Cell division failed for cell at the border #261
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* Fix for Issues #261 - cell division failed at the border * Fix Mesh creation Surface mesh create wasn't create all faces. Now it is fixed. Also : -add two methods to Mesh to list faces and vertices. -generalised coordinates -add `write_polygon_mesh` to export mesh into .ply to visualised with blinder * Add 2D collision solver Add class to solve collision in 2D or in 3D. 3D collision solver need to be fixed * Update README.md Add `How to cite` section Add `Geometry` section Add `Publications` section Update bibliography link * Generalised wich vertex penetrate face * Attempt to set out particular cases * Detect and fix self-crossing face Unable to make this algo works... https://europepmc.org/article/PMC/3660981 Use ordered vertices and their angle position. -> uncrossed face : angles are monotonically increasing -> crossed face : angles are not monotonically increasing * Use `.apply()` Need to recalculate angle_e for twisted face One fix which is only suitable for 2D lateral sheet... * ENH: write `mean_XX` method in `Epithelium` class (Issue #224) * Fix according to comments * Fix Issue #258 ax argument not considered in `plt_draw.sheet_view` * ENH: pass column name to `data_at_opposite` issue (#245) * Add publication and remove bibtex reference * Add check face convexity * Use reset_index and code simplification * yAdd to_mesh function (issue #221) and some test * Remove the use of reset_index in face_self_intersect * use ipv_draw with 2D data * Fix solution after detection point inside polygon * Remove solving collision for 2 same face... * Abord vertex displacement if it creates twisted face * New way to calculate the position of "penetrate" vertices For now, it is the best way to fix collision (compare to what I tried before). So when a vertex is inside an other face. It is pullback by 10% of the length of the ([v-f1]+[v-f2]/2). with v, f1, f2 position of vertices and center of face 1 and face 2, which are the faces to which the vertex belongs. It is not perfect and very arbitrary for now, but it avoids vertex displacement at strange place. * WIP - use force field to fix collision * Small fix * Remove function duplication due to circular import * Calculate "repulsion" gradient in the effector method. Remove loop * Fix tests Remove collisions tests Fix method call in meshes test Comment "update_repulstion" method in planar geometry * Add lateralsheet shapes + test * Update publication + add collapse texte * Add test for Repulsion effector * Add test update repulsion * Remove unused import * Add `drop_face` to allow hole (issues #220 and #141) (associate #221) * Update readme.md * Update publications in README.md * Add `lineage` attribute to `Epithelium` In order to keep track of cell lineage * Remove memory oscillation * dependency (#277) * bug fixes --------- Co-authored-by: Guillaume Gay <[email protected]>
glyg
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* dependency * Update history.py > Added the self.time_stamps() method code for HistoryHdf5 class into the __init__() method so that time_stamps are only calculated once as self._time_stamps > Edited self.time_stamps() method to return self._time_stamps > Greatly improves efficiency of retrieve() method as time_stamps is not computed each time a new time-point is loaded. * Solving mesh collision (#263) * Fix for Issues #261 - cell division failed at the border * Fix Mesh creation Surface mesh create wasn't create all faces. Now it is fixed. Also : -add two methods to Mesh to list faces and vertices. -generalised coordinates -add `write_polygon_mesh` to export mesh into .ply to visualised with blinder * Add 2D collision solver Add class to solve collision in 2D or in 3D. 3D collision solver need to be fixed * Update README.md Add `How to cite` section Add `Geometry` section Add `Publications` section Update bibliography link * Generalised wich vertex penetrate face * Attempt to set out particular cases * Detect and fix self-crossing face Unable to make this algo works... https://europepmc.org/article/PMC/3660981 Use ordered vertices and their angle position. -> uncrossed face : angles are monotonically increasing -> crossed face : angles are not monotonically increasing * Use `.apply()` Need to recalculate angle_e for twisted face One fix which is only suitable for 2D lateral sheet... * ENH: write `mean_XX` method in `Epithelium` class (Issue #224) * Fix according to comments * Fix Issue #258 ax argument not considered in `plt_draw.sheet_view` * ENH: pass column name to `data_at_opposite` issue (#245) * Add publication and remove bibtex reference * Add check face convexity * Use reset_index and code simplification * yAdd to_mesh function (issue #221) and some test * Remove the use of reset_index in face_self_intersect * use ipv_draw with 2D data * Fix solution after detection point inside polygon * Remove solving collision for 2 same face... * Abord vertex displacement if it creates twisted face * New way to calculate the position of "penetrate" vertices For now, it is the best way to fix collision (compare to what I tried before). So when a vertex