Differences

This shows you the differences between two versions of the page.

--- eman2:eman2metadata [2025/07/04 17:33] – created steveludtke
+++ eman2:eman2metadata [2025/07/04 19:35] (current) – steveludtke
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-===== Parameters/Metadata stored in EMData Objects =====
+This page has [[eman2:metadata]]
-The EMData object, and its representation on disk in the BDB local database, XML files, and when serialized in  Python using 'pickle', supports the concept of arbitrary header parameters also known as metadata. This metadata are key/value pairs. The keys are always simple ascii text, and the values may be virtually anything represented as an EMObject, including simple ints, floats and strings, as well as more complicated objects such as Transform classes. If an EMData object is stored in some fashion other than the 3 mechanisms above, some loss of metadata is almost guaranteed. The file i/o objects will try to preserve some of the basic metadata, but most of the  cryoEM formats simply don't support arbitrary header-data. The EMAN2 convention is to use BDB for most internal purposes, and to use HDF5 for data transfer/exchange.
-This page will serve as a repository for the officially supported parameter key/value pairs. While you are free to set any metadata keys/values you like in an EMData object, the names listed here may be interpreted in specific ways by specific modules within EMAN, so it would be unwise to abuse them. Also, if you make up your own name for some purpose, it wouldn't hurt to register it here in the 'unofficial' section, to avoid it being used by someone else for a different purpose.
-==== Native HDF5 Image Compression ====
-EMAN2 supports lossless and lossy (through bit reduction) compression via native HDF5 mechanisms. To write an image with compression, the storage mode must be //EM_COMPRESSED//. //render_bits//, //render_min// and //render_max// should also be set (otherwise lossless compression in floating point mode will take place, which won't save much space. These parameters are not stored under these names in the file). //render_compress_level// may optionally be set (no quality impact, just speed/size tradeoff). Upon storage, the parameters: //stored_rendermin//, //stored_rendermax// and //stored_renderbits// will be set, and when the file is read from disk, the values will be rescaled to match the original image, to within the limits permitted by render_bits.
-==== Special tags (read-only for getting image info) ====
-=== These values are cached and only recomputed if the image changes ===
-||Tag||Type||Description||
-||nx,ny,nz ||int ||Dimensions of the image, also available as get_xsize(),etc. Note: Assignments such as e["nx"] = 30 are an (not preferred) alternative to set_size(nx,ny,nz) ||
-||minimum ||float ||Smallest value in the image ||
-||maximum ||float ||Largest value in the image ||
-||mean ||float ||The average pixel value in the image ||
-||sigma ||float ||The standard deviation of the pixel values in the image ||
-||square_sum ||float ||Sum of the squares of the pixel values ||
-||mean_nonzero ||float ||The mean value of all nonzero pixels ||
-||sigma_nonzero ||float ||The standard deviation of the pixels ignoring pixels which are zero ||
-||all_int||int||True if all values in the image are integers, otherwise false||
-=== These values are computed only when requested, they are not part of get_attr_dict() ===
-||Tag||Type||Description||
-||skewness ||float ||Skewness of the pixel values ||
-||kurtosis ||float ||Kurtosis of the pixel values ||
-||median ||float ||Median value of the pixel values ||
-||nonzero_median ||float ||Median value of nonzero pixels ||
-||moment_inertia||float||Moment of inertia about the image center, considering only positive pixel values||
-||radius_gyration||float||Radius of gyration about the image center, considering only positive pixel values||
-**Official tags (used in EMAN2/SPARX as distributed):**
-||Tag||Type||Description||
