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OSCEM metadata #38

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b153a90
Initial step
lolasanchezzz Jul 5, 2024
2b51262
First part of json generation implemented
lolasanchezzz Jul 9, 2024
cfd749c
First part of json generation implemented
lolasanchezzz Jul 9, 2024
81c2816
Test and protocol refinement
lolasanchezzz Jul 10, 2024
5b7554f
Completing test functions
lolasanchezzz Jul 12, 2024
0d98a68
Completing 6 test functions for protocol
lolasanchezzz Jul 16, 2024
7a4658c
Correcting errors in names
lolasanchezzz Jul 16, 2024
d108c36
Adding histograms generation
lolasanchezzz Jul 17, 2024
5bfa866
Modifying histograms generation
lolasanchezzz Jul 17, 2024
1fa64d6
Addition of particle picking section in json
lolasanchezzz Jul 17, 2024
7ed67be
Addition of Set of particles section and test
lolasanchezzz Jul 19, 2024
5b67045
Addition of setof2Dclasses to protocol
lolasanchezzz Jul 19, 2024
c9aa4ff
Addition of setof2Dclasses to test
lolasanchezzz Jul 19, 2024
37695ef
Updating workflow until setofparticles
lolasanchezzz Jul 22, 2024
301199d
Extending test to initial volume generation
lolasanchezzz Jul 23, 2024
958973c
Extending protocol to 3D classes generation
lolasanchezzz Jul 23, 2024
8651db9
Correcting error in runAlignVol()
lolasanchezzz Jul 23, 2024
c5201af
Reducing test workflow
lolasanchezzz Jul 24, 2024
02187ff
Solving particle histogram error
lolasanchezzz Jul 29, 2024
53c3e98
Re-doing histograms
lolasanchezzz Jul 29, 2024
778859f
Reducing number of tests
lolasanchezzz Jul 29, 2024
a0c1700
new test_data
lolasanchezzz Jul 29, 2024
18c7f51
Finished Classes 2D part
lolasanchezzz Jul 31, 2024
670a122
Updated Classes 2D part
lolasanchezzz Jul 31, 2024
e66e645
Adding initial volume generation part
lolasanchezzz Aug 1, 2024
5a87fb9
Adding classes 3D generation part
lolasanchezzz Aug 1, 2024
bd5ddcf
Adding another option for classes 3D generation
lolasanchezzz Aug 2, 2024
cca114e
Adding initial volume and final test data
lolasanchezzz Aug 2, 2024
f6e823e
Adding units and rounding decimals
lolasanchezzz Aug 21, 2024
1158e94
Adding units to test
lolasanchezzz Aug 21, 2024
1c7c750
Adding units protocol and adding properties in import movies
lolasanchezzz Aug 22, 2024
dd6dd92
Adding histogram for shifts
lolasanchezzz Aug 22, 2024
b87dc91
Adding getting number of particles
lolasanchezzz Aug 22, 2024
3789f06
modifying test data
lolasanchezzz Aug 22, 2024
f082ce5
modifying for gain image
lolasanchezzz Aug 23, 2024
fdfa374
changes in protocol, test and file names
lolasanchezzz Aug 23, 2024
a0cd478
Minor adjustments and unit changes
lolasanchezzz Aug 26, 2024
559ce7e
Shift histogram adjustment
lolasanchezzz Sep 2, 2024
11645d6
classes3D help and volume squeeze
lolasanchezzz Sep 4, 2024
ead7610
change in protocol name
lolasanchezzz Sep 10, 2024
57727d7
update changes.txt
lolasanchezzz Sep 10, 2024
82380aa
update version
lolasanchezzz Sep 10, 2024
d7b25d8
update genereateChimeraView function
lolasanchezzz Sep 10, 2024
d9e6eeb
update max_shift function
lolasanchezzz Sep 10, 2024
2229692
update import_movies function
lolasanchezzz Sep 10, 2024
8eeb9f4
add ylabel of histograms as variable
lolasanchezzz Sep 10, 2024
5f8a35b
add function to generate isosurfaces
lolasanchezzz Sep 10, 2024
0506441
add function for CTF comparison part
lolasanchezzz Sep 10, 2024
3e54a85
update to reduce duplications
lolasanchezzz Sep 10, 2024
f1e7211
function to launch protocol and load json
lolasanchezzz Sep 10, 2024
8b73d04
add condition for particles per class
lolasanchezzz Sep 11, 2024
60abb97
creating micrographs examples for defocus and particles
lolasanchezzz Sep 20, 2024
7ff554f
solve error in input of protocol
lolasanchezzz Sep 20, 2024
b136431
change .png by .jpg
lolasanchezzz Sep 23, 2024
5f3cea2
update in the creation of example micrographs
lolasanchezzz Sep 26, 2024
9d49816
update comments in particle picking
lolasanchezzz Sep 27, 2024
53a793a
updated comments in particle picking
lolasanchezzz Sep 27, 2024
4dfd8ab
change amplitude contrast to ctf_estimation section
lolasanchezzz Oct 11, 2024
5f0366f
change to value-unit system in import movies section
lolasanchezzz Oct 11, 2024
eff4a78
change to value-unit system in movie alignment section
lolasanchezzz Oct 11, 2024
0a0fe95
remove commented code in movie alignment
lolasanchezzz Oct 11, 2024
c1d8143
change to value-unit system in max shift section
lolasanchezzz Oct 11, 2024
ab0ada0
change to value-unit system in CTF estimation section
lolasanchezzz Oct 11, 2024
56e0ad7
update test for value-unit system
