| addConst | addConst(float) add a constant |
| add | add(EMData in) adds 'in' to 'this' |
| addIncoherent | addIncoherent(EMData in) adds 'in' to 'this' |
| addMaskShell | addMaskShell(int shells) Will add additional shells/rings to an existing 1/0 mask image |
| addRadNoise | addRadNoise(int n, float x0, float dx, list y, int interp) |
| aliPeak | float aliPeak() |
| alt | float alt() |
| ap2ri | ap2ri() converts amp/pha to real/imaginary (complex only) |
| applyMask | applyMask(int r,int type) applies a circular mask to the data. type=0 is a step cutoff to the mean value type=4 is a step cutoff to zero type=1 fills in with flatband random noise |
| applyRadFn | applyRadFn(int n,float x0,float dx, list y,int interp=1) |
| autoMask | autoMask(float thresh,float filter=.1) Attempts to automatically mask out the particle, excluding other particles in the box, etc. thresh runs from ~ -2 to 2, negative numbers for dark. protien and positive numbers for light protein (stain) filter is expressed as a fraction of the Fourier radius |
| az | float az() |
| BilateralFilter | void BilateralFilter(float sigma1, float sigma2, int iter=1, int localWidth=1); |
| Busy | int Busy() Returns 1 if data is checked out |
| calcAzDist | calcAzDist(int n,float a0,float da, list data,float rmin,float rmax) |
| calcCCF | EMData calcCCF(EMData with, EMData filter=None) cross correlation between 2 images |
| calcCCFX | EMData calcCCFX(EMData with, int y0=0, int y1=-1, int nosum=0) calculates sum of x-axis CCFs |
| calcHist | calcHist(list hist, int n, float hmin=0, float hmax=0, int add=0) |
| calcMCF | EMData calcMCF(EMData with, EMData filter=None) mutual correlation between 2 images |
| calcRadDist | calcRadDist(int n,float x0,float dx, list y) |
| calcRCF | calcRCF(EMData with, list sum,int NS) |
| cirMean | float cirMean() |
| clearCTF | clearCTF() Clear CTF parameters. |
| clip | EMData clip(int x0, int y0, int xsize, int ysize) EMData clip(int x0, int y0, int z0, int xsize, int ysize, int zsize) inclusive clip. Pads if larger than data |
| cmCenter | cmCenter(int intonly=1) center at center of mass, ignores old dx,dy |
| col | EMData col(int n) extract vector from matrix |
| commonLines | commonLines(EMData d1,EMData d2,int mode=0,int steps=180,int horiz=0) finds common lines between 2 complex images. mode 0 is a summed dot-product mode 1 is weighted phase residualsteps is 1/2 the resolution of the )map |
| commonLinesR | commonLinesR(EMData data1,EMData data2,int steps=180,int horiz=0) |
| convolute | EMData convolute(EMData with) |
| copy | EMData copy(int withfft=0, int withparent=1) returns an exact copy of itself |
| copyHead | EMData copyHead() copies descriptive information without any real data |
| CTFCmp | int CTFCmp(EMData with) used to detect if 2 images have the same CTF parameters |
| ctfMap | ctfMap(int type, XYData sf=None) |
| cutSlice | void cutSlice(EMData *map,float z,Euler *ort=NULL,int interp=1,float x=0,float y=0); this will cut a slice out of a real 3D map |
| dCenter | float dCenter() This will find the density value at the peak of the image histogram, sort of like the mode of the density |
| display | int display() Display the current image. Returns 0 if success; Returns -1 on error. |
| dist | float dist(EMData second, int n=0) |
| doDWT | doDWT(int basis, int level) in place DWT, basis/level defined elsewhere |
| doFFT | EMData doFFT() Apply fourier transform on the data. |
| doIFT | EMData doIFT() Apply inverse fourier transform on the data. |
| doIWT | doIWT(int basis, int level) inverse wavelet x-form |
| doneSlice | doneSlice(int log=0) once all of the slices have been added with insertSlice(), this routine does a normalization and returns a real 3d volume |
| doneSliceWF | doneSliceWF(int log=0) It should only be used in conjunction with insertSliceWF |
| doRadon | EMData doRadon() Radon transform of image, comes out square |
| dot | float dot(EMData data,int evenonly=0) dot product of 2 images (same size !) |
| DWTFilt | DWTFilt(int basis, int level, float thresh) in place nonlinear threshold wavelet filter. thresh is with respect to the 'ideal' threshold |
| Dx | float Dx() |
| Dy | float Dy() |
| Dz | float Dz() |
| edgeMean | float edgeMean() |
| edgeNormalize | edgeNormalize(int cir=0) normalizes so mean -> value at edge of image, if cir=1, uses 2 pixel circular border |
