CHANGELOG.md

Changelog

0.18.3 _{^{2025-01-15 (053715c...053715c)}}

no relevant changes

0.18.2 _{^{2025-01-15 (a245213...25f698c)}}

Merges

• pull request #30 from yzx9/chore/uv (fde7733)

0.18.1 _{^{2025-01-04 (9bbacc8...163776f)}}

no relevant changes

0.18.0 _{^{2025-01-04 (d3a8b93...a07e648)}}

Features

 transforms

• resample tree (close #8 #9) (b5c44bb)

Bug Fixes

• use `np.inf` (close #23) (1111613)

0.17.2 _{^{2024-08-07 (9d5347d...59a5cbf)}}

Bug Fixes

 analysis

• handle zero partition asymmetry in lmeasure (1f332f2)
• workaround with angle (05d2ff7)

 utils

• download with multiprocessing should avoid locals func (6aff3e0)

BREAKING CHANGES

• rename bifurcation to furcation (26e9dec)
• core lazy loading in range indexing (7d38ea8)
  

0.17.1 _{^{2024-04-05 (a8007ac...0ef3c2b)}}

Features

 utils

• set round style (90030e3)

0.17.0 _{^{2024-04-04 (59257cb...2072139)}}

Features

 images

• handle raw file in terafly (67ecd63)
• add image stack dtype support (7313ead)

 transforms

• add new image transformation classes (7b5d805)
• add image flip and notes (5f2a4d1)

BREAKING CHANGES

• images remove deprecated `swap_xy` and `filp_xy` flag (2072139)
  

0.16.0 _{^{2024-03-16 (bf2bf95...7029483)}}

Features

 analysis

• add l-measure support (close #13) (15ddc33)

 core

• `Tree` accpet values with custom names (722f84f)
• add `Population.map` parallel processing support (a1ee5bb)

 images

• add image contrast functions (85b881e)
• stat image stack folder (ffc5e3a)

 transforms

• add basic neuronlucida asc format support (close #12) (619a275)
• add `SGuoImPreProcess` (dab7481)
• add image stack related transforms (7029483)

 utils

• `Tree` support array like inputs (1f228d0)
• download source swc and log from neuromorpho (d4fbfb6)

Bug Fixes

 utils

• expecting a figure from the axes (bf2bf95)

Performance Improvements

 core

• use NamedTuple for SWCNames and SWCTypes (300bfea)

BREAKING CHANGES

• core `Tree` accpet values with custom names (722f84f)
• core remove deprecated `Tree.Node.get_branch` and `Node.child_ids` method (1de86af)

0.15.0 _{^{2024-01-28 (d300b41...8c9e0ab)}}

Features

core

• expose subtree id mapping (35738a3)

images

• add dtype support (d300b41)

transforms

• generate image stack patch (decd3a1)
• add `extra_repr` api (ca19361)

Bug Fixes

core

• fix classmethod typing annotations (0123eeb)

transforms

• should stack images (8c9e0ab)

BREAKING CHANGES

• core remove assembler module (414533d)
  

0.14.0 _{^{2023-12-26 (b9c95f5...cc22018)}}

Features

analysis

• add high accuracy volume calculation (9b51b74)

Bug Fixes

analysis

• subtract volume between frustum cone (dae116e)

utils

• avoid numerical error (a6bd4ad)

Performance Improvements

analysis

• use bvh scene (7a7b988)

utils

• use `sdflit` instead custom impl (a47a190)

BREAKING CHANGES

• transforms rewrite image stack (cc22018)

0.13.2 _{^{2023-12-16 (10f330d...291ae2a)}}

Performance Improvements

• impl a direct algorithm for finding sphere-line intersections (410acad)

0.13.1 _{^{2023-12-15 (0b5b45a...45b4040)}}

Bug Fixes

• import missing volume related file (0b5b45a)

analysis

• add volume between spheres (b8c6dfe)

utils

• remove debug printting (dd1569e)
• solve real values only (2f7459b)

0.13.0 _{^{2023-12-14 (e2add59...06239bd)}}

Features

analysis

• import sholl plot (b03b45c)
• calc volume of tree (close #9) (a5004da)

core

• check if it has a cyclic (#1) (e2add59)

utils

• transform batch of vec3 to vec4 (d2d660c)

Bug Fixes

utils

• should support `StringIO` (de439db)

Performance Improvements

• improve dsu (8b414c3)

0.12.0 _{^{2023-10-12 (d9ba943...0824e9b)}}

Features

core

• support read from io (8fe9df8)
• get neurites and dendrites (a9acfde)
• add swc types (7439288)
• add type check in `Tree.Node.is_soma` (35b53d6)

images

• support `v3dpbd` and `v3draw` (close #6) (ca8267d)

transforms

• sort mst tree by default (7878f3f)
• add path transforms (aaa1b1e)

utils

• change to utf-8 encode (45e971e)

