osiris-utils 1.1.10a0__py3-none-any.whl → 1.2.0__py3-none-any.whl

osiris_utils/utils.py

@@ -8,6 +8,18 @@ import numpy as np
 import pandas as pd
 import scipy
 
+__all__ = [
+    "courant2D",
+    "time_estimation",
+    "filesize_estimation",
+    "transverse_average",
+    "integrate",
+    "save_data",
+    "read_data",
+    "convert_tracks",
+    "create_file_tags",
+]
+
 
 def courant2D(dx: float, dy: float) -> float:
     """
@@ -87,32 +99,29 @@ def transverse_average(data: np.ndarray) -> np.ndarray:
     return cast(np.ndarray, np.mean(data, axis=1))
 
 
-def integrate(array: np.ndarray, dx: float) -> np.ndarray:
+def integrate(array: np.ndarray, dx: float, axis: int = None) -> np.ndarray:
     """
-    Integrate a 1D from the left to the right. This may be changed in the future to allow
-    for integration in both directions or for other more general cases.
+    Integrate a N-D array using the cumulative Simpson's rule, from right to left
+    along a given axis
 
     Parameters
     ----------
     array : numpy.ndarray
-        Dim: 1D.
         The input array.
     dx : float
         The spacing between points.
-
-    Returns
-    -------
-    numpy.ndarray
-        Dim: 1D.
-        The integrated array.
+    axis : int, optional
+        The axis along which to integrate. If None, the default is 0.
+        This will assume that the input array is 1D.
     """
-
-    if len(array.shape) != 1:
-        raise ValueError(f"Array must be 1D\n Array shape: {array.shape}")
-    flip_array = np.flip(array)
+    if axis is None:  # Assume 1D array
+        if len(array.shape) != 1:
+            raise ValueError("The input array must be 1D when axis is None.")
+        axis = 0
+    flip_array = np.flip(array, axis=axis)
     # int = -scipy.integrate.cumulative_trapezoid(flip_array, dx = dx, initial = flip_array[0])
-    int = -scipy.integrate.cumulative_simpson(flip_array, dx=dx, initial=0)
-    return cast(np.ndarray, np.flip(int))
+    int = -scipy.integrate.cumulative_simpson(flip_array, dx=dx, initial=0, axis=axis)
+    return cast(np.ndarray, np.flip(int, axis=axis))
 
 
 def save_data(data: np.ndarray, savename: str, option: str = "numpy") -> None:
@@ -175,7 +184,7 @@ def convert_tracks(filename_in: str) -> str:
 
     try:
         file_in = h5py.File(filename_in, "r")
-    except IOError:
+    except OSError:
         print("cannot open " + filename_in)
         exit()
 

osiris_utils/vis/__init__.py

@@ -0,0 +1,3 @@
+from .plot3d import plot_3d
+
+__all__ = ["plot_3d"]

