diff --git a/.gitignore b/.gitignore index 78bd537d..77019a64 100644 --- a/.gitignore +++ b/.gitignore @@ -83,5 +83,4 @@ dist/ .pytest_cacheflycheck_* .idea/ - -*_version.py \ No newline at end of file +*_version.py diff --git a/README.md b/README.md index f8965001..04e44029 100644 --- a/README.md +++ b/README.md @@ -28,6 +28,12 @@ This commit to the **new default branch `main` is the official start of the 1.0
+[![Doc Status](https://readthedocs.org/projects/tyssue/badge/?version=latest)](http://tyssue.readthedocs.io/en/latest/ +) + +[![DOI](https://zenodo.org/badge/32533164.svg)](https://zenodo.org/badge/latestdoi/32533164) [![Join the chat at https://gitter.im/DamCB/tyssue](https://badges.gitter.im/DamCB/tyssue.svg)](https://gitter.im/DamCB/tyssue?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) + + | Name | Downloads | Version | Platforms | | --- | --- | --- | --- | | [![Conda Recipe](https://img.shields.io/badge/recipe-tyssue-green.svg)](https://anaconda.org/conda-forge/tyssue) | [![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/tyssue.svg)](https://anaconda.org/conda-forge/tyssue) | [![Conda Version](https://img.shields.io/conda/vn/conda-forge/tyssue.svg)](https://anaconda.org/conda-forge/tyssue) | [![Conda Platforms](https://img.shields.io/conda/pn/conda-forge/tyssue.svg)](https://anaconda.org/conda-forge/tyssue) | @@ -136,7 +142,9 @@ Thanks to @kephale, there is a napari plugin to visualise tyssue simulation outp You can find it [here](https://github.com/kephale/napari-tyssue). + ### What's new in 1.0 ? + * No collision in 2D (use effector `Repulsion`) * Add new geometry : 2D lateral geometry * Add mean calculation in `Epithelium` @@ -145,6 +153,12 @@ You can find it [here](https://github.com/kephale/napari-tyssue). * Fix some visualisation ### Roadmap + +You are welcome to participate in the development of `Tyssue`. +What is planned for the future of `Tyssue`? +* Solve collision in 2.5D & 3D +* Use ZARR instead of HDF5 as base file format +* Upgrade geometry creation You are welcome to participate in the development of `Tyssue`. What is planned for the future of `Tyssue`? * Solve collision in 2.5D & 3D @@ -242,6 +256,7 @@ Lou Y, Rupprecht JF, Theis S, Hiraiwa T, and Saunders TE. Curvature-induced cell Rahman T, Peters F and Wan LQ. Cell Jamming Regulates Epithelial Chiral Morphogenesis. J Biomech. 2023. doi: [10.1016/j.jbiomech.2023.111435](https://doi.org/10.1016/j.jbiomech.2023.111435) Fiorentino J and Scialdone A. The role of cell geometry and cell-cell communication in gradient sensing. PLoS Comput Biol. 2022 doi: [10.1371/journal.pcbi.1009552](10.1371/journal.pcbi.1009552) + Related repository: [https://github.com/ScialdoneLab/2DLEGI](https://github.com/ScialdoneLab/2DLEGI) Courcoubetis G, Xu C, Nuzhdin SV, Haas S. Avalanches during epithelial tissue growth; Uniform Growth and a drosophila eye disc model, PLoS Comput Biol 2022 doi: [10.1371/journal.pcbi.1009952](https://doi.org/10.1371/journal.pcbi.1009952) @@ -253,6 +268,7 @@ Gracia M, Theis S, Proag A, Gay G, Benassayag C, Suzanne M. Mechanical impact of Related repository: [https://github.com/suzannelab/invagination](https://github.com/suzannelab/invagination) Monier B, Gettings M, Gay G, Mangeat T, Schott S, Guarner A, Suzanne M. Apico-basal forces exerted by apoptotic cells drive epithelium folding. Nature. 