「機能別コマンド一覧」の版間の差分
(ページの作成：「ここでは、機能別に少しずつ整理をしています。まだまだ整理が終わっていません。すこしずつ進めていますので、ご容赦下...」) |
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ここでは、機能別に少しずつ整理をしています。まだまだ整理が終わっていません。すこしずつ進めていますので、ご容赦下さい。 | ここでは、機能別に少しずつ整理をしています。まだまだ整理が終わっていません。すこしずつ進めていますので、ご容赦下さい。 | ||
| − | + | == 統合環境 == | |
*[[Display2]]: ２Ｄ画像もしくは３Ｄ画像のセクションの表示、処理など | *[[Display2]]: ２Ｄ画像もしくは３Ｄ画像のセクションの表示、処理など | ||
*[[Display3]]: ３Ｄ画像の表示 | *[[Display3]]: ３Ｄ画像の表示 | ||
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*[[obj3Don2DImageView]] | *[[obj3Don2DImageView]] | ||
| + | === molvieシリーズ === | ||
| + | *[[molvie]] | ||
| + | *[[molvieDock]] | ||
| + | *[[molvieFlight]] | ||
| + | *[[molvieMrcViewer]] | ||
| + | *[[molvieProjection]] | ||
| + | *[[molvieViewer]] | ||
| − | === | + | == 開発環境 == |
| + | *[[maketool]] | ||
| + | *[[makeobj]] | ||
| + | *[[protoObjectMethodCreate]] | ||
| + | *[[protoHTMLCreate]] | ||
| + | *[[protoShellCreate]] | ||
| + | *[[protoTestMakefileCreate]] | ||
| + | |||
| + | == コマンドリスト == | ||
[[CheckCommonLineData]] | [[CheckCommonLineData]] | ||
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[[coordRotation]] | [[coordRotation]] | ||
| − | + | == ＣＴＦ関係のコマンド群 == | |
| − | + | === CTF決定のためのプログラム群 === | |
*[[ctfDisplay]]: CTFの決定のためのプログラム(GUI) | *[[ctfDisplay]]: CTFの決定のためのプログラム(GUI) | ||
*[[ctfDeterminationFromMultiImage]] | *[[ctfDeterminationFromMultiImage]] | ||
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*[[ctfDetermine]] | *[[ctfDetermine]] | ||
| − | + | === CTFの関数に関するプログラム === | |
*[[ctfEnvelopFunction]] | *[[ctfEnvelopFunction]] | ||
*[[ctfFunction]] | *[[ctfFunction]] | ||
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*[[ctfFunctionServer]] | *[[ctfFunctionServer]] | ||
| − | + | === CTF補正に関するプログラム群 === | |
*[[ctfInfoSet]] | *[[ctfInfoSet]] | ||
*[[ctfMultiFunction]] | *[[ctfMultiFunction]] | ||
*[[ctfWeightMapCreation]] | *[[ctfWeightMapCreation]] | ||
| − | + | === DCDフォーマットのファイルに関する取り扱い=== | |
*[[dcdAtomChangeDistanceFromAtom]] | *[[dcdAtomChangeDistanceFromAtom]] | ||
*[[dcdAtomDistanceDistribution]] | *[[dcdAtomDistanceDistribution]] | ||
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[[defocusDeterminationFromThonRing]] | [[defocusDeterminationFromThonRing]] | ||
| − | + | ||
[[electronWaveLength]] | [[electronWaveLength]] | ||
[[emData2mrc]] | [[emData2mrc]] | ||
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[[geogeoge]] | [[geogeoge]] | ||
[[gmolvie]] | [[gmolvie]] | ||
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[[homology2PG]] | [[homology2PG]] | ||
[[hostCondition]] | [[hostCondition]] | ||
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[[imodst2mrc]] | [[imodst2mrc]] | ||
[[ip2mrc]] | [[ip2mrc]] | ||
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| − | + | ||
[[khorosFilterGenerate]] | [[khorosFilterGenerate]] | ||
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| − | |||
[[largeIPInfo]] | [[largeIPInfo]] | ||
[[ll2ltlg]] | [[ll2ltlg]] | ||
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[[molecularEnvelopeResampling]] | [[molecularEnvelopeResampling]] | ||
[[molecularWeightCalc]] | [[molecularWeightCalc]] | ||
