	+ //int maxx, maxy;
184	205	int flagEdge;
185	206	double data;
186	207	double data0;

		@@ -211,25 +232,22 @@ lmrcImageMeanFreePathCalcAlongZaxis(mrcImage* in, lmrcImageMeanFreePathCalcInfo*
211	232	linfo->N = in->HeaderN.z;
212	233
213	234	for(y=0; y<in->HeaderN.y; y++) {
214		- miny = floor(y - linfo->LineThickness.y/2.0 + 0.5);
215		- maxy = floor(y + linfo->LineThickness.y/2.0 + 0.5);
	235	+ linfo->min.y = floor(y - linfo->LineThickness.y/2.0 + 0.5);
	236	+ linfo->max.y = floor(y + linfo->LineThickness.y/2.0 + 0.5);
	237	+ linfo->cur.y = y;
216	238	for(x=0; x<in->HeaderN.x; x++) {
217		- minx = floor(x - linfo->LineThickness.x/2.0 + 0.5);
218		- maxx = floor(x + linfo->LineThickness.x/2.0 + 0.5);
	239	+ linfo->min.x = floor(x - linfo->LineThickness.x/2.0 + 0.5);
	240	+ linfo->max.x = floor(x + linfo->LineThickness.x/2.0 + 0.5);
	241	+ linfo->cur.x = x;
219	242
220	243	flagEdge = 1;
221	244	lengthWhite = 0;
222	245	lengthBlack = 0;
223	246
224	247	// Start
225		- data = 1;
226		- for(srcy=miny; srcy<maxy; srcy++) {
227		- for(srcx=minx; srcx<maxx; srcx++) {
228		- mrcPixelDataGet(in, srcx, srcy, 0, &data0, mrcPixelRePart, mrcPixelHowNearest);
229		- data *= data0;
230		- }
231		- }
232		- //mrcPixelDataGet(in, x, y, 0, &data, mrcPixelRePart, mrcPixelHowNearest);
	248	+ linfo->cur.z = 0;
	249	+ data = lmrcImageMeanFreePathCalcBWEvaluation(in, linfo, mode);
	250	+
233	251	if(0<data) {
234	252	countWhiteEdge[0]++;
235	253	lengthWhite++;

		@@ -239,16 +257,10 @@ lmrcImageMeanFreePathCalcAlongZaxis(mrcImage* in, lmrcImageMeanFreePathCalcInfo*
239	257	}
240	258	prevData = data;
241	259
242		- // Interval
	260	+ // Intermediate
243	261	for(z=1; z<in->HeaderN.z-1; z++) {
244		- data = 1;
245		- for(srcy=miny; srcy<maxy; srcy++) {
246		- for(srcx=minx; srcx<maxx; srcx++) {
247		- mrcPixelDataGet(in, srcx, srcy, z, &data0, mrcPixelRePart, mrcPixelHowNearest);
248		- data *= data0;
249		- }
250		- }
251		- //mrcPixelDataGet(in, x, y, z, &data, mrcPixelRePart, mrcPixelHowNearest);
	262	+ linfo->cur.z = z;
	263	+ data = lmrcImageMeanFreePathCalcBWEvaluation(in, linfo, mode);
252	264
253	265	if(0<prevData) {
254	266	if(0<data) { // White continue

		@@ -306,14 +318,8 @@ lmrcImageMeanFreePathCalcAlongZaxis(mrcImage* in, lmrcImageMeanFreePathCalcInfo*
306	318
307	319	// End
308	320	z = in->HeaderN.z-1;
309		- data = 1;
310		- for(srcy=miny; srcy<maxy; srcy++) {
311		- for(srcx=minx; srcx<maxx; srcx++) {
312		- mrcPixelDataGet(in, srcx, srcy, z, &data0, mrcPixelRePart, mrcPixelHowNearest);
313		- data *= data0;
314		- }
315		- }
316		- //mrcPixelDataGet(in, x, y, z, &data, mrcPixelRePart, mrcPixelHowNearest);
	321	+ linfo->cur.z = z;
	322	+ data = lmrcImageMeanFreePathCalcBWEvaluation(in, linfo, mode);
317	323
318	324	if(0<prevData) {
319	325	if(0<data) { // White continue