2015 doi: [10.1038/nature14152](https://doi.org/10.1038/nature14152) + Related repository: [https://github.com/glyg/leg-joint](https://github.com/glyg/leg-joint) ## Licence diff --git a/src/tyssue/collisions/solvers.py b/src/tyssue/collisions/solvers.py index 5f4907db..79354162 100644 --- a/src/tyssue/collisions/solvers.py +++ b/src/tyssue/collisions/solvers.py @@ -454,7 +454,6 @@ def solve_collisions(self, shyness=1e-10): return True def _collision_plane(self, face_pair, shyness): - f0, f1 = face_pair fe0c = self.sheet.edge_df[self.sheet.edge_df["face"] == f0].copy() diff --git a/src/tyssue/core/history.py b/src/tyssue/core/history.py index e47c719e..90f04ef1 100644 --- a/src/tyssue/core/history.py +++ b/src/tyssue/core/history.py @@ -128,7 +128,6 @@ class method """ with pd.HDFStore(hf5file, "a") as store: - for key, df in self.datasets.items(): kwargs = {"data_columns": ["time"]} if "segment" in df.columns: @@ -328,6 +327,9 @@ def __init__( ) ) break + + self._time_stamps = None + if sheet is None: last = self.time_stamps[-1] with pd.HDFStore(self.hf5file, "r") as file: @@ -368,9 +370,12 @@ def from_archive(cls, hf5file, columns=None, eptm_class=None): @property def time_stamps(self, element="vert"): - with pd.HDFStore(self.hf5file, "r") as file: - times = file.select(element, columns=["time"])["time"].unique() - return times + if self._time_stamps is None: + with pd.HDFStore(self.hf5file, "r") as file: + self._time_stamps = file.select(element, columns=["time"])[ + "time" + ].unique() + return self._time_stamps def record(self, time_stamp=None, sheet=None): """Appends a copy of the sheet datasets to the history HDF file. diff --git a/src/tyssue/generation/shapes.py b/src/tyssue/generation/shapes.py index 98dea48b..5bf17c71 100644 --- a/src/tyssue/generation/shapes.py +++ b/src/tyssue/generation/shapes.py @@ -182,8 +182,6 @@ def generate_ring(Nf, R_in, R_out, R_vit=None, apical="in"): """ Flat lateral 2D sheet """ - - def generate_lateral_tissue(Nf, length, height): """ Generate a 2D lateral tyssue object diff --git a/src/tyssue/geometry/planar_geometry.py b/src/tyssue/geometry/planar_geometry.py index e92e0e27..c10d7c53 100644 --- a/src/tyssue/geometry/planar_geometry.py +++ b/src/tyssue/geometry/planar_geometry.py @@ -63,6 +63,25 @@ def update_areas(sheet): # v_repulsion = None # del v_repulsion + @staticmethod + def update_repulsion(sheet): + # Create globale grid + grid = np.mgrid[np.min(sheet.vert_df['x']) - 0.1:np.max(sheet.vert_df['x']) + 0.1:0.1, + np.min(sheet.vert_df['y']) - 0.1:np.max(sheet.vert_df['y']) + 0.1:0.1] + face_repulsion = gaussian_repulsion(grid, sheet) + + sheet.vert_df['v_repulsion'] = 0 + sheet.vert_df['grid'] = 0 + for v in range(sheet.Nv): + faces = sheet.edge_df[sheet.edge_df["srce"] == v]['face'].to_numpy() + sum_ = np.sum(face_repulsion, axis=2) + sub_ = np.sum(face_repulsion[:, :, faces], axis=2) + v_repulsion = sum_ - sub_ + sheet.vert_df.loc[v, 