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[[mrc2dsn6]] | [[mrc2dsn6]] | ||
[[mrc2fld]] | [[mrc2fld]] | ||
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*[[mrcRadon2Dto3D]] | *[[mrcRadon2Dto3D]] | ||
| − | + | === mrcImageフォーマットに対するコマンド群 === | |
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[[mrcFTMeridianEquatorRedece]] | [[mrcFTMeridianEquatorRedece]] | ||
[[mrcImage1DProjectionfrom2D]] | [[mrcImage1DProjectionfrom2D]] | ||
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[[mrcImageSimilarImageSearch]] | [[mrcImageSimilarImageSearch]] | ||
[[mrcImageSimilarityEstimate]] | [[mrcImageSimilarityEstimate]] | ||
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[[mrcImageSmoothing]] | [[mrcImageSmoothing]] | ||
[[mrcImageSolventFlattening]] | [[mrcImageSolventFlattening]] | ||
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[[mrcMirrorImageCreate]] | [[mrcMirrorImageCreate]] | ||
| + | === mrcFFT（フーリエ空間）を処理するためのコマンド群 === | ||
| + | *[[mrcFFTBandPassFilter]] | ||
| + | *[[mrcFFTCTFCompensation]] | ||
| + | *[[mrcFFTDigitize]] | ||
| + | *[[mrcFFTExpression]] | ||
| + | *[[mrcFFTFibreDiagram]] | ||
| + | *[[mrcFFTFiltering]] | ||
| + | *[[mrcFFTIQEstimation]] | ||
| + | *[[mrcFFTInfo]] | ||
| + | *[[mrcFFTLayerLineCheck]] | ||
| + | *[[mrcFFTMedianFilter]] | ||
| + | *[[mrcFFTProjection]] | ||
| + | *[[mrcFFTResampling]] | ||
| + | *[[mrcFFTShellInfo]] | ||
| + | *[[mrcFFTSizeChange]] | ||
| + | *[[mrcFFTSpectrum]] | ||
| + | *[[mrcFFTXFiltering]] | ||
| + | *[[mrcFFTplainreduce]] | ||
| + | === mrcRef関連 === | ||
[[mrcRefCorEstimate]] | [[mrcRefCorEstimate]] | ||
[[mrcRefCorModify]] | [[mrcRefCorModify]] | ||
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[[mrcRefz1ImageCorrelation]] | [[mrcRefz1ImageCorrelation]] | ||
| − | ==== ラドン空間（シノグラム）を用いた解析 === | + | ==== ラドン空間（シノグラム）を用いた解析 ==== |
*[[mrcImageSinogramCreate]] | *[[mrcImageSinogramCreate]] | ||
| + | *[[mrcImageSinogramCorrelation]] | ||
*[[mrcImageSinogramFFT]] | *[[mrcImageSinogramFFT]] | ||
*[[mrcRadon2Dto3D]] | *[[mrcRadon2Dto3D]] | ||
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*[[mrcSinogramFETsmoothParameterMatching]] | *[[mrcSinogramFETsmoothParameterMatching]] | ||
| + | ==== 特徴量を用いた３次元再構成 === | ||
| + | *[[mrcFETnormalizeBySD]] | ||
[[openGLTest]] | [[openGLTest]] | ||
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[[tiff2mrc]] | [[tiff2mrc]] | ||
[[vector2pdb]] | [[vector2pdb]] | ||
| + | [[dos2unix]] | ||
| − | + | ||
| − | + | == その他 == | |
| + | === 乱数の発生 === | ||
[[randomUniformGet]]:一様乱数 | [[randomUniformGet]]:一様乱数 | ||
[[randomNormalGet]]：正規分布に従う乱数 | [[randomNormalGet]]：正規分布に従う乱数 | ||
| + | |||
| + | === 電子顕微鏡制御 === | ||
| + | [[hf2000Init]] | ||
| + | [[hf2000LenzCurrent]] | ||
| + | [[hf2000SpecimenPosition]] | ||
2012年9月23日 (日) 02:43時点における版
ここでは、機能別に少しずつ整理をしています。まだまだ整理が終わっていません。すこしずつ進めていますので、ご容赦下さい。
目次
統合環境
- Display2: ２Ｄ画像もしくは３Ｄ画像のセクションの表示、処理など
- Display3: ３Ｄ画像の表示
- ctfDisplay: For CTF Correlation
- Visualmake: Easy and automatics GUI generator for Makefile
- Eos: Eos on Tcl/Tk, CUI
- smolet: トモグラフィーのためのGUIソフトウェア（傾斜シリーズの表示）
molvieシリーズ
開発環境
コマンドリスト
