nan min/max to handle possible nan ghosts#923
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PhilipDeegan merged 2 commits intoPHAREHUB:masterfrom Nov 12, 2024
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📝 Walkthrough📝 WalkthroughWalkthroughThe changes in this pull request involve modifications to the Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant PatchHierarchy
participant Dataset
User->>PatchHierarchy: Call global_min(qty)
PatchHierarchy->>Dataset: Calculate np.nanmin(pd.dataset[:])
Dataset-->>PatchHierarchy: Return minimum value
PatchHierarchy-->>User: Return global minimum
User->>PatchHierarchy: Call global_max(qty)
PatchHierarchy->>Dataset: Calculate np.nanmax(pd.dataset[:])
Dataset-->>PatchHierarchy: Return maximum value
PatchHierarchy-->>User: Return global maximum
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Comment on lines
+293
to
+297
| m = np.nanmax(pd.dataset[:]) | ||
| first = False | ||
| else: | ||
| m = max(m, pd.dataset[:].max()) | ||
| data_and_max = np.concatenate(([m], pd.dataset[:])) | ||
| m = np.nanmax(data_and_max) |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Refactor to reduce code duplication with global_min.
The global_max implementation duplicates the logic from global_min. Consider extracting a common utility function to handle both cases.
Here's a suggested refactoring:
+ def _global_minmax(self, qty, operation, time=None):
+ """Helper function for global min/max calculations
+ Args:
+ qty: The quantity to compute min/max for
+ operation: np.nanmin or np.nanmax
+ time: Optional timestamp
+ Returns:
+ The global min or max value
+ Raises:
+ ValueError: If all values are NaN
+ """
+ time = time or self._default_time()
+ values = []
+ for _, lvl in self.levels(time).items():
+ for patch in lvl.patches:
+ values.append(patch.patch_datas[qty].dataset[:])
+ all_values = np.concatenate(values)
+ if np.all(np.isnan(all_values)):
+ raise ValueError("All values are NaN")
+ return operation(all_values)
+
+ def global_min(self, qty, **kwargs):
+ return self._global_minmax(qty, np.nanmin, kwargs.get("time"))
+
+ def global_max(self, qty, **kwargs):
+ return self._global_minmax(qty, np.nanmax, kwargs.get("time"))This refactoring:
- Eliminates code duplication
- Improves performance by avoiding repeated array concatenations
- Properly handles the all-NaN case
- Makes the code more maintainable
Committable suggestion skipped: line range outside the PR's diff.
Comment on lines
+278
to
+282
| m = np.nanmin(pd.dataset[:]) | ||
| first = False | ||
| else: | ||
| m = min(m, pd.dataset[:].min()) | ||
| data_and_min = np.concatenate(([m], pd.dataset[:])) | ||
| m = np.nanmin(data_and_min) |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Consider optimizing the min calculation and handling edge cases.
The current implementation using array concatenation in each iteration is not optimal. Additionally, the case where all values are NaN should be handled explicitly.
Consider this more efficient implementation:
- m = np.nanmin(pd.dataset[:])
- first = False
- else:
- data_and_min = np.concatenate(([m], pd.dataset[:]))
- m = np.nanmin(data_and_min)
+ m = pd.dataset[:]
+ first = False
+ else:
+ m = np.append(m, pd.dataset[:])
+ if np.all(np.isnan(m)):
+ raise ValueError("All values are NaN")
+ return np.nanmin(m)Committable suggestion skipped: line range outside the PR's diff.
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Actionable comments posted: 1
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📒 Files selected for processing (1)
pyphare/pyphare/pharesee/hierarchy/hierarchy.py(2 hunks)
🔇 Additional comments (1)
pyphare/pyphare/pharesee/hierarchy/hierarchy.py (1)
293-297: Reduce code duplication with global_min.
The implementation duplicates the logic from global_min.