osiris_utils/vis/plot3d.py

@@ -0,0 +1,148 @@
+import warnings
+from typing import Literal
+
+import matplotlib.pyplot as plt
+import numpy as np
+
+__all__ = ["plot_3d"]
+
+
+def plot_3d(
+    diagnostic,
+    idx: int,
+    scale_type: Literal["zero_centered", "pos", "neg", "default"] = "default",
+    boundaries: np.ndarray = None,
+):
+    """
+    Plots a 3D scatter plot of the diagnostic data (grid data).
+
+    Parameters
+    ----------
+    diagnostic : Diagnostic
+        The diagnostic object containing the data.
+    idx : int
+        Index of the data to plot.
+    scale_type : Literal["zero_centered", "pos", "neg", "default"], optional
+        Type of scaling for the colormap:
+        - "zero_centered": Center colormap around zero.
+        - "pos": Colormap for positive values.
+        - "neg": Colormap for negative values.
+        - "default": Standard colormap.
+    boundaries : np.ndarray, optional
+        Boundaries to plot part of the data. (3,2) If None, uses the default grid boundaries.
+
+    Returns
+    -------
+    fig : matplotlib.figure.Figure
+        The figure object containing the plot.
+    ax : matplotlib.axes._subplots.Axes3DSubplot
+        The 3D axes object of the plot.
+    """
+
+    if diagnostic.dim != 3:
+        raise ValueError("This method is only available for 3D diagnostics.")
+
+    if boundaries is None:
+        boundaries = diagnostic.grid
+
+    if not isinstance(boundaries, np.ndarray):
+        try:
+            boundaries = np.array(boundaries)
+        except Exception:
+            boundaries = diagnostic.grid
+            warnings.warn("boundaries cannot be accessed as a numpy array with shape (3, 2), using default instead", stacklevel=2)
+
+    if boundaries.shape != (3, 2):
+        warnings.warn("boundaries should have shape (3, 2), using default instead", stacklevel=2)
+        boundaries = diagnostic.grid
+
+    # Load data
+    # Access private attributes if necessary, but prefer public properties if available
+    # diagnostic.data is a property, but it might not be loaded for specific index if not load_all
+    # The original code used self._all_loaded and self._data vs self[idx]
+
+    # Check if we can access _all_loaded, otherwise assume we need to load
+    if hasattr(diagnostic, "_all_loaded") and diagnostic._all_loaded:
+        data = diagnostic._data[idx]
+    else:
+        data = diagnostic[idx]
+
+    X, Y, Z = np.meshgrid(diagnostic.x[0], diagnostic.x[1], diagnostic.x[2], indexing="ij")
+
+    # Flatten arrays for scatter plot
+    (
+        X_flat,
+        Y_flat,
+        Z_flat,
+    ) = (
+        X.ravel(),
+        Y.ravel(),
+        Z.ravel(),
+    )
+    data_flat = data.ravel()
+
+    # Apply filter: Keep only chosen points
+    mask = (
+        (X_flat > boundaries[0][0])
+        & (X_flat < boundaries[0][1])
+        & (Y_flat > boundaries[1][0])
+        & (Y_flat < boundaries[1][1])
+        & (Z_flat > boundaries[2][0])
+        & (Z_flat < boundaries[2][1])
+    )
+    X_cut, Y_cut, Z_cut, data_cut = (
+        X_flat[mask],
+        Y_flat[mask],
+        Z_flat[mask],
+        data_flat[mask],
+    )
+
+    if scale_type == "zero_centered":
+        # Center colormap around zero
+        cmap = "seismic"
+        vmax = np.max(np.abs(data_flat))  # Find max absolute value
+        vmin = -vmax
+    elif scale_type == "pos":
+        cmap = "plasma"
+        vmax = np.max(data_flat)
+        vmin = 0
+
+    elif scale_type == "neg":
+        cmap = "plasma"
+        vmax = 0
+        vmin = np.min(data_flat)
+    else:
+        cmap = "plasma"
+        vmax = np.max(data_flat)
+        vmin = np.min(data_flat)
+
+    norm = plt.Normalize(vmin=vmin, vmax=vmax)
+
+    # Plot
+    fig = plt.figure(figsize=(10, 7))
+    ax = fig.add_subplot(111, projection="3d")
+
+    # Scatter plot with seismic colormap
+    sc = ax.scatter(X_cut, Y_cut, Z_cut, c=data_cut, cmap=cmap, norm=norm, alpha=1)
+
+    # Set limits to maintain full background
+    ax.set_xlim(*diagnostic.grid[0])
+    ax.set_ylim(*diagnostic.grid[1])
+    ax.set_zlim(*diagnostic.grid[2])
+
+    # Colorbar
+    cbar = plt.colorbar(sc, ax=ax, shrink=0.6)
+
+    # Labels
+    # Use public properties where possible
+    cbar.set_label(rf"${diagnostic.name}$" + rf"$\  [{diagnostic.units}]$")
+
+    # time(idx) returns [value, unit]
+    t_val, t_unit = diagnostic.time(idx)
+    ax.set_title(rf"$t={t_val:.2f}$" + rf"$\  [{t_unit}]$")
+
+    ax.set_xlabel(r"${}$".format(diagnostic.axis[0]["long_name"]) + r"$\  [{}]$".format(diagnostic.axis[0]["units"]))
+    ax.set_ylabel(r"${}$".format(diagnostic.axis[1]["long_name"]) + r"$\  [{}]$".format(diagnostic.axis[1]["units"]))
+    ax.set_zlabel(r"${}$".format(diagnostic.axis[2]["long_name"]) + r"$\  [{}]$".format(diagnostic.axis[2]["units"]))
+
+    return fig, ax

{osiris_utils-1.1.10a0.dist-info → osiris_utils-1.2.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: osiris_utils
-Version: 1.1.10a0
+Version: 1.2.0
 Summary: Utilities to manipulate and visualise OSIRIS plasma PIC output data
 Author-email: João Pedro Ferreira Biu <joaopedrofbiu@tecnico.ulisboa.pt>
 License: MIT
@@ -12,8 +12,6 @@ Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Natural Language :: English
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
@@ -32,7 +30,6 @@ Requires-Dist: pytest>=8.1; extra == "dev"
 Requires-Dist: pytest-cov; extra == "dev"
 Requires-Dist: pre-commit>=3.7; extra == "dev"
 Requires-Dist: ruff>=0.4; extra == "dev"
-Requires-Dist: isort>=5.13; extra == "dev"
 Requires-Dist: types-tqdm; extra == "dev"
 Requires-Dist: types-Pillow; extra == "dev"
 Provides-Extra: docs
@@ -51,11 +48,13 @@ OSIRIS_UTILS
 .. image:: https://github.com/joaopedrobiu6/osiris_utils/actions/workflows/ci.yml/badge.svg
    :target: https://github.com/joaopedrobiu6/osiris_utils/actions
    :alt: CI status
+
 .. image:: https://codecov.io/gh/joaopedrobiu6/osiris_utils/branch/main/graph/badge.svg
    :target: https://codecov.io/gh/joaopedrobiu6/osiris_utils
    :alt: Coverage
 