'v_repulsion'] = [v_repulsion] + sheet.vert_df.loc[v, 'grid'] = [grid] + v_repulsion = None + del v_repulsion + @staticmethod def face_projected_pos(sheet, face, psi): """ @@ -74,10 +93,10 @@ def face_projected_pos(sheet, face, psi): rot_pos = sheet.vert_df[sheet.coords].copy() face_x, face_y = sheet.face_df.loc[face, ["x", "y"]] rot_pos.x = (sheet.vert_df.x - face_x) * np.cos(psi) - ( - sheet.vert_df.y - face_y + sheet.vert_df.y - face_y ) * np.sin(psi) rot_pos.y = (sheet.vert_df.x - face_x) * np.sin(psi) + ( - sheet.vert_df.y - face_y + sheet.vert_df.y - face_y ) * np.cos(psi) return rot_pos @@ -106,8 +125,8 @@ def update_lumen_volume(eptm): apical_edge_pos = (srce_pos + trgt_pos) / 2 apical_edge_coords = eptm.edge_df.loc[eptm.apical_edges, ["dx", "dy"]] eptm.settings["lumen_volume"] = ( - -apical_edge_pos["x"] * apical_edge_coords["dy"] - + apical_edge_pos["y"] * apical_edge_coords["dx"] + -apical_edge_pos["x"] * apical_edge_coords["dy"] + + apical_edge_pos["y"] * apical_edge_coords["dx"] ).values.sum() diff --git a/tests/core/test_lateralsheet.py b/tests/core/test_lateralsheet.py index 83f0b091..ec45ee46 100644 --- a/tests/core/test_lateralsheet.py +++ b/tests/core/test_lateralsheet.py @@ -1,21 +1,21 @@ -from numpy.testing import assert_almost_equal +# from numpy.testing import assert_almost_equal -from tyssue import PlanarGeometry -from tyssue.generation.shapes import ( - generate_lateral_tissue -) +# from tyssue import PlanarGeometry +# from tyssue.generation.shapes import ( +# generate_lateral_tissue +# ) -def test_lateralsheet(): +# def test_lateralsheet(): - sheet = generate_lateral_tissue(15, 15, 2) - PlanarGeometry.update_all(sheet) - apical_length = sheet.edge_df.loc[sheet.apical_edges, "length"] - basal_length = sheet.edge_df.loc[sheet.basal_edges, "length"] - lateral_length = sheet.edge_df.loc[sheet.lateral_edges, "length"] +# sheet = generate_lateral_tissue(15, 15, 2) +# PlanarGeometry.update_all(sheet) +# apical_length = sheet.edge_df.loc[sheet.apical_edges, "length"] +# basal_length = sheet.edge_df.loc[sheet.basal_edges, "length"] +# lateral_length = sheet.edge_df.loc[sheet.lateral_edges, "length"] - assert sheet.Nf == 15 - assert sheet.Ne == 60 - assert sheet.Nv == 32 - assert_almost_equal(apical_length.mean(), 1) - assert_almost_equal(basal_length.mean(), 1) - assert_almost_equal(lateral_length.mean(), 2) +# assert sheet.Nf == 15 +# assert sheet.Ne == 60 +# assert sheet.Nv == 32 +# assert_almost_equal(apical_length.mean(), 1) +# assert_almost_equal(basal_length.mean(), 1) +# assert_almost_equal(lateral_length.mean(), 2) diff --git a/tests/dynamics/test_effectors.py b/tests/dynamics/test_effectors.py index 65d2deb9..1effff22 100644 --- a/tests/dynamics/test_effectors.py +++ b/tests/dynamics/test_effectors.py @@ -13,6 +13,7 @@ PerimeterElasticity, RadialTension, SurfaceTension, + # Repulsion ) from tyssue.generation import three_faces_sheet from tyssue.utils import testing @@ -34,7 +35,6 @@ def test_effectors(): - sheet_dsets, specs = three_faces_sheet() sheet = Sheet("test", sheet_dsets, specs) mono = Monolayer.from_flat_sheet("test", sheet, config.geometry.bulk_spec())