As suggested in a previous review, consider extracting a common utility function to handle both cases. This would:
- Eliminate code duplication
- Ensure consistent handling of edge cases
- Make the code more maintainable
The previous review comment provided a detailed implementation suggestion.
Comment on lines
+278
to
+282
| m = np.nanmin(pd.dataset[:]) | ||
| first = False | ||
| else: | ||
| m = min(m, pd.dataset[:].min()) | ||
| data_and_min = np.concatenate(([m], pd.dataset[:].flatten())) | ||
| m = np.nanmin(data_and_min) |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Consider optimizing the min calculation and handling edge cases.
While using np.nanmin correctly handles NaN values, the current implementation has some performance concerns:
- Concatenating arrays in a loop is inefficient (O(n²) complexity).
- No explicit handling for the case where all values are NaN.
Consider this more efficient implementation:
- m = np.nanmin(pd.dataset[:])
- first = False
- else:
- data_and_min = np.concatenate(([m], pd.dataset[:].flatten()))
- m = np.nanmin(data_and_min)
+ values = pd.dataset[:]
+ first = False
+ else:
+ values = np.append(values, pd.dataset[:])
+ if np.all(np.isnan(values)):
+ raise ValueError("All values are NaN")
+ return np.nanmin(values)Committable suggestion skipped: line range outside the PR's diff.
UCaromel
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Nov 13, 2024
* nan min/max to handle possible nan ghosts * flatten
UCaromel
pushed a commit
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Nov 13, 2024
* nan min/max to handle possible nan ghosts * flatten
UCaromel
added a commit
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that referenced
this pull request
Jan 6, 2025
…putation improved test, fixed some bugs in godunov-fluxes better timing directory creation (PHAREHUB#914) safer nu (PHAREHUB#911) try fallback for dl on keyerror + ruffage (PHAREHUB#916) convenient utils for mpi/hierarchies keep pyattrs on compute_from_hier nan min/max to handle possible nan ghosts (PHAREHUB#923) * nan min/max to handle possible nan ghosts * flatten rm atefact file fixed missing template keyword for macos-12 build more explicit unwrapping in godunov fluxes with variadic arguments of unclear size fixed lambda capture problem fixed lambda capture problem
UCaromel
added a commit
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that referenced
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Jan 6, 2025
…putation improved test, fixed some bugs in godunov-fluxes better timing directory creation (PHAREHUB#914) safer nu (PHAREHUB#911) try fallback for dl on keyerror + ruffage (PHAREHUB#916) convenient utils for mpi/hierarchies keep pyattrs on compute_from_hier nan min/max to handle possible nan ghosts (PHAREHUB#923) * nan min/max to handle possible nan ghosts * flatten rm atefact file fixed missing template keyword for macos-12 build more explicit unwrapping in godunov fluxes with variadic arguments of unclear size fixed lambda capture problem fixed lambda capture problem
UCaromel
added a commit
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this pull request
Jan 10, 2025
…putation improved test, fixed some bugs in godunov-fluxes better timing directory creation (PHAREHUB#914) safer nu (PHAREHUB#911) try fallback for dl on keyerror + ruffage (PHAREHUB#916) convenient utils for mpi/hierarchies keep pyattrs on compute_from_hier nan min/max to handle possible nan ghosts (PHAREHUB#923) * nan min/max to handle possible nan ghosts * flatten rm atefact file fixed missing template keyword for macos-12 build more explicit unwrapping in godunov fluxes with variadic arguments of unclear size fixed lambda capture problem fixed lambda capture problem
UCaromel
added a commit
to UCaromel/PHARE
that referenced
this pull request
Jan 10, 2025
…putation improved test, fixed some bugs in godunov-fluxes better timing directory creation (PHAREHUB#914) safer nu (PHAREHUB#911) try fallback for dl on keyerror + ruffage (PHAREHUB#916) convenient utils for mpi/hierarchies keep pyattrs on compute_from_hier nan min/max to handle possible nan ghosts (PHAREHUB#923) * nan min/max to handle possible nan ghosts * flatten rm atefact file fixed missing template keyword for macos-12 build more explicit unwrapping in godunov fluxes with variadic arguments of unclear size fixed lambda capture problem fixed lambda capture problem
