dedalus.tools.post
Post-processing helpers.
Module Contents
- logger
- MPI_RANK
- MPI_SIZE
- visit_writes(set_paths, function, **kw)
Apply function to writes from a list of analysis sets.
- Parameters:
set_paths (list of str or pathlib.Path) – List of set paths
function (function(set_path, start, count, **kw)) – A function on an HDF5 file, start index, and count.
Other keyword arguments are passed on to `function`
Notes
This function is parallelized over writes, and so can be effectively parallelized up to the number of writes from all specified sets.
- get_assigned_writes(set_paths)
Divide writes from a list of analysis sets between MPI processes.
- Parameters:
set_paths (list of str or pathlib.Path) – List of set paths
- get_all_writes(set_paths)
Get write numbers from a list of analysis sets.
- Parameters:
set_paths (list of str or pathlib.Path) – List of set paths
- get_assigned_sets(base_path, distributed=False)
Divide analysis sets from a FileHandler between MPI processes.
- Parameters:
base_path (str or pathlib.Path) – Base path of FileHandler output
distributed (bool, optional) – Divide distributed sets instead of merged sets (default: False)
- merge_virtual_analysis(base_path, cleanup=False)
Merge virtual files from a FileHandler into single files.
- Parameters:
base_path (str or pathlib.Path) – Base path of FileHandler output
cleanup (bool, optional) – Delete virtual and distributed files after merging (default: False)
Notes
This function is parallelized over sets, and so can be effectively parallelized up to the number of virtual files.
Merged files are output into a ‘merged_X’ directory, where X is the stem name of the input FileHandler.
- merge_virtual_file(virtual_file_path, cleanup=False)
Merge a virtual file from a FileHandler.
- Parameters:
virtual_file_path (str of pathlib.Path) – Path to a virtual .h5 file
cleanup (bool, optional) – Delete distributed files and virtual file after merging (default: False)
- merge_analysis(base_path, cleanup=False)
Merge distributed analysis sets from a FileHandler.
- Parameters:
base_path (str or pathlib.Path) – Base path of FileHandler output
cleanup (bool, optional) – Delete distributed files after merging (default: False)
Notes
This function is parallelized over sets, and so can be effectively parallelized up to the number of distributed sets.
- merge_distributed_set(set_path, cleanup=False)
Merge a distributed analysis set from a FileHandler.
- Parameters:
set_path (str of pathlib.Path) – Path to distributed analysis set folder
cleanup (bool, optional) – Delete distributed files after merging (default: False)
- merge_setup(joint_file, proc_paths, virtual=False)
Merge HDF5 setup from part of a distributed analysis set into a joint file.
- Parameters:
joint_file (HDF5 file) – Joint file
proc_paths (list of [str or pathlib.Path]) – List of files in a distributed analysis set
virtual (bool, optional) – If True, merging a virtual file into a single file rather than distributed set
- merge_data(joint_file, proc_path)
Merge data from part of a distributed analysis set into a joint file.
- Parameters:
joint_file (HDF5 file) – Joint file
proc_path (str or pathlib.Path) – Path to part of a distributed analysis set
- merge_virtual
- dedalus_h5_to_xarray(dset)
Convert Dedalus HDF5 dataset to an Xarray DataArray.
- load_tasks_to_xarray(filename, tasks=None, squeeze_constant=True)
Load task from Dedalus HDF5 output to an Xarray DataArray.