-||apix_x,y,z ||float ||Angstroms per pixel on the x-axis (also _y and _z). If _y or _z are 0 or not present it will be assumed that they are the same as _x. Note that CTF objects have an independent value for A/pix ||
-||changecount ||int ||An integer which is incremented every time the image is marked as changed ||
-||class_id ||int ||Set by classification routines to indicate which class number the particle is in ||
-||class_ptcl_src ||string ||In a class-average, this is the file containing the raw images used to create the average ||
-||class_ptcl_idxs ||tuple ||In a class-average, this is a list of particle numbers used in the final average (see class_ptcl_src and exc_class_ptcl_idxs) ||
-||class_ptcl_qual ||tuple ||In a class-average, this is the mean quality of the particles vs the average ||
-||class_ptcl_qual_sigma ||tuple ||In a class-average, this is the standard deviation of the quality of the particles vs the average ||
-||class_qual ||float ||The similarity of the class-average to the alignment reference (usually a projection). As usual, smaller is better ||
-||class_ssnr||float list||SSNR computed from the FSC between the class-average and a reference. N points equivalent to the radius(+1) of the particle||
-||ctf ||Ctf subclass ||A subclass of Ctf containing all CTF parameters ||
-||ctf_phase_flipped ||bool ||Set to true if the CTF phases have been flipped ||
-||ctf_wiener_filtered ||bool ||Set to true if a Wiener filter has been applied ||
-||ctf_snr_total ||float list ||Set in class-averages by some averagers indicating the total estimated radial SNR of the average ||
-||data_path ||string ||Used for virtual stacks. References binary file and location for image data as file*location ||
-||data_source ||string ||Used in virtual stacks. This is a reference back to the source image from which this image was derived ||
-||data_n ||int ||Used in virtual stacks. This is the image number ||
-||datatype ||int ||Number format used when storing the file to disk, see format-specific parameters below for formats supported by each file. 0:EM_UNKNOWN, 1:EM_CHAR, 2:EM_UCHAR, 3:EM_SHORT, 4:EM_USHORT, 5:EM_INT, 6:EM_UINT, 7:EM_FLOAT, 8:EM_DOUBLE, 9:EM_SHORT_COMPLEX, 10:EM_USHORT_COMPLEX, 11:EM_FLOAT_COMPLEX,12:EM_COMPRESSED||
-||eigval ||float ||Eigenvalue, only set for images which represent Eigenvectors ||
-||eval_contrast_lowres ||float ||Low-resoluton contrsast in the image (mean power from 25-200 A / mean power >20 A) ||
-||exc_class_ptcl_idxs ||tuple ||In a class-average, this is a list of particle numbers provided to the averager, but excluded from the final average (see class_ptcl_src) ||
-||filter_curve ||float list ||Returned by some processors. List of floats representing an applied radial Fourier filter ||
-||hadzeroedge ||int ||If set, indicates that the mask.zeroedgefill processor detected an edge in need of filling ||
-||hostendian ||str ||Endianness of the computer in use. "big" or "little" ||
-||imageendian ||str ||Endianness of the image. "big" or "little". Only set for image files where this is an important distinction. ||
-||is_complex ||int ||Flag indicating that the image is complex (R/I or A/P pairs) ||
-||is_complex_ri ||int ||Flag indicating that a complex image is R/I not A/P ||
-||lst_comment ||string ||When a file is read from LSX format, any comment present will be stored here ||
-||match_n ||int ||used to represent the number of a reference particle this particle best matched ||
-||match_qual ||float ||used to represent the quality associated with match_n, smaller is a better match ||
-||microscope_voltage ||float ||Voltage of the microscope in kV ||
-||microscope_cs ||float ||Cs of the microscope in mm ||
-||model_id ||int ||in a projection during multi-model refinement, this is the index of the model for the current projection. For single model refinements always 1. In EMAN2.0x the first model was number 0, in EMAN2.1x the first model is number 1. ||
-||movie_frames ||int ||If this is one particle from a direct detector movie, this is the total number of frames in the movie ||
