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| ==== e2ctf.misc ==== ||envelope||list of (x,y) tuples||Computed Envelope*StrucFact curve from CTF maxima from all sets processed during one run|| |
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.micrograph_ccd_filenames |
list of strings |
All micrograph and/or CCD data file names that are associated with a project |
global.imported_micrograph_ccd_files |
list of strings |
All micrograph and/or CCD data file names that have been imported into the raw_data directory using the e2workflow import mechanism |
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 |
EMAN2Ctf object |
An EMAN2Ctf object associated with each filename (without extension) |
e2ctf.misc
envelope |
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.
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 |
EMData |
stores the image generated by the boxertools.CoarsenedFlattenedImage object that is associated with this image |
filename_DD.exclusion_image |
EMData |
stores the binary exclusion image that is associated with this image |
filename_DD.flcf_image |
EMData |
stores the image generated by the boxertools.FLCFImage 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 tag of the image (e.g. hdf, mrc, dm3). This information can be used to check that the user is not trying to box images that have the same file name (minus the tag). This feature should become deprecated |
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.subsampled_image |
EMData |
stores the image generated by the boxertools.SincBlackmanSubsampledImage object that is associated with this image |
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. |