pyvlasiator 0.1.7__tar.gz → 0.1.10__tar.gz

{pyvlasiator-0.1.7 → pyvlasiator-0.1.10}/PKG-INFO

@@ -1,63 +1,68 @@
-Metadata-Version: 2.3
-Name: pyvlasiator
-Version: 0.1.7
-Summary: Python utilities for processing Vlasiator data
-Author: Hongyang Zhou
-Author-email: hyzhou@umich.edu
-Requires-Python: >=3.11,<4.0
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Classifier: Programming Language :: Python :: 3.13
-Provides-Extra: plot
-Requires-Dist: matplotlib (>=3.7.2,<4.0.0) ; extra == "plot"
-Requires-Dist: numpy (>=1.25.1,<2.0.0)
-Description-Content-Type: text/markdown
-
-# pyvlasiator
-
-<p align="center">
-  <a href="https://badge.fury.io/py/pyvlasiator">
-    <img src="https://badge.fury.io/py/pyvlasiator.svg" alt="PyPI version" height="18">
-  </a>
-  <a href="https://github.com/henry2004y/pyvlasiator/actions">
-    <img src="https://github.com/henry2004y/pyvlasiator/actions/workflows/CI.yml/badge.svg">
-  </a>
-  <a href="https://henry2004y.github.io/pyvlasiator/">
-    <img src="https://img.shields.io/badge/docs-dev-blue">
-  </a>
-  <a href="LICENSE">
-    <img src="https://img.shields.io/badge/license-MIT-blue">
-  </a>
-  <a href="https://app.codecov.io/gh/henry2004y/pyvlasiator/">
-    <img src="https://img.shields.io/codecov/c/github/henry2004y/pyvlasiator">
-  </a>
-</p>
-
-Lightweight Python package for processing [Vlasiator](https://github.com/fmihpc/vlasiator) data, alternative to [Analysator](https://github.com/fmihpc/analysator).
-
-## Installation
-
-`pyvlasiator` can be installed via
-
-```bash
-python -m pip install pyvlasiator
-```
-
-## Usage
-
-`pyvlasiator` can be used to process VLSV files generated from Vlasiator.
-
-```python
-from pyvlasiator.vlsv import Vlsv
-
-file = "test.vlsv"
-meta = Vlsv(file)
-```
-
-Plotting is supported via Matplotlib. For more detailed usage, please refer to the [documentation](https://henry2004y.github.io/pyvlasiator/).
-
-## License
-
-`pyvlasiator` was created by Hongyang Zhou. It is licensed under the terms of the MIT license.
-
+Metadata-Version: 2.4
+Name: pyvlasiator
+Version: 0.1.10
+Summary: Python utilities for processing Vlasiator data
+Author-email: Hongyang Zhou <hyzhou@umich.edu>
+Requires-Python: <4.0,>=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE.md
+Requires-Dist: numpy>=1.25.1
+Provides-Extra: plot
+Requires-Dist: matplotlib<4,>=3.7.2; extra == "plot"
+Provides-Extra: dev
+Requires-Dist: pytest<8,>=7.4.0; extra == "dev"
+Requires-Dist: pytest-benchmark<5,>=4.0.0; extra == "dev"
+Requires-Dist: pytest-cov<5,>=4.1.0; extra == "dev"
+Requires-Dist: requests<3,>=2.31.0; extra == "dev"
+Requires-Dist: jupyter<2,>=1.0.0; extra == "dev"
+Requires-Dist: myst-nb<2,>=1.0.0; extra == "dev"
+Requires-Dist: sphinx-autoapi<4,>=3.0.0; extra == "dev"
+Requires-Dist: sphinx-rtd-theme<2,>=1.2.2; extra == "dev"
+Dynamic: license-file
+
+# pyvlasiator
+
+<p align="center">
+  <a href="https://badge.fury.io/py/pyvlasiator">
+    <img src="https://badge.fury.io/py/pyvlasiator.svg" alt="PyPI version" height="18">
+  </a>
+  <a href="https://github.com/henry2004y/pyvlasiator/actions">
+    <img src="https://github.com/henry2004y/pyvlasiator/actions/workflows/CI.yml/badge.svg">
+  </a>
+  <a href="https://henry2004y.github.io/pyvlasiator/">
+    <img src="https://img.shields.io/badge/docs-dev-blue">
+  </a>
+  <a href="LICENSE">
+    <img src="https://img.shields.io/badge/license-MIT-blue">
+  </a>
+  <a href="https://app.codecov.io/gh/henry2004y/pyvlasiator/">
+    <img src="https://img.shields.io/codecov/c/github/henry2004y/pyvlasiator">
+  </a>
+</p>
+
+Lightweight Python package for processing [Vlasiator](https://github.com/fmihpc/vlasiator) data, alternative to [Analysator](https://github.com/fmihpc/analysator).
+
+## Installation
+
+`pyvlasiator` can be installed via
+
+```bash
+python -m pip install pyvlasiator
+```
+
+## Usage
+
+`pyvlasiator` can be used to process VLSV files generated from Vlasiator.
+
+```python
+from pyvlasiator.vlsv import Vlsv
+
+file = "test.vlsv"
+meta = Vlsv(file)
+```
+
+Plotting is supported via Matplotlib. For more detailed usage, please refer to the [documentation](https://henry2004y.github.io/pyvlasiator/).
+
+## License
+
+`pyvlasiator` was created by Hongyang Zhou. It is licensed under the terms of the MIT license.