UCaromel
added a commit
to UCaromel/PHARE
that referenced
this pull request
Jan 10, 2025
…putation improved test, fixed some bugs in godunov-fluxes better timing directory creation (PHAREHUB#914) safer nu (PHAREHUB#911) try fallback for dl on keyerror + ruffage (PHAREHUB#916) convenient utils for mpi/hierarchies keep pyattrs on compute_from_hier nan min/max to handle possible nan ghosts (PHAREHUB#923) * nan min/max to handle possible nan ghosts * flatten rm atefact file fixed missing template keyword for macos-12 build more explicit unwrapping in godunov fluxes with variadic arguments of unclear size fixed lambda capture problem fixed lambda capture problem
UCaromel
added a commit
to UCaromel/PHARE
that referenced
this pull request
Jan 10, 2025
…putation improved test, fixed some bugs in godunov-fluxes better timing directory creation (PHAREHUB#914) safer nu (PHAREHUB#911) try fallback for dl on keyerror + ruffage (PHAREHUB#916) convenient utils for mpi/hierarchies keep pyattrs on compute_from_hier nan min/max to handle possible nan ghosts (PHAREHUB#923) * nan min/max to handle possible nan ghosts * flatten rm atefact file fixed missing template keyword for macos-12 build more explicit unwrapping in godunov fluxes with variadic arguments of unclear size fixed lambda capture problem fixed lambda capture problem
UCaromel
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that referenced
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Jan 13, 2025
* nan min/max to handle possible nan ghosts * flatten
UCaromel
added a commit
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Jan 13, 2025
updated + tested mhd_state, updated mhd_model revert back my typo on hybrid_tagger fixed typo in test_mhd_state preparing mhd usablevecfield new field initialisation logic Added end of file newline in field_user_initializer.hpp added mhd state fixture wrote test for mhd_state_fixtures added mhd yee grid, modified gridlayout to handle both hybrid and mhd up init_functions MHD solver solver mhd update more solver updates preparing rebase formatting riemann reconstruction quick commit fix solved conflict more solver updates initial branch commit: new architecture for reconstruction + flux computation improved test, fixed some bugs in godunov-fluxes better timing directory creation (PHAREHUB#914) safer nu (PHAREHUB#911) try fallback for dl on keyerror + ruffage (PHAREHUB#916) convenient utils for mpi/hierarchies keep pyattrs on compute_from_hier nan min/max to handle possible nan ghosts (PHAREHUB#923) * nan min/max to handle possible nan ghosts * flatten rm atefact file fixed missing template keyword for macos-12 build more explicit unwrapping in godunov fluxes with variadic arguments of unclear size fixed lambda capture problem fixed lambda capture problem added time integration added projection functions for centering, primitive/conservetive converter added projection functions for centering, primitive/conservetive converter solver ref binding in a lambda issue added template deduction guide on for macOS compile on a struct of MHDSolver New approach for template deduction for the struct in MHDSolver added usable ghost cells syntaxe fixes for Werror full boundary conditions in solver changed ghost cells function names to be more consistant with hybrid corrected dummyhierarchy in testmhdsolver (operation on nullptr) MHDMock simulator setup added pybind wrappers and first tests successful orszag-tang test fixed typo fixed typo fixed typo bug fixes (wrong usage of prevIndex nextIndex)
UCaromel
added a commit
to UCaromel/PHARE
that referenced
this pull request
Jan 13, 2025
updated + tested mhd_state, updated mhd_model revert back my typo on hybrid_tagger fixed typo in test_mhd_state preparing mhd usablevecfield new field initialisation logic Added end of file newline in field_user_initializer.hpp added mhd state fixture wrote test for mhd_state_fixtures added mhd yee grid, modified gridlayout to handle both hybrid and mhd up init_functions MHD solver solver mhd update more solver updates preparing rebase formatting riemann reconstruction quick commit fix solved conflict more solver updates initial branch commit: new architecture for reconstruction + flux computation improved test, fixed some bugs in godunov-fluxes better timing directory creation (PHAREHUB#914) safer