diff --git a/NEWS.md b/NEWS.md index b06e4254..abc1aa94 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,11 +1,15 @@ # Changelog -## Version 1.5.0 +## Version 1.5.0 (19 June 2023) #### General - Python 3.12 is now supported, Python 3.8.1 is required for development. - `total_filesize` now errors out when directories are passed. +#### Features +- Added experimental support for reading OpenPMD files (with most of the + heavy-lifting done by @krishivbhatia). Please, report any issue you might find. + ## Version 1.4.0 (2 May 2023) #### General diff --git a/docs/features.rst b/docs/features.rst index 8914f478..6210668c 100644 --- a/docs/features.rst +++ b/docs/features.rst @@ -119,7 +119,7 @@ Units Grid Data --------- -- Read 1D, 2D, and 3D ASCII and HDF5 files as ``HierarchicalGridData``, which supports: +- Read 1D, 2D, and 3D ASCII, HDF5 and OpenPMD (experimental) files as ``HierarchicalGridData``, which supports: - working with multiple components and refinement levels; - handling ghost-zones; diff --git a/docs/index.rst b/docs/index.rst index b3adbe23..307d892f 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -51,7 +51,7 @@ For a full list of available features, see the :doc:`features page `. (:py:mod:`~.tensor`). - Work with 1D, 2D, and 3D grid functions (:py:mod:`~.grid_data`, :py:mod:`~.cactus_grid_functions`) as output by ``CarpetIOHDF5`` or - ``CarpetIOASCII``. + ``CarpetIOASCII``, or in OpenPMD format. - Work with horizon data from (:py:mod:`~.cactus_horizons`) as output by ``QuasiLocalMeasures`` and ``AHFinderDirect``. - Perform common operations with horizons (:py:mod:`~.hor_utils`). diff --git a/kuibit/cactus_grid_functions.py b/kuibit/cactus_grid_functions.py index 73398cde..7df7822e 100755 --- a/kuibit/cactus_grid_functions.py +++ b/kuibit/cactus_grid_functions.py @@ -19,7 +19,6 @@ # # You should have received a copy of the GNU General Public License along with # this program; if not, see . - """The :py:mod:`~.cactus_grid` module provides functions to load grid function in Cactus formats. @@ -30,12 +29,11 @@ object with keys the possible dimensions (e.g., ``x``, ``yz``, ``xyz``). - :py:class`~.AllGridFunctions` takes all the files in SimDir and sort them according the different grid functions they contain. -- There are two :py:class`~.OneGridFunction` classes, one for HDF5 files and one - for ASCII files. They describe one single grid function and they contains the - files associated to that grid function. Both the classes are derived from the - same abstract base class :py:class`~.OneGridFunctionBase`, which implements - the shared methods. - +- There are three :py:class`~.OneGridFunction` classes, one for HDF5 files, one + for ASCII files, and one for OpenPMD files. They describe one single grid + function and they contains the files associated to that grid function. Both + the classes are derived from the same abstract base class + :py:class`~.OneGridFunctionBase`, which implements the shared methods. These are hierarchical classes, one containing the others, so one typically ends up with a series of brackets to access the actual data. For example, if ``sim`` is a :py:class:`~.SimDir`, ``sim.gf.xy['rho_b'][0]`` is ``rho_b`` at iteration 0 @@ -54,6 +52,7 @@ import h5py import numpy as np +import openpmd_api as openpmd_io from kuibit import grid_data, simdir from kuibit.attr_dict import pythonize_name_dict @@ -118,7 +117,6 @@ def __init__(self, allfiles, var_name): # We use this to extract only the information related to the specific # variable self.var_name = var_name - for path in self.allfiles: self._parse_file(path) @@ -170,7 +168,7 @@ def _iterations_in_file(self, path): :rtype: list """ - return sorted(list(self.alldata[path].keys())) + return sorted(self.alldata[path].keys()) def _min_iteration_in_file(self, path): """Return the minimum available iterations