-||movie_n ||int ||If this is one particle from a direct detector movie, this is the sequence number within the movie (0 is the first frame as ususal) ||
-||movie_cc ||float list ||Correlation for each frame in a particle movie ||
-||movie_tx ||float list ||X translation for each frame in a particle movie ||
-||movie_ty ||float list ||Y translation for each frame in a particle movie ||
-||norm_mult ||float ||When images are normalized there is a linear transformation. This is the multiplicative component (happens first). Only some processors provide it. ||
-||norm_add ||float ||When images are normalized there is a linear transformation. This is the additive component for processors that provide it. ||
-||projection_image ||string ||In a class-average, this represents the image file which was used for initial alignment references ||
-||projection_image_idx ||string ||In a class-average, this represents the specific image number in projection_image ||
-||ptcl_repr ||int ||If an image/volume represents the combination of one or more other images, this is the count of the number of particles that went into the average ||
-||ptcl_helix_coords ||tuple ||The two endpoints and a box width that defines a helix box (x1, y1, x2, y2, box_width) ||
-||ptcl_source_coord ||tuple ||The central coordinate of a boxed particle in terms of its source image, normally (x,y), may be (x,y,z) for subtomograms ||
-||ptcl_source_image ||string ||The name of the image from which the particle was extracted. Full path, may be in bdb syntax ||
-||reconstruct_norm ||float ||Normalization factor applied to a single projection/class-average during reconstruction ||
-||reconstruct_qual ||float ||Quality of a single projection/class-average relative to others during reconstruction. Unlike with comparators, larger values are better. ||
-||reconstruct_preproc ||bool ||Set if the image has been preprocessed for use with a reconstructor ||
-||render_min,max ||float ||Used when rendering an image to integer formats. These are the values representing the minimum and maximum integer values. These values are never written to a file, but are set prior to saving. see stored_rendermin ||
-||render_bits||int||Specify the number of bits to keep in integer representation of the data. Bit reduction is lossy, but will not save disk space unless saving with compression enabled. Special value -1 can be used to specify floating point for lossless compression. This is never stored in a file. See stored_renderbits||
-||render_compress_level||int||Specify the compression level to use when writing compressed HDF files. Default is 1, which provides decent compression quickly. Valid range is 1-9. This value will be stored if set.||
-||score_align||float||Score associated with xform.align2d or xform.align3d. Meaning varies with alignment algorithm, but smaller should be better. Not all alignment routines return this.||
-||segment_centers ||float list ||Used when a volume has been segmented into regions. Set of 3*nregions floats in x1,y1,z1,x2,y2,z2,... order, indicating the center of each region as defined by the specific algorithm ||
-||sigma_presub ||float ||The sigma of the input image prior to reference subtraction, optionally returned by math.sub.optimal processor ||
-||source_orig_path ||string ||When an image is copied from one file to another, this can be used to reference its original location ||
-||source_orig_n ||string ||When an image is copied from one file to another, this can be used to reference its original number within the file ||
-||source_path ||string ||When an image is read from a file, this is set to the filename ||
-||source_n ||string ||When an image is read from a file, this is set to the image number (first image is 0) ||
-||stored_rendermin||float ||When an image has been stored in integer mode, this value is used to restore the original floating point range when reading. Any value set for this property prior to saving will be ignored and overwritten. To set this value prior to saving, see render_min.||
