Code

OSCEM metadata#38

Code

Open

lolasanchezzz wants to merge 120 commits intodevelscipion-em/scipion-em-facilities:develfrom LS_OSCEMscipion-em/scipion-em-facilities:LS_OSCEMCopy head branch name to clipboard

+2,039-32

Commits

Commits on Jul 5, 2024

• Initial step

  lolasanchezzz

  committed
  b153a90

  Copy full SHA for b153a90

Commits on Jul 9, 2024

• First part of json generation implemented

  lolasanchezzz

  committed
  2b51262

  Copy full SHA for 2b51262

• First part of json generation implemented

  lolasanchezzz

  committed
  cfd749c

  Copy full SHA for cfd749c

Commits on Jul 10, 2024

• Test and protocol refinement

  lolasanchezzz

  committed
  81c2816

  Copy full SHA for 81c2816

Commits on Jul 12, 2024

• Completing test functions

  lolasanchezzz

  committed
  5b7554f

  Copy full SHA for 5b7554f

Commits on Jul 16, 2024

• Completing 6 test functions for protocol

  lolasanchezzz

  committed
  0d98a68

  Copy full SHA for 0d98a68

• Correcting errors in names

  lolasanchezzz

  committed
  7a4658c

  Copy full SHA for 7a4658c

Commits on Jul 17, 2024

• Adding histograms generation

  lolasanchezzz

  committed
  d108c36

  Copy full SHA for d108c36

• Modifying histograms generation

  lolasanchezzz

  committed
  5bfa866

  Copy full SHA for 5bfa866

• Addition of particle picking section in json

  lolasanchezzz

  committed
  1fa64d6

  Copy full SHA for 1fa64d6

Commits on Jul 19, 2024

• Addition of Set of particles section and test

  lolasanchezzz

  committed
  7ed67be

  Copy full SHA for 7ed67be

• Addition of setof2Dclasses to protocol

  lolasanchezzz

  committed
  5b67045

  Copy full SHA for 5b67045

• Addition of setof2Dclasses to test

  lolasanchezzz

  committed
  c9aa4ff

  Copy full SHA for c9aa4ff

Commits on Jul 22, 2024

• Updating workflow until setofparticles

  lolasanchezzz

  committed
  37695ef

  Copy full SHA for 37695ef

Commits on Jul 23, 2024

• Extending test to initial volume generation

  lolasanchezzz

  committed
  301199d

  Copy full SHA for 301199d

• Extending protocol to 3D classes generation

  lolasanchezzz

  committed
  958973c

  Copy full SHA for 958973c

• Correcting error in runAlignVol()