in the given file. @@ -1006,7 +1004,7 @@ def _parse_file(self, path): # file. We keep a collection of all these in the variable self.alldata try: with h5py.File(path, "r") as f: - for group in f.keys(): + for group in f: matched = self.rx_group_name.match(group) # If this is not an interesting group, just skip it if not matched: @@ -1248,7 +1246,7 @@ def clear_cache(self): for filename, file_reader in self.alldata.items(): for iteration, iteration_reader in file_reader.items(): for ref_level, ref_level_reader in iteration_reader.items(): - for component in ref_level_reader.keys(): + for component in ref_level_reader: self.alldata[filename][iteration][ref_level][ component ] = None @@ -1275,6 +1273,193 @@ def time_at_iteration(self, iteration): return dataset.attrs["time"] +# What is a context manager? +# +# Context managers are useful ways to handle resources in Python. With a +# context manager, we do not have to worry about releasing resources. Here, +# we create a context manager that automatically closes the OpenPMD series +# object. +@contextmanager +def openpmd_series(path: str): + """Context manager to read an OpenPMD file. + + :param path: Path of the file. + :type path: str + + """ + series = openpmd_io.Series(path, openpmd_io.Access.read_only) + try: + yield series + except RuntimeError as exce: + raise RuntimeError(f"File {path} cannot be processed") from exce + finally: + series.close() + + +class OneGridFunctionOpenPMD(BaseOneGridFunction): + """Read grid data produced by CarpetOpenPMD files. + + This class is derived from :py:class:`~.BaseOneGridFunction` and implements + the reading facilities. + """ + + # This class implements the details on how to read the data for OpenPMD + # files, most of the functionalities of the class are in + # OneGridFunctionBase. + + def __init__(self, allfiles, var_name: str, dimension, mesh_basename: str): + """Constructor. + + :param allfiles: Paths of files associated to the variable. + :type allfiles: list of str + :param var_name: Variable name. + :type var_name: str + :param mesh_basename: Basename of the OpenPMD mesh. Typically, _ + :type mesh_basename: str + + """ + self.dimension = dimension + self.mesh_basename = mesh_basename + self.map = None + + self._iterations_to_times = {} + + # Let's unpack the regex + # + # 1. ^ $ match the beginning and end of string + # 2. {mesh_basename} is substituted with the prefix + # 3. _ is the literal underscore + # 4. (?:rl|lev) is a non-capturing group that matches the literals + # rl or lev + # 5. (\d+) matches a number, the refinement level + self._pattern_mesh_name = rf"^{mesh_basename}_(?:rl|lev)(\d+)$" + + super().__init__(allfiles, var_name) + + # super() will fill the other variables that we need for dataset_format + if self.map is None: + self.map = "" + + # OpenPMD data does not contain ghost zones + self.are_ghostzones_in_files = False + + def _parse_file(self, path: str): + """Read the content of the given file (without reading the data). + + For OpenPMD files, a "file" is really a directory. + + :param path: Path of the file. + :type path: str + + """ + rx_mesh = re.compile(self._pattern_mesh_name) + + with openpmd_series(path) as series: + iter_open_pmd = series.iterations + for iteration, iteration_obj in iter_open_pmd.items(): + self._iterations_to_times[iteration] = iteration_obj.time + all_meshes = iteration_obj.meshes + for mesh_name, mesh_obj in all_meshes.items(): + matched = rx_mesh.match(mesh_name) + if matched is not None: + ref_level = matched.group(1) + # Here is where we prepare are nested alldata dictionary + alldata_file = self.alldata.setdefault(path, {}) + alldata_iteration = alldata_file.setdefault( + int(iteration), {} + ) + alldata_ref_level = alldata_iteration.setdefault( + int(ref_level), {} + ) + component = 0 + for _chunk in mesh_obj[ + self.var_name + ].available_chunks(): + # We set the actual data to None, and we will read it in + # _read_component_as_uniform_grid_data upon request + alldata_ref_level.setdefault(component, None) + component += 1 + + def _read_component_as_uniform_grid_data( + self, path: str, iteration: int, ref_level: int, component: int + ): + """Return the component at the given iteration, refinement level, and component. + + :param path: Path of the file. + :type path: str + :param iteration: Iteration. + :type iteration: int + :param ref_level: Refinement level. + :type ref_level: int + :param component: Component. + :type component: int + + :returns: Component as a :py:class:`~.UniformGridData`. + :rtype: :py:class:`~.UniformGridData` + + """ + # ref_level is an integer like 0, 1, 2, 3, 4, 5. + # So it is formatted to 2 digits to give 00, 01, 04, 10, 11 + mesh_name = f"{self.mesh_basename}_lev{ref_level:02d}" + + if self.alldata[path][iteration][ref_level][component] is None: + with openpmd_series(path) as series: + time = series.iterations[iteration].time + mesh_obj = series.iterations[iteration].meshes[mesh_name] + origin = np.array(mesh_obj.grid_global_offset) + dx = np.array(mesh_obj.grid_spacing) + mrc = mesh_obj[self.var_name] + chunk = mrc.available_chunks()[component] + offset = np.array(chunk.offset) + shape = chunk.extent + # Do the actual reading + data = mrc.load_chunk(chunk.offset, chunk.extent) + series.flush() + grid = grid_data.UniformGrid( + shape, + x0=(origin + offset * dx), + dx=dx, + ref_level=ref_level, + num_ghost=[0, 0, 0], + time=time, + iteration=iteration, + component=component, + ) + self.alldata[path][iteration][ref_level][component] = ( + grid_data.UniformGridData(grid, data) + ) + return self.alldata[path][iteration][ref_level][component] + + def clear_cache(self): + """Remove all the cached entries. + + Every time a component is read, :py:class:`~.OneGridFunctionsH5` caches + its value (reading can be expensive). In certain cases, this can lead to + an explosion in the size of this object. For example, when reading + several iterations to make a movie. This method removes all the cached + entries, keeping the size of the object under control. + """ + for filename, file_reader in self.alldata.items(): + for iteration, iteration_reader in file_reader.items(): + for ref_level, ref_level_reader in iteration_reader.items(): + for component in ref_level_reader: + self.alldata[filename][iteration][ref_level][ + component + ] = None + + def time_at_iteration(self, iteration: int): + """Return the time corresponding to the provided iteration. + + :param iteration: Iteration. + :type iteration: int + + :returns: Time corresponding to ``iteration``. + :rtype: float + + """ + return self._iterations_to_times[iteration] + + class AllGridFunctions: """Helper class to read various types of grid data in a list of files and properly order them. The core of this object is the ``_vars`` dictionary @@ -1302,6 +1487,8 @@ class AllGridFunctions: # specific pattern corresponding to the dimension (which are the keys on # the following dictionary). In general, the file name will be: # variable-name.ext.h5, eg rho.xy.h5. + + # Organizes data by dimensions and variables filename_extensions = { (0,): ".x", (1,): ".y", @@ -1322,6 +1509,24 @@ class AllGridFunctions: (0, 1, 2): "xyz", } + # regex to match mesh_name like z4c_allc_lev05, admbasex_curv_lev00, + # admbasex_lapse_lev05 + # Let's uinpack this regex: + # 1. ^ and $ mean that we are matching the entire string + # 2. (\w+) is a capturing group that matches a word. This is thorn_groupname + # For example, wavetoy_state + # 3. _ matches the literal underscore + # 4. (?: ) is a non-capturing group, rl|lev means that we match one of the two + # 5. (\d+) matches numbers + _mesh_name_pattern = r"^(\w+)_(?:rl|lev)(\d+)$" + + # Mapping between a variable name and the prefix for the mesh name in the + # OpenPMD file. Typically, thorname_groupname. + _openpmd_mesh_basenames = {} + + # The oddball case is with OpenPMD files. OpenPMD files are actually folders + # with extension .bp4 and they are always 3D. + def __init__(self, allfiles, dimension, num_ghost=None): """Constructor. @@ -1369,7 +1574,6 @@ def __init__(self, allfiles, dimension, num_ghost=None): # Example of filenames are: # admbase-metric.xyz.file_158.h5 (one group per file) # alp.xy.h5 (one variable per file) - # filename_pattern = r"^([a-zA-Z0-9_]+)(-)?