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Index

A

angast (CTF attribute) append_micrograph_id() (MetaDB.Session method) append_twodclasses_id() (MetaDB.Session method)

avgrot (AVGROT attribute) AVGROT (class in pyp.streampyp.metadb_daemon) avgrot_noastig (AVGROT attribute)

B

BOXX (class in pyp.streampyp.metadb_daemon)

C

cat() (in module pyp.utils) (in module pyp.utils.core) cc (CTF attribute) ccc (CTF attribute) cccc (CTF attribute) cls (BOXX attribute) count() (MetaDB.Micrographs method) (MetaDB.TwoDClassesCollection method)

count_micrographs() (MetaDB.Session method) counts (CTF attribute) create() (MetaDB.Micrograph method) (MetaDB.Session method) (MetaDB.TwoDClasses method) CTF (class in pyp.streampyp.metadb_daemon) ctf_fit (AVGROT attribute)

D

delete_all() (MetaDB.Micrographs method) (MetaDB.TwoDClassesCollection method)

df1 (CTF attribute) df2 (CTF attribute)

E

emit() (MongoHandler method) exists() (MetaDB.Micrograph method) (MetaDB.Session method) (MetaDB.TwoDClasses method)

F

flatten() (in module pyp.utils) (in module pyp.utils.core)

format() (MongoFormatter method) freq (AVGROT attribute)

G

get() (MetaDB.Micrographs method) (MetaDB.Sessions method) (MetaDB.TwoDClassesCollection method) get_avgrot() (MetaDB.Micrograph method) get_boxx() (MetaDB.Micrograph method) get_ctf() (MetaDB.Micrograph method) get_micrograph_ids() (MetaDB.Session method)

get_project_root() (in module pyp.utils.core) get_pyp_config() (MetaDB.Session method) get_relative_path() (in module pyp.utils.core) get_src_path() (in module pyp.utils.core) get_twodclasses_ids() (MetaDB.Session method) get_updated() (MetaDB.Session method) get_xf() (MetaDB.Micrograph method)

H

h (BOXX attribute)

has_files() (in module pyp.utils.core)

I

in_bounds (BOXX attribute)

L

logger() (Timer method)

M

magnification (CTF attribute) makedirs_list() (in module pyp.utils.core) mat00 (XF attribute) mat01 (XF attribute) mat10 (XF attribute) mat11 (XF attribute) mean_df (CTF attribute) MetaDB (class in pyp.streampyp.metadb_daemon) MetaDB.Micrograph (class in pyp.streampyp.metadb_daemon) MetaDB.Micrographs (class in pyp.streampyp.metadb_daemon) MetaDB.Session (class in pyp.streampyp.metadb_daemon) MetaDB.Sessions (class in pyp.streampyp.metadb_daemon) MetaDB.TwoDClasses (class in pyp.streampyp.metadb_daemon) MetaDB.TwoDClassesCollection (class in pyp.streampyp.metadb_daemon) micrograph() (MetaDB.Session method) module pyp pyp.analysis pyp.analysis.geometry.transformations pyp.inout pyp.refine pyp.refine.csp pyp.refine.eman pyp.refine.frealign pyp.refine.relion pyp.refine.tomo_avg pyp.stream pyp.streampyp pyp.streampyp.metadb_daemon pyp.system pyp.system.mongo_handler pyp.utils pyp.utils.core pyp.utils.timer

MongoFormatter (class in pyp.system.mongo_handler) MongoHandler (class in pyp.system.mongo_handler) movie2regex() (in module pyp.utils.core)

N

name (Timer attribute)

noise (AVGROT attribute)

O

open() (in module pyp.streampyp.metadb_daemon)

P

pixel_size (CTF attribute) pyp module pyp.analysis module pyp.analysis.geometry.transformations module pyp.inout module pyp.refine module pyp.refine.csp module pyp.refine.eman module pyp.refine.frealign module pyp.refine.relion module

pyp.refine.tomo_avg module pyp.stream module pyp.streampyp module pyp.streampyp.metadb_daemon module pyp.system module pyp.system.mongo_handler module pyp.utils module pyp.utils.core module pyp.utils.timer module

Q

quality_fit (AVGROT attribute)

S

session() (MetaDB method) set_avgrot() (MetaDB.Micrograph method) set_boxx() (MetaDB.Micrograph method) set_ctf() (MetaDB.Micrograph method) set_micrograph_ids() (MetaDB.Session method) set_pyp_config() (MetaDB.Session method)

set_twodclasses_ids() (MetaDB.Session method) set_updated_now() (MetaDB.Session method) set_xf() (MetaDB.Micrograph method) start() (Timer method) stop() (Timer method) symlink_force() (in module pyp.utils.core) symlink_relative() (in module pyp.utils.core)

T

text (Timer attribute) Timer (class in pyp.utils.timer) TimerError

timers (Timer attribute) to() (MongoHandler class method) twodclasses() (MetaDB.Session method)

U

update() (MetaDB.Micrographs method) (MetaDB.Sessions method) (MetaDB.TwoDClassesCollection method)

V

voltage (CTF attribute)

W

w (BOXX attribute) write() (MetaDB.Micrographs method) (MetaDB.Sessions method) (MetaDB.TwoDClassesCollection method)

X

x (BOXX attribute) (CTF attribute) (XF attribute)

XF (class in pyp.streampyp.metadb_daemon)

Y

y (BOXX attribute) (CTF attribute) (XF attribute)

Z

z (CTF attribute)