  lolasanchezzz

  committed
  8651db9

  Copy full SHA for 8651db9

Commits on Jul 24, 2024

• Reducing test workflow

  lolasanchezzz

  committed
  c5201af

  Copy full SHA for c5201af

Commits on Jul 29, 2024

• Solving particle histogram error

  lolasanchezzz

  committed
  02187ff

  Copy full SHA for 02187ff

• Re-doing histograms

  lolasanchezzz

  committed
  53c3e98

  Copy full SHA for 53c3e98

• Reducing number of tests

  lolasanchezzz

  committed
  778859f

  Copy full SHA for 778859f

• new test_data

  lolasanchezzz

  committed
  a0c1700

  Copy full SHA for a0c1700

Commits on Jul 31, 2024

• Finished Classes 2D part

  lolasanchezzz

  committed
  18c7f51

  Copy full SHA for 18c7f51

• Updated Classes 2D part

  lolasanchezzz

  committed
  670a122

  Copy full SHA for 670a122

Commits on Aug 1, 2024

• Adding initial volume generation part

  lolasanchezzz

  committed
  e66e645

  Copy full SHA for e66e645

• Adding classes 3D generation part

  lolasanchezzz

  committed
  5a87fb9

  Copy full SHA for 5a87fb9

Commits on Aug 2, 2024

• Adding another option for classes 3D generation

  lolasanchezzz

  committed
  bd5ddcf

  Copy full SHA for bd5ddcf

• Adding initial volume and final test data

  lolasanchezzz

  committed
  cca114e

  Copy full SHA for cca114e

Commits on Aug 21, 2024

• Adding units and rounding decimals

  lolasanchezzz

  committed
  f6e823e

  Copy full SHA for f6e823e

• Adding units to test

  lolasanchezzz

  committed
  1158e94

  Copy full SHA for 1158e94

Commits on Aug 22, 2024

• Adding units protocol and adding properties in import movies

  lolasanchezzz

  committed
  1c7c750

  Copy full SHA for 1c7c750

• Adding histogram for shifts

  lolasanchezzz

  committed
  dd6dd92

  Copy full SHA for dd6dd92

• Adding getting number of particles

  lolasanchezzz

  committed
  b87dc91

  Copy full SHA for b87dc91

• modifying test data

  lolasanchezzz

  committed
  3789f06

  Copy full SHA for 3789f06

Commits on Aug 23, 2024

• modifying for gain image

  lolasanchezzz

  committed
  f082ce5

  Copy full SHA for f082ce5

• changes in protocol, test and file names

  lolasanchezzz

  committed
  fdfa374

  Copy full SHA for fdfa374

Commits on Aug 26, 2024

• Minor adjustments and unit changes

  lolasanchezzz

  committed
  a0cd478

  Copy full SHA for a0cd478

Commits on Sep 2, 2024

• Shift histogram adjustment

  lolasanchezzz

  committed
  559ce7e

  Copy full SHA for 559ce7e

Commits on Sep 4, 2024

• classes3D help and volume squeeze

  lolasanchezzz

  committed
  11645d6

  Copy full SHA for 11645d6

Commits on Sep 10, 2024

• change in protocol name

  lolasanchezzz

  committed
  ead7610

  Copy full SHA for ead7610

• update changes.txt

  lolasanchezzz

  committed
  57727d7

  Copy full SHA for 57727d7

• update version

  lolasanchezzz

  committed
  82380aa

  Copy full SHA for 82380aa

• update genereateChimeraView function

  lolasanchezzz

  committed
  d7b25d8

  Copy full SHA for d7b25d8

• update max_shift function

  lolasanchezzz

  committed
  d9e6eeb

  Copy full SHA for d9e6eeb

• update import_movies function

  lolasanchezzz

  committed
  2229692

  Copy full SHA for 2229692

• add ylabel of histograms as variable

  lolasanchezzz

  committed
  8eeb9f4

  Copy full SHA for 8eeb9f4

• add function to generate isosurfaces

  lolasanchezzz

  committed
  5f8a35b

  Copy full SHA for 5f8a35b

• add function for CTF comparison part

  lolasanchezzz

  committed
  0506441

  Copy full SHA for 0506441

• update to reduce duplications

  lolasanchezzz

  committed
  3e54a85

  Copy full SHA for 3e54a85

• function to launch protocol and load json

  lolasanchezzz

  committed
  f1e7211

  Copy full SHA for f1e7211

Commits on Sep 11, 2024

• add condition for particles per class

  lolasanchezzz

  committed
  8b73d04

  Copy full SHA for 8b73d04

Commits on Sep 20, 2024

• creating micrographs examples for defocus and particles

  lolasanchezzz

  committed
  60abb97

  Copy full SHA for 60abb97

• solve error in input of protocol

  lolasanchezzz

  committed
  7ff554f

  Copy full SHA for 7ff554f

Commits on Sep 23, 2024

• change .png by .jpg

  lolasanchezzz

  committed
  b136431

  Copy full SHA for b136431

Commits on Sep 26, 2024

• update in the creation of example micrographs

  lolasanchezzz

