Contents

pyp.streampyp package

pyp.streampyp package

Submodules

pyp.streampyp.jobs module

pyp.streampyp.logging module

pyp.streampyp.metadb_daemon module

class AVGROT(freq, avgrot_noastig, avgrot, ctf_fit, quality_fit, noise)[source]

Bases: tuple

avgrot[source]

Alias for field number 2

avgrot_noastig[source]

Alias for field number 1

ctf_fit[source]

Alias for field number 3

freq[source]

Alias for field number 0

noise[source]

Alias for field number 5

quality_fit[source]

Alias for field number 4

class BOXX(x, y, w, h, in_bounds, cls)[source]

Bases: tuple

cls[source]

Alias for field number 5

h[source]

Alias for field number 3

in_bounds[source]

Alias for field number 4

w[source]

Alias for field number 2

x[source]

Alias for field number 0

y[source]

Alias for field number 1

class CTF(mean_df, cc, df1, df2, angast, ccc, x, y, z, pixel_size, voltage, magnification, cccc, counts)[source]

Bases: tuple

angast[source]

Alias for field number 4

cc[source]

Alias for field number 1

ccc[source]

Alias for field number 5

cccc[source]

Alias for field number 12

counts[source]

Alias for field number 13

df1[source]

Alias for field number 2

df2[source]

Alias for field number 3

magnification[source]

Alias for field number 11

mean_df[source]

Alias for field number 0

pixel_size[source]

Alias for field number 9

voltage[source]

Alias for field number 10

x[source]

Alias for field number 6

y[source]

Alias for field number 7

z[source]

Alias for field number 8

class MetaDB(timeout_ms=30000)[source]

Bases: object

class Micrograph(db, session, id)[source]

Bases: object

create(created)[source]

Create a new micrograph, or re-create an existing micrograph.

Parameters

created (int) – Creation time of the micrograph, in milliseconds since the Unix epoch

exists()[source]

Return True iff the micrograph has already been created.

get_avgrot()[source]
Return type

list[AVGROT]

get_boxx()[source]
Return type

list[BOXX]

get_ctf()[source]
Return type

CTF

get_xf()[source]
Return type

list[XF]

set_avgrot(avgrot)[source]
set_boxx(boxx)[source]
set_ctf(ctf)[source]
set_xf(xf)[source]
class Micrographs(db)[source]

Bases: object

count(group_id, session_id)[source]
delete_all(group_id, session_id)[source]
get(group_id, session_id, micrograph_id)[source]
update(group_id, session_id, micrograph_id, update_doc)[source]
write(group_id, session_id, micrograph_id, doc)[source]
class Session(db, group_id, session_id)[source]

Bases: object

append_micrograph_id(id)[source]
append_twodclasses_id(id)[source]
count_micrographs()[source]

Count the number of micrographs that have been created, not the number of micrograph IDs saved to the session.

Return type

int

create(created)[source]

Create a new session, or re-create an existing session.

Parameters

created (int) – Creation time of the session, in milliseconds since the Unix epoch

exists()[source]

Return True iff the session has already been created.

get_micrograph_ids()[source]
Return type

list[str]

get_pyp_config()[source]
Return type

list[str]

get_twodclasses_ids()[source]
Return type

list[str]

get_updated()[source]

Gets the ‘updated’ timestamp for the session, in milliseconds since the Unix epoch :rtype: int

micrograph(id)[source]
set_micrograph_ids(ids)[source]
set_pyp_config(config)[source]
set_twodclasses_ids(ids)[source]
set_updated_now()[source]

Sets the ‘updated’ timestamp for the session.

twodclasses(id)[source]
class Sessions(db)[source]

Bases: object

get(group_id, session_id)[source]
update(group_id, session_id, update_doc)[source]
write(group_id, session_id, doc)[source]
class TwoDClasses(db, session, id)[source]

Bases: object

create(created, width, height)[source]

Create a new 2D classes image, or re-create an existing 2D classes image.

Parameters

  • created (int) – Creation time of the 2D classes image, in milliseconds since the Unix epoch

  • width (int) – Width of the image, in pixels

  • height (int) – Height of the image, in pixels

exists()[source]

Return True iff the 2D Classes has not already been created.

class TwoDClassesCollection(db)[source]

Bases: object

count(group_id, session_id)[source]
delete_all(group_id, session_id)[source]
get(group_id, session_id, twodclasses_id)[source]
update(group_id, session_id, twodclasses_id, update_doc)[source]
write(group_id, session_id, twodclasses_id, doc)[source]
session(group_id, session_id)[source]
class XF(mat00, mat01, mat10, mat11, x, y)[source]

Bases: tuple

mat00[source]

Alias for field number 0

mat01[source]

Alias for field number 1

mat10[source]

Alias for field number 2

mat11[source]

Alias for field number 3

x[source]

Alias for field number 4

y[source]

Alias for field number 5

open(**kwargs)[source]

pyp.streampyp.web module

Module contents