([a-zA-Z0-9\[\]_]+)%s.%s$" filename_pattern = r"^(([a-zA-Z0-9_]+)-)?([a-zA-Z0-9\[\]_]+)%s.%s$" h5_pattern = filename_pattern % ( self.filename_extensions[self.dimension], @@ -1380,10 +1584,17 @@ def __init__(self, allfiles, dimension, num_ghost=None): r"asc(\.(gz|bz2))?", ) + # OpenPMD files are very different. Instead of being single files, they + # are full directories. We match them by find the data.0 file, which is + # contained in all the OpenPMD directories. Also, OpenPMD files are + # always for 3D variables. + openpmd_pattern = r"^data\.0$" + # Variable files is a dictionary, the keys are the variables, the # values the set of files associated to that variable self._vars_ascii_files = {} self._vars_h5_files = {} + self._vars_openpmd_files = {} # _vars contains the actual data. It is used to cache results. _vars is # a dictionary with keys the variables and values OneGridFunction (H5 or @@ -1392,6 +1603,8 @@ def __init__(self, allfiles, dimension, num_ghost=None): rx_h5 = re.compile(h5_pattern) rx_ascii = re.compile(ascii_pattern) + rx_openpmd = re.compile(openpmd_pattern) + rx_mesh = re.compile(self._mesh_name_pattern) # Here we scan all the files and find those with a name that match # one of our regular expressions. @@ -1400,6 +1613,14 @@ def __init__(self, allfiles, dimension, num_ghost=None): filename = os.path.split(f)[1] matched_h5 = rx_h5.match(filename) matched_ascii = rx_ascii.match(filename) + # OpenPMD files are always 3D, so we ignore them when the dimension + # is not xyz + matched_openpmd = ( + rx_openpmd.match(filename) + if self._dim_names[self.dimension] == "xyz" + else None + ) + # If matched_pattern is not None, this is a Carpet h5 file if matched_h5 is not None: # First, we understand if the file was output with @@ -1430,7 +1651,7 @@ def __init__(self, allfiles, dimension, num_ghost=None): try: with h5py.File(f, "r") as h5f: # Here group is in the sense of HDF5 group - for group in h5f.keys(): + for group in h5f: group_matched = rx_group_name.match(group) # If this is not an interesting group, just skip it if not group_matched: @@ -1497,7 +1718,7 @@ def __init__(self, allfiles, dimension, num_ghost=None): opener=opener, opener_mode=opener_mode, ) - for variable_name in column_description.keys(): + for variable_name in column_description: var_list = self._vars_ascii_files.setdefault( variable_name, set() ) @@ -1505,6 +1726,31 @@ def __init__(self, allfiles, dimension, num_ghost=None): except RuntimeError: pass + elif matched_openpmd is not None: + # We detected a data.0 file. Its parent directory is the actual + # bp4 file. + dir_path = os.path.split(f)[0] + with openpmd_series(dir_path) as series: + for _iteration, iteration_obj in series.iterations.items(): + for ( + mesh_name, + mesh_obj, + ) in iteration_obj.meshes.items(): + matched = rx_mesh.match(mesh_name) + if matched is None: + raise RuntimeError( + f"Could not parse mesh {mesh_name}" + ) + mesh_basename = matched.group(1) + for variable_name in mesh_obj: + var_list = self._vars_openpmd_files.setdefault( + variable_name, set() + ) + var_list.add(dir_path) + self._openpmd_mesh_basenames[variable_name] = ( + mesh_basename + ) + # What pythonize_name_dict does is to make the various variables # accessible as attributes, e.g. self.fields.rho self.fields = pythonize_name_dict(list(self.keys()), self.