-||stored_rendermax||float ||When an image has been stored in integer mode, this value is used to restore the original floating point range when reading. Any value set for this property prior to saving will be ignored and overwritten. To set this value prior to saving, see render_max.||
-||stored_renderbits||float ||The number of bits used when saving this file. Special value -1 can be used to specify floating point for lossless compression. To set this value prior to saving, see render_bits.||
-||stored_truncated||int||Number of pixels with truncated values when saving with rendermin and rendermax||
-||subvolume_x0,y0,z0 ||int ||Used when the EMData stores only a portion of a larger image in certain contexts (notably direct Fourier inversion. This represents the location of the origin of 'this' in the larger virtual volume ||
-||subvolume_full_nx,ny,nz ||int ||Used with subvolume_x0,... Specifies the size of the virtual volume that 'this' is a part of ||
-||threed_ptcl_src ||string ||In a 3-D map, this is the file containing the raw images used to create the reconstruction ||
-||threed_ptcl_idxs ||tuple ||In a 3-D map, this is a list of particle numbers used in the final reconstruction (see threed_ptcl_src) ||
-||threed_excl_ptcl_idxs ||tuple ||In a 3-D map, this is a list of particle numbers excluded from the final map (see threed_ptcl_src) ||
-||tilt_angle || float||Tilt angle of a specific image in a tilt series, derived from recording software||
-||tilt_defocus_est|| float||Estimated defocus of a tilt in a tilt series from recording software||
-||tilt_dose|| float||Dose in a single tilt in a tilt series||
-||tilt_dose_begin|| float||Dose expended in the tilt series at the beginning of a specific tilt image||
-||tilt_seq|| int||Recorded sequence number of a single tilt in a tilt series, starting with 0||
-||timestamp ||string ||When data for an image is being written this is updated with the current time. It is not updated for metadata changes, only when the image data is written ||
-||symxform ||Transform ||A Transform object produced by e2symsearch.py ||
-||xform.projection ||Transform ||A Transform object used by Projectors. It is applied to a 3-D model prior to projecting by summing along Z. The inverse of this Transform is used by Reconstructors ||
-||xform.align2d ||Transform ||A Transform object representing a 2-D transformation used to align this EMData object to a reference in 2-D ||
-||xform.align3d ||Transform ||A Transform object representing a 3-D transformation used to align this (3-D) EMData object to a (3-D) reference ||
-**Proposed new Official tags (comments welcome):**
-||Tag||Type||Description||Comments||
-||apix_scan ||float ||Scan pixel size in Angstroms ||(there are already parameters for apix_x/y/z above. Is this different in some way ?, you could provide this as supplementary information, but apix_x/y/z remain the 'official' values. Is this what you want ?) ||
-||box_location ||int_array ||4 values, x0, y0, xsize, ysize representing the location of the particle in the original (box_source) image ||(Pawel suggested this be changed to the reduced image, because normally we first reduce the micrograph, the window it.)     (No, the box location should be in the coordinates of the referenced 'parent' image. If you want to reference a reduced image you can, but I think it makes a lot more sense to provide the capability of refining the coordinates from the reduced image when you return to the original image.) Pawel: the coordinates in boxer refer to the image from windowing was done.  This is is (or can be) a reduced micrograph. There is more confusion here: name apix_scan suggests this is pixel size of the scan, NOT THE REDUCED MICROGRAPH FROM WHICH PARTICLES WERE WINDOWED. Incidentally, both pixel sizes are needed and have to be in the header. Steve: This differs from the philosophy of e2boxer, which is that you always provide e2boxer with the original image, it may internally downscale it for boxing, but the final box positions are in terms of the original image. I don't understand why you would want to externally downscale, then have to rescale the coordinates again later ? This is very messy.  Anyway, any single image has a particluar A/pix value associated with it. I have no objections to something like apix_original, but what exactly is the point ? You aren't likely to rescale reduced images back to their original size... ||