  committed
  5f3cea2

  Copy full SHA for 5f3cea2

Commits on Sep 27, 2024

• update comments in particle picking

  lolasanchezzz

  committed
  9d49816

  Copy full SHA for 9d49816

• updated comments in particle picking

  lolasanchezzz

  committed
  53a793a

  Copy full SHA for 53a793a

Commits on Oct 11, 2024

• change amplitude contrast to ctf_estimation section

  lolasanchezzz

  committed
  4dfd8ab

  Copy full SHA for 4dfd8ab

• change to value-unit system in import movies section

  lolasanchezzz

  committed
  5f0366f

  Copy full SHA for 5f0366f

• change to value-unit system in movie alignment section

  lolasanchezzz

  committed
  eff4a78

  Copy full SHA for eff4a78

• remove commented code in movie alignment

  lolasanchezzz

  committed
  0a0fe95

  Copy full SHA for 0a0fe95

• change to value-unit system in max shift section

  lolasanchezzz

  committed
  c1d8143

  Copy full SHA for c1d8143

• change to value-unit system in CTF estimation section

  lolasanchezzz

  committed
  ab0ada0

  Copy full SHA for ab0ada0

Commits on Oct 15, 2024

• update test for value-unit system

  lolasanchezzz

  committed
  56e0ad7

  Copy full SHA for 56e0ad7

Commits on Oct 16, 2024

• update import movies removing repeated properties in schemas

  lolasanchezzz

  committed
  4cc5957

  Copy full SHA for 4cc5957

Commits on Nov 20, 2024

• json to yaml

  lolasanchezzz

  committed
  f45b413

  Copy full SHA for f45b413

• update to new movies format

  lolasanchezzz

  committed
  a0b9117

  Copy full SHA for a0b9117

• update to new classes 2D format

  lolasanchezzz

  committed
  1076a4d

  Copy full SHA for 1076a4d

• update to new classes 3D format

  lolasanchezzz

  committed
  5920597

  Copy full SHA for 5920597

Commits on Nov 21, 2024

• update to new volume format

  lolasanchezzz

  committed
  cead1d6

  Copy full SHA for cead1d6

• add micrographs section

  lolasanchezzz

  committed
  25a21c8

  Copy full SHA for 25a21c8

Commits on Nov 22, 2024

• update to accept multiple volumes as input

  lolasanchezzz

  committed
  46f866f

  Copy full SHA for 46f866f

Commits on Nov 25, 2024

• update to retrieve particles number in volumes

  lolasanchezzz

  committed
  e0e8b43

  Copy full SHA for e0e8b43

• solve misspellings

  lolasanchezzz

  committed
  3340b82

  Copy full SHA for 3340b82

Commits on Nov 26, 2024

• add pyyaml in requirements.txt

  lolasanchezzz

  committed
  5f1bc8f

  Copy full SHA for 5f1bc8f

• update in particles num for volumes

  lolasanchezzz

  committed
  8b37f98

  Copy full SHA for 8b37f98

Commits on Nov 27, 2024

• update in classes and slots format

  lolasanchezzz

  committed
  cd0ba35

  Copy full SHA for cd0ba35

• add resolution to volume

  lolasanchezzz

  committed
  39bfb64

  Copy full SHA for 39bfb64

Commits on Nov 28, 2024

• minor changes for micro examples image

  lolasanchezzz

  committed
  d1e7569

  Copy full SHA for d1e7569

• change enhanced by sharpened

  lolasanchezzz

  committed
  16e768e

  Copy full SHA for 16e768e

Commits on Dec 3, 2024

• update resolution calculation

  lolasanchezzz

  committed
  3612991

  Copy full SHA for 3612991

Commits on Dec 10, 2024

• update test data and lower cases

  lolasanchezzz

  committed
  8ab7ca4

  Copy full SHA for 8ab7ca4

• update resolution calculation

  lolasanchezzz

  committed
  d694bf6

  Copy full SHA for d694bf6

• working tests with yaml input

  lolasanchezzz

  committed
  6c6f956

  Copy full SHA for 6c6f956

Commits on Dec 11, 2024

• change to lower case

  lolasanchezzz

  committed
  638ab9a

  Copy full SHA for 638ab9a

• update min-max resolution

  lolasanchezzz

  committed
  97a5585

  Copy full SHA for 97a5585

• Clean up: Remove unnecessary comments and commented-out code

  lolasanchezzz

  committed
  2d9e9c2

  Copy full SHA for 2d9e9c2

Commits on Dec 12, 2024

• change volumes input order

  lolasanchezzz

  committed
  7491dbb

  Copy full SHA for 7491dbb

• updated workflow

  lolasanchezzz

  committed
  4d2ab0b

  Copy full SHA for 4d2ab0b

• clean up of commented code

  lolasanchezzz

  committed
  b6c5b5c

  Copy full SHA for b6c5b5c

Commits on Dec 16, 2024

• add summary with metadata file path

  lolasanchezzz

  committed
  f5e69a0

  Copy full SHA for f5e69a0

• update function names removing 'json'