		@@ -412,3 +418,41 @@ lmrcImageMeanFreePathCalcAlongZaxis(mrcImage* in, lmrcImageMeanFreePathCalcInfo*
412	418	DEBUGPRINT1("mode: %d in Calc: RealLength End\n", mode);
413	419	}
414	420	}
	421	+
	422	+
	423	+double
	424	+lmrcImageMeanFreePathCalcBWEvaluation(mrcImage* in, lmrcImageMeanFreePathCalcInfo* linfo, lmrcImageMeanFreePathCalcMode mode)
	425	+{
	426	+ double data, data0;
	427	+ mrcImageParaTypeReal srcx, srcy;
	428	+
	429	+ switch(linfo->LineShape) {
	430	+ case lmrcImageMeanFreePathCalcLineShapeRectangle: {
	431	+ switch(linfo->LineMode) {
	432	+ case lmrcImageMeanFreePathCalcLineModeAnd: {
	433	+ data = 1;
	434	+ for(srcy=linfo->min.y; srcy<linfo->max.y; srcy++) {
	435	+ for(srcx=linfo->min.x; srcx<linfo->max.x; srcx++) {
	436	+ mrcPixelDataGet(in, srcx, srcy, linfo->cur.z, &data0, mrcPixelRePart, mrcPixelHowNearest);
	437	+ data *= data0;
	438	+ }
	439	+ }
	440	+ break;
	441	+ }
	442	+ default: {
	443	+ fprintf(stderr, "Not supported Line Mode: %d\n", linfo->LineMode);
	444	+ exit(EXIT_FAILURE);
	445	+ break;
	446	+ }
	447	+ }
	448	+ break;
	449	+ }
	450	+ default: {
	451	+ fprintf(stderr, "Not supported Line Shape: %d\n", linfo->LineShape);
	452	+ exit(EXIT_FAILURE);
	453	+ break;
	454	+ }
	455	+ }
	456	+ return data;
	457	+}
	458	+

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

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

		@@ -16,6 +16,8 @@ Options:
16	16	[-O[utput]b[lack]e[dge]OutBlackEdge (NULL ).as(outFile::mrcImage ) ] :Optional :Output: blackEdge
17	17	[-l[ine]t[hickness] LineThicknessX (1 ).as(Real )
18	18	LineThicknessY (1 ).as(Real ) ] :Optional :[pixel]
	19	+ [-l[ine]m[ode] LineMode (0 ).as(Integer ) ] :Optional :LineMode
	20	+ [-l[ine]s[hape] LineShape (0 ).as(Integer ) ] :Optional :LineShape
19	21	[-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile
20	22	[-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode
21	23	----- Additional Usage -----

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

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

		@@ -14,8 +14,10 @@
14	14	-O 1 0 1 0 0 1 -1x1+1+7.500000 ' ' 'OutWhiteEdge' 'Output: whiteEdge' Owe
15	15	-O 1 0 1 0 0 1 -1x1+1+9.000000 ' ' 'OutBlackEdge' 'Output: blackEdge' Obe
16	16	-I 1 0 0 1 0 1 -1x1+1+10 ' ' '1' 'LineThicknessX' [pixel]
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
	17	+ -i 1 0 1 0 0 -1x1+1+12.000000 0 0 0 0 0 'LineMode' 'LineMode' lm
	18	+ -i 1 0 1 0 0 -1x1+1+13.500000 0 0 0 0 0 'LineShape' 'LineShape' ls
	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
19	21	-E
20	22	-E
21	23	-E

--- a/src/Tools/mrcImage/mrcImageMeanFreePathCalc/src/test/Makefile

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

		@@ -3,7 +3,7 @@ include ../../../Config/Define.inc
3	3	include ../../../../Config/Define.inc
4	4	include ../../../../../Config/Define.inc
5	5
6		-all: help exec
	6	+all: help exec exec2
7	7
8	8	help:
9	9	@echo "----- Help Message Check -----"

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

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

		@@ -14,6 +14,8 @@ usage(char* thisProgram)
14	14	fprintf(stderr, " [-O[utput]w[hite]e[dge]OutWhiteEdge (NULL ).as(outFile::mrcImage ) ] :Optional :Output: whiteEdge\n");
15	15	fprintf(stderr, " [-O[utput]b[lack]e[dge]OutBlackEdge (NULL ).as(outFile::mrcImage ) ] :Optional :Output: blackEdge\n");
16	16	fprintf(stderr, " [-l[ine]t[hickness] LineThicknessX (1 ).as(Real ) \n LineThicknessY (1 ).as(Real ) ] :Optional :[pixel]\n");
	17	+ fprintf(stderr, " [-l[ine]m[ode] LineMode (0 ).as(Integer ) ] :Optional :LineMode\n");
	18	+ fprintf(stderr, " [-l[ine]s[hape] LineShape (0 ).as(Integer ) ] :Optional :LineShape\n");
17	19	fprintf(stderr, " [-c[onfig] configFile (NULL ).as(inFile ) ] :Optional :ConfigurationFile\n");
18	20	fprintf(stderr, " [-m[ode] mode (0 ).as(Integer ) ] :Optional :Mode\n");
19	21	additionalUsage();

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