-||box_score ||float ||A value representing the relative quality (meaning may vary) of this particle compared to others ||
-||box_source ||string ||Filename (not full path) of the image this particle was extracted from ||
-||box_source_id ||string ||Other (database) identifier of the image the raw data came from if available ||
-**Unofficial tags (To prevent reuse, used by someone in their own code or for testing):**
-|| || ||
-**Tags used to store header information derived from other file formats:**
-=== Parameters from MRC file ===
-||Tag||Type||Description||
-||datatype ||int ||pixel storage data type in EMAN format: EM_UCHAR, EM_SHORT, EM_USHORT, EM_SHORT_COMPLEX, EM_FLOAT, EM_FLOAT_COMPLEX ||
-||apix_x,y,z ||float ||Angstroms per pixel on the x-axis (also _y and _z). If _y or _z are 0 or not present it will be assumed that they are the same as _x. Note that CTF objects have an independent value for A/pix ||
-||MRC.minimum ||float ||Minimum density value ||
-||MRC.maximum ||float ||Maximum density value ||
-||MRC.mean ||float ||Mean density value ||
-||origin_x, y, z ||float ||image origin for x, y, z axis ||
-||MRC.nxstart ||int ||No. of first column in map ||
-||MRC.nystart ||int ||No. of first row in map ||
-||MRC.nzstart ||int ||No. of first section in map ||
-||MRC.mx ||int ||Number of intervals along X ||
-||MRC.my ||int ||Number of intervals along Y ||
-||MRC.mz ||int ||Number of intervals along Z ||
-||MRC.nx ||int ||number of columns ||
-||MRC.ny ||int ||number of rows ||
-||MRC.nz ||int ||number of sections ||
-||MRC.xlen ||float ||Cell dimensions (Angstroms) ||
-||MRC.ylen ||float ||Cell dimensions (Angstroms) ||
-||MRC.zlen ||float ||Cell dimensions (Angstroms) ||
-||MRC.alpha ||float ||Cell angles (Degrees) ||
-||MRC.beta ||float ||Cell angles (Degrees) ||
-||MRC.gamma ||float ||Cell angles (Degrees) ||
-||MRC.mapc ||int ||Which axis corresponds to Columns ||
-||MRC.mapr ||int ||Which axis corresponds to Rows ||
-||MRC.maps ||int ||Which axis corresponds to Sections ||
-||MRC.ispg ||int ||Space group number (0 for images) ||
-||MRC.nsymbt ||int ||Number of chars used for storing symmetry operators ||
-||MRC.machinestamp ||int ||machine stamp in CCP4 convention: big endian=0x11110000 little endian=0x44440000 ||
-||MRC.rms ||float ||rms deviation of map from mean density ||
-||MRC.nlabels ||int ||Number of labels being used ||
-=== Parameters from FEI MRC file (an extended MRC format for tomography) ===
-||Tag||Type||Description||
-||FEIMRC.a_tilt ||float ||Alpha tilt, in degrees ||
-||FEIMRC.b_tilt ||float ||Beta tilt, in degrees ||
-||FEIMRC.x_stage ||float ||Stage x position. Normally in SI units (meters), but some older files may be in micrometers. Check by looking at values for x,y,z. If one of these exceeds 1, it will be micrometers. ||
-||FEIMRC.y_stage ||float ||Stage y position. For testing of units see x_stage. ||
-||FEIMRC.z_stage ||float ||Stage z position. For testing of units see x_stage. ||
-||FEIMRC.x_shift ||float ||Image shift x. For testing of units see x_stage. ||
-||FEIMRC.y_shift ||float ||Image shift y. For testing of units see x_stage. ||
-||FEIMRC.defocus ||float ||Defocus as read from microscope. For testing of units see x_stage. ||
-||FEIMRC.exp_time ||float ||Exposure time in seconds. ||
-||FEIMRC.mean_int ||float ||Mean value of image. ||
-||FEIMRC.tilt_axis ||float ||The orientation of the tilt axis in the image in degrees. Vertical to the top is 0=B0, the direction of positive rotation is anti-clockwise. ||
-||FEIMRC.pixel_axis ||float ||The pixel size of the images in SI units (meters). ||