is inside an other face. It is pullback by 10% of the length of the ([v-f1]+[v-f2]/2). with v, f1, f2 position of vertices and center of face 1 and face 2, which are the faces to which the vertex belongs. It is not perfect and very arbitrary for now, but it avoids vertex displacement at strange place. * WIP - use force field to fix collision * Small fix * Remove function duplication due to circular import * Calculate "repulsion" gradient in the effector method. Remove loop * Fix tests Remove collisions tests Fix method call in meshes test Comment "update_repulstion" method in planar geometry * Add lateralsheet shapes + test * Update publication + add collapse texte * Add test for Repulsion effector * Add test update repulsion * Remove unused import * Add `drop_face` to allow hole (issues #220 and #141) (associate #221) * Update readme.md * Update publications in README.md * Add `lineage` attribute to `Epithelium` In order to keep track of cell lineage * Remove memory oscillation * dependency (#277) * bug fixes --------- Co-authored-by: Guillaume Gay <[email protected]> * tests pass * fixes unknown namz --------- Co-authored-by: sniffo <[email protected]> Co-authored-by: Sophie THEIS <[email protected]>
glyg
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Feb 13, 2024
* Fix for Issues #261 - cell division failed at the border * Fix Mesh creation Surface mesh create wasn't create all faces. Now it is fixed. Also : -add two methods to Mesh to list faces and vertices. -generalised coordinates -add `write_polygon_mesh` to export mesh into .ply to visualised with blinder * Add 2D collision solver Add class to solve collision in 2D or in 3D. 3D collision solver need to be fixed * Update README.md Add `How to cite` section Add `Geometry` section Add `Publications` section Update bibliography link * Generalised wich vertex penetrate face * Attempt to set out particular cases * Detect and fix self-crossing face Unable to make this algo works... https://europepmc.org/article/PMC/3660981 Use ordered vertices and their angle position. -> uncrossed face : angles are monotonically increasing -> crossed face : angles are not monotonically increasing * Use `.apply()` Need to recalculate angle_e for twisted face One fix which is only suitable for 2D lateral sheet... * ENH: write `mean_XX` method in `Epithelium` class (Issue #224) * Fix according to comments * Fix Issue #258 ax argument not considered in `plt_draw.sheet_view` * ENH: pass column name to `data_at_opposite` issue (#245) * Add publication and remove bibtex reference * Add check face convexity * Use reset_index and code simplification * yAdd to_mesh function (issue #221) and some test * Remove the use of reset_index in face_self_intersect * use ipv_draw with 2D data * Fix solution after detection point inside polygon * Remove solving collision for 2 same face... * Abord vertex displacement if it creates twisted face * New way to calculate the position of "penetrate" vertices For now, it is the best way to fix collision (compare to what I tried before). So when a vertex is inside an other face. It is pullback by 10% of the length of the ([v-f1]+[v-f2]/2). with v, f1, f2 position of vertices and center of face 1 and face 2, which are the faces to which the vertex belongs. It is not perfect and very arbitrary for now, but it avoids vertex displacement at strange place. * WIP - use force field to fix collision * Small fix * Remove function duplication due to circular import * Calculate "repulsion" gradient in the effector method. Remove loop * Fix tests Remove collisions tests Fix method call in meshes test Comment "update_repulstion" method in planar geometry * Add lateralsheet shapes + test * Update publication + add collapse texte * Add test for Repulsion effector * Add test update repulsion * Remove unused import * Add `drop_face` to allow hole (issues #220 and #141) (associate #221) * Update readme.md * Update publications in README.md * Add `lineage` attribute to `Epithelium` In order to keep track of cell lineage * Remove memory oscillation * builds with pip adds pyproject.toml build command: pip install --no-build-isolation --config-settings=editable.rebuild=true -ve. * debugging, still no build apparently * build and tests * update nb submodule * fix pyproject * install with pip in CI * install with pip in CI * install with pip in CI * adds scikit-build dep * python version * python version specifier * remove strang flags * adds _version.py * setuptools_scm dep * simplified I guess * zdds setuptools-scm to env, MakeFilelist shenanigans * restricting to 3.10 * install dev * pyhon version coherence * install cmd * trying to move to modern sckit-build (it's painful) * WIP change build * getting closer I hope * make_spherical test pasess \o/ * tests passing, warnings still to be treated * don't install editable version in gh action * remove diff chars * tagging again to avoid metadata mismatch * Uncomment 2D repulsion + tests Fix pandas issue * Add comments in effectors.py * rmeove _version.py and ignore in git * Update history.py (#274) > Added the self.time_stamps() method code for HistoryHdf5 class into the __init__() method so that time_stamps are only calculated once as self._time_stamps > Edited self.time_stamps() method to return self._time_stamps > Greatly improves efficiency of retrieve() method as time_stamps is not computed each time a new time-point is loaded. * skip 2 tests * fix non existing hdf5 * submodules * adds notebooks submodule * should fix history bug * adds submodules again --------- Co-authored-by: Sophie T <[email protected]> Co-authored-by: sniffo <[email protected]>
