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sync w/ entity v1.0.0
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@haykh
haykh committed Apr 25, 2024
1 parent 867f59d commit 6a3be77
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2 changes: 2 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -157,3 +157,5 @@ cython_debug/
# and can be added to the global gitignore or merged into this file. For a more nuclear
# option (not recommended) you can uncomment the following to ignore the entire idea folder.
#.idea/
test/
temp/
Binary file added dist/nt2py-0.3.0.tar.gz
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2 changes: 1 addition & 1 deletion nt2/__init__.py
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@@ -1 +1 @@
__version__ = ["0.2.1"]
__version__ = "0.3.0"
161 changes: 81 additions & 80 deletions nt2/read.py
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Expand Up @@ -589,8 +589,8 @@ def EdgeToCenter(arr):
"Ttz": "Pz",
}
CoordinateDict = {
"cartesian": {"x": "x", "y": "y", "z": "z", "1": "x", "2": "y", "3": "z"},
"spherical": {
"cart": {"x": "x", "y": "y", "z": "z", "1": "x", "2": "y", "3": "z"},
"sph": {
"r": "r",
"theta": "θ" if useGreek else "th",
"phi": "φ" if useGreek else "ph",
Expand All @@ -600,15 +600,15 @@ def EdgeToCenter(arr):
},
}
PrtlDict = {
"cartesian": {
"cart": {
"X1": "x",
"X2": "y",
"X3": "z",
"U1": "ux",
"U2": "uy",
"U3": "uz",
},
"spherical": {
"sph": {
"X1": "r",
"X2": "θ" if useGreek else "th",
"X3": "φ" if useGreek else "ph",
Expand All @@ -623,40 +623,39 @@ def EdgeToCenter(arr):
except OSError:
raise OSError(f"Could not open file {self.fname}")
step0 = list(self.file.keys())[0]
nsteps = int(self.file.attrs["NumSteps"])
nsteps = len(self.file.keys())
ngh = int(self.file.attrs["NGhosts"])
layout = "right" if self.file.attrs["LayoutRight"] == 1 else "left"
dimension = int(self.file.attrs["Dimension"])
coordinates = self.file.attrs["Coordinates"].decode("UTF-8")
if coordinates == "qspherical":
coordinates = "spherical"
if coordinates == "spherical":
if coordinates == "qsph":
coordinates = "sph"
if coordinates == "sph":
self.metric = SphericalMetric()
else:
self.metric = MinkowskiMetric()
coords = list(CoordinateDict[coordinates].values())[::-1][-dimension:]
# cell-centered coords
cc_coords = {
c: EdgeToCenter(self.file.attrs[f"X{i+1}"])
for i, c in enumerate(coords[::-1])
}
# upper and lower limits of the cell
cc_coords = {c: self.file[step0][f"X{i+1}"] for i, c in enumerate(coords[::-1])}
# cell edges
cell_1 = {
f"{c}_1": (
c,
self.file.attrs[f"X{i+1}"][:-1],
self.file[step0][f"X{i+1}e"][:-1],
)
for i, c in enumerate(coords[::-1])
}
cell_2 = {
f"{c}_2": (
c,
self.file.attrs[f"X{i+1}"][1:],
self.file[step0][f"X{i+1}e"][1:],
)
for i, c in enumerate(coords[::-1])
}

times = np.array([self.file[f"Step{s}"]["Time"][()] for s in range(nsteps)])
times = np.array(
[self.file[f"Step{s}"]["Time"][()] for s in range(nsteps)], dtype=float
)

if dimension == 1:
noghosts = slice(ngh, -ngh) if ngh > 0 else slice(None)
Expand Down Expand Up @@ -700,9 +699,11 @@ def EdgeToCenter(arr):
dask_arrays.append(array[noghosts])

k_ = reduce(
lambda x, y: x.replace(*y)
if "_" not in x
else "_".join([x.split("_")[0].replace(*y)] + x.split("_")[1:]),
lambda x, y: (
x.replace(*y)
if "_" not in x
else "_".join([x.split("_")[0].replace(*y)] + x.split("_")[1:])
),
[k, *list(CoordinateDict[coordinates].items())],
)
k_ = reduce(
Expand All @@ -722,68 +723,68 @@ def EdgeToCenter(arr):
)
self.dataset[k_] = x

prtls = [
k
for k in self.file[step0].keys()
if (k.startswith("X") or k.startswith("U") or k.startswith("W"))
]
# prtls = [
# k
# for k in self.file[step0].keys()
# if (k.startswith("X") or k.startswith("U") or k.startswith("W"))
# ]

species = np.unique(
[int(pq.split("_")[1]) for pq in self.file[step0].keys() if pq in prtls]
)
# species = np.unique(
# [int(pq.split("_")[1]) for pq in self.file[step0].keys() if pq in prtls]
# )

def list_to_ragged(arr):
max_len = np.max([len(a) for a in arr])
return map(
lambda a: np.concatenate([a, np.full(max_len - len(a), np.nan)]), arr
)
# def list_to_ragged(arr):
# max_len = np.max([len(a) for a in arr])
# return map(
# lambda a: np.concatenate([a, np.full(max_len - len(a), np.nan)]), arr
# )

