「機能別コマンド一覧」の版間の差分
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*[[protoTestMakefileCreate]] | *[[protoTestMakefileCreate]] | ||
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== ＣＴＦ関係のコマンド群 == | == ＣＴＦ関係のコマンド群 == | ||
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[[pdbWaterAdd]] | [[pdbWaterAdd]] | ||
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*[[mrc2tiff]] | *[[mrc2tiff]] | ||
*[[mrc2viff]] | *[[mrc2viff]] | ||
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| + | === 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 === | ||
| + | [[psFileMerge]] | ||
| + | [[psFilePageMerge]] | ||
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=== その他 === | === その他 === | ||
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*[[vector2pdb]] | *[[vector2pdb]] | ||
*[[dos2unix]] | *[[dos2unix]] | ||
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| + | == コマンドリスト == | ||
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| + | [[CheckCommonLineData]] | ||
| + | [[CheckOfOrientation]] | ||
| + | [[CheckOrientationByDegree]] | ||
| + | [[CommonLineCalculation]] | ||
| + | [[CommonLineRankCalc_k]] | ||
| + | [[Descartes2Polar]] | ||
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| + | [[EvaluateCorrelationMapwithCommonLine]] | ||
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| + | [[FETOrientationSearchByAnnealing]] | ||
| + | [[FETOrientationSearchByFeatureAlignment]] | ||
| + | [[FETmapOrientationSearchBySimultaneousFitting]] | ||
| + | [[FETsmallMapSetCreate_forSimultaneousMinimization]] | ||
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| + | [[LCalculationForOrientationSearch]] | ||
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| + | [[Polar2Descartes]] | ||
| + | [[ProjectionDirectionMapCreate]] | ||
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| + | [[TestForLcalculationOfOrientationSearchBySimultaneousMinimization]] | ||
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| + | [[WeightCalculationOfCommonLineSearch]] | ||
| + | [[WeightCalculationOfCommonLineSearchByAllSinogram]] | ||
| + | [[WeigthCaluculationOfCommonLineCalculation]] | ||
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| + | [[angleMatchTest_k]] | ||
| + | [[anglediffcalc]] | ||
| + | [[anglediffchk]] | ||
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| + | [[calcCommonLine]] | ||
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| + | [[coordRotation]] | ||
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== その他 == | == その他 == | ||
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*[[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 | ||
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| + | === 点の取り扱い === | ||
| + | [[pointAffineTransform]] | ||
=== 電子顕微鏡制御 === | === 電子顕微鏡制御 === | ||
2012年9月23日 (日) 04:41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
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 energyTransferModelCheck energyTransferModelResultCheck fft2d geogeoge gmolvie homology2PG hostCondition imageView imagesClustering imagesView
khorosFilterGenerate largeIPInfo
らせん対称性を用いた3次元再構成
空間の変換
llExtractのサポートプログラム群
llExtractCtfinfFileCreate llExtractCtrlFileCreate llExtractWithLayerSeparation llExtractWithLayerSeparationCtrlFileCreate llExtractWithLayerSeparationCtrlFileCreateMyosin llExtractWithLayerSeparationFilamentInfo llExtractWithLayerSeparationServer llExtractWithLayerSeparationSingle
G(R, THETA, Z)空間の取り扱い
llDataAverage llDataAxisSearch llDataCTFCompensate llDataCompare llDataContributionCalcDifferentN llDataDump llDataEquatorAdd llDataExtract llDataFit llDataFitServer llDataInfo llDataLowPassFiltering llDataMultiCTFCompensation llDataNEstimation llDataNormalization llDataPrint llDataRescaling llDataResolutionCheck llDataRotation llDataSelectionEstimation llDataSeparate llDataWeightSet llDatarMaxLimit
g(r, theta, Z) の取り扱い
3次元再構成
ラドン空間（シノグラム）を用いた解析
- mrcImageSinogramCreate
- mrcImageSinogramCorrelation
- mrcImageSinogramFFT
- mrcRadon2Dto3D
- commonLinesSearchByVoting
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
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 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
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
クラスター解析に関するツール
mrcImageClusterAnalysis clusterLog2ToLog clusterLogASCII2Binary clusterShow
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
tiltInfoDetermine
vectorImageNearestNeighborMethod
画像フォーマット等のフィルター
他のファイルフォーマットからMRC形式へ変換
MRC形式から他のフォーマットへの変換
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
その他
コマンドリスト
CheckCommonLineData CheckOfOrientation CheckOrientationByDegree CommonLineCalculation CommonLineRankCalc_k Descartes2Polar
EvaluateCorrelationMapwithCommonLine
FETOrientationSearchByAnnealing FETOrientationSearchByFeatureAlignment FETmapOrientationSearchBySimultaneousFitting FETsmallMapSetCreate_forSimultaneousMinimization
LCalculationForOrientationSearch
Polar2Descartes ProjectionDirectionMapCreate
TestForLcalculationOfOrientationSearchBySimultaneousMinimization
WeightCalculationOfCommonLineSearch WeightCalculationOfCommonLineSearchByAllSinogram WeigthCaluculationOfCommonLineCalculation
angleMatchTest_k anglediffcalc anglediffchk
その他
分子の取り扱い
molecularEnvelopeResampling molecularWeightCalc
matrix3Dの取り扱い（3次元空間変換用4x4行列)
matrix3DEulerAngleTransform matrix3DFromEulerAngle matrix3DInverse matrix3DToEulerAngle
乱数の発生
- randomUniformGet:一様乱数
- randomNormalGet：正規分布に従う乱数
