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Changelog

0.1.10

13 December 2024

Documentation Changes

  • Fix stable version on RTD (Adrien Berchet - #20)

0.1.9

13 December 2024

Documentation Changes

  • Fix stable version on RTD (Adrien Berchet - #16)
  • Add banner and badges (Adrien Berchet - #15)

CI Improvements

  • Fix ImageMagick (Adrien Berchet - #18)

0.1.8

26 November 2024

Build

  • Fix dependencies for docs generation (Adrien Berchet - #12)

New Features

  • Add new CLI options and create a specific NodeProvider entry for attractors (Adrien Berchet - #13)

0.1.7

8 November 2024

Chores And Housekeeping

  • Add CITATION.cff file (Adrien Berchet - #9)

Documentation Changes

  • Fix Citation section in README (Adrien Berchet - #10)

0.1.6

23 October 2024

Documentation Changes

  • Use Conda environment in RTD config (#6) (Adrien Berchet - 56f6c38)

0.1.5

22 October 2024

Documentation Changes

  • Fix RTD (Adrien Berchet - #4)

0.1.4

22 October 2024

Chores And Housekeeping

  • Move repo URL (Adrien Berchet - #2)
  • Migrate the code to GitHub and open source it (Adrien Berchet - #1)

0.1.3

22 October 2024

New Features

  • Can pass a parameter file for tuft synthesis in mimic workflow (Adrien Berchet - 9b7aff7)
  • Compute the maximum path extent in tuft properties (Adrien Berchet - ff60d9e)

Chores And Housekeeping

  • Cast paths to str when getting morphology paths (Adrien Berchet - 0e94dd1)

0.1.2

22 October 2024

Fixes

  • Ensure morphology edges are optional (Adrien Berchet - 0ce1694)

Chores And Housekeeping

  • Use grower context to pass the boundary to the tuft grower (Adrien Berchet - e5bd5ff)

0.1.1

22 October 2024

Fixes

  • Fix atlas CLI and remove useless warnings (Adrien Berchet - c1e6afb)

0.1.0

22 October 2024

Build

  • Bump NeuroTS and update the tests (Adrien Berchet - 956e284)
  • Fix m2r2 dependency to docutils<0.21 (Adrien Berchet - 80723f4)

New Features

  • Support nested folders in input morphology directory (Adrien Berchet - af71fac)
  • Add dummy preferred region workflow in mimic validation (Adrien Berchet - 7a0b876)
  • Add tuft creation and grafting (Adrien Berchet - f4dafe3)
  • Compute layer profile coefficients for sub regions (Adrien Berchet - 97625ff)
  • Add parallel computation (Adrien Berchet - c6ab0c0)
  • Add trunk post-processing (Adrien Berchet - 5db264d)
  • Add smoothing and jittering for long-range trunk and some statistics on tuft distributions (Adrien Berchet - 9be74a1)
  • Improve plots (Adrien Berchet - fe65578)
  • Add many options in CLI (Adrien Berchet - 264ac8a)
  • Add functions to generate score matrices (Adrien Berchet - bd495f8)
  • Add favored regions and depth penalties to build the graph (Adrien Berchet - a562aea)
  • Compute inputs in parallel (Adrien Berchet - 16f0336)
  • Can pass multiple clustering configurations (Adrien Berchet - a6434e4)
  • Add script to init empty morphs, add ST solution figure, add some config params (Adrien Berchet - 2720dec)
  • Add boundary handling in tuft synthesis (Adrien Berchet - de004db)
  • Add example and handle multiple axons properly for input creation (Adrien Berchet - d753d96)
  • Enable parallel computation for all mimic workflows (Adrien Berchet - f407f02)
  • Improve random walk along the Steiner solution (Adrien Berchet - 29e3b7b)
  • Parallelize terminal extraction and reduce logger entries from distributed scheduler (Adrien Berchet - 031eb77)
  • Add projection intensities computation (Adrien Berchet - 6ff7da1)
  • Add random walk along the Steiner solution (Adrien Berchet - 10ef6cb)
  • Add parameters to use custom file locations instead of only from inputs directory (Adrien Berchet - 7e51a38)
  • Improve projection intensities and add figures (Adrien Berchet - 9d002ab)
  • Set trunk diameter to 1 by default (Adrien Berchet - 9ae19c5)
  • Improve graph creation in favored regions (Adrien Berchet - 7408f19)
  • Remove extension parameter and find the corresponding files automatically (Adrien Berchet - 3ee6470)
  • Can project multiple tufts in each target population (Rémy Valentin Petkantchin - 9ff53a3)
  • Add WhiteMatterRecipe.exists() and some formatting (Adrien Berchet - 6e7e6fc)
  • Get layer profiles and compute region volumes (Adrien Berchet - fec9b1b)
  • Add config file (Adrien Berchet - 68ae069)
  • Added hemispheres distinction (Rémy Valentin Petkantchin - 350db79)
  • Make the WMR optional for input creation (Adrien Berchet - 118bf50)
  • (mimic preferred region) Allow to keep dummy atlas for later debug (Adrien Berchet - 4156969)
  • Allow to export edges of the initial and final morphologies (Adrien Berchet - 474b069)
  • Rotate the tufts using the atlas orientations (Adrien Berchet - b13f28a)
  • Export more data from the clustering step in debug mode (Adrien Berchet - 840df73)
  • Add many options in CLI (Adrien Berchet - 9dae736)
  • Add export for tuft morphologies (Adrien Berchet - 977902f)
  • Improve buffer computation (Adrien Berchet - 598b848)
  • Add --atlas-enable/--atlas-disable to be able to run synthesis on mimic inputs (Adrien Berchet - 8c8f813)
  • Add neurite type filter to export_morph_edges (Adrien Berchet - 5eb311b)
  • Export morphologies with NEURON order (Adrien Berchet - c65b0f8)
  • Remove unifurcations at the end of the synthesis process (Adrien Berchet - 256b956)