pyvlasiator-0.1.10/pyproject.toml

@@ -0,0 +1,31 @@
+[project]
+name = "pyvlasiator"
+version = "0.1.10"
+description = "Python utilities for processing Vlasiator data"
+authors = [
+    {name = "Hongyang Zhou", email = "hyzhou@umich.edu"},
+]
+readme = "README.md"
+requires-python = ">=3.11, <4.0"
+dependencies = [
+    "numpy>=1.25.1",
+]
+
+[project.optional-dependencies]
+plot = [
+    "matplotlib>=3.7.2, <4",
+]
+dev = [
+    "pytest>=7.4.0, <8",
+    "pytest-benchmark>=4.0.0, <5",
+    "pytest-cov>=4.1.0, <5",
+    "requests>=2.31.0, <3",
+    "jupyter>=1.0.0, <2",
+    "myst-nb>=1.0.0, <2",
+    "sphinx-autoapi>=3.0.0, <4",
+    "sphinx-rtd-theme>=1.2.2, <2",
+]
+
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"

pyvlasiator-0.1.10/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

{pyvlasiator-0.1.7 → pyvlasiator-0.1.10}/src/pyvlasiator/plot/plot.py

@@ -369,11 +369,12 @@ def _plot2d(
     else:
         pArgs = set_args(meta, var, axisunit)
         data = prep2d(meta, var, comp)
+        normal = -1
 
     x1, x2 = get_axis(pArgs.axisunit, pArgs.plotrange, pArgs.sizes)
 
     if var in ("fg_b", "fg_e", "vg_b_vol", "vg_e_vol") or var.endswith("vg_v"):
-        _fillinnerBC(data)
+        _fillinnerBC(data, meta, var, pArgs, normal)
 
     norm, ticks = set_colorbar(colorscale, vmin, vmax, data)
 
@@ -700,17 +701,17 @@ def prep2dslice(meta: Vlsv, var: str, dir: int, comp: int, pArgs: PlotArgs):
             if comp != -1:
                 data = data3D[icut, :, :, comp]
             else:
-                data = np.linalg.norm(data3D[icut, :, :, :], axis=3)
+                data = np.linalg.norm(data3D[icut, :, :, :], axis=2)
         elif dir == 1:
             if comp != -1:
                 data = data3D[:, icut, :, comp]
             else:
-                data = np.linalg.norm(data3D[:, icut, :, :], axis=3)
+                data = np.linalg.norm(data3D[:, icut, :, :], axis=2)
         elif dir == 2:
             if comp != -1:
                 data = data3D[:, :, icut, comp]
             else:
-                data = np.linalg.norm(data3D[:, :, icut, :], axis=3)
+                data = np.linalg.norm(data3D[:, :, icut, :], axis=2)
     else:  # moments, dccrg grid
         # vlasov grid, AMR
         if data3D.ndim == 1:
@@ -797,11 +798,26 @@ def get_axis(axisunit: AxisUnit, plotrange: tuple, sizes: tuple) -> tuple:
     return x, y
 