lolasanchezzz Oct 15, 2024
4cc5957
update import movies removing repeated properties in schemas
lolasanchezzz Oct 16, 2024
f45b413
json to yaml
lolasanchezzz Nov 20, 2024
a0b9117
update to new movies format
lolasanchezzz Nov 20, 2024
1076a4d
update to new classes 2D format
lolasanchezzz Nov 20, 2024
5920597
update to new classes 3D format
lolasanchezzz Nov 20, 2024
cead1d6
update to new volume format
lolasanchezzz Nov 21, 2024
25a21c8
add micrographs section
lolasanchezzz Nov 21, 2024
46f866f
update to accept multiple volumes as input
lolasanchezzz Nov 22, 2024
e0e8b43
update to retrieve particles number in volumes
lolasanchezzz Nov 25, 2024
3340b82
solve misspellings
lolasanchezzz Nov 25, 2024
5f1bc8f
add pyyaml in requirements.txt
lolasanchezzz Nov 26, 2024
8b37f98
update in particles num for volumes
lolasanchezzz Nov 26, 2024
cd0ba35
update in classes and slots format
lolasanchezzz Nov 27, 2024
39bfb64
add resolution to volume
lolasanchezzz Nov 27, 2024
d1e7569
minor changes for micro examples image
lolasanchezzz Nov 28, 2024
16e768e
change enhanced by sharpened
lolasanchezzz Nov 28, 2024
3612991
update resolution calculation
lolasanchezzz Dec 3, 2024
8ab7ca4
update test data and lower cases
lolasanchezzz Dec 10, 2024
d694bf6
update resolution calculation
lolasanchezzz Dec 10, 2024
6c6f956
working tests with yaml input
lolasanchezzz Dec 10, 2024
638ab9a
change to lower case
lolasanchezzz Dec 11, 2024
97a5585
update min-max resolution
lolasanchezzz Dec 11, 2024
2d9e9c2
Clean up: Remove unnecessary comments and commented-out code
lolasanchezzz Dec 11, 2024
7491dbb
change volumes input order
lolasanchezzz Dec 12, 2024
4d2ab0b
updated workflow
lolasanchezzz Dec 12, 2024
b6c5b5c
clean up of commented code
lolasanchezzz Dec 12, 2024
f5e69a0
add summary with metadata file path
lolasanchezzz Dec 16, 2024
2daf30c
update function names removing 'json'
lolasanchezzz Dec 16, 2024
b96b3ab
included resolution unit in volumes
lolasanchezzz Dec 16, 2024
d2325a6
solved error with micrograph number
lolasanchezzz Dec 19, 2024
2d8c40a
updated data folder name for test
lolasanchezzz Jan 15, 2025
898fd45
Merge branch 'devel' into LS_OSCEM
albertmena Jan 28, 2025
2edc976
Update CHANGES.txt
albertmena Jan 28, 2025
9ad0b2b
constant defined for help of threshold for volumes
lolasanchezzz Jan 31, 2025
3dac3d0
constant defined for orthogonal slices file names
lolasanchezzz Jan 31, 2025
95ae8b9
Merge remote-tracking branch 'origin/LS_OSCEM' into LS_OSCEM
lolasanchezzz Jan 31, 2025
6259d74
removed commented line for json generation
lolasanchezzz Feb 4, 2025
e4a832d
merged equal branches om recursive_compare function
lolasanchezzz Feb 4, 2025
68a9be4
replaced the unused local variable "H_jpg" with "_".
lolasanchezzz Feb 4, 2025
340e287
refactored generateChimeraView by removing unnecessary input variables
lolasanchezzz Feb 4, 2025
8015f9c
reduced if conditions in import movies function
lolasanchezzz Feb 4, 2025
a592537
functions created for movie import descriptors
lolasanchezzz Feb 4, 2025
cebdb4a
changed if conditions out of import movie descriptors functions
lolasanchezzz Feb 5, 2025
a2444c4
refactored computation of average and max shift in movie alignment
lolasanchezzz Feb 5, 2025
e323ad4
refactor loop to reduce nesting in movie alignment
lolasanchezzz Feb 5, 2025
be4d40e
removed debug print statement in max shift section
lolasanchezzz Feb 5, 2025
ff55779
Refactor dictionary creation to simplify conditional logic in movie a…
lolasanchezzz Feb 5, 2025
52d4249
refactored recursive_compare function dividing in into functions to r…
lolasanchezzz Feb 5, 2025
0e01c35
added "processing" section in the metadata schema
lolasanchezzz Feb 5, 2025
66897c7
added _devStatus
lolasanchezzz Feb 5, 2025
9d1b4b1
updated all variables names containing 'jsons' to 'metadata'
lolasanchezzz Feb 5, 2025
ae1f409
renamed 'micrograph_examples' slot to 'defocus_micrograph_examples'
lolasanchezzz Feb 6, 2025
7c28525
renamed 'resolution' slot to 'vol_resolution' in volume
lolasanchezzz Feb 6, 2025
6945903
renamed resolution slot volumes
lolasanchezzz Feb 6, 2025
8d49d74
renamed particles per class slot in 2D and 3D classes
lolasanchezzz Feb 6, 2025
3c91d4f
renamed 'number_particles' slot to 'vol_number_particles' in volumes
lolasanchezzz Feb 6, 2025
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6 changes: 5 additions & 1 deletion CHANGES.txt
Original file line number Diff line number Diff line change
@@ -1,4 +1,8 @@
V3.1.0
V3.2.0
- Add OSCEM metadata protocol
- Add streaming protocols: Data counter and Data sampler