Fixes

  • Fix for Pandas<2.2; fix random numbers; recenter morphs in mimic workflow (Adrien Berchet - 9c60298)
  • Handle each clustering config properly (Adrien Berchet - 108635f)
  • Use proper scales in plots and fix morph recentering issues (Adrien Berchet - f6ee18b)
  • The mimic workflow did not produce expected results (Adrien Berchet - 478df02)
  • Fix edge cases with multiple axons and axons with less that 5 points (Adrien Berchet - 7206e3a)
  • Clustering should work for multiple axons and with any neurite order (Adrien Berchet - e6c0dbe)
  • Fix clustering with multiple axons (Adrien Berchet - ae72a79)
  • Graft the tufts to proper sections and propagate rng properly (Adrien Berchet - 25653d7)
  • Fix new edge cases and improve plots to make colors consistent (Adrien Berchet - 4291d8c)
  • Fix orientations, incorrect source point coordinates and MPI computation (Adrien Berchet - 945bb99)
  • Fix target positions in atlas and reduce memory for their computation (Adrien Berchet - f1f0d3f)
  • Fix figures for empty morphologies and target points for missing targets (Adrien Berchet - 9949c4e)
  • Fix input relative path and edge cases with empty morphologies (Adrien Berchet - f9c5d94)
  • Better support of morphologies with no target (Adrien Berchet - 2638c9b)
  • Fix bbox in graph creation (Adrien Berchet - 5dcab1a)
  • Use proper extensions for JSON files and format them (Adrien Berchet - 6ae9e41)
  • Remove points outside the atlas (Adrien Berchet - 4bb0c4a)
  • Handle empty morphs in figures (Adrien Berchet - 7cb116d)
  • Fix synthesis workflow in parallel and fix target point check for multiple axons morphologies (Adrien Berchet - 1a00199)
  • Fixed hemisphere target points symmetry and added option for different h_axis direction (Rémy Valentin Petkantchin - 106a4a7)
  • Skip morphologies without any axons in mimic workflow (Adrien Berchet - b313276)
  • Fix the target orientation storage (Adrien Berchet - 31706ea)
  • Fix clustering path, HDF5 issue with mode=w and minor fixes (Adrien Berchet - f6b10e7)
  • Drop duplicated targets properly (Adrien Berchet - 0a1266c)
  • Add missing tasks in the CreateInputs workflow (Adrien Berchet - 5a9606b)
  • Fix parallel partitions in edge case (Adrien Berchet - ea1cdc7)
  • Properly count the number of synthesized morphologies (Adrien Berchet - 75ea4e6)
  • Compute the tuft barcodes properly (Adrien Berchet - 0b5d0c1)
  • Fix log entry for Steiner Tree solution (Adrien Berchet - 9ddcb6f)
  • Properly call fillna with inplace=True (Adrien Berchet - f6b4489)
  • Use axon ID when removing invalid target points (Adrien Berchet - cdae891)
  • Handle empty list for preferred regions (Adrien Berchet - 5cb2e7c)
  • Reset index after dropping morphs with unknown source brain region (Adrien Berchet - 83c0ca2)