nu (PHAREHUB#911) try fallback for dl on keyerror + ruffage (PHAREHUB#916) convenient utils for mpi/hierarchies keep pyattrs on compute_from_hier nan min/max to handle possible nan ghosts (PHAREHUB#923) * nan min/max to handle possible nan ghosts * flatten rm atefact file fixed missing template keyword for macos-12 build more explicit unwrapping in godunov fluxes with variadic arguments of unclear size fixed lambda capture problem fixed lambda capture problem added time integration added projection functions for centering, primitive/conservetive converter added projection functions for centering, primitive/conservetive converter solver ref binding in a lambda issue added template deduction guide on for macOS compile on a struct of MHDSolver New approach for template deduction for the struct in MHDSolver added usable ghost cells syntaxe fixes for Werror full boundary conditions in solver changed ghost cells function names to be more consistant with hybrid corrected dummyhierarchy in testmhdsolver (operation on nullptr) MHDMock simulator setup added pybind wrappers and first tests successful orszag-tang test fixed typo fixed typo fixed typo bug fixes (wrong usage of prevIndex nextIndex)
nicolasaunai
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Mar 6, 2025
updated + tested mhd_state, updated mhd_model revert back my typo on hybrid_tagger fixed typo in test_mhd_state preparing mhd usablevecfield new field initialisation logic Added end of file newline in field_user_initializer.hpp added mhd state fixture wrote test for mhd_state_fixtures added mhd yee grid, modified gridlayout to handle both hybrid and mhd up init_functions MHD solver solver mhd update more solver updates preparing rebase formatting riemann reconstruction quick commit fix solved conflict more solver updates initial branch commit: new architecture for reconstruction + flux computation improved test, fixed some bugs in godunov-fluxes better timing directory creation (#914) safer nu (#911) try fallback for dl on keyerror + ruffage (#916) convenient utils for mpi/hierarchies keep pyattrs on compute_from_hier nan min/max to handle possible nan ghosts (#923) * nan min/max to handle possible nan ghosts * flatten rm atefact file fixed missing template keyword for macos-12 build more explicit unwrapping in godunov fluxes with variadic arguments of unclear size fixed lambda capture problem fixed lambda capture problem added time integration added projection functions for centering, primitive/conservetive converter added projection functions for centering, primitive/conservetive converter solver ref binding in a lambda issue added template deduction guide on for macOS compile on a struct of MHDSolver New approach for template deduction for the struct in MHDSolver added usable ghost cells syntaxe fixes for Werror full boundary conditions in solver changed ghost cells function names to be more consistant with hybrid corrected dummyhierarchy in testmhdsolver (operation on nullptr) MHDMock simulator setup added pybind wrappers and first tests successful orszag-tang test fixed typo fixed typo fixed typo bug fixes (wrong usage of prevIndex nextIndex)
UCaromel
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Mar 12, 2025
updated + tested mhd_state, updated mhd_model revert back my typo on hybrid_tagger fixed typo in test_mhd_state preparing mhd usablevecfield new field initialisation logic Added end of file newline in field_user_initializer.hpp added mhd state fixture wrote test for mhd_state_fixtures added mhd yee grid, modified gridlayout to handle both hybrid and mhd up init_functions MHD solver solver mhd update more solver updates preparing rebase formatting riemann reconstruction quick commit fix solved conflict more solver updates initial branch commit: new architecture for reconstruction + flux computation improved test, fixed some bugs in godunov-fluxes better timing directory creation (PHAREHUB#914) safer nu (PHAREHUB#911) try fallback for dl on keyerror + ruffage (PHAREHUB#916) convenient utils for mpi/hierarchies keep pyattrs on compute_from_hier nan min/max to handle possible nan ghosts (PHAREHUB#923) * nan min/max to handle possible nan ghosts * flatten rm atefact file fixed missing template keyword for macos-12 build more explicit unwrapping in godunov fluxes with variadic arguments of unclear size fixed lambda