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CHANGELOG.md

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  • 13/02/2020
    • Adding this CHANGELOG file
    • clean_out_data.sh: error correction for ab-inition data directories generation.
    • code/tutorials/synth_sumb/pre/gen_microsomes.py: error correction when the number of microsomes is greater than the number of processes.
    • Corrections in organizations analysis to fit synapse scripts.
  • 25/02/2020
    • Adding statistical analysis for filaments
  • 10/03/2020
    • Updating synapses colocalization routines
    • Adding /code/tutorials/exp_sumb/tracing
    • Bugs correction in /code/tutorials/synth_sumb/tracing/rec_particles.py
  • 16/03/2020
    • Adding AG and Kmeans (with PCA) to /code/tutorials/synth_sumb/class/plane_align_class.py
    • Creating /code/pyorg/diff_geom module
  • 17/03/2020
    • Git Nightly branch created
  • 20/03/2020
    • Adding filament and segmentations analysis in PyOrg
  • 21/03/2020
    • Bug correction in /code/tutorials/exp_sumb/pre/pre_tomo_seg.py
    • Improvement of clean_out_data.sh
    • Adding nighly branch to README.md
  • 26/03/2020
    • Adding file code/tutorials/synth_sumb/class/mbz_cly_mask.m
  • 30/03/2020
    • Correcting bug in code/tutorials/exp_sumb/pre/pre_tomo_seg.m
  • 08/04/2020
    • Updates in rec_particles.py script
    • Synthetic model (ModelFilsRSR) for filaments
  • 30/04/2020
    • Adding /code/tutorials/exp_somb tutorial for processing single oriented membranes.
    • Commenting mask imsave in code/tutorials/synth_sumb/class/plane_align_class.py
  • 06/05/2020
    • Adding membrane signal suppression code/tutorials/exp_somb/post_rec_particles.py
    • Bug fixed for code/tutorials/exp_somb/post_rec_particles.py for non-splitting mode
  • 26/05/2020
    • Adding tutorial exp_domb (/{code,data}/tutorials/exp_domb)
  • 17/07/2020
    • Adding filament analysis scrits in code/pyorg/scripts/filaments
  • 03/09/2020
    • Correction bug in script /code/tutorials/exp_somb/pre_tomos_seg.py
  • 11/09/2020
    • Corrections for test in module /code/pyorg/surf
  • 08/10/2020
    • Corrections for the statistical analysis of filaments organization
  • 26/12/2020
    • Adding comments to explain XML files
  • 27/12/2020
    • Segmentation pre-processing scripts in tutorial using global_analysis function
  • 08/01/2020
    • Eliminating 'WARNING: filament with less than 3 points!' messages
    • Preparing scripts to build an independant repository for filaments quantitative analysis
  • 02/09/2020
    • Adding Gaussian low-pass filtering to script /code/tutorials/exp_somb/post_rec_particles.py
  • 26/12/2020
    • Adding comments to explain XML file
  • 27/12/2020
    • Using global_analysis within pre-procesing segmentation scripts in PySeg tutorials
  • 26/01/2021
    • Adding particle surface overlapping fraction option
  • 06/02/2021
    • Using numpy histogram funtion to increase the speed for computational units in PyOrg.
  • 01/03/2021
    • Adding computation level option (out_level) to plane_align_class.py
  • 15/04/2021
    • Modifications to reduce memory occupancy for PyOrg.
  • 30/08/2021
    • Updating pyto to deal with scipy 1.6.
  • 12/09/2021
    • Updating script for pre-processing tomograms for single un-oriented membranes.
  • 15/09/2021
    • Bug correction: input parsing for Booleans introduced during integration with SCIPION.
  • 02/10/2021
    • Adding MRC I/O TOM-Toolbox functions
  • 21/07/2022
    • Adding system installers for Python3 on Ubuntu 20.04
  • 27/07/2022
    • Adding models in MRC format for generating synthetic tomogras in /data/tutorials/synth_sumb/modes
  • 30/01/2023
    • Since numpy_1.24 types like np.int, np.float and np.bool are no longer used, they have been substituted Python native types int, float and bool respectively.
    • Dockefile with container for Ubuntu 20.04 was added by DimitriosBellos