Chores And Housekeeping

  • Clean research dir (Adrien Berchet - 9fcec1c)
  • Clean random walk (Adrien Berchet - 8e10fb0)
  • Rename cluster-related variables with tuft suffix (Adrien Berchet - 08ded94)
  • Simplify and improve random walk (Adrien Berchet - 26ebf33)
  • Cleaning and always store section ID in steiner morph (Adrien Berchet - 88f2744)
  • Rename favored regions into preferred regions (Adrien Berchet - 523c033)
  • Replace check_min_max by native validators from attrs (Adrien Berchet - 3f0fc51)
  • Improve preferred regions (Adrien Berchet - 511d165)
  • Add more targets to clustering (Adrien Berchet - ce1b356)
  • Define and use the CoordsCols class (Adrien Berchet - 1aa807b)
  • Minor improvements (Adrien Berchet - 25d3a36)
  • Minor improvements (Adrien Berchet - d959d96)
  • Move parameter and distribution keys from apical_dendrite to axon (Adrien Berchet - 278428f)
  • Minor cleaning (Adrien Berchet - 896da34)
  • Reduce memory for trunk properties and improved figures (Adrien Berchet - 5e84e08)
  • Clean code (Adrien Berchet - 2801ad5)
  • Update log entries (Adrien Berchet - f823cb3)
  • Improve optional files handling in Clustering (Adrien Berchet - 961bb46)
  • Bump dir-content-diff (Adrien Berchet - 3324e81)
  • Fix parameters and distributions (Adrien Berchet - f015dc8)
  • Add log entries for source and target points (Adrien Berchet - 0b0d56b)
  • Improve brain region mask creation perf (Adrien Berchet - 0efc681)
  • Fix package name (Adrien Berchet - add00dc)
  • Remove some Pandas warnings (Adrien Berchet - 124a064)
  • Update example scripts (Adrien Berchet - 87c7eb5)
  • Directly cast the 'grafting_section_id' column (Adrien Berchet - b66faa8)
  • Fix language detection (Adrien Berchet - 89f7445)

Documentation Changes

  • Add figure for preferred region point (Adrien Berchet - 54d7050)
  • Add CLI and configuration file details (Adrien Berchet - 8f678e9)
  • Add some general concepts on axon synthesis algorithm (Adrien Berchet - 53a138e)
  • Add input file descriptions (Adrien Berchet - 93dfbe4)
  • Add workflow diagrams and minor improvements (Adrien Berchet - 8e7139a)
  • Add preferred regions in general principles (Adrien Berchet - 23370eb)

Refactoring and Updates

  • Packaging (Adrien Berchet - 6c631a6)
  • Fetch WMR works (Adrien Berchet - 91f1d21)
  • Add mimic workflow and improve global config from file in CLI (Adrien Berchet - 1407c46)
  • Split large modules into smaller ones (Adrien Berchet - a48db16)
  • Reorganize CLI and input creation files (Adrien Berchet - c200363)
  • Remove useless files and improve formatting (Adrien Berchet - 1b17f2e)
  • Move functions from clutering to sub-modules (Adrien Berchet - f9ebab5)
  • Split CreateTuftTerminalProperties run method into smaller functions (Adrien Berchet - 5ce14f4)
  • Reduce run() method size in the ClusterTerminals and FindTargetPoints tasks (Adrien Berchet - ef288e9)
  • Move functions from create_graph to other sub-modules (Adrien Berchet - ea4958a)
  • Simplify the code and fix the tests (Adrien Berchet - 3b81b3b)
  • Extract the trunk properties into a new task (Adrien Berchet - 98e8a2b)
  • Clustering works, at least the sphere-parent method (Adrien Berchet - aeee93d)
  • Move WMR processing (Adrien Berchet - 167119d)
  • Move plot of AddTufs task into an external function (Adrien Berchet - 7022945)

Changes to Test Assests

  • Use not resampled morphologies (Adrien Berchet - 807ccdf)
  • Fix the mimic workflow test and remove a few warnings (Adrien Berchet - 804a48c)
  • Add missing files and minor fixes (Adrien Berchet - 9487823)
  • Add a simple test case and fix revealed bugs (Adrien Berchet - 5384d4a)
  • Fix tests and related issues (Adrien Berchet - 13ce8dd)
  • Add a test for mimic case (Adrien Berchet - a033614)
  • Fix tolerance for Morphology diffs (Adrien Berchet - a7b0a04)
  • Update SteinerTreeSolutions data (Adrien Berchet - 1b3e01c)