CheckCommonLineData CheckOfOrientation CheckOrientationByDegree CommonLineCalculation CommonLineRankCalc_k Descartes2Polar
EvaluateCorrelationMapwithCommonLine FETOrientationSearchByAnnealing FETOrientationSearchByFeatureAlignment FETmapOrientationSearchBySimultaneousFitting FETsmallMapSetCreate_forSimultaneousMinimization LCalculationForOrientationSearch Polar2Descartes ProjectionDirectionMapCreate StereoDisplay TestForLcalculationOfOrientationSearchBySimultaneousMinimization
WeightCalculationOfCommonLineSearch WeightCalculationOfCommonLineSearchByAllSinogram WeigthCaluculationOfCommonLineCalculation angleMatchTest_k anglediffcalc anglediffchk array2mrc bin2mrc calcCommonLine clusterLog2ToLog clusterLogASCII2Binary clusterShow commonLinesSearchByVoting coordRotation
ＣＴＦ関係のコマンド群
CTF決定のためのプログラム群
- ctfDisplay: CTFの決定のためのプログラム(GUI)
- ctfDeterminationFromMultiImage
- ctfDeterminationFromPhaseComparison
- ctfDeterminationFromThonRing
- ctfDetermine
CTFの関数に関するプログラム
CTF補正に関するプログラム群
DCDフォーマットのファイルに関する取り扱い
dcdFilePrint dcdInfo dcdSelectAtoms dcdSerectAtom dcdTest dcdTimeSeriesBehavior
defocusDeterminationFromThonRing
electronWaveLength emData2mrc energyTransferModelCheck energyTransferModelResultCheck fft2d geogeoge gmolvie homology2PG hostCondition imageView imagesClustering imagesView imodst2mrc ip2mrc
khorosFilterGenerate
largeIPInfo
ll2ltlg
llDataAverage
llDataAxisSearch
llDataCTFCompensate
llDataCompare
llDataContributionCalcDifferentN
llDataDump
llDataEquatorAdd
llDataExtract
llDataFit
llDataFitServer
llDataInfo
llDataLowPassFiltering
llDataMultiCTFCompensation
llDataNEstimation
llDataNormalization
llDataPrint
llDataRescaling
llDataResolutionCheck
llDataRotation
llDataSelectionEstimation
llDataSeparate
llDataWeightSet
llDatarMaxLimit
llExtract
llExtractCtfinfFileCreate
llExtractCtrlFileCreate
llExtractWithLayerSeparation
llExtractWithLayerSeparationCtrlFileCreate
llExtractWithLayerSeparationCtrlFileCreateMyosin
llExtractWithLayerSeparationFilamentInfo
llExtractWithLayerSeparationServer
llExtractWithLayerSeparationSingle
ltlg2mrc
ltlg2ps
ltlgDataInfo
mallocCheck
matrix3DEulerAngleTransform
matrix3DFromEulerAngle
matrix3DInverse
matrix3DToEulerAngle
moi2mrc
molecularEnvelopeResampling
molecularWeightCalc
mrc2dsn6 mrc2fld mrc2gif mrc2hdf mrc2lattice mrc2map mrc2pov mrc2tiff mrc2viff mrc3DExtractZ
3次元再構成
mrcImageフォーマットに対するコマンド群
mrcFTMeridianEquatorRedece mrcImage1DProjectionfrom2D mrcImage1dAverageByCorrelation mrcImage1dCutAverage mrcImage1dShiftAverageByAnnealing mrcImage1dShiftByCorrelation mrcImage2DBackProjection mrcImage2DProjection mrcImage2pdb mrcImage3DHighResoEmphasis mrcImage3DPad mrcImage3DPad2 mrcImage3DSymmetryFind mrcImage3DWindowing mrcImageAbnormalValueRemove mrcImageActinSingleParticleAnalysis mrcImageAdaptiveBinalization mrcImageAdd mrcImageAddValue mrcImageAreaCalc mrcImageAssignedToTFofPDB mrcImageAutoCorrelationWithWindowing mrcImageAutoFilamentExtract mrcImageAutoFilamentExtractResultAnalysis mrcImageAutoRotationCorrelation mrcImageAutoRotationCorrelation3D mrcImageAutoRotationCorrelationResultPrint mrcImageAverage mrcImageBandPassFilter mrcImageBinalization mrcImageBlockMerge mrcImageBoundaryInfo mrcImageBtest mrcImageCCDNoiseRemove