| EMData | EMData() construct an empty EMData instance |
| fastTranslate | fastTranslate(int inplace=1) fast integer-only translation |
| fftSlice | EMData fftSlice(float alt,float az,float phi,int mode=5) takes a slice from a 3d complex image for generating projections. |
| fileCount | tuple fileCount(string imagefile) Returns a tuple with the number of images in a file and the image type. |
| filter | filter(float highpass,float lowpass,int type) fourier filters an image, real or imaginary |
| fscmp | float fscmp(EMData with) returns a quality factor based on FSC between images larger numbers indicate a better match |
| getATime | long getATime() Returns access time for the image file. |
| getCTF | list getCTF() Returns the CTF parameters in a list. |
| getEuler | Euler getEuler() |
| getFlags | int getFlags() |
| getImagicHed | imagicH getImagicHed() |
| getMRCHed | mrcH getMRCHed() |
| getSpiHed | SPIDERH getSpiHed() Returns the header of a spider image. |
| gimmeFFT | gimmeFFT() gives the caller ownership of the recently obtained fourier transform, so it won't be freed automatically |
| hasCTFF | int hasCTFF() |
| hasCTF | int hasCTF() |
| hFlip | hFlip() flips image horizontally |
| iftSlice | EMData iftSlice() This does an IFT of a volume reconstructed from slices. Includes a real-space correction for the linear interpolation in Fourier space |
| insertClip | insertClip(EMData block, int x0, int y0) used for 2D only |
| insertSlice3DReal | insertSlice3DReal(EMData slice,float weight) |
| insertSlice | insertSlice(EMData slice, float alt,float az,float phi,int mode=5,float weight=1.0) this inserts a complex slice into an image that has been setup4IS() |
| insertSliceWF | insertSliceWF(EMData slice, float alt,float az,float phi,int mode,list SNR,float padratio) this inserts a complex slice into an image that has been setup4IS() |
| interpFT3d | interpFT3d(float x,float y,float z, list ret,int mode) |
| invert | invert() multiply by -1 |
| isComplex | int isComplex() Returns 1 if the data is in complex number mode; Returns 0 othewise. |
| isComplexX | int isComplexX() |
| isFlipped | int isFlipped() |
| Kurtosis | float Kurtosis() |
| lcmp | tuple lcmp(EMData noisy,int keepzero=0,int invert=0) linear comparison of 2 data sets (smaller better) |
| leastSquareNormalizeTo | tuple leastSquareNormalizeTo(EMData to, float low_thresh=FLT_MIN, float high_thresh=FLT_MAX) |
| littleBigDot | EMData littleBigDot(EMData with, int sigma=0) CCF in real-space, designed for cases where with is small |
| makeAverageCTFC | makeAverageCTFC(list in,float filtr) averages the images in the list with CTF correction filtr is in angstroms, |
| makeAverageCTFCWauto | makeAverageCTFCWauto(list in, string outfile=None) This does CTF correction with a Wiener filter where the filter is estimated directly from the data |
| makeAverageCTFCW | makeAverageCTFCW(list in, XYData sf, list SNR=None) averages the images in the list with CTF correction |
| makeAverage | makeAverage(list in,EMData sigma=None) averages the images in the list, result in 'this' optionally makes a sigma image as well |
| makeAverageIter | makeAverageIter(list in) |
| makeAverageWT | makeAverageWT(list in,EMData curves,XYData sf) averages the images in the list with SNR weightingbut no CTF correction |
| makeMedian | makeMedian(list in) Median of the images in the list, result in 'this' |
| makeRFP | EMData makeRFP(int premasked=0,int unwrap=1) Makes a 'rotational footprint', which is an 'unwound' autocorrelation function. if unwrap is 0 the rfp is not cached. generally the image should be edgenormalized and masked before using this |
| maskNormalize | maskNormalize(EMData mask,int sigmatoo=1) Uses a 1/0 mask defining a region to use for the zero-normalization, if sigma is 0, std-dev not modified |
| Max | float Max() |
| MaxLoc | tuple MaxLoc() Returns maxium value locations in a tuple with (max_x_loc, max_y_loc, max_z_loc) |
| Mean2 | float Mean2() |
| Mean | float Mean() |
| meanShrink | meanShrink(int i) reduces the size of the image by a factor of i, using the average value of the pixels in a block |
| medianShrink | medianShrink(int i) reduces the size of the image by a factor of i using a local median filter |
| Min | float Min() |
| MinLoc | tuple MinLoc() Returns minimum value locations in a tuple with (min_x_loc, min_y_loc, min_z_loc) |