capture problem fixed lambda capture problem added time integration added projection functions for centering, primitive/conservetive converter added projection functions for centering, primitive/conservetive converter solver ref binding in a lambda issue added template deduction guide on for macOS compile on a struct of MHDSolver New approach for template deduction for the struct in MHDSolver added usable ghost cells syntaxe fixes for Werror full boundary conditions in solver changed ghost cells function names to be more consistant with hybrid corrected dummyhierarchy in testmhdsolver (operation on nullptr) MHDMock simulator setup added pybind wrappers and first tests successful orszag-tang test fixed typo fixed typo fixed typo bug fixes (wrong usage of prevIndex nextIndex)
nicolasaunai
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Mar 13, 2025
updated + tested mhd_state, updated mhd_model revert back my typo on hybrid_tagger fixed typo in test_mhd_state preparing mhd usablevecfield new field initialisation logic Added end of file newline in field_user_initializer.hpp added mhd state fixture wrote test for mhd_state_fixtures added mhd yee grid, modified gridlayout to handle both hybrid and mhd up init_functions MHD solver solver mhd update more solver updates preparing rebase formatting riemann reconstruction quick commit fix solved conflict more solver updates initial branch commit: new architecture for reconstruction + flux computation improved test, fixed some bugs in godunov-fluxes better timing directory creation (#914) safer nu (#911) try fallback for dl on keyerror + ruffage (#916) convenient utils for mpi/hierarchies keep pyattrs on compute_from_hier nan min/max to handle possible nan ghosts (#923) * nan min/max to handle possible nan ghosts * flatten rm atefact file fixed missing template keyword for macos-12 build more explicit unwrapping in godunov fluxes with variadic arguments of unclear size fixed lambda capture problem fixed lambda capture problem added time integration added projection functions for centering, primitive/conservetive converter added projection functions for centering, primitive/conservetive converter solver ref binding in a lambda issue added template deduction guide on for macOS compile on a struct of MHDSolver New approach for template deduction for the struct in MHDSolver added usable ghost cells syntaxe fixes for Werror full boundary conditions in solver changed ghost cells function names to be more consistant with hybrid corrected dummyhierarchy in testmhdsolver (operation on nullptr) MHDMock simulator setup added pybind wrappers and first tests successful orszag-tang test fixed typo fixed typo fixed typo bug fixes (wrong usage of prevIndex nextIndex)
UCaromel
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Apr 15, 2025
updated + tested mhd_state, updated mhd_model revert back my typo on hybrid_tagger fixed typo in test_mhd_state preparing mhd usablevecfield new field initialisation logic Added end of file newline in field_user_initializer.hpp added mhd state fixture wrote test for mhd_state_fixtures added mhd yee grid, modified gridlayout to handle both hybrid and mhd up init_functions MHD solver solver mhd update more solver updates preparing rebase formatting riemann reconstruction quick commit fix solved conflict more solver updates initial branch commit: new architecture for reconstruction + flux computation improved test, fixed some bugs in godunov-fluxes better timing directory creation (PHAREHUB#914) safer nu (PHAREHUB#911) try fallback for dl on keyerror + ruffage (PHAREHUB#916) convenient utils for mpi/hierarchies keep pyattrs on compute_from_hier nan min/max to handle possible nan ghosts (PHAREHUB#923) * nan min/max to handle possible nan ghosts * flatten rm atefact file fixed missing template keyword for macos-12 build more explicit unwrapping in godunov fluxes with variadic arguments of unclear size fixed lambda capture problem fixed lambda capture problem added time integration added projection functions for centering, primitive/conservetive converter added projection functions for centering, primitive/conservetive converter solver ref binding in a lambda issue added template deduction guide on for macOS compile on a struct of MHDSolver New approach for template deduction for the struct in MHDSolver added usable ghost cells syntaxe fixes for Werror full boundary conditions in solver changed ghost cells function names to be more consistant with hybrid corrected dummyhierarchy in testmhdsolver (operation on nullptr) MHDMock simulator setup added pybind wrappers and first tests successful orszag-tang test fixed typo fixed typo fixed typo bug fixes (wrong usage of prevIndex nextIndex)
