「File Formats and Other Documentation」の版間の差分

2022年12月30日 (金) 05:41時点における版 (ソースを閲覧) Tacyas (トーク | 投稿記録) (→‎Navigation File Section Data) ←古い編集		2022年12月30日 (金) 05:43時点における版 (ソースを閲覧) Tacyas (トーク | 投稿記録) (→‎Navigation File Section Data) 新しい編集→
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	|-		|-
	|ShiftY ||Float ||shiftY ||Y component of shift in microns		|ShiftY ||Float ||shiftY ||Y component of shift in microns
−	|+	+	|-
−	T|SParam - a section containing tilt series parameters.  See TiltSeriesParam.h in the source code for a description of each item.	+	|colspan="4"|T|SParam - a section containing tilt series parameters.  See TiltSeriesParam.h in the source code for a description of each item.
−	|+	+	|-
−	MontParam - a section containg montage parameters.  See MontageParam.h in the source code for a description of each item.	+	|colspan="4"|MontParam - a section containg montage parameters.  See MontageParam.h in the source code for a description of each item.
−	|+	+	|-
−	FileOptions - a section containing properties for opening a file.  See FileOptions.h in the source code in case this has descriptions.	+	|colspan="4"|FileOptions - a section containing properties for opening a file.  See FileOptions.h in the source code in case this has descriptions.
	|}		|}

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2022年12月30日 (金) 05:43時点における版

Image Metadata Files

SerialEMは、画像のメタデータをIMOD "autodoc" フォーマットでテキストファイルに保存する。 この形式は、キーワードと値のペアをセクションと呼ばれるブロックに整理したものである。 このセクションには、さまざまな種類のデータが含まれているが、 SerialEMのファイルでは、基本的に1種類のセクションしか使用しない。 セクションは、大括弧付きのキーと値のペアで始まります。

 [セクションタイプ = 名前]

ここで、セクションの「名前」または値は通常，ユニークに設定するが、 IMOD autodocリーダーではそうである必要はない。

セクションヘッダ以下の行は、次のような形式で表現される。

キー = 値

そのセクションに関連するデータを提供する。 さらに、キーと値のペアは、セクション・ヘッダの前のファイルの最初に記載することもでき、これらはグローバル値として参照される。

すべての値はオートドキュメントファイルにテキスト文字列として保存されるが、特定の種類の情報を期待するソフトウェアは、これらの文字列を1つまたは複数の浮動小数点または整数値に変換することがよくある。

IMOD ライブラリ libcfshr の autodoc モジュールには、1 つ、2 つ、3 つ、または多数の浮動小数点または整数値をファイルの指定セクションに格納または取得するための関数が含まれている。 autodoc形式がSerialEMに選ばれた理由は、このライブラリがすぐに利用できること、このような関数を利用すると便利なこと、IMODのautodoc読込み機能との互換性があること、などである。

SerialEMが生成する画像関連autodocファイルには2種類ある。

1) ".mdoc "ファイルは、MRCファイルに関するデータを提供し、画像ファイルと同じ名前ですが、拡張子が".mdoc "になっています。 セクションタイプは "ZValue "で、各セクションの名前はファイル内の画像のZ値で、0から順に番号が付けられている。

2) 一連の単一画像TIFFファイルをMRCファイルと同様に扱うための情報を提供する".idoc "ファイル。 ここでのセクションタイプは "Image "で、各セクションの名称はTIFFファイルの名称である。

グローバルデータは、MRCファイルのヘッダーにある情報の一部を複製したものである。 また、MRCファイルのタイトルは "T "型のセクションヘッダに格納されます。

SerialEMが使用するIMODライブラリは、HDFファイルのメタデータにアクセスするために同じ内部オートドック構造を使用する。 したがって、これらのメタデータ情報をすべてautodoc形式のテキストファイルに抽出することは、次のようなコマンドで簡単にできる。

extracttilts -attr filename.hdf filename.hdf.mdoc

のようなコマンドで、これらのメタデータ情報をオートドック形式のテキストファイルに抽出することができる。

Global Data

Global Data

DataMode	MRC file mode
ImageSize	X and Y size of images
Montage	1 if the file is a montage
ImageSeries	1 for an .idoc file describing a series of single-image files
ImageFile	In a .mdoc file, contains the name of the image file
PixelSpacing	Pixel spacing in Angstroms that would be in MRC header (or in 1/Angstroms for diffraction images)