__getitem__) @@ -1521,6 +1767,16 @@ def __getitem__(self, key): self._vars[var_name] = OneGridFunctionH5( self._vars_h5_files[var_name], var_name, self.dimension ) + elif var_name in self._vars_openpmd_files: + self._vars[var_name] = OneGridFunctionOpenPMD( + self._vars_openpmd_files[var_name], + var_name, + self.dimension, + # Get mesh_basenames corresponding to var name from dict. + # mesh_basename is thornname_groupname, where groupname is the + # name of the variable group that contains var_name + self._openpmd_mesh_basenames[var_name], + ) elif var_name in self._vars_ascii_files: if self.num_ghost is None: warnings.warn( @@ -1577,7 +1833,11 @@ def keys(self): """Return the list of all the available variables.""" # We merge the dictionaries and return the keys. # This automatically takes care of making sure that they keys are unique. - return {**self._vars_h5_files, **self._vars_ascii_files}.keys() + return { + **self._vars_h5_files, + **self._vars_ascii_files, + **self._vars_openpmd_files, + }.keys() def __str__(self): ret = "\nAvailable grid data of dimension " @@ -1601,6 +1861,9 @@ def allfiles(self): allfiles.update(file_list) for file_list in self._vars_ascii_files.values(): allfiles.update(file_list) + for dir_list in self._vars_openpmd_files.values(): + # OpenPMD files are actually directory + allfiles.update(dir_list) return allfiles def total_filesize(self, unit="MB"): @@ -1638,6 +1901,7 @@ class GridFunctionsDir: # convenint to index them with numbers. This dictionary provides a way # to go from one notation to the other. Internally, we always use the # index notation. + _dim_indices = { "x": (0,), "y": (1,), @@ -1730,6 +1994,18 @@ def total_filesize(self, unit="MB"): """ # First we find all the unique files allfiles = set() - for dim in self._all_griddata.keys(): + for dim in self._all_griddata: allfiles.update(self[dim].allfiles) + # OpenPMD "files" are really directories, so if we want to measure their + # size accurately we have to open them up + for f_ in set(allfiles): + if f_.endswith(".bp4") or f_.endswith(".bp5"): + # Remove the directory and add all the files inside + allfiles.remove(f_) + allfiles.update( + { + os.path.abspath(os.path.join(f_, p)) + for p in os.listdir(f_) + } + ) return total_filesize(allfiles, unit=unit) diff --git a/poetry.lock b/poetry.lock index 4bcdeef1..4e8b4584 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. 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"sha256:3da69048e4540d84af32131829ff948f1e022c1c6bdb8d6102117aac784f6859"}, + {file = "wcwidth-0.2.13.tar.gz", hash = "sha256:72ea0c06399eb286d978fdedb6923a9eb47e1c486ce63e9b4e64fc18303972b5"}, ] [[package]] @@ -3607,29 +3787,29 @@ files = [ [[package]] name = "websocket-client" -version = "1.6.4" +version = "1.8.0" description = "WebSocket client for Python with low level API options" optional = false python-versions = ">=3.8" files = [ - {file = "websocket-client-1.6.4.tar.gz", hash = "sha256:b3324019b3c28572086c4a319f91d1dcd44e6e11cd340232978c684a7650d0df"}, - {file = "websocket_client-1.6.4-py3-none-any.whl", hash = "sha256:084072e0a7f5f347ef2ac3d8698a5e0b4ffbfcab607628cadabc650fc9a83a24"}, + {file = "websocket_client-1.8.0-py3-none-any.whl", hash = "sha256:17b44cc997f5c498e809b22cdf2d9c7a9e71c02c8cc2b6c56e7c2d1239bfa526"}, + {file = "websocket_client-1.8.0.tar.gz", hash = "sha256:3239df9f44da632f96012472805d40a23281a991027ce11d2f45a6f24ac4c3da"}, ] [package.extras] -docs = ["Sphinx (>=6.0)", "sphinx-rtd-theme (>=1.1.0)"] +docs = ["Sphinx (>=6.0)", "myst-parser (>=2.0.0)", "sphinx-rtd-theme (>=1.1.0)"] optional = ["python-socks", "wsaccel"] test = ["websockets"] [[package]] name = "widgetsnbextension" -version = "4.0.9" +version = "4.0.11" description = "Jupyter interactive widgets for Jupyter Notebook" optional = false python-versions = ">=3.7" files = [ - {file = "widgetsnbextension-4.0.9-py3-none-any.whl", hash = "sha256:91452ca8445beb805792f206e560c1769284267a30ceb1cec9f5bcc887d15175"}, - {file = "widgetsnbextension-4.0.9.tar.gz", hash = "sha256:3c1f5e46dc1166dfd40a42d685e6a51396fd34ff878742a3e47c6f0cc4a2a385"}, + {file = "widgetsnbextension-4.0.11-py3-none-any.whl", hash = "sha256:55d4d6949d100e0d08b94948a42efc3ed6dfdc0e9468b2c4b128c9a2ce3a7a36"}, + {file = "widgetsnbextension-4.0.11.tar.gz", hash = "sha256:8b22a8f1910bfd188e596fe7fc05dcbd87e810c8a4ba010bdb3da86637398474"}, ] [[package]] @@ -3653,4 +3833,4 @@ full = ["numba", "numba"] [metadata] lock-version = "2.0" python-versions = "^3.7, <3.13" -content-hash = "9eb46f1b60e19b1da529a9208dd4c56752d886177e8b49eda707c5c778c758b5" +content-hash = "9361b00b8b4354faa3d85cc41a8790222872823c9eb5b77f46d93f011f2b25c2" diff --git a/pyproject.toml b/pyproject.toml index 17ab6bc3..a051379a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -29,16 +29,19 @@ motionpicture = ">=0.2.0, ^0" argcomplete = "^2.0.0" tikzplotlib = ">=0.9.13, ^0" py-expression-eval = ">=0.3.14, ^0" +openpmd-api = [{ version = "^0.14.0", python = "<3.8" }, + { version = "^0.15.2", python = ">3.8" }] + [tool.poetry.dev-dependencies] -black = "^23.1.0" +black = { version = "^24.1.0", python = ">=3.8.1" } coverage = "^6.3" Sphinx = { version = "^6.0.0", python = ">=3.8.1" } jupyter = { version = "^1.0.0", python = ">=3.8.1" } jedi = ">=0.18.1, ^0" snakeviz = "^2.1.0" nbsphinx = ">0.8.10, ^0" -isort = "^5.10.0" +isort = { version = "^5.13.0", python = ">=3.8.1" } flake8 = [{ version = "^6.0.0", python = ">=3.8.1" }] mypy = ">=0.931, ^0" sphinx-autodoc-typehints = "^1.17.0" diff --git a/tests/grid_functions/batman.it00000000.bp4/data.0 b/tests/grid_functions/batman.it00000000.bp4/data.0 new file mode 100755 index 00000000..e0efea4b Binary files /dev/null and b/tests/grid_functions/batman.it00000000.bp4/data.0 differ diff --git a/tests/grid_functions/batman.it00000000.bp4/md.0 b/tests/grid_functions/batman.it00000000.bp4/md.0 new file mode 100755 index 00000000..2d60c63d Binary files /dev/null and b/tests/grid_functions/batman.it00000000.bp4/md.0 differ diff --git a/tests/grid_functions/batman.it00000000.bp4/md.idx b/tests/grid_functions/batman.it00000000.bp4/md.idx new file mode 100755 index 00000000..d5fb877f Binary files /dev/null and b/tests/grid_functions/batman.it00000000.bp4/md.idx differ diff --git a/tests/grid_functions/batman.it00000000.bp4/profiling.json b/tests/grid_functions/batman.it00000000.bp4/profiling.json new file mode 100755 index 00000000..838a2c6a --- /dev/null +++ b/tests/grid_functions/batman.it00000000.bp4/profiling.json @@ -0,0 +1,3 @@ +[ +{ "rank": 0, "start": "Mon_Nov_27_11:15:33_2023", "threads": 1, "bytes": 2432122, "mkdir_mus": 336, "aggregation_mus": 0, "meta_sort_merge_mus": 94, "minmax_mus": 0, "memcpy_mus": 250, "buffering_mus": 3653, "transport_0": { "type": "File_POSIX", "close_mus": 148, "write_mus": 2606, "open_mus": 3693}, "transport_1": { "type": "File_POSIX", "close_mus": 0, "write_mus": 172, "open_mus": 3241} } +] diff --git a/tests/grid_functions/batman.it00000001.bp4/data.0 b/tests/grid_functions/batman.it00000001.bp4/data.0 new file mode 100644 index 00000000..d23ce73a Binary files /dev/null and b/tests/grid_functions/batman.it00000001.bp4/data.0 differ diff --git a/tests/grid_functions/batman.it00000001.bp4/md.0 b/tests/grid_functions/batman.it00000001.bp4/md.0 new file mode 100644 index 00000000..569718cb Binary files /dev/null and b/tests/grid_functions/batman.it00000001.bp4/md.0 differ diff --git a/tests/grid_functions/batman.it00000001.bp4/md.idx b/tests/grid_functions/batman.it00000001.bp4/md.idx new file mode 100644 index 00000000..d5fb877f Binary files /dev/null and b/tests/grid_functions/batman.it00000001.bp4/md.idx differ diff --git a/tests/grid_functions/batman.it00000001.bp4/profiling.json b/tests/grid_functions/batman.it00000001.bp4/profiling.json new file mode 100644 index 00000000..f5116246 --- /dev/null +++ b/tests/grid_functions/batman.it00000001.bp4/profiling.json @@ -0,0 +1,3 @@ +[ +{ "rank": 0, "start": "Mon_Nov_27_11:15:33_2023", "threads": 1, "bytes": 2432122, "mkdir_mus": 333, "aggregation_mus": 0, "meta_sort_merge_mus": 66, "minmax_mus": 0, "memcpy_mus": 215, "buffering_mus": 1018, "transport_0": { "type": "File_POSIX", "close_mus": 163, "write_mus": 2213, "open_mus": 1891}, "transport_1": { "type": "File_POSIX", "close_mus": 0, "write_mus": 209, "open_mus": 6161} } +] diff --git a/tests/test_cactus_grid_functions.py b/tests/test_cactus_grid_functions.py index 8f50f86b..43d1a065 100755 --- a/tests/test_cactus_grid_functions.py +++ b/tests/test_cactus_grid_functions.py @@ -23,6 +23,7 @@ import numpy as np from kuibit import cactus_grid_functions as cg +from kuibit import cactus_ascii_utils as ca from kuibit import grid_data from kuibit import simdir as sd @@ -58,6 +59,10 @@ def test_GridFunctionsDir_string_or_tuple(self): def test_contains(self): self.assertIn("xyz", self.gd) + def test_contains_OpenPMDVars(self): + vars3D = self.gd.xyz + self.assertIn("wavetoyx_u", vars3D) + def test__getitem(self): self.assertIs(self.gd["xy"], self.gd._all_griddata[(0, 1)]) @@ -90,6 +95,7 @@ def test_total_filesize(self): class TestAllGridFunctions(unittest.TestCase): def setUp(self): self.gf = sd.SimDir("tests/grid_functions").gf.xy + self.gf_xyz = sd.SimDir("tests/grid_functions").gf.xyz def test__init(self): self.assertCountEqual(self.gf.dimension, (0, 1)) @@ -136,6 +142,8 @@ def test__init(self): ], ) + self.assertCountEqual(list(self.gf._vars_openpmd_files.keys()), []) + # Here we are not testing that files are correctly organized... def test_keys(self): @@ -183,7 +191,7 @@ def test__getitem(self): with self.assertRaises(KeyError): self.gf["hey"] - # Test a variable from ASCII and one from HDF5 + # Test a variable from ASCII, one from HDF5, and one from OpenPMD # We don't test the details, we just test that object is initialized # with the correct data @@ -197,6 +205,20 @@ def test__getitem(self): filename, "illinoisgrmhd-grmhd_primitives_allbutbi.xy.h5" ) + # OpenPMD + self.assertTrue( + isinstance(self.gf_xyz["wavetoyx_u"], cg.OneGridFunctionOpenPMD) + ) + self.assertEqual(self.gf_xyz["wavetoyx_u"].var_name, "wavetoyx_u") + # self.gf_xyz['wavetoy-u']allfiles is a set with two elements, the + # two iterations + filenames = { + os.path.split(f)[-1] for f in self.gf_xyz["wavetoyx_u"].allfiles + } + self.assertCountEqual( + filenames, {"batman.it00000000.bp4", "batman.it00000001.bp4"} + ) + # ASCII # First, we test that a warning is emitted when we don't have ghost @@ -254,6 +276,10 @@ def setUp(self): # There's only one file self.rho_star_file = self.rho_star.allfiles[0] + # OpenPMD + self.wavetoy = sd.SimDir("tests/grid_functions").gf.xyz["wavetoyx_rho"] + self.wavetoy_file_it0 = sorted(self.wavetoy.allfiles)[0] + # We are going to test all the methods of the baseclass with # HDF5 files @@ -287,6 +313,28 @@ def test__properties_in_file(self): self.P._components_in_file(self.P_file, 2, 0), [0, 1] ) + self.assertCountEqual( + self.wavetoy._iterations_in_file(self.wavetoy_file_it0), [0] + ) + self.assertEqual( + self.wavetoy._min_iteration_in_file(self.wavetoy_file_it0), 0 + ) + self.assertEqual( + self.wavetoy._max_iteration_in_file(self.wavetoy_file_it0), 0 + ) + self.assertCountEqual( + self.wavetoy._ref_levels_in_file(self.wavetoy_file_it0, 0), + [0, 1], + ) + self.assertCountEqual( + self.wavetoy._components_in_file( + self.wavetoy_file_it0, + 0, + 0, + ), + [0, 1, 2, 3], + ) + def test_restarts(self): # TODO: This test is not robust when we are dealing with only one file... # Add a second file and