 
-def _fillinnerBC(data: np.ndarray):
+def _fillinnerBC(data: np.ndarray, meta: Vlsv, var: str, pArgs: PlotArgs, normal: int):
     """
-    Fill sparsity/inner boundary cells with NaN.
+    Fill sparsity/inner boundary cells with NaN using density as a mask.
     """
-    data[data == 0] = np.nan
+    if "/" in var:
+        species = var.split("/")[0]
+        rho_var = f"{species}/vg_rho"
+    else:
+        # Default to proton density for field quantities
+        rho_var = "proton/vg_rho"
+
+    if not meta.has_variable(rho_var):
+        data[data == 0] = np.nan
+        return
+
+    if normal != -1:
+        rho_data = prep2dslice(meta, rho_var, normal, -1, pArgs)
+    else:
+        rho_data = prep2d(meta, rho_var, -1)
+    data[rho_data == 0] = np.nan
 
 
 def set_colorbar(

{pyvlasiator-0.1.7 → pyvlasiator-0.1.10}/src/pyvlasiator/vlsv/reader.py

@@ -43,6 +43,7 @@ class Vlsv:
         self.celldict = {}
         self.maxamr = -1
         self.vg_indexes_on_fg = np.array([])  # SEE: map_vg_onto_fg(self)
+        self.precipitationenergybins = {}
 
         self._read_xml_footer()
 
@@ -484,8 +485,8 @@ class Vlsv:
 
             return lsize
 
+        nIORanks = self.read_parameter("numWritingRanks")  # Int32
         if fgDecomposition is None:
-            nIORanks = self.read_parameter("numWritingRanks")  # Int32
             fgDecomposition = getDomainDecomposition(bbox, nIORanks)
 
         offsetnow = 0

pyvlasiator-0.1.10/src/pyvlasiator.egg-info/PKG-INFO

@@ -0,0 +1,68 @@
+Metadata-Version: 2.4
+Name: pyvlasiator
+Version: 0.1.10
+Summary: Python utilities for processing Vlasiator data
+Author-email: Hongyang Zhou <hyzhou@umich.edu>
+Requires-Python: <4.0,>=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE.md
+Requires-Dist: numpy>=1.25.1
+Provides-Extra: plot
+Requires-Dist: matplotlib<4,>=3.7.2; extra == "plot"
+Provides-Extra: dev
+Requires-Dist: pytest<8,>=7.4.0; extra == "dev"
+Requires-Dist: pytest-benchmark<5,>=4.0.0; extra == "dev"
+Requires-Dist: pytest-cov<5,>=4.1.0; extra == "dev"
+Requires-Dist: requests<3,>=2.31.0; extra == "dev"
+Requires-Dist: jupyter<2,>=1.0.0; extra == "dev"
+Requires-Dist: myst-nb<2,>=1.0.0; extra == "dev"
+Requires-Dist: sphinx-autoapi<4,>=3.0.0; extra == "dev"
+Requires-Dist: sphinx-rtd-theme<2,>=1.2.2; extra == "dev"
+Dynamic: license-file
+
+# pyvlasiator
+
+<p align="center">
+  <a href="https://badge.fury.io/py/pyvlasiator">
+    <img src="https://badge.fury.io/py/pyvlasiator.svg" alt="PyPI version" height="18">
+  </a>
+  <a href="https://github.com/henry2004y/pyvlasiator/actions">
+    <img src="https://github.com/henry2004y/pyvlasiator/actions/workflows/CI.yml/badge.svg">
+  </a>
+  <a href="https://henry2004y.github.io/pyvlasiator/">
+    <img src="https://img.shields.io/badge/docs-dev-blue">
+  </a>
+  <a href="LICENSE">
+    <img src="https://img.shields.io/badge/license-MIT-blue">
+  </a>
+  <a href="https://app.codecov.io/gh/henry2004y/pyvlasiator/">
+    <img src="https://img.shields.io/codecov/c/github/henry2004y/pyvlasiator">
+  </a>
+</p>
+
+Lightweight Python package for processing [Vlasiator](https://github.com/fmihpc/vlasiator) data, alternative to [Analysator](https://github.com/fmihpc/analysator).
+
+## Installation
+
+`pyvlasiator` can be installed via
+
+```bash
+python -m pip install pyvlasiator
+```
+
+## Usage
+
+`pyvlasiator` can be used to process VLSV files generated from Vlasiator.
+
+```python
+from pyvlasiator.vlsv import Vlsv
+
+file = "test.vlsv"
+meta = Vlsv(file)
+```
+
+Plotting is supported via Matplotlib. For more detailed usage, please refer to the [documentation](https://henry2004y.github.io/pyvlasiator/).
+
+## License
+
+`pyvlasiator` was created by Hongyang Zhou. It is licensed under the terms of the MIT license.