mrcImageCTFCompensation mrcImageCTFCompensationForTiltImage mrcImageCTFDetermination mrcImageCTFObservation mrcImageCTFSN mrcImageCVE mrcImageCenterDensityChange mrcImageCenterGet mrcImageCenterOfMassCalculate mrcImageCircumferentialProjection mrcImageClusterAnalysis mrcImageColoring mrcImageCommonLineSearch mrcImageConnection mrcImageConnectivityNumberCalc mrcImageContourSurfaceCreate mrcImageCoordinateChange mrcImageCoreImageCalc mrcImageCorrelation mrcImageCorrelationInFourierSpace mrcImageCorrelationServer mrcImageCorrelationWithCTFCompensation mrcImageCrystalCreate mrcImageCutAndSetInArray mrcImageCylinderSection mrcImageDeadPixelCorrection mrcImageDensityChangeEstimation mrcImageDensityInfo mrcImageDensityNormalization mrcImageDensityNormalizationByImage mrcImageDisplayDensityAsTempFactor mrcImageDistanceConversion mrcImageDivideInfoForTomography mrcImageDivideIntoTwoImages mrcImageEdgeImageGet mrcImageEnhancementWithFuzzySets mrcImageEstimateTiltImage mrcImageExpression mrcImageFFT mrcImageFFTLayerLineExtraction mrcImageFOMCalc mrcImageFTest mrcImageFeatureExtraction mrcImageFilamentSearch mrcImageFilterCreate mrcImageFilteringbyFile mrcImageFilteringbyFileForVariance mrcImageFourierPowerSpectrum mrcImageFourierShellCorrelation mrcImageFractalFourierShellCorrelation mrcImageFractalFrourierShellCorrelation mrcImageGaussDisc mrcImageGaussSphere mrcImageHeaderChange mrcImageHelicalAveraging mrcImageHelicalConvolution mrcImageHelicalMappingFrom2DImage mrcImageHelicalMasking mrcImageHelicalMaskingBy2DImage mrcImageHelicalProjection mrcImageHighPassFilter mrcImageHighlighting mrcImageInfo mrcImageInverseRadonTransform mrcImageLabeling mrcImageLowPassFilter mrcImageMagnificationChange mrcImageMake2DArrayImage mrcImageMakeCylinder mrcImageMakeDump mrcImageMakeFromTextFile mrcImageMakeSphere mrcImageMappingtoPdb mrcImageMasking mrcImageMaskingByImage mrcImageMergebyside mrcImageMirroring mrcImageModeChange mrcImageModelCreate mrcImageModelSubfilamentsCreate mrcImageMontageCreate mrcImageMove mrcImageMultiCTFCompensation mrcImageMultiCTFDetermination mrcImageMultiplying mrcImageMultiplyingbyFile mrcImageNLMeansFilter mrcImageNeuralNetParticleExtraction mrcImageNeuralNetParticleLearning mrcImageNfoldAxisSearch mrcImageNoiseAdd mrcImageNoiseCreate mrcImageNoiseReductionByRelaxation mrcImageNormalDistributionTest mrcImageNormalizedSubtraction mrcImageNormalizing mrcImageNullImageCreate mrcImageOddBoxel mrcImageOneLineSimilarityCalc mrcImageOrientationSearch mrcImageOrientationSearchByHigherSelection mrcImageOrientationSearchByHybridization mrcImageOrientationSearchBySimultaneousMinimization mrcImagePCA mrcImagePad mrcImageParticleCandidateExtract mrcImagePeakSearch mrcImagePhaseCTFCompensationFromCTFINFO mrcImagePixelDataGet mrcImagePolyROI mrcImagePosterization mrcImagePrint mrcImagePrint3D mrcImageProjection mrcImagePut3D mrcImageROI mrcImageROI3D mrcImageROIs mrcImageROItoPCAoutputImage mrcImageRadialDistribution mrcImageRadonTransform mrcImageRealValueAdd mrcImageRectangleGet mrcImageRectangleGetByCorrelation mrcImageRefConv2D mrcImageRefCreate mrcImageRefFFTConv2D mrcImageRefScaleChangeWithPad