-||FEIMRC.magnification ||float ||The magnification used for recording the images. ||
-||FEIMRC.ht ||float ||Value of the high tension in SI units. (volts) ||
-||FEIMRC.binning ||float ||The binning of the CCD or STEM acquisition. ||
-||FEIMRC.appliedDefocus ||float ||The intended application defocus in SI units (meters), as defined for example in the tomography parameter view. ||
-||FEIMRC.remainder ||float(x128) ||Not used. ||
-=== Parameters from EER file ===
-||Tag||Type||Description||
-||EER.compression ||int ||65001 for EER compressed data 7-bit, COMPRESSION_NONE (1) for final image data ||
-||EER.exposure_time ||float ||Exposure time of the acquisition in s ||
-||EER.total_dose ||float ||Average amount of electrons per pixel in the entire acquisition in e/pixel ||
-||EER.mean_dose_rate ||float ||Average amount of electrons per pixel per second during the acquisition in e/pixel/s ||
-||EER.number_of_frames ||int ||Total number of frames in the acquisition ||
-||EER.sensor_image_height ||int ||Height of the individual images ||
-||EER.sensor_image_width ||int ||Width of the individual images ||
-=== Parameters from IMAGIC file ===
-||Tag||Type||Description||
-||datatype ||int ||pixel storage data type in EMAN format: EM_UCHAR, EM_USHORT, EM_FLOAT, EM_FLOAT_COMPLEX ||
-||IMAGIC.imgnum ||int ||image number, index from 1 to n ||
-||IMAGIC.count ||int ||total number of images - 1 ||
-||IMAGIC.error ||int ||Error code for this image ||
-||IMAGIC.headrec ||int ||number of header records/image (always 1) ||
-||IMAGIC.mday ||int ||image creation date ||
-||IMAGIC.month ||int ||image creation month ||
-||IMAGIC.year ||int ||image creation year ||
-||IMAGIC.hour ||int ||image creation hour ||
-||IMAGIC.minute ||int ||image creation minute ||
-||IMAGIC.sec ||int ||image creation second ||
-||IMAGIC.reals ||int ||image size in reals ||
-||IMAGIC.pixels ||int ||image size in pixels ||
-||IMAGIC.type ||char(4) ||PACK, INTG, REAL, COMP, RECO ||
-||IMAGIC.ixold ||int ||Top left X-coord. in image before windowing ||
-||IMAGIC.iyold ||int ||Top left Y-coord. in image before windowing ||
-||IMAGIC.oldav ||float ||old average density ||
-||IMAGIC.label ||char(80) ||image id string ||
-||ptcl_repr ||int ||raw images represented by this image. Note: non-standard use ||
-||xform.projection ||Transform ||particle orientation, set from the orientation flags(alt, az, phi) in the IMAGIC header ||
-||xform.align3d ||Transform ||particle orientation for 3D image, set from the orientation flags(alt, az, phi) in the IMAGIC header ||
-=== Parameters from IMAGIC2 file ===
-||Tag||Type||Description||
-||datatype ||int ||pixel storage data type in EMAN format: EM_UCHAR, EM_USHORT, EM_FLOAT, EM_FLOAT_COMPLEX ||
-||IMAGIC.imgnum ||int ||image location number (1,2,3,...) ||
-||IMAGIC.count ||int ||total # images in file (1st record only), total number of images - 1 (0,1,2,...) ||
-||IMAGIC.error ||int ||error code for this image during IMAGIC run ||
-||IMAGIC.month ||int ||creation month ||
-||IMAGIC.day ||int ||creation day ||
-||IMAGIC.year ||int ||creation year ||
-||IMAGIC.hour ||int ||creation hour ||
-||IMAGIC.minute ||int ||creation minute ||
-||IMAGIC.sec ||int ||creation second ||
-||IMAGIC.rsize ||int ||image size in bytes ||
-||IMAGIC.izold ||int ||top left Z co-ordinate before THREED-CUT ||
-||IMAGIC.type ||char(4) ||4 characters determining the image type; only 'REAL', or 'INTG' are implemented for EMAN ||
-||IMAGIC.ixold ||int ||top left X co-ordinate before CUT-IMAGE (boxing) ||
-||IMAGIC.iyold ||int ||top left Y co-ordinate before CUT-IMAGE (boxing) ||
-||IMAGIC.complex ||int ||label indicating that data is always complex ||
-||IMAGIC.defocus1 ||float ||defocus value 1 ||
-||IMAGIC.defocus2 ||float ||defocus value 2 ||
-||IMAGIC.defangle ||float ||defocus angle ||
-||IMAGIC.sinostart ||float ||start angle if image is a sinogram ||
-||IMAGIC.sinoend ||float ||end angle if image is a sinogram ||
-||IMAGIC.label ||char(80) ||coded NAME/TITLE of the image ||
-||IMAGIC.ccc3d ||float ||3D similarity criteria ||