  lolasanchezzz

  committed
  2daf30c

  Copy full SHA for 2daf30c

• included resolution unit in volumes

  lolasanchezzz

  committed
  b96b3ab

  Copy full SHA for b96b3ab

Commits on Dec 19, 2024

• solved error with micrograph number

  lolasanchezzz

  committed
  d2325a6

  Copy full SHA for d2325a6

Commits on Jan 15, 2025

• updated data folder name for test

  lolasanchezzz

  committed
  2d8c40a

  Copy full SHA for 2d8c40a

Commits on Jan 28, 2025

• Merge branch 'devel' into LS_OSCEM

  albertmena

  authored
  898fd45

  Copy full SHA for 898fd45

• Update CHANGES.txt

  albertmena

  authored
  2edc976

  Copy full SHA for 2edc976

Commits on Jan 31, 2025

• constant defined for help of threshold for volumes

  lolasanchezzz

  committed
  9ad0b2b

  Copy full SHA for 9ad0b2b

• constant defined for orthogonal slices file names

  lolasanchezzz

  committed
  3dac3d0

  Copy full SHA for 3dac3d0

• Merge remote-tracking branch 'origin/LS_OSCEM' into LS_OSCEM

  lolasanchezzz

  committed
  95ae8b9

  Copy full SHA for 95ae8b9

Commits on Feb 4, 2025

• removed commented line for json generation

  lolasanchezzz

  committed
  6259d74

  Copy full SHA for 6259d74

• merged equal branches om recursive_compare function

  lolasanchezzz

  committed
  e4a832d

  Copy full SHA for e4a832d

• replaced the unused local variable "H_jpg" with "_".

  lolasanchezzz

  committed
  68a9be4

  Copy full SHA for 68a9be4

• refactored generateChimeraView by removing unnecessary input variables

  lolasanchezzz

  committed
  340e287

  Copy full SHA for 340e287

• reduced if conditions in import movies function

  lolasanchezzz

  committed
  8015f9c

  Copy full SHA for 8015f9c

• functions created for movie import descriptors

  lolasanchezzz

  committed
  a592537

  Copy full SHA for a592537

Commits on Feb 5, 2025

• changed if conditions out of import movie descriptors functions

  lolasanchezzz

  committed
  cebdb4a

  Copy full SHA for cebdb4a

• refactored computation of average and max shift in movie alignment

  lolasanchezzz

  committed
  a2444c4

  Copy full SHA for a2444c4

• refactor loop to reduce nesting in movie alignment

  lolasanchezzz

  committed
  e323ad4

  Copy full SHA for e323ad4

• removed debug print statement in max shift section

  lolasanchezzz

  committed
  be4d40e

  Copy full SHA for be4d40e

• Refactor dictionary creation to simplify conditional logic in movie alignment section

  lolasanchezzz

  committed
  ff55779

  Copy full SHA for ff55779

• refactored recursive_compare function dividing in into functions to reduce complexity

  lolasanchezzz

  committed
  52d4249

  Copy full SHA for 52d4249

• added "processing" section in the metadata schema

  lolasanchezzz

  committed
  0e01c35

  Copy full SHA for 0e01c35

• added _devStatus

  lolasanchezzz

  committed
  66897c7

  Copy full SHA for 66897c7

• updated all variables names containing 'jsons' to 'metadata'

  lolasanchezzz

  committed
  9d1b4b1

  Copy full SHA for 9d1b4b1

Commits on Feb 6, 2025

• renamed 'micrograph_examples' slot to 'defocus_micrograph_examples'

  lolasanchezzz

  committed
  ae1f409

  Copy full SHA for ae1f409

• renamed 'resolution' slot to 'vol_resolution' in volume

  lolasanchezzz

  committed
  7c28525

  Copy full SHA for 7c28525

• renamed resolution slot volumes

  lolasanchezzz

  committed
  6945903

  Copy full SHA for 6945903

• renamed particles per class slot in 2D and 3D classes

  lolasanchezzz

  committed
  8d49d74

  Copy full SHA for 8d49d74

• renamed 'number_particles' slot to 'vol_number_particles' in volumes

  lolasanchezzz

  committed
  3c91d4f

  Copy full SHA for 3c91d4f