-
+.. image:: https://zenodo.org/badge/889119723.svg
+  :target: https://doi.org/10.5281/zenodo.17382244
 
 This package contains a set of utilities to open and analyze OSIRIS output files, using Python. All the methods implemented are fully integrated with `NumPy`, and use `np.ndarray` as the main data structure.
 High-level functions are provided to manipulate data from OSIRIS, from reading the data of the diagnostics, to making post-processing calculations.
@@ -95,6 +94,48 @@ Quick-start
    cd osiris_utils
    python examples/quick_start.py examples/example_data/thermal.1d
 
+Command-Line Interface
+----------------------
+
+osiris_utils includes a command-line interface for common operations. After installation, the ``osiris`` command becomes available::
+
+   osiris --version                     # Check version
+   osiris --help                        # Show available commands
+
+**Available Commands:**
+
+- ``osiris info`` - Display metadata about OSIRIS files and simulations
+- ``osiris export`` - Convert data to CSV, JSON, or NumPy formats
+- ``osiris plot`` - Create quick visualizations
+- ``osiris validate`` - Check file integrity
+
+**Examples:**
+
+Show simulation information::
+
+   osiris info path/to/simulation
+   osiris info path/to/file.h5 --brief
+
+Export data to different formats::
+
+   osiris export file.h5 --format csv --output data.csv
+   osiris export diagnostic/dir --format npy --output data.npy
+
+Generate quick plots::
+
+   osiris plot file.h5 --save plot.png
+   osiris plot file.h5 --save plot.png --title "Ez Field" --cmap viridis
+
+Validate simulation data::
+
+   osiris validate path/to/simulation
+   osiris validate path/to/simulation --check-missing
+
+For detailed help on any command::
+
+   osiris <command> --help
+
+
 Documentation
 -------------
 
@@ -106,7 +147,14 @@ The documentation is available at https://osiris-utils.readthedocs.io or via thi
 
 .. _authors:
 
-Authors and Contributors
-------------------------
+Author
+------
 
 - João Biu
+
+Contributors
+------------
+
+- Diogo Carvalho
+- João Cândido
+- Margarida Pereira

