|
Size: 6677
Comment:
|
Size: 17810
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 8: | Line 8: |
| ||nx,ny,nz||int||Dimensions of the image, also available as get_xsize(),etc.|| ||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|| ||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|| ||changecount||int||An integer which is incremented every time the image is marked as changed|| ||data_path||string||Used only in BDB files, to indicate that the binary data for an image should be read from an alternate location. Data cannot be written back to such objects.|| |
||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 || ||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 || ||changecount ||int ||An integer which is incremented every time the image is marked as changed || ||data_path ||string ||Used only in BDB files, to indicate that the binary data for an image should be read from an alternate location. Data cannot be written back to such objects. || |
| Line 21: | Line 23: |
| ||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|| |
||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 || |
| Line 27: | Line 30: |
||apix_x,y,z||float||Angstroms per pixel on the x-axis (also _y and _z)|| ||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|| ||ptcl_repr||int(float?)||If an image represents the average of one or more other images, this is the count of the number of particles that went into the average|| ||class_id||int||Set by classification routines to indicate which class number the particle is in|| ||eigval||float||Eigenvalue, only set for images which represent Eigenvectors|| ||render_min,max||float||Used when rendering an image to 8/16 bit integers. These are the values representing the minimum and maximum integer values|| ||ctf||Ctf subclass||A subclass of Ctf containing all CTF parameters|| ||ctf_phase_flipped||bool||Set to 1 if the CTF phases have been flipped|| ||ptcl_source_coord||tuple||The central coordinate of a boxed particle in terms of its source image|| ||ptcl_source_image||string||The name of the image from which the particle was extracted. Full path, may be in bdb syntax|| |
||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 || ||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) || ||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 ||ing ||Used in virtual stacks. This is the image number || ||eigval ||float ||Eigenvalue, only set for images which represent Eigenvectors || ||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) || ||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 0|| ||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 8/16 bit integers. These are the values representing the minimum and maximum integer values || ||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 || ||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 || ||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) || ||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|| ||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 || |
| Line 42: | Line 75: |
| ||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|| |
||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 || |
| Line 50: | Line 85: |
| ||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|| |
|
| Line 53: | Line 86: |
'''Tags used to store header information derived from other file formats:''' ==== Flags come form MRC file ==== ||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 || ==== Flags come form IMAGIC file ==== ||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 || ==== Flags come form SPIDER file ==== ||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 || ==== Flags come form PGM file ==== ||PGM.max_gray ||int ||maximum value for grey level || ||PGM.min_gray ||int ||minimum value for grey level || ==== Flags come form SAL file ==== ||datatype ||int ||pixel storage data type in EMAN format: EM_SHORT || ||SAL.pixel ||float ||pixel size || ==== Flags come form TIFF file ==== ||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 || ==== Flags from Gatan DM3 files ==== ||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|| || ==== Flags come form XPLOR file ==== ||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 || |
Parameters/Metadata stored in EMData Objects
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.
Special tags (read-only for getting image info)
These values are cached and only recomputed if the image changes
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 |
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 |
changecount |
int |
An integer which is incremented every time the image is marked as changed |
data_path |
string |
Used only in BDB files, to indicate that the binary data for an image should be read from an alternate location. Data cannot be written back to such objects. |
These values are computed on the fly
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 |
Official tags (used in EMAN2/SPARX as distributed):
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 |
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) |
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 |
ing |
Used in virtual stacks. This is the image number |
eigval |
float |
Eigenvalue, only set for images which represent Eigenvectors |
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) |
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 0 |
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 8/16 bit integers. These are the values representing the minimum and maximum integer values |
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 |
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 |
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) |
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 |
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):
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:
Flags come form MRC file
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 |
Flags come form IMAGIC file
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 |
Flags come form SPIDER file
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 |
Flags come form PGM file
PGM.max_gray |
int |
maximum value for grey level |
PGM.min_gray |
int |
minimum value for grey level |
Flags come form SAL file
datatype |
int |
pixel storage data type in EMAN format: EM_SHORT |
SAL.pixel |
float |
pixel size |
Flags come form TIFF file
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 |
Flags from Gatan DM3 files
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 |
|
Flags come form XPLOR file
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 |