Section Data

Section Data

TiltAngle	Tilt angle in degrees
PieceCoordinates	Pixel coordinates in X and Y and section Z value for montage piece
StagePosition	X and Y stage position in microns
StageZ	Z stage position in microns
Magnification	"Film" magnification value
CameraLength	Camera length in mm for image in diffraction mode
MagIndex	Magnification index
Intensity	Raw intensity value between 0 and 1
SuperMontCoords	X and Y pixel coordinates of frame in a supermontage
PixelSpacing	Pixel spacing in Angstroms for individual image (or in 1/Angstroms for diffraction image)
ExposureDose	Dose on specimen during camera exposure in electrons/sq. A
DoseRate	Dose rate to the camera, in electrons per physical pixel per second
SpotSize	Microscope spot size
Defocus	Relative defocus readout from microscope (microns)
TargetDefocus	Current target for autofocus (microns)
ImageShift	X and Y image shift in basic units (close to microns)
RotationAngle	Rotation of image from having tilt axis along X axis (CCW +)
ExposureTime	Image exposure time
Binning	Image binning on the camera
UsingCDS	1 if image was taken with CDS mode on
CameraIndex	Index of the CameraProperties section for the camera used
DividedBy2	1 if image was divided by 2
RotationAndFlip	RotationAndFlip property of K2 or K3 camera
LowDoseConSet	Control set index plus 1 if image taken in Low Dose, or negative of index if not in Low Dose (index 0-6 for View, Focus, Trial, Record, Preview, Search, Mont-map; 7 for tracking, 8 for montage)
MinMaxMean	Minimum, maximum, and mean value for this image
PriorRecordDose	For an image in a tilt series taken in Low Dose mode, the cumulative dose in the Record area prior to this image, including Record and Preview images and View i	mages taken in tasks
XedgeDxy	Edge displacement in X and Y for montage piece to the right of this piece
YedgeDxy	Edge displacement in X and Y for piece above this piece
XedgeDxyVS	Edge displacement for piece to right, computed with very sloppy option
YedgeDxyVS	Edge displacement for piece above, computed with very sloppy option
StageOffsets	minus the nominal stage position of the piece.
AlignedPieceCoords	Piece coordinates adjusted by the solved shifts for each piece when pieces are aligned in overview with 'Very sloppy' option off.
AlignedPieceCoordsVS	Piece coordinates adjusted by the solved shifts for each piece when pieces are aligned in overview with 'Very sloppy' option on.
SubFramePath	Directory or file in which subframes of exposure were stored
NumSubFrames	Number of subframes stored
FrameDosesAndNumbers	Dose per frame in electrons per square Angstrom followed by number of frames at that dose; variable-sized frame sums will have multiple pairs of such values
DateTime	Time and date of image acquisition; the format of the date is dd-Mon-yy regardless of locale.
NavigatorLabel	Label of Navigator item, added if Acquire at Items is being run and a tilt series is not
FilterSlitAndLoss	Energy filter slit width and energy loss if slit is in, 0 0 otherwise
ChannelName	Detector name for a STEM image
MultishotHoleAndPosition	Hole identifier and position within hole when taking multiple record images; peripheral positions are numbered from 1 and the center is numbered 0. For a regular pattern, hole identifiers are a pair of numbers relative to the center of the pattern; for a custom pattern, they are simply numbers starting at 1.
CameraPixelSize	For diffraction image, the size of the image pixel on the camera in microns, namely the physical chip pixel size times the binning.
Voltage	High voltage in kV for diffraction image.

Direct Electron Specific Section Data

DE12-CameraPosition ||Whether camera was retracted or inserted DE12-ProtectionCoverMode ||Whether protection cover is kept open or open and closed for this shot DE12-ProtectionCoverOpenDelay(ms) ||Delay after opening prtection cover DE12-TemperatureDetector(C) ||Detector temperature DE12-FaradayPlatePeakReading(pA/cm2) ||Current reading from Faraday plate during exposure

Direct Electron Specific Section Data

DE12-ServerSoftwareVersion	Server software version
DE12-PreexposureTime(s)	Pre-exposure time
DE12-TotalNumberOfFrames	Total number of frames in acquisition
DE12-FramesPerSecond	Frame rate in frames per second
DE12-SensorModuleSerialNumber	Serial number of sensor
DE12-SensorReadoutDelay(ms)	Delay before starting to read out sensor during exposure
DE12-IgnoredFramesInSummedImage	Number of frames ignored in a summed image

Additional Data in MontSection

Additional Data in MontSection
FullMontSize	Full size of montage in X and Y if all pieces are present
BufISXY	Image shift associated with overview buffer
ProbeMode	1 for microporbe, 0 for nanoprobe
MoveStage	1 if for a stage montage
ConSetUsed	Control set used for the montage (0 = View, 3 = Record, 5 = Search, 6 = MontMap
MontBacklash	The nominal backlash for this montage, or 0 0 if using an anchor at the center
ValidBacklash	The nominal backlash for this montage, or 0 0 if using an anchor at the center or doing a zigzag pattern
DriftSettling	Drift settling in control set used
CameraModes	Shutter mode and read mode
FocusOffset	Focus offset for low dose View or Search, assigned to map item DefocusOffset if a map is made
NetViewShifts	Image shift offsets for low dose View or Search
ViewBeamShifts	Beam shift offsets for low dose View or Search
ViewBeamTilts	Incremental beam tilts for low dose View or Search
ViewDefocus	Focus offset for low dose View or Search, assigned to image buffer when reading in
Alpha	Alpha value on JEOL
FilterState	0/1 if slit is out/in, and slit width