self._particles = {}
for s in species:
prtl_data = {}
for q in [
f"X1_{s}",
f"X2_{s}",
f"X3_{s}",
f"U1_{s}",
f"U2_{s}",
f"U3_{s}",
f"W_{s}",
]:
if q[0] in ["X", "U"]:
q_ = PrtlDict[coordinates][q.split("_")[0]]
else:
q_ = q.split("_")[0]
if q not in prtls:
continue
if q not in prtl_data.keys():
prtl_data[q_] = []
for k in range(nsteps):
step_k = f"Step{k}"
if q in self.file[step_k].keys():
prtl_data[q_].append(self.file[step_k][q])
else:
prtl_data[q_].append(np.full_like(prtl_data[q_][-1], np.nan))
prtl_data[q_] = list_to_ragged(prtl_data[q_])
prtl_data[q_] = da.from_array(list(prtl_data[q_]))
prtl_data[q_] = xr.DataArray(
prtl_data[q_], dims=["t", "id"], name=q_, coords={"t": times}
)
if coordinates == "spherical":
prtl_data["x"] = (
prtl_data[PrtlDict[coordinates]["X1"]]
* np.sin(prtl_data[PrtlDict[coordinates]["X2"]])
* np.cos(prtl_data[PrtlDict[coordinates]["X3"]])
)
prtl_data["y"] = (
prtl_data[PrtlDict[coordinates]["X1"]]
* np.sin(prtl_data[PrtlDict[coordinates]["X2"]])
* np.sin(prtl_data[PrtlDict[coordinates]["X3"]])
)
prtl_data["z"] = prtl_data[PrtlDict[coordinates]["X1"]] * np.cos(
prtl_data[PrtlDict[coordinates]["X2"]]
)
self._particles[s] = xr.Dataset(prtl_data)
# for s in species:
# prtl_data = {}
# for q in [
# f"X1_{s}",
# f"X2_{s}",
# f"X3_{s}",
# f"U1_{s}",
# f"U2_{s}",
# f"U3_{s}",
# f"W_{s}",
# ]:
# if q[0] in ["X", "U"]:
# q_ = PrtlDict[coordinates][q.split("_")[0]]
# else:
# q_ = q.split("_")[0]
# if q not in prtls:
# continue
# if q not in prtl_data.keys():
# prtl_data[q_] = []
# for k in range(nsteps):
# step_k = f"Step{k}"
# if q in self.file[step_k].keys():
# prtl_data[q_].append(self.file[step_k][q])
# else:
# prtl_data[q_].append(np.full_like(prtl_data[q_][-1], np.nan))
# prtl_data[q_] = list_to_ragged(prtl_data[q_])
# prtl_data[q_] = da.from_array(list(prtl_data[q_]))
# prtl_data[q_] = xr.DataArray(
# prtl_data[q_], dims=["t", "id"], name=q_, coords={"t": times}
# )
# if coordinates == "spherical":
# prtl_data["x"] = (
# prtl_data[PrtlDict[coordinates]["X1"]]
# * np.sin(prtl_data[PrtlDict[coordinates]["X2"]])
# * np.cos(prtl_data[PrtlDict[coordinates]["X3"]])
# )
# prtl_data["y"] = (
# prtl_data[PrtlDict[coordinates]["X1"]]
# * np.sin(prtl_data[PrtlDict[coordinates]["X2"]])
# * np.sin(prtl_data[PrtlDict[coordinates]["X3"]])
# )
# prtl_data["z"] = prtl_data[PrtlDict[coordinates]["X1"]] * np.cos(
# prtl_data[PrtlDict[coordinates]["X2"]]
# )
# self._particles[s] = xr.Dataset(prtl_data)

def __del__(self):
self.file.close()
Expand Down Expand Up @@ -878,7 +879,7 @@ def makeMovie(self, plot, makeframes=True, **kwargs):
exp.makeFrames(
plot,
np.arange(len(self.t)),
f"{self.attrs['Title']}/frames",
f"{self.attrs['simulation.name']}/frames",
data=self,
num_cpus=kwargs.pop("num_cpus", None),
)
Expand All @@ -887,9 +888,9 @@ def makeMovie(self, plot, makeframes=True, **kwargs):
makemovie = True
if makemovie:
exp.makeMovie(
input=f"{self.attrs['Title']}/frames/",
input=f"{self.attrs['simulation.name']}/frames/",
overwrite=True,
output=f"{self.attrs['Title']}.mp4",
output=f"{self.attrs['simulation.name']}.mp4",
number=5,
**kwargs,
)
Expand Down
46 changes: 44 additions & 2 deletions pyproject.toml
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Original file line number Diff line number Diff line change
@@ -1,3 +1,45 @@
[build-system]
requires = ["setuptools", "wheel", "setuptools_scm", "pypandoc"]
build-backend = 'setuptools.build_meta'
requires = ["hatchling"]
build-backend = "hatchling.build"

[project]
name = "nt2py"
dynamic = ["version"]
dependencies = [
"types-setuptools",
"dask",
"xarray",
"numpy",
"scipy",
"h5py",
"h5pickle",
"matplotlib",
"tqdm",
"contourpy",
]
requires-python = ">=3.8"
authors = [{ name = "Hayk", email = "haykh.astro@gmail.com" }]
maintainers = [{ name = "Hayk", email = "haykh.astro@gmail.com" }]
description = "Post-processing & visualization toolkit for the Entity PIC code"
readme = "README.md"
license = { file = "LICENSE" }
classifiers = [
"Development Status :: 5 - Production/Stable",
"Intended Audience :: Science/Research",
"Intended Audience :: Education",
"Topic :: Scientific/Engineering :: Physics",
"Topic :: Scientific/Engineering :: Astronomy",
"License :: OSI Approved :: BSD License",
"Programming Language :: Python :: 3 :: Only",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
]

[project.urls]
Repository = "https://github.com/entity-toolkit/nt2py"

[tool.hatch.version]
path = "nt2/__init__.py"
23 changes: 0 additions & 23 deletions setup.cfg
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10 changes: 0 additions & 10 deletions setup.py
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