<> = This page is obsolete = == Global dictionaries/parameters == === 00image_counts database === Every EMAN2DB directory will contain an image count cache database which will contain a number of parameters associated with each image in that directory, updated as necessary. ||filename||(timestamp,# particles,(nx,ny,nz) of particle 1)||Timestamp indicates time other values were last updated|| == Parameters/Metadata for applications stored in the project == These are metadata parameters associated with a 'Project', like a single particle reconstruction, and may be application specific or global. If an application wishes to make parameters available for other applications to see, it should put them in 'bdb:project' in the local directory and name them as described below. Documentation for application specific parameters not really intended for use by other applications appears here as well. This does NOT document parameters stored in the header of individual images, though we strive to use the same names whereever possible. === These parameters can be found in bdb:project === Parameters starting with 'global.' are those which could be used equally by any application, other applications wishing to publish parameters for use by others should prefix them with 'appname.' ||global.apix ||float ||Default A/pix value for a project || ||global.microscope_voltage ||float ||Default microscope voltage in kV for a project || ||global.microscope_cs ||float ||Default microscope Cs in mm for a project || ||global.spr_raw_data_dict ||Dictionary, key is a string, value is a dictionary ||The keys in this dictionary are all the micrograph and/or CCD data file names that are associated with a single particle reconstruction project. The value (which is a dictionary) is currently unused - it is present in anticipation of potential future needs || ||global.spr_stacks_map ||Dictionary, key is a string, value is a dictionary ||In this dictionary the key is the name of the stack file that would be created from the raw particles corresponding to the filtered particles in the filtered stacks enumerated by the dictionary values - The values, which are dictionaries, contains keys which are descriptive strings such as "phase", and values which are the names of filtered file stacks that exist on disk. The raw stack key of this dictionary does not necessarily have to exist, but having this as the 'theoretical' name helps with the management side of things in the workflow || ||global.spr_filt_ptcls_dict ||Dictionary, key is a string, value is a dictionary ||In this dictionary the key is the name of a particle file that should almost certainly also exist in the global.spr_ptcls list. The value, which is a dictionary, contains keys which are descriptive strings such as "phase", and values which are the names of filtered files that exist on disk. || ||global.spr_ref_free_class_aves ||list of strings ||A list of all reference free class averages associated with the project || ||global.spr_rfca_dict ||Dictionary, key is a string, value is a dictionary ||In this dictionary the key is the name of all reference free class averages associated with the project. The dictionary value is currently unused but may be useful in future || ||global.spr_sets_dict||Dictionary, key is a string, value is a dictionary||All of the 'sets' in the project are in this dictionary. The key is the name of the overall 'set'. The value dictionary is keyed by filter type and has values containing the actual filenames of the filtered particles. Standard filter types are: 'Original Data', 'Phase flipped', 'Wiener filtered', 'Phase flipped-hp' (case sensitive).|| ||global.spr_init_models_dict ||Dictionary, key is a string, value is a dictionary ||e keys in this dictionary are a list of all initial models that are associated with the project. The dictionary value is currently unused but may be useful in future || ||global.num_cpus ||int ||Number of cpus available to this project || ||global.memory_available ||int ||Maximum memory usage for this project || ||global.particle_mass ||float ||The mass of the particle in kilodaltons || ||workflow.process_ids ||list of ints ||A list of process ids that is managed by the workflow system || === These parameters are application specific and subject to change === Dictionary names should begin with the application name, the contents of each dictionary can be freely defined by the application. ==== e2ctf.parms ==== ||__filename__ ||[ [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1EMAN2Ctf.html|EMAN2Ctf]] object,1D pow spec,1D bg pow spec,Image Quality] ||A list with a CTF object as a string (from_string to restore), the 2 1-D power spectra, and a user defined image quality value, images default to quality 5, quality 0 images will not be post-processed || ==== e2ctf.im2d ==== ||__filename__ ||[[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1EMData.html|EMData]] ||The averaged 2-D 'signal' power spectrum for all particles from filename || ==== e2ctf.bg2d ==== ||__filename__ ||[[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1EMData.html|EMData]] ||The averaged 2-D 'background' power spectrum for all particles from filename || ==== e2ctf.misc ==== ||strucfac ||list of (x,y) tuples ||Computed Envelope*StrucFact curve from CTF maxima from all sets processed during one run || ==== e2boxer.cache ==== <> This is the cache associated with e2boxer.py. Not that by __filename_DD__ it is meant to be a string constructed from the original file name, for instance if the file name was 123458.mrc then __filename_DD__ would be literally "123458_DD". ||__filename_DD__ ||Python dictionary ||Image Database Dictionary || ||__filename_DD__.auto_boxer_state_TS ||string ||Greenwich Mean time stamp of the associated Autoboxer when it was last used to autobox this image. This information can be used to force reboxing if the associated autoboxer has been updated || ||__filename_DD__.auto_boxer_unique_id ||string ||stores the unique ID of an associated Autoboxer instance which is also stored in the boxer_cache database || ||__filename_DD__.auto_boxes ||boxertools.TrimBox list ||stores the current set of automatically selected boxes by the associated Autoboxer instance || ||__filename_DD__.coarse_flat_image ||[[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1EMData.html|EMData]] ||stores the image generated by the boxertools.CoarsenedFlattenedImage object that is associated with this image || ||__filename_DD__.frozen_state ||boolean ||indicates whether or not the image is frozen. If the image is frozen then no changes can be made to the currently associated boxes || ||__filename_DD__.image_tag ||string ||Stores the original name of the image || ||__filename_DD__.manual_boxes ||boxertools.TrimBox list ||stores boxes that have been manually placed in this image || ||__filename_DD__.moved_boxes ||Python list of 2D coordinates ||effectively a memorization of all the box movements enforced by the user. Can be used to perform collision detection and automatically correct the results of automatic boxing || ||__filename_DD__.quality ||integer [0-4] ||in the special case of the quality being equal to zero this means the image is excluded from boxing and that no boxes should ever be generated for it. Otherwise this is just metadata that may be acted upon autonomously by the user || ||__filename_DD__.reference_boxes ||boxertools.TrimBox list ||stores the reference boxes located in this image that are also being used by the associated Autoboxer instance || ||__filename_DD__.template_ts ||string ||Greenwich Mean time stamp that records when the associated template (that was used to generate the correlation image, which is potentially stored in the database also) was created || ||__autoboxer_ts__ ||Python dictionary ||the key here is literally the string "autobxer_" followed the a unique time stamp as a string. This dictionary object stores the essential parameters of a an Autoboxer instance || ||__autoboxer_ts__.autoboxer ||boxertools.AutoBoxer or boxertools.TrimAutoBoxer ||the Autoboxer instance itself (or similar) || ||__autoboxer_ts__.autoboxer_type ||string ||this is the unique associated with the Autoboxer type, for example "Swarm" or "Gauss" || ||__autoboxer_ts__.convenience_name ||string ||the user may optionally supply a convenience name for this autoboxer in the e2boxer interface, otherwise the name is generated automatically || ||__current_autoboxer__ ||boxertools.AutoBoxer or boxertools.TrimAutoBoxer ||the most recently use Autoboxer instance || ||__current_autoboxer_type__ ||string ||the type of the most recently used Autoboxer instance. This should become deprecated. || ==== e2classaverage.indices ==== ||class number (integer stored as a string)* ||list of integers ||The indexes of particles that went into each class. Generated by e2classaverage if correct command line arguments are passed. Used automatically be e2refine and accessed by e2eulerxplor || * Stored as a string because of some database complication during development ==== emform.e2boxer ==== This dictionary stores the most recently used parameters associated with boxing in [[e2workflow|e2workflow.py]] ||interface_boxsize ||int ||The box size that is used to launch e2boxer from within the project/workflow setting || ||output_boxsize ||int ||The last box size that was used for generating boxed output with e2boxer || ||force ||boolean ||The force flagged used for writing output in e2boxer || ||write_coord_files ||boolean ||The write coordinates flagged used for writing output in e2boxer || ||write_box_images ||boolean ||The write box images flag used for writing output in e2boxer || ||normproc ||string ||The normalization processor name