Navigator File for serialEM

SerialEM Navigator　Fileに関する説明になります。

下記の翻訳に　なります。 [https://bio3d.colorado.edu/SerialEM/stableHlp/html/about_formats.htm#navigator ]

SerialEM 3.6では、Navigatorの出力が1項目につき1行のタブ区切り形式からオートドック形式に変更され、代わりにXMLとして出力するオプションが追加されている。 XMLやautodocファイルは、以前のバージョンのタブ区切りファイルと同様に、読み挙げることができる。

グローバル・データは2行あります。

 AdocVersion = x.xx
 LastSavedAs = xy.nav

という2行のグローバルデータがあり、2行目は最後に保存したときのファイルの完全な絶対パスとファイル名である。

次に、各項目は'Item'タイプのセクションにあり、そのラベル文字列を値として持つ。

次の表は、セクションに出現するすべてのキー、期待される値の種類、それが必須かどうか、必須でない場合はどのようなデフォルト値が設定されるかを示したものである。

Navigation File Section Data

BklshXY ||Two Floats ||0,0 ||mBacklashX/Y ||Backlash when a montage was taken or associated with item SamePosId ||Integer ||0 ||mAtSamePosID ||Items with this matching were taken at same raw stage position RawStageXY ||T|wo Floats ||-10000,-10000 ||mRawStageX/Y ||Raw stage position before adjustments Acquire ||Integer ||0 ||mAcquire ||Flag for acquiring PieceOn ||Integer ||-1 ||mPieceDrawnOn ||Index of montage piece item was drawn on (piece_#_in_X * #_of_pieces_in_Y + piece_#_in_Y), or index |- of nearest piece if item is on a missing piece, in which case XYinPc will not be written to file. XYinPc ||Two Floats ||-1,-1 ||mX/YinPiece ||X,Y coordinates in the montage piece, in right-handed pixels of stored montage MapFile ||String ||Req if Map ||mMapFile ||Full or relative path of map file (see Read & Open) MapID ||Integer ||Req if Map ||mMapID ||Unique ID (all items get one, not just maps) FocusAxisPos Float ||-1.e8 ||mFocusAxisPos ||Stored position of Focus area on inter-area axis LDAxisAngle ||Two integers ||0,0 ||mRotateFocusAxis, mFocusAxisAngle ||First value: 1 to rotate inter-area axis from tilt axis, 0 not to; second |- value: angle of rotation FocusOffsets ||Two Floats ||0,0 ||mFocusX/Yoffset ||Offset of focus subarea in X and Y in unbinned pixels (Y inverted) HoleArray ||Two integers ||0,0 ||mNumX/Yholes ||# of positions in X and Y for multiple Record SkipHoles ||List of integers ||none ||mSkipHolePos ||Pairs of X,Y indexes for positions to skip from that array specified in HoleArray. |- Positions are numbered from 0 at lower-left in stage coordinates TSstartEndAngles Two Floats -1.e8,-1.e8 mTSstartAngle, mTSendAngle Starting and ending angles of range for tilt series item TSbidirAngle Float -1.e8 mTSbidirAngle Bidirectional starting angle for tilt series item TargetDefocus Float -1.e8 mTargetDefocus Target defocus for Acquire or tilt series item FileToOpen String none mFileToOpen Name of file to open for Acquire or tilt series item TSParamIndex Integer -1 mTSParamIndex Index of into parameter array for tilt series MontParamIndex Integer -1 mMontParamIndex Index into array of parameters for montages to open FilePropIndex Integer -1 mFilePropIndex Index into array of file options for file to open MapMontage Integer Req if Map mMapMontage Flag that map is a montage MapSection Integer Req if Map mMapSection Section number in file MapBinning Integer Req if Map mMapBinning Binning at which map was taken, or of initial overview map image for montage MapMagInd Integer Req if Map mMapMagInd Magnification index of map, or of non-map image a point or polygon was drawn on MapCamera Integer Req if Map mMapCamera Camera index MapScaleMat Four Floats Req if Map mMapScaleMat Stage to pixel scale matrix for drawing, based on pixels of initial map image. For |- montage, needs to be adjusted by ratio of currently loaded map width/height to initial map width/height MapWidthHeight Two Integers Req if Map mMapWidth/Height Size of initial map image at which scale matrix was defined MapMinMaxScale Two Floats 0,0 mMapMin/MaxScale Min and max scale values of image when map was defined MapFramesXY Two Integers 0,0 mMapFramesX/Y Number of montage frames when acquired MontBinning Integer 0 mMontBinning Actual binning of montage used to make the map MapExposure Float 0. mMapExposure Exposure time for original map images MapSettling Float 0. mMapSettling Drift settling ShutterMode Integer -1 mShutterMode Shutter mode K2ReadMode Integer 0 mK2ReadMode Read mode for K2/K3 camera MapSpotSize Integer 0 mMapSpotSize Spot size at which map was taken MapIntensity Double 0 mMapIntensity Intensity at which map was taken MapSlitIn Integer 0 mMapSlitIn Filter slit state when map was taken MapSlitWidth Float -1. mMapSlitWidth Filter slit width when map was taken RotOnLoad Integer 0 mRotOnLoad Flag to rotate when load RealignedID Integer 0 mRealignedID ID of lower mag map with nearby realign error RealignErrXY Two Floats 0,0 mRealignErrX/Y Final stage error of that realign operation LocalErrXY Two Floats 0,0 mLocalRealiErrX/Y Error in second round of realign operation RealignReg Integer 0 mRealignReg Original registration of that realign ImageType Integer 0 mImageType Map file type 0-3 for MRC, IMOD, TIFF, IDOC MontUseStage Integer -1 mMontUseStage 1 if montage was taken with stage, 0 if not, -1 if unknown DefocusOffset Float 0. mDefocusOffset Defocus offset for map based on View images K2ReadMode Integer 0 mK2ReadMode Read mode for K2/K3 camera NetViewShiftXY Two Floats 0,0 mNetViewShiftX/Y Net IS offset for a View image map MapAlpha Integer -999 mMapAlpha JEOL alpha value ViewBeamShiftXY Two Floats 0,0 mViewBeamShiftX/Y Incremental beam shift to apply for a View map ViewBeamTiltXY Two Floats 0,0 mViewBeamTiltX/Y Incremental beam tilt to apply for a View map M|apProbeMode Integer -1 mMapProbeMode Probe mode (0 for nano, 1 for micro) MapLDConSet Integer -1 mMapLowDoseConSet Set # (0-4) used for map taken in low dose MapTiltAngle Float -10000. mMapTiltAngle Tilt angle at which map was taken PtsX NumPts Floats Req mPtX X stage cordinates of points PtsY NumPts Floats Req mPtY Y stage cordinates of points UserValueN String none mUserValueMap Arbitrary value set by script; N is # (currently1-8)