glyg
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Feb 13, 2024
* Fix for Issues #261 - cell division failed at the border * Fix Mesh creation Surface mesh create wasn't create all faces. Now it is fixed. Also : -add two methods to Mesh to list faces and vertices. -generalised coordinates -add `write_polygon_mesh` to export mesh into .ply to visualised with blinder * Add 2D collision solver Add class to solve collision in 2D or in 3D. 3D collision solver need to be fixed * Update README.md Add `How to cite` section Add `Geometry` section Add `Publications` section Update bibliography link * Generalised wich vertex penetrate face * Attempt to set out particular cases * Detect and fix self-crossing face Unable to make this algo works... https://europepmc.org/article/PMC/3660981 Use ordered vertices and their angle position. -> uncrossed face : angles are monotonically increasing -> crossed face : angles are not monotonically increasing * Use `.apply()` Need to recalculate angle_e for twisted face One fix which is only suitable for 2D lateral sheet... * ENH: write `mean_XX` method in `Epithelium` class (Issue #224) * Fix according to comments * Fix Issue #258 ax argument not considered in `plt_draw.sheet_view` * ENH: pass column name to `data_at_opposite` issue (#245) * Add publication and remove bibtex reference * Add check face convexity * Use reset_index and code simplification * yAdd to_mesh function (issue #221) and some test * Remove the use of reset_index in face_self_intersect * use ipv_draw with 2D data * Fix solution after detection point inside polygon * Remove solving collision for 2 same face... * Abord vertex displacement if it creates twisted face * New way to calculate the position of "penetrate" vertices For now, it is the best way to fix collision (compare to what I tried before). So when a vertex is inside an other face. It is pullback by 10% of the length of the ([v-f1]+[v-f2]/2). with v, f1, f2 position of vertices and center of face 1 and face 2, which are the faces to which the vertex belongs. It is not perfect and very arbitrary for now, but it avoids vertex displacement at strange place. * WIP - use force field to fix collision * Small fix * Remove function duplication due to circular import * Calculate "repulsion" gradient in the effector method. Remove loop * Fix tests Remove collisions tests Fix method call in meshes test Comment "update_repulstion" method in planar geometry * Add lateralsheet shapes + test * Update publication + add collapse texte * Add test for Repulsion effector * Add test update repulsion * Remove unused import * Add `drop_face` to allow hole (issues #220 and #141) (associate #221) * Update readme.md * Update publications in README.md * Add `lineage` attribute to `Epithelium` In order to keep track of cell lineage * Remove memory oscillation * builds with pip adds pyproject.toml build command: pip install --no-build-isolation --config-settings=editable.rebuild=true -ve. * debugging, still no build apparently * build and tests * update nb submodule * fix pyproject * install with pip in CI * install with pip in CI * install with pip in CI * adds scikit-build dep * python version * python version specifier * remove strang flags * adds _version.py * setuptools_scm dep * simplified I guess * zdds setuptools-scm to env, MakeFilelist shenanigans * restricting to 3.10 * install dev * pyhon version coherence * install cmd * trying to move to modern sckit-build (it's painful) * WIP change build * getting closer I hope * make_spherical test pasess \o/ * tests passing, warnings still to be treated * don't install editable version in gh action * remove diff chars * tagging again to avoid metadata mismatch * Uncomment 2D repulsion + tests Fix pandas issue * Add comments in effectors.py * rmeove _version.py and ignore in git * Update history.py (#274) > Added the self.time_stamps() method code for HistoryHdf5 class into the __init__() method so that time_stamps are only calculated once as self._time_stamps > Edited self.time_stamps() method to return self._time_stamps > Greatly improves efficiency of retrieve() method as time_stamps is not computed each time a new time-point is loaded. * skip 2 tests * fix non existing hdf5 * submodules * adds notebooks submodule * should fix history bug * adds submodules again * minoor fix, notebooks * updates readme and rtd --------- Co-authored-by: Sophie T <[email protected]> Co-authored-by: sniffo <[email protected]>
glyg
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that referenced
this issue
Feb 13, 2024