| multConst | multConst(float) multiply by constant |
| mult | mult(EMData in,int recip=0) multiplies 'in' by 'this', if recip, then divide |
| mxMult | EMData mxMult(EMData second) |
| Name | string Name() |
| NImg | int NImg() Returns the number images in this image file. |
| normalizeMax | normalizeMax() mean -> 0, std dev -> 1 |
| normalizeTo | tuple normalizeTo(EMData noisy,int keepzero=0,int invert=0) This will multiply 'this' by a constant so. it is scaled to the signal in 'to'keepzero will exclude zero values, and keep them at zero in the result |
| normSlice | tuple normSlice(EMData slice,float alt,float az,float phi) try to make sure the slice is normalized properly |
| one | one() Sets all the data values to be 1. |
| Parent | EMData Parent() |
| Path | string Path() |
| PathN | int PathN() |
| pcmp | float pcmp(EMData data, XYData snr=None) amplitude weighted mean phase error, 'data' should be less noisy than 'this' pcmp |
| phi | float phi() |
| Pixel | float Pixel() returns the pixel value. |
| project3d | EMData project3d(float alt,float az, float phi, int mode, float thr=1.0) makes a 3d projection of a volume, mode=-1 does real space projection, 1-5 use fftslice for fourier projection |
| radialAverage | radialAverage() makes image circularly symmetric |
| radialSubtract | radialSubtract() subtracts circularly symmetric part of image |
| readImage | int readImage(filename, n = 0, nodata = 0, imagetype = EMData.ANY) Reads a single image from a file. If image type is not specified, the image type will be determined from file type. return 0 if succeeds; return -1 if fails. |
| readImagesExt | list readImagesExt(string imagefile, string ext, int n0, int n1, int nodata=0) Read a set of filtered images with an automatically generated filename. return a list of EMData instances ranging from image n0 to image n1. If nodata is 0, only read image header information. If nodata is 1, read both image data and image header. |
| readImages | list readImages(string imagefile, int n0, int n1, int nodata=0) Read a set of images. return a list of EMData instances ranging from image n0 to image n1. If nodata is 0, only read image header information. If nodata is 1, read both image data and image header. |
| readLST | int readLST(string filespec, int n, int nodata=0, string file_ext = None) writes a pointer to an image file to a LST file |
| readMRCArea | int readMRCArea(string fsp, int x0, int y0, int xsize, int ysize) read a rectangular area from a mrc file. works ONLY for real 2d images. Also the area MUST reside within the image. int readMRCArea(string fsp, int x0, int y0, int z0, int xsize, int ysize, int zsize) read a cube from a 3D mrc file. works ONLY for real 3d images. Also the area MUST reside within the image. |
| realFilter | realFilter(int type, float val1=0,float val2=0, float val3=0) a variety of real-space filters |
| refineAlign | refineAlign(EMData with,int mode=1) |
| ri2ap | ri2ap() converts real/imaginary to amp/pha (complex only) |
| rot180 | rot180() fast rotation by 180 degrees |
| rotAlignCH | float rotAlignCH(EMData with, int irad=8, int orad=0) rotational alignment via circular harmonic |
| rotAlign | float rotAlign(EMData with) rotational alignment using angular correlation |
| rotAlignPrecen | float rotAlignPrecen(EMData with) rotational alignment assuming centers are correct |
| rotateAndTranslateFast | rotateAndTranslateFast(float scale=1.0) rotate and translate using current settings behavior changes if parent is/not set |
| rotateAndTranslate | rotateAndTranslate(float scale=1.0,float dxc=0,float dyc=0,float dzc=0,int r=0) |
| rotateX | rotateX(int dx) This performs a translation of each line along x with wraparound this is equivalent to a rotation when performed on 'unwrapped' maps |
| row | EMData row(int n) extract vector from matrix |
| RTAlign | EMData RTAlign(EMData with, int usedot=0, int maxshift=0) |
| RTAlignRadon | EMData RTAlignRadon(EMData with,int maxshift=-1,EMData radonwith=None,EMData radonthis=None) |
| RTFAlign | EMData RTFAlign(EMData with=None,EMData flip=None,int usedot=1,int maxshift=-1) rotational, translational and flip alignment |
| RTFAlignRadon | EMData RTFAlignRadon(EMData with,int maxshift=-1,EMData thisf=None,EMData radonwith=None ,EMData radonthis=None,EMData radonthisf=None) rotational, translational and flip alignment with Radon transforms |