mrcImageResolutionEstimateForFilaments mrcImageReverse mrcImageRotation mrcImageRotation3D mrcImageSN mrcImageSamplingUnitChange mrcImageScalarAdd mrcImageSectionGet mrcImageSetFunction mrcImageShapePCA mrcImageShift mrcImageShiftFollowingGC mrcImageShrink mrcImageSiemensStar mrcImageSimilarImageSearch mrcImageSimilarityEstimate mrcImageSmoothing mrcImageSolventFlattening mrcImageSphere mrcImageSplit mrcImageSquare mrcImageStack mrcImageStandardDeviation mrcImageSubtraction mrcImageSuperResolution mrcImageSymmetryAverage mrcImageSymmetryCentreFind mrcImageSymmetryFind mrcImageTTest mrcImageTfunction mrcImageTiltAxisSearch mrcImageTiltAxisSearchHelp mrcImageToNAMDConstantForces mrcImageTrans mrcImageTransformDescartesIntoPolar mrcImageTransformSign mrcImageTranspose mrcImageTwoImageTest mrcImageUnbentROI mrcImageUnexpectedMassFromPDB mrcImageUntwist mrcImageVarianceAnalysis mrcImageVarianceMap mrcImageVolumeCalc mrcImageWindowing mrcImageZPad mrcImagepdbFileReduce mrcImagesSinogramCorrelation mrcImagestoRef mrcInfo mrcInfoSet mrcManipulate_kaya mrcMask mrcMeanYlinePos mrcMirrorImageCreate
mrcFFT（フーリエ空間）を処理するためのコマンド群
- mrcFFTBandPassFilter
- mrcFFTCTFCompensation
- mrcFFTDigitize
- mrcFFTExpression
- mrcFFTFibreDiagram
- mrcFFTFiltering
- mrcFFTIQEstimation
- mrcFFTInfo
- mrcFFTLayerLineCheck
- mrcFFTMedianFilter
- mrcFFTProjection
- mrcFFTResampling
- mrcFFTShellInfo
- mrcFFTSizeChange
- mrcFFTSpectrum
- mrcFFTXFiltering
- mrcFFTplainreduce
mrcRef関連
mrcRefCorEstimate mrcRefCorModify mrcRefCoreGet mrcRefCorrelation mrcRefCorrelationConv mrcRefEstimate mrcRefFFTConvert mrcRefHeaderCreate mrcRefHighPassFilter mrcRefImageCorrelation mrcRefImageOmegaCorrelation mrcRefImagepwzCorEstimate mrcRefImagepwzCorModify mrcRefImagepwzCorPeakFind mrcRefImagepwzCorSmoothing mrcRefImagepwzCorrelation mrcRefImagepwzCorrelationByFFT mrcRefImagexaFit mrcRefLowPassFilter mrcRefNoiseAdd mrcRefNormalizing mrcRefPhaseImageCreate mrcRefSmoothing mrcRefz1ImageCorrelation
ラドン空間（シノグラム）を用いた解析
特徴量を用いたシノグラム解析
- mrcSinogramFET
- mrcSinogramFETcalcSDforNormalize
- mrcSinogramFETcalcWeight
- mrcSinogramFETcorrelationMap
- mrcSinogramFETnormalizedMap
- mrcSinogramFETreferredCorrelation
- mrcSinogramFETsmoothParameterMatching
= 特徴量を用いた３次元再構成
PDB関係のコマンド群
pdb2SketchMacro pdb2bender pdb2mrc pdb2mrc2d pdb2mrc2dWithCTF pdb2ucd pdbAtomSection pdbCAOnly pdbChargeFit pdbCoordAdd pdbCrystalCreate pdbDisplay pdbFileMerge pdbHelix pdbHomologySearch pdbInfo pdbListRMSDCalc pdbMatrixCreate pdbMolecularInterfaceFind pdbMove pdbNAMDRestraintCreate pdbNearAtomListShow pdbOneProteinGet pdbPCA pdbProteinIDSet pdbRhoFit pdbRhoFitCoiledCoil pdbRhoFitTm pdbRotation pdbSecondaryStructurePrint pdbShapeFit pdbSurface pdbTempFactorSet pdbTrans pdbTwoProteinFit pdbView pdbWaterAdd
pgFormat方のファイルに対するプログラム
pgDataBaseSelectServer pgJournalSelect pgJournalSelectCORBAClient pgJournalSelectCORBAServer pgMemoSelectCORBAServer pgSelect
ポストスクリプトファイルの取り扱いに関するプログラム
tiltInfoDetermine
vectorImageNearestNeighborMethod
画像フォーマット等のフィルター
tgaInfo tiff2mrc vector2pdb dos2unix
その他
乱数の発生
randomUniformGet:一様乱数 randomNormalGet：正規分布に従う乱数
電子顕微鏡制御
hf2000Init hf2000LenzCurrent hf2000SpecimenPosition