Tidying of Code eg Whitespace

  • Format according to Ruff (Adrien Berchet - ae36376)
  • Setup mypy checks and add type hints (Adrien Berchet - d6b435f)
  • Fix many linting error (Adrien Berchet - e7ffad1)
  • Setup mypy checks and add type hints (Adrien Berchet - b9b0bac)
  • Lint (Adrien Berchet - 60ea4f9)

Performance Improvements

  • Target points are selected muck quicker (Adrien Berchet - fc9be79)

CI Improvements

  • Fix gitlab config, lint, mypy, ... (Adrien Berchet - 38d8e33)
  • Bump versions in pre-commit config (Adrien Berchet - 1447a46)
  • Fix gitlab configuration (Adrien Berchet - c96fecb)
  • Use build instead setup.py (Adrien Berchet - 914bf25)

General Changes

  • Fix source and target points (Adrien Berchet - 7f75787)
  • Add clustering by regions (Adrien Berchet - c243224)
  • Black and isort (Adrien Berchet - 253804e)
  • Improve logger and add trunk grafting (Adrien Berchet - eb3e3ac)
  • Add graph creation and Steiner Tree solution (Adrien Berchet - f43e414)
  • Add new tasks to synthesize axons from white matter recipe (Adrien Berchet - a809e51)
  • Compute path length of the tufts from the white matter recipe (Adrien Berchet - f59f16d)
  • Refactor several classes to make the code simpler (Adrien Berchet - 721543a)
  • Improve clustrering and use it in later tasks instead of raw morphologies (Adrien Berchet - 42b00a5)
  • Update workflows to synthesize axons in vacuum or using the white matter recipe (Adrien Berchet - 760bfbc)
  • Rework clustering params format and create a class to store results (Adrien Berchet - b14d8be)
  • Improve clustering and tuft statistics, add options in graph creation and fix tuft generation (Adrien Berchet - 6331b2d)
  • Add new clustering method and improve graph creation (Adrien Berchet - 23de2cc)
  • Add a tuft to each terminal (Adrien Berchet - 1c588e3)
  • Add score matrix as validation tool (Adrien Berchet - 82e61a3)
  • Create morphologies from Steiner solutions and plot the morphologies with plotly_helper (Adrien Berchet - 1b04130)
  • Improve clustering and statistics (Adrien Berchet - b202539)
  • Add clustering and use luigi workflows (Adrien Berchet - 0c0d662)
  • Simplify some classes (Adrien Berchet - eafeaca)
  • Add Steiner computation and solution export (Adrien Berchet - c2a2d57)
  • Add some helpers for atlas and white matter repice (Adrien Berchet - 8197b60)
  • Add graph creation step for Steiner Tree computation (Adrien Berchet - 5d8c6a6)
  • Cleaning and start statistics (Adrien Berchet - eae593a)
  • Minor cleaning (Adrien Berchet - 4a02f6f)
  • Minor refactoring and add features to atlas (Adrien Berchet - ffabf3c)
  • Start building the tufts (Adrien Berchet - 44f82ff)
  • Add statistics (Adrien Berchet - 00a524b)
  • Initial commit (Adrien Berchet - 3afee78)
  • Add missing file (Adrien Berchet - 963f5c1)
  • Repair and plot raw morphologies (Adrien Berchet - db16cbb)
  • Add random choice of tufts from the input ones (Adrien Berchet - c2576f2)
  • Add task to automatically fetch the White Matter Recipe file (Adrien Berchet - 6194ce3)
  • Fix clustering and graph creation and use OutputLocalTarget (Adrien Berchet - 59015d3)
  • Add intermediate points before Voronoi points (Adrien Berchet - 8bc1345)
  • Correct the mean length of the tuft by the trunk length (Adrien Berchet - aa684cf)
  • Fix morph export paths (Adrien Berchet - aba4a57)
  • Can add random points before the Voronoi process (Adrien Berchet - b050982)
  • Fix distrs and params for NeuroTS>=3.2 (Adrien Berchet - da83578)
  • Fixes and add new configs (Adrien Berchet - 6ae53e9)
  • Add new task to create specific inputs (Adrien Berchet - 57b61f4)
  • Add requirements.txt (Adrien Berchet - 38142e0)
  • Simplify some classes (Adrien Berchet - 6955e4a)