used writing boxed output in e2boxer || ||outformat ||string ||The image format for boxed images generated when writing output in e2boxer || ||filenames ||string list ||The last set of filenames that was used to launch or spawn e2boxer || ==== emform.e2ctf ==== This dictionary stores the most recently used parameters associated with ctf correction in [[e2workflow|e2workflow.py]] ||ac ||float ||Amplitude contrast constant used to launch e2ctf from within the project/workflow setting || ||oversamp ||float ||Oversample factor used to launch e2ctf from within the project/workflow setting || ||nosmooth ||boolean ||Last nosmooth program argument used to run e2ctf from within the project/workflow setting || ||autohp ||boolean ||Last autohp program argument used to run e2ctf from within the project/workflow setting || ||wiener ||boolean ||Last wiener program argument used to run e2ctf from within the project/workflow setting || ||phaseflip ||boolean ||Last phaseflip program argument used to run e2ctf from within the project/workflow setting || ||filenames ||string list ||The last set of filenames that was used to launch or spawn e2ctf || ==== emform.e2initialmodel ==== ||filenames ||string list ||The last set of filenames that was used to launch or spawn e2initialmodel || ||iter ||int ||Last iterations argument used to run e2initialmodel || ||symname ||string ||Symmetry type, i.e. c,d,icos etc, used to create the symmetry argument last used to run e2initialmodel || ||symnumber ||string ||Symmetry number ("","1","2" and so on) used to create the symmetry argument last used to run e2initialmodel || ||tries ||int ||Last tries argument used to run e2initialmodel || This dictionary stores the most recently used parameters associated with initial model generation in [[e2workflow|e2workflow.py]] ==== emform.e2refine ==== This dictionary stores the most recently used parameters associated with 3D refinement in [[e2workflow|e2workflow.py]] ||amnshellsgauss ||int ||The nshellsgauss parameter of the [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1AutoMask3D2Processor.html|mask.auto3d processor]] || ||amnshells ||int ||The nshells parameter of the [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1AutoMask3D2Processor.html|mask.auto3d processor]] || ||amradius ||int ||The radius parameter of the [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1AutoMask3D2Processor.html|mask.auto3d processor]] || ||amthreshold ||float ||The isosurface threshold parameter of the [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1AutoMask3D2Processor.html|mask.auto3d processor]] || ||automask3d ||boolean ||The last state of the automask3d checkbox on the main page, which cause e2refine to use the [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1AutoMask3D2Processor.html|mask.auto3d processor]] following e2make3d || ||classalign ||string ||The [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Aligner.html|aligner]] used for alignment during iterative class averaging || ||classalignargs ||string ||classalign (The [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Aligner.html|aligner]]) parameters || ||classaligncmp ||string ||The [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Cmp.html|comparator]] used by the main aligner during iterative class averaging || ||classaligncmpargs ||string ||classaligncmp ([[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Cmp.html|comparator]]) parameters || ||classaverager ||string ||[[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Averager.html|Averager]] used for averaging the images in each class || ||classcmp ||string ||The main [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Cmp.html|comparator]] used to quality and exclude bad particles in iterative class averaging || ||classcmpargs ||string ||classcmp ([[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Cmp.html|comparator]]) parameters || ||classiter ||int ||The number of class averaging iterations || ||classkeep ||float ||The keep threshold used for excluding bad particles in iterative class averaging || ||classkeepsig ||bool ||The sigma thresholding flag used in conjunction with classkeep || ||classnormproc ||string ||The normalization [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Processor.html|processor]] used in class averaging || ||classralign ||string ||The refinement [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Aligner.html|aligner]] used in iterative class averagin || ||classralignargs ||string ||classralign ([[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Aligner.html|aligner]]) parameters || ||classraligncmp ||string ||The comparator used by the refinement aligner in iterative class averaging || ||classraligncmpargs ||string ||classraligncmp ([[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Cmp.html|comparator]]) parameters || ||filenames ||string list ||The most recently selected/specified files used to create the input stack from within the workflow setting || ||iter ||int ||The number of refinement iterations || ||lowmem ||boolean ||A low memory flag used to indicate memory should be used as sparsely as possible || ||m3diter ||int ||The number of iterations used my make3d when performing the Fourier inversion method of 3D reconstruction || ||m3dkeep ||float ||The keep threshold used by e2make3d for the purpose of slice exclusion during 3D reconstruction || ||m3dpreprocess ||string:args ||The normalization [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Processor.html|processor]] applied prior to slice insertion during 3D reconstruction || ||model ||string list (length 1) ||The seeding 3D model, this is not an absolute path, but rather the file tag (see get_file_tag in EMAN2.py) of an image in the initial models database || ||orientgen ||string ||The method ([[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1OrientationGenerator.html|OrientationGenerator]]) used to generate orientations in the asymmetric unit of the 3D model || ||orientopt ||string ||Reflects the user's choice between number based and angle based orientation generation (eventually becomes an [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1OrientationGenerator.html|OrientationGenerator]] parameter) || ||orientopt_entry ||float ||A value closely tied with orientopt, this is either an angle of, or the total number of, desired orientations || ||pad ||int ||The amount of padding used by the Fourier inversion 3D reconstruction technique || ||particle_set_choice ||string ||Stores which data set the user chose to supply as main input into the refinement process (e.g. Wiener, phase flipped, etc) || ||projector ||string ||The [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Projector.html|projector]] used for generating projections || ||recon ||string ||The [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Reconstructor.html|reconstructor]] used for performing 3D reconstruction || ||sep ||int ||The number of classes each particles can be associated with || ||shrink ||int ||The shrink factor applied to particles prior to generation of the similarity matrix (e2simmx.py) || ||simalign ||string ||The main [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Aligner.html|aligner]] used during similarity matrix generation || ||simalignargs ||string ||simalign (aligner) parameters || ||simaligncmp ||string ||The [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Cmp.html|comparator]] used by the main aligner during similarity matrix generation || ||simaligncmpargs ||string ||simaligncmp ([[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Cmp.html|comparator]]) parameters || ||simcmp ||string ||The [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Cmp.html|comparator]] used to generate the final score which is stored in the similarity matrix || ||simcmpargs ||string ||simcmp ([[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Cmp.html|comparator]]) parameters || ||simralign ||string ||The refinement aligners used during similarity matrix generation || ||simralignargs ||string ||simralign (aligner) parameters || ||simraligncmp ||string ||The [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Cmp.html|comparator]] used by the refine align in similarity matrix generation || ||simraligncmpargs ||string ||simraligncmp ([[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Cmp.html|comparator]]) arguments || ||symname ||string ||Symmetry type, i.e. c,d,icos etc || ||symnumber ||string ||Symmetry number ("","1","2" and so on) || ||usefilt_choice ||string ||Most recently chosen usefilt option || ||usefilt_string ||string ||Most recently specified usefilt filename || ==== emform.e2refine2d ==== ||filenames ||string list ||The most recently selected/specified files used to create the input stack from within the workflow setting || ||initial ||string ||Name of file containing initial class averages || ||iter ||int ||The number of refinement iterations || ||iterclassav ||int ||The number of iterations to perform when performing class averaging || ||naliref ||int ||e2refine2d argument || ||nbasisfp ||int ||e2refine2d argument || ||ncls ||int ||The number of classes to produce || ||normproj ||boolean ||e2refine2d argument || ||parallel ||int ||The number of available CPUs || ||particle_set_choice ||string ||Stores which data set the user chose to supply as main input into the refinement process (e.g. Wiener, phase flipped, etc) || ||shrink ||int ||Shrink factor for speed || ||simalign ||string ||The main [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Aligner.html|aligner]] used during similarity matrix generation || ||simalignargs ||string ||simalign (aligner) parameters || ||simaligncmp ||string ||The [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Cmp.html|comparator]] used by the main aligner during similarity matrix generation || ||simaligncmpargs ||string ||simaligncmp ([[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Cmp.html|comparator]]) parameters || ||simcmp ||string ||The [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Cmp.html|comparator]] used to generate the final score which is stored in the similarity matrix || ||simcmpargs ||string ||simcmp ([[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Cmp.html|comparator]]) parameters || ||simralign ||string ||The refinement aligners used during similarity matrix generation || ||simralignargs ||string ||simralign (aligner) parameters || ||simraligncmp ||string ||The [[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Cmp.html|comparator]] used by the refine align in similarity matrix generation || ||simraligncmpargs ||string ||simraligncmp ([[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1Cmp.html|comparator]]) arguments || This dictionary stores the most recently used parameters associated with 2D refinement in [[e2workflow|e2workflow.py]] === These parameters can be found in bdb:raw_data# === The raw_directory is used by e2workflow.py for storing imported micrograph/CCD data. The image file tag (e.g. the file tag of /home/somewhere/something.mrc is "something") may be used to access the image, for example {{{#!python a = EMData("bdb:raw_data#something",0) b = EMData() b.read_image("bdb:raw_data#something",0) }}} === These parameters can be found in bdb:particles# === The short story is e2boxer stores particles in this directory, it uses a naming convention where "_ptcls" is appended to the end of the input image names. e2ctf stores particles in this directory and appends "_ctf_flip" or "_ctf_wiener", depending whether the output data are phase flipped or Wiener filtered. The longer story is - The particles directory is used by e2ctf, e2boxer and e2workflow for storing boxed particle data that has optionally been filtered. In general e2boxer will be the first program that stores data here, and it can be done in a number of ways. People can save directly to the particles directory from e2boxer using the 'write box particle images' button (name may be different) and by making sure the output format is 'bdb'. e2boxer can also be used from the command line for writing output (output format is a command line argument). This is precisely what occurs from the context of e2workflow, which spawns output writing processes using e2boxer. Note that a naming convention is employed by e2boxer - if the input image names is something.mrc or "bdb:raw_data#something" then the output particles will be written using the filename "something_ptcls". You can access these images from Python using any of these approaches: {{{#!python a = EMData.read_images("bdb:raw_data#something_ptcls",[]) n = EMUtil.get_image_count("bdb:raw_data#something_ptcls") images = [] for i in range(n): images.append(EMData("bdb:raw_data#something_ptcls",i)) }}} e2ctf will also store filtered particle images in the this directory, and these will be either phase flipped or Wiener filtered. Note that the Wiener filtered data are also phase flipped. These particles are stored in the database with "_ctf_flip" and "_ctf_wiener" appended to the input file names, respectively. === These parameters can be found in bdb:e2boxercache# === The e2boxercache directory has many dedicated particle stacks in it. The currently existing stacks are listed in this table ||exclusion_image ||[[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1EMData.html|EMData]] database ||A binary exclusion image, in shrunken image coordinates || ||image_thumb ||[[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1EMData.html|EMData]] database ||A thumbnail of the image || ||subsampled_image ||[[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1EMData.html|EMData]] database ||A subsampled version of the image generated by the Gauss mode - Sparx group please add details || ||coarse_flat_image ||[[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1EMData.html|EMData]] database ||A coarsened version of the image that has its background flattened || ||coarse_sigma_image ||[[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1EMData.html|EMData]] database ||A specialized image that stores the inverse of the local pixel standard deviation - should probably called inverse_sigma_image - this image is in shrunken image coordinates and is used to normalize the correlation image (Roseman). Note that pixels representing 0 standard deviation are left unchanged || ||flcf_image ||[[http://blake.bcm.edu/eman2/doxygen_html/classEMAN_1_1EMData.html|EMData]] database ||Locally normalized correlation image (Roseman, Ultramicroscopy) || see also [[#e2boxer.cache|the e2boxer.cache database]].