pyvlasiator-0.1.10/src/pyvlasiator.egg-info/SOURCES.txt

@@ -0,0 +1,16 @@
+LICENSE.md
+README.md
+pyproject.toml
+src/pyvlasiator/__init__.py
+src/pyvlasiator/pyvlasiator.py
+src/pyvlasiator.egg-info/PKG-INFO
+src/pyvlasiator.egg-info/SOURCES.txt
+src/pyvlasiator.egg-info/dependency_links.txt
+src/pyvlasiator.egg-info/requires.txt
+src/pyvlasiator.egg-info/top_level.txt
+src/pyvlasiator/plot/__init__.py
+src/pyvlasiator/plot/plot.py
+src/pyvlasiator/vlsv/__init__.py
+src/pyvlasiator/vlsv/reader.py
+src/pyvlasiator/vlsv/variables.py
+tests/test_pyvlasiator.py

pyvlasiator-0.1.10/src/pyvlasiator.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

pyvlasiator-0.1.10/src/pyvlasiator.egg-info/requires.txt

@@ -0,0 +1,14 @@
+numpy>=1.25.1
+
+[dev]
+pytest<8,>=7.4.0
+pytest-benchmark<5,>=4.0.0
+pytest-cov<5,>=4.1.0
+requests<3,>=2.31.0
+jupyter<2,>=1.0.0
+myst-nb<2,>=1.0.0
+sphinx-autoapi<4,>=3.0.0
+sphinx-rtd-theme<2,>=1.2.2
+
+[plot]
+matplotlib<4,>=3.7.2