nicolasaunai
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Apr 16, 2025
updated + tested mhd_state, updated mhd_model revert back my typo on hybrid_tagger fixed typo in test_mhd_state preparing mhd usablevecfield new field initialisation logic Added end of file newline in field_user_initializer.hpp added mhd state fixture wrote test for mhd_state_fixtures added mhd yee grid, modified gridlayout to handle both hybrid and mhd up init_functions MHD solver solver mhd update more solver updates preparing rebase formatting riemann reconstruction quick commit fix solved conflict more solver updates initial branch commit: new architecture for reconstruction + flux computation improved test, fixed some bugs in godunov-fluxes better timing directory creation (#914) safer nu (#911) try fallback for dl on keyerror + ruffage (#916) convenient utils for mpi/hierarchies keep pyattrs on compute_from_hier nan min/max to handle possible nan ghosts (#923) * nan min/max to handle possible nan ghosts * flatten rm atefact file fixed missing template keyword for macos-12 build more explicit unwrapping in godunov fluxes with variadic arguments of unclear size fixed lambda capture problem fixed lambda capture problem added time integration added projection functions for centering, primitive/conservetive converter added projection functions for centering, primitive/conservetive converter solver ref binding in a lambda issue added template deduction guide on for macOS compile on a struct of MHDSolver New approach for template deduction for the struct in MHDSolver added usable ghost cells syntaxe fixes for Werror full boundary conditions in solver changed ghost cells function names to be more consistant with hybrid corrected dummyhierarchy in testmhdsolver (operation on nullptr) MHDMock simulator setup added pybind wrappers and first tests successful orszag-tang test fixed typo fixed typo fixed typo bug fixes (wrong usage of prevIndex nextIndex)
UCaromel
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updated + tested mhd_state, updated mhd_model revert back my typo on hybrid_tagger fixed typo in test_mhd_state preparing mhd usablevecfield new field initialisation logic Added end of file newline in field_user_initializer.hpp added mhd state fixture wrote test for mhd_state_fixtures added mhd yee grid, modified gridlayout to handle both hybrid and mhd up init_functions MHD solver solver mhd update more solver updates preparing rebase formatting riemann reconstruction quick commit fix solved conflict more solver updates initial branch commit: new architecture for reconstruction + flux computation improved test, fixed some bugs in godunov-fluxes better timing directory creation (PHAREHUB#914) safer nu (PHAREHUB#911) try fallback for dl on keyerror + ruffage (PHAREHUB#916) convenient utils for mpi/hierarchies keep pyattrs on compute_from_hier nan min/max to handle possible nan ghosts (PHAREHUB#923) * nan min/max to handle possible nan ghosts * flatten rm atefact file fixed missing template keyword for macos-12 build more explicit unwrapping in godunov fluxes with variadic arguments of unclear size fixed lambda capture problem fixed lambda capture problem added time integration added projection functions for centering, primitive/conservetive converter added projection functions for centering, primitive/conservetive converter solver ref binding in a lambda issue added template deduction guide on for macOS compile on a struct of MHDSolver New approach for template deduction for the struct in MHDSolver added usable ghost cells syntaxe fixes for Werror full boundary conditions in solver changed ghost cells function names to be more consistant with hybrid corrected dummyhierarchy in testmhdsolver (operation on nullptr) MHDMock simulator setup added pybind wrappers and first tests successful orszag-tang test fixed typo fixed typo fixed typo bug fixes (wrong usage of prevIndex nextIndex)
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PatchHierarchyclass.