Bug Fixes

core

• avoid duplicate cols comments (f99eaf3)
• inherit source (702efab)
• remove original point when cat tree (065125e)

images

• shape should be vec4i (0824e9b)

transforms

• add missing exports (93bf8e6)

Performance Improvements

transforms

• disable `detach` operation (204d44c)

0.11.1 _{^{2023-08-12 (36fa413...36fa413)}}

no relevant changes

0.11.0 _{^{2023-08-05 (a8adae5...c075ec4)}}

Features

analysis

• draw trunk (4d2e069)
• draw point at the start of subtree (2c9938f)

core

• detect swc encoding (06087bd)
• preserve original swc comments(close #2) (ac49e25)
• accept non-positive radius (47c29b5)
• accept space before comments in swc (c075ec4)

utils

• add neuromorpho related util (4a22e3d)
• convert neuromorpho lmdb to swc (e48c1a8)
• retry download neuromorpho (ebd9255)
• mark invalid neuromorpho data (43a96c6)

Bug Fixes

core

• forward names (52192ce)

transform

• cut by dynamic type (3293a67)

utils

• should throw http error (7fb4ee2)

0.10.0 _{^{2023-05-23 (bc48787...8991fe0)}}

Features

• dict-like swc (a1f52d7)

analysis

• add str input support (f98aea5)

core

• check if is sorted topology (bc48787)

images

• detect tiff axes (b1e44bb)
• change terafly to a left-handed coordinate system (b22b69a)

transforms

• cut tree by type (184482b)
• reset radius (e697e34)

Bug Fixes

*

• np.nonzero returns a tuple (091e6eb)

core

• forwarding init kwargs (226b3ef)

transforms

• crop fixed shape (e1078d3)

Performance Improvements

transforms

• flat transforms (f824651)

BREAKING CHANGES

• * export common classes and methods only (39de173)
• core set `check_same` arg to false by default (0f576e9)
• images change terafly to a left-handed coordinate system (b22b69a)

0.9.0 _{^{2023-05-04 (1a3e9d4...797934f)}}

Features

analysis

• plot sholl circles by default (797934f)

images

• add transform support to folder (167f67c)
• support disable compression (9db01e9)
• check if is a valid fname (4d98abc)

transform

• add image stack center transform (0fd1441)
• expose static method (c65c0cb)

Bug Fixes

core

• change `w` to ones (325ff1e)

BREAKING CHANGES

• analysis plot sholl circles by default (797934f)
• images folder do not move channel to first (fd3a3cb)

0.8.0 _{^{2023-04-18 (3d2d660...bfee570)}}

Features

analysis

• add node count (149ecec)
• transform each tree in population (fcd5fd7)
• plot sholl in populations (466cd3a)

core

• check is it a binary tree (b919de9)
• support create population from trees (73792a0)
• check valid population (199db95)

images

• add image stack folder (0318f0d)
• pathed image stack folder (bfee570)

transforms

• add `LinesToTree` (5083f26)
• add branch smoother (a4e8cd2)
• add tree smoother (082b05d)
• add transform `TranslateOorigin` (5ef9c43)
• expose `AffineTransform` (93d6ca9)

transfroms

• get tree longest path (17b6eda)

Bug Fixes

analysis

• handle different number of trees (94ffd2e)
• wrong x-ticks (ebd2e91)

core

• set new root (54cecf2)
• detach with new id and pid (a5f1791)

images

• patch has 4 dim (ccdb4d7)

transform

• typo (7bfa106)

Performance Improvements

images

• add lru cache for terafly (f288710)

0.7.0 _{^{2023-04-02 (e45b520...df0b693)}}

Features

core

• update root orf tree (13395d4)
• concat tree (93abf8c)
• check is it an binary tree (ba1b5b9)
• remove duplicate nodes (95596de)
• update waning message (f745626)

images

• support rgb (e45b520)

transforms

• add mst tree (529a530)

BREAKING CHANGES

• utils `utils.numpy_printoptions` has been remove, use `np.printoptions`instead of (df0b693)

0.6.0 _{^{2023-03-22 (97cb9b2...d40ccf6)}}

Features

analysis

• improve node_branch_order plotting (97cb9b2)
• add tip and bifurcation node feature (c1594d9)
• show fig by default (1587488)
• filter tips node (c3dd567)
• rebuild sholl (a43bc01)

core

• traverse from node (9f64d31)
• support index by np.integer (1b1699f)
• get subtree rooted at n (b57fb62)
• add high-level subtree api (eb91d7f)

images

• add io of image stack (f7b27be)

transforms

• add geometry transforms (6fd1166)

0.5.0 _{^{2023-03-09 (711ebb1...80acd75)}}

Features

analysis

• custom draw (bdc1291)
• re-design feature_extractor (e5affa7)
• add populations feature extractor (94a2bc6)
• plot histogram (0dc05d7)
• custom length plot (d32272d)
• custom position of direction indicator (b84b57e)
• support hidden swc in legend (80acd75)

core

• add populations (711ebb1)
• rename class method option (7003c1d)
• take intersection among populations (6442572)
• add pure-func style utils (7f9cba1)
• add `BranchTree.from_eswc` (d01cd04)
• add labels for populations (998566e)