-||IMAGIC.ref3d ||int ||3D membership ||
-||IMAGIC.mident ||int ||micrograph identification number ||
-||IMAGIC.ezshift ||int ||equivalent shift in Z direction ||
-||IMAGIC.ealpha ||int ||equivalent Euler angle alpha ||
-||IMAGIC.ebeta ||int ||equivalent Euler angle beta ||
-||IMAGIC.egamma ||int ||equivalent Euler angle gamma ||
-||IMAGIC.nalisum ||int ||number of image summed ||
-||IMAGIC.pgroup ||int ||point-group symmetry in international notation (622, for example) ||
-||IMAGIC.i4lp ||int ||number of objects in file ||
-||IMAGIC.alpha ||float ||Euler angle alpha (3D and Angular Reconst. ||
-||IMAGIC.beta ||float ||Euler angle beta (3D and Angular Reconst.) ||
-||IMAGIC.gamma ||float ||Euler angle gamma (3D and Angular Reconst.) ||
-||IMAGIC.imavers ||int ||IMAGIC version, which created the file (yyyymmdd) ||
-||IMAGIC.realtype ||int ||floating point type, machine stamp ||
-||IMAGIC.angle ||float ||last rotation angle ||
-||IMAGIC.voltage ||float ||acceleration voltage (kv) ||
-||IMAGIC.spaberr ||int ||sperical aberration (mm) ||
-||IMAGIC.pcoher ||int ||partial coherence ||
-||IMAGIC.ccc ||float ||cross correlation peak hight ||
-||IMAGIC.errar ||float ||error in angular reconstitution,  if -1.0: the file is a special file (FABOSA) ||
-||IMAGIC.err3d ||float ||error in 3D reconstruction ||
-||IMAGIC.ref ||int ||(multi-) reference number ||
-||IMAGIC.classno ||float ||class number in MSA classification ||
-||IMAGIC.locold ||float ||location number before CUT-IMAGE (boxing), or before copy in ANG-RECONST and EX-COPY ||
-||IMAGIC.repqual ||float ||representation quality, used in MSA-RUN and MSA (eigen) filtering ||
-||IMAGIC.zshift ||float ||last shift in Z direction ||
-||IMAGIC.xshift ||float ||last shift in X direction ||
-||IMAGIC.yshift ||float ||last shift in Y direction ||
-||IMAGIC.numcls ||float ||number members in the class specified in CLASSNO, if this image represents a class average (class-sum image) ||
-||IMAGIC.ovqual ||float ||overall quality of the class in CLASSNO ||
-||IMAGIC.eangle ||float ||equivalent angle ||
-||IMAGIC.exshift ||float ||equivalent shift in X direction ||
-||IMAGIC.eyshift ||float ||equivalent shift in Y direction ||
-||IMAGIC.cmtotvar ||float ||total variance in data matrix relative to center of mass (MSA calculations) ||
-||IMAGIC.informat ||float ||Gauss norm / real*FT Space information of the data set ||
-||IMAGIC.numeigen ||int ||number of eigen values in MSA ||
-||IMAGIC.niactive ||int ||number of active images in MSA calculations ||
-||IMAGIC.fabosa1 ||float ||Euler angle alpha (from projection matching), Special FABOSA variables if DAT1(105) = -1.0 ||
-||IMAGIC.fabosa2 ||float ||Euler angle beta (from projection matching), Special FABOSA variables if DAT1(105) = -1.0 ||
-||IMAGIC.fabosa3 ||float ||Euler angle gamma (from projection matching), Special FABOSA variables if DAT1(105) = -1.0 ||
-||IMAGIC.alpha2 ||float ||Euler angle alpha (from projection matching), Special FABOSA variables if DAT1(105) = -1.0 ||
-||IMAGIC.beta2 ||float ||Euler angle beta (from projection matching), Special FABOSA variables if DAT1(105) = -1.0 ||
-||IMAGIC.gamma2 ||float ||Euler angle gamma (from projection matching), Special FABOSA variables if DAT1(105) = -1.0 ||
-||IMAGIC.nmetric ||float ||Metric used in MSA calculations ||
-||IMAGIC.actmsa ||float ||a flag indicating whether the "image" is active or not. Used during MSA calculations ||
-||IMAGIC.coosmsa ||float(69) ||co-ordinates of "image" along factorial axis ||
-||IMAGIC.history ||char(228) ||coded history of image (228 characters) ||
-||ptcl_repr ||int ||raw images represented by this image. Note: non-standard use ||
-||xform.projection ||Transform ||particle orientation, set from the orientation flags(alt, az, phi) in the IMAGIC header ||
-||xform.align3d ||Transform ||particle orientation for 3D image, set from the orientation flags(alt, az, phi) in the IMAGIC header ||
-=== Parameters from SPIDER file ===
-||Tag||Type||Description||
-||datatype ||int ||pixel storage data type in EMAN format: EM_FLOAT ||