BaseMarkerShift - a section containing a stored shift from Shift to Marker (names are from BaseMarkerShift structure).

Key	Type of value	Default value, or Required	CMapDrawItem member(s)	Description
Color	Integer	Req	mColor	Color index (0-5)
StageXYZ	Three Floats	Req (unless external)	mStageX/Y/Z	Stage position adjusted for current mag
NumPts	Integer	Req	mNumPoints	Number of points
Corner	Integer	0	mCorner	Flag for corner point
Draw	Integer	1	mDraw	Flag to draw
RegPt	Integer	0	mRegPoint	Registration point number
Regis	Integer	Req	mRegistration	Registration at which item exists
Type	Integer	Req	mType	Type: 0-2 for point, polygon, map
Note	String	blank	mNote	Note string
GroupID	Integer	0	mGroupID	ID of group thatitem belongs to
PolyID	Integer	0	mPolygonID	ID of polygon used to define supermontage
FitToPolygonID	Integer	0	mFitToPolygonID ID of polygon that this montage map was fit to
Imported	Integer	0	mImported	Indicator of an imported map or point drawn on one
RegisteredToID	Integer	0	mRegisteredToID	For an imported map, ID of map that it was registered to for transforming
SuperMontXY	Two Integers	-1,-1	SuperMontX/Y	Camera coordinate of a montage in supermontage
OrigReg	Integer	Regis	mOriginalReg	Original registration (default is Registration)
DrawnID	Integer	0	mDrawnOnMapID	ID of map point/polygon was drawn on
FromMag	Integer	fromMagInd Mag index of map item was marked on
ToMag	Integer	toMagInd	Mag index of image with marker point
ShiftX	Float	shiftX	X component of shift in microns
ShiftY	Float	shiftY	Y component of shift in microns
T|SParam - a section containing tilt series parameters. See TiltSeriesParam.h in the source code for a description of each item.
MontParam - a section containg montage parameters. See MontageParam.h in the source code for a description of each item.
FileOptions - a section containing properties for opening a file. See FileOptions.h in the source code in case this has descriptions.