Merges

• branch 'feature/populations' (1c7d1e8)

BREAKING CHANGES

• analysis (e5affa7)
  • `extract_feature` has been fully re-designed
  • `NodeFeatures.get_distribution` has been removed
  • `Sholl.get_distribution` has been removed
• analysis remove filters in `NodeFeatures` (f0b37bf)
• core `Population.from_swc` and `Population.from_eswc` argument `suffix` has been renamed to `ext` (7003c1d)
• core add pure-func style utils (7f9cba1)

0.4.1 _{^{2023-03-01 (4efbcef...4efbcef)}}

Bug Fixes

core

• should count nonzero nodes (4efbcef)

0.4.0 _{^{2023-02-27 (af51d11...1d9aeb5)}}

Features

analysis

• forward kwarg to plot method (1d9aeb5)

core

• add `Tree.from_data_frame` (b36f382)
• assemble lines into swc (382df7b)
• sort nodes after assemble (d00687c)
• rename `sort_swc` to `sort_nodes` (b7f27d6)
• support export swc without source (a8da734)

transform

• support cut short branch (0bc2f2c)

Performance Improvements

core

• reduce the number of value fetches (33169d1)

BREAKING CHANGES

• analysis forward kwarg to plot method (1d9aeb5)

0.3.1 _{^{2023-02-13 (557693b...fc9335f)}}

no relevant changes

0.3.0 _{^{2023-02-12 (40ff824...cedf52f)}}

Features

• add tree cutter (e8f1e68)
• support smart color swither (a6df232)
• add debug helper (f3819a5)
• sort tree (5f1d53e)
• support to swc string (0b68b65)
• sort swc tree (d812c0d)

analysis

• add get distribution (ea44851)
• add population feature extractor (7f3ff59)
• plot feature distribution (460f7d1)
• support plot sholl (a253d60)
• expose plot ax (9bb7585)

analysis/feature

• expose ax (2f98884)
• minor (bf18b4d)
• change default options (c6891b0)

analysis/visualization

• add legend (3739d93)

core

• add suffix option (ad8b1b0)_ rename `get_branch` to `branch` (7adca54)_ export eswc (0bce6a8)

core/swc

• write 1 as root id by default (946084b)
• support eswc (f49906a)
• fix multi roots (de75ee2)
• sort tree (a7ac4c7)
• rename read params (cb55c2b)

core/tree

• expose ndata id (0464b3f)

datasets

• rename `TreeToBranchTree` to `ToBranchTree` (5f6c93c)

transform

• rename option (ced31b1)
• add image stack (114f119)
• add verbose option (31a32a2)
• improve perf (40c650d)

transform/image-stack

• transforms population (a686fb1)

transform/image_stack

• support big image stack (bbe5bd1)
• add photometric (35e40c5)

Bug Fixes

• should copy ndata (cedf52f)

analysis/visulization

• handle draw too many neurons in same axes (de48fe2)

core

• avoid duplicate export tree (4a506bb)
• tip should not be parent (ce22ea0)
• branch should be nodes (3f1dcb0)
• should returns id (c622666)
• handle zero length (0112949)
• should propagate removal (f87ab43)

datasets/dgl

• copy prop (40ff824)

transfrom/image_stack

• handle root sdf (ce8cae2)

Performance Improvements

transform/image_stack

• boost intersect (8003026)

transforms

• boost is_in of sdf (45fee56)

BREAKING CHANGES

• analysis `get_distribution` returns both `x` and `y`, before (460f7d1)
  only `y`.
• anlysis/node_feature change default options (c6891b0)

0.2.0 _^2022-09-28

BREAKING CHANGE

• several features have been activatedm, take advantage
• migrate to numpy-based, remove networkx

0.1.7 _^2022-08-28

Features

core

• expose branch standardize method

data/torch

• support tree transfroms
• expose BranchToTensor transform, and support more options

data/transforms

• add branch transforms

Bug Fixes

core

• stack arrays to get the correct shape
• update node correctly

data/torch

• super object is not subscriptable

Performance Improvements

data

• delay log formatting

0.1.6 _^2022-08-25

Features

• add Branch.from_numpy
• rename Branch.from_numpy to Branch.from_numpy_batch
• expose branch resampler

Bug Fixes

data/torch

• avoid cycle reference

BREAKING CHANGES

• resample args should be named arguments now
• rename Branch.from_numpy to Branch.from_numpy_batch, and drop the support for squeezed input

0.1.5 _^2022-08-24

BREAKING CHANGE

• now node attributes are all dictionary attributes

Features

• convert node to dict

data/torch

• add datasets

0.1.4 _^2022-08-22

Bug Fixes

• import version correctly

0.1.3 _^2022-08-21

0.1.2 _^2022-08-21

0.1.1 _^2022-08-21

0.1.0 _^2022-08-21

Features

• import codes