* Fix for Issues #261 - cell division failed at the border * Fix Mesh creation Surface mesh create wasn't create all faces. Now it is fixed. Also : -add two methods to Mesh to list faces and vertices. -generalised coordinates -add `write_polygon_mesh` to export mesh into .ply to visualised with blinder * Add 2D collision solver Add class to solve collision in 2D or in 3D. 3D collision solver need to be fixed * Update README.md Add `How to cite` section Add `Geometry` section Add `Publications` section Update bibliography link * Generalised wich vertex penetrate face * Attempt to set out particular cases * Detect and fix self-crossing face Unable to make this algo works... https://europepmc.org/article/PMC/3660981 Use ordered vertices and their angle position. -> uncrossed face : angles are monotonically increasing -> crossed face : angles are not monotonically increasing * Use `.apply()` Need to recalculate angle_e for twisted face One fix which is only suitable for 2D lateral sheet... * ENH: write `mean_XX` method in `Epithelium` class (Issue #224) * Fix according to comments * Fix Issue #258 ax argument not considered in `plt_draw.sheet_view` * ENH: pass column name to `data_at_opposite` issue (#245) * Add publication and remove bibtex reference * Add check face convexity * Use reset_index and code simplification * yAdd to_mesh function (issue #221) and some test * Remove the use of reset_index in face_self_intersect * use ipv_draw with 2D data * Fix solution after detection point inside polygon * Remove solving collision for 2 same face... * Abord vertex displacement if it creates twisted face * New way to calculate the position of "penetrate" vertices For now, it is the best way to fix collision (compare to what I tried before). So when a vertex is inside an other face. It is pullback by 10% of the length of the ([v-f1]+[v-f2]/2). with v, f1, f2 position of vertices and center of face 1 and face 2, which are the faces to which the vertex belongs. It is not perfect and very arbitrary for now, but it avoids vertex displacement at strange place. * WIP - use force field to fix collision * Small fix * Remove function duplication due to circular import * Calculate "repulsion" gradient in the effector method. Remove loop * Fix tests Remove collisions tests Fix method call in meshes test Comment "update_repulstion" method in planar geometry * Add lateralsheet shapes + test * Update publication + add collapse texte * Add test for Repulsion effector * Add test update repulsion * Remove unused import * Add `drop_face` to allow hole (issues #220 and #141) (associate #221) * Update readme.md * Update publications in README.md * Add `lineage` attribute to `Epithelium` In order to keep track of cell lineage * Remove memory oscillation * builds with pip adds pyproject.toml build command: pip install --no-build-isolation --config-settings=editable.rebuild=true -ve. * debugging, still no build apparently * build and tests * update nb submodule * fix pyproject * install with pip in CI * install with pip in CI * install with pip in CI * adds scikit-build dep * python version * python version specifier * remove strang flags * adds _version.py * setuptools_scm dep * simplified I guess * zdds setuptools-scm to env, MakeFilelist shenanigans * restricting to 3.10 * install dev * pyhon version coherence * install cmd * trying to move to modern sckit-build (it's painful) * WIP change build * getting closer I hope * make_spherical test pasess \o/ * tests passing, warnings still to be treated * don't install editable version in gh action * remove diff chars * tagging again to avoid metadata mismatch * Uncomment 2D repulsion + tests Fix pandas issue * Add comments in effectors.py * rmeove _version.py and ignore in git * Update history.py (#274) > Added the self.time_stamps() method code for HistoryHdf5 class into the __init__() method so that time_stamps are only calculated once as self._time_stamps > Edited self.time_stamps() method to return self._time_stamps > Greatly improves efficiency of retrieve() method as time_stamps is not computed each time a new time-point is loaded. * skip 2 tests * fix non existing hdf5 * submodules * adds notebooks submodule * should fix history bug * adds submodules again * minoor fix, notebooks * updates readme and rtd * fixing pyproject --------- Co-authored-by: Sophie T <[email protected]> Co-authored-by: sniffo <[email protected]>
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Hi,
Cell division can fail for cell at the border. Especially when the axis of division involves junction that has no opposite.
Fix is easy. Inside base_topology file, modify line 122-126 :
[...] eptm.edge_df.loc[opposites.index, "srce"] = new_vert eptm.edge_df = pd.concat([eptm.edge_df, opposites], ignore_index=True) new_opp_edges = eptm.edge_df.index[-opposites.index.size :] eptm.edge_df.loc[new_opp_edges, "trgt"] = new_vert eptm.edge_df.loc[new_opp_edges, "srce"] = trgt [...]by :
[...] new_opp_edges = [] if len(opposites.index) != 0: eptm.edge_df.loc[opposites.index, "srce"] = new_vert eptm.edge_df = pd.concat([eptm.edge_df, opposites], ignore_index=True) new_opp_edges = eptm.edge_df.index[-opposites.index.size :] eptm.edge_df.loc[new_opp_edges, "trgt"] = new_vert eptm.edge_df.loc[new_opp_edges, "srce"] = trgt [...]Need to add the modification in the next PR.
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