| RTFAlignSlowest | EMData RTFAlignSlowest(EMData with,EMData flip=None,int maxshift=-1) rotational, translational and flip alignment using exhaustive search. VERY SLOW |
| RTFAlignSlow | EMData RTFAlignSlow(EMData with,EMData flip=None,int maxshift=-1) rotational, translational and flip alignment using real-space methods, SLOW |
| serialIn | serialIn(int file_descriptor) |
| serialOut | serialOut(int file_descriptor) used ONLY for FILESERVER operation, not safe otherwise |
| setCol | setCol(EMData d,int n) insert vector into matrix |
| setComplex | setComplex(int i) |
| setComplexX | setComplexX(int i) |
| setCTFF | setCTF(list new_ctf) Sets CTF parameters with new values from a list. setCTFF(string s) Sets CTF parameters with new values from a string. |
| setCTF | setCTF(list new_ctf) Sets CTF parameters with new values from a list. setCTFF(string s) Sets CTF parameters with new values from a string. |
| setFlipped | setFlipped(int f) |
| setImagicHed | setImagicHed(imagicH hed) |
| setName | setName(string name) |
| setParent | setParent(EMData data) |
| setPath | setPath(string path) |
| setPathN | setPathN(int n) |
| setPixel | setPixel(float pix) set the pixel value. |
| setRAlign | setRAlign(Euler angle) |
| setRI | setRI(int i) |
| setRow | setRow(EMData d,int n) insert vector into matrix |
| setSize | int setSize(int x, int y=1, int z=1) Sets x, y, z dimension sizes |
| setTAlign | setTAlign(float x, float y, float z=0) |
| setup4IS | setup4IS(int size) |
| setup4Slice | setup4Slice(int redo=1) |
| setValueAt | setValueAt(int x, int y, int z, float v) it does not set the changed flag |
| sigDiff | float sigDiff() Calculates sigma above and below the mean and returns the difference between them |
| Sigma2 | float Sigma2() |
| Sigma | float Sigma() |
| Skewness | float Skewness() |
| subNoise | subNoise() Subtract average noise from intensity. Negative results allowed. |
| subtract | subtract(EMData data) subtracts 'data' from the current set |
| SumSq | float SumSq() |
| swapin | int swapin() Swaps the data in from the swap file. |
| swapout | int swapout() Swaps the data out to a temporary file. |
| transAlign3d | float transAlign3d(EMData with,int useparent=0,int intonly=0) translational alignment using CCF |
| transAlign | tuple transAlign(EMData with, int useparent, int intonly, int maxshift) translational alignment using CCF |
| uncutSlice | void uncutSlice(EMData *map,float z,Euler *ort=NULL,float x=0,float y=0); Opposite of cutSlice(). It will take a slice and insert the data into a real 3D map. It does not interpolate, it uses the nearest neighbor. |
| unwrap | EMData unwrap(int r1=-1,int r2=-1,int xs=-1,int dx=0,int dy=0,int do360=0) maps polar coordinates to cylindrical coordinates |
| update | update() Tells EMData to update itself in the future. |
| valueAt | float valueAt(int x, int y) Return data at a 2D position. float valueAt(int x, int y, int z) Return data at a 3D position. |
| valueAtInterp | float valueAtInterp(float x, float y) Returns a data value at a 2D position. |
| valueAtSafe | float valueAtSafe(int x, int y) Return a data value at a 2D position. It has no locking. float valueAtSafe(int x, int y, int z) Return a data value at a 3D position. It has no locking. |
| vertACF | EMData vertACF(int maxdy) vertical autocorrelation calculated in real-space over a range of translations |
| vFlip | vFlip() flips image vertically |
| Wait | Wait() Waits until the data becomes available. |
| waitReady | int waitReady(int readonly) Waits for data to become available; Returns 0 if OK; Returns non-zero if any error. |
| writeDebug | writeDebug(int n) write to a special graphical debug viewer |
| writeImage | int writeImage(filename, n=0, imagetype=EMData.ANY, nolock=0, swap = 0, mode=MODE_float) Writes a single image to a file. If image type is not specified, teh image type will be determined from given file type. return 0 if succeeds; return -1 if fails. |
| writeLST | int writeLST(string filespec, int n, string reffile, int refn, string comment) |
| xNormalize | xNormalize(int mode=0) normalizes each row in the image individually |
| xSize | int xSize() Returns x dimension size |
| ySize | int ySize() Returns y dimension size |
| zero | zero() Sets all the data values to be 0. |
| zSize | int zSize() Returns z dimension size |