V3.1.0
- Monitor summary: validation for publish command
- Monitor summary: verbose error if publish command fails
- Updated workflow template
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2 changes: 1 addition & 1 deletion emfacilities/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@

from .constants import *

__version__ = "3.1.1"
__version__ = "3.2.0"
_logo = "facilityLogo.png"
_references = ["delaRosaTrevin201693"]

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4 changes: 1 addition & 3 deletions emfacilities/protocols/__init__.py
Original file line number Diff line number Diff line change
@@ -1,16 +1,14 @@

from .protocol_OSCEM_metadata import ProtOSCEM
from .protocol_data_counter import ProtDataCounter
from .protocol_data_sampler import ProtDataSampler
from .protocol_monitor import ProtMonitor, Monitor, PrintNotifier
from .protocol_monitor_system import SYSTEM_LOG_SQLITE

from .protocol_monitor_summary import ProtMonitorSummary
from .summary_provider import SummaryProvider

from .protocol_monitor_ctf import ProtMonitorCTF, MonitorCTF, CTF_LOG_SQLITE
from .protocol_monitor_system import ProtMonitorSystem
from .protocol_monitor_movie_gain import ProtMonitorMovieGain, MonitorMovieGain

from .protocol_monitor_2d_streamer import ProtMonitor2dStreamer
from .protocol_good_classes_extractor import ProtGoodClassesExtractor
from .protocol_volume_extractor import ProtVolumeExtractor
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