pyvlasiator-0.1.10/src/pyvlasiator.egg-info/top_level.txt

@@ -0,0 +1 @@
+pyvlasiator

pyvlasiator-0.1.10/tests/test_pyvlasiator.py

@@ -0,0 +1,172 @@
+import pytest
+import requests
+import tarfile
+import os
+import numpy as np
+from pyvlasiator.vlsv import Vlsv
+import pyvlasiator.plot
+import matplotlib as mpl
+import packaging.version
+
+filedir = os.path.dirname(__file__)
+
+if os.path.isfile(filedir + "/data/bulk.1d.vlsv"):
+    pass
+else:
+    url = (
+        "https://raw.githubusercontent.com/henry2004y/vlsv_data/master/testdata.tar.gz"
+    )
+    testfiles = url.rsplit("/", 1)[1]
+    r = requests.get(url, allow_redirects=True)
+    open(testfiles, "wb").write(r.content)
+
+    path = filedir + "/data"
+
+    if not os.path.exists(path):
+        os.makedirs(path)
+
+    with tarfile.open(testfiles) as file:
+        file.extractall(path)
+    os.remove(testfiles)
+
+
+class TestVlsv:
+    dir = "tests/data/"
+    files = (dir + "bulk.1d.vlsv", dir + "bulk.2d.vlsv", dir + "bulk.amr.vlsv")
+
+    def test_load(self):
+        meta = Vlsv(self.files[0])
+        assert meta.__repr__().startswith("File")
+        assert meta.time == 10.0
+
+    def test_load_error(self):
+        with pytest.raises(FileNotFoundError):
+            meta = Vlsv("None")
+
+    def test_read_variable(self):
+        meta = Vlsv(self.files[0])
+        assert np.array_equal(meta.cellindex, np.arange(9, -1, -1, dtype=np.uint64))
+        # unsorted ID
+        cellid = meta.read_variable("CellID", sorted=False)
+        assert np.array_equal(cellid, np.arange(10, 0, -1, dtype=np.uint64))
+        # sorted var by default
+        data = meta.read_variable("vg_boundarytype")
+        assert np.array_equal(data, np.array([4, 4, 1, 1, 1, 1, 1, 1, 3, 3]))
+        # ID finding (noAMR)
+        loc = [2.0, 0.0, 0.0]
+        id = meta.getcell(loc)
+        coords = meta.getcellcoordinates(id)
+        assert coords == pytest.approx([3.0, 0.0, 0.0])
+        assert meta.read_variable("proton/vg_rho", id) == pytest.approx(1.2288102e0)
+        assert meta.read_variable("proton/vg_rho", [id]) == pytest.approx(1.2288102e0)
+        # Nearest ID with VDF stored
+        assert meta.getnearestcellwithvdf(id) == 5
+
+    def test_read_vspace(self):
+        meta = Vlsv(self.files[0])
+        vcellids, vcellf = meta.read_vcells(5)
+        V = meta.getvcellcoordinates(vcellids)
+        assert V[-1] == pytest.approx((2.45, 1.95, 1.95))
+
+    def test_read_amr(self):
+        metaAMR = Vlsv(self.files[2])
+        assert metaAMR.maxamr == 2
+        # AMR data reading, DCCRG grid
+        sliceoffset = abs(metaAMR.coordmin[1])
+        idlist, indexlist = metaAMR.getslicecell(
+            sliceoffset, 1, metaAMR.coordmin[1], metaAMR.coordmax[1]
+        )
+
+        # ID finding (AMR)
+        loc = [2.5e6, 2.5e6, 2.5e6]  # exact cell center
+        id = metaAMR.getcell(loc)
+        assert metaAMR.getcellcoordinates(id) == pytest.approx(loc)
+
+        data = metaAMR.read_variable("proton/vg_rho")
+        dataslice = metaAMR.refineslice(idlist, data[indexlist], 1)
+        assert np.sum(dataslice) == pytest.approx(7.6903526e8)
+
+    def test_read_fg_variable(self):
+        metaAMR = Vlsv(self.files[2])
+        data = metaAMR.read_variable("fg_e")
+        ncells, namr = metaAMR.ncells, metaAMR.maxamr
+        assert data.shape == (
+            ncells[0] * namr**2,
+            ncells[1] * namr**2,
+            ncells[2] * namr**2,
+            3,