-||SPIDER.nslice ||int ||number of slices in volume; 1 for a 2D image ||
-||SPIDER.type ||int ||file type ||
-||SPIDER.irec ||float ||total number of records in the file (unused) ||
-||SPIDER.angvalid ||int ||1 if tilt angles have been computed ||
-||SPIDER.phi ||float ||tilt angle phi ||
-||SPIDER.theta ||float ||tilt angle theta ||
-||SPIDER.gamma ||float ||tilt angle gamma ||
-||SPIDER.headrec ||int ||number of records in header ||
-||SPIDER.headlen ||int ||header length in bytes ||
-||SPIDER.reclen ||int ||record length in bytes ||
-||SPIDER.dx ||float ||x translation ||
-||SPIDER.dy ||float ||y translation ||
-||SPIDER.dz ||float ||z translation ||
-||SPIDER.istack ||int ||0 for simple 2D or 3D (non-stack) files. for stacked image, istack=2 in overall header, istack =-1 in following individual images. ||
-||SPIDER.maxim ||int ||maxim is only used in the overall header for a stacked image file. It is the number of the highest image currently used in the stack. The number is updated, if necessary, when an image is added or deleted from the stack. ||
-||SPIDER.imgnum ||int ||imgnum is only used in a stacked image header. It is the number of the current image or zero if the image is unused. ||
-||SPIDER.Kangle ||int ||flag that additional angles are present in header. 1 = one additional rotation is present, 2 = additional rotation that preceeds the rotation that was stored in words 15..20. ||
-||SPIDER.phi1 ||float || ||
-||SPIDER.theta1 ||float || ||
-||SPIDER.psi1 ||float || ||
-||SPIDER.phi2 ||float || ||
-||SPIDER.theta2 ||float || ||
-||SPIDER.psi2 ||float || ||
-||SPIDER.date ||char(11) ||creation date ||
-||SPIDER.time ||char(8) ||creation time ||
-||SPIDER.title ||char(160) ||title ||
-||SPIDER.scale ||float ||scale factor ||
-||xform.projection ||Transform ||particle orientation, set from the orientation flags(phi, theta, psi, tx, ty, tz, scale) in the SPIDER header ||
-||xform.align3d ||Transform ||particle orientation for 3D image, set from the orientation flags(phi, theta, psi, tx, ty, tz, scale) in the SPIDER header ||
-=== Parameters from PGM file ===
-||Tag||Type||Description||
-||PGM.max_gray ||int ||maximum value for grey level ||
-||PGM.min_gray ||int ||minimum value for grey level ||
-=== Parameters from SAL file ===
-||Tag||Type||Description||
-||datatype ||int ||pixel storage data type in EMAN format: EM_SHORT ||
-||SAL.pixel ||float ||pixel size ||
-=== Parameters from TIFF file ===
-||Tag||Type||Description||
-||datatype ||int ||pixel storage data type in EMAN format: EM_UCHAR, EM_USHORT, EM_FLOAT ||
-||TIFF.bitspersample ||unsigned short ||bits per pixel sample ||
-||TIFF.resolution_x ||float ||x dimension resolution ||
-||TIFF.resolution_y ||float ||y dimension resolution ||
-=== Parameters from Gatan DM3 files ===
-||Tag||Type||Description||
-||DM3.acq_date ||string ||Acquisition date ||
-||DM3.acq_time ||string ||Acquisition time ||
-||DM3.actual_mag ||float ||Calibrated magnification ||
-||DM3.antiblooming ||int || ||
-||DM3.binning_x ||int ||Binning (X) ||
-||DM3.binning_y ||int ||Binning (Y) ||
-||DM3.camera_x ||int ||Camera size (X) ||
-||DM3.camera_y ||int ||Camera size (Y) ||
-||DM3.cs ||float ||Microscope Cs ||
-||DM3.exposure_number ||int ||Camera exposure number ||
-||DM3.exposure_time ||float ||Exposure time ||
-||DM3.frame_type ||string ||Frame type ||
-||DM3.indicated_mag ||float ||Indicated magnification ||
-||DM3.name ||string ||Filename ||
-||DM3.pixel_size ||float ||Pixel size (microns) ||
-||DM3.source ||string ||Camera name ||
-||DM3.voltage ||float ||Microscope voltage ||
-||DM3.zoom ||float || ||
-=== Parameters from XPLOR file ===
-||Tag||Type||Description||
-||apix_x,y,z ||float ||Angstroms per pixel on the x-axis (also _y and _z). If _y or _z are 0 or not present it will be assumed that they are the same as _x. Note that CTF objects have an independent value for A/pix ||
-||XPLOR.alpha ||float ||alpha angle of the cell ||
-||XPLOR.beta ||float ||beta angle of the cell ||
-||XPLOR.gamma ||float ||gamma angle of the cell ||