{osiris_utils-1.1.10a0.dist-info → osiris_utils-1.2.0.dist-info}/RECORD

@@ -1,17 +1,26 @@
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 docs/source/contrib.rst,sha256=CkYSzy3msde38fy0zROAjDsdRHYYvQSAJwjkJczFmGI,35
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 docs/source/_static/custom.css,sha256=aLsKMK8rejJzzCdISkHhDG8Eq-f7T4v4DmQInYzeRDI,909
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 examples/example_data/thermal.1d,sha256=w4PuwO4RHr9GbAQnwh2YEUI0JpH_2icG9QaynE4rwKo,1010
@@ -1036,27 +1045,35 @@ examples/example_data/MS/UDIST/electrons/vfl1/vfl1-electrons-000251.h5,sha256=Y5
 examples/example_data/MS/UDIST/electrons/vfl1/vfl1-electrons-000252.h5,sha256=uehzDEpMDT1iPAnD12HjB5Lpy59p5VR39HWRmouiFJ0,15368
 examples/example_data/MS/UDIST/electrons/vfl1/vfl1-electrons-000253.h5,sha256=Kt6DXemyVU6l0jhNYb10NYFo3xWZsQRQStUaWaEZJAE,15368
 examples/example_data/TIMINGS/timings-final,sha256=1i_dcQ1hIxs78eeD4e6WNWUxJ_vXKRvbIVDAPGl9_R4,2910
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+osiris_utils/data/data.py,sha256=VtoMDoTj8nXZlGZeCjIgIZUICtwkST9TxBFShzYsnAI,22059
+osiris_utils/data/diagnostic.py,sha256=sy-e4hz4G8Am9wjtkeTr3w64elMLXGizsfGcA9xfHAw,39181
+osiris_utils/data/simulation.py,sha256=bn5-Uv894dm38PNhUtMl9TZCmEBQlVqN4DuteM6ui-Y,7256
+osiris_utils/decks/__init__.py,sha256=m6lNzGk5DSHs9wpRmW6d3vdir4Wg28ImWkeg5fzQx3k,114
+osiris_utils/decks/decks.py,sha256=HW9iAGP2xjtJ5VpHceLhXYK2tnB4rcYdsfDquRQVv3o,12194
+osiris_utils/decks/species.py,sha256=f8BY-Zb_LhHP5KFlkQNbzF3uQZl7vtDKXHXZvlKzps8,1106
+osiris_utils/postprocessing/__init__.py,sha256=bN8YlzTXd1Kr8eYqyWtGv8WFF0N_9f5XlsN1uUIHyLc,1180
+osiris_utils/postprocessing/derivative.py,sha256=OIp71mfjhNWxhW_HzEQ6NTUKSgWeqpbujCrp0NX-CRE,19715
+osiris_utils/postprocessing/fft.py,sha256=EN44iH8nvhMnHbBBTKT5ZFB1A_8DCgexVFoK7SomHuI,14009
+osiris_utils/postprocessing/field_centering.py,sha256=YTYzdEvRFh6fhxPYn95UAZ1eQcC9AP2kf7En2ynRfPs,12952
+osiris_utils/postprocessing/heatflux_correction.py,sha256=NtCOkjQuW95v3PHpDJODZBYFFetfsCS3AWNu5DoVA_I,8105
+osiris_utils/postprocessing/mft.py,sha256=MOGHpiDBsfZdbCHWP1999NGt8j790RB39GHjdcQp0Mw,13128
+osiris_utils/postprocessing/postprocess.py,sha256=-_zydCuK7RsH2kTT5vGpIZd5dQco9iIaSMKwUSex5Ww,1144
+osiris_utils/postprocessing/pressure_correction.py,sha256=N0UwUmW7eEcr1OdgzyIwY-rFxUKXomfsQvTUobKXBlw,7223
+osiris_utils/vis/__init__.py,sha256=Vr0o8wtRFtPOJdSK5cRIa_bDvbylAe2sHTk8c7qO_tM,51
+osiris_utils/vis/plot3d.py,sha256=ywP9UGI4i3SRgUdsz-ILHxc7W_StCSN1D1U4Tmpd_6o,4658
+osiris_utils-1.2.0.dist-info/licenses/LICENSE.txt,sha256=z1lVzLA_QsfcnLffhfWMrFw5cR_nuwpvbOGCOFUN7iY,1066
+osiris_utils-1.2.0.dist-info/METADATA,sha256=7IgAe88iZbzaZ53jT5toI4FEnM9LZXyb6GWAHAtRI84,5436
+osiris_utils-1.2.0.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+osiris_utils-1.2.0.dist-info/entry_points.txt,sha256=s3WXJWsWF5AWEFhJ8rXscjGttQCOXvViOiNmX45AJjo,49
+osiris_utils-1.2.0.dist-info/top_level.txt,sha256=tSs2XcOs-JtYsqVepo5WVSNcilf6ALHfKyYuPaVZLco,38
+osiris_utils-1.2.0.dist-info/RECORD,,

{osiris_utils-1.1.10a0.dist-info → osiris_utils-1.2.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.9.0)
+Generator: setuptools (80.10.2)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

osiris_utils-1.2.0.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+osiris = osiris_utils.cli:main

{osiris_utils-1.1.10a0.dist-info → osiris_utils-1.2.0.dist-info}/top_level.txt

@@ -1,3 +1,4 @@
+benchmarks
 docs
 examples
 osiris_utils

osiris_utils/postprocessing/mft_for_gridfile.py

@@ -1,55 +0,0 @@
-import numpy as np
-
-from ..data.data import OsirisGridFile
-
-
-# Deprecated
-class MFT_Single(OsirisGridFile):
-    """
-    Class to handle the mean field theory on data. Inherits from OsirisGridFile.
-
-    Parameters
-    ----------
-    source : str or OsirisGridFile
-        The filename or an OsirisGridFile object.
-    axis : int
-        The axis to average over.
-    """
-
-    def __init__(self, source, axis=1):
-        if isinstance(source, OsirisGridFile):
-            self.__dict__.update(source.__dict__)
-        else:
-            super().__init__(source)
-        self._compute_mean_field(axis=axis)
-
-    def _compute_mean_field(self, axis=1):
-        self._average = np.expand_dims(np.mean(self.data, axis=axis), axis=axis)
-        self._fluctuations = self.data - self._average
-
-    def __array__(self):
-        return self.data
-
-    @property
-    def average(self):
-        return self._average
-
-    @property
-    def delta(self):
-        return self._fluctuations
-
-    def __str__(self):
-        return super().__str__() + f"\nAverage: {self.average.shape}\nDelta: {self.delta.shape}"
-
-    def derivative(self, field, axis=0):
-        """
-        Compute the derivative of the average or the fluctuations.
-
-        Parameters
-        ----------
-        field : MeanFieldTheory.average or MeanFieldTheory.delta
-            The field to compute the derivative.
-        axis : int
-            The axis to compute the derivative.
-        """
-        return np.gradient(field, self.dx[axis], axis=0)