+        ) and data[4, 0, 0, :] == pytest.approx([7.603512e-07, 2e-04, -2e-04])
+
+
+class TestPlot:
+    dir = "tests/data/"
+    files = (dir + "bulk.1d.vlsv", dir + "bulk.2d.vlsv", dir + "bulk.amr.vlsv")
+    mpl.use("Agg")
+    version_str = mpl.__version__
+    version = packaging.version.parse(version_str)
+
+    def test_1d_plot(self):
+        meta = Vlsv(self.files[0])
+        v = meta.plot("proton/vg_rho")[0].get_ydata()
+        assert np.array_equal(v, meta.read_variable("proton/vg_rho"))
+        v = meta.scatter("proton/vg_rho").get_offsets()
+        assert np.array_equal(v[0].data[0], -10.0)
+
+    def test_2d_plot(self):
+        meta = Vlsv(self.files[1])
+        v = meta.pcolormesh("proton/vg_rho").get_array()
+        assert v[99, 60] == pytest.approx(999535.8) and v.data.size == 6300
+        v = meta.pcolormesh(
+            "proton/vg_rho", axisunit=pyvlasiator.plot.AxisUnit.SI
+        ).get_array()
+        assert v[99, 60] == pytest.approx(999535.8) and v.data.size == 6300
+        v = meta.contour("proton/vg_rho").get_array()
+        assert v[-3] == 4000000.0
+        v = meta.contourf("proton/vg_rho").get_array()
+        assert v[-3] == 3600000.0
+        v = meta.contourf(
+            "proton/vg_rho", colorscale=pyvlasiator.plot.ColorScale.Log
+        ).get_array()
+        assert v[-3] == 3600000.0
+        v = meta.pcolormesh("vg_b_vol").get_array()
+        assert v[0, 1] == pytest.approx(3.0051286e-09)
+        v = meta.pcolormesh(
+            "vg_b_vol", comp=1, colorscale=pyvlasiator.plot.ColorScale.SymLog
+        ).get_array()
+        assert v[0, 1] == pytest.approx(-9.284285146238247e-12)
+        v = meta.pcolormesh("fg_b", comp=0).get_array()
+        assert v[99, 60] == pytest.approx(-2.999047e-09) and v.data.size == 6300
+
+    def test_3d_amr_slice(self):
+        meta = Vlsv(self.files[2])
+        v = meta.pcolormesh("proton/vg_rho").get_array()
+        assert v[15, 31] == pytest.approx(1.0483886e6) and v.data.size == 512
+
+    def test_stream_plot(self):
+        meta = Vlsv(self.files[1])
+        p = meta.streamplot("proton/vg_v", comp="xy")
+        assert type(p) == mpl.streamplot.StreamplotSet
+
+    def test_vdf_plot(self):
+        meta = Vlsv(self.files[0])
+        loc = [2.0, 0.0, 0.0]
+        v = meta.vdfslice(loc, verbose=True).get_array()
+        assert v[19, 25] == 238.24398578141802
+
+
+def load(files):
+    """
+    Benchmarking VLSV loading.
+    """
+    meta = Vlsv(files[0])
+    meta = Vlsv(files[1])
+    meta = Vlsv(files[2])
+    return meta
+
+
+def test_load(benchmark):
+    dir = "tests/data/"
+    files = (dir + "bulk.1d.vlsv", dir + "bulk.2d.vlsv", dir + "bulk.amr.vlsv")
+    result = benchmark(load, files)
+
+    assert type(result) == Vlsv

pyvlasiator-0.1.7/pyproject.toml

@@ -1,28 +0,0 @@
-[tool.poetry]
-name = "pyvlasiator"
-version = "0.1.7"
-description = "Python utilities for processing Vlasiator data"
-authors = ["Hongyang Zhou <hyzhou@umich.edu>"]
-readme = "README.md"
-
-[tool.poetry.dependencies]
-python = "^3.11"
-numpy = "^1.25.1"
-matplotlib = {version = "^3.7.2", optional = true}
-
-[tool.poetry.extras]
-plot = ["matplotlib"]
-
-[tool.poetry.group.dev.dependencies]
-pytest = "^7.4.0"
-pytest-benchmark = "^4.0.0"
-pytest-cov = "^4.1.0"
-requests = "^2.31.0"
-jupyter = "^1.0.0"
-myst-nb = "^1.0.0"
-sphinx-autoapi = "^3.0.0"
-sphinx-rtd-theme = "^1.2.2"
-
-[build-system]
-requires = ["poetry-core"]
-build-backend = "poetry.core.masonry.api"