rewrite tests. @@ -299,6 +347,11 @@ def test_iterations(self): self.assertCountEqual(self.P.available_iterations, [0, 1, 2]) self.assertCountEqual(self.P.iterations, [0, 1, 2]) + self.assertEqual(self.wavetoy.min_iteration, 0) + self.assertEqual(self.wavetoy.max_iteration, 1) + self.assertCountEqual(self.wavetoy.available_iterations, [0, 1]) + self.assertCountEqual(self.wavetoy.iterations, [0, 1]) + # Iteration not available with self.assertRaises(ValueError): self.P._files_with_iteration(3) @@ -311,9 +364,14 @@ def test_times(self): self.assertCountEqual(self.P.available_times, [0, 0.25, 0.5]) self.assertCountEqual(self.P.times, [0, 0.25, 0.5]) + self.assertCountEqual(self.wavetoy.available_times, [0, 0.0078125]) + self.assertCountEqual(self.wavetoy.times, [0, 0.0078125]) + def test_iteration_at_time(self): self.assertEqual(self.P.iteration_at_time(0.5), 2) + self.assertEqual(self.wavetoy.iteration_at_time(0.0078125), 1) + # Time not available with self.assertRaises(ValueError): self.P.iteration_at_time(5) @@ -489,6 +547,40 @@ def test_init(self): with self.assertRaises(RuntimeError): self.rho_star._parse_file("/tmp/wrongname") + def test_openpmd(self): + iteration = 0 + component = 0 + + with cg.openpmd_series(self.wavetoy_file_it0) as series: + variable = series.iterations[iteration].meshes[ + "wavetoyx_state_lev00" + ]["wavetoyx_u"] + chunk = variable.available_chunks()[component] + + # Do the actual reading + data = variable.load_chunk(chunk.offset, chunk.extent) + series.flush() + + expected_grid = grid_data.UniformGrid( + [9, 33, 33], + x0=[-1.0, -1.0, -1.0], + x1=[1.0, 0.0, 0.0], + ref_level=0, + num_ghost=[0, 0, 0], + time=0, + iteration=0, + component=0, + ) + + expected_grid_data = grid_data.UniformGridData(expected_grid, data) + + self.assertEqual( + self.wavetoy._read_component_as_uniform_grid_data( + self.wavetoy_file_it0, 0, 0, 0 + ), + expected_grid_data, + ) + def test_clear_cache(self): # Read something self.P[0] @@ -501,3 +593,57 @@ def test_clear_cache(self): # Check that we are clear self.assertIsNone(self.P.alldata[self.P_file][0][0][0]) + + +class TestOneGridFunctionOpenPMD(unittest.TestCase): + def setUp(self): + self.gf = sd.SimDir("tests/grid_functions").gf.xyz + + def test__init(self): + self.assertCountEqual(self.gf.dimension, (0, 1, 2)) + # Here we check that we indexed the correct variables. We must check + # the OpenPMD file + + # There are five files including one OpenPMD file in the test folder: + # 1. illinoisgrmhd-grmhd_primitives_allbutbi.xyz.asc (ASCII one group) + # 2. rho_star.xyz.asc (ASCII one var) + # 3. illinoisgrmhd-grmhd_primitives_allbutbi.xyz.file_0.h5 (HDF5 one group) + # 4. illinoisgrmhd-grmhd_primitives_allbutbi.xyz.file_1.h5 (HDF5 one group) + # 5. batman.it00000000.bp4 (OpenPMD bp4) + + # Here we can we find all the variables + + # assert variables from OpenPMD bp4 file + self.assertCountEqual( + list(self.gf._vars_openpmd_files.keys()), + [ + "wavetoyx_rho", + "wavetoyx_u", + ], + ) + + # assert variables from h5 file + self.assertCountEqual( + list(self.gf._vars_h5_files.keys()), + ["P", "rho_b", "vx", "vy", "vz"], + ) + + # assert variables from ascii file + self.assertCountEqual( + list(self.gf._vars_ascii_files.keys()), + ["P", "rho_b", "vx", "vy", "vz", "rho_star"], + ) + + def test_allfiles(self): + # This is a weak test, we are just testing how many files we have... + # There should be 6 files including the OpenPMD bp4 files + self.assertEqual(len(self.gf.allfiles), 6) + + def test_iterations(self): + wavetoyx_rho = self.gf.fields.wavetoyx_rho + self.assertEqual(wavetoyx_rho.iterations, [0, 1]) + + def test_multiple_mesh_refinement_levels(self): + # wavetouyx_rho variable in the OpenPMD file has 2 mesh refinement levels + wavetoyx_rho0 = self.gf.fields.wavetoyx_rho[0] + self.assertEqual(wavetoyx_rho0.refinement_levels, [0, 1])